From 8433cca3985cf5309b753dc8d000c66406ce7cf6 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 3 May 2023 18:27:04 -0400 Subject: [PATCH 001/176] initial commit --- CMakeLists.txt | 1 + src/simsopt/geo/boozersurface.py | 227 ++++++++++++++- src/simsopt/geo/surfaceobjectives.py | 412 +++++++++++++++++++++------ src/simsopt/geo/surfacerzfourier.py | 8 +- src/simsoptpp/python.cpp | 36 +-- src/simsoptpp/surface.cpp | 111 +++++++- 6 files changed, 664 insertions(+), 131 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index bb37a56f9..73c0491b5 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -101,6 +101,7 @@ set(XTENSOR_USE_TBB 0) pybind11_add_module(${PROJECT_NAME} src/simsoptpp/python.cpp src/simsoptpp/python_surfaces.cpp src/simsoptpp/python_curves.cpp + src/simsoptpp/boozerresidual.cpp src/simsoptpp/python_magneticfield.cpp src/simsoptpp/python_tracing.cpp src/simsoptpp/python_distance.cpp src/simsoptpp/biot_savart_py.cpp src/simsoptpp/biot_savart_vjp_py.cpp src/simsoptpp/regular_grid_interpolant_3d_py.cpp diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index e8d564e40..6a5e2f7d6 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -2,7 +2,8 @@ from scipy.linalg import lu from scipy.optimize import minimize, least_squares -from .surfaceobjectives import boozer_surface_residual +import simsoptpp as sopp +from .surfaceobjectives import boozer_surface_residual, boozer_surface_dexactresidual_dcoils_dcurrents_vjp, boozer_surface_dlsqgrad_dcoils_vjp from .._core.optimizable import Optimizable __all__ = ['BoozerSurface'] @@ -39,17 +40,42 @@ class BoozerSurface(Optimizable): where Newton is used to solve the first order necessary conditions for optimality. """ - - def __init__(self, biotsavart, surface, label, targetlabel): + + def __init__(self, biotsavart, surface, label, targetlabel, constraint_weight=None, reg=None): super().__init__(depends_on=[biotsavart]) self.biotsavart = biotsavart self.surface = surface self.label = label self.targetlabel = targetlabel + self.constraint_weight = constraint_weight + self.reg = reg self.need_to_run_code = True def recompute_bell(self, parent=None): self.need_to_run_code = True + + def run_code(self, boozer_type, iota, G=None): + """ + Run the default solvers. + """ + if not self.need_to_run_code: + return + + if boozer_type == 'exact': + res = self.boozer_surface.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=iota, G=G) + return res + + elif boozer_type == 'ls': + # first try BFGS + res = self.compute_boozerls_BFGS(tol=1e-10, maxiter=1e3, constraint_weight=self.constraint_weight, iota=iota, G=G) + iota, G = res['iota'], res['G'] + + ## polish off using Newton's method + self.need_to_run_code = True + res = self.compute_boozerls_newton(tol=1e-11, maxiter=20, constraint_weight=self.constraint_weight, iota=iota, G=G) + return res + else: + raise Exception(f"boozer_type not supported: {boozer_type}") def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., scalarize=True, optimize_G=False): r""" @@ -583,9 +609,202 @@ def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., P, L, U = lu(J) res = { "residual": r, "jacobian": J, "iter": i, "success": norm <= tol, "G": G, "s": s, "iota": iota, "PLU": (P, L, U), - "mask": mask, 'type': 'exact' + "mask": mask, 'type': 'exact', "vjp": boozer_surface_dexactresidual_dcoils_dcurrents_vjp } self.res = res self.need_to_run_code = False return res + def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G=False): + # this is essentially the scalarize option in previous implementation. This should be merged in that case... + assert derivatives in [0, 1, 2] + if optimize_G: + sdofs = dofs[:-2] + iota = dofs[-2] + G = dofs[-1] + else: + sdofs = dofs[:-1] + iota = dofs[-1] + G = None + + s = self.surface + nphi = s.quadpoints_phi.size + ntheta = s.quadpoints_theta.size + nsurfdofs = sdofs.size + + s.set_dofs(sdofs) + + #boozer = residual(s, iota, G, self.bs, derivatives=derivatives) + # initialize + surface = self.surface + biotsavart = self.biotsavart + x = surface.gamma() + xphi = surface.gammadash1() + xtheta = surface.gammadash2() + nphi = x.shape[0] + ntheta = x.shape[1] + + xsemiflat = x.reshape((x.size//3, 3)).copy() + biotsavart.set_points(xsemiflat) + biotsavart.compute(derivatives) + B = biotsavart.B().reshape((nphi, ntheta, 3)) + + if derivatives >= 1: + dx_dc = surface.dgamma_by_dcoeff() + dxphi_dc = surface.dgammadash1_by_dcoeff() + dxtheta_dc = surface.dgammadash2_by_dcoeff() + dB_dx = biotsavart.dB_by_dX().reshape((nphi, ntheta, 3, 3)) + if derivatives == 2: + d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) + + if derivatives == 0: + val = sopp.boozer_residual(G, iota, xphi, xtheta, B) + boozer = val, + elif derivatives == 1: + val, dval = sopp.boozer_residual_ds(G, iota, B, dB_dx, xphi, xtheta, dx_dc, dxphi_dc, dxtheta_dc) + boozer = val, dval + elif derivatives == 2: + val, dval, d2val = sopp.boozer_residual_ds2(G, iota, B, dB_dx, d2B_by_dXdX, xphi, xtheta, dx_dc, dxphi_dc, dxtheta_dc) + boozer = val, dval, d2val + + lab = self.label.J() + + rnl = boozer[0] + rl = np.sqrt(constraint_weight) * (lab-self.targetlabel) + rz = np.sqrt(constraint_weight) * (s.gamma()[0, 0, 2] - 0.) + r = rnl + 0.5*rl**2 + 0.5*rz**2 + + if self.reg is not None: + r += self.reg.J() + + if derivatives == 0: + return r + + dl = np.zeros(dofs.shape) + drz = np.zeros(dofs.shape) + dl[:nsurfdofs] = self.label.dJ() + drz[:nsurfdofs] = s.dgamma_by_dcoeff()[0, 0, 2, :] + + Jnl = boozer[1] + drl = np.sqrt(constraint_weight) * dl + drz = np.sqrt(constraint_weight) * drz + J = Jnl + rl * drl + rz * drz + if self.reg is not None: + J[:nsurfdofs] += self.reg.dJ() + + if derivatives == 1: + return r, J + + Hnl = boozer[2] + d2rl = np.zeros((dofs.shape[0], dofs.shape[0])) + d2rl[:nsurfdofs, :nsurfdofs] = np.sqrt(constraint_weight)*self.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() + H = Hnl + drl[:,None] @ drl[None,:] + drz[:,None] @ drz[None, :] + rl * d2rl + if self.reg is not None: + H[:nsurfdofs, :nsurfdofs] += self.reg.d2J() + return r, J, H + + def compute_boozerls_BFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, hessian=False): + r""" + """ + if not self.need_to_run_code: + return self.res + + s = self.surface + if G is None: + x = np.concatenate((s.get_dofs(), [iota])) + else: + x = np.concatenate((s.get_dofs(), [iota, G])) + + fun = lambda x: self.boozerls_penalty( + x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) + res = minimize( + fun, x, jac=True, method='BFGS', + options={'maxiter': maxiter, 'gtol': tol}) + + resdict = { + "residual": res.fun, "gradient": res.jac, "iter": res.nit, "info": res, "success": res.success, "G": None, 'type':'ls', 'solver':'BFGS', + "firstorderop":res.jac, "constraint_weight":constraint_weight, "labelerr":np.abs((self.label.J()-self.targetlabel)/self.targetlabel), + "vjp":boozer_surface_dlsqgrad_dcoils_vjp + } + + if G is None: + s.set_dofs(res.x[:-1]) + iota = res.x[-1] + else: + s.set_dofs(res.x[:-2]) + iota = res.x[-2] + G = res.x[-1] + resdict['G'] = G + resdict['s'] = s + resdict['iota'] = iota + + if hessian: + val, dval, d2val = self.boozerls_penalty( + x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + P, L, U = lu(d2val) + resdict["PLU"] = (P, L, U) + + self.res = resdict + self.need_to_run_code = False + + print(f"BFGS solve - {resdict['success']} iter={resdict['iter']}, iota={resdict['iota']:.16f}, ||grad||_inf = {np.linalg.norm(resdict['firstorderop'], ord=np.inf):.3e}", flush=True) + return resdict + + def compute_boozerls_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0.): + """ + """ + if not self.need_to_run_code: + return self.res + + s = self.surface + if G is None: + x = np.concatenate((s.get_dofs(), [iota])) + else: + x = np.concatenate((s.get_dofs(), [iota, G])) + i = 0 + + val, dval, d2val = self.boozerls_penalty( + x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + norm = np.linalg.norm(dval, ord=np.inf) + + while i < maxiter and norm > tol: + d2val += stab*np.identity(d2val.shape[0]) + dx = np.linalg.solve(d2val, dval) + if norm < 1e-9: + dx += np.linalg.solve(d2val, dval - d2val@dx) + x = x - dx + val, dval, d2val = self.boozerls_penalty( + x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + norm = np.linalg.norm(dval, ord=np.inf) + + if norm > 1e2: + break + + i = i+1 + + P, L, U = lu(d2val) + if G is None: + s.set_dofs(x[:-1]) + iota = x[-1] + else: + s.set_dofs(x[:-2]) + iota = x[-2] + G = x[-1] + + #res = { + # "residual": val, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "type": "ls", + # "PLU":(P,L,U), "firstorderop":dval, "constraint_weight":constraint_weight, "iota":iota, "G":G, + # "type":'ls', "labelerr":np.abs((self.label.J()-self.targetlabel)/self.targetlabel), "cond":np.linalg.cond(d2val),- + # "reg": self.reg.J() if self.reg is not None else 0. + #} + + res = { + "residual": val, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "firstorderop": dval, + "PLU" : (P, L, U), 'iota': iota, "G": G, "type": "ls", "vjp": boozer_surface_dlsqgrad_dcoils_vjp + } + + self.res = res + self.need_to_run_code = False + + print(f"NEWTON solve - {res['success']} iter={res['iter']}, iota={res['iota']:.16f}, ||grad||_inf = {np.linalg.norm(res['firstorderop'], ord=np.inf):.3e}", flush=True) + return res diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index e18ae1a31..9319df30e 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -12,7 +12,7 @@ __all__ = ['Area', 'Volume', 'ToroidalFlux', 'PrincipalCurvature', 'QfmResidual', 'boozer_surface_residual', 'Iotas', - 'MajorRadius', 'NonQuasiSymmetricRatio'] + 'MajorRadius', 'NonQuasiSymmetricRatio', 'BoozerResidual'] class Area(Optimizable): @@ -287,21 +287,24 @@ def dJ(self): return Derivative({self.surface: deriv}) -def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0): +def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_inv_modB=False): r""" For a given surface, this function computes the residual .. math:: - G\mathbf B(\mathbf x) - \|\mathbf B(\mathbf x)\|^2 (\mathbf x_\varphi + \iota \mathbf x_\theta) + G\mathbf B_\text{BS}(\mathbf x) - ||\mathbf B_\text{BS}(\mathbf x)||^2 (\mathbf x_\varphi + \iota \mathbf x_\theta) as well as the derivatives of this residual with respect to surface dofs, iota, and G. In the above, :math:`\mathbf x` are points on the surface, :math:`\iota` is the - rotational transform on that surface, and :math:`\mathbf B` is the magnetic field. + rotational transform on that surface, and :math:`\mathbf B_{\text{BS}}` is the magnetic field + computed using the Biot-Savart law. :math:`G` is known for exact boozer surfaces, so if ``G=None`` is passed, then that value is used instead. """ + + assert derivatives in [0, 1] user_provided_G = G is not None if not user_provided_G: @@ -324,8 +327,15 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0): B2 = np.sum(B**2, axis=2) residual = G*B - B2[..., None] * tang - residual_flattened = residual.reshape((nphi*ntheta*3, )) - r = residual_flattened + if weight_inv_modB: + modB = np.sqrt(B2) + w = 1./modB + rtil = w[:, :, None] * residual + else: + rtil = residual.copy() + + rtil_flattened = rtil.reshape((nphi*ntheta*3, )) + r = rtil_flattened if derivatives == 0: return r, @@ -341,64 +351,81 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0): dresidual_dc = sopp.boozer_dresidual_dc(G, dB_dc, B, tang, B2, dxphi_dc, iota, dxtheta_dc) dresidual_diota = -B2[..., None] * xtheta - dresidual_dc_flattened = dresidual_dc.reshape((nphi*ntheta*3, nsurfdofs)) - dresidual_diota_flattened = dresidual_diota.reshape((nphi*ntheta*3, 1)) - - if user_provided_G: - dresidual_dG = B - dresidual_dG_flattened = dresidual_dG.reshape((nphi*ntheta*3, 1)) - J = np.concatenate((dresidual_dc_flattened, dresidual_diota_flattened, dresidual_dG_flattened), axis=1) + if weight_inv_modB: + dB2_dc = 2*np.einsum('ijk,ijkl->ijl', B, dB_dc, optimize=True) + dmodB_dc = 0.5*dB2_dc/np.sqrt(B2[:, :, None]) + dw_dc = -dmodB_dc/modB[:, :, None]**2 + # d/dc(r*dS) = dr/dc * dS + dS_dc * r + drtil_dc = residual[..., None] * dw_dc[:, :, None, :] + w[:, :, None, None] * dresidual_dc + drtil_diota = w[:, :, None] * dresidual_diota else: - J = np.concatenate((dresidual_dc_flattened, dresidual_diota_flattened), axis=1) - if derivatives == 1: - return r, J + drtil_dc = dresidual_dc.copy() + drtil_diota = dresidual_diota.copy() - d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) - d2B_dcdc = np.einsum('ijkpl,ijpn,ijkm->ijlmn', d2B_by_dXdX, dx_dc, dx_dc) - dB2_dc = 2. * np.einsum('ijl,ijlm->ijm', B, dB_dc) - - term1 = np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc) - term2 = np.einsum('ijlmn,ijl->ijmn', d2B_dcdc, B) - d2B2_dcdc = 2*(term1 + term2) - - term1 = -(dxphi_dc[..., None, :] + iota * dxtheta_dc[..., None, :]) * dB2_dc[..., None, :, None] - term2 = -(dxphi_dc[..., :, None] + iota * dxtheta_dc[..., :, None]) * dB2_dc[..., None, None, :] - term3 = -(xphi[..., None, None] + iota * xtheta[..., None, None]) * d2B2_dcdc[..., None, :, :] - d2residual_by_dcdc = G * d2B_dcdc + term1 + term2 + term3 - d2residual_by_dcdiota = -(dB2_dc[..., None, :] * xtheta[..., :, None] + B2[..., None, None] * dxtheta_dc) - d2residual_by_diotadiota = np.zeros(dresidual_diota.shape) - - d2residual_by_dcdc_flattened = d2residual_by_dcdc.reshape((nphi*ntheta*3, nsurfdofs, nsurfdofs)) - d2residual_by_dcdiota_flattened = d2residual_by_dcdiota.reshape((nphi*ntheta*3, nsurfdofs)) - d2residual_by_diotadiota_flattened = d2residual_by_diotadiota.reshape((nphi*ntheta*3,)) + drtil_dc_flattened = drtil_dc.reshape((nphi*ntheta*3, nsurfdofs)) + drtil_diota_flattened = drtil_diota.reshape((nphi*ntheta*3, 1)) if user_provided_G: - d2residual_by_dcdG = dB_dc - d2residual_by_diotadG = np.zeros(dresidual_diota.shape) - d2residual_by_dGdG = np.zeros(dresidual_dG.shape) - d2residual_by_dcdG_flattened = d2residual_by_dcdG.reshape((nphi*ntheta*3, nsurfdofs)) - d2residual_by_diotadG_flattened = d2residual_by_diotadG.reshape((nphi*ntheta*3,)) - d2residual_by_dGdG_flattened = d2residual_by_dGdG.reshape((nphi*ntheta*3,)) - H = np.zeros((nphi*ntheta*3, nsurfdofs + 2, nsurfdofs + 2)) - # noqa turns out linting so that we can align everything neatly - H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc - H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota - H[:, :nsurfdofs, nsurfdofs+1] = d2residual_by_dcdG_flattened # noqa (0, 2) dcdG - H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc - H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota - H[:, nsurfdofs, nsurfdofs+1] = d2residual_by_diotadiota_flattened # noqa (1, 2) diotadG - H[:, nsurfdofs+1, :nsurfdofs] = d2residual_by_dcdG_flattened # noqa (2, 0) dGdc - H[:, nsurfdofs+1, nsurfdofs] = d2residual_by_diotadG_flattened # noqa (2, 1) dGdiota - H[:, nsurfdofs+1, nsurfdofs+1] = d2residual_by_dGdG_flattened # noqa (2, 2) dGdG - else: - H = np.zeros((nphi*ntheta*3, nsurfdofs + 1, nsurfdofs + 1)) - - H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc - H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota - H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc - H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota + dresidual_dG = B + + if weight_inv_modB: + drtil_dG = w[:, :, None] * dresidual_dG + else: + drtil_dG = dresidual_dG.copy() - return r, J, H + drtil_dG_flattened = drtil_dG.reshape((nphi*ntheta*3, 1)) + J = np.concatenate((drtil_dc_flattened, drtil_diota_flattened, drtil_dG_flattened), axis=1) + else: + J = np.concatenate((drtil_dc_flattened, drtil_diota_flattened), axis=1) + + return r, J + +# d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) +# d2B_dcdc = np.einsum('ijkpl,ijpn,ijkm->ijlmn', d2B_by_dXdX, dx_dc, dx_dc) +# dB2_dc = 2. * np.einsum('ijl,ijlm->ijm', B, dB_dc) +# +# term1 = np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc) +# term2 = np.einsum('ijlmn,ijl->ijmn', d2B_dcdc, B) +# d2B2_dcdc = 2*(term1 + term2) +# +# term1 = -(dxphi_dc[..., None, :] + iota * dxtheta_dc[..., None, :]) * dB2_dc[..., None, :, None] +# term2 = -(dxphi_dc[..., :, None] + iota * dxtheta_dc[..., :, None]) * dB2_dc[..., None, None, :] +# term3 = -(xphi[..., None, None] + iota * xtheta[..., None, None]) * d2B2_dcdc[..., None, :, :] +# d2residual_by_dcdc = G * d2B_dcdc + term1 + term2 + term3 +# d2residual_by_dcdiota = -(dB2_dc[..., None, :] * xtheta[..., :, None] + B2[..., None, None] * dxtheta_dc) +# d2residual_by_diotadiota = np.zeros(dresidual_diota.shape) +# +# d2residual_by_dcdc_flattened = d2residual_by_dcdc.reshape((nphi*ntheta*3, nsurfdofs, nsurfdofs)) +# d2residual_by_dcdiota_flattened = d2residual_by_dcdiota.reshape((nphi*ntheta*3, nsurfdofs)) +# d2residual_by_diotadiota_flattened = d2residual_by_diotadiota.reshape((nphi*ntheta*3,)) +# +# if user_provided_G: +# d2residual_by_dcdG = dB_dc +# d2residual_by_diotadG = np.zeros(dresidual_diota.shape) +# d2residual_by_dGdG = np.zeros(dresidual_dG.shape) +# d2residual_by_dcdG_flattened = d2residual_by_dcdG.reshape((nphi*ntheta*3, nsurfdofs)) +# d2residual_by_diotadG_flattened = d2residual_by_diotadG.reshape((nphi*ntheta*3,)) +# d2residual_by_dGdG_flattened = d2residual_by_dGdG.reshape((nphi*ntheta*3,)) +# H = np.zeros((nphi*ntheta*3, nsurfdofs + 2, nsurfdofs + 2)) +# # noqa turns out linting so that we can align everything neatly +# H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc +# H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota +# H[:, :nsurfdofs, nsurfdofs+1] = d2residual_by_dcdG_flattened # noqa (0, 2) dcdG +# H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc +# H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota +# H[:, nsurfdofs, nsurfdofs+1] = d2residual_by_diotadiota_flattened # noqa (1, 2) diotadG +# H[:, nsurfdofs+1, :nsurfdofs] = d2residual_by_dcdG_flattened # noqa (2, 0) dGdc +# H[:, nsurfdofs+1, nsurfdofs] = d2residual_by_diotadG_flattened # noqa (2, 1) dGdiota +# H[:, nsurfdofs+1, nsurfdofs+1] = d2residual_by_dGdG_flattened # noqa (2, 2) dGdG +# else: +# H = np.zeros((nphi*ntheta*3, nsurfdofs + 1, nsurfdofs + 1)) +# +# H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc +# H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota +# H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc +# H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota +# +# return r, J, H def parameter_derivatives(surface: Surface, @@ -545,7 +572,7 @@ def recompute_bell(self, parent=None): def compute(self): if self.boozer_surface.need_to_run_code: res = self.boozer_surface.res - res = self.boozer_surface.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=res['iota'], G=res['G']) + res = self.boozer_surface.run_code(res['type'], res['iota'], G=res['G']) surface = self.surface self._J = surface.major_radius() @@ -554,7 +581,7 @@ def compute(self): iota = booz_surf.res['iota'] G = booz_surf.res['G'] P, L, U = booz_surf.res['PLU'] - dconstraint_dcoils_vjp = boozer_surface_dexactresidual_dcoils_dcurrents_vjp + dconstraint_dcoils_vjp = self.boozer_surface.res['vjp'] # tack on dJ_diota = dJ_dG = 0 to the end of dJ_ds dJ_ds = np.zeros(L.shape[0]) @@ -597,8 +624,6 @@ class NonQuasiSymmetricRatio(Optimizable): """ def __init__(self, boozer_surface, bs, sDIM=20, quasi_poloidal=False): - # only BoozerExact surfaces work for now - assert boozer_surface.res['type'] == 'exact' # only SurfaceXYZTensorFourier for now assert type(boozer_surface.surface) is SurfaceXYZTensorFourier @@ -635,7 +660,7 @@ def dJ(self): def compute(self): if self.boozer_surface.need_to_run_code: res = self.boozer_surface.res - res = self.boozer_surface.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=res['iota'], G=res['G']) + res = self.boozer_surface.run_code(res['type'], res['iota'], G=res['G']) self.biotsavart.set_points(self.surface.gamma().reshape((-1, 3))) axis = self.axis @@ -666,7 +691,7 @@ def compute(self): iota = booz_surf.res['iota'] G = booz_surf.res['G'] P, L, U = booz_surf.res['PLU'] - dconstraint_dcoils_vjp = boozer_surface_dexactresidual_dcoils_dcurrents_vjp + dconstraint_dcoils_vjp = self.boozer_surface.res['vjp'] dJ_by_dB = self.dJ_by_dB().reshape((-1, 3)) dJ_by_dcoils = self.biotsavart.B_vjp(dJ_by_dB) @@ -797,7 +822,7 @@ def recompute_bell(self, parent=None): def compute(self): if self.boozer_surface.need_to_run_code: res = self.boozer_surface.res - res = self.boozer_surface.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=res['iota'], G=res['G']) + res = self.boozer_surface.run_code(res['type'], res['iota'], G=res['G']) self._J = self.boozer_surface.res['iota'] @@ -805,7 +830,7 @@ def compute(self): iota = booz_surf.res['iota'] G = booz_surf.res['G'] P, L, U = booz_surf.res['PLU'] - dconstraint_dcoils_vjp = boozer_surface_dexactresidual_dcoils_dcurrents_vjp + dconstraint_dcoils_vjp = self.boozer_surface.res['vjp'] # tack on dJ_diota = dJ_dG = 0 to the end of dJ_ds dJ_ds = np.zeros(L.shape[0]) @@ -815,6 +840,103 @@ def compute(self): adj_times_dg_dcoil = dconstraint_dcoils_vjp(adj, booz_surf, iota, G) self._dJ = -1.*adj_times_dg_dcoil +class BoozerResidual(Optimizable): + r""" + """ + def __init__(self, boozer_surface, bs): + Optimizable.__init__(self, depends_on=[boozer_surface]) + in_surface=boozer_surface.surface + self.boozer_surface = boozer_surface + + # same number of points as on the solved surface + phis = in_surface.quadpoints_phi + thetas = in_surface.quadpoints_theta + + s = SurfaceXYZTensorFourier(mpol=in_surface.mpol, ntor=in_surface.ntor, stellsym=in_surface.stellsym, nfp=in_surface.nfp, quadpoints_phi=phis, quadpoints_theta=thetas) + s.set_dofs(in_surface.get_dofs()) + + self.constraint_weight= boozer_surface.constraint_weight + self.in_surface = in_surface + self.surface = s + self.biotsavart = bs + self.recompute_bell() + + def J(self): + if self._J is None: + self.compute() + return self._J + + @derivative_dec + def dJ(self): + if self._dJ is None: + self.compute() + return self._dJ + + def recompute_bell(self, parent=None): + self._J = None + self._dJ = None + + def compute(self): + if self.boozer_surface.need_to_run_code: + res = self.boozer_surface.res + res = self.boozer_surface.run_code(res['type'], res['iota'], G=res['G']) + + self.surface.set_dofs(self.in_surface.get_dofs()) + self.biotsavart.set_points(self.surface.gamma().reshape((-1,3))) + + nphi = self.surface.quadpoints_phi.size + ntheta = self.surface.quadpoints_theta.size + num_points = 3 * nphi * ntheta + + # compute J + surface = self.surface + iota = self.boozer_surface.res['iota'] + G = self.boozer_surface.res['G'] + r, J = boozer_surface_residual(surface, iota, G, self.biotsavart, derivatives=1, weight_inv_modB=True) + rtil = np.concatenate((r/np.sqrt(num_points), [np.sqrt(self.constraint_weight)*(self.boozer_surface.label.J()-self.boozer_surface.targetlabel)] ) ) + self._J = 0.5*np.sum(rtil**2) + + booz_surf = self.boozer_surface + P, L, U = booz_surf.res['PLU'] + dconstraint_dcoils_vjp = booz_surf.res['vjp'] + + dJ_by_dB = self.dJ_by_dB() + dJ_by_dcoils = self.biotsavart.B_vjp(dJ_by_dB) + + # dJ_diota, dJ_dG to the end of dJ_ds are on the end + dl = np.zeros((J.shape[1],)) + dl[:-2] = self.boozer_surface.label.dJ_by_dsurfacecoefficients() + Jtil = np.concatenate((J/np.sqrt(num_points), np.sqrt(self.constraint_weight) * dl[None, :]), axis=0) + dJ_ds = Jtil.T@rtil + + if booz_surf.res['type'] == 'lscons': + if booz_surf.surface.stellsym: + dJ_ds = np.concatenate((dJ_ds, [0.])) + else: + dJ_ds = np.concatenate((dJ_ds, [0., 0.])) + + adj = forward_backward(P, L, U, dJ_ds) + + adj_times_dg_dcoil = dconstraint_dcoils_vjp(adj, booz_surf, iota, G) + self._dJ = dJ_by_dcoils - adj_times_dg_dcoil + + def dJ_by_dB(self): + """ + Return the partial derivative of the objective with respect to the magnetic field + """ + + surface = self.surface + nphi = self.surface.quadpoints_phi.size + ntheta = self.surface.quadpoints_theta.size + num_points = 3 * nphi * ntheta + r, r_dB = boozer_surface_residual_dB(surface, self.boozer_surface.res['iota'], self.boozer_surface.res['G'], self.biotsavart, derivatives=0, weight_inv_modB=True) + + r/=np.sqrt(num_points) + r_dB/=np.sqrt(num_points) + + dJ_by_dB = r[:, None]*r_dB + dJ_by_dB = np.sum(dJ_by_dB.reshape((-1, 3, 3)), axis=1) + return dJ_by_dB def boozer_surface_dexactresidual_dcoils_dcurrents_vjp(lm, booz_surf, iota, G): r""" @@ -855,21 +977,53 @@ def boozer_surface_dexactresidual_dcoils_dcurrents_vjp(lm, booz_surf, iota, G): return lm_times_dres_dcoils+lm_times_dlabel_dcoils - -def boozer_surface_residual_dB(surface, iota, G, biotsavart): - r""" +def boozer_surface_dlsqgrad_dcoils_vjp(lm, booz_surf, iota, G): + """ For a given surface with points x on it, this function computes the - differentiated residual + vector-Jacobian product of \lm^T * dlsqgrad_dcoils, \lm^T * dlsqgrad_dcurrents: + lm^T dresidual_dcoils = lm^T [dr_dsurface]^T[dr_dcoils] + sum r_i lm^T d2ri_dsdc + lm^T dresidual_dcurrents = lm^T [dr_dsurface]^T[dr_dcurrents] + sum r_i lm^T d2ri_dsdcurrents - .. math:: - \frac{d}{dB_{i,j,k}}[ G B_{i,j,k} - \|\mathbf{B}_{i,j}\|^2 (\mathbf{x}_{\varphi} + \iota \mathbf{x}_{\theta}) ] + G is known for exact boozer surfaces, so if G=None is passed, then that + value is used instead. + """ + + if booz_surf.res['type'] == 'lscons': + if booz_surf.surface.stellsym: + lm = lm[:-1] + else: + lm = lm[:-2] - where :math:`B_{i,j,k}` is the kth component of the magnetic field :math:`\mathbf B_{i,j}` at quadrature point :math:`(i,j)` + surface = booz_surf.surface + biotsavart = booz_surf.biotsavart + nphi = surface.quadpoints_phi.size + ntheta = surface.quadpoints_theta.size + num_points = 3 * nphi * ntheta + # r, dr_dB, J, d2residual_dsurfacedB, d2residual_dsurfacedgradB + boozer = boozer_surface_residual_dB(surface, iota, G, biotsavart, derivatives=1, weight_inv_modB=True) + r = boozer[0]/np.sqrt(num_points) + dr_dB = boozer[1].reshape((-1, 3, 3))/np.sqrt(num_points) + dr_ds = boozer[2]/np.sqrt(num_points) + d2r_dsdB = boozer[3]/np.sqrt(num_points) + d2r_dsdgradB = boozer[4]/np.sqrt(num_points) + + v1 = np.sum(np.sum(lm[:, None]*dr_ds.T, axis=0).reshape((-1, 3, 1)) * dr_dB, axis=1) + v2 = np.sum(r.reshape((-1, 3, 1))*np.sum(lm[None, None, :]*d2r_dsdB, axis=-1).reshape((-1, 3, 3)), axis=1) + v3 = np.sum(r.reshape((-1, 3, 1, 1))*np.sum(lm[None, None, None, :]*d2r_dsdgradB, axis=-1).reshape((-1, 3, 3, 3)), axis=1) + dres_dcoils = biotsavart.B_and_dB_vjp(v1+v2, v3) + return dres_dcoils[0]+dres_dcoils[1] + +def boozer_surface_residual_dB(surface, iota, G, biotsavart, derivatives=0, weight_inv_modB=False): + """ + For a given surface with points x on it, this function computes the + differentiated residual + d/dB[ G*B_BS(x) - ||B_BS(x)||^2 * (x_phi + iota * x_theta) ] as well as the derivatives of this residual with respect to surface dofs, - :math:`\iota`, and :math:`G`. :math:`G` is known for exact boozer surfaces, so if - G=None is passed, then that value is used instead. + iota, and G. + G is known for exact boozer surfaces, so if G=None is passed, then that + value is used instead. """ - + user_provided_G = G is not None if not user_provided_G: G = 2. * np.pi * np.sum(np.abs(biotsavart.coil_currents)) * (4 * np.pi * 10**(-7) / (2 * np.pi)) @@ -891,11 +1045,105 @@ def boozer_surface_residual_dB(surface, iota, G, biotsavart): GI = np.eye(3, 3) * G dresidual_dB = GI[None, None, :, :] - 2. * tang[:, :, :, None] * B[:, :, None, :] + + if weight_inv_modB: + B2 = np.sum(B**2, axis=2) + modB = np.sqrt(B2) + w = 1./modB + dw_dB = -B/B2[:, :, None]**1.5 + rtil = w[:, :, None] * residual + drtil_dB = residual[:, :, :, None] * dw_dB[:, :, None, :] + dresidual_dB * w[:, :, None, None] + else: + rtil = residual.copy() + drtil_dB = dresidual_dB.copy() - residual_flattened = residual.reshape((nphi*ntheta*3, )) - dresidual_dB_flattened = dresidual_dB.reshape((nphi*ntheta*3, 3)) - r = residual_flattened - dr_dB = dresidual_dB_flattened + rtil_flattened = rtil.reshape((nphi*ntheta*3, )) + drtil_dB_flattened = drtil_dB.reshape((nphi*ntheta*3, 3)) - return r, dr_dB + if derivatives == 0: + return rtil_flattened, drtil_dB_flattened + + dx_dc = surface.dgamma_by_dcoeff() + dxphi_dc = surface.dgammadash1_by_dcoeff() + dxtheta_dc = surface.dgammadash2_by_dcoeff() + nsurfdofs = dx_dc.shape[-1] + dB_by_dX = biotsavart.dB_by_dX().reshape((nphi, ntheta, 3, 3)) + dB_dc = np.einsum('ijkl,ijkm->ijlm', dB_by_dX, dx_dc, optimize=True) + dtang_dc = dxphi_dc + iota * dxtheta_dc + dresidual_dc = G*dB_dc \ + - 2*np.sum(B[..., None]*dB_dc, axis=2)[:, :, None, :] * tang[..., None] \ + - np.sum(B**2, axis=2)[..., None, None] * dtang_dc + dresidual_diota = -np.sum(B**2, axis=2)[..., None] * xtheta + + d2residual_dcdB = -2*dB_dc[:, :, None, :, :] * tang[:, :, :, None, None] - 2*B[:, :, None, :, None] * dtang_dc[:, :, :, None, :] + d2residual_diotadB = -2.*B[:, :, None, :] * xtheta[:, :, :, None] + d2residual_dcdgradB = -2.*B[:, :, None, None, :, None]*dx_dc[:, :, None, :, None, :]*tang[:, :, :, None, None, None] + idx = np.arange(3) + d2residual_dcdgradB[:, :, idx, :, idx, :] += dx_dc * G + + if weight_inv_modB: + dB2_dc = 2*np.einsum('ijk,ijkl->ijl', B, dB_dc, optimize=True) + dmodB_dc = 0.5*dB2_dc/modB[:, :, None] + dw_dc = -dmodB_dc/B2[:, :, None] + + d2w_dcdB = -(dB_dc * B2[:, :, None, None]**1.5 - 1.5*dB2_dc[:, :, None, :]*modB[:, :, None, None]*B[:, :, :, None])/B2[:, :, None, None]**3 + d2w_dcdgradB = dw_dB[:, :, None, :, None] * dx_dc[:, :, :, None, :] + + drtil_dc = dresidual_dc * w[:, :, None, None] + dw_dc[:, :, None, :] * residual[..., None] + drtil_diota = w[:, :, None] * dresidual_diota + d2rtil_dcdB = dresidual_dc[:, :, :, None, :]*dw_dB[:, :, None, :, None] \ + + dresidual_dB[:, :, :, :, None]*dw_dc[:, :, None, None, :] \ + + d2residual_dcdB*w[:, :, None, None, None] \ + + residual[:, :, :, None, None]*d2w_dcdB[:, :, None, :, :] + d2rtil_diotadB = dw_dB[:, :, None, :]*dresidual_diota[:, :, :, None] + w[:, :, None, None]*d2residual_diotadB + d2rtil_dcdgradB = d2w_dcdgradB[:, :, None, :, :, :]*residual[:, :, :, None, None, None] + d2residual_dcdgradB*w[:, :, None, None, None, None] + else: + drtil_dc = dresidual_dc.copy() + drtil_diota = dresidual_diota.copy() + d2rtil_dcdB = d2residual_dcdB.copy() + d2rtil_diotadB = d2residual_diotadB.copy() + d2rtil_dcdgradB = d2residual_dcdgradB.copy() + + + drtil_dc_flattened = drtil_dc.reshape((nphi*ntheta*3, nsurfdofs)) + drtil_diota_flattened = drtil_diota.reshape((nphi*ntheta*3, 1)) + d2rtil_dcdB_flattened = d2rtil_dcdB.reshape((nphi*ntheta*3, 3, nsurfdofs)) + d2rtil_diotadB_flattened = d2rtil_diotadB.reshape((nphi*ntheta*3, 3, 1)) + d2rtil_dcdgradB_flattened = d2rtil_dcdgradB.reshape((nphi*ntheta*3, 3, 3, nsurfdofs)) + d2rtil_diotadgradB_flattened = np.zeros((nphi*ntheta*3, 3, 3, 1)) + + if user_provided_G: + dresidual_dG = B + d2residual_dGdB = np.ones((nphi*ntheta, 3, 3)) + d2residual_dGdB[:, :, :] = np.eye(3)[None, :, :] + d2residual_dGdB = d2residual_dGdB.reshape((nphi,ntheta, 3, 3)) + d2residual_dGdgradB = np.zeros((nphi, ntheta, 3, 3, 3)) + + if weight_inv_modB: + drtil_dG = dresidual_dG * w[:, :, None] + d2rtil_dGdB = d2residual_dGdB * w[:, :, None, None] + dw_dB[:, :, None, :]*dresidual_dG[:, :, :, None] + d2rtil_dGdgradB = d2residual_dGdgradB.copy() + else: + drtil_dG = dresidual_dG.copy() + d2rtil_dGdB = d2residual_dGdB.copy() + d2rtil_dGdgradB = d2residual_dGdgradB.copy() + + drtil_dG_flattened = drtil_dG.reshape((nphi*ntheta*3, 1)) + d2rtil_dGdB_flattened = d2rtil_dGdB.reshape((nphi*ntheta*3, 3, 1)) + d2rtil_dGdgradB_flattened = d2rtil_dGdgradB.reshape((nphi*ntheta*3, 3, 3, 1)) + + J = np.concatenate((drtil_dc_flattened, drtil_diota_flattened, drtil_dG_flattened), axis=1) + d2rtil_dsurfacedB = np.concatenate((d2rtil_dcdB_flattened, + d2rtil_diotadB_flattened, + d2rtil_dGdB_flattened), axis=-1) + d2rtil_dsurfacedgradB = np.concatenate((d2rtil_dcdgradB_flattened, + d2rtil_diotadgradB_flattened, + d2rtil_dGdgradB_flattened), axis=-1) + else: + J = np.concatenate((drtil_dc_flattened, drtil_diota_flattened), axis=1) + d2rtil_dsurfacedB = np.concatenate((d2rtil_dcdB_flattened, d2rtil_diotadB_flattened), axis=-1) + d2rtil_dsurfacedgradB = np.concatenate((d2rtil_dcdgradB_flattened, d2rtil_diotadgradB_flattened), axis=-1) + + if derivatives == 1: + return rtil_flattened, drtil_dB_flattened, J, d2rtil_dsurfacedB, d2rtil_dsurfacedgradB diff --git a/src/simsopt/geo/surfacerzfourier.py b/src/simsopt/geo/surfacerzfourier.py index 7d430c343..7bfc8c863 100644 --- a/src/simsopt/geo/surfacerzfourier.py +++ b/src/simsopt/geo/surfacerzfourier.py @@ -406,11 +406,11 @@ def from_pyQSC(cls, stel: Qsc, r: float = 0.1, ntheta=20, mpol=10, ntor=20, **kw surf = cls(mpol=mpol, ntor=ntor, nfp=stel.nfp, stellsym=not stel.lasym, **kwargs) - surf.rc = RBC.transpose() - surf.zs = ZBS.transpose() + surf.rc[:, :] = RBC.transpose() + surf.zs[:, :] = ZBS.transpose() if stel.lasym: - surf.rs = RBS.transpose() - surf.zc = ZBC.transpose() + surf.rs[:, :] = RBS.transpose() + surf.zc[:, :] = ZBC.transpose() surf.local_full_x = surf.get_dofs() return surf diff --git a/src/simsoptpp/python.cpp b/src/simsoptpp/python.cpp index 168206477..f6a92a553 100644 --- a/src/simsoptpp/python.cpp +++ b/src/simsoptpp/python.cpp @@ -16,6 +16,7 @@ typedef xt::pyarray PyArray; #include "dommaschk.h" #include "reiman.h" #include "boozerradialinterpolant.h" +#include "boozerresidual.h" namespace py = pybind11; @@ -61,37 +62,10 @@ PYBIND11_MODULE(simsoptpp, m) { m.def("compute_kmnc_kmns",&compute_kmnc_kmns); // the computation below is used in boozer_surface_residual. - // - // G*dB_dc - 2*np.sum(B[..., None]*dB_dc, axis=2)[:, :, None, :] * tang[..., None] - B2[..., None, None] * (dxphi_dc + iota * dxtheta_dc) - m.def("boozer_dresidual_dc", [](double G, PyArray& dB_dc, PyArray& B, PyArray& tang, PyArray& B2, PyArray& dxphi_dc, double iota, PyArray& dxtheta_dc) { - int nphi = dB_dc.shape(0); - int ntheta = dB_dc.shape(1); - int ndofs = dB_dc.shape(3); - PyArray res = xt::zeros({nphi, ntheta, 3, ndofs}); - double* B_dB_dc = new double[ndofs]; - for(int i=0; i::dvolume_by_dcoeff_impl(Array& data) { data(m) = temp(m); } } + + + +#include "xsimd/xsimd.hpp" +#include "simdhelpers.h" +#include "vec3dsimd.h" + template void Surface::d2volume_by_dcoeffdcoeff_impl(Array& data) { + constexpr int simd_size = xsimd::simd_type::size; data *= 0.; auto nor = this->normal(); - auto dnor_dc = this->dnormal_by_dcoeff(); - auto d2nor_dcdc = this->d2normal_by_dcoeffdcoeff(); auto xyz = this->gamma(); auto dxyz_dc = this->dgamma_by_dcoeff(); + auto dnor_dc = this->dnormal_by_dcoeff(); + auto dg1_dc = this->dgammadash1_by_dcoeff(); + auto dg2_dc = this->dgammadash2_by_dcoeff(); int ndofs = num_dofs(); + + auto dg1x_dc = AlignedPaddedVec(ndofs, 0); + auto dg1y_dc = AlignedPaddedVec(ndofs, 0); + auto dg1z_dc = AlignedPaddedVec(ndofs, 0); + + auto dg2x_dc = AlignedPaddedVec(ndofs, 0); + auto dg2y_dc = AlignedPaddedVec(ndofs, 0); + auto dg2z_dc = AlignedPaddedVec(ndofs, 0); + + auto dnorx_dc = AlignedPaddedVec(ndofs, 0); + auto dnory_dc = AlignedPaddedVec(ndofs, 0); + auto dnorz_dc = AlignedPaddedVec(ndofs, 0); + + auto dxyzx_dc = AlignedPaddedVec(ndofs, 0); + auto dxyzy_dc = AlignedPaddedVec(ndofs, 0); + auto dxyzz_dc = AlignedPaddedVec(ndofs, 0); + for (int i = 0; i < numquadpoints_phi; ++i) { for (int j = 0; j < numquadpoints_theta; ++j) { - for (int m = 0; m < ndofs; ++m){ - for (int n = 0; n < ndofs; ++n){ - data(m,n) += (1./3) * (dxyz_dc(i,j,0,m)*dnor_dc(i,j,0,n) - +dxyz_dc(i,j,1,m)*dnor_dc(i,j,1,n) - +dxyz_dc(i,j,2,m)*dnor_dc(i,j,2,n)); - data(m,n) += (1./3) * (xyz(i,j,0)*d2nor_dcdc(i,j,0,m,n) + dxyz_dc(i,j,0,n) * dnor_dc(i,j,0,m) - +xyz(i,j,1)*d2nor_dcdc(i,j,1,m,n) + dxyz_dc(i,j,1,n) * dnor_dc(i,j,1,m) - +xyz(i,j,2)*d2nor_dcdc(i,j,2,m,n) + dxyz_dc(i,j,2,n) * dnor_dc(i,j,2,m)); + simd_t xyzij0(xyz(i,j,0)); + simd_t xyzij1(xyz(i,j,1)); + simd_t xyzij2(xyz(i,j,2)); + + for (int n = 0; n < ndofs; ++n) { + dg1x_dc[n] = dg1_dc(i, j, 0, n); + dg1y_dc[n] = dg1_dc(i, j, 1, n); + dg1z_dc[n] = dg1_dc(i, j, 2, n); + + dg2x_dc[n] = dg2_dc(i, j, 0, n); + dg2y_dc[n] = dg2_dc(i, j, 1, n); + dg2z_dc[n] = dg2_dc(i, j, 2, n); + + dnorx_dc[n] = dnor_dc(i, j, 0, n); + dnory_dc[n] = dnor_dc(i, j, 1, n); + dnorz_dc[n] = dnor_dc(i, j, 2, n); + + dxyzx_dc[n] = dxyz_dc(i, j, 0, n); + dxyzy_dc[n] = dxyz_dc(i, j, 1, n); + dxyzz_dc[n] = dxyz_dc(i, j, 2, n); + } + + for (int m = 0; m < ndofs; ++m){ + simd_t dg1_dc_ij0m(dg1_dc(i, j, 0, m)); + simd_t dg1_dc_ij1m(dg1_dc(i, j, 1, m)); + simd_t dg1_dc_ij2m(dg1_dc(i, j, 2, m)); + + simd_t dg2_dc_ij0m(dg2_dc(i, j, 0, m)); + simd_t dg2_dc_ij1m(dg2_dc(i, j, 1, m)); + simd_t dg2_dc_ij2m(dg2_dc(i, j, 2, m)); + + simd_t dxyz_dc_ij0m(dxyz_dc(i, j, 0, m)); + simd_t dxyz_dc_ij1m(dxyz_dc(i, j, 1, m)); + simd_t dxyz_dc_ij2m(dxyz_dc(i, j, 2, m)); + + simd_t dnor_dc_ij0m(dnor_dc(i, j, 0, m)); + simd_t dnor_dc_ij1m(dnor_dc(i, j, 1, m)); + simd_t dnor_dc_ij2m(dnor_dc(i, j, 2, m)); + + for (int n = 0; n < ndofs; n+=simd_size){ + simd_t dg1_dc_ij0n = xs::load_aligned(&dg1x_dc[n]); + simd_t dg1_dc_ij1n = xs::load_aligned(&dg1y_dc[n]); + simd_t dg1_dc_ij2n = xs::load_aligned(&dg1z_dc[n]); + + simd_t dg2_dc_ij0n = xs::load_aligned(&dg2x_dc[n]); + simd_t dg2_dc_ij1n = xs::load_aligned(&dg2y_dc[n]); + simd_t dg2_dc_ij2n = xs::load_aligned(&dg2z_dc[n]); + + simd_t dnor_dc_ij0n = xs::load_aligned(&dnorx_dc[n]); + simd_t dnor_dc_ij1n = xs::load_aligned(&dnory_dc[n]); + simd_t dnor_dc_ij2n = xs::load_aligned(&dnorz_dc[n]); + + simd_t dxyz_dc_ij0n = xs::load_aligned(&dxyzx_dc[n]); + simd_t dxyz_dc_ij1n = xs::load_aligned(&dxyzy_dc[n]); + simd_t dxyz_dc_ij2n = xs::load_aligned(&dxyzz_dc[n]); + + auto d2nor_dcdc_ij0mn = xsimd::fms(dg1_dc_ij1m, dg2_dc_ij2n, dg1_dc_ij2m*dg2_dc_ij1n); + d2nor_dcdc_ij0mn += xsimd::fms(dg1_dc_ij1n, dg2_dc_ij2m, dg1_dc_ij2n*dg2_dc_ij1m); + auto d2nor_dcdc_ij1mn = xsimd::fms(dg1_dc_ij2m, dg2_dc_ij0n, dg1_dc_ij0m*dg2_dc_ij2n); + d2nor_dcdc_ij1mn += xsimd::fms(dg1_dc_ij2n, dg2_dc_ij0m, dg1_dc_ij0n*dg2_dc_ij2m); + auto d2nor_dcdc_ij2mn = xsimd::fms(dg1_dc_ij0m, dg2_dc_ij1n, dg1_dc_ij1m*dg2_dc_ij0n); + d2nor_dcdc_ij2mn += xsimd::fms(dg1_dc_ij0n, dg2_dc_ij1m, dg1_dc_ij1n*dg2_dc_ij0m); + + auto temp = xsimd::fma(dxyz_dc_ij0m, dnor_dc_ij0n, dxyz_dc_ij1m*dnor_dc_ij1n); + auto data1 = (1./3) * xsimd::fma(dxyz_dc_ij2m, dnor_dc_ij2n, temp); + auto data2 = (1./3) * (xsimd::fma(xyzij0, d2nor_dcdc_ij0mn , dxyz_dc_ij0n * dnor_dc_ij0m) + +xsimd::fma(xyzij1, d2nor_dcdc_ij1mn , dxyz_dc_ij1n * dnor_dc_ij1m) + +xsimd::fma(xyzij2, d2nor_dcdc_ij2mn , dxyz_dc_ij2n * dnor_dc_ij2m) ); + + int jjlimit = std::min(simd_size, ndofs-n); + for(int jj=0; jj Date: Wed, 3 May 2023 18:27:34 -0400 Subject: [PATCH 002/176] add example --- examples/2_Intermediate/boozerQA_ls_mpi.py | 194 +++++++++++++++++++++ 1 file changed, 194 insertions(+) create mode 100755 examples/2_Intermediate/boozerQA_ls_mpi.py diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py new file mode 100755 index 000000000..a2979851a --- /dev/null +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -0,0 +1,194 @@ +#!/usr/bin/env python3 +from simsopt.geo import SurfaceXYZTensorFourier, SurfaceRZFourier, BoozerSurface, curves_to_vtk, boozer_surface_residual, \ + ToroidalFlux, Volume, MajorRadius, CurveLength, CurveCurveDistance, NonQuasiSymmetricRatio, Iotas, BoozerResidual, \ + LpCurveCurvature, MeanSquaredCurvature, ArclengthVariation +from simsopt._core import load +from simsopt.objectives import MPIObjective +from simsopt.field import BiotSavart, coils_via_symmetries +from simsopt.configs import get_ncsx_data +from simsopt.objectives import QuadraticPenalty +from scipy.optimize import minimize +from qsc import Qsc as Qsc +import numpy as np +import os +try: + from mpi4py import MPI + comm = MPI.COMM_WORLD + rank = comm.rank + size = comm.size +except ImportError: + comm = None + rank = 0 + size = 1 + +""" +""" + +# Directory for output +IN_DIR = "./inputs/input_ncsx/" +OUT_DIR = "./output/" +os.makedirs(OUT_DIR, exist_ok=True) + +print("Running 2_Intermediate/boozerQA_ls.py") +print("================================") + +base_curves, base_currents, ma = get_ncsx_data() +coils = coils_via_symmetries(base_curves, base_currents, 3, True) +curves = [c.curve for c in coils] +bs = BiotSavart(coils) +bs_tf = BiotSavart(coils) +current_sum = sum(abs(c.current.get_value()) for c in coils) +ncoils = len(base_curves) + +## COMPUTE THE INITIAL SURFACE ON WHICH WE WANT TO OPTIMIZE FOR QA## +# Resolution details of surface on which we optimize for qa +mpol = 6 +ntor = 6 +stellsym = True +nfp = 3 + +phis = np.linspace(0, 1/nfp, 2*ntor+1+5, endpoint=False) +thetas = np.linspace(0, 1, 2*mpol+1+5, endpoint=False) +s = SurfaceXYZTensorFourier(mpol=mpol, ntor=ntor, stellsym=stellsym, nfp=nfp, quadpoints_phi=phis, quadpoints_theta=thetas) + +boozer_surface, res = load(IN_DIR + f"surface_{rank}.json") +res = boozer_surface.run_code('ls', res['iota'], res['G']) + +## SET UP THE OPTIMIZATION PROBLEM AS A SUM OF OPTIMIZABLES ## +bs_nonQS = BiotSavart(coils) +mr = MajorRadius(boozer_surface) +ls = [CurveLength(c) for c in base_curves] +iotas = Iotas(boozer_surface) +mean_iota = MPIObjective([iotas], comm) + + +CC_THRESHOLD = 0.15 +KAPPA_THRESHOLD = 15. +MSC_THRESHOLD = 15. +IOTAS_TARGET = -0.4 + +RES_WEIGHT = 1e3 +LENGTH_WEIGHT = 1. +MR_WEIGHT = 1. +CC_WEIGHT = 1e2 +KAPPA_WEIGHT = 1. +MSC_WEIGHT = 1. +IOTAS_WEIGHT = 1. +ARCLENGTH_WEIGHT = 1e-2 + +Jnqs = NonQuasiSymmetricRatio(boozer_surface, bs_nonQS) +Jbr = BoozerResidual(boozer_surface, BiotSavart(coils)) +J_nonQSRatio = MPIObjective([Jnqs], comm) +JBoozerResidual = MPIObjective([Jbr], comm) +Jiotas = IOTAS_WEIGHT * QuadraticPenalty(mean_iota, IOTAS_TARGET, 'identity') +if rank == 0: + J_major_radius = QuadraticPenalty(mr, mr.J(), 'identity') # target major radius only on innermost surface +else: + J_major_radius = 0 * QuadraticPenalty(mr, mr.J(), 'identity') # target major radius only on innermost surface + +Jls = LENGTH_WEIGHT * QuadraticPenalty(sum(ls), float(sum(ls).J()), 'max') +Jccdist = CurveCurveDistance(curves, CC_THRESHOLD, num_basecurves=ncoils) +Jcs = KAPPA_WEIGHT * sum([LpCurveCurvature(c, 2, KAPPA_THRESHOLD) for c in base_curves]) +Jmscs = [MeanSquaredCurvature(c) for c in base_curves] +Jmr = MR_WEIGHT * MPIObjective([J_major_radius], comm) +Jals = [ArclengthVariation(c) for c in base_curves] + +JF = J_nonQSRatio + RES_WEIGHT * JBoozerResidual + Jiotas + Jmr \ + + Jls + CC_WEIGHT * Jccdist + Jcs\ + + MSC_WEIGHT * sum(QuadraticPenalty(J, MSC_THRESHOLD, "max") for J in Jmscs) \ + + ARCLENGTH_WEIGHT * sum(Jals) + +boozer_surface.surface.to_vtk(OUT_DIR + f"surf_init_{rank}") +if comm is None or comm.rank == 0: + curves_to_vtk(curves, OUT_DIR + f"curves_init") + +# let's fix the coil current +base_currents[0].fix_all() + +def fun(dofs): + # save these as a backup in case the boozer surface Newton solve fails + sdofs_prev = boozer_surface.surface.x + iota_prev = boozer_surface.res['iota'] + G_prev = boozer_surface.res['G'] + + JF.x = dofs + J = JF.J() + grad = JF.dJ() + + success = boozer_surface.res['success'] if comm is not None else MPI.COMM_WORLD.allreduce(boozer_surface.res['success'], op=MPI.LAND) + if not success: + # failed, so reset back to previous surface and return a large value + # of the objective. The purpose is to trigger the line search to reduce + # the step size. + J = 1e3 + boozer_surface.surface.x = sdofs_prev + boozer_surface.res['iota'] = iota_prev + boozer_surface.res['G'] = G_prev + + return J, grad + +def callback(x): + J = JF.J() + grad = JF.dJ() + + cl_string = ", ".join([f"{J.J():.3f}" for J in ls]) + kappa_string = ", ".join([f"{np.max(c.kappa()):.3f}" for c in base_curves]) + msc_string = ", ".join([f"{Jmsc.J():.3f}" for Jmsc in Jmscs]) + iotas_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(iotas.J()) if comm is not None else iotas.J()) ]) + mr_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(boozer_surface.surface.major_radius()) if comm is not None else boozer_surface.surface.major_radius() ) ]) + ar_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(boozer_surface.surface.aspect_ratio()) if comm is not None else boozer_surface.surface.aspect_ratio() ) ]) + br_string = ", ".join([f"{val:.3e}" for val in (comm.allgather(Jbr.J()) if comm is not None else Jbr.J() ) ]) + nqs_ratio_string = ", ".join([f"{val:.3e}" for val in (comm.allgather(Jnqs.J()) if comm is not None else Jnqs.J() ) ]) + outstr = f"\nJ={J:.3e}\n" + outstr += f"nqas_ratio_string=[{nqs_ratio_string}], \n" + outstr += f"br=[{br_string}], \n" + outstr += f"mean_iota={mean_iota.J():.3f}, \n" + outstr += f"iotas=[{iotas_string}], \n" + outstr += f"mr=[{mr_string}], \n" + outstr += f"AR=[{ar_string}], \n" + outstr += f"Len=sum([{cl_string}])={sum(J.J() for J in ls):.3f},\n" + outstr += f"kappa=[{kappa_string}], \n" + outstr += f"msc=[{msc_string}], \n" + outstr += f"cc_dist={Jccdist.shortest_distance():.3f}, \n" + outstr += f"ā•‘āˆ‡Jā•‘={np.linalg.norm(grad):.3e}\n\n" + if comm is None or comm.rank == 0: + print(outstr, flush=True) + + +#print(""" +################################################################################# +#### Perform a Taylor test ###################################################### +################################################################################# +#""") +#f = fun +#dofs = JF.x +#np.random.seed(1) +#h = np.random.uniform(size=dofs.shape) +#J0, dJ0 = f(dofs) +#dJh = sum(dJ0 * h) +#for eps in [1e-3, 1e-4, 1e-5, 1e-6, 1e-7, 1e-8, 1e-9]: +# J1, _ = f(dofs + 2*eps*h) +# J2, _ = f(dofs + eps*h) +# J3, _ = f(dofs - eps*h) +# J4, _ = f(dofs - 2*eps*h) +# print("err", ((J1*(-1/12) + J2*(8/12) + J3*(-8/12) + J4*(1/12))/eps - dJh)/np.linalg.norm(dJh)) + +dofs = JF.x +callback(dofs) +#quit() + +print(""" +################################################################################ +### Run the optimization ####################################################### +################################################################################ +""") +# Number of iterations to perform: +ci = "CI" in os.environ and os.environ['CI'].lower() in ['1', 'true'] +MAXITER = 50 if ci else 1e3 + +res = minimize(fun, dofs, jac=True, method='BFGS', options={'maxiter': MAXITER}, tol=1e-15, callback=callback) +curves_to_vtk(curves, OUT_DIR + f"curves_opt") +boozer_surface.surface.to_vtk(OUT_DIR + "surf_opt") + +print("End of 2_Intermediate/boozerQA_ls.py") +print("================================") From ec3dfe4288992dea3011cad02501972732631754 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 3 May 2023 18:28:19 -0400 Subject: [PATCH 003/176] missing cpp files --- src/simsoptpp/boozerresidual.cpp | 703 +++++++++++++++++++++++++++++++ src/simsoptpp/boozerresidual.h | 14 + 2 files changed, 717 insertions(+) create mode 100644 src/simsoptpp/boozerresidual.cpp create mode 100644 src/simsoptpp/boozerresidual.h diff --git a/src/simsoptpp/boozerresidual.cpp b/src/simsoptpp/boozerresidual.cpp new file mode 100644 index 000000000..13931d3c8 --- /dev/null +++ b/src/simsoptpp/boozerresidual.cpp @@ -0,0 +1,703 @@ +#include "boozerresidual.h" + +#include "xsimd/xsimd.hpp" +#include "simdhelpers.h" +#include "vec3dsimd.h" +#include "xtensor/xarray.hpp" +#include "xtensor/xview.hpp" +#include "xtensor/xstrided_view.hpp" +#include +#include "xtensor/xadapt.hpp" + +double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B){ + int nphi = B.shape(0); + int ntheta = B.shape(1); + Array res = xt::zeros({nphi, ntheta, 3}); + int num_points = 3 * nphi * ntheta; + for(int i=0; i +void boozer_residual_ds_impl(double G, double iota, T& B, T& dB_dx, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres){ + int nphi = xphi.shape(0); + int ntheta = xtheta.shape(1); + int ndofs = dx_ds.shape(3); + int num_points = 3 * nphi * ntheta; + + constexpr int simd_size = xsimd::simd_type::size; + auto dx_ds_ij0 = AlignedPaddedVec(ndofs, 0); + auto dx_ds_ij1 = AlignedPaddedVec(ndofs, 0); + auto dx_ds_ij2 = AlignedPaddedVec(ndofs, 0); + auto dxphi_ds_ij0 = AlignedPaddedVec(ndofs, 0); + auto dxphi_ds_ij1 = AlignedPaddedVec(ndofs, 0); + auto dxphi_ds_ij2 = AlignedPaddedVec(ndofs, 0); + auto dxtheta_ds_ij0 = AlignedPaddedVec(ndofs, 0); + auto dxtheta_ds_ij1 = AlignedPaddedVec(ndofs, 0); + auto dxtheta_ds_ij2 = AlignedPaddedVec(ndofs, 0); + + simd_t it(iota); + simd_t GG(G); + for(int i=0; i boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds){ + // flatten the quadrature points + int nphi = xphi.shape(0); + int ntheta = xtheta.shape(1); + int ndofs = dx_ds.shape(3); + int num_points = nphi * ntheta; + + int num_threads= 0; + #pragma omp parallel reduction(+:num_threads) + num_threads += 1; + + int batch_size = num_points / num_threads; + if(num_points % num_threads != 0) + batch_size++; + + vector res_list(num_threads, 0.); + vector> dres_list; + + for(int idx = 0; idx < num_threads; idx++){ + dres_list.push_back(xt::zeros({ndofs+2})); + } + + double res =0.; + xt::xarray dres =xt::zeros({ndofs+2}); + + + #pragma omp parallel for + for (int idx = 0; idx < num_threads; ++idx) { + int idx_start = batch_size * idx; + int idx_end = batch_size * (idx+1) > num_points ? num_points : batch_size*(idx+1); + size_t diff = idx_end-idx_start; + + size_t size_B = 3; + size_t size_dB_dx = 3 * 3; + size_t size_d2B_dx2 = 3 * 3 * 3; + size_t size_xphi = 3; + size_t size_xtheta = 3; + size_t size_dx_ds = 3 * ndofs; + size_t size_dxphi_ds = 3 * ndofs; + size_t size_dxtheta_ds = 3 * ndofs; + + vector shape_B = {diff, 1, 3}; + vector shape_dB_dx = {diff, 1, 3, 3}; + vector shape_d2B_dx2 = {diff, 1, 3, 3, 3}; + vector shape_xphi = {diff, 1, 3}; + vector shape_xtheta = {diff, 1, 3}; + vector shape_dx_ds = {diff, 1, 3, ndofs}; + vector shape_dxphi_ds = {diff, 1, 3, ndofs}; + vector shape_dxtheta_ds = {diff, 1, 3, ndofs}; + + xt::xarray bB = xt::adapt(B.data() + idx_start*size_B , diff*size_B , xt::no_ownership(), shape_B ); + xt::xarray bdB_dx = xt::adapt(dB_dx.data() + idx_start*size_dB_dx , diff*size_dB_dx , xt::no_ownership(), shape_dB_dx ); + xt::xarray bxphi = xt::adapt(xphi.data() + idx_start*size_xphi , diff*size_xphi , xt::no_ownership(), shape_xphi ); + xt::xarray bxtheta = xt::adapt(xtheta.data() + idx_start*size_xtheta , diff*size_xtheta , xt::no_ownership(), shape_xtheta ); + xt::xarray bdx_ds = xt::adapt(dx_ds.data() + idx_start*size_dx_ds , diff*size_dx_ds , xt::no_ownership(), shape_dx_ds ); + xt::xarray bdxphi_ds = xt::adapt(dxphi_ds.data() + idx_start*size_dxphi_ds , diff*size_dxphi_ds , xt::no_ownership(), shape_dxphi_ds ); + xt::xarray bdxtheta_ds = xt::adapt(dxtheta_ds.data()+ idx_start*size_dxtheta_ds, diff*size_dxtheta_ds, xt::no_ownership(), shape_dxtheta_ds); + + boozer_residual_ds_impl>(G, iota, bB, bdB_dx, bxphi, bxtheta, bdx_ds, bdxphi_ds, bdxtheta_ds, res_list[idx], dres_list[idx]); + res_list[idx] *= (idx_end-idx_start)*3; + dres_list[idx] *= (idx_end-idx_start)*3; + } + + for(int i=0; i < num_threads; i++){ + res+=res_list[i]/num_points/3.; + dres+=dres_list[i]/num_points/3.; + } + + auto tup = std::make_tuple(res, dres); + return tup; +} + + + + +template +void boozer_residual_ds2_impl(double G, double iota, T& B, T& dB_dx, T& d2B_dx2, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres, T& d2res){ + int nphi = xphi.shape(0); + int ntheta = xtheta.shape(1); + int ndofs = dx_ds.shape(3); + int num_points = 3 * nphi * ntheta; + + constexpr int simd_size = xsimd::simd_type::size; + auto dx_ds_ij0 = AlignedPaddedVec(ndofs, 0); + auto dx_ds_ij1 = AlignedPaddedVec(ndofs, 0); + auto dx_ds_ij2 = AlignedPaddedVec(ndofs, 0); + auto dxphi_ds_ij0 = AlignedPaddedVec(ndofs, 0); + auto dxphi_ds_ij1 = AlignedPaddedVec(ndofs, 0); + auto dxphi_ds_ij2 = AlignedPaddedVec(ndofs, 0); + auto dxtheta_ds_ij0 = AlignedPaddedVec(ndofs, 0); + auto dxtheta_ds_ij1 = AlignedPaddedVec(ndofs, 0); + auto dxtheta_ds_ij2 = AlignedPaddedVec(ndofs, 0); + + auto drtilij0 = AlignedPaddedVec(ndofs+2, 0); + auto drtilij1 = AlignedPaddedVec(ndofs+2, 0); + auto drtilij2 = AlignedPaddedVec(ndofs+2, 0); + + auto dresij0 = AlignedPaddedVec(ndofs+2, 0); + auto dresij1 = AlignedPaddedVec(ndofs+2, 0); + auto dresij2 = AlignedPaddedVec(ndofs+2, 0); + + auto dw_ij = AlignedPaddedVec(ndofs+2, 0); + + auto dtang_ij0 = AlignedPaddedVec(ndofs+2, 0); + auto dtang_ij1 = AlignedPaddedVec(ndofs+2, 0); + auto dtang_ij2 = AlignedPaddedVec(ndofs+2, 0); + + auto dB2_ij = AlignedPaddedVec(ndofs+2, 0); + auto dBij0 = AlignedPaddedVec(ndofs+2, 0); + auto dBij1 = AlignedPaddedVec(ndofs+2, 0); + auto dBij2 = AlignedPaddedVec(ndofs+2, 0); + auto dmodB_ij = AlignedPaddedVec(ndofs+2, 0); + + simd_t it(iota); + simd_t GG(G); + + for(int i=0; i boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds){ + // flatten the quadrature points + int nphi = xphi.shape(0); + int ntheta = xtheta.shape(1); + int ndofs = dx_ds.shape(3); + int num_points = nphi * ntheta; + + int num_threads= 0; + #pragma omp parallel reduction(+:num_threads) + num_threads += 1; + + int batch_size = num_points / num_threads; + if(num_points % num_threads != 0) + batch_size++; + + vector res_list(num_threads, 0.); + vector> dres_list; + vector> d2res_list; + + for(int idx = 0; idx < num_threads; idx++){ + dres_list.push_back(xt::zeros({ndofs+2})); + d2res_list.push_back(xt::zeros({ndofs+2, ndofs+2})); + } + + double res =0.; + xt::xarray dres =xt::zeros({ndofs+2}); + xt::xarray d2res=xt::zeros({ndofs+2, ndofs+2}); + + + #pragma omp parallel for + for (int idx = 0; idx < num_threads; ++idx) { + int idx_start = batch_size * idx; + int idx_end = batch_size * (idx+1) > num_points ? num_points : batch_size*(idx+1); + size_t diff = idx_end-idx_start; + + size_t size_B = 3; + size_t size_dB_dx = 3 * 3; + size_t size_d2B_dx2 = 3 * 3 * 3; + size_t size_xphi = 3; + size_t size_xtheta = 3; + size_t size_dx_ds = 3 * ndofs; + size_t size_dxphi_ds = 3 * ndofs; + size_t size_dxtheta_ds = 3 * ndofs; + + vector shape_B = {diff, 1, 3}; + vector shape_dB_dx = {diff, 1, 3, 3}; + vector shape_d2B_dx2 = {diff, 1, 3, 3, 3}; + vector shape_xphi = {diff, 1, 3}; + vector shape_xtheta = {diff, 1, 3}; + vector shape_dx_ds = {diff, 1, 3, ndofs}; + vector shape_dxphi_ds = {diff, 1, 3, ndofs}; + vector shape_dxtheta_ds = {diff, 1, 3, ndofs}; + + xt::xarray bB = xt::adapt(B.data() + idx_start*size_B , diff*size_B , xt::no_ownership(), shape_B ); + xt::xarray bdB_dx = xt::adapt(dB_dx.data() + idx_start*size_dB_dx , diff*size_dB_dx , xt::no_ownership(), shape_dB_dx ); + xt::xarray bdB2_dx2 = xt::adapt(d2B_dx2.data() + idx_start*size_d2B_dx2 , diff*size_d2B_dx2 , xt::no_ownership(), shape_d2B_dx2 ); + xt::xarray bxphi = xt::adapt(xphi.data() + idx_start*size_xphi , diff*size_xphi , xt::no_ownership(), shape_xphi ); + xt::xarray bxtheta = xt::adapt(xtheta.data() + idx_start*size_xtheta , diff*size_xtheta , xt::no_ownership(), shape_xtheta ); + xt::xarray bdx_ds = xt::adapt(dx_ds.data() + idx_start*size_dx_ds , diff*size_dx_ds , xt::no_ownership(), shape_dx_ds ); + xt::xarray bdxphi_ds = xt::adapt(dxphi_ds.data() + idx_start*size_dxphi_ds , diff*size_dxphi_ds , xt::no_ownership(), shape_dxphi_ds ); + xt::xarray bdxtheta_ds = xt::adapt(dxtheta_ds.data()+ idx_start*size_dxtheta_ds, diff*size_dxtheta_ds, xt::no_ownership(), shape_dxtheta_ds); + + boozer_residual_ds2_impl>(G, iota, bB, bdB_dx, bdB2_dx2, bxphi, bxtheta, bdx_ds, bdxphi_ds, bdxtheta_ds, res_list[idx], dres_list[idx], d2res_list[idx]); + res_list[idx] *= (idx_end-idx_start)*3; + dres_list[idx] *= (idx_end-idx_start)*3; + d2res_list[idx] *= (idx_end-idx_start)*3; + } + + for(int i=0; i < num_threads; i++){ + res+=res_list[i]/num_points/3.; + dres+=dres_list[i]/num_points/3.; + d2res+=d2res_list[i]/num_points/3.; + } + + auto tup = std::make_tuple(res, dres, d2res); + return tup; +} + +Array boozer_residual_dc(double G, Array& dB_dc, Array& B, Array& tang, Array& B2, Array& dxphi_dc, double iota, Array& dxtheta_dc){ + int nphi = dB_dc.shape(0); + int ntheta = dB_dc.shape(1); + int ndofs = dB_dc.shape(3); + Array res = xt::zeros({nphi, ntheta, 3, ndofs}); + double* B_dB_dc = new double[ndofs]; + for(int i=0; i Array; +using std::vector; + +double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B); +std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds); +std::tuple boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds); + + +Array boozer_residual_dc(double G, Array& dB_dc, Array& B, Array& tang, Array& B2, Array& dxphi_dc, double iota, Array& dxtheta_dc); From 7a2d98c9b32c126a99c493318157cb427de0fa6c Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Thu, 4 May 2023 12:31:25 -0400 Subject: [PATCH 004/176] edits --- examples/2_Intermediate/boozerQA_ls_mpi.py | 92 +++++++++++++++------- src/simsopt/geo/boozersurface.py | 1 + 2 files changed, 64 insertions(+), 29 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index a2979851a..504efd2b0 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -67,7 +67,7 @@ MSC_THRESHOLD = 15. IOTAS_TARGET = -0.4 -RES_WEIGHT = 1e3 +RES_WEIGHT = 1e4 LENGTH_WEIGHT = 1. MR_WEIGHT = 1. CC_WEIGHT = 1e2 @@ -80,23 +80,35 @@ Jbr = BoozerResidual(boozer_surface, BiotSavart(coils)) J_nonQSRatio = MPIObjective([Jnqs], comm) JBoozerResidual = MPIObjective([Jbr], comm) -Jiotas = IOTAS_WEIGHT * QuadraticPenalty(mean_iota, IOTAS_TARGET, 'identity') +Jiotas = QuadraticPenalty(mean_iota, IOTAS_TARGET, 'identity') if rank == 0: J_major_radius = QuadraticPenalty(mr, mr.J(), 'identity') # target major radius only on innermost surface else: J_major_radius = 0 * QuadraticPenalty(mr, mr.J(), 'identity') # target major radius only on innermost surface -Jls = LENGTH_WEIGHT * QuadraticPenalty(sum(ls), float(sum(ls).J()), 'max') +Jls = QuadraticPenalty(sum(ls), float(sum(ls).J()), 'max') Jccdist = CurveCurveDistance(curves, CC_THRESHOLD, num_basecurves=ncoils) -Jcs = KAPPA_WEIGHT * sum([LpCurveCurvature(c, 2, KAPPA_THRESHOLD) for c in base_curves]) -Jmscs = [MeanSquaredCurvature(c) for c in base_curves] -Jmr = MR_WEIGHT * MPIObjective([J_major_radius], comm) -Jals = [ArclengthVariation(c) for c in base_curves] - -JF = J_nonQSRatio + RES_WEIGHT * JBoozerResidual + Jiotas + Jmr \ - + Jls + CC_WEIGHT * Jccdist + Jcs\ - + MSC_WEIGHT * sum(QuadraticPenalty(J, MSC_THRESHOLD, "max") for J in Jmscs) \ - + ARCLENGTH_WEIGHT * sum(Jals) +Jcs = sum([LpCurveCurvature(c, 2, KAPPA_THRESHOLD) for c in base_curves]) +msc_list = [MeanSquaredCurvature(c) for c in base_curves] +J_msc = sum(QuadraticPenalty(J, MSC_THRESHOLD, "max") for J in msc_list) +Jmr = MPIObjective([J_major_radius], comm) +Jals = sum([ArclengthVariation(c) for c in base_curves]) + + +JF = J_nonQSRatio + RES_WEIGHT * JBoozerResidual + IOTAS_WEIGHT * Jiotas + MR_WEIGHT * Jmr \ + + LENGTH_WEIGHT * Jls + CC_WEIGHT * Jccdist + KAPPA_WEIGHT * Jcs\ + + MSC_WEIGHT * J_msc \ + + ARCLENGTH_WEIGHT * Jals + +penalty_list = {"JnonQSRatio":[1, J_nonQSRatio], + "JBoozerResidual":[RES_WEIGHT, JBoozerResidual], + "JIotas":[IOTAS_WEIGHT, Jiotas], + "JMr":[MR_WEIGHT, Jmr], + "Jls":[LENGTH_WEIGHT, Jls], + "Jccdist":[CC_WEIGHT, Jccdist], + "Jcurv":[KAPPA_WEIGHT, Jcs], + "Jmsc":[MSC_WEIGHT, J_msc], + "Jals":[ARCLENGTH_WEIGHT, Jals]} boozer_surface.surface.to_vtk(OUT_DIR + f"surf_init_{rank}") if comm is None or comm.rank == 0: @@ -126,31 +138,53 @@ def fun(dofs): boozer_surface.res['G'] = G_prev return J, grad - +#JF = J_nonQSRatio + RES_WEIGHT * JBoozerResidual + IOTAS_WEIGHT * Jiotas + MR_WEIGHT * Jmr \ +# + LENGTH_WEIGHT * Jls + CC_WEIGHT * Jccdist + Jcs\ +# + MSC_WEIGHT * sum(QuadraticPenalty(J, MSC_THRESHOLD, "max") for J in Jmscs) \ +# + ARCLENGTH_WEIGHT * sum(Jals) def callback(x): J = JF.J() grad = JF.dJ() - cl_string = ", ".join([f"{J.J():.3f}" for J in ls]) + cl_string = ", ".join([f"{J.J():5.3f}" for J in ls]) kappa_string = ", ".join([f"{np.max(c.kappa()):.3f}" for c in base_curves]) - msc_string = ", ".join([f"{Jmsc.J():.3f}" for Jmsc in Jmscs]) + msc_string = ", ".join([f"{Jmsc.J():.3f}" for Jmsc in msc_list]) iotas_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(iotas.J()) if comm is not None else iotas.J()) ]) - mr_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(boozer_surface.surface.major_radius()) if comm is not None else boozer_surface.surface.major_radius() ) ]) + mr_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(boozer_surface.surface.minor_radius()) if comm is not None else boozer_surface.surface.minor_radius() ) ]) + mR_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(boozer_surface.surface.major_radius()) if comm is not None else boozer_surface.surface.major_radius() ) ]) ar_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(boozer_surface.surface.aspect_ratio()) if comm is not None else boozer_surface.surface.aspect_ratio() ) ]) br_string = ", ".join([f"{val:.3e}" for val in (comm.allgather(Jbr.J()) if comm is not None else Jbr.J() ) ]) nqs_ratio_string = ", ".join([f"{val:.3e}" for val in (comm.allgather(Jnqs.J()) if comm is not None else Jnqs.J() ) ]) - outstr = f"\nJ={J:.3e}\n" - outstr += f"nqas_ratio_string=[{nqs_ratio_string}], \n" - outstr += f"br=[{br_string}], \n" - outstr += f"mean_iota={mean_iota.J():.3f}, \n" - outstr += f"iotas=[{iotas_string}], \n" - outstr += f"mr=[{mr_string}], \n" - outstr += f"AR=[{ar_string}], \n" - outstr += f"Len=sum([{cl_string}])={sum(J.J() for J in ls):.3f},\n" - outstr += f"kappa=[{kappa_string}], \n" - outstr += f"msc=[{msc_string}], \n" - outstr += f"cc_dist={Jccdist.shortest_distance():.3f}, \n" - outstr += f"ā•‘āˆ‡Jā•‘={np.linalg.norm(grad):.3e}\n\n" + + width = 35 + outstr = "\n" + s = "J"; outstr += f"{s:{width}} {J:.3e} \n" + s = "ā•‘āˆ‡Jā•‘"; outstr += f"{s:{width}} {np.linalg.norm(grad):.3e} \n\n" + + width = 15 + for pen in penalty_list.keys(): + s = pen; outstr+=f"{s:<{width}} " + outstr+="\n" + for pen in penalty_list.keys(): + w = penalty_list[pen][0] + val = penalty_list[pen][1].J() + outstr+=f"{w*val:<{width}.3e} " + + outstr+="\n\n" + width = 35 + s = "nonQS ratio"; outstr += f"{s:{width}} {nqs_ratio_string} \n" + s = "Boozer Residual"; outstr += f"{s:{width}} {br_string} \n" + s = "<Ī¹>"; outstr += f"{s:{width}} {mean_iota.J():.3f} \n" + s = "Ī¹ on surfaces"; outstr += f"{s:{width}} {iotas_string} \n" + s = "major radius on surfaces"; outstr += f"{s:{width}} {mR_string} \n" + s = "minor radius on surfaces"; outstr += f"{s:{width}} {mr_string} \n" + s = "aspect ratio on surfaces"; outstr += f"{s:{width}} {ar_string} \n" + s = "shortest coil to coil distance"; outstr += f"{s:{width}} {Jccdist.shortest_distance():.3f} \n" + s = "coil lengths"; outstr += f"{s:{width}} {cl_string} \n" + s = "coil length sum"; outstr += f"{s:{width}} {sum(J.J() for J in ls):.3f} \n" + s = "max Īŗ"; outstr += f"{s:{width}} {kappa_string} \n" + s = "āˆ« Īŗ^2 dl / āˆ« dl"; outstr += f"{s:{width}} {msc_string} \n" + outstr+="\n\n" if comm is None or comm.rank == 0: print(outstr, flush=True) @@ -175,7 +209,7 @@ def callback(x): dofs = JF.x callback(dofs) -#quit() +quit() print(""" ################################################################################ diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 6a5e2f7d6..69e8a0cbe 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -67,6 +67,7 @@ def run_code(self, boozer_type, iota, G=None): elif boozer_type == 'ls': # first try BFGS + #res = self.minimize_boozer_penalty_constraints_ls(tol=1e-10, maxiter=100, constraint_weight=self.constraint_weight, iota=iota, G=G, method='manual') res = self.compute_boozerls_BFGS(tol=1e-10, maxiter=1e3, constraint_weight=self.constraint_weight, iota=iota, G=G) iota, G = res['iota'], res['G'] From e9ab133b33792bebe3469f8f654ad86a4b899fe5 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 5 May 2023 18:00:33 -0400 Subject: [PATCH 005/176] cleaned up NCSX example --- examples/2_Intermediate/boozerQA_ls_mpi.py | 219 +++++++++------------ src/simsopt/geo/boozersurface.py | 24 ++- src/simsopt/objectives/utilities.py | 38 +++- 3 files changed, 142 insertions(+), 139 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 504efd2b0..911113197 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -3,12 +3,11 @@ ToroidalFlux, Volume, MajorRadius, CurveLength, CurveCurveDistance, NonQuasiSymmetricRatio, Iotas, BoozerResidual, \ LpCurveCurvature, MeanSquaredCurvature, ArclengthVariation from simsopt._core import load -from simsopt.objectives import MPIObjective +from simsopt.objectives import MPIObjective, MPIOptimizable from simsopt.field import BiotSavart, coils_via_symmetries from simsopt.configs import get_ncsx_data from simsopt.objectives import QuadraticPenalty from scipy.optimize import minimize -from qsc import Qsc as Qsc import numpy as np import os try: @@ -16,53 +15,43 @@ comm = MPI.COMM_WORLD rank = comm.rank size = comm.size + def pprint(*args, **kwargs): + if comm.rank == 0: # only print on rank 0 + print(*args, **kwargs) + except ImportError: comm = None - rank = 0 size = 1 - -""" -""" + pprint = print # Directory for output IN_DIR = "./inputs/input_ncsx/" OUT_DIR = "./output/" os.makedirs(OUT_DIR, exist_ok=True) -print("Running 2_Intermediate/boozerQA_ls.py") -print("================================") - -base_curves, base_currents, ma = get_ncsx_data() -coils = coils_via_symmetries(base_curves, base_currents, 3, True) -curves = [c.curve for c in coils] -bs = BiotSavart(coils) -bs_tf = BiotSavart(coils) -current_sum = sum(abs(c.current.get_value()) for c in coils) -ncoils = len(base_curves) +pprint("Running 2_Intermediate/boozerQA_ls.py") +pprint("================================") -## COMPUTE THE INITIAL SURFACE ON WHICH WE WANT TO OPTIMIZE FOR QA## -# Resolution details of surface on which we optimize for qa -mpol = 6 -ntor = 6 -stellsym = True -nfp = 3 +base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress= load(IN_DIR + f"ncsx_init.json") +nsurfaces = 2 +surfaces = surfaces[:nsurfaces] +boozer_surfaces = boozer_surfaces[:nsurfaces] +ress = ress[:nsurfaces] -phis = np.linspace(0, 1/nfp, 2*ntor+1+5, endpoint=False) -thetas = np.linspace(0, 1, 2*mpol+1+5, endpoint=False) -s = SurfaceXYZTensorFourier(mpol=mpol, ntor=ntor, stellsym=stellsym, nfp=nfp, quadpoints_phi=phis, quadpoints_theta=thetas) +for boozer_surface, res in zip(boozer_surfaces, ress): + boozer_surface.run_code('ls', res['iota'], res['G'], verbose=False) -boozer_surface, res = load(IN_DIR + f"surface_{rank}.json") -res = boozer_surface.run_code('ls', res['iota'], res['G']) +ncoils = len(base_curves) -## SET UP THE OPTIMIZATION PROBLEM AS A SUM OF OPTIMIZABLES ## -bs_nonQS = BiotSavart(coils) -mr = MajorRadius(boozer_surface) -ls = [CurveLength(c) for c in base_curves] -iotas = Iotas(boozer_surface) -mean_iota = MPIObjective([iotas], comm) +mpi_surfaces = MPIOptimizable(surfaces, ["x"], comm) +mpi_boozer_surfaces = MPIOptimizable(boozer_surfaces, ["res", "need_to_run_code"], comm) +mrs = [MajorRadius(boozer_surface) for boozer_surface in boozer_surfaces] +iotas = [Iotas(boozer_surface) for boozer_surface in boozer_surfaces] +nonQSs = [NonQuasiSymmetricRatio(boozer_surface, BiotSavart(coils)) for boozer_surface in boozer_surfaces] +brs = [BoozerResidual(boozer_surface, BiotSavart(coils)) for boozer_surface in boozer_surfaces] -CC_THRESHOLD = 0.15 +MIN_DIST_THRESHOLD = 0.15 KAPPA_THRESHOLD = 15. MSC_THRESHOLD = 15. IOTAS_TARGET = -0.4 @@ -70,148 +59,120 @@ RES_WEIGHT = 1e4 LENGTH_WEIGHT = 1. MR_WEIGHT = 1. -CC_WEIGHT = 1e2 +MIN_DIST_WEIGHT = 1e2 KAPPA_WEIGHT = 1. MSC_WEIGHT = 1. IOTAS_WEIGHT = 1. ARCLENGTH_WEIGHT = 1e-2 -Jnqs = NonQuasiSymmetricRatio(boozer_surface, bs_nonQS) -Jbr = BoozerResidual(boozer_surface, BiotSavart(coils)) -J_nonQSRatio = MPIObjective([Jnqs], comm) -JBoozerResidual = MPIObjective([Jbr], comm) +mean_iota = MPIObjective(iotas, comm, needs_splitting=True) Jiotas = QuadraticPenalty(mean_iota, IOTAS_TARGET, 'identity') -if rank == 0: - J_major_radius = QuadraticPenalty(mr, mr.J(), 'identity') # target major radius only on innermost surface -else: - J_major_radius = 0 * QuadraticPenalty(mr, mr.J(), 'identity') # target major radius only on innermost surface +JnonQSRatio = MPIObjective(nonQSs, comm, needs_splitting=True) +JBoozerResidual = MPIObjective(brs, comm, needs_splitting=True) +Jmajor_radius = MPIObjective([len(mrs)*QuadraticPenalty(mr, mr.J(), 'identity') if idx == 0 else 0*QuadraticPenalty(mr, mr.J(), 'identity') for idx, mr in enumerate(mrs)], comm, needs_splitting=True) +ls = [CurveLength(c) for c in base_curves] Jls = QuadraticPenalty(sum(ls), float(sum(ls).J()), 'max') -Jccdist = CurveCurveDistance(curves, CC_THRESHOLD, num_basecurves=ncoils) +Jccdist = CurveCurveDistance(curves, MIN_DIST_THRESHOLD, num_basecurves=ncoils) Jcs = sum([LpCurveCurvature(c, 2, KAPPA_THRESHOLD) for c in base_curves]) msc_list = [MeanSquaredCurvature(c) for c in base_curves] -J_msc = sum(QuadraticPenalty(J, MSC_THRESHOLD, "max") for J in msc_list) -Jmr = MPIObjective([J_major_radius], comm) +Jmsc = sum(QuadraticPenalty(J, MSC_THRESHOLD, "max") for J in msc_list) Jals = sum([ArclengthVariation(c) for c in base_curves]) - -JF = J_nonQSRatio + RES_WEIGHT * JBoozerResidual + IOTAS_WEIGHT * Jiotas + MR_WEIGHT * Jmr \ - + LENGTH_WEIGHT * Jls + CC_WEIGHT * Jccdist + KAPPA_WEIGHT * Jcs\ - + MSC_WEIGHT * J_msc \ +JF = JnonQSRatio + RES_WEIGHT * JBoozerResidual + IOTAS_WEIGHT * Jiotas + MR_WEIGHT * Jmajor_radius \ + + LENGTH_WEIGHT * Jls + MIN_DIST_WEIGHT * Jccdist + KAPPA_WEIGHT * Jcs\ + + MSC_WEIGHT * Jmsc \ + ARCLENGTH_WEIGHT * Jals -penalty_list = {"JnonQSRatio":[1, J_nonQSRatio], - "JBoozerResidual":[RES_WEIGHT, JBoozerResidual], - "JIotas":[IOTAS_WEIGHT, Jiotas], - "JMr":[MR_WEIGHT, Jmr], - "Jls":[LENGTH_WEIGHT, Jls], - "Jccdist":[CC_WEIGHT, Jccdist], - "Jcurv":[KAPPA_WEIGHT, Jcs], - "Jmsc":[MSC_WEIGHT, J_msc], - "Jals":[ARCLENGTH_WEIGHT, Jals]} +# let's fix the coil current +base_currents[0].fix_all() boozer_surface.surface.to_vtk(OUT_DIR + f"surf_init_{rank}") if comm is None or comm.rank == 0: curves_to_vtk(curves, OUT_DIR + f"curves_init") -# let's fix the coil current -base_currents[0].fix_all() +prevs = {'sdofs':[surface.x.copy() for surface in mpi_surfaces], + 'iota':[boozer_surface.res['iota'] for boozer_surface in mpi_boozer_surfaces], + 'G': [boozer_surface.res['G'] for boozer_surface in mpi_boozer_surfaces], + 'J': JF.J(), + 'dJ':JF.dJ().copy(), + 'it': 0} def fun(dofs): + # initialize to last accepted surface values + for idx, surface in enumerate(mpi_surfaces): + surface.x = prevs['sdofs'][idx] + for idx, boozer_surface in enumerate(mpi_boozer_surfaces): + boozer_surface.res['iota'] = prevs['iota'][idx] + boozer_surface.res['G'] = prevs['G'][idx] + # save these as a backup in case the boozer surface Newton solve fails - sdofs_prev = boozer_surface.surface.x - iota_prev = boozer_surface.res['iota'] - G_prev = boozer_surface.res['G'] - + alldofs = MPI.COMM_WORLD.allgather(dofs) + assert np.all(np.norm(alldofs[0]-d)==0 for d in alldofs) + JF.x = dofs J = JF.J() grad = JF.dJ() - success = boozer_surface.res['success'] if comm is not None else MPI.COMM_WORLD.allreduce(boozer_surface.res['success'], op=MPI.LAND) + success = np.all([boozer_surface.res['success'] for boozer_surface in mpi_boozer_surfaces]) if not success: - # failed, so reset back to previous surface and return a large value - # of the objective. The purpose is to trigger the line search to reduce - # the step size. - J = 1e3 - boozer_surface.surface.x = sdofs_prev - boozer_surface.res['iota'] = iota_prev - boozer_surface.res['G'] = G_prev - + J = prevs['J'] + grad = -prevs['dJ'] + for idx, boozer_surface in enumerate(mpi_boozer_surfaces): + boozer_surface.surface.x = prevs['sdofs'][idx] + boozer_surface.res['iota'] = prevs['iota'][idx] + boozer_surface.res['G'] = prevs['G'][idx] return J, grad -#JF = J_nonQSRatio + RES_WEIGHT * JBoozerResidual + IOTAS_WEIGHT * Jiotas + MR_WEIGHT * Jmr \ -# + LENGTH_WEIGHT * Jls + CC_WEIGHT * Jccdist + Jcs\ -# + MSC_WEIGHT * sum(QuadraticPenalty(J, MSC_THRESHOLD, "max") for J in Jmscs) \ -# + ARCLENGTH_WEIGHT * sum(Jals) + def callback(x): - J = JF.J() - grad = JF.dJ() - - cl_string = ", ".join([f"{J.J():5.3f}" for J in ls]) - kappa_string = ", ".join([f"{np.max(c.kappa()):.3f}" for c in base_curves]) - msc_string = ", ".join([f"{Jmsc.J():.3f}" for Jmsc in msc_list]) - iotas_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(iotas.J()) if comm is not None else iotas.J()) ]) - mr_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(boozer_surface.surface.minor_radius()) if comm is not None else boozer_surface.surface.minor_radius() ) ]) - mR_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(boozer_surface.surface.major_radius()) if comm is not None else boozer_surface.surface.major_radius() ) ]) - ar_string = ", ".join([f"{val:.3f}" for val in (comm.allgather(boozer_surface.surface.aspect_ratio()) if comm is not None else boozer_surface.surface.aspect_ratio() ) ]) - br_string = ", ".join([f"{val:.3e}" for val in (comm.allgather(Jbr.J()) if comm is not None else Jbr.J() ) ]) - nqs_ratio_string = ", ".join([f"{val:.3e}" for val in (comm.allgather(Jnqs.J()) if comm is not None else Jnqs.J() ) ]) + for idx, surface in enumerate(mpi_surfaces): + prevs['sdofs'][idx] = surface.x.copy() + for idx, boozer_surface in enumerate(mpi_boozer_surfaces): + prevs['iota'][idx] = boozer_surface.res['iota'] + prevs['G'][idx] = boozer_surface.res['G'] + prevs['J'] = JF.J() + prevs['dJ'] = JF.dJ().copy() + cl_string = ", ".join([f"{J.J():5.6f}" for J in ls]) + kappa_string = ", ".join([f"{np.max(c.kappa()):.6f}" for c in base_curves]) + msc_string = ", ".join([f"{Jmsc.J():.6f}" for Jmsc in msc_list]) + iotas_string = ", ".join([f"{boozer_surface.res['iota']:.6f}" for boozer_surface in boozer_surfaces]) + mr_string = ", ".join([f"{surface.minor_radius():.6f}" for surface in surfaces]) + mR_string = ", ".join([f"{surface.major_radius():.6f}" for surface in surfaces]) + ar_string = ", ".join([f"{surface.aspect_ratio():.6f}" for surface in surfaces]) + vol_string = ", ".join([f"{surface.volume():.6f}" for surface in surfaces]) + br_string = ", ".join([f"{br.J():.6e}" for br in brs]) + nqs_ratio_string = ", ".join([f"{np.sqrt(nonqs.J()):.6e}" for nonqs in nonQSs]) + width = 35 - outstr = "\n" - s = "J"; outstr += f"{s:{width}} {J:.3e} \n" - s = "ā•‘āˆ‡Jā•‘"; outstr += f"{s:{width}} {np.linalg.norm(grad):.3e} \n\n" - - width = 15 - for pen in penalty_list.keys(): - s = pen; outstr+=f"{s:<{width}} " - outstr+="\n" - for pen in penalty_list.keys(): - w = penalty_list[pen][0] - val = penalty_list[pen][1].J() - outstr+=f"{w*val:<{width}.3e} " + outstr = f"\nIteration {prevs['it']}\n" + s = "J"; outstr += f"{s:{width}} {JF.J():.6e} \n" + s = "ā•‘āˆ‡Jā•‘"; outstr += f"{s:{width}} {np.linalg.norm(JF.dJ()):.6e} \n\n" - outstr+="\n\n" width = 35 s = "nonQS ratio"; outstr += f"{s:{width}} {nqs_ratio_string} \n" s = "Boozer Residual"; outstr += f"{s:{width}} {br_string} \n" - s = "<Ī¹>"; outstr += f"{s:{width}} {mean_iota.J():.3f} \n" + s = "<Ī¹>"; outstr += f"{s:{width}} {mean_iota.J():.6f} \n" s = "Ī¹ on surfaces"; outstr += f"{s:{width}} {iotas_string} \n" s = "major radius on surfaces"; outstr += f"{s:{width}} {mR_string} \n" s = "minor radius on surfaces"; outstr += f"{s:{width}} {mr_string} \n" s = "aspect ratio on surfaces"; outstr += f"{s:{width}} {ar_string} \n" + s = "volume"; outstr += f"{s:{width}} {vol_string} \n" s = "shortest coil to coil distance"; outstr += f"{s:{width}} {Jccdist.shortest_distance():.3f} \n" s = "coil lengths"; outstr += f"{s:{width}} {cl_string} \n" s = "coil length sum"; outstr += f"{s:{width}} {sum(J.J() for J in ls):.3f} \n" s = "max Īŗ"; outstr += f"{s:{width}} {kappa_string} \n" s = "āˆ« Īŗ^2 dl / āˆ« dl"; outstr += f"{s:{width}} {msc_string} \n" outstr+="\n\n" - if comm is None or comm.rank == 0: - print(outstr, flush=True) - - -#print(""" -################################################################################# -#### Perform a Taylor test ###################################################### -################################################################################# -#""") -#f = fun -#dofs = JF.x -#np.random.seed(1) -#h = np.random.uniform(size=dofs.shape) -#J0, dJ0 = f(dofs) -#dJh = sum(dJ0 * h) -#for eps in [1e-3, 1e-4, 1e-5, 1e-6, 1e-7, 1e-8, 1e-9]: -# J1, _ = f(dofs + 2*eps*h) -# J2, _ = f(dofs + eps*h) -# J3, _ = f(dofs - eps*h) -# J4, _ = f(dofs - 2*eps*h) -# print("err", ((J1*(-1/12) + J2*(8/12) + J3*(-8/12) + J4*(1/12))/eps - dJh)/np.linalg.norm(dJh)) + + pprint(outstr) + prevs['it']+=1 + dofs = JF.x callback(dofs) -quit() -print(""" +pprint(""" ################################################################################ ### Run the optimization ####################################################### ################################################################################ @@ -224,5 +185,5 @@ def callback(x): curves_to_vtk(curves, OUT_DIR + f"curves_opt") boozer_surface.surface.to_vtk(OUT_DIR + "surf_opt") -print("End of 2_Intermediate/boozerQA_ls.py") -print("================================") +pprint("End of 2_Intermediate/boozerQA_ls.py") +pprint("================================") diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 69e8a0cbe..a2c9016e0 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -54,7 +54,7 @@ def __init__(self, biotsavart, surface, label, targetlabel, constraint_weight=No def recompute_bell(self, parent=None): self.need_to_run_code = True - def run_code(self, boozer_type, iota, G=None): + def run_code(self, boozer_type, iota, G=None, verbose=True): """ Run the default solvers. """ @@ -62,18 +62,18 @@ def run_code(self, boozer_type, iota, G=None): return if boozer_type == 'exact': - res = self.boozer_surface.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=iota, G=G) + res = self.boozer_surface.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=iota, G=G, verbose=verbose) return res elif boozer_type == 'ls': # first try BFGS #res = self.minimize_boozer_penalty_constraints_ls(tol=1e-10, maxiter=100, constraint_weight=self.constraint_weight, iota=iota, G=G, method='manual') - res = self.compute_boozerls_BFGS(tol=1e-10, maxiter=1e3, constraint_weight=self.constraint_weight, iota=iota, G=G) + res = self.compute_boozerls_BFGS(tol=1e-10, maxiter=1e3, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) iota, G = res['iota'], res['G'] ## polish off using Newton's method self.need_to_run_code = True - res = self.compute_boozerls_newton(tol=1e-11, maxiter=20, constraint_weight=self.constraint_weight, iota=iota, G=G) + res = self.compute_boozerls_newton(tol=1e-11, maxiter=20, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) return res else: raise Exception(f"boozer_type not supported: {boozer_type}") @@ -472,7 +472,7 @@ def minimize_boozer_exact_constraints_newton(self, tol=1e-12, maxiter=10, iota=0 self.need_to_run_code = False return res - def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., G=None): + def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., G=None, verbose=False): """ This function solves the Boozer Surface residual equation exactly. For this to work, we need the right balance of quadrature points, degrees @@ -612,6 +612,10 @@ def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., "residual": r, "jacobian": J, "iter": i, "success": norm <= tol, "G": G, "s": s, "iota": iota, "PLU": (P, L, U), "mask": mask, 'type': 'exact', "vjp": boozer_surface_dexactresidual_dcoils_dcurrents_vjp } + + if verbose: + print(f"NEWTON solve - {res['success']} iter={res['iter']}, iota={res['iota']:.16f}, ||residual||_inf = {np.linalg.norm(res['residual'], ord=np.inf):.3e}", flush=True) + self.res = res self.need_to_run_code = False return res @@ -704,7 +708,7 @@ def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G H[:nsurfdofs, :nsurfdofs] += self.reg.d2J() return r, J, H - def compute_boozerls_BFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, hessian=False): + def compute_boozerls_BFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, hessian=False, verbose=False): r""" """ if not self.need_to_run_code: @@ -748,10 +752,11 @@ def compute_boozerls_BFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., io self.res = resdict self.need_to_run_code = False - print(f"BFGS solve - {resdict['success']} iter={resdict['iter']}, iota={resdict['iota']:.16f}, ||grad||_inf = {np.linalg.norm(resdict['firstorderop'], ord=np.inf):.3e}", flush=True) + if verbose: + print(f"BFGS solve - {resdict['success']} iter={resdict['iter']}, iota={resdict['iota']:.16f}, ||grad||_inf = {np.linalg.norm(resdict['firstorderop'], ord=np.inf):.3e}", flush=True) return resdict - def compute_boozerls_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0.): + def compute_boozerls_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0., verbose=False): """ """ if not self.need_to_run_code: @@ -807,5 +812,6 @@ def compute_boozerls_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., i self.res = res self.need_to_run_code = False - print(f"NEWTON solve - {res['success']} iter={res['iter']}, iota={res['iota']:.16f}, ||grad||_inf = {np.linalg.norm(res['firstorderop'], ord=np.inf):.3e}", flush=True) + if verbose: + print(f"NEWTON solve - {res['success']} iter={res['iter']}, iota={res['iota']:.16f}, ||grad||_inf = {np.linalg.norm(res['firstorderop'], ord=np.inf):.3e}", flush=True) return res diff --git a/src/simsopt/objectives/utilities.py b/src/simsopt/objectives/utilities.py index c3bec9d25..8720d426e 100644 --- a/src/simsopt/objectives/utilities.py +++ b/src/simsopt/objectives/utilities.py @@ -6,7 +6,7 @@ from .._core.derivative import Derivative, derivative_dec from .._core.json import GSONable -__all__ = ['MPIObjective', 'QuadraticPenalty', 'Weight', 'forward_backward'] +__all__ = ['MPIOptimizable', 'MPIObjective', 'QuadraticPenalty', 'Weight', 'forward_backward'] def forward_backward(P, L, U, rhs, iterative_refinement=False): @@ -50,6 +50,42 @@ def sum_across_comm(derivative, comm): return Derivative(newdict) +class MPIOptimizable(Optimizable): + + def __init__(self, optimizables, attributes, comm): + r""" + + """ + + from simsopt._core.util import parallel_loop_bounds + startidx, endidx = parallel_loop_bounds(comm, len(optimizables)) + self.local_optimizables = optimizables[startidx:endidx] + self.global_optimizables = optimizables + + self.comm = comm + self.attributes = attributes + Optimizable.__init__(self, x0=np.asarray([]), depends_on=optimizables) + + def __getitem__(self, key): + if self.need_to_communicate: + self.communicate() + return self.global_optimizables[key] + + def communicate(self): + if self.need_to_communicate: + for attr in self.attributes: + local_vals = [getattr(J, attr) for J in self.local_optimizables] + global_vals = local_vals if self.comm is None else [i for o in self.comm.allgather(local_vals) for i in o] + for val, J in zip(global_vals, self.global_optimizables): + if J in self.local_optimizables: + continue + setattr(J, attr, val) + self.need_to_communicate = False + + def recompute_bell(self, parent=None): + self.need_to_communicate = True + + class MPIObjective(Optimizable): def __init__(self, objectives, comm, needs_splitting=False): From 3a7ae14b23a8d67b2bf84e3094f7bbba5fd2aaf5 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 8 May 2023 11:38:36 -0400 Subject: [PATCH 006/176] added support for computing whether surfaces are self-intersecting --- examples/2_Intermediate/boozerQA_ls_mpi.py | 6 ++--- src/simsopt/geo/surface.py | 28 +++++++++++++++++++++- 2 files changed, 30 insertions(+), 4 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 911113197..12f869daa 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -41,8 +41,6 @@ def pprint(*args, **kwargs): for boozer_surface, res in zip(boozer_surfaces, ress): boozer_surface.run_code('ls', res['iota'], res['G'], verbose=False) -ncoils = len(base_curves) - mpi_surfaces = MPIOptimizable(surfaces, ["x"], comm) mpi_boozer_surfaces = MPIOptimizable(boozer_surfaces, ["res", "need_to_run_code"], comm) @@ -73,7 +71,7 @@ def pprint(*args, **kwargs): ls = [CurveLength(c) for c in base_curves] Jls = QuadraticPenalty(sum(ls), float(sum(ls).J()), 'max') -Jccdist = CurveCurveDistance(curves, MIN_DIST_THRESHOLD, num_basecurves=ncoils) +Jccdist = CurveCurveDistance(curves, MIN_DIST_THRESHOLD, num_basecurves=len(base_curves)) Jcs = sum([LpCurveCurvature(c, 2, KAPPA_THRESHOLD) for c in base_curves]) msc_list = [MeanSquaredCurvature(c) for c in base_curves] Jmsc = sum(QuadraticPenalty(J, MSC_THRESHOLD, "max") for J in msc_list) @@ -143,6 +141,7 @@ def callback(x): vol_string = ", ".join([f"{surface.volume():.6f}" for surface in surfaces]) br_string = ", ".join([f"{br.J():.6e}" for br in brs]) nqs_ratio_string = ", ".join([f"{np.sqrt(nonqs.J()):.6e}" for nonqs in nonQSs]) + is_self_intersecting_string = ", ".join([f"{surface.is_self_intersecting()}" for surface in surfaces]) width = 35 outstr = f"\nIteration {prevs['it']}\n" @@ -158,6 +157,7 @@ def callback(x): s = "minor radius on surfaces"; outstr += f"{s:{width}} {mr_string} \n" s = "aspect ratio on surfaces"; outstr += f"{s:{width}} {ar_string} \n" s = "volume"; outstr += f"{s:{width}} {vol_string} \n" + s = "surfaces are self-intersecting"; outstr += f"{s:{width}} {is_self_intersecting_string} \n" s = "shortest coil to coil distance"; outstr += f"{s:{width}} {Jccdist.shortest_distance():.3f} \n" s = "coil lengths"; outstr += f"{s:{width}} {cl_string} \n" s = "coil length sum"; outstr += f"{s:{width}} {sum(J.J() for J in ls):.3f} \n" diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index aef17c773..e245c14dc 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -7,6 +7,16 @@ except ImportError: gridToVTK = None +try: + from ground.base import get_context +except ImportError: + get_context = None + +try: + from bentley_ottmann.planar import contour_self_intersects +except ImportError: + contour_self_intersects = None + import simsoptpp as sopp from .._core.optimizable import Optimizable from .._core.dev import SimsoptRequires @@ -309,7 +319,7 @@ def to_RZFourier(self): implement this abstract method. """ raise NotImplementedError - + def cross_section(self, phi, thetas=None): """ This function takes in a cylindrical angle :math:`\phi` and returns the cross @@ -421,6 +431,22 @@ def bisection(phia, a, phic, c): cross_section = np.zeros((sol.size, 3)) self.gamma_lin(cross_section, sol, theta) return cross_section + + @SimsoptRequires(get_context is not None, "is_self_intersecting requires ground package") + @SimsoptRequires(contour_self_intersects is not None, "is_self_intersecting requires the bentley_ottmann package") + def is_self_intersecting(self, angle=0.): + """ + + """ + + cs = self.cross_section(angle) + R = np.sqrt( cs[:,0]**2 + cs[:,1]**2) + Z = cs[:, 2] + + context = get_context() + Point, Contour = context.point_cls, context.contour_cls + contour = Contour([ Point(R[i], Z[i]) for i in range(cs.shape[0]) ]) + return contour_self_intersects(contour) def aspect_ratio(self): r""" From 04749f39a7ec781e0a03585640d6b00c25b89f2b Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 8 May 2023 12:08:02 -0400 Subject: [PATCH 007/176] edits to example --- examples/2_Intermediate/boozerQA_ls_mpi.py | 36 +++++++--------------- 1 file changed, 11 insertions(+), 25 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 12f869daa..dd17c248e 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -131,38 +131,24 @@ def callback(x): prevs['J'] = JF.J() prevs['dJ'] = JF.dJ().copy() - cl_string = ", ".join([f"{J.J():5.6f}" for J in ls]) - kappa_string = ", ".join([f"{np.max(c.kappa()):.6f}" for c in base_curves]) - msc_string = ", ".join([f"{Jmsc.J():.6f}" for Jmsc in msc_list]) - iotas_string = ", ".join([f"{boozer_surface.res['iota']:.6f}" for boozer_surface in boozer_surfaces]) - mr_string = ", ".join([f"{surface.minor_radius():.6f}" for surface in surfaces]) - mR_string = ", ".join([f"{surface.major_radius():.6f}" for surface in surfaces]) - ar_string = ", ".join([f"{surface.aspect_ratio():.6f}" for surface in surfaces]) - vol_string = ", ".join([f"{surface.volume():.6f}" for surface in surfaces]) - br_string = ", ".join([f"{br.J():.6e}" for br in brs]) - nqs_ratio_string = ", ".join([f"{np.sqrt(nonqs.J()):.6e}" for nonqs in nonQSs]) - is_self_intersecting_string = ", ".join([f"{surface.is_self_intersecting()}" for surface in surfaces]) - width = 35 outstr = f"\nIteration {prevs['it']}\n" s = "J"; outstr += f"{s:{width}} {JF.J():.6e} \n" s = "ā•‘āˆ‡Jā•‘"; outstr += f"{s:{width}} {np.linalg.norm(JF.dJ()):.6e} \n\n" - - width = 35 - s = "nonQS ratio"; outstr += f"{s:{width}} {nqs_ratio_string} \n" - s = "Boozer Residual"; outstr += f"{s:{width}} {br_string} \n" + s = "nonQS ratio"; outstr += f"{s:{width}}" + ", ".join([f'{np.sqrt(nonqs.J()):.6e}' for nonqs in nonQSs]) +"\n" + s = "Boozer Residual"; outstr += f"{s:{width}}" + ", ".join([f'{br.J():.6e}' for br in brs]) + "\n" s = "<Ī¹>"; outstr += f"{s:{width}} {mean_iota.J():.6f} \n" - s = "Ī¹ on surfaces"; outstr += f"{s:{width}} {iotas_string} \n" - s = "major radius on surfaces"; outstr += f"{s:{width}} {mR_string} \n" - s = "minor radius on surfaces"; outstr += f"{s:{width}} {mr_string} \n" - s = "aspect ratio on surfaces"; outstr += f"{s:{width}} {ar_string} \n" - s = "volume"; outstr += f"{s:{width}} {vol_string} \n" - s = "surfaces are self-intersecting"; outstr += f"{s:{width}} {is_self_intersecting_string} \n" + s = "Ī¹ on surfaces"; outstr += f"{s:{width}}" + ", ".join([f"{boozer_surface.res['iota']:.6f}" for boozer_surface in boozer_surfaces]) + "\n" + s = "major radius on surfaces"; outstr += f"{s:{width}}" + ', '.join([f'{surface.major_radius():.6f}' for surface in surfaces]) + "\n" + s = "minor radius on surfaces"; outstr += f"{s:{width}}" + ', '.join([f'{surface.minor_radius():.6f}' for surface in surfaces]) + "\n" + s = "aspect ratio on surfaces"; outstr += f"{s:{width}}" + ', '.join([f'{surface.aspect_ratio():.6f}' for surface in surfaces]) + "\n" + s = "volume"; outstr += f"{s:{width}}" + ', '.join([f'{surface.volume():.6f}' for surface in surfaces]) + "\n" + s = "surfaces are self-intersecting"; outstr += f"{s:{width}}" + ', '.join([f'{surface.is_self_intersecting()}' for surface in surfaces]) + "\n" s = "shortest coil to coil distance"; outstr += f"{s:{width}} {Jccdist.shortest_distance():.3f} \n" - s = "coil lengths"; outstr += f"{s:{width}} {cl_string} \n" + s = "coil lengths"; outstr += f"{s:{width}}" + ', '.join([f'{J.J():5.6f}' for J in ls]) + "\n" s = "coil length sum"; outstr += f"{s:{width}} {sum(J.J() for J in ls):.3f} \n" - s = "max Īŗ"; outstr += f"{s:{width}} {kappa_string} \n" - s = "āˆ« Īŗ^2 dl / āˆ« dl"; outstr += f"{s:{width}} {msc_string} \n" + s = "max Īŗ"; outstr += f"{s:{width}}" + ', '.join([f'{np.max(c.kappa()):.6f}' for c in base_curves]) + "\n" + s = "āˆ« Īŗ^2 dl / āˆ« dl"; outstr += f"{s:{width}}" + ', '.join([f'{Jmsc.J():.6f}' for Jmsc in msc_list]) + "\n" outstr+="\n\n" pprint(outstr) From f9c81054a4c189c3c7094875e9a0a5ce69cfb6ce Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 8 May 2023 12:30:13 -0400 Subject: [PATCH 008/176] edits to example --- examples/2_Intermediate/boozerQA_ls_mpi.py | 34 +++++++++++----------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index dd17c248e..4104d9e0c 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -29,7 +29,7 @@ def pprint(*args, **kwargs): OUT_DIR = "./output/" os.makedirs(OUT_DIR, exist_ok=True) -pprint("Running 2_Intermediate/boozerQA_ls.py") +pprint("Running 2_Intermediate/boozerQA.py") pprint("================================") base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress= load(IN_DIR + f"ncsx_init.json") @@ -133,22 +133,22 @@ def callback(x): width = 35 outstr = f"\nIteration {prevs['it']}\n" - s = "J"; outstr += f"{s:{width}} {JF.J():.6e} \n" - s = "ā•‘āˆ‡Jā•‘"; outstr += f"{s:{width}} {np.linalg.norm(JF.dJ()):.6e} \n\n" - s = "nonQS ratio"; outstr += f"{s:{width}}" + ", ".join([f'{np.sqrt(nonqs.J()):.6e}' for nonqs in nonQSs]) +"\n" - s = "Boozer Residual"; outstr += f"{s:{width}}" + ", ".join([f'{br.J():.6e}' for br in brs]) + "\n" - s = "<Ī¹>"; outstr += f"{s:{width}} {mean_iota.J():.6f} \n" - s = "Ī¹ on surfaces"; outstr += f"{s:{width}}" + ", ".join([f"{boozer_surface.res['iota']:.6f}" for boozer_surface in boozer_surfaces]) + "\n" - s = "major radius on surfaces"; outstr += f"{s:{width}}" + ', '.join([f'{surface.major_radius():.6f}' for surface in surfaces]) + "\n" - s = "minor radius on surfaces"; outstr += f"{s:{width}}" + ', '.join([f'{surface.minor_radius():.6f}' for surface in surfaces]) + "\n" - s = "aspect ratio on surfaces"; outstr += f"{s:{width}}" + ', '.join([f'{surface.aspect_ratio():.6f}' for surface in surfaces]) + "\n" - s = "volume"; outstr += f"{s:{width}}" + ', '.join([f'{surface.volume():.6f}' for surface in surfaces]) + "\n" - s = "surfaces are self-intersecting"; outstr += f"{s:{width}}" + ', '.join([f'{surface.is_self_intersecting()}' for surface in surfaces]) + "\n" - s = "shortest coil to coil distance"; outstr += f"{s:{width}} {Jccdist.shortest_distance():.3f} \n" - s = "coil lengths"; outstr += f"{s:{width}}" + ', '.join([f'{J.J():5.6f}' for J in ls]) + "\n" - s = "coil length sum"; outstr += f"{s:{width}} {sum(J.J() for J in ls):.3f} \n" - s = "max Īŗ"; outstr += f"{s:{width}}" + ', '.join([f'{np.max(c.kappa()):.6f}' for c in base_curves]) + "\n" - s = "āˆ« Īŗ^2 dl / āˆ« dl"; outstr += f"{s:{width}}" + ', '.join([f'{Jmsc.J():.6f}' for Jmsc in msc_list]) + "\n" + outstr += f"{'J':{width}} {JF.J():.6e} \n" + outstr += f"{'ā•‘āˆ‡Jā•‘':{width}} {np.linalg.norm(JF.dJ()):.6e} \n\n" + outstr += f"{'nonQS ratio':{width}}" + ", ".join([f'{np.sqrt(nonqs.J()):.6e}' for nonqs in nonQSs]) +"\n" + outstr += f"{'Boozer Residual':{width}}" + ", ".join([f'{br.J():.6e}' for br in brs]) + "\n" + outstr += f"{'<Ī¹>':{width}} {mean_iota.J():.6f} \n" + outstr += f"{'Ī¹ on surfaces':{width}}" + ", ".join([f"{boozer_surface.res['iota']:.6f}" for boozer_surface in boozer_surfaces]) + "\n" + outstr += f"{'major radius on surfaces':{width}}" + ', '.join([f'{surface.major_radius():.6f}' for surface in surfaces]) + "\n" + outstr += f"{'minor radius on surfaces':{width}}" + ', '.join([f'{surface.minor_radius():.6f}' for surface in surfaces]) + "\n" + outstr += f"{'aspect ratio radius on surfaces':{width}}" + ', '.join([f'{surface.aspect_ratio():.6f}' for surface in surfaces]) + "\n" + outstr += f"{'volume':{width}}" + ', '.join([f'{surface.volume():.6f}' for surface in surfaces]) + "\n" + outstr += f"{'surfaces are self-intersecting':{width}}" + ', '.join([f'{surface.is_self_intersecting()}' for surface in surfaces]) + "\n" + outstr += f"{'shortest coil to coil distance':{width}} {Jccdist.shortest_distance():.3f} \n" + outstr += f"{'coil lengths':{width}}" + ', '.join([f'{J.J():5.6f}' for J in ls]) + "\n" + outstr += f"{'coil length sum':{width}} {sum(J.J() for J in ls):.3f} \n" + outstr += f"{'max Īŗ':{width}}" + ', '.join([f'{np.max(c.kappa()):.6f}' for c in base_curves]) + "\n" + outstr += f"{'āˆ« Īŗ^2 dl / āˆ« dl':{width}}" + ', '.join([f'{Jmsc.J():.6f}' for Jmsc in msc_list]) + "\n" outstr+="\n\n" pprint(outstr) From cf4bc39853e20c8fdb36c626416b1db1b9e16413 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 8 May 2023 13:55:58 -0400 Subject: [PATCH 009/176] linting --- examples/2_Intermediate/boozerQA_ls_mpi.py | 35 +++++++------- src/simsopt/geo/boozersurface.py | 21 +++------ src/simsopt/geo/surface.py | 4 +- src/simsopt/geo/surfaceobjectives.py | 54 ++++++++++++---------- 4 files changed, 55 insertions(+), 59 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 4104d9e0c..c55893e3c 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -15,6 +15,7 @@ comm = MPI.COMM_WORLD rank = comm.rank size = comm.size + def pprint(*args, **kwargs): if comm.rank == 0: # only print on rank 0 print(*args, **kwargs) @@ -32,7 +33,7 @@ def pprint(*args, **kwargs): pprint("Running 2_Intermediate/boozerQA.py") pprint("================================") -base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress= load(IN_DIR + f"ncsx_init.json") +base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress = load(IN_DIR + f"ncsx_init.json") nsurfaces = 2 surfaces = surfaces[:nsurfaces] boozer_surfaces = boozer_surfaces[:nsurfaces] @@ -89,24 +90,21 @@ def pprint(*args, **kwargs): if comm is None or comm.rank == 0: curves_to_vtk(curves, OUT_DIR + f"curves_init") -prevs = {'sdofs':[surface.x.copy() for surface in mpi_surfaces], - 'iota':[boozer_surface.res['iota'] for boozer_surface in mpi_boozer_surfaces], - 'G': [boozer_surface.res['G'] for boozer_surface in mpi_boozer_surfaces], - 'J': JF.J(), - 'dJ':JF.dJ().copy(), - 'it': 0} +prevs = {'sdofs': [surface.x.copy() for surface in mpi_surfaces], 'iota': [boozer_surface.res['iota'] for boozer_surface in mpi_boozer_surfaces], + 'G': [boozer_surface.res['G'] for boozer_surface in mpi_boozer_surfaces], 'J': JF.J(), 'dJ': JF.dJ().copy(), 'it': 0} + def fun(dofs): # initialize to last accepted surface values for idx, surface in enumerate(mpi_surfaces): - surface.x = prevs['sdofs'][idx] + surface.x = prevs['sdofs'][idx] for idx, boozer_surface in enumerate(mpi_boozer_surfaces): boozer_surface.res['iota'] = prevs['iota'][idx] - boozer_surface.res['G'] = prevs['G'][idx] + boozer_surface.res['G'] = prevs['G'][idx] # save these as a backup in case the boozer surface Newton solve fails alldofs = MPI.COMM_WORLD.allgather(dofs) - assert np.all(np.norm(alldofs[0]-d)==0 for d in alldofs) + assert np.all(np.norm(alldofs[0]-d) == 0 for d in alldofs) JF.x = dofs J = JF.J() @@ -122,20 +120,21 @@ def fun(dofs): boozer_surface.res['G'] = prevs['G'][idx] return J, grad + def callback(x): for idx, surface in enumerate(mpi_surfaces): prevs['sdofs'][idx] = surface.x.copy() for idx, boozer_surface in enumerate(mpi_boozer_surfaces): - prevs['iota'][idx] = boozer_surface.res['iota'] - prevs['G'][idx] = boozer_surface.res['G'] - prevs['J'] = JF.J() - prevs['dJ'] = JF.dJ().copy() + prevs['iota'][idx] = boozer_surface.res['iota'] + prevs['G'][idx] = boozer_surface.res['G'] + prevs['J'] = JF.J() + prevs['dJ'] = JF.dJ().copy() width = 35 outstr = f"\nIteration {prevs['it']}\n" outstr += f"{'J':{width}} {JF.J():.6e} \n" outstr += f"{'ā•‘āˆ‡Jā•‘':{width}} {np.linalg.norm(JF.dJ()):.6e} \n\n" - outstr += f"{'nonQS ratio':{width}}" + ", ".join([f'{np.sqrt(nonqs.J()):.6e}' for nonqs in nonQSs]) +"\n" + outstr += f"{'nonQS ratio':{width}}" + ", ".join([f'{np.sqrt(nonqs.J()):.6e}' for nonqs in nonQSs]) + "\n" outstr += f"{'Boozer Residual':{width}}" + ", ".join([f'{br.J():.6e}' for br in brs]) + "\n" outstr += f"{'<Ī¹>':{width}} {mean_iota.J():.6f} \n" outstr += f"{'Ī¹ on surfaces':{width}}" + ", ".join([f"{boozer_surface.res['iota']:.6f}" for boozer_surface in boozer_surfaces]) + "\n" @@ -148,11 +147,11 @@ def callback(x): outstr += f"{'coil lengths':{width}}" + ', '.join([f'{J.J():5.6f}' for J in ls]) + "\n" outstr += f"{'coil length sum':{width}} {sum(J.J() for J in ls):.3f} \n" outstr += f"{'max Īŗ':{width}}" + ', '.join([f'{np.max(c.kappa()):.6f}' for c in base_curves]) + "\n" - outstr += f"{'āˆ« Īŗ^2 dl / āˆ« dl':{width}}" + ', '.join([f'{Jmsc.J():.6f}' for Jmsc in msc_list]) + "\n" - outstr+="\n\n" + outstr += f"{'āˆ« Īŗ^2 dl / āˆ« dl':{width}}" + ', '.join([f'{Jmsc.J():.6f}' for Jmsc in msc_list]) + "\n" + outstr += "\n\n" pprint(outstr) - prevs['it']+=1 + prevs['it'] += 1 dofs = JF.x diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index a2c9016e0..b5a5dea69 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -703,7 +703,7 @@ def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G Hnl = boozer[2] d2rl = np.zeros((dofs.shape[0], dofs.shape[0])) d2rl[:nsurfdofs, :nsurfdofs] = np.sqrt(constraint_weight)*self.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() - H = Hnl + drl[:,None] @ drl[None,:] + drz[:,None] @ drz[None, :] + rl * d2rl + H = Hnl + drl[:, None] @ drl[None, :] + drz[:, None] @ drz[None, :] + rl * d2rl if self.reg is not None: H[:nsurfdofs, :nsurfdofs] += self.reg.d2J() return r, J, H @@ -727,9 +727,9 @@ def compute_boozerls_BFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., io options={'maxiter': maxiter, 'gtol': tol}) resdict = { - "residual": res.fun, "gradient": res.jac, "iter": res.nit, "info": res, "success": res.success, "G": None, 'type':'ls', 'solver':'BFGS', - "firstorderop":res.jac, "constraint_weight":constraint_weight, "labelerr":np.abs((self.label.J()-self.targetlabel)/self.targetlabel), - "vjp":boozer_surface_dlsqgrad_dcoils_vjp + "residual": res.fun, "gradient": res.jac, "iter": res.nit, "info": res, "success": res.success, "G": None, 'type': 'ls', 'solver': 'BFGS', + "firstorderop": res.jac, "constraint_weight": constraint_weight, "labelerr": np.abs((self.label.J()-self.targetlabel)/self.targetlabel), + "vjp": boozer_surface_dlsqgrad_dcoils_vjp } if G is None: @@ -796,18 +796,11 @@ def compute_boozerls_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., i s.set_dofs(x[:-2]) iota = x[-2] G = x[-1] - - #res = { - # "residual": val, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "type": "ls", - # "PLU":(P,L,U), "firstorderop":dval, "constraint_weight":constraint_weight, "iota":iota, "G":G, - # "type":'ls', "labelerr":np.abs((self.label.J()-self.targetlabel)/self.targetlabel), "cond":np.linalg.cond(d2val),- - # "reg": self.reg.J() if self.reg is not None else 0. - #} res = { - "residual": val, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "firstorderop": dval, - "PLU" : (P, L, U), 'iota': iota, "G": G, "type": "ls", "vjp": boozer_surface_dlsqgrad_dcoils_vjp - } + "residual": val, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "firstorderop": dval, + "PLU": (P, L, U), 'iota': iota, "G": G, "type": "ls", "vjp": boozer_surface_dlsqgrad_dcoils_vjp + } self.res = res self.need_to_run_code = False diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index e245c14dc..0aca5df57 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -440,12 +440,12 @@ def is_self_intersecting(self, angle=0.): """ cs = self.cross_section(angle) - R = np.sqrt( cs[:,0]**2 + cs[:,1]**2) + R = np.sqrt(cs[:, 0]**2 + cs[:, 1]**2) Z = cs[:, 2] context = get_context() Point, Contour = context.point_cls, context.contour_cls - contour = Contour([ Point(R[i], Z[i]) for i in range(cs.shape[0]) ]) + contour = Contour([Point(R[i], Z[i]) for i in range(cs.shape[0])]) return contour_self_intersects(contour) def aspect_ratio(self): diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 9319df30e..aff9722d5 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -354,15 +354,15 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ if weight_inv_modB: dB2_dc = 2*np.einsum('ijk,ijkl->ijl', B, dB_dc, optimize=True) dmodB_dc = 0.5*dB2_dc/np.sqrt(B2[:, :, None]) - dw_dc = -dmodB_dc/modB[:, :, None]**2 + dw_dc = -dmodB_dc/modB[:, :, None]**2 # d/dc(r*dS) = dr/dc * dS + dS_dc * r drtil_dc = residual[..., None] * dw_dc[:, :, None, :] + w[:, :, None, None] * dresidual_dc drtil_diota = w[:, :, None] * dresidual_diota else: - drtil_dc = dresidual_dc.copy() + drtil_dc = dresidual_dc.copy() drtil_diota = dresidual_diota.copy() - drtil_dc_flattened = drtil_dc.reshape((nphi*ntheta*3, nsurfdofs)) + drtil_dc_flattened = drtil_dc.reshape((nphi*ntheta*3, nsurfdofs)) drtil_diota_flattened = drtil_diota.reshape((nphi*ntheta*3, 1)) if user_provided_G: @@ -840,22 +840,24 @@ def compute(self): adj_times_dg_dcoil = dconstraint_dcoils_vjp(adj, booz_surf, iota, G) self._dJ = -1.*adj_times_dg_dcoil + class BoozerResidual(Optimizable): r""" """ + def __init__(self, boozer_surface, bs): Optimizable.__init__(self, depends_on=[boozer_surface]) - in_surface=boozer_surface.surface + in_surface = boozer_surface.surface self.boozer_surface = boozer_surface # same number of points as on the solved surface - phis = in_surface.quadpoints_phi + phis = in_surface.quadpoints_phi thetas = in_surface.quadpoints_theta s = SurfaceXYZTensorFourier(mpol=in_surface.mpol, ntor=in_surface.ntor, stellsym=in_surface.stellsym, nfp=in_surface.nfp, quadpoints_phi=phis, quadpoints_theta=thetas) s.set_dofs(in_surface.get_dofs()) - self.constraint_weight= boozer_surface.constraint_weight + self.constraint_weight = boozer_surface.constraint_weight self.in_surface = in_surface self.surface = s self.biotsavart = bs @@ -882,7 +884,7 @@ def compute(self): res = self.boozer_surface.run_code(res['type'], res['iota'], G=res['G']) self.surface.set_dofs(self.in_surface.get_dofs()) - self.biotsavart.set_points(self.surface.gamma().reshape((-1,3))) + self.biotsavart.set_points(self.surface.gamma().reshape((-1, 3))) nphi = self.surface.quadpoints_phi.size ntheta = self.surface.quadpoints_theta.size @@ -893,7 +895,7 @@ def compute(self): iota = self.boozer_surface.res['iota'] G = self.boozer_surface.res['G'] r, J = boozer_surface_residual(surface, iota, G, self.biotsavart, derivatives=1, weight_inv_modB=True) - rtil = np.concatenate((r/np.sqrt(num_points), [np.sqrt(self.constraint_weight)*(self.boozer_surface.label.J()-self.boozer_surface.targetlabel)] ) ) + rtil = np.concatenate((r/np.sqrt(num_points), [np.sqrt(self.constraint_weight)*(self.boozer_surface.label.J()-self.boozer_surface.targetlabel)])) self._J = 0.5*np.sum(rtil**2) booz_surf = self.boozer_surface @@ -918,7 +920,7 @@ def compute(self): adj = forward_backward(P, L, U, dJ_ds) adj_times_dg_dcoil = dconstraint_dcoils_vjp(adj, booz_surf, iota, G) - self._dJ = dJ_by_dcoils - adj_times_dg_dcoil + self._dJ = dJ_by_dcoils - adj_times_dg_dcoil def dJ_by_dB(self): """ @@ -931,13 +933,14 @@ def dJ_by_dB(self): num_points = 3 * nphi * ntheta r, r_dB = boozer_surface_residual_dB(surface, self.boozer_surface.res['iota'], self.boozer_surface.res['G'], self.biotsavart, derivatives=0, weight_inv_modB=True) - r/=np.sqrt(num_points) - r_dB/=np.sqrt(num_points) + r /= np.sqrt(num_points) + r_dB /= np.sqrt(num_points) dJ_by_dB = r[:, None]*r_dB dJ_by_dB = np.sum(dJ_by_dB.reshape((-1, 3, 3)), axis=1) return dJ_by_dB + def boozer_surface_dexactresidual_dcoils_dcurrents_vjp(lm, booz_surf, iota, G): r""" For a given surface with points :math:`x` on it, this function computes the @@ -977,6 +980,7 @@ def boozer_surface_dexactresidual_dcoils_dcurrents_vjp(lm, booz_surf, iota, G): return lm_times_dres_dcoils+lm_times_dlabel_dcoils + def boozer_surface_dlsqgrad_dcoils_vjp(lm, booz_surf, iota, G): """ For a given surface with points x on it, this function computes the @@ -1013,6 +1017,7 @@ def boozer_surface_dlsqgrad_dcoils_vjp(lm, booz_surf, iota, G): dres_dcoils = biotsavart.B_and_dB_vjp(v1+v2, v3) return dres_dcoils[0]+dres_dcoils[1] + def boozer_surface_residual_dB(surface, iota, G, biotsavart, derivatives=0, weight_inv_modB=False): """ For a given surface with points x on it, this function computes the @@ -1085,27 +1090,26 @@ def boozer_surface_residual_dB(surface, iota, G, biotsavart, derivatives=0, weig if weight_inv_modB: dB2_dc = 2*np.einsum('ijk,ijkl->ijl', B, dB_dc, optimize=True) dmodB_dc = 0.5*dB2_dc/modB[:, :, None] - dw_dc = -dmodB_dc/B2[:, :, None] + dw_dc = -dmodB_dc/B2[:, :, None] d2w_dcdB = -(dB_dc * B2[:, :, None, None]**1.5 - 1.5*dB2_dc[:, :, None, :]*modB[:, :, None, None]*B[:, :, :, None])/B2[:, :, None, None]**3 d2w_dcdgradB = dw_dB[:, :, None, :, None] * dx_dc[:, :, :, None, :] - drtil_dc = dresidual_dc * w[:, :, None, None] + dw_dc[:, :, None, :] * residual[..., None] - drtil_diota = w[:, :, None] * dresidual_diota - d2rtil_dcdB = dresidual_dc[:, :, :, None, :]*dw_dB[:, :, None, :, None] \ - + dresidual_dB[:, :, :, :, None]*dw_dc[:, :, None, None, :] \ - + d2residual_dcdB*w[:, :, None, None, None] \ - + residual[:, :, :, None, None]*d2w_dcdB[:, :, None, :, :] - d2rtil_diotadB = dw_dB[:, :, None, :]*dresidual_diota[:, :, :, None] + w[:, :, None, None]*d2residual_diotadB + drtil_dc = dresidual_dc * w[:, :, None, None] + dw_dc[:, :, None, :] * residual[..., None] + drtil_diota = w[:, :, None] * dresidual_diota + d2rtil_dcdB = dresidual_dc[:, :, :, None, :]*dw_dB[:, :, None, :, None] \ + + dresidual_dB[:, :, :, :, None]*dw_dc[:, :, None, None, :] \ + + d2residual_dcdB*w[:, :, None, None, None] \ + + residual[:, :, :, None, None]*d2w_dcdB[:, :, None, :, :] + d2rtil_diotadB = dw_dB[:, :, None, :]*dresidual_diota[:, :, :, None] + w[:, :, None, None]*d2residual_diotadB d2rtil_dcdgradB = d2w_dcdgradB[:, :, None, :, :, :]*residual[:, :, :, None, None, None] + d2residual_dcdgradB*w[:, :, None, None, None, None] else: - drtil_dc = dresidual_dc.copy() - drtil_diota = dresidual_diota.copy() - d2rtil_dcdB = d2residual_dcdB.copy() - d2rtil_diotadB = d2residual_diotadB.copy() + drtil_dc = dresidual_dc.copy() + drtil_diota = dresidual_diota.copy() + d2rtil_dcdB = d2residual_dcdB.copy() + d2rtil_diotadB = d2residual_diotadB.copy() d2rtil_dcdgradB = d2residual_dcdgradB.copy() - drtil_dc_flattened = drtil_dc.reshape((nphi*ntheta*3, nsurfdofs)) drtil_diota_flattened = drtil_diota.reshape((nphi*ntheta*3, 1)) d2rtil_dcdB_flattened = d2rtil_dcdB.reshape((nphi*ntheta*3, 3, nsurfdofs)) @@ -1117,7 +1121,7 @@ def boozer_surface_residual_dB(surface, iota, G, biotsavart, derivatives=0, weig dresidual_dG = B d2residual_dGdB = np.ones((nphi*ntheta, 3, 3)) d2residual_dGdB[:, :, :] = np.eye(3)[None, :, :] - d2residual_dGdB = d2residual_dGdB.reshape((nphi,ntheta, 3, 3)) + d2residual_dGdB = d2residual_dGdB.reshape((nphi, ntheta, 3, 3)) d2residual_dGdgradB = np.zeros((nphi, ntheta, 3, 3, 3)) if weight_inv_modB: From 4761643745042f9eaa614f31abbbbcc3ab010c66 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 8 May 2023 14:43:03 -0400 Subject: [PATCH 010/176] added more docstrings --- src/simsopt/geo/surfaceobjectives.py | 36 +++++++++++++++++++++++++++- src/simsopt/objectives/utilities.py | 17 +++++++++++++ 2 files changed, 52 insertions(+), 1 deletion(-) diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index aff9722d5..8790f69c0 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -302,6 +302,22 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ :math:`G` is known for exact boozer surfaces, so if ``G=None`` is passed, then that value is used instead. + + Args: + surface: The surface to use for the computation + iota: the surface rotational transform + G: a constant that is a function of the coil currents in vacuum field + biotsavart: the Biot-Savart magnetic field + derivatives: how many spatial derivatives of the residual to compute + weight_inv_modB: whether or not to weight the residual by :math:`\|\mathbf B\|`. This + is useful to activate so that the residual does not scale with the + coil currents. + + Returns: + the residual at the surface quadrature points and optionally the spatial derivatives + of the residual. + + """ assert derivatives in [0, 1] @@ -843,8 +859,18 @@ def compute(self): class BoozerResidual(Optimizable): r""" - """ + This term returns the Boozer residual penalty term + + .. math:: + J = \int_0^{1/n_{\text{fp}}} \int_0^1 \| \mathbf r \|^2 ~d\theta ~d\varphi + w (\text{label.J()-boozer_surface.constraint_weight})^2. + + where + .. math:: + \mathbf r = \frac{1}{\|\mathbf B\|}[G\mathbf B_\text{BS}(\mathbf x) - ||\mathbf B_\text{BS}(\mathbf x)||^2 (\mathbf x_\varphi + \iota \mathbf x_\theta)] + + """ + def __init__(self, boozer_surface, bs): Optimizable.__init__(self, depends_on=[boozer_surface]) in_surface = boozer_surface.surface @@ -864,12 +890,20 @@ def __init__(self, boozer_surface, bs): self.recompute_bell() def J(self): + """ + Return the value of the penalty function. + """ + if self._J is None: self.compute() return self._J @derivative_dec def dJ(self): + """ + Return the derivative of the penalty function with respect to the coil degrees of freedom. + """ + if self._dJ is None: self.compute() return self._dJ diff --git a/src/simsopt/objectives/utilities.py b/src/simsopt/objectives/utilities.py index 8720d426e..4919cff96 100644 --- a/src/simsopt/objectives/utilities.py +++ b/src/simsopt/objectives/utilities.py @@ -54,7 +54,19 @@ class MPIOptimizable(Optimizable): def __init__(self, optimizables, attributes, comm): r""" + Ensures that a list of Optimizables on separate ranks have a consistent set of attributes on all ranks. + For example, say that all ranks have the list ``optimizables``. Rank ``i`` modifies attributes + of ``optimizable[i]``. The value attribute ``attr``, i.e., ``optimizables[i].attr`` potentially + will be different on ranks ``i`` and ``j``, for ``i`` not equal to ``j``. This class ensures that + if the cache is invalidated on the ``Optimizables`` in the list ``optimizables``, then when the list + is accessed, the attributes in ``attributes`` will be communicated accross all ranks. + Args: + objectives: A python list of ``Optimizables`` with attributes in ``attributes`` that can be + communicated using ``mpi4py``. + attributes: A python list of strings corresponding to the list of attributes that is to be + maintained consistent across all ranks. + comm: The MPI communicator to use. """ from simsopt._core.util import parallel_loop_bounds @@ -65,6 +77,11 @@ def __init__(self, optimizables, attributes, comm): self.comm = comm self.attributes = attributes Optimizable.__init__(self, x0=np.asarray([]), depends_on=optimizables) + + for opt in self.optimizables: + for attr in self.attributes: + if not hasattr(opt, attr): + raise Exception(f'All Optimizables in the optimizable list must contain the attribute {attr}') def __getitem__(self, key): if self.need_to_communicate: From 289219acc245cc338e692032a6b0682b97c5936d Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 9 May 2023 12:20:58 -0400 Subject: [PATCH 011/176] added a few more unit tests --- examples/2_Intermediate/boozerQA_ls_mpi.py | 5 +- src/simsopt/geo/boozersurface.py | 25 ++++-- src/simsopt/geo/surfaceobjectives.py | 100 ++++++++++----------- tests/geo/test_boozersurface.py | 56 ++++++++++++ 4 files changed, 127 insertions(+), 59 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index c55893e3c..16b13240b 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -90,10 +90,10 @@ def pprint(*args, **kwargs): if comm is None or comm.rank == 0: curves_to_vtk(curves, OUT_DIR + f"curves_init") +# dictionary used to save the last accepted surface dofs in the line search, in case Newton's method fails prevs = {'sdofs': [surface.x.copy() for surface in mpi_surfaces], 'iota': [boozer_surface.res['iota'] for boozer_surface in mpi_boozer_surfaces], 'G': [boozer_surface.res['G'] for boozer_surface in mpi_boozer_surfaces], 'J': JF.J(), 'dJ': JF.dJ().copy(), 'it': 0} - def fun(dofs): # initialize to last accepted surface values for idx, surface in enumerate(mpi_surfaces): @@ -102,7 +102,6 @@ def fun(dofs): boozer_surface.res['iota'] = prevs['iota'][idx] boozer_surface.res['G'] = prevs['G'][idx] - # save these as a backup in case the boozer surface Newton solve fails alldofs = MPI.COMM_WORLD.allgather(dofs) assert np.all(np.norm(alldofs[0]-d) == 0 for d in alldofs) @@ -122,6 +121,8 @@ def fun(dofs): def callback(x): + # since this set of coil dofs was accepted, set the backup surface dofs + # to accepted ones in case future Newton solves fail. for idx, surface in enumerate(mpi_surfaces): prevs['sdofs'][idx] = surface.x.copy() for idx, boozer_surface in enumerate(mpi_boozer_surfaces): diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index b5a5dea69..acb6d66c8 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -78,7 +78,7 @@ def run_code(self, boozer_type, iota, G=None, verbose=True): else: raise Exception(f"boozer_type not supported: {boozer_type}") - def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., scalarize=True, optimize_G=False): + def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., scalarize=True, optimize_G=False, weight_inv_modB=False): r""" Define the residual @@ -116,7 +116,7 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca s.set_dofs(sdofs) - boozer = boozer_surface_residual(s, iota, G, biotsavart, derivatives=derivatives) + boozer = boozer_surface_residual(s, iota, G, biotsavart, derivatives=derivatives, weight_inv_modB=weight_inv_modB) r = boozer[0] @@ -621,6 +621,11 @@ def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., return res def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G=False): + """ + This function returns the same thing as `boozer_penalty_constraints` when `scalarized=True` and `weight_inv_modB=True`. It + is much faster since it calls a vectorized implementation in cpp. + """ + # this is essentially the scalarize option in previous implementation. This should be merged in that case... assert derivatives in [0, 1, 2] if optimize_G: @@ -630,7 +635,7 @@ def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G else: sdofs = dofs[:-1] iota = dofs[-1] - G = None + G = 2. * np.pi * np.sum(np.abs([coil.current.get_value() for coil in self.biotsavart._coils])) * (4 * np.pi * 10**(-7) / (2 * np.pi)) s = self.surface nphi = s.quadpoints_phi.size @@ -639,8 +644,6 @@ def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G s.set_dofs(sdofs) - #boozer = residual(s, iota, G, self.bs, derivatives=derivatives) - # initialize surface = self.surface biotsavart = self.biotsavart x = surface.gamma() @@ -659,6 +662,7 @@ def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G dxphi_dc = surface.dgammadash1_by_dcoeff() dxtheta_dc = surface.dgammadash2_by_dcoeff() dB_dx = biotsavart.dB_by_dX().reshape((nphi, ntheta, 3, 3)) + if derivatives == 2: d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) @@ -687,25 +691,32 @@ def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G dl = np.zeros(dofs.shape) drz = np.zeros(dofs.shape) - dl[:nsurfdofs] = self.label.dJ() + dl[:nsurfdofs] = self.label.dJ(partials=True)(s) drz[:nsurfdofs] = s.dgamma_by_dcoeff()[0, 0, 2, :] Jnl = boozer[1] + if not optimize_G: + Jnl = Jnl[:-1] + drl = np.sqrt(constraint_weight) * dl drz = np.sqrt(constraint_weight) * drz J = Jnl + rl * drl + rz * drz if self.reg is not None: J[:nsurfdofs] += self.reg.dJ() - + if derivatives == 1: return r, J Hnl = boozer[2] + if not optimize_G: + Hnl = Hnl[:-1, :-1] + d2rl = np.zeros((dofs.shape[0], dofs.shape[0])) d2rl[:nsurfdofs, :nsurfdofs] = np.sqrt(constraint_weight)*self.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() H = Hnl + drl[:, None] @ drl[None, :] + drz[:, None] @ drz[None, :] + rl * d2rl if self.reg is not None: H[:nsurfdofs, :nsurfdofs] += self.reg.d2J() + return r, J, H def compute_boozerls_BFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, hessian=False, verbose=False): diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 8790f69c0..d2e4db7a7 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -320,7 +320,7 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ """ - assert derivatives in [0, 1] + assert derivatives in [0, 1, 2] user_provided_G = G is not None if not user_provided_G: @@ -371,7 +371,6 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ dB2_dc = 2*np.einsum('ijk,ijkl->ijl', B, dB_dc, optimize=True) dmodB_dc = 0.5*dB2_dc/np.sqrt(B2[:, :, None]) dw_dc = -dmodB_dc/modB[:, :, None]**2 - # d/dc(r*dS) = dr/dc * dS + dS_dc * r drtil_dc = residual[..., None] * dw_dc[:, :, None, :] + w[:, :, None, None] * dresidual_dc drtil_diota = w[:, :, None] * dresidual_diota else: @@ -394,54 +393,55 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ else: J = np.concatenate((drtil_dc_flattened, drtil_diota_flattened), axis=1) - return r, J - -# d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) -# d2B_dcdc = np.einsum('ijkpl,ijpn,ijkm->ijlmn', d2B_by_dXdX, dx_dc, dx_dc) -# dB2_dc = 2. * np.einsum('ijl,ijlm->ijm', B, dB_dc) -# -# term1 = np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc) -# term2 = np.einsum('ijlmn,ijl->ijmn', d2B_dcdc, B) -# d2B2_dcdc = 2*(term1 + term2) -# -# term1 = -(dxphi_dc[..., None, :] + iota * dxtheta_dc[..., None, :]) * dB2_dc[..., None, :, None] -# term2 = -(dxphi_dc[..., :, None] + iota * dxtheta_dc[..., :, None]) * dB2_dc[..., None, None, :] -# term3 = -(xphi[..., None, None] + iota * xtheta[..., None, None]) * d2B2_dcdc[..., None, :, :] -# d2residual_by_dcdc = G * d2B_dcdc + term1 + term2 + term3 -# d2residual_by_dcdiota = -(dB2_dc[..., None, :] * xtheta[..., :, None] + B2[..., None, None] * dxtheta_dc) -# d2residual_by_diotadiota = np.zeros(dresidual_diota.shape) -# -# d2residual_by_dcdc_flattened = d2residual_by_dcdc.reshape((nphi*ntheta*3, nsurfdofs, nsurfdofs)) -# d2residual_by_dcdiota_flattened = d2residual_by_dcdiota.reshape((nphi*ntheta*3, nsurfdofs)) -# d2residual_by_diotadiota_flattened = d2residual_by_diotadiota.reshape((nphi*ntheta*3,)) -# -# if user_provided_G: -# d2residual_by_dcdG = dB_dc -# d2residual_by_diotadG = np.zeros(dresidual_diota.shape) -# d2residual_by_dGdG = np.zeros(dresidual_dG.shape) -# d2residual_by_dcdG_flattened = d2residual_by_dcdG.reshape((nphi*ntheta*3, nsurfdofs)) -# d2residual_by_diotadG_flattened = d2residual_by_diotadG.reshape((nphi*ntheta*3,)) -# d2residual_by_dGdG_flattened = d2residual_by_dGdG.reshape((nphi*ntheta*3,)) -# H = np.zeros((nphi*ntheta*3, nsurfdofs + 2, nsurfdofs + 2)) -# # noqa turns out linting so that we can align everything neatly -# H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc -# H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota -# H[:, :nsurfdofs, nsurfdofs+1] = d2residual_by_dcdG_flattened # noqa (0, 2) dcdG -# H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc -# H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota -# H[:, nsurfdofs, nsurfdofs+1] = d2residual_by_diotadiota_flattened # noqa (1, 2) diotadG -# H[:, nsurfdofs+1, :nsurfdofs] = d2residual_by_dcdG_flattened # noqa (2, 0) dGdc -# H[:, nsurfdofs+1, nsurfdofs] = d2residual_by_diotadG_flattened # noqa (2, 1) dGdiota -# H[:, nsurfdofs+1, nsurfdofs+1] = d2residual_by_dGdG_flattened # noqa (2, 2) dGdG -# else: -# H = np.zeros((nphi*ntheta*3, nsurfdofs + 1, nsurfdofs + 1)) -# -# H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc -# H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota -# H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc -# H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota -# -# return r, J, H + if derivatives == 1: + return r, J + + d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) + d2B_dcdc = np.einsum('ijkpl,ijpn,ijkm->ijlmn', d2B_by_dXdX, dx_dc, dx_dc) + dB2_dc = 2. * np.einsum('ijl,ijlm->ijm', B, dB_dc) + + term1 = np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc) + term2 = np.einsum('ijlmn,ijl->ijmn', d2B_dcdc, B) + d2B2_dcdc = 2*(term1 + term2) + + term1 = -(dxphi_dc[..., None, :] + iota * dxtheta_dc[..., None, :]) * dB2_dc[..., None, :, None] + term2 = -(dxphi_dc[..., :, None] + iota * dxtheta_dc[..., :, None]) * dB2_dc[..., None, None, :] + term3 = -(xphi[..., None, None] + iota * xtheta[..., None, None]) * d2B2_dcdc[..., None, :, :] + d2residual_by_dcdc = G * d2B_dcdc + term1 + term2 + term3 + d2residual_by_dcdiota = -(dB2_dc[..., None, :] * xtheta[..., :, None] + B2[..., None, None] * dxtheta_dc) + d2residual_by_diotadiota = np.zeros(dresidual_diota.shape) + + d2residual_by_dcdc_flattened = d2residual_by_dcdc.reshape((nphi*ntheta*3, nsurfdofs, nsurfdofs)) + d2residual_by_dcdiota_flattened = d2residual_by_dcdiota.reshape((nphi*ntheta*3, nsurfdofs)) + d2residual_by_diotadiota_flattened = d2residual_by_diotadiota.reshape((nphi*ntheta*3,)) + + if user_provided_G: + d2residual_by_dcdG = dB_dc + d2residual_by_diotadG = np.zeros(dresidual_diota.shape) + d2residual_by_dGdG = np.zeros(dresidual_dG.shape) + d2residual_by_dcdG_flattened = d2residual_by_dcdG.reshape((nphi*ntheta*3, nsurfdofs)) + d2residual_by_diotadG_flattened = d2residual_by_diotadG.reshape((nphi*ntheta*3,)) + d2residual_by_dGdG_flattened = d2residual_by_dGdG.reshape((nphi*ntheta*3,)) + H = np.zeros((nphi*ntheta*3, nsurfdofs + 2, nsurfdofs + 2)) + # noqa turns out linting so that we can align everything neatly + H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc + H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota + H[:, :nsurfdofs, nsurfdofs+1] = d2residual_by_dcdG_flattened # noqa (0, 2) dcdG + H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc + H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota + H[:, nsurfdofs, nsurfdofs+1] = d2residual_by_diotadiota_flattened # noqa (1, 2) diotadG + H[:, nsurfdofs+1, :nsurfdofs] = d2residual_by_dcdG_flattened # noqa (2, 0) dGdc + H[:, nsurfdofs+1, nsurfdofs] = d2residual_by_diotadG_flattened # noqa (2, 1) dGdiota + H[:, nsurfdofs+1, nsurfdofs+1] = d2residual_by_dGdG_flattened # noqa (2, 2) dGdG + else: + H = np.zeros((nphi*ntheta*3, nsurfdofs + 1, nsurfdofs + 1)) + + H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc + H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota + H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc + H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota + + return r, J, H def parameter_derivatives(surface: Surface, diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 06ae8aeff..4c3adf5a4 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -349,6 +349,62 @@ def subtest_boozer_serialization(self, label): # check that BoozerSurface.surface and label.surface are the same surfaces assert bs_regen.label.surface is bs_regen.surface + def test_boozer_penalty_constraints_cpp_notcpp(self): + """ + Test to verify cpp and python implementations of the BoozerLS objective return the same thing. + """ + for surfacetype in surfacetypes_list: + for stellsym in stellsym_list: + for optimize_G in [True, False]: + for nphi in [10, 11, 14, 15]: + for ntheta in [10, 11, 14, 15]: + with self.subTest(surfacetype=surfacetype, + stellsym=stellsym, + optimize_G=optimize_G): + self.subtest_boozer_penalty_constraints_cpp_notcpp(surfacetype, stellsym, optimize_G, nphi, ntheta) + + def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, optimize_G, nphi, ntheta): + + np.random.seed(1) + curves, currents, ma = get_ncsx_data() + coils = coils_via_symmetries(curves, currents, 3, stellsym) + bs = BiotSavart(coils) + bs_tf = BiotSavart(coils) + current_sum = sum(abs(c.current.get_value()) for c in coils) + + s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta) + s.fit_to_curve(ma, 0.1) + tf = ToroidalFlux(s, bs_tf, nphi=51, ntheta=51) + + tf_target = 0.1 + boozer_surface = BoozerSurface(bs, s, tf, tf_target) + + iota = -0.3 + x = np.concatenate((s.get_dofs(), [iota])) + if optimize_G: + x = np.concatenate( + (x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) + + f0, J0 = boozer_surface.boozer_penalty_constraints( + x, derivatives=1, constraint_weight=1e2, optimize_G=optimize_G, weight_inv_modB=True) + f1, J1 = boozer_surface.boozerls_penalty( + x, derivatives=1, constraint_weight=1e2, optimize_G=optimize_G) + + f1 -= 0.5 * 1e2 * (boozer_surface.label.J() - boozer_surface.targetlabel)**2 + f1 *= (3 * len(s.quadpoints_phi)*len(s.quadpoints_theta)) + f1 += 0.5 * 1e2 * (boozer_surface.label.J() - boozer_surface.targetlabel)**2 + + to_add = [0] + if optimize_G: + to_add = [0, 0] + + J1 -= 1e2 * (boozer_surface.label.J() - boozer_surface.targetlabel) * np.append(boozer_surface.label.dJ(partials=True)(s), to_add) + J1 *= (3*len(s.quadpoints_phi)*len(s.quadpoints_theta)) + J1 += 1e2 * (boozer_surface.label.J() - boozer_surface.targetlabel) * np.append(boozer_surface.label.dJ(partials=True)(s), to_add) + + self.assertAlmostEqual(f0, f1) + np.testing.assert_allclose(J0, J1) + if __name__ == "__main__": unittest.main() From c7e9ba87bac5ba556bfe5dd8683f5338a4a147b3 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 9 May 2023 16:05:49 -0400 Subject: [PATCH 012/176] edits to unit test --- src/simsopt/geo/boozersurface.py | 4 +- src/simsopt/geo/surfaceobjectives.py | 73 ++++++++++++++++++---------- tests/geo/test_boozersurface.py | 51 ++++++++++++------- 3 files changed, 83 insertions(+), 45 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index acb6d66c8..e33e0522e 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -62,7 +62,7 @@ def run_code(self, boozer_type, iota, G=None, verbose=True): return if boozer_type == 'exact': - res = self.boozer_surface.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=iota, G=G, verbose=verbose) + res = self.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=iota, G=G, verbose=verbose) return res elif boozer_type == 'ls': @@ -160,7 +160,7 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca d2l = np.zeros((x.shape[0], x.shape[0])) d2l[:nsurfdofs, :nsurfdofs] = self.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() - + H = np.concatenate(( H, np.sqrt(constraint_weight) * d2l[None, :, :], diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index d2e4db7a7..8ed36c823 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -397,11 +397,11 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ return r, J d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) - d2B_dcdc = np.einsum('ijkpl,ijpn,ijkm->ijlmn', d2B_by_dXdX, dx_dc, dx_dc) - dB2_dc = 2. * np.einsum('ijl,ijlm->ijm', B, dB_dc) + d2B_dcdc = np.einsum('ijkpl,ijpn,ijkm->ijlmn', d2B_by_dXdX, dx_dc, dx_dc, optimize=True) + dB2_dc = 2. * np.einsum('ijl,ijlm->ijm', B, dB_dc, optimize=True) - term1 = np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc) - term2 = np.einsum('ijlmn,ijl->ijmn', d2B_dcdc, B) + term1 = np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc, optimize=True) + term2 = np.einsum('ijlmn,ijl->ijmn', d2B_dcdc, B, optimize=True) d2B2_dcdc = 2*(term1 + term2) term1 = -(dxphi_dc[..., None, :] + iota * dxtheta_dc[..., None, :]) * dB2_dc[..., None, :, None] @@ -411,35 +411,56 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ d2residual_by_dcdiota = -(dB2_dc[..., None, :] * xtheta[..., :, None] + B2[..., None, None] * dxtheta_dc) d2residual_by_diotadiota = np.zeros(dresidual_diota.shape) - d2residual_by_dcdc_flattened = d2residual_by_dcdc.reshape((nphi*ntheta*3, nsurfdofs, nsurfdofs)) - d2residual_by_dcdiota_flattened = d2residual_by_dcdiota.reshape((nphi*ntheta*3, nsurfdofs)) - d2residual_by_diotadiota_flattened = d2residual_by_diotadiota.reshape((nphi*ntheta*3,)) + if weight_inv_modB: + d2B2_dcdc = 2*(np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc, optimize=True)+np.einsum('ijkpl,ijpn,ijkm,ijl->ijmn', d2B_by_dXdX, dx_dc, dx_dc, B, optimize=True)) + d2modB_dc2 = (2*B2[:, :, None, None] * d2B2_dcdc -dB2_dc[:, :, :, None]*dB2_dc[:, :, None, :])*(1/(4*B2[:, :, None, None]**1.5)) + d2w_dc2 = (2*dmodB_dc[:, :, :, None] * dmodB_dc[:, :, None, :] - modB[:, :, None, None] * d2modB_dc2)/modB[:, :, None, None]**3. + + d2rtil_dcdc = residual[..., None, None] * d2w_dc2[:, :, None, ...] \ + + dw_dc[:, :, None, :, None] * dresidual_dc[:, :, :, None, :] \ + + dw_dc[:, :, None, None, :] * dresidual_dc[:, :, :, :, None] \ + + w[:, :, None, None, None] * d2residual_by_dcdc + d2rtil_dcdiota = w[:, :, None, None] * d2residual_by_dcdiota + dw_dc[:, :, None, :] * dresidual_diota[..., None] + d2rtil_diotadiota = np.zeros(dresidual_diota.shape) + else: + d2rtil_dcdc = d2residual_by_dcdc.copy() + d2rtil_dcdiota = d2residual_by_dcdiota.copy() + d2rtil_diotadiota = d2residual_by_diotadiota.copy() + + d2rtil_dcdc_flattened = d2rtil_dcdc.reshape((nphi*ntheta*3, nsurfdofs, nsurfdofs)) + d2rtil_dcdiota_flattened = d2rtil_dcdiota.reshape((nphi*ntheta*3, nsurfdofs)) + d2rtil_diotadiota_flattened = d2rtil_diotadiota.reshape((nphi*ntheta*3,)) + if user_provided_G: d2residual_by_dcdG = dB_dc - d2residual_by_diotadG = np.zeros(dresidual_diota.shape) - d2residual_by_dGdG = np.zeros(dresidual_dG.shape) - d2residual_by_dcdG_flattened = d2residual_by_dcdG.reshape((nphi*ntheta*3, nsurfdofs)) - d2residual_by_diotadG_flattened = d2residual_by_diotadG.reshape((nphi*ntheta*3,)) - d2residual_by_dGdG_flattened = d2residual_by_dGdG.reshape((nphi*ntheta*3,)) + if weight_inv_modB: + d2rtil_dcdG = dw_dc[:, :, None, :] * dresidual_dG[..., None] + w[:, :, None, None] * d2residual_by_dcdG + else: + d2rtil_dcdG = d2residual_by_dcdG.copy() + + d2rtil_dGdG = np.zeros(dresidual_dG.shape) + d2rtil_dcdG_flattened = d2rtil_dcdG.reshape((nphi*ntheta*3, nsurfdofs)) + d2rtil_diotadG_flattened = np.zeros((nphi*ntheta*3,)) + d2rtil_dGdG_flattened = d2rtil_dGdG.reshape((nphi*ntheta*3,)) + H = np.zeros((nphi*ntheta*3, nsurfdofs + 2, nsurfdofs + 2)) # noqa turns out linting so that we can align everything neatly - H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc - H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota - H[:, :nsurfdofs, nsurfdofs+1] = d2residual_by_dcdG_flattened # noqa (0, 2) dcdG - H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc - H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota - H[:, nsurfdofs, nsurfdofs+1] = d2residual_by_diotadiota_flattened # noqa (1, 2) diotadG - H[:, nsurfdofs+1, :nsurfdofs] = d2residual_by_dcdG_flattened # noqa (2, 0) dGdc - H[:, nsurfdofs+1, nsurfdofs] = d2residual_by_diotadG_flattened # noqa (2, 1) dGdiota - H[:, nsurfdofs+1, nsurfdofs+1] = d2residual_by_dGdG_flattened # noqa (2, 2) dGdG + H[:, :nsurfdofs, :nsurfdofs] = d2rtil_dcdc_flattened # noqa (0, 0) dcdc + H[:, :nsurfdofs, nsurfdofs] = d2rtil_dcdiota_flattened # noqa (0, 1) dcdiota + H[:, :nsurfdofs, nsurfdofs+1] = d2rtil_dcdG_flattened # noqa (0, 2) dcdG + H[:, nsurfdofs, :nsurfdofs] = d2rtil_dcdiota_flattened # noqa (1, 0) diotadc + H[:, nsurfdofs, nsurfdofs] = d2rtil_diotadiota_flattened # noqa (1, 1) diotadiota + H[:, nsurfdofs, nsurfdofs+1] = d2rtil_diotadiota_flattened # noqa (1, 2) diotadG + H[:, nsurfdofs+1, :nsurfdofs] = d2rtil_dcdG_flattened # noqa (2, 0) dGdc + H[:, nsurfdofs+1, nsurfdofs] = d2rtil_diotadG_flattened # noqa (2, 1) dGdiota + H[:, nsurfdofs+1, nsurfdofs+1] = d2rtil_dGdG_flattened # noqa (2, 2) dGdG else: H = np.zeros((nphi*ntheta*3, nsurfdofs + 1, nsurfdofs + 1)) - - H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc - H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota - H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc - H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota + H[:, :nsurfdofs, :nsurfdofs] = d2rtil_dcdc_flattened # noqa (0, 0) dcdc + H[:, :nsurfdofs, nsurfdofs] = d2rtil_dcdiota_flattened # noqa (0, 1) dcdiota + H[:, nsurfdofs, :nsurfdofs] = d2rtil_dcdiota_flattened # noqa (1, 0) diotadc + H[:, nsurfdofs, nsurfdofs] = d2rtil_diotadiota_flattened # noqa (1, 1) diotadiota return r, J, H diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 4c3adf5a4..7287ceb30 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -355,13 +355,11 @@ def test_boozer_penalty_constraints_cpp_notcpp(self): """ for surfacetype in surfacetypes_list: for stellsym in stellsym_list: - for optimize_G in [True, False]: - for nphi in [10, 11, 14, 15]: - for ntheta in [10, 11, 14, 15]: - with self.subTest(surfacetype=surfacetype, - stellsym=stellsym, - optimize_G=optimize_G): - self.subtest_boozer_penalty_constraints_cpp_notcpp(surfacetype, stellsym, optimize_G, nphi, ntheta) + for (optimize_G, nphi, ntheta) in [(True, 10, 17), (False, 13, 21)]: + with self.subTest(surfacetype=surfacetype, + stellsym=stellsym, + optimize_G=optimize_G): + self.subtest_boozer_penalty_constraints_cpp_notcpp(surfacetype, stellsym, optimize_G, nphi, ntheta) def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, optimize_G, nphi, ntheta): @@ -374,6 +372,7 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta) s.fit_to_curve(ma, 0.1) + s.x = s.x + np.random.rand(s.x.size)*1e-6 tf = ToroidalFlux(s, bs_tf, nphi=51, ntheta=51) @@ -386,25 +385,43 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o x = np.concatenate( (x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) - f0, J0 = boozer_surface.boozer_penalty_constraints( - x, derivatives=1, constraint_weight=1e2, optimize_G=optimize_G, weight_inv_modB=True) - f1, J1 = boozer_surface.boozerls_penalty( - x, derivatives=1, constraint_weight=1e2, optimize_G=optimize_G) + w = 1e2 + f0, J0, H0 = boozer_surface.boozer_penalty_constraints( + x, derivatives=2, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=True) + f1, J1, H1 = boozer_surface.boozerls_penalty( + x, derivatives=2, constraint_weight=w, optimize_G=optimize_G) - f1 -= 0.5 * 1e2 * (boozer_surface.label.J() - boozer_surface.targetlabel)**2 + # f1, and J1 scale the quadratic residual terms by 1/(number of residuals), while f0 and J0 do not. + # rescale below so that both quantities are comparable. + diff1 = (boozer_surface.label.J() - boozer_surface.targetlabel) + diff2 = s.gamma()[0, 0, 2] + f1 -= 0.5 * w * (diff1**2 + diff2**2) f1 *= (3 * len(s.quadpoints_phi)*len(s.quadpoints_theta)) - f1 += 0.5 * 1e2 * (boozer_surface.label.J() - boozer_surface.targetlabel)**2 - + f1 += 0.5 * w * (diff1**2 + diff2**2) + to_add = [0] if optimize_G: to_add = [0, 0] - - J1 -= 1e2 * (boozer_surface.label.J() - boozer_surface.targetlabel) * np.append(boozer_surface.label.dJ(partials=True)(s), to_add) + + dl = np.append(boozer_surface.label.dJ(partials=True)(s), to_add) + drz = np.append(s.dgamma_by_dcoeff()[0, 0, 2, :], to_add) + J1 -= w * (diff1 * dl + diff2 * drz) J1 *= (3*len(s.quadpoints_phi)*len(s.quadpoints_theta)) - J1 += 1e2 * (boozer_surface.label.J() - boozer_surface.targetlabel) * np.append(boozer_surface.label.dJ(partials=True)(s), to_add) + J1 += w * (diff1 * dl + diff2 * drz) + nsurfdofs = s.x.size + d2l = np.zeros((x.size, x.size)) + d2l[:nsurfdofs, :nsurfdofs] = boozer_surface.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() + H1 -= w * dl[:, None] * dl[None, :] + w * diff1 * d2l + H1 -= w * drz[:, None] * drz[None, :] + H1 *= (3*len(s.quadpoints_phi)*len(s.quadpoints_theta)) + H1 += w * dl[:, None] * dl[None, :] + w * diff1 * d2l + H1 += w * drz[:, None] * drz[None, :] + self.assertAlmostEqual(f0, f1) np.testing.assert_allclose(J0, J1) + norm = np.max(np.abs(H0)) + assert np.all(np.abs((H0-H1)/norm) < 1e-13) if __name__ == "__main__": unittest.main() From 0dc5f35ac8c87c8cfa6b3bf966c181487960f90c Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 9 May 2023 16:09:32 -0400 Subject: [PATCH 013/176] linting --- src/simsopt/geo/surfaceobjectives.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 8ed36c823..00cf7d13b 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -411,16 +411,15 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ d2residual_by_dcdiota = -(dB2_dc[..., None, :] * xtheta[..., :, None] + B2[..., None, None] * dxtheta_dc) d2residual_by_diotadiota = np.zeros(dresidual_diota.shape) - if weight_inv_modB: d2B2_dcdc = 2*(np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc, optimize=True)+np.einsum('ijkpl,ijpn,ijkm,ijl->ijmn', d2B_by_dXdX, dx_dc, dx_dc, B, optimize=True)) - d2modB_dc2 = (2*B2[:, :, None, None] * d2B2_dcdc -dB2_dc[:, :, :, None]*dB2_dc[:, :, None, :])*(1/(4*B2[:, :, None, None]**1.5)) + d2modB_dc2 = (2*B2[:, :, None, None] * d2B2_dcdc - dB2_dc[:, :, :, None]*dB2_dc[:, :, None, :])*(1/(4*B2[:, :, None, None]**1.5)) d2w_dc2 = (2*dmodB_dc[:, :, :, None] * dmodB_dc[:, :, None, :] - modB[:, :, None, None] * d2modB_dc2)/modB[:, :, None, None]**3. d2rtil_dcdc = residual[..., None, None] * d2w_dc2[:, :, None, ...] \ - + dw_dc[:, :, None, :, None] * dresidual_dc[:, :, :, None, :] \ - + dw_dc[:, :, None, None, :] * dresidual_dc[:, :, :, :, None] \ - + w[:, :, None, None, None] * d2residual_by_dcdc + + dw_dc[:, :, None, :, None] * dresidual_dc[:, :, :, None, :] \ + + dw_dc[:, :, None, None, :] * dresidual_dc[:, :, :, :, None] \ + + w[:, :, None, None, None] * d2residual_by_dcdc d2rtil_dcdiota = w[:, :, None, None] * d2residual_by_dcdiota + dw_dc[:, :, None, :] * dresidual_diota[..., None] d2rtil_diotadiota = np.zeros(dresidual_diota.shape) else: From 158fa046b4065e7d7698697a102f4872841735bd Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 9 May 2023 16:13:08 -0400 Subject: [PATCH 014/176] linting pt 2 --- examples/2_Intermediate/boozerQA_ls_mpi.py | 1 + tests/geo/test_boozersurface.py | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 16b13240b..b984b28c7 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -94,6 +94,7 @@ def pprint(*args, **kwargs): prevs = {'sdofs': [surface.x.copy() for surface in mpi_surfaces], 'iota': [boozer_surface.res['iota'] for boozer_surface in mpi_boozer_surfaces], 'G': [boozer_surface.res['G'] for boozer_surface in mpi_boozer_surfaces], 'J': JF.J(), 'dJ': JF.dJ().copy(), 'it': 0} + def fun(dofs): # initialize to last accepted surface values for idx, surface in enumerate(mpi_surfaces): diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 7287ceb30..095ef41b4 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -422,6 +422,7 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o np.testing.assert_allclose(J0, J1) norm = np.max(np.abs(H0)) assert np.all(np.abs((H0-H1)/norm) < 1e-13) - + + if __name__ == "__main__": unittest.main() From 85a6cdd516efd8ede8c3620856ed0fe11cb9eb59 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 9 May 2023 16:53:04 -0400 Subject: [PATCH 015/176] added unit test for self intersection --- tests/geo/test_surface.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/tests/geo/test_surface.py b/tests/geo/test_surface.py index a395350ae..6474d19ee 100755 --- a/tests/geo/test_surface.py +++ b/tests/geo/test_surface.py @@ -369,5 +369,22 @@ def test_gauss_bonnet(self): assert np.abs(np.sum(K*N)) < 1e-12 +class isSelfIntersecting(unittest.TestCase): + """ + Tests the self-intersection algorithm: + """ + + def test_is_self_intersecting(self): + # dofs1 results in a surface that is self-intersecting + # dofs2 results in a surface that is not self-intersecting + dofs1 = np.array([1. , 0. , 0. , 0. , 0. , 0.1, 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0.1, 0. , 0. , 0. , 0. , 0. , 0. , 0.1]) + s = get_surface('SurfaceRZFourier', True, full=True, nphi=200, ntheta=200, mpol=2, ntor=2) + s.x = dofs1 + assert s.is_self_intersecting() + + dofs2 = np.array([1. , 0. , 0. , 0. , 0. , 0.1, 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0.1, 0. , 0. , 0. , 0. , 0. , 0. , 0. ]) + s.x = dofs2 + assert not s.is_self_intersecting() + if __name__ == "__main__": unittest.main() From f3904df2d214d43ecd62865f32f45ff58caf91fd Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 9 May 2023 17:01:00 -0400 Subject: [PATCH 016/176] linting --- tests/geo/test_surface.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/tests/geo/test_surface.py b/tests/geo/test_surface.py index 6474d19ee..00156f2ed 100755 --- a/tests/geo/test_surface.py +++ b/tests/geo/test_surface.py @@ -377,14 +377,17 @@ class isSelfIntersecting(unittest.TestCase): def test_is_self_intersecting(self): # dofs1 results in a surface that is self-intersecting # dofs2 results in a surface that is not self-intersecting - dofs1 = np.array([1. , 0. , 0. , 0. , 0. , 0.1, 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0.1, 0. , 0. , 0. , 0. , 0. , 0. , 0.1]) + dofs1 = np.array([1., 0., 0., 0., 0., 0.1, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.1,\ + 0., 0., 0., 0., 0., 0., 0.1]) s = get_surface('SurfaceRZFourier', True, full=True, nphi=200, ntheta=200, mpol=2, ntor=2) s.x = dofs1 assert s.is_self_intersecting() - dofs2 = np.array([1. , 0. , 0. , 0. , 0. , 0.1, 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0.1, 0. , 0. , 0. , 0. , 0. , 0. , 0. ]) + dofs2 = np.array([1., 0., 0., 0., 0., 0.1, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.1, + 0., 0., 0., 0., 0., 0., 0.1]) s.x = dofs2 assert not s.is_self_intersecting() + if __name__ == "__main__": unittest.main() From 965014458c551ba7c8b36a75e6e800483b5db6b4 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Thu, 18 May 2023 13:34:04 -0400 Subject: [PATCH 017/176] added second derivative --- src/simsopt/geo/surface.py | 58 +++++++++++++++++++++++++++++ src/simsopt/objectives/utilities.py | 2 +- 2 files changed, 59 insertions(+), 1 deletion(-) diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index 0aca5df57..e4af95592 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -651,6 +651,64 @@ def dmean_cross_sectional_area_by_dcoeff(self): dmean_area_ds = np.mean((1/(r**2))*((xvarphi * y * ztheta - xtheta * y * zvarphi + x * (-yvarphi * ztheta + ytheta * zvarphi)) * dr_ds + r * (-zvarphi * (ytheta * dx_ds - y * dxtheta_ds - xtheta * dy_ds + x * dytheta_ds) + ztheta * (yvarphi * dx_ds - y * dxvarphi_ds - xvarphi * dy_ds + x * dyvarphi_ds) + (-xvarphi * y + x * yvarphi) * dztheta_ds + (xtheta * y - x * ytheta) * dzvarphi_ds)), axis=(0, 1)) return np.sign(mean_area) * dmean_area_ds/(2*np.pi) + def d2mean_cross_sectional_area_by_dcoeff_dcoeff(self): + """ + Return the second derivative of the mean cross sectional area wrt surface coefficients + """ + + g = self.gamma() + g1 = self.gammadash1() + g2 = self.gammadash2() + + dg_ds = self.dgamma_by_dcoeff() + dg1_ds = self.dgammadash1_by_dcoeff() + dg2_ds = self.dgammadash2_by_dcoeff() + + x = g[:, :, 0, None] + y = g[:, :, 1, None] + + dx_ds = dg_ds[:, :, 0, :] + dy_ds = dg_ds[:, :, 1, :] + + r = np.sqrt(x**2+y**2) + dr_ds = (x*dx_ds+y*dy_ds)/r + dr2_ds2 = -(2*x*dx_ds + 2*y*dy_ds)**2/(4*r**3) + (2*dx_ds**2 + 2*dy_ds**2)/(2*r) + + xvarphi = g1[:, :, 0, None] + yvarphi = g1[:, :, 1, None] + zvarphi = g1[:, :, 2, None] + + xtheta = g2[:, :, 0, None] + ytheta = g2[:, :, 1, None] + ztheta = g2[:, :, 2, None] + + dxvarphi_ds = dg1_ds[:, :, 0, :] + dyvarphi_ds = dg1_ds[:, :, 1, :] + dzvarphi_ds = dg1_ds[:, :, 2, :] + + dxtheta_ds = dg2_ds[:, :, 0, :] + dytheta_ds = dg2_ds[:, :, 1, :] + dztheta_ds = dg2_ds[:, :, 2, :] + + mean_area = np.mean((1/r) * (ztheta*(x*yvarphi-y*xvarphi)-zvarphi*(x*ytheta-y*xtheta)))/(2.*np.pi) + dmean_area_ds = np.mean((1/(r**2))*((xvarphi * y * ztheta - xtheta * y * zvarphi + x * (-yvarphi * ztheta + ytheta * zvarphi)) * dr_ds + r * (-zvarphi * (ytheta * dx_ds - y * dxtheta_ds - xtheta * dy_ds + x * dytheta_ds) + ztheta * (yvarphi * dx_ds - y * dxvarphi_ds - xvarphi * dy_ds + x * dyvarphi_ds) + (-xvarphi * y + x * yvarphi) * dztheta_ds + (xtheta * y - x * ytheta) * dzvarphi_ds)), axis=(0, 1)) + d2mean_area_ds2 = (-2*dr_ds*((yvarphi*ztheta - ytheta*zvarphi)*dx_ds + \ + y*zvarphi*dxtheta_ds - y*ztheta*dxvarphi_ds - xvarphi*ztheta*dy_ds + \ + xtheta*zvarphi*dy_ds - xvarphi*y*dztheta_ds + xtheta*y*dzvarphi_ds + \ + x*(-(zvarphi*dytheta_ds) + ztheta*dyvarphi_ds + yvarphi*dztheta_ds - \ + ytheta*dzvarphi_ds)))/r**2 + (2*zvarphi*dxtheta_ds*dy_ds - \ + 2*xvarphi*dy_ds*dztheta_ds - 2*dxvarphi_ds*(ztheta*dy_ds + \ + y*dztheta_ds) + 2*(y*dxtheta_ds + xtheta*dy_ds)*dzvarphi_ds + \ + 2*dx_ds*(-(zvarphi*dytheta_ds) + ztheta*dyvarphi_ds + \ + yvarphi*dztheta_ds - ytheta*dzvarphi_ds) + \ + x*(2*dyvarphi_ds*dztheta_ds - 2*dytheta_ds*dzvarphi_ds))/r + \ + (-(xvarphi*y*ztheta) + xtheta*y*zvarphi + x*(yvarphi*ztheta - \ + ytheta*zvarphi))*((2*dr_ds**2)/r^3 - dr2_ds2/r**2) + + return d2mean_area_ds2 + + + def arclength_poloidal_angle(self): """ Computes poloidal angle based on arclenth along magnetic surface at diff --git a/src/simsopt/objectives/utilities.py b/src/simsopt/objectives/utilities.py index 4919cff96..a45a0b9ea 100644 --- a/src/simsopt/objectives/utilities.py +++ b/src/simsopt/objectives/utilities.py @@ -78,7 +78,7 @@ def __init__(self, optimizables, attributes, comm): self.attributes = attributes Optimizable.__init__(self, x0=np.asarray([]), depends_on=optimizables) - for opt in self.optimizables: + for opt in optimizables: for attr in self.attributes: if not hasattr(opt, attr): raise Exception(f'All Optimizables in the optimizable list must contain the attribute {attr}') From f3974955dd60495d2ca5fe6544284cda0b2e71d2 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Sat, 20 May 2023 19:53:11 -0400 Subject: [PATCH 018/176] added second derivative of aspect ratio wrt surface coefficients --- src/simsopt/geo/surface.py | 133 +++++++++++++++++++++++-------- tests/geo/test_surface_taylor.py | 78 +++++++++++++++++- 2 files changed, 178 insertions(+), 33 deletions(-) diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index e4af95592..f8fc973ec 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -471,7 +471,7 @@ def aspect_ratio(self): """ R_minor = self.minor_radius() - R_major = np.abs(self.volume()) / (2. * np.pi**2 * R_minor**2) + R_major = self.major_radius() AR = R_major/R_minor return AR @@ -485,6 +485,22 @@ def daspect_ratio_by_dcoeff(self): dAR_ds = (self.dmajor_radius_by_dcoeff()*R_minor - self.dminor_radius_by_dcoeff() * R_major)/R_minor**2 return dAR_ds + def d2aspect_ratio_by_dcoeff_dcoeff(self): + """ + Return the derivative of the aspect ratio with respect to the surface coefficients + """ + r = self.minor_radius() + dr_ds = self.dminor_radius_by_dcoeff()[:, None] + dr_dt = self.dminor_radius_by_dcoeff()[None, :] + d2r_dsdt = self.d2minor_radius_by_dcoeff_dcoeff() + R = self.major_radius() + dR_ds = self.dmajor_radius_by_dcoeff()[:, None] + dR_dt = self.dmajor_radius_by_dcoeff()[None, :] + d2R_dsdt = self.d2major_radius_by_dcoeff_dcoeff() + + return (2*R*dr_dt*dr_ds)/r**3 - (dR_dt*dr_ds)/r**2 - \ + (dr_dt*dR_ds)/r**2 - (R*d2r_dsdt)/r**2 + d2R_dsdt/r + def minor_radius(self): r""" Return the minor radius of the surface using the formula @@ -507,6 +523,17 @@ def dminor_radius_by_dcoeff(self): return (0.5/np.pi)*self.dmean_cross_sectional_area_by_dcoeff()/np.sqrt(self.mean_cross_sectional_area() / np.pi) + def d2minor_radius_by_dcoeff_dcoeff(self): + """ + Return the second derivative of the minor radius wrt surface coefficients + + """ + A = self.mean_cross_sectional_area() + dA_ds = self.dmean_cross_sectional_area_by_dcoeff()[:, None] + dA_dt = self.dmean_cross_sectional_area_by_dcoeff()[None, :] + d2A_ds2 = self.d2mean_cross_sectional_area_by_dcoeff_dcoeff() + return (-(dA_dt*dA_ds) + 2*A*d2A_ds2)/(4*np.sqrt(np.pi)*A**(3/2)) + def major_radius(self): r""" Return the major radius of the surface using the formula @@ -534,6 +561,23 @@ def dmajor_radius_by_dcoeff(self): dR_major_ds = (-self.volume() * dmean_area_ds + self.dvolume_by_dcoeff() * mean_area) / mean_area**2 return dR_major_ds * np.sign(self.volume()) / (2. * np.pi) + def d2major_radius_by_dcoeff_dcoeff(self): + """ + Return the second derivative of the major radius wrt surface coefficients + """ + V = self.volume() + dV_ds = self.dvolume_by_dcoeff()[:, None] + dV_dt = self.dvolume_by_dcoeff()[None, :] + d2V_dsdt = self.d2volume_by_dcoeffdcoeff() + r = self.minor_radius() + dr_ds = self.dminor_radius_by_dcoeff()[:, None] + dr_dt = self.dminor_radius_by_dcoeff()[None, :] + d2r_dsdt = self.d2minor_radius_by_dcoeff_dcoeff() + + return ((6*V*dr_dt*dr_ds)/r**4 - (2*dV_dt*dr_ds)/r**3 - \ + (2*dr_dt*dV_ds)/r**3 - (2*V*d2r_dsdt)/r**3 + \ + d2V_dsdt/r**2)* np.sign(V)/(2*np.pi**2) + def mean_cross_sectional_area(self): r""" Note: cylindrical coordinates are :math:`(R, \phi, Z)`, where @@ -664,47 +708,72 @@ def d2mean_cross_sectional_area_by_dcoeff_dcoeff(self): dg1_ds = self.dgammadash1_by_dcoeff() dg2_ds = self.dgammadash2_by_dcoeff() - x = g[:, :, 0, None] - y = g[:, :, 1, None] + x = g[:, :, 0, None, None] + y = g[:, :, 1, None, None] - dx_ds = dg_ds[:, :, 0, :] - dy_ds = dg_ds[:, :, 1, :] + dx_ds = dg_ds[:, :, 0, :, None] + dy_ds = dg_ds[:, :, 1, :, None] + + dx_dt = dg_ds[:, :, 0, None, :] + dy_dt = dg_ds[:, :, 1, None, :] r = np.sqrt(x**2+y**2) dr_ds = (x*dx_ds+y*dy_ds)/r - dr2_ds2 = -(2*x*dx_ds + 2*y*dy_ds)**2/(4*r**3) + (2*dx_ds**2 + 2*dy_ds**2)/(2*r) + dr_dt = (x*dx_dt+y*dy_dt)/r + dr2_dsdt = -((2*x*dx_dt + 2*y*dy_dt)*(2*x*dx_ds + 2*y*dy_ds))/(4*(x**2 + y**2)**(3/2)) + (2*dx_dt*dx_ds + 2*dy_dt*dy_ds)/(2*r) + + xvarphi = g1[:, :, 0, None, None] + yvarphi = g1[:, :, 1, None, None] + zvarphi = g1[:, :, 2, None, None] - xvarphi = g1[:, :, 0, None] - yvarphi = g1[:, :, 1, None] - zvarphi = g1[:, :, 2, None] + xtheta = g2[:, :, 0, None, None] + ytheta = g2[:, :, 1, None, None] + ztheta = g2[:, :, 2, None, None] - xtheta = g2[:, :, 0, None] - ytheta = g2[:, :, 1, None] - ztheta = g2[:, :, 2, None] + dxvarphi_ds = dg1_ds[:, :, 0, :, None] + dyvarphi_ds = dg1_ds[:, :, 1, :, None] + dzvarphi_ds = dg1_ds[:, :, 2, :, None] - dxvarphi_ds = dg1_ds[:, :, 0, :] - dyvarphi_ds = dg1_ds[:, :, 1, :] - dzvarphi_ds = dg1_ds[:, :, 2, :] + dxtheta_ds = dg2_ds[:, :, 0, :, None] + dytheta_ds = dg2_ds[:, :, 1, :, None] + dztheta_ds = dg2_ds[:, :, 2, :, None] + + dxvarphi_dt = dg1_ds[:, :, 0, None, :] + dyvarphi_dt = dg1_ds[:, :, 1, None, :] + dzvarphi_dt = dg1_ds[:, :, 2, None, :] + + dxtheta_dt = dg2_ds[:, :, 0, None, :] + dytheta_dt = dg2_ds[:, :, 1, None, :] + dztheta_dt = dg2_ds[:, :, 2, None, :] - dxtheta_ds = dg2_ds[:, :, 0, :] - dytheta_ds = dg2_ds[:, :, 1, :] - dztheta_ds = dg2_ds[:, :, 2, :] mean_area = np.mean((1/r) * (ztheta*(x*yvarphi-y*xvarphi)-zvarphi*(x*ytheta-y*xtheta)))/(2.*np.pi) - dmean_area_ds = np.mean((1/(r**2))*((xvarphi * y * ztheta - xtheta * y * zvarphi + x * (-yvarphi * ztheta + ytheta * zvarphi)) * dr_ds + r * (-zvarphi * (ytheta * dx_ds - y * dxtheta_ds - xtheta * dy_ds + x * dytheta_ds) + ztheta * (yvarphi * dx_ds - y * dxvarphi_ds - xvarphi * dy_ds + x * dyvarphi_ds) + (-xvarphi * y + x * yvarphi) * dztheta_ds + (xtheta * y - x * ytheta) * dzvarphi_ds)), axis=(0, 1)) - d2mean_area_ds2 = (-2*dr_ds*((yvarphi*ztheta - ytheta*zvarphi)*dx_ds + \ - y*zvarphi*dxtheta_ds - y*ztheta*dxvarphi_ds - xvarphi*ztheta*dy_ds + \ - xtheta*zvarphi*dy_ds - xvarphi*y*dztheta_ds + xtheta*y*dzvarphi_ds + \ - x*(-(zvarphi*dytheta_ds) + ztheta*dyvarphi_ds + yvarphi*dztheta_ds - \ - ytheta*dzvarphi_ds)))/r**2 + (2*zvarphi*dxtheta_ds*dy_ds - \ - 2*xvarphi*dy_ds*dztheta_ds - 2*dxvarphi_ds*(ztheta*dy_ds + \ - y*dztheta_ds) + 2*(y*dxtheta_ds + xtheta*dy_ds)*dzvarphi_ds + \ - 2*dx_ds*(-(zvarphi*dytheta_ds) + ztheta*dyvarphi_ds + \ - yvarphi*dztheta_ds - ytheta*dzvarphi_ds) + \ - x*(2*dyvarphi_ds*dztheta_ds - 2*dytheta_ds*dzvarphi_ds))/r + \ - (-(xvarphi*y*ztheta) + xtheta*y*zvarphi + x*(yvarphi*ztheta - \ - ytheta*zvarphi))*((2*dr_ds**2)/r^3 - dr2_ds2/r**2) - + d2mean_area_ds2 = np.sign(mean_area)*np.mean( + (2*(-(xvarphi*y*ztheta) + xtheta*y*zvarphi + x*(yvarphi*ztheta - \ + ytheta*zvarphi))*dr_dt*dr_ds - r*((yvarphi*ztheta - \ + ytheta*zvarphi)*dx_dt + y*zvarphi*dxtheta_dt - y*ztheta*dxvarphi_dt - \ + xvarphi*ztheta*dy_dt + xtheta*zvarphi*dy_dt - xvarphi*y*dztheta_dt + \ + xtheta*y*dzvarphi_dt + x*(-(zvarphi*dytheta_dt) + ztheta*dyvarphi_dt \ + + yvarphi*dztheta_dt - ytheta*dzvarphi_dt))*dr_ds - \ + r*dr_dt*((yvarphi*ztheta - ytheta*zvarphi)*dx_ds + \ + y*zvarphi*dxtheta_ds - y*ztheta*dxvarphi_ds - xvarphi*ztheta*dy_ds + \ + xtheta*zvarphi*dy_ds - xvarphi*y*dztheta_ds + xtheta*y*dzvarphi_ds + \ + x*(-(zvarphi*dytheta_ds) + ztheta*dyvarphi_ds + yvarphi*dztheta_ds - \ + ytheta*dzvarphi_ds)) + r**2*((-(zvarphi*dytheta_dt) + \ + ztheta*dyvarphi_dt + yvarphi*dztheta_dt - ytheta*dzvarphi_dt)*dx_ds + \ + zvarphi*dy_dt*dxtheta_ds + y*dzvarphi_dt*dxtheta_ds - \ + ztheta*dy_dt*dxvarphi_ds - y*dztheta_dt*dxvarphi_ds + \ + zvarphi*dxtheta_dt*dy_ds - ztheta*dxvarphi_dt*dy_ds - \ + xvarphi*dztheta_dt*dy_ds + xtheta*dzvarphi_dt*dy_ds - \ + y*dxvarphi_dt*dztheta_ds - xvarphi*dy_dt*dztheta_ds + \ + y*dxtheta_dt*dzvarphi_ds + xtheta*dy_dt*dzvarphi_ds + \ + dx_dt*(-(zvarphi*dytheta_ds) + ztheta*dyvarphi_ds + \ + yvarphi*dztheta_ds - ytheta*dzvarphi_ds) + \ + x*(-(dzvarphi_dt*dytheta_ds) + dztheta_dt*dyvarphi_ds + \ + dyvarphi_dt*dztheta_ds - dytheta_dt*dzvarphi_ds)) + \ + r*(xvarphi*y*ztheta - xtheta*y*zvarphi + x*(-(yvarphi*ztheta) + \ + ytheta*zvarphi))*dr2_dsdt)/r**3 + , axis=(0, 1))/(2*np.pi) return d2mean_area_ds2 diff --git a/tests/geo/test_surface_taylor.py b/tests/geo/test_surface_taylor.py index 7b64ed0f7..a3594f1a0 100644 --- a/tests/geo/test_surface_taylor.py +++ b/tests/geo/test_surface_taylor.py @@ -109,7 +109,7 @@ def taylor_test2(f, df, d2f, x, epsilons=None, direction1=None, d2fest = (fpluseps-df0)/eps err = np.abs(d2fest - d2fval) - print(err/err_old) + print(err, err/err_old) assert err < 0.6 * err_old err_old = err print("###################################################################") @@ -410,6 +410,82 @@ def test_surface_volume_coefficient_derivative(self): s = get_surface(surfacetype, stellsym) self.subtest_surface_volume_coefficient_derivative(s) + def test_mean_area_second_derivative(self): + """ + Taylor test for the second derivative of the volume w.r.t. the dofs + """ + for surfacetype in self.surfacetypes: + for stellsym in [True, False]: + with self.subTest(surfacetype=surfacetype, stellsym=stellsym): + s = get_surface(surfacetype, stellsym) + self.subtest_mean_area_second_derivative(s) + + def subtest_mean_area_second_derivative(self, s): + x = s.x + s.invalidate_cache() + + def f(dofs): + s.x = dofs + return s.mean_cross_sectional_area() + + def df(dofs): + s.x = dofs + return s.dmean_cross_sectional_area_by_dcoeff() + + def d2f(dofs): + s.x = dofs + return s.d2mean_cross_sectional_area_by_dcoeff_dcoeff() + np.random.seed(1) + direction1 = np.random.rand(*(x.shape))-0.5 + direction2 = np.random.rand(*(x.shape))-0.5 + + f0 = f(x) + df0 = df(x) @ direction1 + d2fval = direction2.T @ d2f(x) @ direction1 + epsilons = np.power(2., -np.asarray(range(7, 16))) + print("###################################################################") + err_old = 1e9 + for eps in epsilons: + fpluseps = df(x + eps * direction2) @ direction1 + d2fest = (fpluseps-df0)/eps + err = np.abs(d2fest - d2fval) + + print(err, err/err_old) + assert err < 0.6 * err_old or err < 1e-10 + err_old = err + print("###################################################################") + + def test_AR_second_derivative(self): + """ + Taylor test for the second derivative of the volume w.r.t. the dofs + """ + for surfacetype in self.surfacetypes: + for stellsym in [True, False]: + with self.subTest(surfacetype=surfacetype, stellsym=stellsym): + s = get_surface(surfacetype, stellsym) + self.subtest_AR_second_derivative(s) + + def subtest_AR_second_derivative(self, s): + coeffs = s.x + s.invalidate_cache() + + def f(dofs): + s.x = dofs + return s.aspect_ratio() + + def df(dofs): + s.x = dofs + return s.daspect_ratio_by_dcoeff() + + def d2f(dofs): + s.x = dofs + return s.d2aspect_ratio_by_dcoeff_dcoeff() + taylor_test2(f, df, d2f, coeffs, + epsilons=np.power(2., -np.asarray(range(13, 20)))) + + + + def subtest_surface_phi_derivative(self, surfacetype, stellsym): epss = [0.5**i for i in range(10, 15)] phis = np.asarray([0.6] + [0.6 + eps for eps in epss]) From b7cd6cab190df4b786ce570897d0ed2c9fdbf769 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Sat, 20 May 2023 20:04:04 -0400 Subject: [PATCH 019/176] added AspectRatio surface label --- src/simsopt/geo/surfaceobjectives.py | 55 +++++++++++++++++++++++++++- 1 file changed, 54 insertions(+), 1 deletion(-) diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 00cf7d13b..13f896ba4 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -12,7 +12,60 @@ __all__ = ['Area', 'Volume', 'ToroidalFlux', 'PrincipalCurvature', 'QfmResidual', 'boozer_surface_residual', 'Iotas', - 'MajorRadius', 'NonQuasiSymmetricRatio', 'BoozerResidual'] + 'MajorRadius', 'NonQuasiSymmetricRatio', 'BoozerResidual', + 'AspectRatio'] + +class AspectRatio(Optimizable): + """ + Wrapper class for surface area label. + """ + + def __init__(self, surface, range=None, nphi=None, ntheta=None): + + if range is not None or nphi is not None or ntheta is not None: + if range is None: + if surface.stellsym: + range = Surface.RANGE_HALF_PERIOD + else: + range = Surface.RANGE_FIELD_PERIOD + if nphi is None: + nphi = len(surface.quadpoints_phi) + if ntheta is None: + ntheta = len(surface.quadpoints_theta) + self.surface = surface.__class__.from_nphi_ntheta(nphi=nphi, ntheta=ntheta, range=range, nfp=surface.nfp, stellsym=surface.stellsym, \ + mpol=surface.mpol, ntor=surface.ntor, dofs=surface.dofs) + else: + self.surface = surface + + self.range = range + self.nphi = nphi + self.ntheta = ntheta + + super().__init__(depends_on=[self.surface]) + + def J(self): + """ + Compute the area of a surface. + """ + return self.surface.aspect_ratio() + + @derivative_dec + def dJ(self): + return Derivative({self.surface: self.dJ_by_dsurfacecoefficients()}) + + def dJ_by_dsurfacecoefficients(self): + """ + Calculate the partial derivatives with respect to the surface coefficients. + """ + return self.surface.daspect_ratio_by_dcoeff() + + def d2J_by_dsurfacecoefficientsdsurfacecoefficients(self): + """ + Calculate the second partial derivatives with respect to the surface coefficients. + """ + return self.surface.d2aspect_ratio_by_dcoeff_dcoeff() + + class Area(Optimizable): From f1b588d7f75ad8ffe086ec623be6900b7e055c64 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Thu, 15 Jun 2023 08:38:02 -0700 Subject: [PATCH 020/176] edits --- CMakeLists.txt | 5 ++++ src/simsopt/geo/boozersurface.py | 10 +++---- src/simsopt/geo/curve.py | 2 +- src/simsopt/geo/surfacexyztensorfourier.py | 4 +++ src/simsoptpp/python.cpp | 31 ++++++++++++++++++++++ 5 files changed, 46 insertions(+), 6 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 73c0491b5..a2e33ff0a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -117,6 +117,11 @@ set_target_properties(${PROJECT_NAME} CXX_STANDARD 14 CXX_STANDARD_REQUIRED ON) +target_include_directories(${PROJECT_NAME} PRIVATE "thirdparty/LinkingNumber/toolbox/src/") +target_link_directories(${PROJECT_NAME} PRIVATE "thirdparty/LinkingNumber/build/") +target_link_libraries(${PROJECT_NAME} PRIVATE LinkingNumber_linux) + + target_include_directories(${PROJECT_NAME} PRIVATE "thirdparty/xtensor/include" "thirdparty/xtensor-python/include" "thirdparty/xsimd/include" "thirdparty/xtl/include" "thirdparty/eigen" ${Python_NumPy_INCLUDE_DIRS} "src/simsoptpp/") target_link_libraries(${PROJECT_NAME} PRIVATE fmt::fmt) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index e33e0522e..0f3126167 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -62,18 +62,18 @@ def run_code(self, boozer_type, iota, G=None, verbose=True): return if boozer_type == 'exact': - res = self.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=iota, G=G, verbose=verbose) + res = self.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=40, iota=iota, G=G, verbose=verbose) return res elif boozer_type == 'ls': # first try BFGS #res = self.minimize_boozer_penalty_constraints_ls(tol=1e-10, maxiter=100, constraint_weight=self.constraint_weight, iota=iota, G=G, method='manual') - res = self.compute_boozerls_BFGS(tol=1e-10, maxiter=1e3, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) + res = self.compute_boozerls_BFGS(tol=1e-10, maxiter=1500, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) iota, G = res['iota'], res['G'] ## polish off using Newton's method self.need_to_run_code = True - res = self.compute_boozerls_newton(tol=1e-11, maxiter=20, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) + res = self.compute_boozerls_newton(tol=1e-11, maxiter=40, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) return res else: raise Exception(f"boozer_type not supported: {boozer_type}") @@ -609,7 +609,7 @@ def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., P, L, U = lu(J) res = { - "residual": r, "jacobian": J, "iter": i, "success": norm <= tol, "G": G, "s": s, "iota": iota, "PLU": (P, L, U), + "residual": r, "jacobian": J, "iter": i, "success": norm <= tol, "G": G, "iota": iota, "PLU": (P, L, U), "mask": mask, 'type': 'exact', "vjp": boozer_surface_dexactresidual_dcoils_dcurrents_vjp } @@ -794,7 +794,7 @@ def compute_boozerls_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., i x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) norm = np.linalg.norm(dval, ord=np.inf) - if norm > 1e2: + if norm > 1e1: break i = i+1 diff --git a/src/simsopt/geo/curve.py b/src/simsopt/geo/curve.py index bc52be1ac..695643b73 100644 --- a/src/simsopt/geo/curve.py +++ b/src/simsopt/geo/curve.py @@ -878,4 +878,4 @@ def create_equally_spaced_curves(ncurves, nfp, stellsym, R0=1.0, R1=0.5, order=6 curve.set("zs(1)", R1) curve.x = curve.x # need to do this to transfer data to C++ curves.append(curve) - return curves \ No newline at end of file + return curves diff --git a/src/simsopt/geo/surfacexyztensorfourier.py b/src/simsopt/geo/surfacexyztensorfourier.py index 493a6370a..6015ab4e6 100644 --- a/src/simsopt/geo/surfacexyztensorfourier.py +++ b/src/simsopt/geo/surfacexyztensorfourier.py @@ -166,4 +166,8 @@ def npsame(a, b): if npsame(phis, np.linspace(0, 1/(2*self.nfp), ntor+1, endpoint=False)) and \ npsame(thetas, np.linspace(0, 1, 2*mpol+1, endpoint=False)): mask[0, mpol+1:] = False + if npsame(phis, np.linspace(0, 1/self.nfp, 2*ntor+1, endpoint=False)[:ntor+1]) and \ + npsame(thetas, np.linspace(0, 1, 2*mpol+1, endpoint=False)): + mask[0, mpol+1:] = False + return mask diff --git a/src/simsoptpp/python.cpp b/src/simsoptpp/python.cpp index f6a92a553..3312fa891 100644 --- a/src/simsoptpp/python.cpp +++ b/src/simsoptpp/python.cpp @@ -18,6 +18,11 @@ typedef xt::pyarray PyArray; #include "boozerradialinterpolant.h" #include "boozerresidual.h" +#include "linking_number.hh" +typedef LK::LinkingNumber LK_class; + + + namespace py = pybind11; using std::vector; @@ -143,6 +148,32 @@ PYBIND11_MODULE(simsoptpp, m) { return 0.5 * res / (nphi*ntheta); }); + m.def("ln", [](PyArray& A, PyArray& B) { + LK_class lk(2); + int nseg1 = A.shape(0); + int nseg2 = B.shape(0); + + double c1[10000][3]; + double c2[10000][3]; + for(int i; i < nseg1; i++){ + c1[i][0] = A(i, 0); + c1[i][1] = A(i, 1); + c1[i][2] = A(i, 2); + } + + for(int i; i < nseg2; i++){ + c2[i][0] = B(i, 0); + c2[i][1] = B(i, 1); + c2[i][2] = B(i, 2); + } + + return lk.eval(c1, nseg1, c2, nseg2) ; + }); + + + + + #ifdef VERSION_INFO m.attr("__version__") = VERSION_INFO; #else From e237c4d8126512afc5f23429f1e9e6203833cefa Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 6 Oct 2023 11:38:40 -0400 Subject: [PATCH 021/176] initial commit --- src/simsopt/_core/derivative.py | 28 ++++++++++++++++++---------- tests/geo/test_surface_objectives.py | 12 ++++++++---- 2 files changed, 26 insertions(+), 14 deletions(-) diff --git a/src/simsopt/_core/derivative.py b/src/simsopt/_core/derivative.py index c3acfce6e..394677f92 100644 --- a/src/simsopt/_core/derivative.py +++ b/src/simsopt/_core/derivative.py @@ -176,20 +176,28 @@ def __call__(self, optim, as_derivative=False): """ from .optimizable import Optimizable # Import here to avoid circular import assert isinstance(optim, Optimizable) - derivs = [] - keys = [] - for k in optim.unique_dof_lineage: - if np.any(k.dofs_free_status): - local_derivs = np.zeros(k.local_dof_size) + + if not as_derivative: + derivs = [] + keys = [] + for k in optim.unique_dof_lineage: + if np.any(k.dofs_free_status): + local_derivs = np.zeros(k.local_dof_size) + for opt in k.dofs.dep_opts(): + local_derivs += self.data[opt][opt.local_dofs_free_status] + keys.append(opt) + derivs.append(local_derivs) + return np.concatenate(derivs) + else: + derivs = [] + keys = [] + for k in optim.unique_dof_lineage: + local_derivs = np.zeros(k.local_full_dof_size) for opt in k.dofs.dep_opts(): - local_derivs += self.data[opt][opt.local_dofs_free_status] + local_derivs += self.data[opt] keys.append(opt) derivs.append(local_derivs) - - if as_derivative: return Derivative({k: d for k, d in zip(keys, derivs)}) - else: - return np.concatenate(derivs) # https://stackoverflow.com/questions/11624955/avoiding-python-sum-default-start-arg-behavior def __radd__(self, other): diff --git a/tests/geo/test_surface_objectives.py b/tests/geo/test_surface_objectives.py index 0f7d82db6..990952638 100644 --- a/tests/geo/test_surface_objectives.py +++ b/tests/geo/test_surface_objectives.py @@ -318,14 +318,18 @@ def test_nonQSratio_derivative(self): """ for label in ["Volume", "ToroidalFlux"]: for axis in [False, True]: - with self.subTest(label=label, axis=axis): - self.subtest_nonQSratio_derivative(label, axis) + for fix_coil_dof in [True, False]: + with self.subTest(label=label, axis=axis, fix_coil_dof=fix_coil_dof): + self.subtest_nonQSratio_derivative(label, axis, fix_coil_dof) - def subtest_nonQSratio_derivative(self, label, axis): + def subtest_nonQSratio_derivative(self, label, axis, fix_coil_dof): bs, boozer_surface = get_boozer_surface(label=label) - coeffs = bs.x io = NonQuasiSymmetricRatio(boozer_surface, bs, quasi_poloidal=axis) + + if fix_coil_dof: + bs.coils[0].curve.fix('xc(0)') + coeffs = bs.x def f(dofs): bs.x = dofs return io.J() From eabe058e102fab5ce4a4ce5dbee6eaeebb21b6b4 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 6 Oct 2023 11:42:15 -0400 Subject: [PATCH 022/176] linting fix --- tests/geo/test_surface_objectives.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/geo/test_surface_objectives.py b/tests/geo/test_surface_objectives.py index 990952638..36d787df9 100644 --- a/tests/geo/test_surface_objectives.py +++ b/tests/geo/test_surface_objectives.py @@ -330,6 +330,7 @@ def subtest_nonQSratio_derivative(self, label, axis, fix_coil_dof): bs.coils[0].curve.fix('xc(0)') coeffs = bs.x + def f(dofs): bs.x = dofs return io.J() From f723178ac58e6b34dc5384b73eeeebd8a995a2a6 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 6 Oct 2023 12:49:11 -0400 Subject: [PATCH 023/176] rearrange --- src/simsopt/_core/derivative.py | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/src/simsopt/_core/derivative.py b/src/simsopt/_core/derivative.py index 394677f92..d983c2e17 100644 --- a/src/simsopt/_core/derivative.py +++ b/src/simsopt/_core/derivative.py @@ -177,27 +177,28 @@ def __call__(self, optim, as_derivative=False): from .optimizable import Optimizable # Import here to avoid circular import assert isinstance(optim, Optimizable) - if not as_derivative: + if as_derivative: + derivs = [] + keys = [] + for k in optim.unique_dof_lineage: + local_derivs = np.zeros(k.local_full_dof_size) + for opt in k.dofs.dep_opts(): + local_derivs += self.data[opt] #return the full derivative here, including the derivatives of fixed dofs + keys.append(opt) + derivs.append(local_derivs) + return Derivative({k: d for k, d in zip(keys, derivs)}) + else: derivs = [] keys = [] for k in optim.unique_dof_lineage: if np.any(k.dofs_free_status): local_derivs = np.zeros(k.local_dof_size) for opt in k.dofs.dep_opts(): - local_derivs += self.data[opt][opt.local_dofs_free_status] + local_derivs += self.data[opt][opt.local_dofs_free_status] # filter out the derivatives of fixed dofs keys.append(opt) derivs.append(local_derivs) return np.concatenate(derivs) - else: - derivs = [] - keys = [] - for k in optim.unique_dof_lineage: - local_derivs = np.zeros(k.local_full_dof_size) - for opt in k.dofs.dep_opts(): - local_derivs += self.data[opt] - keys.append(opt) - derivs.append(local_derivs) - return Derivative({k: d for k, d in zip(keys, derivs)}) + # https://stackoverflow.com/questions/11624955/avoiding-python-sum-default-start-arg-behavior def __radd__(self, other): From c8b4ccb4b90b35444cc65f67ad744bc6a3e066eb Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 6 Oct 2023 14:25:29 -0400 Subject: [PATCH 024/176] linting fix --- src/simsopt/_core/derivative.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/simsopt/_core/derivative.py b/src/simsopt/_core/derivative.py index d983c2e17..33abe3576 100644 --- a/src/simsopt/_core/derivative.py +++ b/src/simsopt/_core/derivative.py @@ -183,7 +183,7 @@ def __call__(self, optim, as_derivative=False): for k in optim.unique_dof_lineage: local_derivs = np.zeros(k.local_full_dof_size) for opt in k.dofs.dep_opts(): - local_derivs += self.data[opt] #return the full derivative here, including the derivatives of fixed dofs + local_derivs += self.data[opt] # return the full derivative here, including the derivatives of fixed dofs keys.append(opt) derivs.append(local_derivs) return Derivative({k: d for k, d in zip(keys, derivs)}) @@ -194,12 +194,11 @@ def __call__(self, optim, as_derivative=False): if np.any(k.dofs_free_status): local_derivs = np.zeros(k.local_dof_size) for opt in k.dofs.dep_opts(): - local_derivs += self.data[opt][opt.local_dofs_free_status] # filter out the derivatives of fixed dofs + local_derivs += self.data[opt][opt.local_dofs_free_status] # filter out the derivatives of fixed dofs keys.append(opt) derivs.append(local_derivs) return np.concatenate(derivs) - # https://stackoverflow.com/questions/11624955/avoiding-python-sum-default-start-arg-behavior def __radd__(self, other): # This allows sum() to work (the default start value is zero) From 067fa1c6518ae3f5b833090c771db65981380427 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 9 Oct 2023 11:26:17 -0400 Subject: [PATCH 025/176] initial commit --- CMakeLists.txt | 5 - .../inputs/input_ncsx/ncsx_init.json | 35315 ++++++++++++++++ .../inputs/input_ncsx/surface_0.json | 7022 +++ .../inputs/input_ncsx/surface_0.vts | Bin 0 -> 31872 bytes .../inputs/input_ncsx/surface_1.json | 7022 +++ .../inputs/input_ncsx/surface_1.vts | Bin 0 -> 31872 bytes .../inputs/input_ncsx/surface_2.json | 7022 +++ .../inputs/input_ncsx/surface_2.vts | Bin 0 -> 31872 bytes .../inputs/input_ncsx/surface_3.json | 7022 +++ .../inputs/input_ncsx/surface_3.vts | Bin 0 -> 31872 bytes .../inputs/input_ncsx/surface_4.json | 7022 +++ .../inputs/input_ncsx/surface_4.vts | Bin 0 -> 31872 bytes .../inputs/input_ncsx/surface_5.json | 7022 +++ .../inputs/input_ncsx/surface_5.vts | Bin 0 -> 31872 bytes .../inputs/input_ncsx/surface_6.json | 7022 +++ .../inputs/input_ncsx/surface_6.vts | Bin 0 -> 31872 bytes .../inputs/input_ncsx/surface_7.json | 7022 +++ .../inputs/input_ncsx/surface_7.vts | Bin 0 -> 31872 bytes .../inputs/input_ncsx/surface_8.json | 7022 +++ .../inputs/input_ncsx/surface_8.vts | Bin 0 -> 31872 bytes .../inputs/input_ncsx/surface_9.json | 7022 +++ .../inputs/input_ncsx/surface_9.vts | Bin 0 -> 31872 bytes src/simsoptpp/python.cpp | 27 - 23 files changed, 105535 insertions(+), 32 deletions(-) create mode 100644 examples/2_Intermediate/inputs/input_ncsx/ncsx_init.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_0.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_0.vts create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_1.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_1.vts create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_2.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_2.vts create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_3.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_3.vts create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_4.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_4.vts create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_5.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_5.vts create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_6.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_6.vts create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_7.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_7.vts create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_8.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_8.vts create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_9.json create mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_9.vts diff --git a/CMakeLists.txt b/CMakeLists.txt index a2e33ff0a..73c0491b5 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -117,11 +117,6 @@ set_target_properties(${PROJECT_NAME} CXX_STANDARD 14 CXX_STANDARD_REQUIRED ON) -target_include_directories(${PROJECT_NAME} PRIVATE "thirdparty/LinkingNumber/toolbox/src/") -target_link_directories(${PROJECT_NAME} PRIVATE 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z-m(A;37?n3*&~tPYC%+!|C!d3Iq-_`{F?rqZ?6ngp@gGfDX?c8Tq68`_XDj4hQ4lO zck(f9(D`oQN&EuKrSyE&pg}Zl`6~T(X+QWz{Don0?!P#593>7o^{e>J0(;^|>^>X0xIx9c&{0 zi2u6(1(b>ZRZsjcyLPXRk54Icvv=LvlhV}&ii!VX=wQ9eVqyU#ES@^Y)zt?gh+lKC z^6dSq8|T0c7}a?0wCr*BiBg7{4_$Di}F>ka_TV^#NKp3Q=@#GgXbY9UW~dceQQ z^N&U57r+GZvzYcTsBRpo1^VGi7J8#|U_bG{I{uzKvS>-UZ}yQ}`K0C$Fe82$hp>xL zgJ~b?eHr>=-^xdjN&L0u)FfN3hCXz5?$Xm$fuG2f_;D)Ko`Tw*ZD`6lG~%j64d5mI z-RN0UzbDbZ(eQZuZ^xel;5G64rvD_b4raBXjuN?Dx)i;Gh(8!?e(h7NTrYa`D`M61 t=M=a}{KT^y{&}--7)iNp(TLQg+{;S*N6L-P|NjNf|8v7LxnO+X{{!m7zQ6zg From 291b0a02644c683302f6a1c5e3f0e805cedfc4aa Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 5 Apr 2024 14:21:05 -0400 Subject: [PATCH 032/176] cleaning up [skip ci] --- examples/2_Intermediate/boozerQA_ls_mpi.py | 12 ++++++------ src/simsopt/geo/boozersurface.py | 10 +--------- 2 files changed, 7 insertions(+), 15 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index b984b28c7..88404c521 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -139,12 +139,12 @@ def callback(x): outstr += f"{'nonQS ratio':{width}}" + ", ".join([f'{np.sqrt(nonqs.J()):.6e}' for nonqs in nonQSs]) + "\n" outstr += f"{'Boozer Residual':{width}}" + ", ".join([f'{br.J():.6e}' for br in brs]) + "\n" outstr += f"{'<Ī¹>':{width}} {mean_iota.J():.6f} \n" - outstr += f"{'Ī¹ on surfaces':{width}}" + ", ".join([f"{boozer_surface.res['iota']:.6f}" for boozer_surface in boozer_surfaces]) + "\n" - outstr += f"{'major radius on surfaces':{width}}" + ', '.join([f'{surface.major_radius():.6f}' for surface in surfaces]) + "\n" - outstr += f"{'minor radius on surfaces':{width}}" + ', '.join([f'{surface.minor_radius():.6f}' for surface in surfaces]) + "\n" - outstr += f"{'aspect ratio radius on surfaces':{width}}" + ', '.join([f'{surface.aspect_ratio():.6f}' for surface in surfaces]) + "\n" - outstr += f"{'volume':{width}}" + ', '.join([f'{surface.volume():.6f}' for surface in surfaces]) + "\n" - outstr += f"{'surfaces are self-intersecting':{width}}" + ', '.join([f'{surface.is_self_intersecting()}' for surface in surfaces]) + "\n" + outstr += f"{'Ī¹ on surfaces':{width}}" + ", ".join([f"{boozer_surface.res['iota']:.6f}" for boozer_surface in mpi_boozer_surfaces]) + "\n" + outstr += f"{'major radius on surfaces':{width}}" + ', '.join([f'{surface.major_radius():.6f}' for surface in mpi_surfaces]) + "\n" + outstr += f"{'minor radius on surfaces':{width}}" + ', '.join([f'{surface.minor_radius():.6f}' for surface in mpi_surfaces]) + "\n" + outstr += f"{'aspect ratio radius on surfaces':{width}}" + ', '.join([f'{surface.aspect_ratio():.6f}' for surface in mpi_surfaces]) + "\n" + outstr += f"{'volume':{width}}" + ', '.join([f'{surface.volume():.6f}' for surface in mpi_surfaces]) + "\n" + outstr += f"{'surfaces are self-intersecting':{width}}" + ', '.join([f'{surface.is_self_intersecting()}' for surface in mpi_surfaces]) + "\n" outstr += f"{'shortest coil to coil distance':{width}} {Jccdist.shortest_distance():.3f} \n" outstr += f"{'coil lengths':{width}}" + ', '.join([f'{J.J():5.6f}' for J in ls]) + "\n" outstr += f"{'coil length sum':{width}} {sum(J.J() for J in ls):.3f} \n" diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 0f3126167..4278cc5f8 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -41,14 +41,13 @@ class BoozerSurface(Optimizable): where Newton is used to solve the first order necessary conditions for optimality. """ - def __init__(self, biotsavart, surface, label, targetlabel, constraint_weight=None, reg=None): + def __init__(self, biotsavart, surface, label, targetlabel, constraint_weight=None): super().__init__(depends_on=[biotsavart]) self.biotsavart = biotsavart self.surface = surface self.label = label self.targetlabel = targetlabel self.constraint_weight = constraint_weight - self.reg = reg self.need_to_run_code = True def recompute_bell(self, parent=None): @@ -683,9 +682,6 @@ def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G rz = np.sqrt(constraint_weight) * (s.gamma()[0, 0, 2] - 0.) r = rnl + 0.5*rl**2 + 0.5*rz**2 - if self.reg is not None: - r += self.reg.J() - if derivatives == 0: return r @@ -701,8 +697,6 @@ def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G drl = np.sqrt(constraint_weight) * dl drz = np.sqrt(constraint_weight) * drz J = Jnl + rl * drl + rz * drz - if self.reg is not None: - J[:nsurfdofs] += self.reg.dJ() if derivatives == 1: return r, J @@ -714,8 +708,6 @@ def boozerls_penalty(self, dofs, derivatives=0, constraint_weight=1., optimize_G d2rl = np.zeros((dofs.shape[0], dofs.shape[0])) d2rl[:nsurfdofs, :nsurfdofs] = np.sqrt(constraint_weight)*self.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() H = Hnl + drl[:, None] @ drl[None, :] + drz[:, None] @ drz[None, :] + rl * d2rl - if self.reg is not None: - H[:nsurfdofs, :nsurfdofs] += self.reg.d2J() return r, J, H From 63bfaf98ad2fce92de7bcd0d67d6b8165bd59082 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 5 Apr 2024 14:37:32 -0400 Subject: [PATCH 033/176] docstring [skip ci] --- examples/2_Intermediate/boozerQA_ls_mpi.py | 23 +++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 88404c521..104f09764 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -25,12 +25,33 @@ def pprint(*args, **kwargs): size = 1 pprint = print +""" +This example optimizes the NCSX coils and currents for QA on potentially multiple surfaces using the BoozerLS approach. +For a single surface, the objective is: + + J = ( \int_S B_nonQA**2 dS )/(\int_S B_QA dS) + + 0.5*(iota - iota_0)**2 + + 0.5*(major_radius - target_major_radius)**2 + + 0.5*max(\sum_{coils} CurveLength - CurveLengthTarget, 0)**2 + +We first load a surface close to the magnetic axis, then optimize for QA on that surface. +The objective also includes penalty terms on the rotational transform, major radius, +and total coil length. The rotational transform and major radius penalty ensures that the surface's +rotational transform and aspect ratio do not stray too far from the value in the initial configuration. +There is also a penalty on the total coil length as a regularizer to prevent the coils from becoming +too complex. The BFGS optimizer is used, and quasisymmetry is improved substantially on the surface. +Surface solves using the BoozerLS approach can be costly, so this script supports distributing the solves +across multiple MPI ranks. + +More details on this work can be found at or doi:10.1063/5.0129716 arxiv:2210.03248. +""" + # Directory for output IN_DIR = "./inputs/input_ncsx/" OUT_DIR = "./output/" os.makedirs(OUT_DIR, exist_ok=True) -pprint("Running 2_Intermediate/boozerQA.py") +pprint("Running 2_Intermediate/boozerQA_ls_mpi.py") pprint("================================") base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress = load(IN_DIR + f"ncsx_init.json") From 9cd851431a23bef6b1eb6da53b51f30f223b39ef Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Thu, 11 Apr 2024 15:44:21 -0400 Subject: [PATCH 034/176] cleaning up [skip ci] --- src/simsopt/geo/surfacexyztensorfourier.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/simsopt/geo/surfacexyztensorfourier.py b/src/simsopt/geo/surfacexyztensorfourier.py index 7f4eeac20..a6e2197aa 100644 --- a/src/simsopt/geo/surfacexyztensorfourier.py +++ b/src/simsopt/geo/surfacexyztensorfourier.py @@ -165,8 +165,4 @@ def npsame(a, b): if npsame(phis, np.linspace(0, 1/(2*self.nfp), ntor+1, endpoint=False)) and \ npsame(thetas, np.linspace(0, 1, 2*mpol+1, endpoint=False)): mask[0, mpol+1:] = False - if npsame(phis, np.linspace(0, 1/self.nfp, 2*ntor+1, endpoint=False)[:ntor+1]) and \ - npsame(thetas, np.linspace(0, 1, 2*mpol+1, endpoint=False)): - mask[0, mpol+1:] = False - return mask From bd9c09128bc171c3d9bb703fbc37c612bb7b8f71 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 15 Apr 2024 16:38:38 -0400 Subject: [PATCH 035/176] initial commit --- CMakeLists.txt | 1 + src/simsopt/geo/boozersurface.py | 235 +++++++++++++++- src/simsopt/geo/surfaceobjectives.py | 138 +++++++--- src/simsoptpp/boozerresidual.cpp | 382 +++++++++++++++++++++++++++ src/simsoptpp/boozerresidual.h | 11 + src/simsoptpp/python.cpp | 7 + tests/geo/test_boozersurface.py | 73 +++++ 7 files changed, 802 insertions(+), 45 deletions(-) create mode 100644 src/simsoptpp/boozerresidual.cpp create mode 100644 src/simsoptpp/boozerresidual.h diff --git a/CMakeLists.txt b/CMakeLists.txt index e6e63ec9b..2d0a93f54 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -119,6 +119,7 @@ set(XTENSOR_USE_TBB 0) pybind11_add_module(${PROJECT_NAME} src/simsoptpp/python.cpp src/simsoptpp/python_surfaces.cpp src/simsoptpp/python_curves.cpp + src/simsoptpp/boozerresidual.cpp src/simsoptpp/python_magneticfield.cpp src/simsoptpp/python_tracing.cpp src/simsoptpp/python_distance.cpp src/simsoptpp/biot_savart_py.cpp src/simsoptpp/biot_savart_vjp_py.cpp diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index e8d564e40..74ad2ac5a 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -2,6 +2,7 @@ from scipy.linalg import lu from scipy.optimize import minimize, least_squares +import simsoptpp as sopp from .surfaceobjectives import boozer_surface_residual from .._core.optimizable import Optimizable @@ -39,19 +40,42 @@ class BoozerSurface(Optimizable): where Newton is used to solve the first order necessary conditions for optimality. """ - - def __init__(self, biotsavart, surface, label, targetlabel): + + def __init__(self, biotsavart, surface, label, targetlabel, constraint_weight=None): super().__init__(depends_on=[biotsavart]) self.biotsavart = biotsavart self.surface = surface self.label = label self.targetlabel = targetlabel + self.constraint_weight = constraint_weight self.need_to_run_code = True def recompute_bell(self, parent=None): self.need_to_run_code = True + + def run_code(self, boozer_type, iota, G=None, verbose=True): + """ + Run the default solvers. + """ + if not self.need_to_run_code: + return + + if boozer_type == 'exact': + res = self.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=40, iota=iota, G=G, verbose=verbose) + return res + elif boozer_type == 'ls': + # first try BFGS + res = self.minimize_boozer_penalty_constraints_BFGS(tol=1e-10, maxiter=1500, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) + iota, G = res['iota'], res['G'] + + ## polish off using Newton's method + self.need_to_run_code = True + res = self.minimize_boozer_penalty_constraints_newton(tol=1e-11, maxiter=40, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) + return res + else: + raise Exception(f"boozer_type not supported: {boozer_type}") - def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., scalarize=True, optimize_G=False): + def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., scalarize=True, optimize_G=False, weight_inv_modB=False): r""" Define the residual @@ -89,7 +113,7 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca s.set_dofs(sdofs) - boozer = boozer_surface_residual(s, iota, G, biotsavart, derivatives=derivatives) + boozer = boozer_surface_residual(s, iota, G, biotsavart, derivatives=derivatives, weight_inv_modB=weight_inv_modB) r = boozer[0] @@ -133,7 +157,7 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca d2l = np.zeros((x.shape[0], x.shape[0])) d2l[:nsurfdofs, :nsurfdofs] = self.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() - + H = np.concatenate(( H, np.sqrt(constraint_weight) * d2l[None, :, :], @@ -141,6 +165,99 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca d2val = J.T @ J + np.sum(r[:, None, None] * H, axis=0) return val, dval, d2val + def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_weight=1., optimize_G=False): + """ + This function returns the same thing as `boozer_penalty_constraints` when `scalarized=True` and `weight_inv_modB=True`. It + is much faster since it calls a vectorized implementation in cpp. + """ + + # this is essentially the scalarize option in previous implementation. This should be merged in that case... + assert derivatives in [0, 1, 2] + if optimize_G: + sdofs = dofs[:-2] + iota = dofs[-2] + G = dofs[-1] + else: + sdofs = dofs[:-1] + iota = dofs[-1] + G = 2. * np.pi * np.sum(np.abs([coil.current.get_value() for coil in self.biotsavart._coils])) * (4 * np.pi * 10**(-7) / (2 * np.pi)) + + s = self.surface + nphi = s.quadpoints_phi.size + ntheta = s.quadpoints_theta.size + nsurfdofs = sdofs.size + + s.set_dofs(sdofs) + + surface = self.surface + biotsavart = self.biotsavart + x = surface.gamma() + xphi = surface.gammadash1() + xtheta = surface.gammadash2() + nphi = x.shape[0] + ntheta = x.shape[1] + + xsemiflat = x.reshape((x.size//3, 3)).copy() + biotsavart.set_points(xsemiflat) + biotsavart.compute(derivatives) + B = biotsavart.B().reshape((nphi, ntheta, 3)) + + if derivatives >= 1: + dx_dc = surface.dgamma_by_dcoeff() + dxphi_dc = surface.dgammadash1_by_dcoeff() + dxtheta_dc = surface.dgammadash2_by_dcoeff() + dB_dx = biotsavart.dB_by_dX().reshape((nphi, ntheta, 3, 3)) + + if derivatives == 2: + d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) + + if derivatives == 0: + val = sopp.boozer_residual(G, iota, xphi, xtheta, B) + boozer = val, + elif derivatives == 1: + val, dval = sopp.boozer_residual_ds(G, iota, B, dB_dx, xphi, xtheta, dx_dc, dxphi_dc, dxtheta_dc) + boozer = val, dval + elif derivatives == 2: + val, dval, d2val = sopp.boozer_residual_ds2(G, iota, B, dB_dx, d2B_by_dXdX, xphi, xtheta, dx_dc, dxphi_dc, dxtheta_dc) + boozer = val, dval, d2val + + lab = self.label.J() + + rnl = boozer[0] + rl = np.sqrt(constraint_weight) * (lab-self.targetlabel) + rz = np.sqrt(constraint_weight) * (s.gamma()[0, 0, 2] - 0.) + r = rnl + 0.5*rl**2 + 0.5*rz**2 + + if derivatives == 0: + return r + + dl = np.zeros(dofs.shape) + drz = np.zeros(dofs.shape) + dl[:nsurfdofs] = self.label.dJ(partials=True)(s) + drz[:nsurfdofs] = s.dgamma_by_dcoeff()[0, 0, 2, :] + + Jnl = boozer[1] + if not optimize_G: + Jnl = Jnl[:-1] + + drl = np.sqrt(constraint_weight) * dl + drz = np.sqrt(constraint_weight) * drz + J = Jnl + rl * drl + rz * drz + + if derivatives == 1: + return r, J + + Hnl = boozer[2] + if not optimize_G: + Hnl = Hnl[:-1, :-1] + + d2rl = np.zeros((dofs.shape[0], dofs.shape[0])) + d2rl[:nsurfdofs, :nsurfdofs] = np.sqrt(constraint_weight)*self.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() + H = Hnl + drl[:, None] @ drl[None, :] + drz[:, None] @ drz[None, :] + rl * d2rl + + return r, J, H + + def boozer_exact_constraints(self, xl, derivatives=0, optimize_G=True): r""" This function returns the optimality conditions corresponding to the minimization problem @@ -252,6 +369,106 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons self.need_to_run_code = False return resdict + def minimize_boozer_penalty_constraints_BFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, hessian=False, verbose=False): + r""" + """ + if not self.need_to_run_code: + return self.res + + s = self.surface + if G is None: + x = np.concatenate((s.get_dofs(), [iota])) + else: + x = np.concatenate((s.get_dofs(), [iota, G])) + + fun = lambda x: self.boozer_penalty_constraints_vectorized( + x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) + res = minimize( + fun, x, jac=True, method='BFGS', + options={'maxiter': maxiter, 'gtol': tol}) + + resdict = { + "residual": res.fun, "gradient": res.jac, "iter": res.nit, "info": res, "success": res.success, "G": None, 'type': 'ls', 'solver': 'BFGS', + "firstorderop": res.jac, "constraint_weight": constraint_weight, "labelerr": np.abs((self.label.J()-self.targetlabel)/self.targetlabel) + } + + if G is None: + s.set_dofs(res.x[:-1]) + iota = res.x[-1] + else: + s.set_dofs(res.x[:-2]) + iota = res.x[-2] + G = res.x[-1] + resdict['G'] = G + resdict['s'] = s + resdict['iota'] = iota + + if hessian: + val, dval, d2val = self.boozer_penalty_constraints_vectorized( + x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + P, L, U = lu(d2val) + resdict["PLU"] = (P, L, U) + + self.res = resdict + self.need_to_run_code = False + + if verbose: + print(f"BFGS solve - {resdict['success']} iter={resdict['iter']}, iota={resdict['iota']:.16f}, ||grad||_inf = {np.linalg.norm(resdict['firstorderop'], ord=np.inf):.3e}", flush=True) + return resdict + + def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0., verbose=False): + """ + """ + if not self.need_to_run_code: + return self.res + + s = self.surface + if G is None: + x = np.concatenate((s.get_dofs(), [iota])) + else: + x = np.concatenate((s.get_dofs(), [iota, G])) + i = 0 + + val, dval, d2val = self.boozer_penalty_constraints_vectorized( + x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + norm = np.linalg.norm(dval, ord=np.inf) + + while i < maxiter and norm > tol: + d2val += stab*np.identity(d2val.shape[0]) + dx = np.linalg.solve(d2val, dval) + if norm < 1e-9: + dx += np.linalg.solve(d2val, dval - d2val@dx) + x = x - dx + val, dval, d2val = self.boozer_penalty_constraints_vectorized( + x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + norm = np.linalg.norm(dval, ord=np.inf) + + if norm > 1e1: + break + + i = i+1 + + P, L, U = lu(d2val) + if G is None: + s.set_dofs(x[:-1]) + iota = x[-1] + else: + s.set_dofs(x[:-2]) + iota = x[-2] + G = x[-1] + + res = { + "residual": val, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "firstorderop": dval, + "PLU": (P, L, U), 'iota': iota, "G": G, "type": "ls" + } + + self.res = res + self.need_to_run_code = False + + if verbose: + print(f"NEWTON solve - {res['success']} iter={res['iter']}, iota={res['iota']:.16f}, ||grad||_inf = {np.linalg.norm(res['firstorderop'], ord=np.inf):.3e}", flush=True) + return res + def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0.): """ This function does the same as :mod:`minimize_boozer_penalty_constraints_LBFGS`, but instead of LBFGS it uses @@ -445,7 +662,7 @@ def minimize_boozer_exact_constraints_newton(self, tol=1e-12, maxiter=10, iota=0 self.need_to_run_code = False return res - def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., G=None): + def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., G=None, verbose=False): """ This function solves the Boozer Surface residual equation exactly. For this to work, we need the right balance of quadrature points, degrees @@ -582,9 +799,13 @@ def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., P, L, U = lu(J) res = { - "residual": r, "jacobian": J, "iter": i, "success": norm <= tol, "G": G, "s": s, "iota": iota, "PLU": (P, L, U), + "residual": r, "jacobian": J, "iter": i, "success": norm <= tol, "G": G, "iota": iota, "PLU": (P, L, U), "mask": mask, 'type': 'exact' } + + if verbose: + print(f"NEWTON solve - {res['success']} iter={res['iter']}, iota={res['iota']:.16f}, ||residual||_inf = {np.linalg.norm(res['residual'], ord=np.inf):.3e}", flush=True) + self.res = res self.need_to_run_code = False return res diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index bfe3ebf21..bd3f73e76 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -287,21 +287,40 @@ def dJ(self): return Derivative({self.surface: deriv}) -def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0): +def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_inv_modB=False): r""" For a given surface, this function computes the residual .. math:: - G\mathbf B(\mathbf x) - \|\mathbf B(\mathbf x)\|^2 (\mathbf x_\varphi + \iota \mathbf x_\theta) + G\mathbf B_\text{BS}(\mathbf x) - ||\mathbf B_\text{BS}(\mathbf x)||^2 (\mathbf x_\varphi + \iota \mathbf x_\theta) as well as the derivatives of this residual with respect to surface dofs, iota, and G. In the above, :math:`\mathbf x` are points on the surface, :math:`\iota` is the - rotational transform on that surface, and :math:`\mathbf B` is the magnetic field. + rotational transform on that surface, and :math:`\mathbf B_{\text{BS}}` is the magnetic field + computed using the Biot-Savart law. :math:`G` is known for exact boozer surfaces, so if ``G=None`` is passed, then that value is used instead. + + Args: + surface: The surface to use for the computation + iota: the surface rotational transform + G: a constant that is a function of the coil currents in vacuum field + biotsavart: the Biot-Savart magnetic field + derivatives: how many spatial derivatives of the residual to compute + weight_inv_modB: whether or not to weight the residual by :math:`\|\mathbf B\|`. This + is useful to activate so that the residual does not scale with the + coil currents. + + Returns: + the residual at the surface quadrature points and optionally the spatial derivatives + of the residual. + + """ + + assert derivatives in [0, 1, 2] user_provided_G = G is not None if not user_provided_G: @@ -324,8 +343,15 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0): B2 = np.sum(B**2, axis=2) residual = G*B - B2[..., None] * tang - residual_flattened = residual.reshape((nphi*ntheta*3, )) - r = residual_flattened + if weight_inv_modB: + modB = np.sqrt(B2) + w = 1./modB + rtil = w[:, :, None] * residual + else: + rtil = residual.copy() + + rtil_flattened = rtil.reshape((nphi*ntheta*3, )) + r = rtil_flattened if derivatives == 0: return r, @@ -341,24 +367,41 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0): dresidual_dc = sopp.boozer_dresidual_dc(G, dB_dc, B, tang, B2, dxphi_dc, iota, dxtheta_dc) dresidual_diota = -B2[..., None] * xtheta - dresidual_dc_flattened = dresidual_dc.reshape((nphi*ntheta*3, nsurfdofs)) - dresidual_diota_flattened = dresidual_diota.reshape((nphi*ntheta*3, 1)) + if weight_inv_modB: + dB2_dc = 2*np.einsum('ijk,ijkl->ijl', B, dB_dc, optimize=True) + dmodB_dc = 0.5*dB2_dc/np.sqrt(B2[:, :, None]) + dw_dc = -dmodB_dc/modB[:, :, None]**2 + drtil_dc = residual[..., None] * dw_dc[:, :, None, :] + w[:, :, None, None] * dresidual_dc + drtil_diota = w[:, :, None] * dresidual_diota + else: + drtil_dc = dresidual_dc.copy() + drtil_diota = dresidual_diota.copy() + + drtil_dc_flattened = drtil_dc.reshape((nphi*ntheta*3, nsurfdofs)) + drtil_diota_flattened = drtil_diota.reshape((nphi*ntheta*3, 1)) if user_provided_G: dresidual_dG = B - dresidual_dG_flattened = dresidual_dG.reshape((nphi*ntheta*3, 1)) - J = np.concatenate((dresidual_dc_flattened, dresidual_diota_flattened, dresidual_dG_flattened), axis=1) + + if weight_inv_modB: + drtil_dG = w[:, :, None] * dresidual_dG + else: + drtil_dG = dresidual_dG.copy() + + drtil_dG_flattened = drtil_dG.reshape((nphi*ntheta*3, 1)) + J = np.concatenate((drtil_dc_flattened, drtil_diota_flattened, drtil_dG_flattened), axis=1) else: - J = np.concatenate((dresidual_dc_flattened, dresidual_diota_flattened), axis=1) + J = np.concatenate((drtil_dc_flattened, drtil_diota_flattened), axis=1) + if derivatives == 1: return r, J d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) - d2B_dcdc = np.einsum('ijkpl,ijpn,ijkm->ijlmn', d2B_by_dXdX, dx_dc, dx_dc) - dB2_dc = 2. * np.einsum('ijl,ijlm->ijm', B, dB_dc) + d2B_dcdc = np.einsum('ijkpl,ijpn,ijkm->ijlmn', d2B_by_dXdX, dx_dc, dx_dc, optimize=True) + dB2_dc = 2. * np.einsum('ijl,ijlm->ijm', B, dB_dc, optimize=True) - term1 = np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc) - term2 = np.einsum('ijlmn,ijl->ijmn', d2B_dcdc, B) + term1 = np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc, optimize=True) + term2 = np.einsum('ijlmn,ijl->ijmn', d2B_dcdc, B, optimize=True) d2B2_dcdc = 2*(term1 + term2) term1 = -(dxphi_dc[..., None, :] + iota * dxtheta_dc[..., None, :]) * dB2_dc[..., None, :, None] @@ -368,39 +411,58 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0): d2residual_by_dcdiota = -(dB2_dc[..., None, :] * xtheta[..., :, None] + B2[..., None, None] * dxtheta_dc) d2residual_by_diotadiota = np.zeros(dresidual_diota.shape) - d2residual_by_dcdc_flattened = d2residual_by_dcdc.reshape((nphi*ntheta*3, nsurfdofs, nsurfdofs)) - d2residual_by_dcdiota_flattened = d2residual_by_dcdiota.reshape((nphi*ntheta*3, nsurfdofs)) - d2residual_by_diotadiota_flattened = d2residual_by_diotadiota.reshape((nphi*ntheta*3,)) - + if weight_inv_modB: + d2B2_dcdc = 2*(np.einsum('ijlm,ijln->ijmn', dB_dc, dB_dc, optimize=True)+np.einsum('ijkpl,ijpn,ijkm,ijl->ijmn', d2B_by_dXdX, dx_dc, dx_dc, B, optimize=True)) + d2modB_dc2 = (2*B2[:, :, None, None] * d2B2_dcdc - dB2_dc[:, :, :, None]*dB2_dc[:, :, None, :])*(1/(4*B2[:, :, None, None]**1.5)) + d2w_dc2 = (2*dmodB_dc[:, :, :, None] * dmodB_dc[:, :, None, :] - modB[:, :, None, None] * d2modB_dc2)/modB[:, :, None, None]**3. + + d2rtil_dcdc = residual[..., None, None] * d2w_dc2[:, :, None, ...] \ + + dw_dc[:, :, None, :, None] * dresidual_dc[:, :, :, None, :] \ + + dw_dc[:, :, None, None, :] * dresidual_dc[:, :, :, :, None] \ + + w[:, :, None, None, None] * d2residual_by_dcdc + d2rtil_dcdiota = w[:, :, None, None] * d2residual_by_dcdiota + dw_dc[:, :, None, :] * dresidual_diota[..., None] + d2rtil_diotadiota = np.zeros(dresidual_diota.shape) + else: + d2rtil_dcdc = d2residual_by_dcdc.copy() + d2rtil_dcdiota = d2residual_by_dcdiota.copy() + d2rtil_diotadiota = d2residual_by_diotadiota.copy() + + d2rtil_dcdc_flattened = d2rtil_dcdc.reshape((nphi*ntheta*3, nsurfdofs, nsurfdofs)) + d2rtil_dcdiota_flattened = d2rtil_dcdiota.reshape((nphi*ntheta*3, nsurfdofs)) + d2rtil_diotadiota_flattened = d2rtil_diotadiota.reshape((nphi*ntheta*3,)) + if user_provided_G: d2residual_by_dcdG = dB_dc - d2residual_by_diotadG = np.zeros(dresidual_diota.shape) - d2residual_by_dGdG = np.zeros(dresidual_dG.shape) - d2residual_by_dcdG_flattened = d2residual_by_dcdG.reshape((nphi*ntheta*3, nsurfdofs)) - d2residual_by_diotadG_flattened = d2residual_by_diotadG.reshape((nphi*ntheta*3,)) - d2residual_by_dGdG_flattened = d2residual_by_dGdG.reshape((nphi*ntheta*3,)) + if weight_inv_modB: + d2rtil_dcdG = dw_dc[:, :, None, :] * dresidual_dG[..., None] + w[:, :, None, None] * d2residual_by_dcdG + else: + d2rtil_dcdG = d2residual_by_dcdG.copy() + + d2rtil_dGdG = np.zeros(dresidual_dG.shape) + d2rtil_dcdG_flattened = d2rtil_dcdG.reshape((nphi*ntheta*3, nsurfdofs)) + d2rtil_diotadG_flattened = np.zeros((nphi*ntheta*3,)) + d2rtil_dGdG_flattened = d2rtil_dGdG.reshape((nphi*ntheta*3,)) + H = np.zeros((nphi*ntheta*3, nsurfdofs + 2, nsurfdofs + 2)) # noqa turns out linting so that we can align everything neatly - H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc - H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota - H[:, :nsurfdofs, nsurfdofs+1] = d2residual_by_dcdG_flattened # noqa (0, 2) dcdG - H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc - H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota - H[:, nsurfdofs, nsurfdofs+1] = d2residual_by_diotadiota_flattened # noqa (1, 2) diotadG - H[:, nsurfdofs+1, :nsurfdofs] = d2residual_by_dcdG_flattened # noqa (2, 0) dGdc - H[:, nsurfdofs+1, nsurfdofs] = d2residual_by_diotadG_flattened # noqa (2, 1) dGdiota - H[:, nsurfdofs+1, nsurfdofs+1] = d2residual_by_dGdG_flattened # noqa (2, 2) dGdG + H[:, :nsurfdofs, :nsurfdofs] = d2rtil_dcdc_flattened # noqa (0, 0) dcdc + H[:, :nsurfdofs, nsurfdofs] = d2rtil_dcdiota_flattened # noqa (0, 1) dcdiota + H[:, :nsurfdofs, nsurfdofs+1] = d2rtil_dcdG_flattened # noqa (0, 2) dcdG + H[:, nsurfdofs, :nsurfdofs] = d2rtil_dcdiota_flattened # noqa (1, 0) diotadc + H[:, nsurfdofs, nsurfdofs] = d2rtil_diotadiota_flattened # noqa (1, 1) diotadiota + H[:, nsurfdofs, nsurfdofs+1] = d2rtil_diotadiota_flattened # noqa (1, 2) diotadG + H[:, nsurfdofs+1, :nsurfdofs] = d2rtil_dcdG_flattened # noqa (2, 0) dGdc + H[:, nsurfdofs+1, nsurfdofs] = d2rtil_diotadG_flattened # noqa (2, 1) dGdiota + H[:, nsurfdofs+1, nsurfdofs+1] = d2rtil_dGdG_flattened # noqa (2, 2) dGdG else: H = np.zeros((nphi*ntheta*3, nsurfdofs + 1, nsurfdofs + 1)) - - H[:, :nsurfdofs, :nsurfdofs] = d2residual_by_dcdc_flattened # noqa (0, 0) dcdc - H[:, :nsurfdofs, nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (0, 1) dcdiota - H[:, nsurfdofs, :nsurfdofs] = d2residual_by_dcdiota_flattened # noqa (1, 0) diotadc - H[:, nsurfdofs, nsurfdofs] = d2residual_by_diotadiota_flattened # noqa (1, 1) diotadiota + H[:, :nsurfdofs, :nsurfdofs] = d2rtil_dcdc_flattened # noqa (0, 0) dcdc + H[:, :nsurfdofs, nsurfdofs] = d2rtil_dcdiota_flattened # noqa (0, 1) dcdiota + H[:, nsurfdofs, :nsurfdofs] = d2rtil_dcdiota_flattened # noqa (1, 0) diotadc + H[:, nsurfdofs, nsurfdofs] = d2rtil_diotadiota_flattened # noqa (1, 1) diotadiota return r, J, H - def parameter_derivatives(surface: Surface, shape_gradient: NDArray[Any, Float] ) -> NDArray[Any, Float]: diff --git a/src/simsoptpp/boozerresidual.cpp b/src/simsoptpp/boozerresidual.cpp new file mode 100644 index 000000000..340cdfd65 --- /dev/null +++ b/src/simsoptpp/boozerresidual.cpp @@ -0,0 +1,382 @@ +#include "boozerresidual.h" + +#include "xsimd/xsimd.hpp" +#include "simdhelpers.h" +#include "vec3dsimd.h" +#include "xtensor/xarray.hpp" +#include +#include "xtensor/xadapt.hpp" + +#if __cplusplus >= 201703L +#define MYIF(c) if constexpr(c) +#else +#define MYIF(c) if(c) +#endif + +#if defined(USE_XSIMD) +template void boozer_residual_impl(double G, double iota, T& B, T& dB_dx, T& d2B_dx2, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres, T& d2res, size_t ndofs){ + int nphi = xphi.shape(0); + int ntheta = xtheta.shape(1); + int num_points = 3 * nphi * ntheta; + + constexpr size_t simd_size = xsimd::simd_type::size; + auto dx_ds_ij0 = AlignedPaddedVec(ndofs, 0); + auto dx_ds_ij1 = AlignedPaddedVec(ndofs, 0); + auto dx_ds_ij2 = AlignedPaddedVec(ndofs, 0); + auto dxphi_ds_ij0 = AlignedPaddedVec(ndofs, 0); + auto dxphi_ds_ij1 = AlignedPaddedVec(ndofs, 0); + auto dxphi_ds_ij2 = AlignedPaddedVec(ndofs, 0); + auto dxtheta_ds_ij0 = AlignedPaddedVec(ndofs, 0); + auto dxtheta_ds_ij1 = AlignedPaddedVec(ndofs, 0); + auto dxtheta_ds_ij2 = AlignedPaddedVec(ndofs, 0); + + auto drtilij0 = AlignedPaddedVec(ndofs+2, 0); + auto drtilij1 = AlignedPaddedVec(ndofs+2, 0); + auto drtilij2 = AlignedPaddedVec(ndofs+2, 0); + + auto dresij0 = AlignedPaddedVec(ndofs+2, 0); + auto dresij1 = AlignedPaddedVec(ndofs+2, 0); + auto dresij2 = AlignedPaddedVec(ndofs+2, 0); + + auto dw_ij = AlignedPaddedVec(ndofs+2, 0); + + auto dtang_ij0 = AlignedPaddedVec(ndofs+2, 0); + auto dtang_ij1 = AlignedPaddedVec(ndofs+2, 0); + auto dtang_ij2 = AlignedPaddedVec(ndofs+2, 0); + + auto dB2_ij = AlignedPaddedVec(ndofs+2, 0); + auto dBij0 = AlignedPaddedVec(ndofs+2, 0); + auto dBij1 = AlignedPaddedVec(ndofs+2, 0); + auto dBij2 = AlignedPaddedVec(ndofs+2, 0); + auto dmodB_ij = AlignedPaddedVec(ndofs+2, 0); + + simd_t it(iota); + simd_t GG(G); + + for(int i=0; i0){ + simd_t Bij0(B(i, j, 0)); + simd_t Bij1(B(i, j, 1)); + simd_t Bij2(B(i, j, 2)); + + simd_t dB_dxij00(dB_dx(i, j, 0, 0)); + simd_t dB_dxij10(dB_dx(i, j, 1, 0)); + simd_t dB_dxij20(dB_dx(i, j, 2, 0)); + simd_t dB_dxij01(dB_dx(i, j, 0, 1)); + simd_t dB_dxij11(dB_dx(i, j, 1, 1)); + simd_t dB_dxij21(dB_dx(i, j, 2, 1)); + simd_t dB_dxij02(dB_dx(i, j, 0, 2)); + simd_t dB_dxij12(dB_dx(i, j, 1, 2)); + simd_t dB_dxij22(dB_dx(i, j, 2, 2)); + + simd_t bw_ij(wij); + simd_t btang_ij0(tang_ij0); + simd_t btang_ij1(tang_ij1); + simd_t btang_ij2(tang_ij2); + + simd_t brtil_ij0(rtil_ij0); + simd_t brtil_ij1(rtil_ij1); + simd_t brtil_ij2(rtil_ij2); + + for (int m = 0; m < ndofs; ++m) { + dx_ds_ij0[m] = dx_ds(i,j,0,m); + dx_ds_ij1[m] = dx_ds(i,j,1,m); + dx_ds_ij2[m] = dx_ds(i,j,2,m); + + dxphi_ds_ij0[m] = dxphi_ds(i,j,0,m); + dxphi_ds_ij1[m] = dxphi_ds(i,j,1,m); + dxphi_ds_ij2[m] = dxphi_ds(i,j,2,m); + + dxtheta_ds_ij0[m] = dxtheta_ds(i,j,0,m); + dxtheta_ds_ij1[m] = dxtheta_ds(i,j,1,m); + dxtheta_ds_ij2[m] = dxtheta_ds(i,j,2,m); + + } + + for (int m = 0; m < ndofs; m+=simd_size) { + simd_t dx_ds_ij0m = xs::load_aligned(&dx_ds_ij0[m]); + simd_t dx_ds_ij1m = xs::load_aligned(&dx_ds_ij1[m]); + simd_t dx_ds_ij2m = xs::load_aligned(&dx_ds_ij2[m]); + + simd_t dxphi_ds_ij0m = xs::load_aligned(&dxphi_ds_ij0[m]); + simd_t dxphi_ds_ij1m = xs::load_aligned(&dxphi_ds_ij1[m]); + simd_t dxphi_ds_ij2m = xs::load_aligned(&dxphi_ds_ij2[m]); + + simd_t dxtheta_ds_ij0m = xs::load_aligned(&dxtheta_ds_ij0[m]); + simd_t dxtheta_ds_ij1m = xs::load_aligned(&dxtheta_ds_ij1[m]); + simd_t dxtheta_ds_ij2m = xs::load_aligned(&dxtheta_ds_ij2[m]); + + auto dBij0m = xsimd::fma(dB_dxij00,dx_ds_ij0m,xsimd::fma(dB_dxij10,dx_ds_ij1m,dB_dxij20*dx_ds_ij2m)); + auto dBij1m = xsimd::fma(dB_dxij01,dx_ds_ij0m,xsimd::fma(dB_dxij11,dx_ds_ij1m,dB_dxij21*dx_ds_ij2m)); + auto dBij2m = xsimd::fma(dB_dxij02,dx_ds_ij0m,xsimd::fma(dB_dxij12,dx_ds_ij1m,dB_dxij22*dx_ds_ij2m)); + + auto dB2_ijm = 2*(Bij0 * dBij0m + Bij1 * dBij1m + Bij2 * dBij2m); + auto tang_ij0m = xsimd::fma(it, dxtheta_ds_ij0m , dxphi_ds_ij0m); + auto tang_ij1m = xsimd::fma(it, dxtheta_ds_ij1m , dxphi_ds_ij1m); + auto tang_ij2m = xsimd::fma(it, dxtheta_ds_ij2m , dxphi_ds_ij2m); + + auto dresij0m = xsimd::fms(GG , dBij0m , xsimd::fma(dB2_ijm , btang_ij0 , B2ij * tang_ij0m)); + auto dresij1m = xsimd::fms(GG , dBij1m , xsimd::fma(dB2_ijm , btang_ij1 , B2ij * tang_ij1m)); + auto dresij2m = xsimd::fms(GG , dBij2m , xsimd::fma(dB2_ijm , btang_ij2 , B2ij * tang_ij2m)); + + auto dmodB_ijm = 0.5 * dB2_ijm * wij; + auto dw_ijm = -dmodB_ijm * rB2ij; + auto drtil_ij0m = xsimd::fma(dresij0m , bw_ij , dw_ijm * resij0); + auto drtil_ij1m = xsimd::fma(dresij1m , bw_ij , dw_ijm * resij1); + auto drtil_ij2m = xsimd::fma(dresij2m , bw_ij , dw_ijm * resij2); + + // sum_k (r_k grad r_k) + auto dresm = xsimd::fma(brtil_ij0, drtil_ij0m, xsimd::fma(brtil_ij1, drtil_ij1m , brtil_ij2 * drtil_ij2m)); + + int jjlimit = std::min(simd_size, ndofs-m); + for(int jj = 0; jj < jjlimit; jj++){ + dres(m+jj) += dresm[jj]; + + drtilij0[m+jj] = drtil_ij0m[jj]; + drtilij1[m+jj] = drtil_ij1m[jj]; + drtilij2[m+jj] = drtil_ij2m[jj]; + + dB2_ij[m+jj] = dB2_ijm[jj]; + dtang_ij0[m+jj] = tang_ij0m[jj]; + dtang_ij1[m+jj] = tang_ij1m[jj]; + dtang_ij2[m+jj] = tang_ij2m[jj]; + dresij0[m+jj] = dresij0m[jj]; + dresij1[m+jj] = dresij1m[jj]; + dresij2[m+jj] = dresij2m[jj]; + + dBij0[m+jj] = dBij0m[jj]; + dBij1[m+jj] = dBij1m[jj]; + dBij2[m+jj] = dBij2m[jj]; + + dw_ij[m+jj] = dw_ijm[jj]; + + dmodB_ij[m+jj] = dmodB_ijm[jj]; + } + } + + double dres_ij0iota = -B2ij * xtheta(i, j, 0); + double dres_ij1iota = -B2ij * xtheta(i, j, 1); + double dres_ij2iota = -B2ij * xtheta(i, j, 2); + + double drtil_ij0iota = dres_ij0iota * wij; + double drtil_ij1iota = dres_ij1iota * wij; + double drtil_ij2iota = dres_ij2iota * wij; + dres(ndofs + 0) += rtil_ij0 * drtil_ij0iota + rtil_ij1 * drtil_ij1iota + rtil_ij2 * drtil_ij2iota; + + drtilij0[ndofs + 0] = drtil_ij0iota; + drtilij1[ndofs + 0] = drtil_ij1iota; + drtilij2[ndofs + 0] = drtil_ij2iota; + + + double dres_ij0_dG = B(i, j, 0); + double dres_ij1_dG = B(i, j, 1); + double dres_ij2_dG = B(i, j, 2); + + double drtil_ij0_dG = wij * dres_ij0_dG; + double drtil_ij1_dG = wij * dres_ij1_dG; + double drtil_ij2_dG = wij * dres_ij2_dG; + dres(ndofs + 1) += rtil_ij0 * drtil_ij0_dG + rtil_ij1 * drtil_ij1_dG + rtil_ij2 * drtil_ij2_dG; + + drtilij0[ndofs + 1] = drtil_ij0_dG; + drtilij1[ndofs + 1] = drtil_ij1_dG; + drtilij2[ndofs + 1] = drtil_ij2_dG; + + MYIF(deriv > 1) { + // outer product d_rij0_dm (x) d_rij0_dm + for(int m = 0; m < ndofs + 2; m++){ + simd_t drtilij0_dm(drtilij0[m]); + simd_t drtilij1_dm(drtilij1[m]); + simd_t drtilij2_dm(drtilij2[m]); + for(int n = m; n < ndofs + 2; n+=simd_size){ + simd_t drtilij0_dn = xs::load_aligned(&drtilij0[n]); + simd_t drtilij1_dn = xs::load_aligned(&drtilij1[n]); + simd_t drtilij2_dn = xs::load_aligned(&drtilij2[n]); + simd_t d2res_mn = drtilij0_dm * drtilij0_dn + drtilij1_dm * drtilij1_dn + drtilij2_dm * drtilij2_dn; + + int jjlimit = std::min(simd_size, ndofs+2-n); + for(int jj = 0; jj < jjlimit; jj++){ + d2res(m, n+jj) += d2res_mn[jj]; + } + } + } + + // rij * d2rij_dmn + for(int m = 0; m < ndofs; m+=simd_size){ + simd_t dx_ds_ij0m = xsimd::load_aligned(&dx_ds_ij0[m]); + simd_t dx_ds_ij1m = xsimd::load_aligned(&dx_ds_ij1[m]); + simd_t dx_ds_ij2m = xsimd::load_aligned(&dx_ds_ij2[m]); + + simd_t dxphi_ds_ij0m = xsimd::load_aligned(&dxphi_ds_ij0[m]); + simd_t dxphi_ds_ij1m = xsimd::load_aligned(&dxphi_ds_ij1[m]); + simd_t dxphi_ds_ij2m = xsimd::load_aligned(&dxphi_ds_ij2[m]); + + simd_t dxtheta_ds_ij0m = xsimd::load_aligned(&dxtheta_ds_ij0[m]); + simd_t dxtheta_ds_ij1m = xsimd::load_aligned(&dxtheta_ds_ij1[m]); + simd_t dxtheta_ds_ij2m = xsimd::load_aligned(&dxtheta_ds_ij2[m]); + + simd_t dBij0m = xsimd::load_aligned(&dBij0[m]); + simd_t dBij1m = xsimd::load_aligned(&dBij1[m]); + simd_t dBij2m = xsimd::load_aligned(&dBij2[m]); + + simd_t dB2_ijm = xsimd::load_aligned(&dB2_ij[m]); + simd_t dmodB_ijm = xsimd::load_aligned(&dmodB_ij[m]); + simd_t dw_ijm = xsimd::load_aligned(&dw_ij[m]); + + simd_t dresij0m = xsimd::load_aligned(&dresij0[m]); + simd_t dresij1m = xsimd::load_aligned(&dresij1[m]); + simd_t dresij2m = xsimd::load_aligned(&dresij2[m]); + + simd_t dtang_ij0m = xsimd::load_aligned(&dtang_ij0[m]); + simd_t dtang_ij1m = xsimd::load_aligned(&dtang_ij1[m]); + simd_t dtang_ij2m = xsimd::load_aligned(&dtang_ij2[m]); + + for(int n = m; n < ndofs; n++){ + simd_t d2Bij0_mn(0.); + simd_t d2Bij1_mn(0.); + simd_t d2Bij2_mn(0.); + for(int l = 0; l < 3; l++){ + simd_t dx_ds_ijln(dx_ds(i, j, l, n)); + + d2Bij0_mn = d2B_dx2(i, j, 0, l, 0) * dx_ds_ij0m * dx_ds_ijln+ d2Bij0_mn; + d2Bij1_mn = d2B_dx2(i, j, 0, l, 1) * dx_ds_ij0m * dx_ds_ijln+ d2Bij1_mn; + d2Bij2_mn = d2B_dx2(i, j, 0, l, 2) * dx_ds_ij0m * dx_ds_ijln+ d2Bij2_mn; + d2Bij0_mn = d2B_dx2(i, j, 1, l, 0) * dx_ds_ij1m * dx_ds_ijln+ d2Bij0_mn; + d2Bij1_mn = d2B_dx2(i, j, 1, l, 1) * dx_ds_ij1m * dx_ds_ijln+ d2Bij1_mn; + d2Bij2_mn = d2B_dx2(i, j, 1, l, 2) * dx_ds_ij1m * dx_ds_ijln+ d2Bij2_mn; + d2Bij0_mn = d2B_dx2(i, j, 2, l, 0) * dx_ds_ij2m * dx_ds_ijln+ d2Bij0_mn; + d2Bij1_mn = d2B_dx2(i, j, 2, l, 1) * dx_ds_ij2m * dx_ds_ijln+ d2Bij1_mn; + d2Bij2_mn = d2B_dx2(i, j, 2, l, 2) * dx_ds_ij2m * dx_ds_ijln+ d2Bij2_mn; + } + + auto d2B2_ijmn = 2*(dBij0m*dBij0[n] + dBij1m*dBij1[n] + dBij2m*dBij2[n]+ B(i,j,0) * d2Bij0_mn + B(i,j,1) * d2Bij1_mn + B(i,j,2) * d2Bij2_mn); + auto term1_0 = -dtang_ij0[n] * dB2_ijm; + auto term1_1 = -dtang_ij1[n] * dB2_ijm; + auto term1_2 = -dtang_ij2[n] * dB2_ijm; + + auto term2_0 = -dtang_ij0m * dB2_ij[n]; + auto term2_1 = -dtang_ij1m * dB2_ij[n]; + auto term2_2 = -dtang_ij2m * dB2_ij[n]; + + auto term3_0 = -tang_ij0 * d2B2_ijmn; + auto term3_1 = -tang_ij1 * d2B2_ijmn; + auto term3_2 = -tang_ij2 * d2B2_ijmn; + + auto d2res_ij0mn = xsimd::fma(GG , d2Bij0_mn , term1_0) + term2_0 + term3_0; + auto d2res_ij1mn = xsimd::fma(GG , d2Bij1_mn , term1_1) + term2_1 + term3_1; + auto d2res_ij2mn = xsimd::fma(GG , d2Bij2_mn , term1_2) + term2_2 + term3_2; + + auto d2modB_ijmn = (2 * B2ij * d2B2_ijmn - dB2_ijm*dB2_ij[n]) * powrmodBijthree / 4. ; + auto d2wij_mn = (2. * dmodB_ijm * dmodB_ij[n] - modB_ij * d2modB_ijmn) * powrmodBijthree; + + auto d2rtil_0mn = dresij0m *dw_ij[n] + dresij0[n] * dw_ijm + d2res_ij0mn * wij + resij0 * d2wij_mn; + auto d2rtil_1mn = dresij1m *dw_ij[n] + dresij1[n] * dw_ijm + d2res_ij1mn * wij + resij1 * d2wij_mn; + auto d2rtil_2mn = dresij2m *dw_ij[n] + dresij2[n] * dw_ijm + d2res_ij2mn * wij + resij2 * d2wij_mn; + + auto d2res_mn = rtil_ij0 * d2rtil_0mn + rtil_ij1 * d2rtil_1mn +rtil_ij2 * d2rtil_2mn; + + int jjlimit = std::min(simd_size, ndofs-m); + for(int jj = 0; jj < jjlimit; jj++){ + d2res(m+jj, n) += d2res_mn[jj]; + } + } + auto d2res_ij0miota = -(dB2_ijm * xtheta(i, j, 0) + B2ij * dxtheta_ds_ij0m); + auto d2res_ij1miota = -(dB2_ijm * xtheta(i, j, 1) + B2ij * dxtheta_ds_ij1m); + auto d2res_ij2miota = -(dB2_ijm * xtheta(i, j, 2) + B2ij * dxtheta_ds_ij2m); + + + auto d2rtil_ij0miota = d2res_ij0miota * wij + dres_ij0iota * dw_ijm ; + auto d2rtil_ij1miota = d2res_ij1miota * wij + dres_ij1iota * dw_ijm ; + auto d2rtil_ij2miota = d2res_ij2miota * wij + dres_ij2iota * dw_ijm ; + auto d2res_miota = rtil_ij0*d2rtil_ij0miota+rtil_ij1*d2rtil_ij1miota+rtil_ij2*d2rtil_ij2miota; + + int jjlimit = std::min(simd_size, ndofs-m); + for(int jj = 0; jj < jjlimit; jj++){ + d2res(m+jj, ndofs) += d2res_miota[jj]; + } + + auto d2res_ij0mG = dBij0m; + auto d2res_ij1mG = dBij1m; + auto d2res_ij2mG = dBij2m; + + auto d2rtil_ij0mG = d2res_ij0mG * wij + dres_ij0_dG * dw_ijm; + auto d2rtil_ij1mG = d2res_ij1mG * wij + dres_ij1_dG * dw_ijm; + auto d2rtil_ij2mG = d2res_ij2mG * wij + dres_ij2_dG * dw_ijm; + auto d2res_mG = rtil_ij0*d2rtil_ij0mG+rtil_ij1*d2rtil_ij1mG+rtil_ij2*d2rtil_ij2mG; + + for(int jj = 0; jj < jjlimit; jj++){ + d2res(m+jj, ndofs+1) += d2res_mG[jj]; + } + + } + } + } + } + } + + res/=num_points; + dres/=num_points; + d2res/=num_points; + + // symmetrize the Hessian + for(int m = 0; m < ndofs+2; m++){ + for(int n = m+1; n < ndofs+2; n++){ + d2res(n, m) = d2res(m, n); + } + } +} + +#else +#endif + +double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B){ + double res = 0.; + Array dummy = xt::zeros({1}); + boozer_residual_impl(G, iota, B, dummy, dummy, xphi, xtheta, dummy, dummy, dummy, res, dummy, dummy, 0); + return res; +} + +std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds){ + size_t ndofs = dx_ds.shape(3); + + double res = 0.; + Array dres = xt::zeros({ndofs+2}); + Array dummy = xt::zeros({1}); + boozer_residual_impl(G, iota, B, dB_dx, dummy, xphi, xtheta, dx_ds, dxphi_ds, dxtheta_ds, res, dres, dummy, ndofs); + auto tup = std::make_tuple(res, dres); + return tup; +} + +std::tuple boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds){ + size_t ndofs = dx_ds.shape(3); + + double res = 0.; + Array dres = xt::zeros({ndofs+2}); + Array d2res = xt::zeros({ndofs+2, ndofs+2}); + boozer_residual_impl(G, iota, B, dB_dx, d2B_dx2, xphi, xtheta, dx_ds, dxphi_ds, dxtheta_ds, res, dres, d2res, ndofs); + auto tup = std::make_tuple(res, dres, d2res); + return tup; +} + diff --git a/src/simsoptpp/boozerresidual.h b/src/simsoptpp/boozerresidual.h new file mode 100644 index 000000000..a30558c46 --- /dev/null +++ b/src/simsoptpp/boozerresidual.h @@ -0,0 +1,11 @@ +#pragma once + +#include "xtensor/xarray.hpp" +#include "xtensor/xmath.hpp" +#include "xtensor-python/pyarray.hpp" // Numpy bindings +typedef xt::pyarray Array; +using std::vector; + +double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B); +std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds); +std::tuple boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds); diff --git a/src/simsoptpp/python.cpp b/src/simsoptpp/python.cpp index 83a1c93f2..f965ec567 100644 --- a/src/simsoptpp/python.cpp +++ b/src/simsoptpp/python.cpp @@ -12,6 +12,8 @@ typedef xt::pytensor PyTensor; #include + + #include "biot_savart_py.h" #include "biot_savart_vjp_py.h" #include "boozerradialinterpolant.h" @@ -21,6 +23,7 @@ typedef xt::pytensor PyTensor; #include "permanent_magnet_optimization.h" #include "reiman.h" #include "simdhelpers.h" +#include "boozerresidual.h" namespace py = pybind11; @@ -123,6 +126,10 @@ PYBIND11_MODULE(simsoptpp, m) { return res; }); + m.def("boozer_residual", &boozer_residual); + m.def("boozer_residual_ds", &boozer_residual_ds); + m.def("boozer_residual_ds2", &boozer_residual_ds2); + m.def("matmult", [](PyArray& A, PyArray&B) { // Product of an lxm matrix with an mxn matrix, results in an l x n matrix int l = A.shape(0); diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 06ae8aeff..8b82fbd9b 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -349,6 +349,79 @@ def subtest_boozer_serialization(self, label): # check that BoozerSurface.surface and label.surface are the same surfaces assert bs_regen.label.surface is bs_regen.surface + def test_boozer_penalty_constraints_cpp_notcpp(self): + """ + Test to verify cpp and python implementations of the BoozerLS objective return the same thing. + """ + for surfacetype in surfacetypes_list: + for stellsym in stellsym_list: + for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 10, 17), (False, 13, 21)]: + with self.subTest(surfacetype=surfacetype, + stellsym=stellsym, + optimize_G=optimize_G): + self.subtest_boozer_penalty_constraints_cpp_notcpp(surfacetype, stellsym, optimize_G, nphi, ntheta) + + def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, optimize_G, nphi, ntheta): + + np.random.seed(1) + curves, currents, ma = get_ncsx_data() + coils = coils_via_symmetries(curves, currents, 3, stellsym) + bs = BiotSavart(coils) + bs_tf = BiotSavart(coils) + current_sum = sum(abs(c.current.get_value()) for c in coils) + + s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta) + s.fit_to_curve(ma, 0.1) + s.x = s.x + np.random.rand(s.x.size)*1e-6 + + tf = ToroidalFlux(s, bs_tf, nphi=51, ntheta=51) + + tf_target = 0.1 + boozer_surface = BoozerSurface(bs, s, tf, tf_target) + + iota = -0.3 + x = np.concatenate((s.get_dofs(), [iota])) + if optimize_G: + x = np.concatenate( + (x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) + + w = 1e2 + f0, J0, H0 = boozer_surface.boozer_penalty_constraints( + x, derivatives=2, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=True) + f1, J1, H1 = boozer_surface.boozer_penalty_constraints_vectorized( + x, derivatives=2, constraint_weight=w, optimize_G=optimize_G) + + # f1, and J1 scale the quadratic residual terms by 1/(number of residuals), while f0 and J0 do not. + # rescale below so that both quantities are comparable. + diff1 = (boozer_surface.label.J() - boozer_surface.targetlabel) + diff2 = s.gamma()[0, 0, 2] + f1 -= 0.5 * w * (diff1**2 + diff2**2) + f1 *= (3 * len(s.quadpoints_phi)*len(s.quadpoints_theta)) + f1 += 0.5 * w * (diff1**2 + diff2**2) + + to_add = [0] + if optimize_G: + to_add = [0, 0] + + dl = np.append(boozer_surface.label.dJ(partials=True)(s), to_add) + drz = np.append(s.dgamma_by_dcoeff()[0, 0, 2, :], to_add) + J1 -= w * (diff1 * dl + diff2 * drz) + J1 *= (3*len(s.quadpoints_phi)*len(s.quadpoints_theta)) + J1 += w * (diff1 * dl + diff2 * drz) + + nsurfdofs = s.x.size + d2l = np.zeros((x.size, x.size)) + d2l[:nsurfdofs, :nsurfdofs] = boozer_surface.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() + H1 -= w * dl[:, None] * dl[None, :] + w * diff1 * d2l + H1 -= w * drz[:, None] * drz[None, :] + H1 *= (3*len(s.quadpoints_phi)*len(s.quadpoints_theta)) + H1 += w * dl[:, None] * dl[None, :] + w * diff1 * d2l + H1 += w * drz[:, None] * drz[None, :] + + self.assertAlmostEqual(f0, f1) + np.testing.assert_allclose(J0, J1) + norm = np.max(np.abs(H0)) + assert np.all(np.abs((H0-H1)/norm) < 1e-13) if __name__ == "__main__": unittest.main() From 290dab1dcd43ad03e781abbb05a939f7f3447062 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 15 Apr 2024 18:32:57 -0400 Subject: [PATCH 036/176] cleaning up unit tests --- src/simsopt/geo/boozersurface.py | 19 +++++-- src/simsoptpp/boozerresidual.cpp | 23 ++++----- src/simsoptpp/boozerresidual.h | 6 +-- tests/geo/test_boozersurface.py | 85 +++++++++++++++----------------- 4 files changed, 66 insertions(+), 67 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 74ad2ac5a..81fdc6635 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -165,9 +165,9 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca d2val = J.T @ J + np.sum(r[:, None, None] * H, axis=0) return val, dval, d2val - def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_weight=1., optimize_G=False): + def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_weight=1., optimize_G=False, weight_inv_modB=False): """ - This function returns the same thing as `boozer_penalty_constraints` when `scalarized=True` and `weight_inv_modB=True`. It + This function returns the same thing as `boozer_penalty_constraints` when `scalarized=True`. It is much faster since it calls a vectorized implementation in cpp. """ @@ -212,13 +212,13 @@ def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_ d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) if derivatives == 0: - val = sopp.boozer_residual(G, iota, xphi, xtheta, B) + val = sopp.boozer_residual(G, iota, xphi, xtheta, B, weight_inv_modB) boozer = val, elif derivatives == 1: - val, dval = sopp.boozer_residual_ds(G, iota, B, dB_dx, xphi, xtheta, dx_dc, dxphi_dc, dxtheta_dc) + val, dval = sopp.boozer_residual_ds(G, iota, B, dB_dx, xphi, xtheta, dx_dc, dxphi_dc, dxtheta_dc, weight_inv_modB) boozer = val, dval elif derivatives == 2: - val, dval, d2val = sopp.boozer_residual_ds2(G, iota, B, dB_dx, d2B_by_dXdX, xphi, xtheta, dx_dc, dxphi_dc, dxtheta_dc) + val, dval, d2val = sopp.boozer_residual_ds2(G, iota, B, dB_dx, d2B_by_dXdX, xphi, xtheta, dx_dc, dxphi_dc, dxtheta_dc, weight_inv_modB) boozer = val, dval, d2val lab = self.label.J() @@ -371,6 +371,15 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons def minimize_boozer_penalty_constraints_BFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, hessian=False, verbose=False): r""" + This function tries to find the surface that approximately solves + + .. math:: + \text{min}_x ~J(x) + \frac{1}{2} w_c (l - l_0)^2 + + \frac{1}{2} w_c (z(\varphi=0, \theta=0) - 0)^2 + + where :math:`J(x) = \frac{1}{2}\mathbf r(x)^T \mathbf r(x)`, and :math:`\mathbf r(x)` contains + the Boozer residuals at quadrature points :math:`1,\dots,n`. + This is done using BFGS. """ if not self.need_to_run_code: return self.res diff --git a/src/simsoptpp/boozerresidual.cpp b/src/simsoptpp/boozerresidual.cpp index 340cdfd65..c64f32a34 100644 --- a/src/simsoptpp/boozerresidual.cpp +++ b/src/simsoptpp/boozerresidual.cpp @@ -14,7 +14,7 @@ #endif #if defined(USE_XSIMD) -template void boozer_residual_impl(double G, double iota, T& B, T& dB_dx, T& d2B_dx2, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres, T& d2res, size_t ndofs){ +template void boozer_residual_impl(double G, double iota, T& B, T& dB_dx, T& d2B_dx2, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres, T& d2res, size_t ndofs, bool weight_inv_modB){ int nphi = xphi.shape(0); int ntheta = xtheta.shape(1); int num_points = 3 * nphi * ntheta; @@ -57,7 +57,7 @@ template void boozer_residual_impl(double G, double iota, T& for(int j=0; j void boozer_residual_impl(double G, double iota, T& auto dresij2m = xsimd::fms(GG , dBij2m , xsimd::fma(dB2_ijm , btang_ij2 , B2ij * tang_ij2m)); auto dmodB_ijm = 0.5 * dB2_ijm * wij; - auto dw_ijm = -dmodB_ijm * rB2ij; + auto dw_ijm = weight_inv_modB ? -dmodB_ijm * rB2ij : simd_t(0.); auto drtil_ij0m = xsimd::fma(dresij0m , bw_ij , dw_ijm * resij0); auto drtil_ij1m = xsimd::fma(dresij1m , bw_ij , dw_ijm * resij1); auto drtil_ij2m = xsimd::fma(dresij2m , bw_ij , dw_ijm * resij2); @@ -289,7 +289,7 @@ template void boozer_residual_impl(double G, double iota, T& auto d2res_ij2mn = xsimd::fma(GG , d2Bij2_mn , term1_2) + term2_2 + term3_2; auto d2modB_ijmn = (2 * B2ij * d2B2_ijmn - dB2_ijm*dB2_ij[n]) * powrmodBijthree / 4. ; - auto d2wij_mn = (2. * dmodB_ijm * dmodB_ij[n] - modB_ij * d2modB_ijmn) * powrmodBijthree; + auto d2wij_mn = weight_inv_modB ? (2. * dmodB_ijm * dmodB_ij[n] - modB_ij * d2modB_ijmn) * powrmodBijthree : simd_t(0.); auto d2rtil_0mn = dresij0m *dw_ij[n] + dresij0[n] * dw_ijm + d2res_ij0mn * wij + resij0 * d2wij_mn; auto d2rtil_1mn = dresij1m *dw_ij[n] + dresij1[n] * dw_ijm + d2res_ij1mn * wij + resij1 * d2wij_mn; @@ -336,9 +336,6 @@ template void boozer_residual_impl(double G, double iota, T& } } - res/=num_points; - dres/=num_points; - d2res/=num_points; // symmetrize the Hessian for(int m = 0; m < ndofs+2; m++){ @@ -351,31 +348,31 @@ template void boozer_residual_impl(double G, double iota, T& #else #endif -double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B){ +double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B, bool weight_inv_modB){ double res = 0.; Array dummy = xt::zeros({1}); - boozer_residual_impl(G, iota, B, dummy, dummy, xphi, xtheta, dummy, dummy, dummy, res, dummy, dummy, 0); + boozer_residual_impl(G, iota, B, dummy, dummy, xphi, xtheta, dummy, dummy, dummy, res, dummy, dummy, 0, weight_inv_modB); return res; } -std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds){ +std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds, bool weight_inv_modB){ size_t ndofs = dx_ds.shape(3); double res = 0.; Array dres = xt::zeros({ndofs+2}); Array dummy = xt::zeros({1}); - boozer_residual_impl(G, iota, B, dB_dx, dummy, xphi, xtheta, dx_ds, dxphi_ds, dxtheta_ds, res, dres, dummy, ndofs); + boozer_residual_impl(G, iota, B, dB_dx, dummy, xphi, xtheta, dx_ds, dxphi_ds, dxtheta_ds, res, dres, dummy, ndofs, weight_inv_modB); auto tup = std::make_tuple(res, dres); return tup; } -std::tuple boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds){ +std::tuple boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds, bool weight_inv_modB){ size_t ndofs = dx_ds.shape(3); double res = 0.; Array dres = xt::zeros({ndofs+2}); Array d2res = xt::zeros({ndofs+2, ndofs+2}); - boozer_residual_impl(G, iota, B, dB_dx, d2B_dx2, xphi, xtheta, dx_ds, dxphi_ds, dxtheta_ds, res, dres, d2res, ndofs); + boozer_residual_impl(G, iota, B, dB_dx, d2B_dx2, xphi, xtheta, dx_ds, dxphi_ds, dxtheta_ds, res, dres, d2res, ndofs, weight_inv_modB); auto tup = std::make_tuple(res, dres, d2res); return tup; } diff --git a/src/simsoptpp/boozerresidual.h b/src/simsoptpp/boozerresidual.h index a30558c46..2c11650a4 100644 --- a/src/simsoptpp/boozerresidual.h +++ b/src/simsoptpp/boozerresidual.h @@ -6,6 +6,6 @@ typedef xt::pyarray Array; using std::vector; -double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B); -std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds); -std::tuple boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds); +double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B, bool weight_inv_modB); +std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds, bool weight_inv_modB); +std::tuple boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds, bool weight_inv_modB); diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 8b82fbd9b..e897f48e6 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -355,13 +355,15 @@ def test_boozer_penalty_constraints_cpp_notcpp(self): """ for surfacetype in surfacetypes_list: for stellsym in stellsym_list: - for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 10, 17), (False, 13, 21)]: - with self.subTest(surfacetype=surfacetype, - stellsym=stellsym, - optimize_G=optimize_G): - self.subtest_boozer_penalty_constraints_cpp_notcpp(surfacetype, stellsym, optimize_G, nphi, ntheta) + for weight_inv_modB in [False, True]: + for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 10, 17), (False, 13, 21),(True, 3, 3), (False, 3, 3)]: + with self.subTest(surfacetype=surfacetype, + stellsym=stellsym, + optimize_G=optimize_G, + weight_inv_modB=weight_inv_modB): + self.subtest_boozer_penalty_constraints_cpp_notcpp(surfacetype, stellsym, optimize_G, nphi, ntheta, weight_inv_modB) - def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, optimize_G, nphi, ntheta): + def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, optimize_G, nphi, ntheta, weight_inv_modB): np.random.seed(1) curves, currents, ma = get_ncsx_data() @@ -369,59 +371,50 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o bs = BiotSavart(coils) bs_tf = BiotSavart(coils) current_sum = sum(abs(c.current.get_value()) for c in coils) - - s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta) + + phis = None + thetas = None + if nphi == 1: + phis = [0.2234567989] + elif nphi == 2: + phis = [0.2234567989, 0.432123451] + + if ntheta == 1: + thetas = [0.2432101234] + elif ntheta == 2: + thetas = [0.2432101234, 0.9832134] + + + s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta, thetas=thetas, phis=phis) s.fit_to_curve(ma, 0.1) s.x = s.x + np.random.rand(s.x.size)*1e-6 tf = ToroidalFlux(s, bs_tf, nphi=51, ntheta=51) - + tf_target = 0.1 boozer_surface = BoozerSurface(bs, s, tf, tf_target) iota = -0.3 x = np.concatenate((s.get_dofs(), [iota])) if optimize_G: - x = np.concatenate( - (x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) + x = np.concatenate((x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) - w = 1e2 + w = 0. f0, J0, H0 = boozer_surface.boozer_penalty_constraints( - x, derivatives=2, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=True) + x, derivatives=2, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) f1, J1, H1 = boozer_surface.boozer_penalty_constraints_vectorized( - x, derivatives=2, constraint_weight=w, optimize_G=optimize_G) - - # f1, and J1 scale the quadratic residual terms by 1/(number of residuals), while f0 and J0 do not. - # rescale below so that both quantities are comparable. - diff1 = (boozer_surface.label.J() - boozer_surface.targetlabel) - diff2 = s.gamma()[0, 0, 2] - f1 -= 0.5 * w * (diff1**2 + diff2**2) - f1 *= (3 * len(s.quadpoints_phi)*len(s.quadpoints_theta)) - f1 += 0.5 * w * (diff1**2 + diff2**2) - - to_add = [0] - if optimize_G: - to_add = [0, 0] - - dl = np.append(boozer_surface.label.dJ(partials=True)(s), to_add) - drz = np.append(s.dgamma_by_dcoeff()[0, 0, 2, :], to_add) - J1 -= w * (diff1 * dl + diff2 * drz) - J1 *= (3*len(s.quadpoints_phi)*len(s.quadpoints_theta)) - J1 += w * (diff1 * dl + diff2 * drz) - - nsurfdofs = s.x.size - d2l = np.zeros((x.size, x.size)) - d2l[:nsurfdofs, :nsurfdofs] = boozer_surface.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() - H1 -= w * dl[:, None] * dl[None, :] + w * diff1 * d2l - H1 -= w * drz[:, None] * drz[None, :] - H1 *= (3*len(s.quadpoints_phi)*len(s.quadpoints_theta)) - H1 += w * dl[:, None] * dl[None, :] + w * diff1 * d2l - H1 += w * drz[:, None] * drz[None, :] - - self.assertAlmostEqual(f0, f1) - np.testing.assert_allclose(J0, J1) - norm = np.max(np.abs(H0)) - assert np.all(np.abs((H0-H1)/norm) < 1e-13) + x, derivatives=2, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) + + np.testing.assert_allclose(f0, f1, atol=1e-13, rtol=1e-13) + np.testing.assert_allclose(J0, J1, atol=1e-11, rtol=1e-11) + np.testing.assert_allclose(H0, H1, atol=1e-10, rtol=1e-10) + + h1 = np.random.rand(J0.size)-0.5 + h2 = np.random.rand(J0.size)-0.5 + np.testing.assert_allclose(f0, f1, atol=1e-13, rtol=1e-13) + np.testing.assert_allclose(J0@h1, J1@h1, atol=1e-13, rtol=1e-13) + np.testing.assert_allclose((H0@h1)@h2, (H1@h1)@h2, atol=1e-13, rtol=1e-13) + print(np.abs(f0-f1)/np.abs(f0), np.abs(J0@h1-J1@h1)/np.abs(J0@h1), np.abs((H0@h1)@h2-(H1@h1)@h2)/np.abs((H0@h1)@h2)) if __name__ == "__main__": unittest.main() From fd33c3d46f74f0ef7c735f9bf73669111ea92f01 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 15 Apr 2024 22:07:42 -0400 Subject: [PATCH 037/176] added non-xsimd implementation --- src/simsoptpp/boozerresidual.cpp | 242 +++++++++++++++++++++++++++++-- tests/geo/test_boozersurface.py | 11 +- 2 files changed, 234 insertions(+), 19 deletions(-) diff --git a/src/simsoptpp/boozerresidual.cpp b/src/simsoptpp/boozerresidual.cpp index c64f32a34..3da78ee52 100644 --- a/src/simsoptpp/boozerresidual.cpp +++ b/src/simsoptpp/boozerresidual.cpp @@ -13,6 +13,7 @@ #define MYIF(c) if(c) #endif +//#if false #if defined(USE_XSIMD) template void boozer_residual_impl(double G, double iota, T& B, T& dB_dx, T& d2B_dx2, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres, T& d2res, size_t ndofs, bool weight_inv_modB){ int nphi = xphi.shape(0); @@ -260,15 +261,15 @@ template void boozer_residual_impl(double G, double iota, T& for(int l = 0; l < 3; l++){ simd_t dx_ds_ijln(dx_ds(i, j, l, n)); - d2Bij0_mn = d2B_dx2(i, j, 0, l, 0) * dx_ds_ij0m * dx_ds_ijln+ d2Bij0_mn; - d2Bij1_mn = d2B_dx2(i, j, 0, l, 1) * dx_ds_ij0m * dx_ds_ijln+ d2Bij1_mn; - d2Bij2_mn = d2B_dx2(i, j, 0, l, 2) * dx_ds_ij0m * dx_ds_ijln+ d2Bij2_mn; - d2Bij0_mn = d2B_dx2(i, j, 1, l, 0) * dx_ds_ij1m * dx_ds_ijln+ d2Bij0_mn; - d2Bij1_mn = d2B_dx2(i, j, 1, l, 1) * dx_ds_ij1m * dx_ds_ijln+ d2Bij1_mn; - d2Bij2_mn = d2B_dx2(i, j, 1, l, 2) * dx_ds_ij1m * dx_ds_ijln+ d2Bij2_mn; - d2Bij0_mn = d2B_dx2(i, j, 2, l, 0) * dx_ds_ij2m * dx_ds_ijln+ d2Bij0_mn; - d2Bij1_mn = d2B_dx2(i, j, 2, l, 1) * dx_ds_ij2m * dx_ds_ijln+ d2Bij1_mn; - d2Bij2_mn = d2B_dx2(i, j, 2, l, 2) * dx_ds_ij2m * dx_ds_ijln+ d2Bij2_mn; + d2Bij0_mn += d2B_dx2(i, j, 0, l, 0) * dx_ds_ij0m * dx_ds_ijln; + d2Bij1_mn += d2B_dx2(i, j, 0, l, 1) * dx_ds_ij0m * dx_ds_ijln; + d2Bij2_mn += d2B_dx2(i, j, 0, l, 2) * dx_ds_ij0m * dx_ds_ijln; + d2Bij0_mn += d2B_dx2(i, j, 1, l, 0) * dx_ds_ij1m * dx_ds_ijln; + d2Bij1_mn += d2B_dx2(i, j, 1, l, 1) * dx_ds_ij1m * dx_ds_ijln; + d2Bij2_mn += d2B_dx2(i, j, 1, l, 2) * dx_ds_ij1m * dx_ds_ijln; + d2Bij0_mn += d2B_dx2(i, j, 2, l, 0) * dx_ds_ij2m * dx_ds_ijln; + d2Bij1_mn += d2B_dx2(i, j, 2, l, 1) * dx_ds_ij2m * dx_ds_ijln; + d2Bij2_mn += d2B_dx2(i, j, 2, l, 2) * dx_ds_ij2m * dx_ds_ijln; } auto d2B2_ijmn = 2*(dBij0m*dBij0[n] + dBij1m*dBij1[n] + dBij2m*dBij2[n]+ B(i,j,0) * d2Bij0_mn + B(i,j,1) * d2Bij1_mn + B(i,j,2) * d2Bij2_mn); @@ -336,16 +337,229 @@ template void boozer_residual_impl(double G, double iota, T& } } - - // symmetrize the Hessian - for(int m = 0; m < ndofs+2; m++){ - for(int n = m+1; n < ndofs+2; n++){ - d2res(n, m) = d2res(m, n); + MYIF(deriv > 1){ + // symmetrize the Hessian + for(int m = 0; m < ndofs+2; m++){ + for(int n = m+1; n < ndofs+2; n++){ + d2res(n, m) = d2res(m, n); + } } } } #else +template void boozer_residual_impl(double G, double iota, T& B, T& dB_dx, T& d2B_dx2, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres, T& d2res, size_t ndofs, bool weight_inv_modB){ + int nphi = xphi.shape(0); + int ntheta = xtheta.shape(1); + + for(int i=0; i0){ + auto drtilij0 = AlignedPaddedVec(ndofs+2, 0); + auto drtilij1 = AlignedPaddedVec(ndofs+2, 0); + auto drtilij2 = AlignedPaddedVec(ndofs+2, 0); + + auto dresij0 = AlignedPaddedVec(ndofs+2, 0); + auto dresij1 = AlignedPaddedVec(ndofs+2, 0); + auto dresij2 = AlignedPaddedVec(ndofs+2, 0); + + auto dw_ij = AlignedPaddedVec(ndofs+2, 0); + + auto dtang_ij0 = AlignedPaddedVec(ndofs+2, 0); + auto dtang_ij1 = AlignedPaddedVec(ndofs+2, 0); + auto dtang_ij2 = AlignedPaddedVec(ndofs+2, 0); + + auto dB2_ij = AlignedPaddedVec(ndofs+2, 0); + auto dBij0 = AlignedPaddedVec(ndofs+2, 0); + auto dBij1 = AlignedPaddedVec(ndofs+2, 0); + auto dBij2 = AlignedPaddedVec(ndofs+2, 0); + auto dmodB_ij = AlignedPaddedVec(ndofs+2, 0); + + for (int m = 0; m < ndofs; m++) { + double dBij0m = dB_dx(i,j,0,0)*dx_ds(i,j,0,m)+dB_dx(i,j,1,0)*dx_ds(i,j,1,m)+dB_dx(i,j,2,0)*dx_ds(i,j,2,m); + double dBij1m = dB_dx(i,j,0,1)*dx_ds(i,j,0,m)+dB_dx(i,j,1,1)*dx_ds(i,j,1,m)+dB_dx(i,j,2,1)*dx_ds(i,j,2,m); + double dBij2m = dB_dx(i,j,0,2)*dx_ds(i,j,0,m)+dB_dx(i,j,1,2)*dx_ds(i,j,1,m)+dB_dx(i,j,2,2)*dx_ds(i,j,2,m); + + double dB2_ijm = 2*(B(i,j,0) * dBij0m + B(i,j,1) * dBij1m + B(i,j,2) * dBij2m); + double tang_ij0m = iota*dxtheta_ds(i,j,0,m) + dxphi_ds(i,j,0,m); + double tang_ij1m = iota*dxtheta_ds(i,j,1,m) + dxphi_ds(i,j,1,m); + double tang_ij2m = iota*dxtheta_ds(i,j,2,m) + dxphi_ds(i,j,2,m); + + double dresij0m = G * dBij0m - (dB2_ijm * tang_ij0 + B2ij * tang_ij0m); + double dresij1m = G * dBij1m - (dB2_ijm * tang_ij1 + B2ij * tang_ij1m); + double dresij2m = G * dBij2m - (dB2_ijm * tang_ij2 + B2ij * tang_ij2m); + + double dmodB_ijm = 0.5 * dB2_ijm * wij; + double dw_ijm = weight_inv_modB ? -dmodB_ijm * rB2ij : 0.; + double drtil_ij0m = dresij0m * wij + dw_ijm * resij0; + double drtil_ij1m = dresij1m * wij + dw_ijm * resij1; + double drtil_ij2m = dresij2m * wij + dw_ijm * resij2; + + // sum_k (r_k grad r_k) + dres(m) += rtil_ij0 * drtil_ij0m + rtil_ij1 * drtil_ij1m + rtil_ij2 * drtil_ij2m; + + drtilij0[m] = drtil_ij0m; + drtilij1[m] = drtil_ij1m; + drtilij2[m] = drtil_ij2m; + + dB2_ij[m] = dB2_ijm; + dtang_ij0[m] = tang_ij0m; + dtang_ij1[m] = tang_ij1m; + dtang_ij2[m] = tang_ij2m; + dresij0[m] = dresij0m; + dresij1[m] = dresij1m; + dresij2[m] = dresij2m; + + dBij0[m] = dBij0m; + dBij1[m] = dBij1m; + dBij2[m] = dBij2m; + + dw_ij[m] = dw_ijm; + + dmodB_ij[m] = dmodB_ijm; + } + + double dres_ij0iota = -B2ij * xtheta(i, j, 0); + double dres_ij1iota = -B2ij * xtheta(i, j, 1); + double dres_ij2iota = -B2ij * xtheta(i, j, 2); + + double drtil_ij0iota = dres_ij0iota * wij; + double drtil_ij1iota = dres_ij1iota * wij; + double drtil_ij2iota = dres_ij2iota * wij; + dres(ndofs + 0) += rtil_ij0 * drtil_ij0iota + rtil_ij1 * drtil_ij1iota + rtil_ij2 * drtil_ij2iota; + + drtilij0[ndofs + 0] = drtil_ij0iota; + drtilij1[ndofs + 0] = drtil_ij1iota; + drtilij2[ndofs + 0] = drtil_ij2iota; + + + double dres_ij0_dG = B(i, j, 0); + double dres_ij1_dG = B(i, j, 1); + double dres_ij2_dG = B(i, j, 2); + + double drtil_ij0_dG = wij * dres_ij0_dG; + double drtil_ij1_dG = wij * dres_ij1_dG; + double drtil_ij2_dG = wij * dres_ij2_dG; + dres(ndofs + 1) += rtil_ij0 * drtil_ij0_dG + rtil_ij1 * drtil_ij1_dG + rtil_ij2 * drtil_ij2_dG; + + drtilij0[ndofs + 1] = drtil_ij0_dG; + drtilij1[ndofs + 1] = drtil_ij1_dG; + drtilij2[ndofs + 1] = drtil_ij2_dG; + MYIF(deriv > 1) { + // outer product d_rij0_dm (x) d_rij0_dm + for(int m = 0; m < ndofs + 2; m++){ + for(int n = m; n < ndofs + 2; n++){ + d2res(m, n) += drtilij0[m] * drtilij0[n] + drtilij1[m] * drtilij1[n] + drtilij2[m] * drtilij2[n]; + } + } + + // rij * d2rij_dmn + for(int m = 0; m < ndofs; m++){ + for(int n = m; n < ndofs; n++){ + double d2Bij0_mn = 0.; + double d2Bij1_mn = 0.; + double d2Bij2_mn = 0.; + for(int l = 0; l < 3; l++){ + d2Bij0_mn += d2B_dx2(i, j, 0, l, 0) * dx_ds(i,j,0,m) * dx_ds(i, j, l, n); + d2Bij1_mn += d2B_dx2(i, j, 0, l, 1) * dx_ds(i,j,0,m) * dx_ds(i, j, l, n); + d2Bij2_mn += d2B_dx2(i, j, 0, l, 2) * dx_ds(i,j,0,m) * dx_ds(i, j, l, n); + d2Bij0_mn += d2B_dx2(i, j, 1, l, 0) * dx_ds(i,j,1,m) * dx_ds(i, j, l, n); + d2Bij1_mn += d2B_dx2(i, j, 1, l, 1) * dx_ds(i,j,1,m) * dx_ds(i, j, l, n); + d2Bij2_mn += d2B_dx2(i, j, 1, l, 2) * dx_ds(i,j,1,m) * dx_ds(i, j, l, n); + d2Bij0_mn += d2B_dx2(i, j, 2, l, 0) * dx_ds(i,j,2,m) * dx_ds(i, j, l, n); + d2Bij1_mn += d2B_dx2(i, j, 2, l, 1) * dx_ds(i,j,2,m) * dx_ds(i, j, l, n); + d2Bij2_mn += d2B_dx2(i, j, 2, l, 2) * dx_ds(i,j,2,m) * dx_ds(i, j, l, n); + } + + auto d2B2_ijmn = 2*(dBij0[m]*dBij0[n] + dBij1[m]*dBij1[n] + dBij2[m]*dBij2[n]+ B(i,j,0) * d2Bij0_mn + B(i,j,1) * d2Bij1_mn + B(i,j,2) * d2Bij2_mn); + auto term1_0 = -dtang_ij0[n] * dB2_ij[m]; + auto term1_1 = -dtang_ij1[n] * dB2_ij[m]; + auto term1_2 = -dtang_ij2[n] * dB2_ij[m]; + + auto term2_0 = -dtang_ij0[m] * dB2_ij[n]; + auto term2_1 = -dtang_ij1[m] * dB2_ij[n]; + auto term2_2 = -dtang_ij2[m] * dB2_ij[n]; + + auto term3_0 = -tang_ij0 * d2B2_ijmn; + auto term3_1 = -tang_ij1 * d2B2_ijmn; + auto term3_2 = -tang_ij2 * d2B2_ijmn; + + auto d2res_ij0mn = G * d2Bij0_mn + term1_0 + term2_0 + term3_0; + auto d2res_ij1mn = G * d2Bij1_mn + term1_1 + term2_1 + term3_1; + auto d2res_ij2mn = G * d2Bij2_mn + term1_2 + term2_2 + term3_2; + + auto d2modB_ijmn = (2 * B2ij * d2B2_ijmn - dB2_ij[m]*dB2_ij[n]) * powrmodBijthree / 4. ; + auto d2wij_mn = weight_inv_modB ? (2. * dmodB_ij[m] * dmodB_ij[n] - modB_ij * d2modB_ijmn) * powrmodBijthree : 0.; + + auto d2rtil_0mn = dresij0[m] *dw_ij[n] + dresij0[n] * dw_ij[m] + d2res_ij0mn * wij + resij0 * d2wij_mn; + auto d2rtil_1mn = dresij1[m] *dw_ij[n] + dresij1[n] * dw_ij[m] + d2res_ij1mn * wij + resij1 * d2wij_mn; + auto d2rtil_2mn = dresij2[m] *dw_ij[n] + dresij2[n] * dw_ij[m] + d2res_ij2mn * wij + resij2 * d2wij_mn; + + auto d2res_mn = rtil_ij0 * d2rtil_0mn + rtil_ij1 * d2rtil_1mn +rtil_ij2 * d2rtil_2mn; + + d2res(m, n) += d2res_mn; + } + auto d2res_ij0miota = -(dB2_ij[m] * xtheta(i, j, 0) + B2ij * dxtheta_ds(i,j,0,m)); + auto d2res_ij1miota = -(dB2_ij[m] * xtheta(i, j, 1) + B2ij * dxtheta_ds(i,j,1,m)); + auto d2res_ij2miota = -(dB2_ij[m] * xtheta(i, j, 2) + B2ij * dxtheta_ds(i,j,2,m)); + + + auto d2rtil_ij0miota = d2res_ij0miota * wij + dres_ij0iota * dw_ij[m] ; + auto d2rtil_ij1miota = d2res_ij1miota * wij + dres_ij1iota * dw_ij[m] ; + auto d2rtil_ij2miota = d2res_ij2miota * wij + dres_ij2iota * dw_ij[m] ; + auto d2res_miota = rtil_ij0*d2rtil_ij0miota+rtil_ij1*d2rtil_ij1miota+rtil_ij2*d2rtil_ij2miota; + + d2res(m, ndofs) += d2res_miota; + + auto d2res_ij0mG = dBij0[m]; + auto d2res_ij1mG = dBij1[m]; + auto d2res_ij2mG = dBij2[m]; + + auto d2rtil_ij0mG = d2res_ij0mG * wij + dres_ij0_dG * dw_ij[m]; + auto d2rtil_ij1mG = d2res_ij1mG * wij + dres_ij1_dG * dw_ij[m]; + auto d2rtil_ij2mG = d2res_ij2mG * wij + dres_ij2_dG * dw_ij[m]; + auto d2res_mG = rtil_ij0*d2rtil_ij0mG+rtil_ij1*d2rtil_ij1mG+rtil_ij2*d2rtil_ij2mG; + + d2res(m, ndofs+1) += d2res_mG; + + } + } + } + } + } + + MYIF(deriv > 1){ + // symmetrize the Hessian + for(int m = 0; m < ndofs+2; m++){ + for(int n = m+1; n < ndofs+2; n++){ + d2res(n, m) = d2res(m, n); + } + } + } +} + #endif double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B, bool weight_inv_modB){ diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index e897f48e6..43f65a603 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -231,11 +231,12 @@ def test_boozer_surface_optimisation_convergence(self): ] for surfacetype, stellsym, optimize_G, second_stage in configs: for get_data in [get_hsx_data, get_ncsx_data, get_giuliani_data]: - with self.subTest( - surfacetype=surfacetype, stellsym=stellsym, - optimize_G=optimize_G, second_stage=second_stage, get_data=get_data): - self.subtest_boozer_surface_optimisation_convergence( - surfacetype, stellsym, optimize_G, second_stage, get_data) + for vectorize in [True, False]: + with self.subTest( + surfacetype=surfacetype, stellsym=stellsym, + optimize_G=optimize_G, second_stage=second_stage, get_data=get_data, vectorize=vectorize): + self.subtest_boozer_surface_optimisation_convergence( + surfacetype, stellsym, optimize_G, second_stage, get_data) def subtest_boozer_surface_optimisation_convergence(self, surfacetype, stellsym, optimize_G, From ad73f7c9e601cf6ec79130af54e58697adb5cd62 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 16 Apr 2024 15:32:47 -0400 Subject: [PATCH 038/176] removing some changes to make this PR simpler [skip ci] --- src/simsopt/geo/boozersurface.py | 173 ++++++------------------------- tests/geo/test_boozersurface.py | 57 ++++++++-- 2 files changed, 79 insertions(+), 151 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 81fdc6635..904d4dbbf 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -53,28 +53,6 @@ def __init__(self, biotsavart, surface, label, targetlabel, constraint_weight=No def recompute_bell(self, parent=None): self.need_to_run_code = True - def run_code(self, boozer_type, iota, G=None, verbose=True): - """ - Run the default solvers. - """ - if not self.need_to_run_code: - return - - if boozer_type == 'exact': - res = self.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=40, iota=iota, G=G, verbose=verbose) - return res - elif boozer_type == 'ls': - # first try BFGS - res = self.minimize_boozer_penalty_constraints_BFGS(tol=1e-10, maxiter=1500, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) - iota, G = res['iota'], res['G'] - - ## polish off using Newton's method - self.need_to_run_code = True - res = self.minimize_boozer_penalty_constraints_newton(tol=1e-11, maxiter=40, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) - return res - else: - raise Exception(f"boozer_type not supported: {boozer_type}") - def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., scalarize=True, optimize_G=False, weight_inv_modB=False): r""" Define the residual @@ -95,6 +73,8 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca J(x) = \frac{1}{2}\mathbf r(x)^T \mathbf r(x), i.e. the least squares residual and optionally the gradient and the Hessian of :math:`J(x)`. + + For ``weight_inv_modB=False``, the residuals are unweighted, and they are multiplied by 1/ """ assert derivatives in [0, 1, 2] @@ -324,7 +304,7 @@ def boozer_exact_constraints(self, xl, derivatives=0, optimize_G=True): dres[-1, :-2] = drz return res, dres - def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None): + def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, vectorize=False): r""" This function tries to find the surface that approximately solves @@ -345,8 +325,13 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons x = np.concatenate((s.get_dofs(), [iota])) else: x = np.concatenate((s.get_dofs(), [iota, G])) - fun = lambda x: self.boozer_penalty_constraints( - x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) + + if vectorize: + fun = lambda x: self.boozer_penalty_constraints_vectorized( + x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) + else: + fun = lambda x: self.boozer_penalty_constraints( + x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) res = minimize( fun, x, jac=True, method='L-BFGS-B', options={'maxiter': maxiter, 'ftol': tol, 'gtol': tol, 'maxcor': 200}) @@ -369,132 +354,27 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons self.need_to_run_code = False return resdict - def minimize_boozer_penalty_constraints_BFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, hessian=False, verbose=False): - r""" - This function tries to find the surface that approximately solves - - .. math:: - \text{min}_x ~J(x) + \frac{1}{2} w_c (l - l_0)^2 - + \frac{1}{2} w_c (z(\varphi=0, \theta=0) - 0)^2 - - where :math:`J(x) = \frac{1}{2}\mathbf r(x)^T \mathbf r(x)`, and :math:`\mathbf r(x)` contains - the Boozer residuals at quadrature points :math:`1,\dots,n`. - This is done using BFGS. - """ - if not self.need_to_run_code: - return self.res - - s = self.surface - if G is None: - x = np.concatenate((s.get_dofs(), [iota])) - else: - x = np.concatenate((s.get_dofs(), [iota, G])) - - fun = lambda x: self.boozer_penalty_constraints_vectorized( - x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) - res = minimize( - fun, x, jac=True, method='BFGS', - options={'maxiter': maxiter, 'gtol': tol}) - - resdict = { - "residual": res.fun, "gradient": res.jac, "iter": res.nit, "info": res, "success": res.success, "G": None, 'type': 'ls', 'solver': 'BFGS', - "firstorderop": res.jac, "constraint_weight": constraint_weight, "labelerr": np.abs((self.label.J()-self.targetlabel)/self.targetlabel) - } - - if G is None: - s.set_dofs(res.x[:-1]) - iota = res.x[-1] - else: - s.set_dofs(res.x[:-2]) - iota = res.x[-2] - G = res.x[-1] - resdict['G'] = G - resdict['s'] = s - resdict['iota'] = iota - - if hessian: - val, dval, d2val = self.boozer_penalty_constraints_vectorized( - x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) - P, L, U = lu(d2val) - resdict["PLU"] = (P, L, U) - - self.res = resdict - self.need_to_run_code = False - - if verbose: - print(f"BFGS solve - {resdict['success']} iter={resdict['iter']}, iota={resdict['iota']:.16f}, ||grad||_inf = {np.linalg.norm(resdict['firstorderop'], ord=np.inf):.3e}", flush=True) - return resdict - - def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0., verbose=False): + def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0., vectorize=False): """ + This function does the same as :mod:`minimize_boozer_penalty_constraints_LBFGS`, but instead of LBFGS it uses + Newton's method. """ if not self.need_to_run_code: return self.res - + s = self.surface if G is None: x = np.concatenate((s.get_dofs(), [iota])) else: x = np.concatenate((s.get_dofs(), [iota, G])) i = 0 - - val, dval, d2val = self.boozer_penalty_constraints_vectorized( - x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) - norm = np.linalg.norm(dval, ord=np.inf) - while i < maxiter and norm > tol: - d2val += stab*np.identity(d2val.shape[0]) - dx = np.linalg.solve(d2val, dval) - if norm < 1e-9: - dx += np.linalg.solve(d2val, dval - d2val@dx) - x = x - dx + if vectorize: val, dval, d2val = self.boozer_penalty_constraints_vectorized( x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) - norm = np.linalg.norm(dval, ord=np.inf) - - if norm > 1e1: - break - - i = i+1 - - P, L, U = lu(d2val) - if G is None: - s.set_dofs(x[:-1]) - iota = x[-1] - else: - s.set_dofs(x[:-2]) - iota = x[-2] - G = x[-1] - - res = { - "residual": val, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "firstorderop": dval, - "PLU": (P, L, U), 'iota': iota, "G": G, "type": "ls" - } - - self.res = res - self.need_to_run_code = False - - if verbose: - print(f"NEWTON solve - {res['success']} iter={res['iter']}, iota={res['iota']:.16f}, ||grad||_inf = {np.linalg.norm(res['firstorderop'], ord=np.inf):.3e}", flush=True) - return res - - def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0.): - """ - This function does the same as :mod:`minimize_boozer_penalty_constraints_LBFGS`, but instead of LBFGS it uses - Newton's method. - """ - if not self.need_to_run_code: - return self.res - - s = self.surface - if G is None: - x = np.concatenate((s.get_dofs(), [iota])) else: - x = np.concatenate((s.get_dofs(), [iota, G])) - i = 0 - - val, dval, d2val = self.boozer_penalty_constraints( - x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + val, dval, d2val = self.boozer_penalty_constraints( + x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) norm = np.linalg.norm(dval) while i < maxiter and norm > tol: d2val += stab*np.identity(d2val.shape[0]) @@ -527,7 +407,7 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons self.need_to_run_code = False return res - def minimize_boozer_penalty_constraints_ls(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, method='lm'): + def minimize_boozer_penalty_constraints_ls(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, method='lm', vectorize=False): """ This function does the same as :mod:`minimize_boozer_penalty_constraints_LBFGS`, but instead of LBFGS it uses a nonlinear least squares algorithm when ``method='lm'``. Options for the method @@ -547,15 +427,24 @@ def minimize_boozer_penalty_constraints_ls(self, tol=1e-12, maxiter=10, constrai if method == 'manual': i = 0 lam = 1. - r, J = self.boozer_penalty_constraints( - x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) + if vectorize: + r, J = self.boozer_penalty_constraints_vectorized( + x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) + else: + r, J = self.boozer_penalty_constraints( + x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) b = J.T@r JTJ = J.T@J while i < maxiter and norm > tol: dx = np.linalg.solve(JTJ + lam * np.diag(np.diag(JTJ)), b) x -= dx - r, J = self.boozer_penalty_constraints( - x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) + + if vectorize: + r, J = self.boozer_penalty_constraints_vectorized( + x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) + else: + r, J = self.boozer_penalty_constraints( + x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) b = J.T@r JTJ = J.T@J norm = np.linalg.norm(b) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 43f65a603..30c986909 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -236,11 +236,12 @@ def test_boozer_surface_optimisation_convergence(self): surfacetype=surfacetype, stellsym=stellsym, optimize_G=optimize_G, second_stage=second_stage, get_data=get_data, vectorize=vectorize): self.subtest_boozer_surface_optimisation_convergence( - surfacetype, stellsym, optimize_G, second_stage, get_data) + surfacetype, stellsym, optimize_G, second_stage, get_data, vectorize) def subtest_boozer_surface_optimisation_convergence(self, surfacetype, stellsym, optimize_G, - second_stage, get_data): + second_stage, get_data, + vectorize): curves, currents, ma = get_data() if stellsym: coils = coils_via_symmetries(curves, currents, ma.nfp, True) @@ -284,18 +285,19 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, # compute surface first using LBFGS exact and an area constraint res = boozer_surface.minimize_boozer_penalty_constraints_LBFGS( - tol=1e-9, maxiter=500, constraint_weight=100., iota=iota, G=G) + tol=1e-9, maxiter=500, constraint_weight=100., iota=iota, G=G, + vectorize=vectorize) print('Residual norm after LBFGS', np.sqrt(2*res['fun'])) boozer_surface.recompute_bell() if second_stage == 'ls': res = boozer_surface.minimize_boozer_penalty_constraints_ls( tol=1e-11, maxiter=100, constraint_weight=1000., - iota=res['iota'], G=res['G']) + iota=res['iota'], G=res['G'], vectorize=vectorize) elif second_stage == 'newton': res = boozer_surface.minimize_boozer_penalty_constraints_newton( tol=1e-9, maxiter=15, constraint_weight=100., - iota=res['iota'], G=res['G'], stab=1e-4) + iota=res['iota'], G=res['G'], stab=1e-4, vectorize=vectorize) elif second_stage == 'newton_exact': res = boozer_surface.minimize_boozer_exact_constraints_newton( tol=1e-9, maxiter=15, iota=res['iota'], G=res['G']) @@ -399,8 +401,31 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o x = np.concatenate((s.get_dofs(), [iota])) if optimize_G: x = np.concatenate((x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) - + + # deriv = 0 w = 0. + f0 = boozer_surface.boozer_penalty_constraints( + x, derivatives=0, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) + f1 = boozer_surface.boozer_penalty_constraints_vectorized( + x, derivatives=0, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) + np.testing.assert_allclose(f0, f1, atol=1e-13, rtol=1e-13) + #print(np.abs(f0-f1)/np.abs(f0)) + + + # deriv = 1 + f0, J0 = boozer_surface.boozer_penalty_constraints( + x, derivatives=1, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) + f1, J1 = boozer_surface.boozer_penalty_constraints_vectorized( + x, derivatives=1, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) + np.testing.assert_allclose(f0, f1, atol=1e-13, rtol=1e-13) + np.testing.assert_allclose(J0, J1, atol=1e-11, rtol=1e-11) + + # check directional derivative + h1 = np.random.rand(J0.size)-0.5 + np.testing.assert_allclose(J0@h1, J1@h1, atol=1e-13, rtol=1e-13) + #print(np.abs(f0-f1)/np.abs(f0), np.abs(J0@h1-J1@h1)/np.abs(J0@h1)) + + f0, J0, H0 = boozer_surface.boozer_penalty_constraints( x, derivatives=2, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) f1, J1, H1 = boozer_surface.boozer_penalty_constraints_vectorized( @@ -409,13 +434,27 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o np.testing.assert_allclose(f0, f1, atol=1e-13, rtol=1e-13) np.testing.assert_allclose(J0, J1, atol=1e-11, rtol=1e-11) np.testing.assert_allclose(H0, H1, atol=1e-10, rtol=1e-10) - - h1 = np.random.rand(J0.size)-0.5 h2 = np.random.rand(J0.size)-0.5 + np.testing.assert_allclose(f0, f1, atol=1e-13, rtol=1e-13) np.testing.assert_allclose(J0@h1, J1@h1, atol=1e-13, rtol=1e-13) np.testing.assert_allclose((H0@h1)@h2, (H1@h1)@h2, atol=1e-13, rtol=1e-13) - print(np.abs(f0-f1)/np.abs(f0), np.abs(J0@h1-J1@h1)/np.abs(J0@h1), np.abs((H0@h1)@h2-(H1@h1)@h2)/np.abs((H0@h1)@h2)) + #print(np.abs(f0-f1)/np.abs(f0), np.abs(J0@h1-J1@h1)/np.abs(J0@h1), np.abs((H0@h1)@h2-(H1@h1)@h2)/np.abs((H0@h1)@h2)) + + + def compute_differences(Ha, Hb): + diff = np.abs(Ha.flatten() - Hb.flatten()) + rel_diff = diff/np.abs(Ha.flatten()) + ij1 = np.where(diff.reshape(Ha.shape) == np.max(diff)) + i1 = ij1[0][0] + j1 = ij1[1][0] + + + ij2 = np.where(rel_diff.reshape(Ha.shape) == np.max(rel_diff)) + i2 = ij2[0][0] + j2 = ij2[1][0] + print(f'max err ({i1:03}, {j1:03}): {np.max(diff):.6e}, {Ha[i1, j1]:.6e}\nmax rel err ({i2:03}, {j2:03}): {np.max(rel_diff):.6e}, {Ha[i2,j2]:.6e}\n') + compute_differences(H0, H1) if __name__ == "__main__": unittest.main() From cc77bd79bc2a97d0e2680c6051ab7a4b8c41d44e Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 16 Apr 2024 15:50:11 -0400 Subject: [PATCH 039/176] more unit tests --- tests/geo/test_boozersurface.py | 65 +++++++++++++++++++++------------ 1 file changed, 42 insertions(+), 23 deletions(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 30c986909..8e5a4d12a 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -55,11 +55,13 @@ def test_boozer_penalty_constraints_gradient(self): for surfacetype in surfacetypes_list: for stellsym in stellsym_list: for optimize_G in [True, False]: - with self.subTest(surfacetype=surfacetype, - stellsym=stellsym, - optimize_G=optimize_G): - self.subtest_boozer_penalty_constraints_gradient( - surfacetype, stellsym, optimize_G) + for vectorize in [True, False]: + with self.subTest(surfacetype=surfacetype, + stellsym=stellsym, + optimize_G=optimize_G, + vectorize=vectorize): + self.subtest_boozer_penalty_constraints_gradient( + surfacetype, stellsym, optimize_G, vectorize) def test_boozer_penalty_constraints_hessian(self): """ @@ -69,14 +71,16 @@ def test_boozer_penalty_constraints_hessian(self): for surfacetype in surfacetypes_list: for stellsym in stellsym_list: for optimize_G in [True, False]: - with self.subTest(surfacetype=surfacetype, - stellsym=stellsym, - optimize_G=optimize_G): - self.subtest_boozer_penalty_constraints_hessian( - surfacetype, stellsym, optimize_G) + for vectorize in [True, False]: + with self.subTest(surfacetype=surfacetype, + stellsym=stellsym, + optimize_G=optimize_G, + vectorize=vectorize): + self.subtest_boozer_penalty_constraints_hessian( + surfacetype, stellsym, optimize_G, vectorize) def subtest_boozer_penalty_constraints_gradient(self, surfacetype, stellsym, - optimize_G=False): + optimize_G=False, vectorize=False): np.random.seed(1) curves, currents, ma = get_ncsx_data() coils = coils_via_symmetries(curves, currents, 3, True) @@ -98,9 +102,12 @@ def subtest_boozer_penalty_constraints_gradient(self, surfacetype, stellsym, x = np.concatenate((s.get_dofs(), [iota])) if optimize_G: x = np.concatenate((x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) - f0, J0 = boozer_surface.boozer_penalty_constraints( - x, derivatives=1, constraint_weight=weight, optimize_G=optimize_G) - + if vectorize: + f0, J0 = boozer_surface.boozer_penalty_constraints_vectorized( + x, derivatives=1, constraint_weight=weight, optimize_G=optimize_G) + else: + f0, J0 = boozer_surface.boozer_penalty_constraints( + x, derivatives=1, constraint_weight=weight, optimize_G=optimize_G) h = np.random.uniform(size=x.shape)-0.5 Jex = J0@h @@ -108,9 +115,14 @@ def subtest_boozer_penalty_constraints_gradient(self, surfacetype, stellsym, epsilons = np.power(2., -np.asarray(range(7, 20))) print("###############################################################") for eps in epsilons: - f1 = boozer_surface.boozer_penalty_constraints( - x + eps*h, derivatives=0, constraint_weight=weight, - optimize_G=optimize_G) + if vectorize: + f1 = boozer_surface.boozer_penalty_constraints_vectorized( + x + eps*h, derivatives=0, constraint_weight=weight, + optimize_G=optimize_G) + else: + f1 = boozer_surface.boozer_penalty_constraints( + x + eps*h, derivatives=0, constraint_weight=weight, + optimize_G=optimize_G) Jfd = (f1-f0)/eps err = np.linalg.norm(Jfd-Jex)/np.linalg.norm(Jex) print(err/err_old, f0, f1) @@ -119,7 +131,7 @@ def subtest_boozer_penalty_constraints_gradient(self, surfacetype, stellsym, print("###############################################################") def subtest_boozer_penalty_constraints_hessian(self, surfacetype, stellsym, - optimize_G=False): + optimize_G=False, vectorize=False): np.random.seed(1) curves, currents, ma = get_ncsx_data() coils = coils_via_symmetries(curves, currents, 3, True) @@ -140,9 +152,12 @@ def subtest_boozer_penalty_constraints_hessian(self, surfacetype, stellsym, if optimize_G: x = np.concatenate( (x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) - f0, J0, H0 = boozer_surface.boozer_penalty_constraints( - x, derivatives=2, optimize_G=optimize_G) - + if vectorize: + f0, J0, H0 = boozer_surface.boozer_penalty_constraints_vectorized( + x, derivatives=2, optimize_G=optimize_G) + else: + f0, J0, H0 = boozer_surface.boozer_penalty_constraints( + x, derivatives=2, optimize_G=optimize_G) h1 = np.random.uniform(size=x.shape)-0.5 h2 = np.random.uniform(size=x.shape)-0.5 d2f = h1 @ H0 @ h2 @@ -151,8 +166,12 @@ def subtest_boozer_penalty_constraints_hessian(self, surfacetype, stellsym, epsilons = np.power(2., -np.asarray(range(10, 20))) print("###############################################################") for eps in epsilons: - fp, Jp = boozer_surface.boozer_penalty_constraints( - x + eps*h1, derivatives=1, optimize_G=optimize_G) + if vectorize: + fp, Jp = boozer_surface.boozer_penalty_constraints_vectorized( + x + eps*h1, derivatives=1, optimize_G=optimize_G) + else: + fp, Jp = boozer_surface.boozer_penalty_constraints( + x + eps*h1, derivatives=1, optimize_G=optimize_G) d2f_fd = (Jp@h2-J0@h2)/eps err = np.abs(d2f_fd-d2f)/np.abs(d2f) print(err/err_old) From 9e5f6216c4c317149696dd16c0541eec51a05321 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 16 Apr 2024 16:05:23 -0400 Subject: [PATCH 040/176] remove unused header --- src/simsoptpp/boozerresidual.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/simsoptpp/boozerresidual.cpp b/src/simsoptpp/boozerresidual.cpp index 3da78ee52..1a1b55782 100644 --- a/src/simsoptpp/boozerresidual.cpp +++ b/src/simsoptpp/boozerresidual.cpp @@ -4,7 +4,6 @@ #include "simdhelpers.h" #include "vec3dsimd.h" #include "xtensor/xarray.hpp" -#include #include "xtensor/xadapt.hpp" #if __cplusplus >= 201703L @@ -13,7 +12,6 @@ #define MYIF(c) if(c) #endif -//#if false #if defined(USE_XSIMD) template void boozer_residual_impl(double G, double iota, T& B, T& dB_dx, T& d2B_dx2, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres, T& d2res, size_t ndofs, bool weight_inv_modB){ int nphi = xphi.shape(0); From 09c17c244b37a434c5747bfbff09e8e30fac254f Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 16 Apr 2024 16:29:44 -0400 Subject: [PATCH 041/176] removing vectorization option in the boozer_surface.minimize_boozer_penalty_constraints_ls function [skip ci] --- src/simsopt/geo/boozersurface.py | 21 ++++++--------------- tests/geo/test_boozersurface.py | 2 +- 2 files changed, 7 insertions(+), 16 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 904d4dbbf..22d05836d 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -407,7 +407,7 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons self.need_to_run_code = False return res - def minimize_boozer_penalty_constraints_ls(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, method='lm', vectorize=False): + def minimize_boozer_penalty_constraints_ls(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, method='lm'): """ This function does the same as :mod:`minimize_boozer_penalty_constraints_LBFGS`, but instead of LBFGS it uses a nonlinear least squares algorithm when ``method='lm'``. Options for the method @@ -417,7 +417,7 @@ def minimize_boozer_penalty_constraints_ls(self, tol=1e-12, maxiter=10, constrai if not self.need_to_run_code: return self.res - + s = self.surface if G is None: x = np.concatenate((s.get_dofs(), [iota])) @@ -427,24 +427,15 @@ def minimize_boozer_penalty_constraints_ls(self, tol=1e-12, maxiter=10, constrai if method == 'manual': i = 0 lam = 1. - if vectorize: - r, J = self.boozer_penalty_constraints_vectorized( - x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) - else: - r, J = self.boozer_penalty_constraints( - x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) + r, J = self.boozer_penalty_constraints( + x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) b = J.T@r JTJ = J.T@J while i < maxiter and norm > tol: dx = np.linalg.solve(JTJ + lam * np.diag(np.diag(JTJ)), b) x -= dx - - if vectorize: - r, J = self.boozer_penalty_constraints_vectorized( - x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) - else: - r, J = self.boozer_penalty_constraints( - x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) + r, J = self.boozer_penalty_constraints( + x, derivatives=1, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) b = J.T@r JTJ = J.T@J norm = np.linalg.norm(b) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 8e5a4d12a..84dd49e76 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -312,7 +312,7 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, if second_stage == 'ls': res = boozer_surface.minimize_boozer_penalty_constraints_ls( tol=1e-11, maxiter=100, constraint_weight=1000., - iota=res['iota'], G=res['G'], vectorize=vectorize) + iota=res['iota'], G=res['G']) elif second_stage == 'newton': res = boozer_surface.minimize_boozer_penalty_constraints_newton( tol=1e-9, maxiter=15, constraint_weight=100., From 0e2c3926a3a1daade57d6db2ea9f4d7925ff7f8b Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 16 Apr 2024 16:31:42 -0400 Subject: [PATCH 042/176] removed constraint_weight [skip ci] --- src/simsopt/geo/boozersurface.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 22d05836d..49f83bdcb 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -41,13 +41,12 @@ class BoozerSurface(Optimizable): where Newton is used to solve the first order necessary conditions for optimality. """ - def __init__(self, biotsavart, surface, label, targetlabel, constraint_weight=None): + def __init__(self, biotsavart, surface, label, targetlabel): super().__init__(depends_on=[biotsavart]) self.biotsavart = biotsavart self.surface = surface self.label = label self.targetlabel = targetlabel - self.constraint_weight = constraint_weight self.need_to_run_code = True def recompute_bell(self, parent=None): From 005b0e0363807dac368ba32917bf05faf5177507 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 16 Apr 2024 16:45:18 -0400 Subject: [PATCH 043/176] increasing maxiter in one of the unit tests [skip ci] --- tests/geo/test_boozersurface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 84dd49e76..80171186c 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -304,7 +304,7 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, # compute surface first using LBFGS exact and an area constraint res = boozer_surface.minimize_boozer_penalty_constraints_LBFGS( - tol=1e-9, maxiter=500, constraint_weight=100., iota=iota, G=G, + tol=1e-9, maxiter=600, constraint_weight=100., iota=iota, G=G, vectorize=vectorize) print('Residual norm after LBFGS', np.sqrt(2*res['fun'])) From d1e71db13de4852833664b6a67945f62d4f7e90a Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 16 Apr 2024 16:50:03 -0400 Subject: [PATCH 044/176] removing a verbose optional argument --- src/simsopt/geo/boozersurface.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 49f83bdcb..58acc02e4 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -550,7 +550,7 @@ def minimize_boozer_exact_constraints_newton(self, tol=1e-12, maxiter=10, iota=0 self.need_to_run_code = False return res - def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., G=None, verbose=False): + def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., G=None): """ This function solves the Boozer Surface residual equation exactly. For this to work, we need the right balance of quadrature points, degrees @@ -691,8 +691,6 @@ def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., "mask": mask, 'type': 'exact' } - if verbose: - print(f"NEWTON solve - {res['success']} iter={res['iter']}, iota={res['iota']:.16f}, ||residual||_inf = {np.linalg.norm(res['residual'], ord=np.inf):.3e}", flush=True) self.res = res self.need_to_run_code = False From 464b3e5237e7f8dc724a115495caba8ceb0b2a7e Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 16 Apr 2024 17:04:26 -0400 Subject: [PATCH 045/176] added another unit test for self-intersecting surfaces --- tests/geo/test_boozersurface.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 80171186c..d17d4663a 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -285,7 +285,7 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, s = get_surface(surfacetype, stellsym, nfp=ma.nfp) s.fit_to_curve(ma, 0.1) if get_data is get_ncsx_data: - iota = -0.3 + iota = -0.4 elif get_data is get_giuliani_data: iota = 0.4 elif get_data is get_hsx_data: @@ -326,6 +326,8 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, print('Residual norm after second stage', np.linalg.norm(res['residual'])) assert res['success'] + assert boozer_surface.surface.is_self_intersecting(thetas=100) + # For the stellsym case we have z(0, 0) = y(0, 0) = 0. For the not # stellsym case, we enforce z(0, 0) = 0, but expect y(0, 0) \neq 0 gammazero = s.gamma()[0, 0, :] From 4c418f59468a11361ee957e3a847f4d5b10785df Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 16 Apr 2024 17:30:20 -0400 Subject: [PATCH 046/176] making problem smaller to avoid issues with CI --- tests/geo/test_boozersurface.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index d17d4663a..23152767e 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -380,7 +380,7 @@ def test_boozer_penalty_constraints_cpp_notcpp(self): for surfacetype in surfacetypes_list: for stellsym in stellsym_list: for weight_inv_modB in [False, True]: - for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 10, 17), (False, 13, 21),(True, 3, 3), (False, 3, 3)]: + for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 6, 13), (False, 7, 13),(True, 3, 3), (False, 3, 3)]: with self.subTest(surfacetype=surfacetype, stellsym=stellsym, optimize_G=optimize_G, @@ -447,6 +447,7 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o #print(np.abs(f0-f1)/np.abs(f0), np.abs(J0@h1-J1@h1)/np.abs(J0@h1)) + # deriv = 2 f0, J0, H0 = boozer_surface.boozer_penalty_constraints( x, derivatives=2, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) f1, J1, H1 = boozer_surface.boozer_penalty_constraints_vectorized( From 80e23bc67a2b8d6adebc4509b27a4656558651fa Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 16 Apr 2024 18:04:13 -0400 Subject: [PATCH 047/176] making problem smaller to avoid issues with CI --- tests/geo/test_boozersurface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 23152767e..635415dad 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -380,7 +380,7 @@ def test_boozer_penalty_constraints_cpp_notcpp(self): for surfacetype in surfacetypes_list: for stellsym in stellsym_list: for weight_inv_modB in [False, True]: - for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 6, 13), (False, 7, 13),(True, 3, 3), (False, 3, 3)]: + for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 6, 9), (False, 7, 8),(True, 3, 3), (False, 3, 3)]: with self.subTest(surfacetype=surfacetype, stellsym=stellsym, optimize_G=optimize_G, From 56f67be059643d3a226faf5a21aeb8d28dde86ab Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 17 Apr 2024 10:06:34 -0400 Subject: [PATCH 048/176] trying to avoid segfault in unit tests --- tests/geo/test_boozersurface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 635415dad..7580f4df7 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -409,7 +409,7 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o thetas = [0.2432101234, 0.9832134] - s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta, thetas=thetas, phis=phis) + s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta, thetas=thetas, phis=phis, mpol=3, ntor=3) s.fit_to_curve(ma, 0.1) s.x = s.x + np.random.rand(s.x.size)*1e-6 From 77ca9148b055dca3504de1d5546d6c2154cb8ec0 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 17 Apr 2024 13:07:12 -0400 Subject: [PATCH 049/176] made unit test even easier, minor changes to file naming --- CMakeLists.txt | 4 +-- ...ozerresidual.cpp => boozerresidual_impl.h} | 33 ------------------- src/simsoptpp/boozerresidual_py.cpp | 32 ++++++++++++++++++ .../{boozerresidual.h => boozerresidual_py.h} | 4 +-- src/simsoptpp/python.cpp | 2 +- tests/geo/test_boozersurface.py | 3 +- 6 files changed, 37 insertions(+), 41 deletions(-) rename src/simsoptpp/{boozerresidual.cpp => boozerresidual_impl.h} (94%) create mode 100644 src/simsoptpp/boozerresidual_py.cpp rename src/simsoptpp/{boozerresidual.h => boozerresidual_py.h} (95%) diff --git a/CMakeLists.txt b/CMakeLists.txt index 2d0a93f54..046f45db4 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -119,7 +119,7 @@ set(XTENSOR_USE_TBB 0) pybind11_add_module(${PROJECT_NAME} src/simsoptpp/python.cpp src/simsoptpp/python_surfaces.cpp src/simsoptpp/python_curves.cpp - src/simsoptpp/boozerresidual.cpp + src/simsoptpp/boozerresidual_py.cpp src/simsoptpp/python_magneticfield.cpp src/simsoptpp/python_tracing.cpp src/simsoptpp/python_distance.cpp src/simsoptpp/biot_savart_py.cpp src/simsoptpp/biot_savart_vjp_py.cpp @@ -159,8 +159,6 @@ set_target_properties(profiling target_include_directories(profiling PRIVATE "thirdparty/xtensor/include" "thirdparty/xsimd/include" "thirdparty/xtl/include" "thirdparty/eigen" "src/simsoptpp/") target_link_libraries(profiling PRIVATE fmt::fmt-header-only) - - #get_cmake_property(_variableNames VARIABLES) #list (SORT _variableNames) #foreach (_variableName ${_variableNames}) diff --git a/src/simsoptpp/boozerresidual.cpp b/src/simsoptpp/boozerresidual_impl.h similarity index 94% rename from src/simsoptpp/boozerresidual.cpp rename to src/simsoptpp/boozerresidual_impl.h index 1a1b55782..c432e275d 100644 --- a/src/simsoptpp/boozerresidual.cpp +++ b/src/simsoptpp/boozerresidual_impl.h @@ -1,10 +1,7 @@ -#include "boozerresidual.h" - #include "xsimd/xsimd.hpp" #include "simdhelpers.h" #include "vec3dsimd.h" #include "xtensor/xarray.hpp" -#include "xtensor/xadapt.hpp" #if __cplusplus >= 201703L #define MYIF(c) if constexpr(c) @@ -559,33 +556,3 @@ template void boozer_residual_impl(double G, double iota, T& } #endif - -double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B, bool weight_inv_modB){ - double res = 0.; - Array dummy = xt::zeros({1}); - boozer_residual_impl(G, iota, B, dummy, dummy, xphi, xtheta, dummy, dummy, dummy, res, dummy, dummy, 0, weight_inv_modB); - return res; -} - -std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds, bool weight_inv_modB){ - size_t ndofs = dx_ds.shape(3); - - double res = 0.; - Array dres = xt::zeros({ndofs+2}); - Array dummy = xt::zeros({1}); - boozer_residual_impl(G, iota, B, dB_dx, dummy, xphi, xtheta, dx_ds, dxphi_ds, dxtheta_ds, res, dres, dummy, ndofs, weight_inv_modB); - auto tup = std::make_tuple(res, dres); - return tup; -} - -std::tuple boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds, bool weight_inv_modB){ - size_t ndofs = dx_ds.shape(3); - - double res = 0.; - Array dres = xt::zeros({ndofs+2}); - Array d2res = xt::zeros({ndofs+2, ndofs+2}); - boozer_residual_impl(G, iota, B, dB_dx, d2B_dx2, xphi, xtheta, dx_ds, dxphi_ds, dxtheta_ds, res, dres, d2res, ndofs, weight_inv_modB); - auto tup = std::make_tuple(res, dres, d2res); - return tup; -} - diff --git a/src/simsoptpp/boozerresidual_py.cpp b/src/simsoptpp/boozerresidual_py.cpp new file mode 100644 index 000000000..d8d41e85b --- /dev/null +++ b/src/simsoptpp/boozerresidual_py.cpp @@ -0,0 +1,32 @@ +#include "boozerresidual_impl.h" +#include "boozerresidual_py.h" + +double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B, bool weight_inv_modB){ + double res = 0.; + Array dummy = xt::zeros({1}); + boozer_residual_impl(G, iota, B, dummy, dummy, xphi, xtheta, dummy, dummy, dummy, res, dummy, dummy, 0, weight_inv_modB); + return res; +} + +std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds, bool weight_inv_modB){ + size_t ndofs = dx_ds.shape(3); + + double res = 0.; + Array dres = xt::zeros({ndofs+2}); + Array dummy = xt::zeros({1}); + boozer_residual_impl(G, iota, B, dB_dx, dummy, xphi, xtheta, dx_ds, dxphi_ds, dxtheta_ds, res, dres, dummy, ndofs, weight_inv_modB); + auto tup = std::make_tuple(res, dres); + return tup; +} + +std::tuple boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds, bool weight_inv_modB){ + size_t ndofs = dx_ds.shape(3); + + double res = 0.; + Array dres = xt::zeros({ndofs+2}); + Array d2res = xt::zeros({ndofs+2, ndofs+2}); + boozer_residual_impl(G, iota, B, dB_dx, d2B_dx2, xphi, xtheta, dx_ds, dxphi_ds, dxtheta_ds, res, dres, d2res, ndofs, weight_inv_modB); + auto tup = std::make_tuple(res, dres, d2res); + return tup; +} + diff --git a/src/simsoptpp/boozerresidual.h b/src/simsoptpp/boozerresidual_py.h similarity index 95% rename from src/simsoptpp/boozerresidual.h rename to src/simsoptpp/boozerresidual_py.h index 2c11650a4..8b5fc5f9b 100644 --- a/src/simsoptpp/boozerresidual.h +++ b/src/simsoptpp/boozerresidual_py.h @@ -1,10 +1,8 @@ -#pragma once - #include "xtensor/xarray.hpp" #include "xtensor/xmath.hpp" #include "xtensor-python/pyarray.hpp" // Numpy bindings + typedef xt::pyarray Array; -using std::vector; double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B, bool weight_inv_modB); std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds, bool weight_inv_modB); diff --git a/src/simsoptpp/python.cpp b/src/simsoptpp/python.cpp index f965ec567..2f153c5a3 100644 --- a/src/simsoptpp/python.cpp +++ b/src/simsoptpp/python.cpp @@ -23,7 +23,7 @@ typedef xt::pytensor PyTensor; #include "permanent_magnet_optimization.h" #include "reiman.h" #include "simdhelpers.h" -#include "boozerresidual.h" +#include "boozerresidual_py.h" namespace py = pybind11; diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 7580f4df7..2be3bfa95 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -380,7 +380,8 @@ def test_boozer_penalty_constraints_cpp_notcpp(self): for surfacetype in surfacetypes_list: for stellsym in stellsym_list: for weight_inv_modB in [False, True]: - for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 6, 9), (False, 7, 8),(True, 3, 3), (False, 3, 3)]: + for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1)]: + #for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 6, 9), (False, 7, 8),(True, 3, 3), (False, 3, 3)]: with self.subTest(surfacetype=surfacetype, stellsym=stellsym, optimize_G=optimize_G, From 71db8b9faf1852924b5a665d044232947277192d Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 17 Apr 2024 20:11:35 -0400 Subject: [PATCH 050/176] initial commit --- src/simsopt/geo/curvexyzhelical.py | 120 +++++++++++++++++++++++++++++ tests/geo/test_curve.py | 50 +++++++++++- 2 files changed, 166 insertions(+), 4 deletions(-) create mode 100644 src/simsopt/geo/curvexyzhelical.py diff --git a/src/simsopt/geo/curvexyzhelical.py b/src/simsopt/geo/curvexyzhelical.py new file mode 100644 index 000000000..bc9d190d7 --- /dev/null +++ b/src/simsopt/geo/curvexyzhelical.py @@ -0,0 +1,120 @@ +import jax.numpy as jnp +from math import pi +import numpy as np +from .curve import JaxCurve + +__all__ = ['CurveXYZHelical'] + + +def jaxXYZHelicalFouriercurve_pure(dofs, quadpoints, order, nfp, stellsym): + + if stellsym: + xc = dofs[:order+1] + ys = dofs[order+1:2*order+1] + zs = dofs[2*order+1:] + + theta, m = jnp.meshgrid(quadpoints, jnp.arange(order+1), indexing='ij') + xhat = np.sum(xc[None, :] * jnp.cos(2 * jnp.pi * nfp*m*theta), axis=1) + yhat = np.sum(ys[None, :] * jnp.sin(2 * jnp.pi * nfp*m[:, 1:]*theta[:, 1:]), axis=1) + + x = jnp.cos(2*jnp.pi*quadpoints) * xhat - jnp.sin(2*jnp.pi*quadpoints) * yhat + y = jnp.sin(2*jnp.pi*quadpoints) * xhat + jnp.cos(2*jnp.pi*quadpoints) * yhat + z = jnp.sum(zs[None, :] * jnp.sin(2*jnp.pi*nfp * m[:, 1:]*theta[:, 1:]), axis=1) + else: + xc = dofs[0 : order+1] + xs = dofs[order+1 : 2*order+1] + yc = dofs[2*order+1: 3*order+2] + ys = dofs[3*order+2: 4*order+2] + zc = dofs[4*order+2: 5*order+3] + zs = dofs[5*order+3: ] + + theta, m = jnp.meshgrid(quadpoints, jnp.arange(order+1), indexing='ij') + xhat = np.sum(xc[None, :] * jnp.cos(2*jnp.pi*nfp*m*theta), axis=1) + np.sum(xs[None, :] * jnp.sin(2*jnp.pi*nfp*m[:, 1:]*theta[:, 1:]), axis=1) + yhat = np.sum(yc[None, :] * jnp.cos(2*jnp.pi*nfp*m*theta), axis=1) + np.sum(ys[None, :] * jnp.sin(2*jnp.pi*nfp*m[:, 1:]*theta[:, 1:]), axis=1) + + x = jnp.cos(2*jnp.pi*quadpoints) * xhat - jnp.sin(2*jnp.pi*quadpoints) * yhat + y = jnp.sin(2*jnp.pi*quadpoints) * xhat + jnp.cos(2*jnp.pi*quadpoints) * yhat + z = np.sum(zc[None, :] * jnp.cos(2*jnp.pi*nfp*m*theta), axis=1) + np.sum(zs[None, :] * jnp.sin(2*jnp.pi*nfp*m[:, 1:]*theta[:, 1:]), axis=1) + + gamma = jnp.zeros((len(quadpoints),3)) + gamma = gamma.at[:, 0].add(x) + gamma = gamma.at[:, 1].add(y) + gamma = gamma.at[:, 2].add(z) + return gamma + + +class CurveXYZHelical(JaxCurve): + r'''A curve representation for a helical coil that does not lie on a torus. The coordinates of the curve are given by: + .. math:: + \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} x_{c,m} cos(2pi n_{\text{fp}} m \theta)\\ + \hat y(\theta) &= \sum_{m=1}^{\text{order}} y_{s,m} sin(2pi n_{\text{fp}} m \theta)\\ + x(\theta) &= \hat x(\theta) \cos(2pi \theta) - \hat y(\theta) \sin(2pi \theta)\\ + y(\theta) &= \hat x(\theta) \sin(2pi \theta) + \hat y(\theta) \cos(2pi \theta)\\ + z(\theta) &= \sum_{i=0}^{\text{order}} z_{s,m} sin(2pi n_{\text{fp}} \theta) + if the coil is stellarator symmetric. When the coil is not stellarator symmetric, the formulas above + become + .. math:: + \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} x_{c, m} cos(2pi m \theta) + x_{s, m} sin(2pi m \theta)\\ + \hat y(\theta) &= y_{c, 0} + \sum_{m=1}^{\text{order}} y_{c, m} cos(2pi m \theta) + y_{s, m} sin(2pi m \theta)\\ + x(\theta) &= \hat x(\theta) \cos(2pi \theta) - \hat y(\theta) \sin(2pi \theta)\\ + y(\theta) &= \hat x(\theta) \sin(2pi \theta) + \hat y(\theta) \cos(2pi \theta)\\ + z(\theta) &= z_{c, 0} + \sum_{m=1}^{\text{order}} z_{c, m} cos(2pi \theta) + z_{s, m} sin(2pi \theta) + + Args: + quadpoints: number of grid points/resolution along the curve, + order: how many Fourier harmonics to include in the Fourier representation, + nfp: discrete rotational symmetry number, + stellsym: stellaratory symmetry if True, not stellarator symmetric otherwise. + ''' + + def __init__(self, quadpoints, order, nfp, stellsym, **kwargs): + if isinstance(quadpoints, int): + quadpoints = np.linspace(0, 1, quadpoints, endpoint=False) + pure = lambda dofs, points: jaxXYZHelicalFouriercurve_pure( + dofs, points, order, nfp, stellsym) + + self.order = order + self.nfp = nfp + self.stellsym = stellsym + self.coefficients = np.zeros(self.num_dofs()) + if "dofs" not in kwargs: + if "x0" not in kwargs: + kwargs["x0"] = self.coefficients + else: + self.set_dofs_impl(kwargs["x0"]) + + super().__init__(quadpoints, pure, names=self._make_names(order), **kwargs) + + def _make_names(self, order): + if self.stellsym: + x_cos_names = [f'xc({i})' for i in range(0, order + 1)] + x_names = x_cos_names + y_sin_names = [f'ys({i})' for i in range(1, order + 1)] + y_names = y_sin_names + z_sin_names = [f'zs({i})' for i in range(1, order + 1)] + z_names = z_sin_names + else: + x_names = ['xc(0)'] + x_cos_names = [f'xc({i})' for i in range(1, order + 1)] + x_sin_names = [f'xs({i})' for i in range(1, order + 1)] + x_names += x_cos_names + x_sin_names + y_names = ['yc(0)'] + y_cos_names = [f'yc({i})' for i in range(1, order + 1)] + y_sin_names = [f'ys({i})' for i in range(1, order + 1)] + y_names += y_cos_names + y_sin_names + z_names = ['zc(0)'] + z_cos_names = [f'zc({i})' for i in range(1, order + 1)] + z_sin_names = [f'zs({i})' for i in range(1, order + 1)] + z_names += z_cos_names + z_sin_names + + return x_names + y_names + z_names + + def num_dofs(self): + return (self.order+1) + self.order + self.order if self.stellsym else 3*(2*self.order+1) + + def get_dofs(self): + return self.coefficients + + def set_dofs_impl(self, dofs): + self.coefficients[:] = dofs[:] + diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index acf3314bf..979359e27 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -11,6 +11,7 @@ from simsopt.geo.curverzfourier import CurveRZFourier from simsopt.geo.curveplanarfourier import CurvePlanarFourier from simsopt.geo.curvehelical import CurveHelical +from simsopt.geo.curvexyzhelical import CurveXYZHelical from simsopt.geo.curve import RotatedCurve, curves_to_vtk from simsopt.geo import parameters from simsopt.configs.zoo import get_ncsx_data, get_w7x_data @@ -36,7 +37,7 @@ def taylor_test(f, df, x, epsilons=None, direction=None): dfx = df(x)@direction if epsilons is None: epsilons = np.power(2., -np.asarray(range(7, 20))) - # print("################################################################################") + print("################################################################################") err_old = 1e9 counter = 0 for eps in epsilons: @@ -46,6 +47,8 @@ def taylor_test(f, df, x, epsilons=None, direction=None): fminuseps = f(x - eps * direction) dfest = (fpluseps-fminuseps)/(2*eps) err = np.linalg.norm(dfest - dfx) + print(err, err/err_old) + assert err < 1e-9 or err < 0.3 * err_old if err < 1e-9: break @@ -53,9 +56,10 @@ def taylor_test(f, df, x, epsilons=None, direction=None): counter += 1 if err > 1e-10: assert counter > 3 - # print("################################################################################") + print("################################################################################") +#def get_curve(curvetype, rotated, x=np.linspace(0, 1, 100, endpoint=False)): def get_curve(curvetype, rotated, x=np.asarray([0.5])): np.random.seed(2) rand_scale = 0.01 @@ -73,9 +77,13 @@ def get_curve(curvetype, rotated, x=np.asarray([0.5])): curve = CurveHelical(x, order, 5, 2, 1.0, 0.3, x0=np.ones((2*order,))) elif curvetype == "CurvePlanarFourier": curve = CurvePlanarFourier(x, order, 2, True) + elif curvetype == "CurveXYZHelical1": + curve = CurveXYZHelical(x, order, 2, True) + elif curvetype == "CurveXYZHelical2": + curve = CurveXYZHelical(x, order, 2, False) else: assert False - + dofs = np.zeros((curve.dof_size, )) if curvetype in ["CurveXYZFourier", "JaxCurveXYZFourier"]: dofs[1] = 1. @@ -87,10 +95,28 @@ def get_curve(curvetype, rotated, x=np.asarray([0.5])): dofs[order+1] = 0.1 elif curvetype in ["CurveHelical", "CurveHelicalInitx0"]: dofs[0] = np.pi/2 + elif curvetype == "CurveXYZHelical1": + R = 1 + r = 0.5 + curve.set('xc(0)', R) + curve.set('xc(1)', -r) + curve.set('zs(1)', -r) + dofs = curve.get_dofs() + elif curvetype == "CurveXYZHelical2": + R = 1 + r = 0.5 + curve.set('xc(0)', R) + curve.set('xs(1)', -0.1*r) + curve.set('xc(1)', -r) + curve.set('zs(1)', -r) + curve.set('zc(0)', 1) + curve.set('zs(1)', r) + dofs = curve.get_dofs() else: assert False curve.x = dofs + rand_scale * np.random.rand(len(dofs)).reshape(dofs.shape) + if rotated: curve = RotatedCurve(curve, 0.5, flip=False) return curve @@ -98,7 +124,23 @@ def get_curve(curvetype, rotated, x=np.asarray([0.5])): class Testing(unittest.TestCase): - curvetypes = ["CurveXYZFourier", "JaxCurveXYZFourier", "CurveRZFourier", "CurvePlanarFourier", "CurveHelical", "CurveHelicalInitx0"] + curvetypes = ["CurveXYZFourier", "JaxCurveXYZFourier", "CurveRZFourier", "CurvePlanarFourier", "CurveHelical", "CurveXYZHelical1","CurveXYZHelical2", "CurveHelicalInitx0"] + + def test_curve_xyzhelical_xyzfourier(self): + # this test checks that both helical coil representations can produce the same helical curve on a torus + + order = 1 + nfp = 2 + x = np.linspace(0, 1, 100, endpoint=False) + curve1 = CurveXYZHelical(x, 10, nfp, True) + R = 1 + r = 0.5 + curve1.set('xc(0)', R) + curve1.set('xc(1)', r) + curve1.set('zs(1)', -r) + dofs = curve1.get_dofs() + curve2 = CurveHelical(x, order, nfp, 1, R, r, x0=np.zeros((2*order,))) + assert np.mean(np.linalg.norm(curve1.gamma()-curve2.gamma(), axis=-1)) == 0 def test_curve_helical_xyzfourier(self): x = np.asarray([0.6]) From c03467852f7bc5f06c25b95b22932253b839aa61 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 17 Apr 2024 20:19:31 -0400 Subject: [PATCH 051/176] linting --- tests/geo/test_curve.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 979359e27..e1d5210dc 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -128,7 +128,7 @@ class Testing(unittest.TestCase): def test_curve_xyzhelical_xyzfourier(self): # this test checks that both helical coil representations can produce the same helical curve on a torus - + order = 1 nfp = 2 x = np.linspace(0, 1, 100, endpoint=False) @@ -138,7 +138,6 @@ def test_curve_xyzhelical_xyzfourier(self): curve1.set('xc(0)', R) curve1.set('xc(1)', r) curve1.set('zs(1)', -r) - dofs = curve1.get_dofs() curve2 = CurveHelical(x, order, nfp, 1, R, r, x0=np.zeros((2*order,))) assert np.mean(np.linalg.norm(curve1.gamma()-curve2.gamma(), axis=-1)) == 0 From 9ef07b1011cf7eb38255c02aa072d16572afc37a Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 17 Apr 2024 20:23:41 -0400 Subject: [PATCH 052/176] more linting --- src/simsopt/geo/curvexyzhelical.py | 1 - tests/geo/test_curve.py | 1 - 2 files changed, 2 deletions(-) diff --git a/src/simsopt/geo/curvexyzhelical.py b/src/simsopt/geo/curvexyzhelical.py index bc9d190d7..e78ba9ca8 100644 --- a/src/simsopt/geo/curvexyzhelical.py +++ b/src/simsopt/geo/curvexyzhelical.py @@ -1,5 +1,4 @@ import jax.numpy as jnp -from math import pi import numpy as np from .curve import JaxCurve diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index e1d5210dc..c3301e2e4 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -128,7 +128,6 @@ class Testing(unittest.TestCase): def test_curve_xyzhelical_xyzfourier(self): # this test checks that both helical coil representations can produce the same helical curve on a torus - order = 1 nfp = 2 x = np.linspace(0, 1, 100, endpoint=False) From c74f81b3b77514b4c1dad2ba222c651899c85f42 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 17 Apr 2024 21:21:43 -0400 Subject: [PATCH 053/176] added more unit tests --- src/simsopt/geo/curvexyzhelical.py | 2 +- tests/geo/test_curve.py | 91 +++++++++++++++++++++++++++++- 2 files changed, 91 insertions(+), 2 deletions(-) diff --git a/src/simsopt/geo/curvexyzhelical.py b/src/simsopt/geo/curvexyzhelical.py index e78ba9ca8..6fcc83690 100644 --- a/src/simsopt/geo/curvexyzhelical.py +++ b/src/simsopt/geo/curvexyzhelical.py @@ -46,7 +46,7 @@ class CurveXYZHelical(JaxCurve): r'''A curve representation for a helical coil that does not lie on a torus. The coordinates of the curve are given by: .. math:: \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} x_{c,m} cos(2pi n_{\text{fp}} m \theta)\\ - \hat y(\theta) &= \sum_{m=1}^{\text{order}} y_{s,m} sin(2pi n_{\text{fp}} m \theta)\\ + \hat y(\theta) &= \sum_{m=1}^{\text{order}} y_{s,m} sin(2pi n_{\text{fp}} m \theta)\\ x(\theta) &= \hat x(\theta) \cos(2pi \theta) - \hat y(\theta) \sin(2pi \theta)\\ y(\theta) &= \hat x(\theta) \sin(2pi \theta) + \hat y(\theta) \cos(2pi \theta)\\ z(\theta) &= \sum_{i=0}^{\text{order}} z_{s,m} sin(2pi n_{\text{fp}} \theta) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index c3301e2e4..1bf8be5ef 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -131,7 +131,7 @@ def test_curve_xyzhelical_xyzfourier(self): order = 1 nfp = 2 x = np.linspace(0, 1, 100, endpoint=False) - curve1 = CurveXYZHelical(x, 10, nfp, True) + curve1 = CurveXYZHelical(x, order, nfp, True) R = 1 r = 0.5 curve1.set('xc(0)', R) @@ -140,6 +140,95 @@ def test_curve_xyzhelical_xyzfourier(self): curve2 = CurveHelical(x, order, nfp, 1, R, r, x0=np.zeros((2*order,))) assert np.mean(np.linalg.norm(curve1.gamma()-curve2.gamma(), axis=-1)) == 0 + def test_xyzhelical_symmetries(self): + # does the stellarator symmetric curve have rotational symmetry? + np.random.seed(1) + rand_scale = 1e-2 + order = 2 + nfp = 3 + x = np.array([0.123, 0.123+1/nfp]) + curve = CurveXYZHelical(x, order, nfp, True) + R = 1 + r = 0.25 + curve.set('xc(0)', R) + curve.set('xc(2)', r) + curve.set('ys(2)', -r) + curve.set('zs(1)', -2*r) + curve.set('zs(2)', r) + dofs = curve.x.copy() + curve.x = dofs + rand_scale * np.random.rand(len(dofs)).reshape(dofs.shape) + + out = curve.gamma() + alpha = -2*np.pi/nfp + R = np.array([[np.cos(alpha), np.sin(alpha), 0], [-np.sin(alpha), np.cos(alpha), 0], [0, 0, 1]]) + print(R@out[0], out[1]) + assert np.linalg.norm(out[1]-R@out[0])<1e-15 + + # is the stellarator symmetric curve actually stellarator symmetric? + order = 2 + nfp = 3 + x = np.array([0.123, -0.123]) + curve = CurveXYZHelical(x, order, nfp, True) + R = 1 + r = 0.25 + curve.set('xc(0)', R) + curve.set('xc(2)', r) + curve.set('ys(2)', -r) + curve.set('zs(1)', -2*r) + curve.set('zs(2)', r) + dofs = curve.x.copy() + curve.x = dofs + rand_scale * np.random.rand(len(dofs)).reshape(dofs.shape) + pts = curve.gamma() + assert np.abs(pts[0, 0]-pts[1, 0]) <1e-15 + assert np.abs(pts[0, 1]+pts[1, 1]) <1e-15 + assert np.abs(pts[0, 2]+pts[1, 2]) <1e-15 + + + # is the field from the stellarator symmetric curve actually stellarator symmetric? + order = 2 + nfp = 3 + x = np.array([0.123, -0.123]) + curve = CurveXYZHelical(100, order, nfp, True) + R = 1 + r = 0.25 + curve.set('xc(0)', R) + curve.set('xc(2)', r) + curve.set('ys(2)', -r) + curve.set('zs(1)', -2*r) + curve.set('zs(2)', r) + dofs = curve.x.copy() + curve.x = dofs + rand_scale * np.random.rand(len(dofs)).reshape(dofs.shape) + from simsopt.field import BiotSavart, Current, Coil + current = Current(1e5) + coil = Coil(curve, current) + bs = BiotSavart([coil]) + bs.set_points([[1, 1, 1], [1, -1, -1]]) + B=bs.B_cyl() + assert np.abs(B[0, 0]+B[1, 0]) <1e-15 + assert np.abs(B[0, 1]-B[1, 1]) <1e-15 + assert np.abs(B[0, 2]-B[1, 2]) <1e-15 + + # does the non-stellarator symmetric curve have rotational symmetry still? + order = 2 + nfp = 5 + x = np.array([0.123, 0.123+1/nfp]) + curve = CurveXYZHelical(x, order, nfp, False) + R = 1 + r = 0.25 + curve.set('xc(0)', R) + curve.set('xc(2)', r) + curve.set('ys(2)', -r) + curve.set('zs(1)', -2*r) + curve.set('zs(2)', r) + dofs = curve.x.copy() + curve.x = dofs + rand_scale * np.random.rand(len(dofs)).reshape(dofs.shape) + + out = curve.gamma() + alpha = -2*np.pi/nfp + R = np.array([[np.cos(alpha), np.sin(alpha), 0], [-np.sin(alpha), np.cos(alpha), 0], [0, 0, 1]]) + print(R@out[0], out[1]) + assert np.linalg.norm(out[1]-R@out[0])<1e-15 + def test_curve_helical_xyzfourier(self): x = np.asarray([0.6]) curve1 = CurveHelical(x, 2, 5, 2, 1.0, 0.3) From a5b97523ce614a198230ec22799713fb8dafcbbb Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 17 Apr 2024 22:03:37 -0400 Subject: [PATCH 054/176] fixing typo in docstring --- src/simsopt/geo/curvexyzhelical.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/simsopt/geo/curvexyzhelical.py b/src/simsopt/geo/curvexyzhelical.py index 6fcc83690..3d690dc1d 100644 --- a/src/simsopt/geo/curvexyzhelical.py +++ b/src/simsopt/geo/curvexyzhelical.py @@ -49,7 +49,7 @@ class CurveXYZHelical(JaxCurve): \hat y(\theta) &= \sum_{m=1}^{\text{order}} y_{s,m} sin(2pi n_{\text{fp}} m \theta)\\ x(\theta) &= \hat x(\theta) \cos(2pi \theta) - \hat y(\theta) \sin(2pi \theta)\\ y(\theta) &= \hat x(\theta) \sin(2pi \theta) + \hat y(\theta) \cos(2pi \theta)\\ - z(\theta) &= \sum_{i=0}^{\text{order}} z_{s,m} sin(2pi n_{\text{fp}} \theta) + z(\theta) &= \sum_{i=1}^{\text{order}} z_{s,m} sin(2pi n_{\text{fp}} \theta) if the coil is stellarator symmetric. When the coil is not stellarator symmetric, the formulas above become .. math:: From cdebaf33f153aa3cb213ded5801a58f284569253 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Thu, 18 Apr 2024 12:15:59 -0400 Subject: [PATCH 055/176] cleaning up unit tests --- tests/geo/test_curve.py | 113 ++++++++++++++++++++-------------------- 1 file changed, 56 insertions(+), 57 deletions(-) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 1bf8be5ef..53340a933 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -126,7 +126,32 @@ class Testing(unittest.TestCase): curvetypes = ["CurveXYZFourier", "JaxCurveXYZFourier", "CurveRZFourier", "CurvePlanarFourier", "CurveHelical", "CurveXYZHelical1","CurveXYZHelical2", "CurveHelicalInitx0"] - def test_curve_xyzhelical_xyzfourier(self): + def get_curvexyzhelical(self, stellsym=True, x=None, nfp=None): + # returns a CurveXYZHelical that is randomly perturbed + + np.random.seed(1) + rand_scale = 1e-2 + + if nfp is None: + nfp = 3 + if x is None: + x = np.linspace(0, 1, 200, endpoint=False) + + order = 2 + curve = CurveXYZHelical(x, order, nfp, stellsym) + R = 1 + r = 0.25 + curve.set('xc(0)', R) + curve.set('xc(2)', r) + curve.set('ys(2)', -r) + curve.set('zs(1)', -2*r) + curve.set('zs(2)', r) + dofs = curve.x.copy() + curve.x = dofs + rand_scale * np.random.rand(len(dofs)).reshape(dofs.shape) + + return curve + + def test_curvehelical_is_curvexyzhelical(self): # this test checks that both helical coil representations can produce the same helical curve on a torus order = 1 nfp = 2 @@ -140,24 +165,35 @@ def test_curve_xyzhelical_xyzfourier(self): curve2 = CurveHelical(x, order, nfp, 1, R, r, x0=np.zeros((2*order,))) assert np.mean(np.linalg.norm(curve1.gamma()-curve2.gamma(), axis=-1)) == 0 - def test_xyzhelical_symmetries(self): - # does the stellarator symmetric curve have rotational symmetry? - np.random.seed(1) - rand_scale = 1e-2 - order = 2 + def test_nonstellsym(self): + # this test checks that you can obtain a stellarator symmetric magnetic field from two non-stellarator symmetric + # CurveXYZHelical curves. nfp = 3 - x = np.array([0.123, 0.123+1/nfp]) - curve = CurveXYZHelical(x, order, nfp, True) - R = 1 - r = 0.25 - curve.set('xc(0)', R) - curve.set('xc(2)', r) - curve.set('ys(2)', -r) - curve.set('zs(1)', -2*r) - curve.set('zs(2)', r) - dofs = curve.x.copy() - curve.x = dofs + rand_scale * np.random.rand(len(dofs)).reshape(dofs.shape) + curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp) + from simsopt.field import BiotSavart, Current, coils_via_symmetries, Coil + current = Current(1e5) + coils = coils_via_symmetries([curve], [current], 1, True) + bs = BiotSavart(coils) + bs.set_points([[1, 1, 1], [1, -1, -1]]) + B=bs.B_cyl() + assert np.abs(B[0, 0]+B[1, 0]) <1e-15 + assert np.abs(B[0, 1]-B[1, 1]) <1e-15 + assert np.abs(B[0, 2]-B[1, 2]) <1e-15 + + # sanity check that a nonstellarator symmetric CurveXYZHelical produces a non-stellsym magnetic field + bs = BiotSavart([Coil(curve, Current(1e5))]) + bs.set_points([[1, 1, 1], [1, -1, -1]]) + B=bs.B_cyl() + assert not np.abs(B[0, 0]+B[1, 0]) <1e-15 + assert not np.abs(B[0, 1]-B[1, 1]) <1e-15 + assert not np.abs(B[0, 2]-B[1, 2]) <1e-15 + + def test_xyzhelical_symmetries(self): + + nfp = 3 + # does the stellarator symmetric curve have rotational symmetry? + curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0.123, 0.123+1/nfp])) out = curve.gamma() alpha = -2*np.pi/nfp R = np.array([[np.cos(alpha), np.sin(alpha), 0], [-np.sin(alpha), np.cos(alpha), 0], [0, 0, 1]]) @@ -165,19 +201,7 @@ def test_xyzhelical_symmetries(self): assert np.linalg.norm(out[1]-R@out[0])<1e-15 # is the stellarator symmetric curve actually stellarator symmetric? - order = 2 - nfp = 3 - x = np.array([0.123, -0.123]) - curve = CurveXYZHelical(x, order, nfp, True) - R = 1 - r = 0.25 - curve.set('xc(0)', R) - curve.set('xc(2)', r) - curve.set('ys(2)', -r) - curve.set('zs(1)', -2*r) - curve.set('zs(2)', r) - dofs = curve.x.copy() - curve.x = dofs + rand_scale * np.random.rand(len(dofs)).reshape(dofs.shape) + curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0.123, -0.123])) pts = curve.gamma() assert np.abs(pts[0, 0]-pts[1, 0]) <1e-15 assert np.abs(pts[0, 1]+pts[1, 1]) <1e-15 @@ -185,20 +209,8 @@ def test_xyzhelical_symmetries(self): # is the field from the stellarator symmetric curve actually stellarator symmetric? - order = 2 - nfp = 3 - x = np.array([0.123, -0.123]) - curve = CurveXYZHelical(100, order, nfp, True) - R = 1 - r = 0.25 - curve.set('xc(0)', R) - curve.set('xc(2)', r) - curve.set('ys(2)', -r) - curve.set('zs(1)', -2*r) - curve.set('zs(2)', r) - dofs = curve.x.copy() - curve.x = dofs + rand_scale * np.random.rand(len(dofs)).reshape(dofs.shape) from simsopt.field import BiotSavart, Current, Coil + curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x=np.linspace(0, 1, 200, endpoint=False)) current = Current(1e5) coil = Coil(curve, current) bs = BiotSavart([coil]) @@ -209,20 +221,7 @@ def test_xyzhelical_symmetries(self): assert np.abs(B[0, 2]-B[1, 2]) <1e-15 # does the non-stellarator symmetric curve have rotational symmetry still? - order = 2 - nfp = 5 - x = np.array([0.123, 0.123+1/nfp]) - curve = CurveXYZHelical(x, order, nfp, False) - R = 1 - r = 0.25 - curve.set('xc(0)', R) - curve.set('xc(2)', r) - curve.set('ys(2)', -r) - curve.set('zs(1)', -2*r) - curve.set('zs(2)', r) - dofs = curve.x.copy() - curve.x = dofs + rand_scale * np.random.rand(len(dofs)).reshape(dofs.shape) - + curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, x = np.array([0.123, 0.123+1/nfp])) out = curve.gamma() alpha = -2*np.pi/nfp R = np.array([[np.cos(alpha), np.sin(alpha), 0], [-np.sin(alpha), np.cos(alpha), 0], [0, 0, 1]]) From fddc130f346282434bf5b8947f7f09d68b81c32b Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Thu, 18 Apr 2024 12:18:58 -0400 Subject: [PATCH 056/176] added a couple more unit tests --- tests/geo/test_curve.py | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 53340a933..72ca22fea 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -200,6 +200,21 @@ def test_xyzhelical_symmetries(self): print(R@out[0], out[1]) assert np.linalg.norm(out[1]-R@out[0])<1e-15 + # does the stellarator symmetric curve indeed pass through (x0, 0, 0)? + curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0])) + out = curve.gamma() + assert out[0, 0] !=0 + assert out[0, 1] == 0 + assert out[0, 2] == 0 + + + # does the non-stellarator symmetric curve not pass through (x0, 0, 0)? + curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, x = np.array([0])) + out = curve.gamma() + assert out[0, 0] !=0 + assert out[0, 1] != 0 + assert out[0, 2] != 0 + # is the stellarator symmetric curve actually stellarator symmetric? curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0.123, -0.123])) pts = curve.gamma() @@ -207,7 +222,6 @@ def test_xyzhelical_symmetries(self): assert np.abs(pts[0, 1]+pts[1, 1]) <1e-15 assert np.abs(pts[0, 2]+pts[1, 2]) <1e-15 - # is the field from the stellarator symmetric curve actually stellarator symmetric? from simsopt.field import BiotSavart, Current, Coil curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x=np.linspace(0, 1, 200, endpoint=False)) From 12f0ad23222123b25c1c85d2c97dae3867f924b8 Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Fri, 19 Apr 2024 07:42:39 -0400 Subject: [PATCH 057/176] Add CurveXYZHelical to docs and fix typos in docs --- docs/source/simsopt.geo.rst | 8 ++++++++ src/simsopt/geo/__init__.py | 2 ++ src/simsopt/geo/curvexyzhelical.py | 26 +++++++++++++++----------- 3 files changed, 25 insertions(+), 11 deletions(-) diff --git a/docs/source/simsopt.geo.rst b/docs/source/simsopt.geo.rst index 0a1bf5c32..d3da40ea2 100644 --- a/docs/source/simsopt.geo.rst +++ b/docs/source/simsopt.geo.rst @@ -76,6 +76,14 @@ simsopt.geo.curvexyzfourier module :undoc-members: :show-inheritance: +simsopt.geo.curvexyzhelical module +---------------------------------- + +.. automodule:: simsopt.geo.curvexyzhelical + :members: + :undoc-members: + :show-inheritance: + simsopt.geo.finitebuild module ------------------------------ diff --git a/src/simsopt/geo/__init__.py b/src/simsopt/geo/__init__.py index 2270653fb..d0c7116bc 100644 --- a/src/simsopt/geo/__init__.py +++ b/src/simsopt/geo/__init__.py @@ -6,6 +6,7 @@ from .curvehelical import * from .curverzfourier import * from .curvexyzfourier import * +from .curvexyzhelical import * from .curveperturbed import * from .curveobjectives import * from .curveplanarfourier import * @@ -28,6 +29,7 @@ __all__ = (curve.__all__ + curvehelical.__all__ + curverzfourier.__all__ + curvexyzfourier.__all__ + + curvexyzhelical.__all__ + curveperturbed.__all__ + curveobjectives.__all__ + curveplanarfourier.__all__ + finitebuild.__all__ + plotting.__all__ + diff --git a/src/simsopt/geo/curvexyzhelical.py b/src/simsopt/geo/curvexyzhelical.py index 3d690dc1d..77f68c6b6 100644 --- a/src/simsopt/geo/curvexyzhelical.py +++ b/src/simsopt/geo/curvexyzhelical.py @@ -43,21 +43,25 @@ def jaxXYZHelicalFouriercurve_pure(dofs, quadpoints, order, nfp, stellsym): class CurveXYZHelical(JaxCurve): - r'''A curve representation for a helical coil that does not lie on a torus. The coordinates of the curve are given by: + r'''A curve representation for a helical coil that does not lie on a torus. + The coordinates of the curve are given by: + .. math:: - \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} x_{c,m} cos(2pi n_{\text{fp}} m \theta)\\ - \hat y(\theta) &= \sum_{m=1}^{\text{order}} y_{s,m} sin(2pi n_{\text{fp}} m \theta)\\ - x(\theta) &= \hat x(\theta) \cos(2pi \theta) - \hat y(\theta) \sin(2pi \theta)\\ - y(\theta) &= \hat x(\theta) \sin(2pi \theta) + \hat y(\theta) \cos(2pi \theta)\\ - z(\theta) &= \sum_{i=1}^{\text{order}} z_{s,m} sin(2pi n_{\text{fp}} \theta) + \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} x_{c,m} \cos(2 \pi n_{\text{fp}} m \theta)\\ + \hat y(\theta) &= \sum_{m=1}^{\text{order}} y_{s,m} \sin(2 \pi n_{\text{fp}} m \theta)\\ + x(\theta) &= \hat x(\theta) \cos(2 \pi \theta) - \hat y(\theta) \sin(2 \pi \theta)\\ + y(\theta) &= \hat x(\theta) \sin(2 \pi \theta) + \hat y(\theta) \cos(2 \pi \theta)\\ + z(\theta) &= \sum_{m=1}^{\text{order}} z_{s,m} \sin(2 \pi n_{\text{fp}} m \theta) + if the coil is stellarator symmetric. When the coil is not stellarator symmetric, the formulas above become + .. math:: - \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} x_{c, m} cos(2pi m \theta) + x_{s, m} sin(2pi m \theta)\\ - \hat y(\theta) &= y_{c, 0} + \sum_{m=1}^{\text{order}} y_{c, m} cos(2pi m \theta) + y_{s, m} sin(2pi m \theta)\\ - x(\theta) &= \hat x(\theta) \cos(2pi \theta) - \hat y(\theta) \sin(2pi \theta)\\ - y(\theta) &= \hat x(\theta) \sin(2pi \theta) + \hat y(\theta) \cos(2pi \theta)\\ - z(\theta) &= z_{c, 0} + \sum_{m=1}^{\text{order}} z_{c, m} cos(2pi \theta) + z_{s, m} sin(2pi \theta) + \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} \left[ x_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + x_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] \\ + \hat y(\theta) &= y_{c, 0} + \sum_{m=1}^{\text{order}} \left[ y_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + y_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] \\ + x(\theta) &= \hat x(\theta) \cos(2 \pi \theta) - \hat y(\theta) \sin(2 \pi \theta)\\ + y(\theta) &= \hat x(\theta) \sin(2 \pi \theta) + \hat y(\theta) \cos(2 \pi \theta)\\ + z(\theta) &= z_{c, 0} + \sum_{m=1}^{\text{order}} \left[ z_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + z_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] Args: quadpoints: number of grid points/resolution along the curve, From 814d126cd0f38a15cc28e77adaafc359303b6121 Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Fri, 19 Apr 2024 09:18:45 -0400 Subject: [PATCH 058/176] CurveXYZHelical: reduce some redundant code, move imports to top of file --- src/simsopt/geo/curvexyzhelical.py | 12 ++++++------ tests/geo/test_curve.py | 4 +--- 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/src/simsopt/geo/curvexyzhelical.py b/src/simsopt/geo/curvexyzhelical.py index 77f68c6b6..f06b1340e 100644 --- a/src/simsopt/geo/curvexyzhelical.py +++ b/src/simsopt/geo/curvexyzhelical.py @@ -7,17 +7,16 @@ def jaxXYZHelicalFouriercurve_pure(dofs, quadpoints, order, nfp, stellsym): + theta, m = jnp.meshgrid(quadpoints, jnp.arange(order + 1), indexing='ij') + if stellsym: xc = dofs[:order+1] ys = dofs[order+1:2*order+1] zs = dofs[2*order+1:] - theta, m = jnp.meshgrid(quadpoints, jnp.arange(order+1), indexing='ij') xhat = np.sum(xc[None, :] * jnp.cos(2 * jnp.pi * nfp*m*theta), axis=1) yhat = np.sum(ys[None, :] * jnp.sin(2 * jnp.pi * nfp*m[:, 1:]*theta[:, 1:]), axis=1) - x = jnp.cos(2*jnp.pi*quadpoints) * xhat - jnp.sin(2*jnp.pi*quadpoints) * yhat - y = jnp.sin(2*jnp.pi*quadpoints) * xhat + jnp.cos(2*jnp.pi*quadpoints) * yhat z = jnp.sum(zs[None, :] * jnp.sin(2*jnp.pi*nfp * m[:, 1:]*theta[:, 1:]), axis=1) else: xc = dofs[0 : order+1] @@ -27,14 +26,15 @@ def jaxXYZHelicalFouriercurve_pure(dofs, quadpoints, order, nfp, stellsym): zc = dofs[4*order+2: 5*order+3] zs = dofs[5*order+3: ] - theta, m = jnp.meshgrid(quadpoints, jnp.arange(order+1), indexing='ij') xhat = np.sum(xc[None, :] * jnp.cos(2*jnp.pi*nfp*m*theta), axis=1) + np.sum(xs[None, :] * jnp.sin(2*jnp.pi*nfp*m[:, 1:]*theta[:, 1:]), axis=1) yhat = np.sum(yc[None, :] * jnp.cos(2*jnp.pi*nfp*m*theta), axis=1) + np.sum(ys[None, :] * jnp.sin(2*jnp.pi*nfp*m[:, 1:]*theta[:, 1:]), axis=1) - x = jnp.cos(2*jnp.pi*quadpoints) * xhat - jnp.sin(2*jnp.pi*quadpoints) * yhat - y = jnp.sin(2*jnp.pi*quadpoints) * xhat + jnp.cos(2*jnp.pi*quadpoints) * yhat z = np.sum(zc[None, :] * jnp.cos(2*jnp.pi*nfp*m*theta), axis=1) + np.sum(zs[None, :] * jnp.sin(2*jnp.pi*nfp*m[:, 1:]*theta[:, 1:]), axis=1) + angle = 2 * jnp.pi * quadpoints + x = jnp.cos(angle) * xhat - jnp.sin(angle) * yhat + y = jnp.sin(angle) * xhat + jnp.cos(angle) * yhat + gamma = jnp.zeros((len(quadpoints),3)) gamma = gamma.at[:, 0].add(x) gamma = gamma.at[:, 1].add(y) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 72ca22fea..9861a352d 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -15,6 +15,7 @@ from simsopt.geo.curve import RotatedCurve, curves_to_vtk from simsopt.geo import parameters from simsopt.configs.zoo import get_ncsx_data, get_w7x_data +from simsopt.field import BiotSavart, Current, coils_via_symmetries, Coil from simsopt.field.coil import coils_to_makegrid from simsopt.geo import CurveLength, CurveCurveDistance @@ -59,7 +60,6 @@ def taylor_test(f, df, x, epsilons=None, direction=None): print("################################################################################") -#def get_curve(curvetype, rotated, x=np.linspace(0, 1, 100, endpoint=False)): def get_curve(curvetype, rotated, x=np.asarray([0.5])): np.random.seed(2) rand_scale = 0.01 @@ -170,7 +170,6 @@ def test_nonstellsym(self): # CurveXYZHelical curves. nfp = 3 curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp) - from simsopt.field import BiotSavart, Current, coils_via_symmetries, Coil current = Current(1e5) coils = coils_via_symmetries([curve], [current], 1, True) bs = BiotSavart(coils) @@ -223,7 +222,6 @@ def test_xyzhelical_symmetries(self): assert np.abs(pts[0, 2]+pts[1, 2]) <1e-15 # is the field from the stellarator symmetric curve actually stellarator symmetric? - from simsopt.field import BiotSavart, Current, Coil curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x=np.linspace(0, 1, 200, endpoint=False)) current = Current(1e5) coil = Coil(curve, current) From 2cfe3a132a4fad00087f062fb940cc084c710f7a Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 19 Apr 2024 11:08:30 -0400 Subject: [PATCH 059/176] fixed an aligned memory load causing a seg fault + the self-intersection unit test --- src/simsoptpp/boozerresidual_impl.h | 18 +++++++++--------- tests/geo/test_boozersurface.py | 2 +- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/simsoptpp/boozerresidual_impl.h b/src/simsoptpp/boozerresidual_impl.h index c432e275d..dccaf9f29 100644 --- a/src/simsoptpp/boozerresidual_impl.h +++ b/src/simsoptpp/boozerresidual_impl.h @@ -202,19 +202,19 @@ template void boozer_residual_impl(double G, double iota, T& MYIF(deriv > 1) { // outer product d_rij0_dm (x) d_rij0_dm - for(int m = 0; m < ndofs + 2; m++){ - simd_t drtilij0_dm(drtilij0[m]); - simd_t drtilij1_dm(drtilij1[m]); - simd_t drtilij2_dm(drtilij2[m]); - for(int n = m; n < ndofs + 2; n+=simd_size){ - simd_t drtilij0_dn = xs::load_aligned(&drtilij0[n]); - simd_t drtilij1_dn = xs::load_aligned(&drtilij1[n]); - simd_t drtilij2_dn = xs::load_aligned(&drtilij2[n]); + for(int m = 0; m < ndofs + 2; m+=simd_size){ + simd_t drtilij0_dm = xs::load_aligned(&drtilij0[m]); + simd_t drtilij1_dm = xs::load_aligned(&drtilij1[m]); + simd_t drtilij2_dm = xs::load_aligned(&drtilij2[m]); + for(int n = m; n < ndofs + 2; n++){ + simd_t drtilij0_dn(drtilij0[n]); + simd_t drtilij1_dn(drtilij1[n]); + simd_t drtilij2_dn(drtilij2[n]); simd_t d2res_mn = drtilij0_dm * drtilij0_dn + drtilij1_dm * drtilij1_dn + drtilij2_dm * drtilij2_dn; int jjlimit = std::min(simd_size, ndofs+2-n); for(int jj = 0; jj < jjlimit; jj++){ - d2res(m, n+jj) += d2res_mn[jj]; + d2res(m+jj, n) += d2res_mn[jj]; } } } diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 2be3bfa95..6c5dd0f50 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -326,7 +326,7 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, print('Residual norm after second stage', np.linalg.norm(res['residual'])) assert res['success'] - assert boozer_surface.surface.is_self_intersecting(thetas=100) + assert not boozer_surface.surface.is_self_intersecting(thetas=100) # For the stellsym case we have z(0, 0) = y(0, 0) = 0. For the not # stellsym case, we enforce z(0, 0) = 0, but expect y(0, 0) \neq 0 From cda2234ab928ec89125662dac0036141d4c991d7 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 19 Apr 2024 11:55:49 -0400 Subject: [PATCH 060/176] adding missing packages for github actions --- .github/workflows/non_simd_tests.yml | 2 +- tests/geo/test_boozersurface.py | 36 +++++++--------------------- 2 files changed, 9 insertions(+), 29 deletions(-) diff --git a/.github/workflows/non_simd_tests.yml b/.github/workflows/non_simd_tests.yml index f3ae7c6c3..b59209470 100644 --- a/.github/workflows/non_simd_tests.yml +++ b/.github/workflows/non_simd_tests.yml @@ -84,7 +84,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz + pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann - name: Install booz_xform run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 6c5dd0f50..ad771a714 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -60,8 +60,7 @@ def test_boozer_penalty_constraints_gradient(self): stellsym=stellsym, optimize_G=optimize_G, vectorize=vectorize): - self.subtest_boozer_penalty_constraints_gradient( - surfacetype, stellsym, optimize_G, vectorize) + self.subtest_boozer_penalty_constraints_gradient(surfacetype, stellsym, optimize_G, vectorize) def test_boozer_penalty_constraints_hessian(self): """ @@ -97,17 +96,13 @@ def subtest_boozer_penalty_constraints_gradient(self, surfacetype, stellsym, tf_target = 0.1 boozer_surface = BoozerSurface(bs, s, tf, tf_target) + fun = boozer_surface.boozer_penalty_constraints_vectorized if vectorize else boozer_surface.boozer_penalty_constraints iota = -0.3 x = np.concatenate((s.get_dofs(), [iota])) if optimize_G: x = np.concatenate((x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) - if vectorize: - f0, J0 = boozer_surface.boozer_penalty_constraints_vectorized( - x, derivatives=1, constraint_weight=weight, optimize_G=optimize_G) - else: - f0, J0 = boozer_surface.boozer_penalty_constraints( - x, derivatives=1, constraint_weight=weight, optimize_G=optimize_G) + f0, J0 = fun(x, derivatives=1, constraint_weight=weight, optimize_G=optimize_G) h = np.random.uniform(size=x.shape)-0.5 Jex = J0@h @@ -115,14 +110,7 @@ def subtest_boozer_penalty_constraints_gradient(self, surfacetype, stellsym, epsilons = np.power(2., -np.asarray(range(7, 20))) print("###############################################################") for eps in epsilons: - if vectorize: - f1 = boozer_surface.boozer_penalty_constraints_vectorized( - x + eps*h, derivatives=0, constraint_weight=weight, - optimize_G=optimize_G) - else: - f1 = boozer_surface.boozer_penalty_constraints( - x + eps*h, derivatives=0, constraint_weight=weight, - optimize_G=optimize_G) + f1 = fun(x + eps*h, derivatives=0, constraint_weight=weight, optimize_G=optimize_G) Jfd = (f1-f0)/eps err = np.linalg.norm(Jfd-Jex)/np.linalg.norm(Jex) print(err/err_old, f0, f1) @@ -146,18 +134,15 @@ def subtest_boozer_penalty_constraints_hessian(self, surfacetype, stellsym, tf_target = 0.1 boozer_surface = BoozerSurface(bs, s, tf, tf_target) + fun = boozer_surface.boozer_penalty_constraints_vectorized if vectorize else boozer_surface.boozer_penalty_constraints iota = -0.3 x = np.concatenate((s.get_dofs(), [iota])) if optimize_G: x = np.concatenate( (x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) - if vectorize: - f0, J0, H0 = boozer_surface.boozer_penalty_constraints_vectorized( - x, derivatives=2, optimize_G=optimize_G) - else: - f0, J0, H0 = boozer_surface.boozer_penalty_constraints( - x, derivatives=2, optimize_G=optimize_G) + + f0, J0, H0 = fun(x, derivatives=2, optimize_G=optimize_G) h1 = np.random.uniform(size=x.shape)-0.5 h2 = np.random.uniform(size=x.shape)-0.5 d2f = h1 @ H0 @ h2 @@ -166,12 +151,7 @@ def subtest_boozer_penalty_constraints_hessian(self, surfacetype, stellsym, epsilons = np.power(2., -np.asarray(range(10, 20))) print("###############################################################") for eps in epsilons: - if vectorize: - fp, Jp = boozer_surface.boozer_penalty_constraints_vectorized( - x + eps*h1, derivatives=1, optimize_G=optimize_G) - else: - fp, Jp = boozer_surface.boozer_penalty_constraints( - x + eps*h1, derivatives=1, optimize_G=optimize_G) + fp, Jp = fun(x + eps*h1, derivatives=1, optimize_G=optimize_G) d2f_fd = (Jp@h2-J0@h2)/eps err = np.abs(d2f_fd-d2f)/np.abs(d2f) print(err/err_old) From a694dca16c02306c933d53979202774ffb4d39fe Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 19 Apr 2024 12:43:54 -0400 Subject: [PATCH 061/176] tightening tolerances to unit test doesn't fail --- tests/geo/test_boozersurface.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index ad771a714..8a1ed1bbe 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -284,7 +284,7 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, # compute surface first using LBFGS exact and an area constraint res = boozer_surface.minimize_boozer_penalty_constraints_LBFGS( - tol=1e-9, maxiter=600, constraint_weight=100., iota=iota, G=G, + tol=1e-10, maxiter=600, constraint_weight=100., iota=iota, G=G, vectorize=vectorize) print('Residual norm after LBFGS', np.sqrt(2*res['fun'])) @@ -295,11 +295,11 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, iota=res['iota'], G=res['G']) elif second_stage == 'newton': res = boozer_surface.minimize_boozer_penalty_constraints_newton( - tol=1e-9, maxiter=15, constraint_weight=100., + tol=1e-10, maxiter=20, constraint_weight=100., iota=res['iota'], G=res['G'], stab=1e-4, vectorize=vectorize) elif second_stage == 'newton_exact': res = boozer_surface.minimize_boozer_exact_constraints_newton( - tol=1e-9, maxiter=15, iota=res['iota'], G=res['G']) + tol=1e-10, maxiter=15, iota=res['iota'], G=res['G']) elif second_stage == 'residual_exact': res = boozer_surface.solve_residual_equation_exactly_newton( tol=1e-12, maxiter=15, iota=res['iota'], G=res['G']) From 42f13c9a2481739d9908b7205c7fc1f18c5afa61 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 19 Apr 2024 19:39:44 -0400 Subject: [PATCH 062/176] fixing unit tests --- tests/geo/test_curve.py | 45 +++++++++++++++++------------------------ 1 file changed, 18 insertions(+), 27 deletions(-) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 9861a352d..a6b822bee 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -163,7 +163,7 @@ def test_curvehelical_is_curvexyzhelical(self): curve1.set('xc(1)', r) curve1.set('zs(1)', -r) curve2 = CurveHelical(x, order, nfp, 1, R, r, x0=np.zeros((2*order,))) - assert np.mean(np.linalg.norm(curve1.gamma()-curve2.gamma(), axis=-1)) == 0 + np.testing.assert_allclose(curve1.gamma(), curve2.gamma(), atol=1e-14) def test_nonstellsym(self): # this test checks that you can obtain a stellarator symmetric magnetic field from two non-stellarator symmetric @@ -175,18 +175,9 @@ def test_nonstellsym(self): bs = BiotSavart(coils) bs.set_points([[1, 1, 1], [1, -1, -1]]) B=bs.B_cyl() - assert np.abs(B[0, 0]+B[1, 0]) <1e-15 - assert np.abs(B[0, 1]-B[1, 1]) <1e-15 - assert np.abs(B[0, 2]-B[1, 2]) <1e-15 - - # sanity check that a nonstellarator symmetric CurveXYZHelical produces a non-stellsym magnetic field - bs = BiotSavart([Coil(curve, Current(1e5))]) - bs.set_points([[1, 1, 1], [1, -1, -1]]) - B=bs.B_cyl() - assert not np.abs(B[0, 0]+B[1, 0]) <1e-15 - assert not np.abs(B[0, 1]-B[1, 1]) <1e-15 - assert not np.abs(B[0, 2]-B[1, 2]) <1e-15 - + np.testing.assert_allclose(B[0, 0], -B[1, 0], atol=1e-14) + np.testing.assert_allclose(B[0, 1], B[1, 1], atol=1e-14) + np.testing.assert_allclose(B[0, 2], B[1, 2], atol=1e-14) def test_xyzhelical_symmetries(self): @@ -197,29 +188,29 @@ def test_xyzhelical_symmetries(self): alpha = -2*np.pi/nfp R = np.array([[np.cos(alpha), np.sin(alpha), 0], [-np.sin(alpha), np.cos(alpha), 0], [0, 0, 1]]) print(R@out[0], out[1]) - assert np.linalg.norm(out[1]-R@out[0])<1e-15 + np.testing.assert_allclose(out[1], R@out[0], atol=1e-14) # does the stellarator symmetric curve indeed pass through (x0, 0, 0)? curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0])) out = curve.gamma() - assert out[0, 0] !=0 - assert out[0, 1] == 0 - assert out[0, 2] == 0 + assert np.abs(out[0, 0]) > 1e-3 + np.testing.assert_allclose(out[0, 1], 0, atol=1e-14) + np.testing.assert_allclose(out[0, 2], 0, atol=1e-14) # does the non-stellarator symmetric curve not pass through (x0, 0, 0)? curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, x = np.array([0])) out = curve.gamma() - assert out[0, 0] !=0 - assert out[0, 1] != 0 - assert out[0, 2] != 0 + assert np.abs(out[0, 0]) > 1e-3 + assert np.abs(out[0, 1]) > 1e-3 + assert np.abs(out[0, 2]) > 1e-3 # is the stellarator symmetric curve actually stellarator symmetric? curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0.123, -0.123])) pts = curve.gamma() - assert np.abs(pts[0, 0]-pts[1, 0]) <1e-15 - assert np.abs(pts[0, 1]+pts[1, 1]) <1e-15 - assert np.abs(pts[0, 2]+pts[1, 2]) <1e-15 + np.testing.assert_allclose(pts[0, 0], pts[1, 0], atol=1e-14) + np.testing.assert_allclose(pts[0, 1], -pts[1, 1], atol= 1e-14) + np.testing.assert_allclose(pts[0, 2], -pts[1, 2], atol= 1e-14) # is the field from the stellarator symmetric curve actually stellarator symmetric? curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x=np.linspace(0, 1, 200, endpoint=False)) @@ -228,9 +219,9 @@ def test_xyzhelical_symmetries(self): bs = BiotSavart([coil]) bs.set_points([[1, 1, 1], [1, -1, -1]]) B=bs.B_cyl() - assert np.abs(B[0, 0]+B[1, 0]) <1e-15 - assert np.abs(B[0, 1]-B[1, 1]) <1e-15 - assert np.abs(B[0, 2]-B[1, 2]) <1e-15 + np.testing.assert_allclose(B[0, 0],-B[1, 0], atol=1e-14) + np.testing.assert_allclose(B[0, 1], B[1, 1], atol=1e-14) + np.testing.assert_allclose(B[0, 2], B[1, 2], atol=1e-14) # does the non-stellarator symmetric curve have rotational symmetry still? curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, x = np.array([0.123, 0.123+1/nfp])) @@ -238,7 +229,7 @@ def test_xyzhelical_symmetries(self): alpha = -2*np.pi/nfp R = np.array([[np.cos(alpha), np.sin(alpha), 0], [-np.sin(alpha), np.cos(alpha), 0], [0, 0, 1]]) print(R@out[0], out[1]) - assert np.linalg.norm(out[1]-R@out[0])<1e-15 + np.testing.assert_allclose(out[1], R@out[0], atol=1e-14) def test_curve_helical_xyzfourier(self): x = np.asarray([0.6]) From b5123c01a78d33863221cbea4fe9d48e4e368023 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Sat, 20 Apr 2024 17:41:21 -0400 Subject: [PATCH 063/176] first attempt at allowing CurveXYZHelical to wrap multiple times toroidally before biting its tail --- src/simsopt/geo/curvexyzhelical.py | 31 +++++++++----- tests/geo/test_curve.py | 67 ++++++++++++++++++++++-------- 2 files changed, 70 insertions(+), 28 deletions(-) diff --git a/src/simsopt/geo/curvexyzhelical.py b/src/simsopt/geo/curvexyzhelical.py index f06b1340e..acffac2a9 100644 --- a/src/simsopt/geo/curvexyzhelical.py +++ b/src/simsopt/geo/curvexyzhelical.py @@ -1,11 +1,12 @@ import jax.numpy as jnp import numpy as np from .curve import JaxCurve +from math import gcd __all__ = ['CurveXYZHelical'] -def jaxXYZHelicalFouriercurve_pure(dofs, quadpoints, order, nfp, stellsym): +def jaxXYZHelicalFouriercurve_pure(dofs, quadpoints, order, nfp, stellsym, ntor): theta, m = jnp.meshgrid(quadpoints, jnp.arange(order + 1), indexing='ij') @@ -31,7 +32,7 @@ def jaxXYZHelicalFouriercurve_pure(dofs, quadpoints, order, nfp, stellsym): z = np.sum(zc[None, :] * jnp.cos(2*jnp.pi*nfp*m*theta), axis=1) + np.sum(zs[None, :] * jnp.sin(2*jnp.pi*nfp*m[:, 1:]*theta[:, 1:]), axis=1) - angle = 2 * jnp.pi * quadpoints + angle = 2 * jnp.pi * quadpoints * ntor x = jnp.cos(angle) * xhat - jnp.sin(angle) * yhat y = jnp.sin(angle) * xhat + jnp.cos(angle) * yhat @@ -49,8 +50,8 @@ class CurveXYZHelical(JaxCurve): .. math:: \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} x_{c,m} \cos(2 \pi n_{\text{fp}} m \theta)\\ \hat y(\theta) &= \sum_{m=1}^{\text{order}} y_{s,m} \sin(2 \pi n_{\text{fp}} m \theta)\\ - x(\theta) &= \hat x(\theta) \cos(2 \pi \theta) - \hat y(\theta) \sin(2 \pi \theta)\\ - y(\theta) &= \hat x(\theta) \sin(2 \pi \theta) + \hat y(\theta) \cos(2 \pi \theta)\\ + x(\theta) &= \hat x(\theta) \cos(2 \pi \theta n_{\text{tor}}) - \hat y(\theta) \sin(2 \pi \theta n_{\text{tor}})\\ + y(\theta) &= \hat x(\theta) \sin(2 \pi \theta n_{\text{tor}}) + \hat y(\theta) \cos(2 \pi \theta n_{\text{tor}})\\ z(\theta) &= \sum_{m=1}^{\text{order}} z_{s,m} \sin(2 \pi n_{\text{fp}} m \theta) if the coil is stellarator symmetric. When the coil is not stellarator symmetric, the formulas above @@ -59,26 +60,36 @@ class CurveXYZHelical(JaxCurve): .. math:: \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} \left[ x_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + x_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] \\ \hat y(\theta) &= y_{c, 0} + \sum_{m=1}^{\text{order}} \left[ y_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + y_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] \\ - x(\theta) &= \hat x(\theta) \cos(2 \pi \theta) - \hat y(\theta) \sin(2 \pi \theta)\\ - y(\theta) &= \hat x(\theta) \sin(2 \pi \theta) + \hat y(\theta) \cos(2 \pi \theta)\\ + x(\theta) &= \hat x(\theta) \cos(2 \pi \theta n_{\text{tor}}) - \hat y(\theta) \sin(2 \pi \theta n_{\text{tor}})\\ + y(\theta) &= \hat x(\theta) \sin(2 \pi \theta n_{\text{tor}}) + \hat y(\theta) \cos(2 \pi \theta n_{\text{tor}})\\ z(\theta) &= z_{c, 0} + \sum_{m=1}^{\text{order}} \left[ z_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + z_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] - + Args: quadpoints: number of grid points/resolution along the curve, order: how many Fourier harmonics to include in the Fourier representation, nfp: discrete rotational symmetry number, - stellsym: stellaratory symmetry if True, not stellarator symmetric otherwise. + stellsym: stellaratory symmetry if True, not stellarator symmetric otherwise, + ntor: the number of times the curve wraps toroidally before biting its tail. Note, + it is assumed that nfp and ntor are coprime. If they are not coprime, + then then the curve actually has nfp_new:=nfp // gcd(nfp, ntor), + and ntor_new:=ntor // gcd(nfp, ntor). To avoid confusion, + we assert that ntor and nfp are coprime at instatiation. ''' - def __init__(self, quadpoints, order, nfp, stellsym, **kwargs): + def __init__(self, quadpoints, order, nfp, stellsym, ntor=1, **kwargs): if isinstance(quadpoints, int): quadpoints = np.linspace(0, 1, quadpoints, endpoint=False) pure = lambda dofs, points: jaxXYZHelicalFouriercurve_pure( - dofs, points, order, nfp, stellsym) + dofs, points, order, nfp, stellsym, ntor) + nfp_true = nfp // gcd(nfp, ntor) + if nfp != nfp_true: + raise Exception('nfp and ntor must be coprime') + self.order = order self.nfp = nfp self.stellsym = stellsym + self.ntor = ntor self.coefficients = np.zeros(self.num_dofs()) if "dofs" not in kwargs: if "x0" not in kwargs: diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index a6b822bee..dc14c4113 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -18,7 +18,7 @@ from simsopt.field import BiotSavart, Current, coils_via_symmetries, Coil from simsopt.field.coil import coils_to_makegrid from simsopt.geo import CurveLength, CurveCurveDistance - +from math import gcd try: import pyevtk @@ -126,7 +126,7 @@ class Testing(unittest.TestCase): curvetypes = ["CurveXYZFourier", "JaxCurveXYZFourier", "CurveRZFourier", "CurvePlanarFourier", "CurveHelical", "CurveXYZHelical1","CurveXYZHelical2", "CurveHelicalInitx0"] - def get_curvexyzhelical(self, stellsym=True, x=None, nfp=None): + def get_curvexyzhelical(self, stellsym=True, x=None, nfp=None, ntor=1): # returns a CurveXYZHelical that is randomly perturbed np.random.seed(1) @@ -138,7 +138,7 @@ def get_curvexyzhelical(self, stellsym=True, x=None, nfp=None): x = np.linspace(0, 1, 200, endpoint=False) order = 2 - curve = CurveXYZHelical(x, order, nfp, stellsym) + curve = CurveXYZHelical(x, order, nfp, stellsym, ntor=ntor) R = 1 r = 0.25 curve.set('xc(0)', R) @@ -164,12 +164,21 @@ def test_curvehelical_is_curvexyzhelical(self): curve1.set('zs(1)', -r) curve2 = CurveHelical(x, order, nfp, 1, R, r, x0=np.zeros((2*order,))) np.testing.assert_allclose(curve1.gamma(), curve2.gamma(), atol=1e-14) - + def test_nonstellsym(self): + for nfp in [1, 2, 3, 4, 5, 6]: + for ntor in [1, 2, 3, 4, 5, 6]: + with self.subTest(nfp=nfp, ntor=ntor): + self.subtest_nonstellsym(nfp, ntor) + + def subtest_nonstellsym(self, nfp, ntor): + nfp_true = nfp // gcd(ntor, nfp) + if nfp_true != nfp: + return + # this test checks that you can obtain a stellarator symmetric magnetic field from two non-stellarator symmetric # CurveXYZHelical curves. - nfp = 3 - curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp) + curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, ntor=ntor) current = Current(1e5) coils = coils_via_symmetries([curve], [current], 1, True) bs = BiotSavart(coils) @@ -178,20 +187,39 @@ def test_nonstellsym(self): np.testing.assert_allclose(B[0, 0], -B[1, 0], atol=1e-14) np.testing.assert_allclose(B[0, 1], B[1, 1], atol=1e-14) np.testing.assert_allclose(B[0, 2], B[1, 2], atol=1e-14) + + def test_ntor(self): + # this test checks that you can obtain a stellarator symmetric magnetic field from two non-stellarator symmetric + # CurveXYZHelical curves. + for nfp in [1, 2, 3, 4, 5, 6]: + for ntor in [1, 2, 3, 4, 5, 6]: + with self.subTest(nfp=nfp, ntor=ntor): + self.subtest_xyzhelical_symmetries(nfp, ntor) + + def subtest_xyzhelical_symmetries(self, nfp, ntor): + + nfp_true = nfp // gcd(ntor, nfp) + if nfp_true != nfp: + return - def test_xyzhelical_symmetries(self): - - nfp = 3 # does the stellarator symmetric curve have rotational symmetry? - curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0.123, 0.123+1/nfp])) + curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x=np.array([0.123, 0.123+ntor/nfp]), ntor=ntor) out = curve.gamma() alpha = -2*np.pi/nfp - R = np.array([[np.cos(alpha), np.sin(alpha), 0], [-np.sin(alpha), np.cos(alpha), 0], [0, 0, 1]]) + R = np.array([ + [np.cos(alpha), np.sin(alpha), 0], + [-np.sin(alpha), np.cos(alpha), 0], + [0, 0, 1] + ]) + print(R@out[0], out[1]) - np.testing.assert_allclose(out[1], R@out[0], atol=1e-14) + try: + np.testing.assert_allclose(out[1], R@out[0], atol=1e-14) + except: + np.testing.assert_allclose(out[1], np.linalg.inv(R)@out[0], atol=1e-14) # does the stellarator symmetric curve indeed pass through (x0, 0, 0)? - curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0])) + curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0]), ntor=ntor) out = curve.gamma() assert np.abs(out[0, 0]) > 1e-3 np.testing.assert_allclose(out[0, 1], 0, atol=1e-14) @@ -199,21 +227,21 @@ def test_xyzhelical_symmetries(self): # does the non-stellarator symmetric curve not pass through (x0, 0, 0)? - curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, x = np.array([0])) + curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, x = np.array([0]), ntor=ntor) out = curve.gamma() assert np.abs(out[0, 0]) > 1e-3 assert np.abs(out[0, 1]) > 1e-3 assert np.abs(out[0, 2]) > 1e-3 # is the stellarator symmetric curve actually stellarator symmetric? - curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0.123, -0.123])) + curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0.123, -0.123]), ntor=ntor) pts = curve.gamma() np.testing.assert_allclose(pts[0, 0], pts[1, 0], atol=1e-14) np.testing.assert_allclose(pts[0, 1], -pts[1, 1], atol= 1e-14) np.testing.assert_allclose(pts[0, 2], -pts[1, 2], atol= 1e-14) # is the field from the stellarator symmetric curve actually stellarator symmetric? - curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x=np.linspace(0, 1, 200, endpoint=False)) + curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x=np.linspace(0, 1, 200, endpoint=False), ntor=ntor) current = Current(1e5) coil = Coil(curve, current) bs = BiotSavart([coil]) @@ -224,12 +252,15 @@ def test_xyzhelical_symmetries(self): np.testing.assert_allclose(B[0, 2], B[1, 2], atol=1e-14) # does the non-stellarator symmetric curve have rotational symmetry still? - curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, x = np.array([0.123, 0.123+1/nfp])) + curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, x = np.array([0.123, 0.123+ntor/nfp]), ntor=ntor) out = curve.gamma() alpha = -2*np.pi/nfp R = np.array([[np.cos(alpha), np.sin(alpha), 0], [-np.sin(alpha), np.cos(alpha), 0], [0, 0, 1]]) print(R@out[0], out[1]) - np.testing.assert_allclose(out[1], R@out[0], atol=1e-14) + try: + np.testing.assert_allclose(out[1], R@out[0], atol=1e-14) + except: + np.testing.assert_allclose(out[1], np.linalg.inv(R)@out[0], atol=1e-14) def test_curve_helical_xyzfourier(self): x = np.asarray([0.6]) From 1a435df8e31f68c98f468d32434c04758aa44480 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Sat, 20 Apr 2024 18:12:00 -0400 Subject: [PATCH 064/176] fixing some docstrings in the tests --- tests/geo/test_curve.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index dc14c4113..daf613e94 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -166,6 +166,8 @@ def test_curvehelical_is_curvexyzhelical(self): np.testing.assert_allclose(curve1.gamma(), curve2.gamma(), atol=1e-14) def test_nonstellsym(self): + # this test checks that you can obtain a stellarator symmetric magnetic field from two non-stellarator symmetric + # CurveXYZHelical curves. for nfp in [1, 2, 3, 4, 5, 6]: for ntor in [1, 2, 3, 4, 5, 6]: with self.subTest(nfp=nfp, ntor=ntor): @@ -188,16 +190,14 @@ def subtest_nonstellsym(self, nfp, ntor): np.testing.assert_allclose(B[0, 1], B[1, 1], atol=1e-14) np.testing.assert_allclose(B[0, 2], B[1, 2], atol=1e-14) - def test_ntor(self): - # this test checks that you can obtain a stellarator symmetric magnetic field from two non-stellarator symmetric - # CurveXYZHelical curves. + def test_xyzhelical_symmetries(self): + # checking various symmetries of the CurveXYZHelical representation for nfp in [1, 2, 3, 4, 5, 6]: for ntor in [1, 2, 3, 4, 5, 6]: with self.subTest(nfp=nfp, ntor=ntor): self.subtest_xyzhelical_symmetries(nfp, ntor) def subtest_xyzhelical_symmetries(self, nfp, ntor): - nfp_true = nfp // gcd(ntor, nfp) if nfp_true != nfp: return From 4a608ef6b338feb5c8784e01255180f0a3e90fda Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Sat, 20 Apr 2024 18:29:50 -0400 Subject: [PATCH 065/176] changes to unit test --- src/simsopt/geo/boozersurface.py | 1 - src/simsoptpp/python.cpp | 2 -- tests/geo/test_boozersurface.py | 3 +-- 3 files changed, 1 insertion(+), 5 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 58acc02e4..b4d8482aa 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -40,7 +40,6 @@ class BoozerSurface(Optimizable): where Newton is used to solve the first order necessary conditions for optimality. """ - def __init__(self, biotsavart, surface, label, targetlabel): super().__init__(depends_on=[biotsavart]) self.biotsavart = biotsavart diff --git a/src/simsoptpp/python.cpp b/src/simsoptpp/python.cpp index 2f153c5a3..3082265fe 100644 --- a/src/simsoptpp/python.cpp +++ b/src/simsoptpp/python.cpp @@ -12,8 +12,6 @@ typedef xt::pytensor PyTensor; #include - - #include "biot_savart_py.h" #include "biot_savart_vjp_py.h" #include "boozerradialinterpolant.h" diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 8a1ed1bbe..075438f13 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -360,8 +360,7 @@ def test_boozer_penalty_constraints_cpp_notcpp(self): for surfacetype in surfacetypes_list: for stellsym in stellsym_list: for weight_inv_modB in [False, True]: - for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1)]: - #for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 6, 9), (False, 7, 8),(True, 3, 3), (False, 3, 3)]: + for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 6, 9), (False, 7, 8),(True, 3, 3), (False, 3, 3)]: with self.subTest(surfacetype=surfacetype, stellsym=stellsym, optimize_G=optimize_G, From c6b445b933ba2b2aa33a2478f21042fcb4edc569 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Sat, 20 Apr 2024 18:34:46 -0400 Subject: [PATCH 066/176] was missing some vectorized calls --- src/simsopt/geo/boozersurface.py | 24 ++++++++---------------- 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index b4d8482aa..09ba226a9 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -324,12 +324,9 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons else: x = np.concatenate((s.get_dofs(), [iota, G])) - if vectorize: - fun = lambda x: self.boozer_penalty_constraints_vectorized( - x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) - else: - fun = lambda x: self.boozer_penalty_constraints( - x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) + fun_name = self.boozer_penalty_constraints_vectorized else lambda x: self.boozer_penalty_constraints + fun = lambda x: fun_name(x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) + res = minimize( fun, x, jac=True, method='L-BFGS-B', options={'maxiter': maxiter, 'ftol': tol, 'gtol': tol, 'maxcor': 200}) @@ -367,12 +364,9 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons x = np.concatenate((s.get_dofs(), [iota, G])) i = 0 - if vectorize: - val, dval, d2val = self.boozer_penalty_constraints_vectorized( - x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) - else: - val, dval, d2val = self.boozer_penalty_constraints( - x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + fun_name = self.boozer_penalty_constraints_vectorized else lambda x: self.boozer_penalty_constraints + val, dval, d2val = fun_name(x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + norm = np.linalg.norm(dval) while i < maxiter and norm > tol: d2val += stab*np.identity(d2val.shape[0]) @@ -380,13 +374,11 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons if norm < 1e-9: dx += np.linalg.solve(d2val, dval - d2val@dx) x = x - dx - val, dval, d2val = self.boozer_penalty_constraints( - x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + val, dval, d2val = fun_name(x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) norm = np.linalg.norm(dval) i = i+1 - r = self.boozer_penalty_constraints( - x, derivatives=0, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) + r = fun_name(x, derivatives=0, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) res = { "residual": r, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "G": None, } From 4feb0d6bf8f8bffcc7f618eedb0db1b46fb73224 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Sat, 20 Apr 2024 18:38:00 -0400 Subject: [PATCH 067/176] syntax error --- src/simsopt/geo/boozersurface.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 09ba226a9..7d9a068a7 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -324,7 +324,7 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons else: x = np.concatenate((s.get_dofs(), [iota, G])) - fun_name = self.boozer_penalty_constraints_vectorized else lambda x: self.boozer_penalty_constraints + fun_name = self.boozer_penalty_constraints_vectorized if vectorize else self.boozer_penalty_constraints fun = lambda x: fun_name(x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) res = minimize( @@ -364,7 +364,7 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons x = np.concatenate((s.get_dofs(), [iota, G])) i = 0 - fun_name = self.boozer_penalty_constraints_vectorized else lambda x: self.boozer_penalty_constraints + fun_name = self.boozer_penalty_constraints_vectorized if vectorize else self.boozer_penalty_constraints val, dval, d2val = fun_name(x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) norm = np.linalg.norm(dval) From eb2ed513e5224077b45a1edfd90090d193c15ce9 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 22 Apr 2024 12:18:26 -0400 Subject: [PATCH 068/176] renaming class, adding a trefoil unit test --- src/simsopt/geo/__init__.py | 4 +- ...elical.py => curvexyzfouriersymmetries.py} | 12 +-- tests/geo/test_curve.py | 82 +++++++++++++------ 3 files changed, 67 insertions(+), 31 deletions(-) rename src/simsopt/geo/{curvexyzhelical.py => curvexyzfouriersymmetries.py} (92%) diff --git a/src/simsopt/geo/__init__.py b/src/simsopt/geo/__init__.py index d0c7116bc..25cf7ea42 100644 --- a/src/simsopt/geo/__init__.py +++ b/src/simsopt/geo/__init__.py @@ -6,7 +6,7 @@ from .curvehelical import * from .curverzfourier import * from .curvexyzfourier import * -from .curvexyzhelical import * +from .curvexyzfouriersymmetries import * from .curveperturbed import * from .curveobjectives import * from .curveplanarfourier import * @@ -29,7 +29,7 @@ __all__ = (curve.__all__ + curvehelical.__all__ + curverzfourier.__all__ + curvexyzfourier.__all__ + - curvexyzhelical.__all__ + + curvexyzfouriersymmetries.__all__ + curveperturbed.__all__ + curveobjectives.__all__ + curveplanarfourier.__all__ + finitebuild.__all__ + plotting.__all__ + diff --git a/src/simsopt/geo/curvexyzhelical.py b/src/simsopt/geo/curvexyzfouriersymmetries.py similarity index 92% rename from src/simsopt/geo/curvexyzhelical.py rename to src/simsopt/geo/curvexyzfouriersymmetries.py index acffac2a9..c796d29ba 100644 --- a/src/simsopt/geo/curvexyzhelical.py +++ b/src/simsopt/geo/curvexyzfouriersymmetries.py @@ -3,10 +3,10 @@ from .curve import JaxCurve from math import gcd -__all__ = ['CurveXYZHelical'] +__all__ = ['CurveXYZFourierSymmetries'] -def jaxXYZHelicalFouriercurve_pure(dofs, quadpoints, order, nfp, stellsym, ntor): +def jaxXYZFourierSymmetriescurve_pure(dofs, quadpoints, order, nfp, stellsym, ntor): theta, m = jnp.meshgrid(quadpoints, jnp.arange(order + 1), indexing='ij') @@ -43,9 +43,9 @@ def jaxXYZHelicalFouriercurve_pure(dofs, quadpoints, order, nfp, stellsym, ntor) return gamma -class CurveXYZHelical(JaxCurve): - r'''A curve representation for a helical coil that does not lie on a torus. - The coordinates of the curve are given by: +class CurveXYZFourierSymmetries(JaxCurve): + r'''A curve representation that allows for stellarator and discrete rotational symmetries. This class can be used to + represent a helical coil that does not lie on a torus. The coordinates of the curve are given by: .. math:: \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} x_{c,m} \cos(2 \pi n_{\text{fp}} m \theta)\\ @@ -79,7 +79,7 @@ class CurveXYZHelical(JaxCurve): def __init__(self, quadpoints, order, nfp, stellsym, ntor=1, **kwargs): if isinstance(quadpoints, int): quadpoints = np.linspace(0, 1, quadpoints, endpoint=False) - pure = lambda dofs, points: jaxXYZHelicalFouriercurve_pure( + pure = lambda dofs, points: jaxXYZFourierSymmetriescurve_pure( dofs, points, order, nfp, stellsym, ntor) nfp_true = nfp // gcd(nfp, ntor) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index daf613e94..664ce7aab 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -11,7 +11,7 @@ from simsopt.geo.curverzfourier import CurveRZFourier from simsopt.geo.curveplanarfourier import CurvePlanarFourier from simsopt.geo.curvehelical import CurveHelical -from simsopt.geo.curvexyzhelical import CurveXYZHelical +from simsopt.geo.curvexyzfouriersymmetries import CurveXYZFourierSymmetries from simsopt.geo.curve import RotatedCurve, curves_to_vtk from simsopt.geo import parameters from simsopt.configs.zoo import get_ncsx_data, get_w7x_data @@ -77,10 +77,10 @@ def get_curve(curvetype, rotated, x=np.asarray([0.5])): curve = CurveHelical(x, order, 5, 2, 1.0, 0.3, x0=np.ones((2*order,))) elif curvetype == "CurvePlanarFourier": curve = CurvePlanarFourier(x, order, 2, True) - elif curvetype == "CurveXYZHelical1": - curve = CurveXYZHelical(x, order, 2, True) - elif curvetype == "CurveXYZHelical2": - curve = CurveXYZHelical(x, order, 2, False) + elif curvetype == "CurveXYZFourierSymmetries1": + curve = CurveXYZFourierSymmetries(x, order, 2, True) + elif curvetype == "CurveXYZFourierSymmetries2": + curve = CurveXYZFourierSymmetries(x, order, 2, False) else: assert False @@ -95,14 +95,14 @@ def get_curve(curvetype, rotated, x=np.asarray([0.5])): dofs[order+1] = 0.1 elif curvetype in ["CurveHelical", "CurveHelicalInitx0"]: dofs[0] = np.pi/2 - elif curvetype == "CurveXYZHelical1": + elif curvetype == "CurveXYZFourierSymmetries1": R = 1 r = 0.5 curve.set('xc(0)', R) curve.set('xc(1)', -r) curve.set('zs(1)', -r) dofs = curve.get_dofs() - elif curvetype == "CurveXYZHelical2": + elif curvetype == "CurveXYZFourierSymmetries2": R = 1 r = 0.5 curve.set('xc(0)', R) @@ -124,10 +124,10 @@ def get_curve(curvetype, rotated, x=np.asarray([0.5])): class Testing(unittest.TestCase): - curvetypes = ["CurveXYZFourier", "JaxCurveXYZFourier", "CurveRZFourier", "CurvePlanarFourier", "CurveHelical", "CurveXYZHelical1","CurveXYZHelical2", "CurveHelicalInitx0"] + curvetypes = ["CurveXYZFourier", "JaxCurveXYZFourier", "CurveRZFourier", "CurvePlanarFourier", "CurveHelical", "CurveXYZFourierSymmetries1","CurveXYZFourierSymmetries2", "CurveHelicalInitx0"] - def get_curvexyzhelical(self, stellsym=True, x=None, nfp=None, ntor=1): - # returns a CurveXYZHelical that is randomly perturbed + def get_curvexyzfouriersymmetries(self, stellsym=True, x=None, nfp=None, ntor=1): + # returns a CurveXYZFourierSymmetries that is randomly perturbed np.random.seed(1) rand_scale = 1e-2 @@ -138,7 +138,7 @@ def get_curvexyzhelical(self, stellsym=True, x=None, nfp=None, ntor=1): x = np.linspace(0, 1, 200, endpoint=False) order = 2 - curve = CurveXYZHelical(x, order, nfp, stellsym, ntor=ntor) + curve = CurveXYZFourierSymmetries(x, order, nfp, stellsym, ntor=ntor) R = 1 r = 0.25 curve.set('xc(0)', R) @@ -151,12 +151,12 @@ def get_curvexyzhelical(self, stellsym=True, x=None, nfp=None, ntor=1): return curve - def test_curvehelical_is_curvexyzhelical(self): + def test_curvehelical_is_curvexyzfouriersymmetries(self): # this test checks that both helical coil representations can produce the same helical curve on a torus order = 1 nfp = 2 x = np.linspace(0, 1, 100, endpoint=False) - curve1 = CurveXYZHelical(x, order, nfp, True) + curve1 = CurveXYZFourierSymmetries(x, order, nfp, True) R = 1 r = 0.5 curve1.set('xc(0)', R) @@ -165,9 +165,45 @@ def test_curvehelical_is_curvexyzhelical(self): curve2 = CurveHelical(x, order, nfp, 1, R, r, x0=np.zeros((2*order,))) np.testing.assert_allclose(curve1.gamma(), curve2.gamma(), atol=1e-14) + def test_trefoil(self): + r''' This test checks that a CurveXYZFourierSymmetries can represent a trefoil knot. + A parametric representation of a trefoil knot is given by: + x(t) = sin(t) + 2sin(t) + y(t) = cos(t) - 2cos(t) + z(t) = -sin(3t) + + The above can be rewritten the CurveXYZFourierSymmetries representation, with + order = 1, nfp = 3, and ntor = 2: + + xhat(t) = sin(nfp*t) + yhat(t) = -2 + cos(nfp*t), + x(t) = xhat(t) * cos(ntor*t) - yhat(t) * sin(ntor*t), + y(t) = xhat(t) * sin(ntor*t) + yhat(t) * cos(ntor*t), + z(t) = -sin(nfp*t), + + i.e., xs(1)=1, yc(0)=-2, yc(1)=1, zs(1)=-1. + ''' + + order = 1 + nfp = 3 + ntor = 2 + x = np.linspace(0, 1, 500, endpoint=False) + curve = CurveXYZFourierSymmetries(x, order, nfp, False, ntor=ntor) + + X = np.sin(2*np.pi * x) + 2 * np.sin(2*2*np.pi * x) + Y = np.cos(2*np.pi * x) - 2 * np.cos(2*2*np.pi*x) + Z = -np.sin(3*2*np.pi*x) + XYZ = np.concatenate([X[:, None], Y[:, None], Z[:, None]], axis=1) + + curve.set('xs(1)', 1.) + curve.set('yc(0)', -2.) + curve.set('yc(1)', 1.) + curve.set('zs(1)', -1.) + np.testing.assert_allclose(curve.gamma(), XYZ, atol=1e-14) + def test_nonstellsym(self): # this test checks that you can obtain a stellarator symmetric magnetic field from two non-stellarator symmetric - # CurveXYZHelical curves. + # CurveXYZFourierSymmetries curves. for nfp in [1, 2, 3, 4, 5, 6]: for ntor in [1, 2, 3, 4, 5, 6]: with self.subTest(nfp=nfp, ntor=ntor): @@ -179,8 +215,8 @@ def subtest_nonstellsym(self, nfp, ntor): return # this test checks that you can obtain a stellarator symmetric magnetic field from two non-stellarator symmetric - # CurveXYZHelical curves. - curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, ntor=ntor) + # CurveXYZFourierSymmetries curves. + curve = self.get_curvexyzfouriersymmetries(stellsym=False, nfp=nfp, ntor=ntor) current = Current(1e5) coils = coils_via_symmetries([curve], [current], 1, True) bs = BiotSavart(coils) @@ -191,7 +227,7 @@ def subtest_nonstellsym(self, nfp, ntor): np.testing.assert_allclose(B[0, 2], B[1, 2], atol=1e-14) def test_xyzhelical_symmetries(self): - # checking various symmetries of the CurveXYZHelical representation + # checking various symmetries of the CurveXYZFourierSymmetries representation for nfp in [1, 2, 3, 4, 5, 6]: for ntor in [1, 2, 3, 4, 5, 6]: with self.subTest(nfp=nfp, ntor=ntor): @@ -203,7 +239,7 @@ def subtest_xyzhelical_symmetries(self, nfp, ntor): return # does the stellarator symmetric curve have rotational symmetry? - curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x=np.array([0.123, 0.123+ntor/nfp]), ntor=ntor) + curve = self.get_curvexyzfouriersymmetries(stellsym=True, nfp=nfp, x=np.array([0.123, 0.123+ntor/nfp]), ntor=ntor) out = curve.gamma() alpha = -2*np.pi/nfp R = np.array([ @@ -219,7 +255,7 @@ def subtest_xyzhelical_symmetries(self, nfp, ntor): np.testing.assert_allclose(out[1], np.linalg.inv(R)@out[0], atol=1e-14) # does the stellarator symmetric curve indeed pass through (x0, 0, 0)? - curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0]), ntor=ntor) + curve = self.get_curvexyzfouriersymmetries(stellsym=True, nfp=nfp, x = np.array([0]), ntor=ntor) out = curve.gamma() assert np.abs(out[0, 0]) > 1e-3 np.testing.assert_allclose(out[0, 1], 0, atol=1e-14) @@ -227,21 +263,21 @@ def subtest_xyzhelical_symmetries(self, nfp, ntor): # does the non-stellarator symmetric curve not pass through (x0, 0, 0)? - curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, x = np.array([0]), ntor=ntor) + curve = self.get_curvexyzfouriersymmetries(stellsym=False, nfp=nfp, x = np.array([0]), ntor=ntor) out = curve.gamma() assert np.abs(out[0, 0]) > 1e-3 assert np.abs(out[0, 1]) > 1e-3 assert np.abs(out[0, 2]) > 1e-3 # is the stellarator symmetric curve actually stellarator symmetric? - curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x = np.array([0.123, -0.123]), ntor=ntor) + curve = self.get_curvexyzfouriersymmetries(stellsym=True, nfp=nfp, x = np.array([0.123, -0.123]), ntor=ntor) pts = curve.gamma() np.testing.assert_allclose(pts[0, 0], pts[1, 0], atol=1e-14) np.testing.assert_allclose(pts[0, 1], -pts[1, 1], atol= 1e-14) np.testing.assert_allclose(pts[0, 2], -pts[1, 2], atol= 1e-14) # is the field from the stellarator symmetric curve actually stellarator symmetric? - curve = self.get_curvexyzhelical(stellsym=True, nfp=nfp, x=np.linspace(0, 1, 200, endpoint=False), ntor=ntor) + curve = self.get_curvexyzfouriersymmetries(stellsym=True, nfp=nfp, x=np.linspace(0, 1, 200, endpoint=False), ntor=ntor) current = Current(1e5) coil = Coil(curve, current) bs = BiotSavart([coil]) @@ -252,7 +288,7 @@ def subtest_xyzhelical_symmetries(self, nfp, ntor): np.testing.assert_allclose(B[0, 2], B[1, 2], atol=1e-14) # does the non-stellarator symmetric curve have rotational symmetry still? - curve = self.get_curvexyzhelical(stellsym=False, nfp=nfp, x = np.array([0.123, 0.123+ntor/nfp]), ntor=ntor) + curve = self.get_curvexyzfouriersymmetries(stellsym=False, nfp=nfp, x = np.array([0.123, 0.123+ntor/nfp]), ntor=ntor) out = curve.gamma() alpha = -2*np.pi/nfp R = np.array([[np.cos(alpha), np.sin(alpha), 0], [-np.sin(alpha), np.cos(alpha), 0], [0, 0, 1]]) From 4ae7c54cc530212dbbb9fe10e6ce965ac129a42a Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 22 Apr 2024 13:14:58 -0400 Subject: [PATCH 069/176] fixing unit tests --- tests/geo/test_curve.py | 49 +++++++++++++++++++++-------------------- 1 file changed, 25 insertions(+), 24 deletions(-) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 664ce7aab..0eec5faef 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -168,18 +168,21 @@ def test_curvehelical_is_curvexyzfouriersymmetries(self): def test_trefoil(self): r''' This test checks that a CurveXYZFourierSymmetries can represent a trefoil knot. A parametric representation of a trefoil knot is given by: - x(t) = sin(t) + 2sin(t) - y(t) = cos(t) - 2cos(t) - z(t) = -sin(3t) + + .. math:: + x(t) &= sin(t) + 2sin(t) \\ + y(t) &= cos(t) - 2cos(t) \\ + z(t) &= -sin(3t) The above can be rewritten the CurveXYZFourierSymmetries representation, with order = 1, nfp = 3, and ntor = 2: - xhat(t) = sin(nfp*t) - yhat(t) = -2 + cos(nfp*t), - x(t) = xhat(t) * cos(ntor*t) - yhat(t) * sin(ntor*t), - y(t) = xhat(t) * sin(ntor*t) + yhat(t) * cos(ntor*t), - z(t) = -sin(nfp*t), + .. math:: + xhat(t) &= sin(nfp*t) \\ + yhat(t) &= -2 + cos(nfp*t), \\ + x(t) &= xhat(t) * cos(ntor*t) - yhat(t) * sin(ntor*t), \\ + y(t) &= xhat(t) * sin(ntor*t) + yhat(t) * cos(ntor*t), \\ + z(t) &= -sin(nfp*t), i.e., xs(1)=1, yc(0)=-2, yc(1)=1, zs(1)=-1. ''' @@ -191,7 +194,7 @@ def test_trefoil(self): curve = CurveXYZFourierSymmetries(x, order, nfp, False, ntor=ntor) X = np.sin(2*np.pi * x) + 2 * np.sin(2*2*np.pi * x) - Y = np.cos(2*np.pi * x) - 2 * np.cos(2*2*np.pi*x) + Y = np.cos(2*np.pi * x) - 2 * np.cos(2*2*np.pi * x) Z = -np.sin(3*2*np.pi*x) XYZ = np.concatenate([X[:, None], Y[:, None], Z[:, None]], axis=1) @@ -239,20 +242,17 @@ def subtest_xyzhelical_symmetries(self, nfp, ntor): return # does the stellarator symmetric curve have rotational symmetry? - curve = self.get_curvexyzfouriersymmetries(stellsym=True, nfp=nfp, x=np.array([0.123, 0.123+ntor/nfp]), ntor=ntor) + curve = self.get_curvexyzfouriersymmetries(stellsym=True, nfp=nfp, x=np.array([0.123, 0.123+1/nfp]), ntor=ntor) out = curve.gamma() - alpha = -2*np.pi/nfp + alpha = 2*np.pi*ntor/nfp R = np.array([ - [np.cos(alpha), np.sin(alpha), 0], - [-np.sin(alpha), np.cos(alpha), 0], + [np.cos(alpha), -np.sin(alpha), 0], + [np.sin(alpha), np.cos(alpha), 0], [0, 0, 1] ]) print(R@out[0], out[1]) - try: - np.testing.assert_allclose(out[1], R@out[0], atol=1e-14) - except: - np.testing.assert_allclose(out[1], np.linalg.inv(R)@out[0], atol=1e-14) + np.testing.assert_allclose(out[1], R@out[0], atol=1e-14) # does the stellarator symmetric curve indeed pass through (x0, 0, 0)? curve = self.get_curvexyzfouriersymmetries(stellsym=True, nfp=nfp, x = np.array([0]), ntor=ntor) @@ -288,15 +288,16 @@ def subtest_xyzhelical_symmetries(self, nfp, ntor): np.testing.assert_allclose(B[0, 2], B[1, 2], atol=1e-14) # does the non-stellarator symmetric curve have rotational symmetry still? - curve = self.get_curvexyzfouriersymmetries(stellsym=False, nfp=nfp, x = np.array([0.123, 0.123+ntor/nfp]), ntor=ntor) + curve = self.get_curvexyzfouriersymmetries(stellsym=False, nfp=nfp, x = np.array([0.123, 0.123+1./nfp]), ntor=ntor) out = curve.gamma() - alpha = -2*np.pi/nfp - R = np.array([[np.cos(alpha), np.sin(alpha), 0], [-np.sin(alpha), np.cos(alpha), 0], [0, 0, 1]]) + alpha = 2*np.pi*ntor/nfp + R = np.array([ + [np.cos(alpha), -np.sin(alpha), 0], + [np.sin(alpha), np.cos(alpha), 0], + [0, 0, 1] + ]) print(R@out[0], out[1]) - try: - np.testing.assert_allclose(out[1], R@out[0], atol=1e-14) - except: - np.testing.assert_allclose(out[1], np.linalg.inv(R)@out[0], atol=1e-14) + np.testing.assert_allclose(out[1], R@out[0], atol=1e-14) def test_curve_helical_xyzfourier(self): x = np.asarray([0.6]) From c91431fc2be9c2171e0fdd872214714b47a95925 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 22 Apr 2024 13:20:41 -0400 Subject: [PATCH 070/176] cleaning up the condition checking if ntor and nfp are coprime --- src/simsopt/geo/curvexyzfouriersymmetries.py | 3 +-- tests/geo/test_curve.py | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/src/simsopt/geo/curvexyzfouriersymmetries.py b/src/simsopt/geo/curvexyzfouriersymmetries.py index c796d29ba..d334086c3 100644 --- a/src/simsopt/geo/curvexyzfouriersymmetries.py +++ b/src/simsopt/geo/curvexyzfouriersymmetries.py @@ -82,8 +82,7 @@ def __init__(self, quadpoints, order, nfp, stellsym, ntor=1, **kwargs): pure = lambda dofs, points: jaxXYZFourierSymmetriescurve_pure( dofs, points, order, nfp, stellsym, ntor) - nfp_true = nfp // gcd(nfp, ntor) - if nfp != nfp_true: + if gcd(ntor, nfp) != 1: raise Exception('nfp and ntor must be coprime') self.order = order diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 0eec5faef..4209f9da8 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -213,8 +213,7 @@ def test_nonstellsym(self): self.subtest_nonstellsym(nfp, ntor) def subtest_nonstellsym(self, nfp, ntor): - nfp_true = nfp // gcd(ntor, nfp) - if nfp_true != nfp: + if gcd(ntor, nfp) != 1: return # this test checks that you can obtain a stellarator symmetric magnetic field from two non-stellarator symmetric From 5cec5ac6fd936285cccc0196552c2ac8f0640ebb Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 22 Apr 2024 13:40:18 -0400 Subject: [PATCH 071/176] testing on a stellsym and nonstellsym trefoil --- tests/geo/test_curve.py | 48 +++++++++++++++++++++++++++++++++++++---- 1 file changed, 44 insertions(+), 4 deletions(-) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 4209f9da8..22f9f4ecf 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -165,9 +165,9 @@ def test_curvehelical_is_curvexyzfouriersymmetries(self): curve2 = CurveHelical(x, order, nfp, 1, R, r, x0=np.zeros((2*order,))) np.testing.assert_allclose(curve1.gamma(), curve2.gamma(), atol=1e-14) - def test_trefoil(self): - r''' This test checks that a CurveXYZFourierSymmetries can represent a trefoil knot. - A parametric representation of a trefoil knot is given by: + def test_trefoil_nonstellsym(self): + r''' This test checks that a CurveXYZFourierSymmetries can represent a non-stellarator symmetric + trefoil knot. A parametric representation of a trefoil knot is given by: .. math:: x(t) &= sin(t) + 2sin(t) \\ @@ -184,7 +184,7 @@ def test_trefoil(self): y(t) &= xhat(t) * sin(ntor*t) + yhat(t) * cos(ntor*t), \\ z(t) &= -sin(nfp*t), - i.e., xs(1)=1, yc(0)=-2, yc(1)=1, zs(1)=-1. + i.e., The dofs are xs(1)=1, yc(0)=-2, yc(1)=1, zs(1)=-1, and zero otherwise. ''' order = 1 @@ -204,6 +204,46 @@ def test_trefoil(self): curve.set('zs(1)', -1.) np.testing.assert_allclose(curve.gamma(), XYZ, atol=1e-14) + def test_trefoil_stellsym(self): + r''' This test checks that a CurveXYZFourierSymmetries can represent a stellarator symmetric + trefoil knot. A parametric representation of a trefoil knot is given by: + + .. math:: + x(t) &= cos(t) - 2cos(t) \\ + y(t) &=-sin(t) - 2sin(t) \\ + z(t) &= -sin(3t) + + The above can be rewritten the CurveXYZFourierSymmetries representation, with + order = 1, nfp = 3, and ntor = 2: + + .. math:: + xhat(t) &= -2 + cos(t)\\ + yhat(t) &= -sin(t)\\ + x(t) &= xhat(t) * cos(ntor*t) - yhat(t) * sin(ntor*t), \\ + y(t) &= xhat(t) * sin(ntor*t) + yhat(t) * cos(ntor*t), \\ + z(t) &= -sin(nfp*t), + + i.e., xc(0)=-2, xc(1)=1, ys(1)=-1, zs(1)=-1. + ''' + + order = 1 + nfp = 3 + ntor = 2 + x = np.linspace(0, 1, 500, endpoint=False) + curve = CurveXYZFourierSymmetries(x, order, nfp, True, ntor=ntor) + + X = np.cos(2*np.pi * x) - 2 * np.cos(2*2*np.pi * x) + Y =-np.sin(2*np.pi * x) - 2 * np.sin(2*2*np.pi * x) + Z = -np.sin(3*2*np.pi*x) + XYZ = np.concatenate([X[:, None], Y[:, None], Z[:, None]], axis=1) + + curve.set('xc(0)', -2) + curve.set('xc(1)', 1) + curve.set('ys(1)', -1) + curve.set('zs(1)', -1) + np.testing.assert_allclose(curve.gamma(), XYZ, atol=1e-14) + + def test_nonstellsym(self): # this test checks that you can obtain a stellarator symmetric magnetic field from two non-stellarator symmetric # CurveXYZFourierSymmetries curves. From ee48c83b37fcbd15eda6f41dba4414f68860545d Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 22 Apr 2024 15:15:36 -0400 Subject: [PATCH 072/176] fixing docstrings --- src/simsopt/geo/curvexyzfouriersymmetries.py | 2 +- tests/geo/test_curve.py | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/src/simsopt/geo/curvexyzfouriersymmetries.py b/src/simsopt/geo/curvexyzfouriersymmetries.py index d334086c3..16f557330 100644 --- a/src/simsopt/geo/curvexyzfouriersymmetries.py +++ b/src/simsopt/geo/curvexyzfouriersymmetries.py @@ -73,7 +73,7 @@ class CurveXYZFourierSymmetries(JaxCurve): it is assumed that nfp and ntor are coprime. If they are not coprime, then then the curve actually has nfp_new:=nfp // gcd(nfp, ntor), and ntor_new:=ntor // gcd(nfp, ntor). To avoid confusion, - we assert that ntor and nfp are coprime at instatiation. + we assert that ntor and nfp are coprime at instantiation. ''' def __init__(self, quadpoints, order, nfp, stellsym, ntor=1, **kwargs): diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 22f9f4ecf..7202128e6 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -276,13 +276,14 @@ def test_xyzhelical_symmetries(self): self.subtest_xyzhelical_symmetries(nfp, ntor) def subtest_xyzhelical_symmetries(self, nfp, ntor): - nfp_true = nfp // gcd(ntor, nfp) - if nfp_true != nfp: + if gcd(nfp, ntor) != 1 : return # does the stellarator symmetric curve have rotational symmetry? curve = self.get_curvexyzfouriersymmetries(stellsym=True, nfp=nfp, x=np.array([0.123, 0.123+1/nfp]), ntor=ntor) out = curve.gamma() + + # NOTE: the point at angle t+1/nfp is the point at angle t, but rotated by 2pi *(ntor/nfp) radians. alpha = 2*np.pi*ntor/nfp R = np.array([ [np.cos(alpha), -np.sin(alpha), 0], @@ -327,6 +328,7 @@ def subtest_xyzhelical_symmetries(self, nfp, ntor): np.testing.assert_allclose(B[0, 2], B[1, 2], atol=1e-14) # does the non-stellarator symmetric curve have rotational symmetry still? + # NOTE: the point at angle t+1/nfp is the point at angle t, but rotated by 2pi *(ntor/nfp) radians. curve = self.get_curvexyzfouriersymmetries(stellsym=False, nfp=nfp, x = np.array([0.123, 0.123+1./nfp]), ntor=ntor) out = curve.gamma() alpha = 2*np.pi*ntor/nfp From ccea42129dd3962e3bb18a19ec603b128fa287b8 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 22 Apr 2024 16:19:43 -0400 Subject: [PATCH 073/176] fixing documentation so it compiles --- docs/source/simsopt.geo.rst | 6 +- src/simsopt/geo/curvexyzfouriersymmetries.py | 65 +++++++++++--------- tests/geo/test_curve.py | 55 ++++++++++------- 3 files changed, 74 insertions(+), 52 deletions(-) diff --git a/docs/source/simsopt.geo.rst b/docs/source/simsopt.geo.rst index d3da40ea2..92859f7c7 100644 --- a/docs/source/simsopt.geo.rst +++ b/docs/source/simsopt.geo.rst @@ -76,10 +76,10 @@ simsopt.geo.curvexyzfourier module :undoc-members: :show-inheritance: -simsopt.geo.curvexyzhelical module ----------------------------------- +simsopt.geo.curvexyzfouriersymmetries module +-------------------------------------------- -.. automodule:: simsopt.geo.curvexyzhelical +.. automodule:: simsopt.geo.curvexyzfouriersymmetries :members: :undoc-members: :show-inheritance: diff --git a/src/simsopt/geo/curvexyzfouriersymmetries.py b/src/simsopt/geo/curvexyzfouriersymmetries.py index 16f557330..b537e94f3 100644 --- a/src/simsopt/geo/curvexyzfouriersymmetries.py +++ b/src/simsopt/geo/curvexyzfouriersymmetries.py @@ -46,35 +46,44 @@ def jaxXYZFourierSymmetriescurve_pure(dofs, quadpoints, order, nfp, stellsym, nt class CurveXYZFourierSymmetries(JaxCurve): r'''A curve representation that allows for stellarator and discrete rotational symmetries. This class can be used to represent a helical coil that does not lie on a torus. The coordinates of the curve are given by: + + .. math:: + x(\theta) &= \hat x(\theta) \cos(2 \pi \theta n_{\text{tor}}) - \hat y(\theta) \sin(2 \pi \theta n_{\text{tor}})\\ + y(\theta) &= \hat x(\theta) \sin(2 \pi \theta n_{\text{tor}}) + \hat y(\theta) \cos(2 \pi \theta n_{\text{tor}})\\ + z(\theta) &= \sum_{m=1}^{\text{order}} z_{s,m} \sin(2 \pi n_{\text{fp}} m \theta) + + where + + .. math:: + \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} x_{c,m} \cos(2 \pi n_{\text{fp}} m \theta)\\ + \hat y(\theta) &= \sum_{m=1}^{\text{order}} y_{s,m} \sin(2 \pi n_{\text{fp}} m \theta)\\ + - .. math:: - \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} x_{c,m} \cos(2 \pi n_{\text{fp}} m \theta)\\ - \hat y(\theta) &= \sum_{m=1}^{\text{order}} y_{s,m} \sin(2 \pi n_{\text{fp}} m \theta)\\ - x(\theta) &= \hat x(\theta) \cos(2 \pi \theta n_{\text{tor}}) - \hat y(\theta) \sin(2 \pi \theta n_{\text{tor}})\\ - y(\theta) &= \hat x(\theta) \sin(2 \pi \theta n_{\text{tor}}) + \hat y(\theta) \cos(2 \pi \theta n_{\text{tor}})\\ - z(\theta) &= \sum_{m=1}^{\text{order}} z_{s,m} \sin(2 \pi n_{\text{fp}} m \theta) - - if the coil is stellarator symmetric. When the coil is not stellarator symmetric, the formulas above - become - - .. math:: - \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} \left[ x_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + x_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] \\ - \hat y(\theta) &= y_{c, 0} + \sum_{m=1}^{\text{order}} \left[ y_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + y_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] \\ - x(\theta) &= \hat x(\theta) \cos(2 \pi \theta n_{\text{tor}}) - \hat y(\theta) \sin(2 \pi \theta n_{\text{tor}})\\ - y(\theta) &= \hat x(\theta) \sin(2 \pi \theta n_{\text{tor}}) + \hat y(\theta) \cos(2 \pi \theta n_{\text{tor}})\\ - z(\theta) &= z_{c, 0} + \sum_{m=1}^{\text{order}} \left[ z_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + z_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] - - Args: - quadpoints: number of grid points/resolution along the curve, - order: how many Fourier harmonics to include in the Fourier representation, - nfp: discrete rotational symmetry number, - stellsym: stellaratory symmetry if True, not stellarator symmetric otherwise, - ntor: the number of times the curve wraps toroidally before biting its tail. Note, - it is assumed that nfp and ntor are coprime. If they are not coprime, - then then the curve actually has nfp_new:=nfp // gcd(nfp, ntor), - and ntor_new:=ntor // gcd(nfp, ntor). To avoid confusion, - we assert that ntor and nfp are coprime at instantiation. - ''' + if the coil is stellarator symmetric. When the coil is not stellarator symmetric, the formulas above + become + + .. math:: + x(\theta) &= \hat x(\theta) \cos(2 \pi \theta n_{\text{tor}}) - \hat y(\theta) \sin(2 \pi \theta n_{\text{tor}})\\ + y(\theta) &= \hat x(\theta) \sin(2 \pi \theta n_{\text{tor}}) + \hat y(\theta) \cos(2 \pi \theta n_{\text{tor}})\\ + z(\theta) &= z_{c, 0} + \sum_{m=1}^{\text{order}} \left[ z_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + z_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] + + where + + .. math:: + \hat x(\theta) &= x_{c, 0} + \sum_{m=1}^{\text{order}} \left[ x_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + x_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] \\ + \hat y(\theta) &= y_{c, 0} + \sum_{m=1}^{\text{order}} \left[ y_{c, m} \cos(2 \pi n_{\text{fp}} m \theta) + y_{s, m} \sin(2 \pi n_{\text{fp}} m \theta) \right] \\ + + Args: + quadpoints: number of grid points/resolution along the curve, + order: how many Fourier harmonics to include in the Fourier representation, + nfp: discrete rotational symmetry number, + stellsym: stellaratory symmetry if True, not stellarator symmetric otherwise, + ntor: the number of times the curve wraps toroidally before biting its tail. Note, + it is assumed that nfp and ntor are coprime. If they are not coprime, + then then the curve actually has nfp_new:=nfp // gcd(nfp, ntor), + and ntor_new:=ntor // gcd(nfp, ntor). The operator `//` is integer division. + To avoid confusion, we assert that ntor and nfp are coprime at instantiation. + ''' def __init__(self, quadpoints, order, nfp, stellsym, ntor=1, **kwargs): if isinstance(quadpoints, int): diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 7202128e6..48ed68305 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -81,6 +81,8 @@ def get_curve(curvetype, rotated, x=np.asarray([0.5])): curve = CurveXYZFourierSymmetries(x, order, 2, True) elif curvetype == "CurveXYZFourierSymmetries2": curve = CurveXYZFourierSymmetries(x, order, 2, False) + elif curvetype == "CurveXYZFourierSymmetries3": + curve = CurveXYZFourierSymmetries(x, order, 2, False, ntor=3) else: assert False @@ -112,6 +114,16 @@ def get_curve(curvetype, rotated, x=np.asarray([0.5])): curve.set('zc(0)', 1) curve.set('zs(1)', r) dofs = curve.get_dofs() + elif curvetype == "CurveXYZFourierSymmetries3": + R = 1 + r = 0.5 + curve.set('xc(0)', R) + curve.set('xs(1)', -0.1*r) + curve.set('xc(1)', -r) + curve.set('zs(1)', -r) + curve.set('zc(0)', 1) + curve.set('zs(1)', r) + dofs = curve.get_dofs() else: assert False @@ -124,7 +136,7 @@ def get_curve(curvetype, rotated, x=np.asarray([0.5])): class Testing(unittest.TestCase): - curvetypes = ["CurveXYZFourier", "JaxCurveXYZFourier", "CurveRZFourier", "CurvePlanarFourier", "CurveHelical", "CurveXYZFourierSymmetries1","CurveXYZFourierSymmetries2", "CurveHelicalInitx0"] + curvetypes = ["CurveXYZFourier", "JaxCurveXYZFourier", "CurveRZFourier", "CurvePlanarFourier", "CurveHelical", "CurveXYZFourierSymmetries1","CurveXYZFourierSymmetries2", "CurveXYZFourierSymmetries3", "CurveHelicalInitx0"] def get_curvexyzfouriersymmetries(self, stellsym=True, x=None, nfp=None, ntor=1): # returns a CurveXYZFourierSymmetries that is randomly perturbed @@ -169,21 +181,21 @@ def test_trefoil_nonstellsym(self): r''' This test checks that a CurveXYZFourierSymmetries can represent a non-stellarator symmetric trefoil knot. A parametric representation of a trefoil knot is given by: - .. math:: - x(t) &= sin(t) + 2sin(t) \\ - y(t) &= cos(t) - 2cos(t) \\ - z(t) &= -sin(3t) + x(t) = sin(t) + 2sin(t) + y(t) = cos(t) - 2cos(t) + z(t) = -sin(3t) The above can be rewritten the CurveXYZFourierSymmetries representation, with order = 1, nfp = 3, and ntor = 2: - .. math:: - xhat(t) &= sin(nfp*t) \\ - yhat(t) &= -2 + cos(nfp*t), \\ - x(t) &= xhat(t) * cos(ntor*t) - yhat(t) * sin(ntor*t), \\ - y(t) &= xhat(t) * sin(ntor*t) + yhat(t) * cos(ntor*t), \\ - z(t) &= -sin(nfp*t), + x(t) = xhat(t) * cos(ntor*t) - yhat(t) * sin(ntor*t), + y(t) = xhat(t) * sin(ntor*t) + yhat(t) * cos(ntor*t), + z(t) = -sin(nfp*t), + where + xhat(t) &= sin(nfp*t), + yhat(t) &= -2 + cos(nfp*t), + i.e., The dofs are xs(1)=1, yc(0)=-2, yc(1)=1, zs(1)=-1, and zero otherwise. ''' @@ -208,21 +220,22 @@ def test_trefoil_stellsym(self): r''' This test checks that a CurveXYZFourierSymmetries can represent a stellarator symmetric trefoil knot. A parametric representation of a trefoil knot is given by: - .. math:: - x(t) &= cos(t) - 2cos(t) \\ - y(t) &=-sin(t) - 2sin(t) \\ - z(t) &= -sin(3t) + x(t) = cos(t) - 2cos(t), + y(t) =-sin(t) - 2sin(t), + z(t) = -sin(3t). The above can be rewritten the CurveXYZFourierSymmetries representation, with order = 1, nfp = 3, and ntor = 2: - .. math:: - xhat(t) &= -2 + cos(t)\\ - yhat(t) &= -sin(t)\\ - x(t) &= xhat(t) * cos(ntor*t) - yhat(t) * sin(ntor*t), \\ - y(t) &= xhat(t) * sin(ntor*t) + yhat(t) * cos(ntor*t), \\ - z(t) &= -sin(nfp*t), + x(t) = xhat(t) * cos(ntor*t) - yhat(t) * sin(ntor*t), + y(t) = xhat(t) * sin(ntor*t) + yhat(t) * cos(ntor*t), + z(t) = -sin(nfp*t), + where + + xhat(t) = -2 + cos(nfp*t) + yhat(t) = -sin(nfp*t) + i.e., xc(0)=-2, xc(1)=1, ys(1)=-1, zs(1)=-1. ''' From 1c122674cf9694c421514ca1a1768b624f17b94b Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 22 Apr 2024 16:23:08 -0400 Subject: [PATCH 074/176] minor change to docstring --- tests/geo/test_curve.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 48ed68305..1f3e92d06 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -193,8 +193,8 @@ def test_trefoil_nonstellsym(self): z(t) = -sin(nfp*t), where - xhat(t) &= sin(nfp*t), - yhat(t) &= -2 + cos(nfp*t), + xhat(t) = sin(nfp*t), + yhat(t) = -2 + cos(nfp*t), i.e., The dofs are xs(1)=1, yc(0)=-2, yc(1)=1, zs(1)=-1, and zero otherwise. ''' From 4e75515fb8779fc074f17605d08eb72ad94f53c0 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 22 Apr 2024 22:01:28 -0400 Subject: [PATCH 075/176] adding one final unit test [skip ci] --- tests/geo/test_boozersurface.py | 46 +++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 075438f13..6e30d2201 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -352,6 +352,52 @@ def subtest_boozer_serialization(self, label): # check that BoozerSurface.surface and label.surface are the same surfaces assert bs_regen.label.surface is bs_regen.surface + + def test_convergence_cpp_and_notcpp_same(self): + """ + This unit test verifies that that the cpp and not cpp implementations converge to + the same solutions + """ + x_vec = self.subtest_convergence_cpp_and_notcpp_same(True) + x_nonvec = self.subtest_convergence_cpp_and_notcpp_same(False) + np.testing.assert_allclose(x_vec, x_nonvec, atol=1e-14) + + def subtest_convergence_cpp_and_notcpp_same(self, vectorize): + """ + compute a surface using either the vectorized or non-vectorized subroutines + """ + curves, currents, ma = get_ncsx_data() + coils = coils_via_symmetries(curves, currents, ma.nfp, True) + current_sum = sum(abs(c.current.get_value()) for c in coils) + bs = BiotSavart(coils) + + s = get_surface('SurfaceXYZTensorFourier', True, nfp=ma.nfp) + s.fit_to_curve(ma, 0.1) + iota = -0.4 + + ar = Area(s) + ar_target = ar.J() + boozer_surface = BoozerSurface(bs, s, ar, ar_target) + + G = 2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi)) + + # vectorized solution first + res = boozer_surface.minimize_boozer_penalty_constraints_LBFGS( + tol=1e-10, maxiter=600, constraint_weight=100., iota=iota, G=G, + vectorize=vectorize) + print('Residual norm after LBFGS', np.sqrt(2*res['fun'])) + + boozer_surface.recompute_bell() + res = boozer_surface.minimize_boozer_penalty_constraints_newton( + tol=1e-10, maxiter=20, constraint_weight=100., + iota=res['iota'], G=res['G'], stab=1e-4, vectorize=vectorize) + + assert res['success'] + x = boozer_surface.surface.x.copy() + iota = res['iota'] + G = res['G'] + return np.concatenate([x, [iota, G]]) + def test_boozer_penalty_constraints_cpp_notcpp(self): """ From 2c453bc62e60c5975766c1d6d4c26d564951d357 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 22 Apr 2024 22:04:04 -0400 Subject: [PATCH 076/176] undoing a change to what is output during minimize_boozer_penalty_constraints_newton [skip ci] --- src/simsopt/geo/boozersurface.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 7d9a068a7..a4c412452 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -377,8 +377,9 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons val, dval, d2val = fun_name(x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) norm = np.linalg.norm(dval) i = i+1 - - r = fun_name(x, derivatives=0, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) + + r = self.boozer_penalty_constraints( + x, derivatives=0, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) res = { "residual": r, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "G": None, } From f595c3dabfee61fb3a9d7f46763418ea99f304e1 Mon Sep 17 00:00:00 2001 From: Bharat Medasani Date: Tue, 23 Apr 2024 10:22:19 -0400 Subject: [PATCH 077/176] Disable avx512 code in simsopt --- src/simsoptpp/simdhelpers.h | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/simsoptpp/simdhelpers.h b/src/simsoptpp/simdhelpers.h index b5485febc..994292d9d 100644 --- a/src/simsoptpp/simdhelpers.h +++ b/src/simsoptpp/simdhelpers.h @@ -129,6 +129,7 @@ using AlignedPaddedVec = std::vector>; #endif #if defined(USE_XSIMD) +/* #if __AVX512F__ // On skylake _mm512_sqrt_pd takes 24 CPI and _mm512_div_pd takes 16 CPI, so // 1/sqrt(vec) takes 40 CPI. Instead we can use the approximate inverse square @@ -147,6 +148,7 @@ inline simd_t rsqrt(simd_t r2){ return rinv; } #else +*/ inline simd_t rsqrt(const simd_t& r2){ //On my avx2 machine, computing the sqrt and then the inverse is actually a //bit faster. just keeping this line here to remind myself how to compute @@ -155,7 +157,7 @@ inline simd_t rsqrt(const simd_t& r2){ return 1./sqrt(r2); } -#endif +//#endif #endif inline double rsqrt(const double& r2){ From f7bdc53e481abb0604a96c370dcfffe8271da674 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 23 Apr 2024 15:22:19 -0400 Subject: [PATCH 078/176] modified unit tests for code coverage --- tests/geo/test_curve.py | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index 1f3e92d06..c7a31066b 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -163,18 +163,34 @@ def get_curvexyzfouriersymmetries(self, stellsym=True, x=None, nfp=None, ntor=1) return curve - def test_curvehelical_is_curvexyzfouriersymmetries(self): + def test_curvexyzsymmetries_raisesexception(self): + # test ensures that an exception is raised when you try and create a curvexyzfouriersymmetries + # where gcd(ntor, nfp) != 1. + + order = 1 + nfp = 1 + ntor = 2 + # nfp = 1 and ntor = 2 here, so it should work + curve = CurveXYZFourierSymmetries(100, order, nfp, True, ntor=ntor, x0=np.ones(3*order+1)) + + with self.assertRaises(Exception): + order = 1 + nfp = 2 + ntor = 2 + # nfp = 2 and ntor = 2 here, so an exception should be raised + curve = CurveXYZFourierSymmetries(100, order, nfp, True, ntor=ntor, x0=np.ones(3*order+1)) + + def test_curvexyzsymmetries_is_curvexyzfouriersymmetries(self): # this test checks that both helical coil representations can produce the same helical curve on a torus order = 1 nfp = 2 - x = np.linspace(0, 1, 100, endpoint=False) - curve1 = CurveXYZFourierSymmetries(x, order, nfp, True) + curve1 = CurveXYZFourierSymmetries(100, order, nfp, True) R = 1 r = 0.5 curve1.set('xc(0)', R) curve1.set('xc(1)', r) curve1.set('zs(1)', -r) - curve2 = CurveHelical(x, order, nfp, 1, R, r, x0=np.zeros((2*order,))) + curve2 = CurveHelical(np.linspace(0, 1, 100, endpoint=False), order, nfp, 1, R, r, x0=np.zeros((2*order,))) np.testing.assert_allclose(curve1.gamma(), curve2.gamma(), atol=1e-14) def test_trefoil_nonstellsym(self): From 6841058bb74eb5e89323045acf4696f788daf33e Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 23 Apr 2024 15:30:40 -0400 Subject: [PATCH 079/176] linting fix --- tests/geo/test_curve.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/tests/geo/test_curve.py b/tests/geo/test_curve.py index c7a31066b..a997a6e84 100644 --- a/tests/geo/test_curve.py +++ b/tests/geo/test_curve.py @@ -172,15 +172,16 @@ def test_curvexyzsymmetries_raisesexception(self): ntor = 2 # nfp = 1 and ntor = 2 here, so it should work curve = CurveXYZFourierSymmetries(100, order, nfp, True, ntor=ntor, x0=np.ones(3*order+1)) - + print(curve.x) + with self.assertRaises(Exception): order = 1 nfp = 2 ntor = 2 # nfp = 2 and ntor = 2 here, so an exception should be raised - curve = CurveXYZFourierSymmetries(100, order, nfp, True, ntor=ntor, x0=np.ones(3*order+1)) - - def test_curvexyzsymmetries_is_curvexyzfouriersymmetries(self): + _ = CurveXYZFourierSymmetries(100, order, nfp, True, ntor=ntor, x0=np.ones(3*order+1)) + + def test_curvehelical_is_curvexyzfouriersymmetries(self): # this test checks that both helical coil representations can produce the same helical curve on a torus order = 1 nfp = 2 From e87861aaf5631dda75cc299caaa5607edca29593 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 23 Apr 2024 15:43:08 -0400 Subject: [PATCH 080/176] minor linting changes --- src/simsopt/geo/boozersurface.py | 15 ++++++--------- src/simsopt/geo/surfaceobjectives.py | 2 +- 2 files changed, 7 insertions(+), 10 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index a4c412452..863bb3079 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -40,6 +40,7 @@ class BoozerSurface(Optimizable): where Newton is used to solve the first order necessary conditions for optimality. """ + def __init__(self, biotsavart, surface, label, targetlabel): super().__init__(depends_on=[biotsavart]) self.biotsavart = biotsavart @@ -50,7 +51,7 @@ def __init__(self, biotsavart, surface, label, targetlabel): def recompute_bell(self, parent=None): self.need_to_run_code = True - + def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., scalarize=True, optimize_G=False, weight_inv_modB=False): r""" Define the residual @@ -135,7 +136,7 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca d2l = np.zeros((x.shape[0], x.shape[0])) d2l[:nsurfdofs, :nsurfdofs] = self.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() - + H = np.concatenate(( H, np.sqrt(constraint_weight) * d2l[None, :, :], @@ -235,7 +236,6 @@ def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_ return r, J, H - def boozer_exact_constraints(self, xl, derivatives=0, optimize_G=True): r""" This function returns the optimality conditions corresponding to the minimization problem @@ -377,7 +377,7 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons val, dval, d2val = fun_name(x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) norm = np.linalg.norm(dval) i = i+1 - + r = self.boozer_penalty_constraints( x, derivatives=0, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) res = { @@ -408,7 +408,7 @@ def minimize_boozer_penalty_constraints_ls(self, tol=1e-12, maxiter=10, constrai if not self.need_to_run_code: return self.res - + s = self.surface if G is None: x = np.concatenate((s.get_dofs(), [iota])) @@ -679,12 +679,9 @@ def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., P, L, U = lu(J) res = { - "residual": r, "jacobian": J, "iter": i, "success": norm <= tol, "G": G, "iota": iota, "PLU": (P, L, U), + "residual": r, "jacobian": J, "iter": i, "success": norm <= tol, "G": G, "s":s, "iota": iota, "PLU": (P, L, U), "mask": mask, 'type': 'exact' } - - self.res = res self.need_to_run_code = False return res - diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index bd3f73e76..db228ecc2 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -293,7 +293,7 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ residual .. math:: - G\mathbf B_\text{BS}(\mathbf x) - ||\mathbf B_\text{BS}(\mathbf x)||^2 (\mathbf x_\varphi + \iota \mathbf x_\theta) + G\mathbf B_\text{BS}(\mathbf x) - \|\mathbf B_\text{BS}(\mathbf x)\|^2 (\mathbf x_\varphi + \iota \mathbf x_\theta) as well as the derivatives of this residual with respect to surface dofs, iota, and G. In the above, :math:`\mathbf x` are points on the surface, :math:`\iota` is the From a094ca550745d28e192566e3b8aadcd500fd07bc Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 23 Apr 2024 15:45:49 -0400 Subject: [PATCH 081/176] removing a comment --- src/simsopt/geo/boozersurface.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 863bb3079..24e37e18b 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -150,7 +150,6 @@ def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_ is much faster since it calls a vectorized implementation in cpp. """ - # this is essentially the scalarize option in previous implementation. This should be merged in that case... assert derivatives in [0, 1, 2] if optimize_G: sdofs = dofs[:-2] From 6e034d258b5950effc81c9bd0f0c24a1562c8ec5 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 23 Apr 2024 15:57:27 -0400 Subject: [PATCH 082/176] more linting changes --- src/simsopt/geo/boozersurface.py | 2 +- src/simsopt/geo/surfaceobjectives.py | 1 + tests/geo/test_boozersurface.py | 15 +++++---------- 3 files changed, 7 insertions(+), 11 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 24e37e18b..f4edceea4 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -678,7 +678,7 @@ def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., P, L, U = lu(J) res = { - "residual": r, "jacobian": J, "iter": i, "success": norm <= tol, "G": G, "s":s, "iota": iota, "PLU": (P, L, U), + "residual": r, "jacobian": J, "iter": i, "success": norm <= tol, "G": G, "s": s, "iota": iota, "PLU": (P, L, U), "mask": mask, 'type': 'exact' } self.res = res diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index db228ecc2..6d5f0dfd3 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -463,6 +463,7 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ return r, J, H + def parameter_derivatives(surface: Surface, shape_gradient: NDArray[Any, Float] ) -> NDArray[Any, Float]: diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 6e30d2201..e02824fea 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -398,7 +398,6 @@ def subtest_convergence_cpp_and_notcpp_same(self, vectorize): G = res['G'] return np.concatenate([x, [iota, G]]) - def test_boozer_penalty_constraints_cpp_notcpp(self): """ Test to verify cpp and python implementations of the BoozerLS objective return the same thing. @@ -406,7 +405,7 @@ def test_boozer_penalty_constraints_cpp_notcpp(self): for surfacetype in surfacetypes_list: for stellsym in stellsym_list: for weight_inv_modB in [False, True]: - for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 6, 9), (False, 7, 8),(True, 3, 3), (False, 3, 3)]: + for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 6, 9), (False, 7, 8), (True, 3, 3), (False, 3, 3)]: with self.subTest(surfacetype=surfacetype, stellsym=stellsym, optimize_G=optimize_G, @@ -434,7 +433,6 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o elif ntheta == 2: thetas = [0.2432101234, 0.9832134] - s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta, thetas=thetas, phis=phis, mpol=3, ntor=3) s.fit_to_curve(ma, 0.1) s.x = s.x + np.random.rand(s.x.size)*1e-6 @@ -456,9 +454,8 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o f1 = boozer_surface.boozer_penalty_constraints_vectorized( x, derivatives=0, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) np.testing.assert_allclose(f0, f1, atol=1e-13, rtol=1e-13) - #print(np.abs(f0-f1)/np.abs(f0)) + print(np.abs(f0-f1)/np.abs(f0)) - # deriv = 1 f0, J0 = boozer_surface.boozer_penalty_constraints( x, derivatives=1, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) @@ -470,8 +467,7 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o # check directional derivative h1 = np.random.rand(J0.size)-0.5 np.testing.assert_allclose(J0@h1, J1@h1, atol=1e-13, rtol=1e-13) - #print(np.abs(f0-f1)/np.abs(f0), np.abs(J0@h1-J1@h1)/np.abs(J0@h1)) - + print(np.abs(f0-f1)/np.abs(f0), np.abs(J0@h1-J1@h1)/np.abs(J0@h1)) # deriv = 2 f0, J0, H0 = boozer_surface.boozer_penalty_constraints( @@ -487,8 +483,7 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o np.testing.assert_allclose(f0, f1, atol=1e-13, rtol=1e-13) np.testing.assert_allclose(J0@h1, J1@h1, atol=1e-13, rtol=1e-13) np.testing.assert_allclose((H0@h1)@h2, (H1@h1)@h2, atol=1e-13, rtol=1e-13) - #print(np.abs(f0-f1)/np.abs(f0), np.abs(J0@h1-J1@h1)/np.abs(J0@h1), np.abs((H0@h1)@h2-(H1@h1)@h2)/np.abs((H0@h1)@h2)) - + print(np.abs(f0-f1)/np.abs(f0), np.abs(J0@h1-J1@h1)/np.abs(J0@h1), np.abs((H0@h1)@h2-(H1@h1)@h2)/np.abs((H0@h1)@h2)) def compute_differences(Ha, Hb): diff = np.abs(Ha.flatten() - Hb.flatten()) @@ -497,12 +492,12 @@ def compute_differences(Ha, Hb): i1 = ij1[0][0] j1 = ij1[1][0] - ij2 = np.where(rel_diff.reshape(Ha.shape) == np.max(rel_diff)) i2 = ij2[0][0] j2 = ij2[1][0] print(f'max err ({i1:03}, {j1:03}): {np.max(diff):.6e}, {Ha[i1, j1]:.6e}\nmax rel err ({i2:03}, {j2:03}): {np.max(rel_diff):.6e}, {Ha[i2,j2]:.6e}\n') compute_differences(H0, H1) + if __name__ == "__main__": unittest.main() From 0cf68fe61130210d300a815f6ae571254f457ef9 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 23 Apr 2024 16:04:40 -0400 Subject: [PATCH 083/176] more linting --- CMakeLists.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CMakeLists.txt b/CMakeLists.txt index 046f45db4..6a41b4654 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -159,6 +159,8 @@ set_target_properties(profiling target_include_directories(profiling PRIVATE "thirdparty/xtensor/include" "thirdparty/xsimd/include" "thirdparty/xtl/include" "thirdparty/eigen" "src/simsoptpp/") target_link_libraries(profiling PRIVATE fmt::fmt-header-only) + + #get_cmake_property(_variableNames VARIABLES) #list (SORT _variableNames) #foreach (_variableName ${_variableNames}) From 30e2420eea1277f7e2f45f9e8cc08a56a71d53d2 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 23 Apr 2024 16:43:19 -0400 Subject: [PATCH 084/176] more docstring and linting changes --- src/simsopt/geo/boozersurface.py | 7 +++++-- src/simsopt/geo/surface.py | 2 +- src/simsopt/geo/surfaceobjectives.py | 2 +- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index f4edceea4..1bef2e825 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -73,7 +73,9 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca i.e. the least squares residual and optionally the gradient and the Hessian of :math:`J(x)`. - For ``weight_inv_modB=False``, the residuals are unweighted, and they are multiplied by 1/ + If ``weight_inv_modB=True``, the Boozer residuals are weighted by the inverse of the field strength + (i.e. multiplied by :math:`1/\|\mathbf B \|`), otherwise, they are unweighted (multiplied by 1). Setting + this to True is useful to prevent the least squares residual from scaling with the coil currents. """ assert derivatives in [0, 1, 2] @@ -147,7 +149,8 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_weight=1., optimize_G=False, weight_inv_modB=False): """ This function returns the same thing as `boozer_penalty_constraints` when `scalarized=True`. It - is much faster since it calls a vectorized implementation in cpp. + is much faster and uses less memory since it calls a vectorized implementation in cpp. This is + especially true when `derivatives=2`, i.e., when the Hessian is requested. """ assert derivatives in [0, 1, 2] diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index ef12cb80d..9da6fba97 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -518,7 +518,7 @@ def minor_radius(self): Return the minor radius of the surface using the formula .. math:: - R_{\text{minor}} &= \sqrt{ \overline{A} / \pi } + R_{\text{minor}} = \sqrt{ \overline{A} / \pi } where :math:`\overline{A}` is the average cross sectional area. diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 6d5f0dfd3..83e831dc5 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -309,7 +309,7 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ G: a constant that is a function of the coil currents in vacuum field biotsavart: the Biot-Savart magnetic field derivatives: how many spatial derivatives of the residual to compute - weight_inv_modB: whether or not to weight the residual by :math:`\|\mathbf B\|`. This + weight_inv_modB: whether or not to weight the residual by :math:`1/\|\mathbf B\|`. This is useful to activate so that the residual does not scale with the coil currents. From 939a8594e3c20acaafb71f00c1cde6aca77a75b2 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 23 Apr 2024 19:20:05 -0400 Subject: [PATCH 085/176] missed a bug introduced when I was fixing the aligned memory access --- src/simsoptpp/boozerresidual_impl.h | 2 +- tests/geo/test_boozersurface.py | 12 +++++++----- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/src/simsoptpp/boozerresidual_impl.h b/src/simsoptpp/boozerresidual_impl.h index dccaf9f29..cb9ab3832 100644 --- a/src/simsoptpp/boozerresidual_impl.h +++ b/src/simsoptpp/boozerresidual_impl.h @@ -212,7 +212,7 @@ template void boozer_residual_impl(double G, double iota, T& simd_t drtilij2_dn(drtilij2[n]); simd_t d2res_mn = drtilij0_dm * drtilij0_dn + drtilij1_dm * drtilij1_dn + drtilij2_dm * drtilij2_dn; - int jjlimit = std::min(simd_size, ndofs+2-n); + int jjlimit = std::min(simd_size, ndofs+2-m); for(int jj = 0; jj < jjlimit; jj++){ d2res(m+jj, n) += d2res_mn[jj]; } diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index e02824fea..903ac27a9 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -405,14 +405,16 @@ def test_boozer_penalty_constraints_cpp_notcpp(self): for surfacetype in surfacetypes_list: for stellsym in stellsym_list: for weight_inv_modB in [False, True]: - for (optimize_G, nphi, ntheta) in [(True, 1, 1), (False, 1, 1), (True, 2, 2), (False, 2, 1), (True, 6, 9), (False, 7, 8), (True, 3, 3), (False, 3, 3)]: + for (optimize_G, nphi, ntheta, mpol, ntor) in [(True, 1, 1, 3, 3), (False, 1, 1, 13, 2), (True, 2, 2, 10, 3), (False, 2, 1, 3, 4), (True, 6, 9, 3, 3), (False, 7, 8, 3, 4), (True, 3, 3, 3, 3), (False, 3, 3, 3, 5)]: with self.subTest(surfacetype=surfacetype, stellsym=stellsym, optimize_G=optimize_G, - weight_inv_modB=weight_inv_modB): - self.subtest_boozer_penalty_constraints_cpp_notcpp(surfacetype, stellsym, optimize_G, nphi, ntheta, weight_inv_modB) + weight_inv_modB=weight_inv_modB, + mpol=mpol, + ntor=ntor): + self.subtest_boozer_penalty_constraints_cpp_notcpp(surfacetype, stellsym, optimize_G, nphi, ntheta, weight_inv_modB, mpol, ntor) - def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, optimize_G, nphi, ntheta, weight_inv_modB): + def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, optimize_G, nphi, ntheta, weight_inv_modB, mpol, ntor): np.random.seed(1) curves, currents, ma = get_ncsx_data() @@ -433,7 +435,7 @@ def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, o elif ntheta == 2: thetas = [0.2432101234, 0.9832134] - s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta, thetas=thetas, phis=phis, mpol=3, ntor=3) + s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta, thetas=thetas, phis=phis, mpol=mpol, ntor=ntor) s.fit_to_curve(ma, 0.1) s.x = s.x + np.random.rand(s.x.size)*1e-6 From 773b9ec6cc55aaf1c80404943f5ed125627adeed Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 23 Apr 2024 20:28:17 -0400 Subject: [PATCH 086/176] adding packages missing, but needed for unit tests --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 637981a4c..269c9588d 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -93,7 +93,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install numpy cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec pyoculus h5py + pip install numpy cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec pyoculus h5py ground bentley_ottmann - name: Install booz_xform run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform From 736d6ebf72e3f92aa2d2721447407e90fe4d1f42 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 23 Apr 2024 21:39:41 -0400 Subject: [PATCH 087/176] tightening tolerances again for unit test --- tests/geo/test_boozersurface.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 903ac27a9..98956473a 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -284,9 +284,9 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, # compute surface first using LBFGS exact and an area constraint res = boozer_surface.minimize_boozer_penalty_constraints_LBFGS( - tol=1e-10, maxiter=600, constraint_weight=100., iota=iota, G=G, + tol=1e-11, maxiter=700, constraint_weight=100., iota=iota, G=G, vectorize=vectorize) - print('Residual norm after LBFGS', np.sqrt(2*res['fun'])) + print('Residual norm after LBFGS', res['iter'], np.sqrt(2*res['fun'])) boozer_surface.recompute_bell() if second_stage == 'ls': From dbd99ba51fe7420c0fcb7b853e8b3d9c51dd0a79 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 1 May 2024 12:04:56 -0400 Subject: [PATCH 088/176] making weight_inv_modB default to True --- examples/2_Intermediate/boozer.py | 2 ++ src/simsopt/geo/boozersurface.py | 4 ++-- src/simsopt/geo/surfaceobjectives.py | 2 +- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/examples/2_Intermediate/boozer.py b/examples/2_Intermediate/boozer.py index 222a763d7..3b847d2fc 100755 --- a/examples/2_Intermediate/boozer.py +++ b/examples/2_Intermediate/boozer.py @@ -50,6 +50,8 @@ print(f"After LBFGS: iota={res['iota']:.3f}, tf={tf.J():.3f}, area={s.area():.3f}, ||residual||={np.linalg.norm(boozer_surface_residual(s, res['iota'], res['G'], bs, derivatives=0)):.3e}") if "DISPLAY" in os.environ: s.plot() + +boozer_surface.need_to_run_code = True # now drive the residual down using a specialised least squares algorithm res = boozer_surface.minimize_boozer_penalty_constraints_ls(tol=1e-10, maxiter=100, constraint_weight=100., iota=res['iota'], G=res['G'], method='manual') print(f"After Lev-Mar: iota={res['iota']:.3f}, tf={tf.J():.3f}, area={s.area():.3f}, ||residual||={np.linalg.norm(boozer_surface_residual(s, res['iota'], res['G'], bs, derivatives=0)):.3e}") diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 1bef2e825..0f4606623 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -52,7 +52,7 @@ def __init__(self, biotsavart, surface, label, targetlabel): def recompute_bell(self, parent=None): self.need_to_run_code = True - def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., scalarize=True, optimize_G=False, weight_inv_modB=False): + def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., scalarize=True, optimize_G=False, weight_inv_modB=True): r""" Define the residual @@ -146,7 +146,7 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca d2val = J.T @ J + np.sum(r[:, None, None] * H, axis=0) return val, dval, d2val - def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_weight=1., optimize_G=False, weight_inv_modB=False): + def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_weight=1., optimize_G=False, weight_inv_modB=True): """ This function returns the same thing as `boozer_penalty_constraints` when `scalarized=True`. It is much faster and uses less memory since it calls a vectorized implementation in cpp. This is diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 83e831dc5..03c2373ce 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -287,7 +287,7 @@ def dJ(self): return Derivative({self.surface: deriv}) -def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_inv_modB=False): +def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_inv_modB=True): r""" For a given surface, this function computes the residual From f4c993179c4d880b71ef297dfa219112b7a471f0 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 1 May 2024 13:45:47 -0400 Subject: [PATCH 089/176] making weight_inv_modB default to False on one function --- src/simsopt/geo/surfaceobjectives.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 03c2373ce..83e831dc5 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -287,7 +287,7 @@ def dJ(self): return Derivative({self.surface: deriv}) -def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_inv_modB=True): +def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_inv_modB=False): r""" For a given surface, this function computes the residual From e8c5433757f9d65b87f76afef7da67c6dc34f98b Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Thu, 2 May 2024 07:31:24 -0400 Subject: [PATCH 090/176] Saving residuals file for least-squares solves is now optional --- src/simsopt/solve/mpi.py | 45 ++++++++++++++++++------------- src/simsopt/solve/serial.py | 45 ++++++++++++++++++------------- tests/mhd/test_integrated_mpi.py | 2 +- tests/solve/test_least_squares.py | 11 ++++---- 4 files changed, 59 insertions(+), 44 deletions(-) diff --git a/src/simsopt/solve/mpi.py b/src/simsopt/solve/mpi.py index 6876cecaf..0f6a6988b 100644 --- a/src/simsopt/solve/mpi.py +++ b/src/simsopt/solve/mpi.py @@ -79,6 +79,7 @@ def least_squares_mpi_solve(prob: LeastSquaresProblem, abs_step: float = 1.0e-7, rel_step: float = 0.0, diff_method: str = "forward", + save_residuals: bool = False, **kwargs): """ Solve a nonlinear-least-squares minimization problem using @@ -101,6 +102,8 @@ def least_squares_mpi_solve(prob: LeastSquaresProblem, "forward". If ``centered``, centered finite differences will be used. If ``forward``, one-sided finite differences will be used. Else, error is raised. + save_residuals: Whether to save the residuals at each iteration. + This may be useful for debugging, although the file can become large. kwargs: Any arguments to pass to `scipy.optimize.least_squares `_. For instance, you can supply ``max_nfev=100`` to set @@ -159,20 +162,21 @@ def _f_proc0(x): objective_file.write(f"Problem type:\nleast_squares\nnparams:\n{prob.dof_size}\n") objective_file.write("function_evaluation,seconds") - residuals_file = open(f"residuals_{datestr}.dat", 'w') - residuals_file.write(f"Problem type:\nleast_squares\nnparams:\n{prob.dof_size}\n") - residuals_file.write("function_evaluation,seconds") - for j in range(prob.dof_size): objective_file.write(f",x({j})") objective_file.write(",objective_function\n") - for j in range(prob.dof_size): - residuals_file.write(f",x({j})") - residuals_file.write(",objective_function") - for j in range(len(residuals)): - residuals_file.write(f",F({j})") - residuals_file.write("\n") + if save_residuals: + residuals_file = open(f"residuals_{datestr}.dat", 'w') + residuals_file.write(f"Problem type:\nleast_squares\nnparams:\n{prob.dof_size}\n") + residuals_file.write("function_evaluation,seconds") + + for j in range(prob.dof_size): + residuals_file.write(f",x({j})") + residuals_file.write(",objective_function") + for j in range(len(residuals)): + residuals_file.write(f",F({j})") + residuals_file.write("\n") del_t = time() - start_time objective_file.write(f"{nevals:6d},{del_t:12.4e}") @@ -181,14 +185,16 @@ def _f_proc0(x): objective_file.write(f",{objective_val:24.16e}\n") objective_file.flush() - residuals_file.write(f"{nevals:6d},{del_t:12.4e}") - for xj in x: - residuals_file.write(f",{xj:24.16e}") - residuals_file.write(f",{objective_val:24.16e}") - for fj in unweighted_residuals: - residuals_file.write(f",{fj:24.16e}") - residuals_file.write("\n") - residuals_file.flush() + if save_residuals: + residuals_file.write(f"{nevals:6d},{del_t:12.4e}") + for xj in x: + residuals_file.write(f",{xj:24.16e}") + residuals_file.write(f",{objective_val:24.16e}") + for fj in unweighted_residuals: + residuals_file.write(f",{fj:24.16e}") + residuals_file.write("\n") + residuals_file.flush() + nevals += 1 logger.debug(f"residuals are {residuals}") return residuals @@ -225,7 +231,8 @@ def _f_proc0(x): x = result.x objective_file.close() - residuals_file.close() + if save_residuals: + residuals_file.close() datalog_started = False logger.info("Completed solve.") diff --git a/src/simsopt/solve/serial.py b/src/simsopt/solve/serial.py index 5096d828c..14865da7b 100644 --- a/src/simsopt/solve/serial.py +++ b/src/simsopt/solve/serial.py @@ -33,6 +33,7 @@ def least_squares_serial_solve(prob: LeastSquaresProblem, abs_step: float = 1.0e-7, rel_step: float = 0.0, diff_method: str = "forward", + save_residuals: bool = False, **kwargs): """ Solve a nonlinear-least-squares minimization problem using @@ -52,6 +53,8 @@ def least_squares_serial_solve(prob: LeastSquaresProblem, ``"forward"``. If ``"centered"``, centered finite differences will be used. If ``"forward"``, one-sided finite differences will be used. Else, error is raised. + save_residuals: Whether to save the residuals at each iteration. + This can be useful for debugging, although the file can become large. kwargs: Any arguments to pass to `scipy.optimize.least_squares `_. For instance, you can supply ``max_nfev=100`` to set @@ -62,7 +65,8 @@ def least_squares_serial_solve(prob: LeastSquaresProblem, datestr = datetime.now().strftime("%Y-%m-%d-%H-%M-%S") objective_file = open(f"simsopt_{datestr}.dat", 'w') - residuals_file = open(f"residuals_{datestr}.dat", 'w') + if save_residuals: + residuals_file = open(f"residuals_{datestr}.dat", 'w') nevals = 0 start_time = time() @@ -105,15 +109,16 @@ def objective(x): objective_file.write(f",x({j})") objective_file.write(",objective_function\n") - residuals_file.write( - f"Problem type:\nleast_squares\nnparams:\n{ndofs}\n") - residuals_file.write("function_evaluation,seconds") - for j in range(ndofs): - residuals_file.write(f",x({j})") - residuals_file.write(",objective_function") - for j in range(len(residuals)): - residuals_file.write(f",F({j})") - residuals_file.write("\n") + if save_residuals: + residuals_file.write( + f"Problem type:\nleast_squares\nnparams:\n{ndofs}\n") + residuals_file.write("function_evaluation,seconds") + for j in range(ndofs): + residuals_file.write(f",x({j})") + residuals_file.write(",objective_function") + for j in range(len(residuals)): + residuals_file.write(f",F({j})") + residuals_file.write("\n") elapsed_t = time() - start_time objective_file.write(f"{nevals:6d},{elapsed_t:12.4e}") @@ -123,14 +128,15 @@ def objective(x): objective_file.write("\n") objective_file.flush() - residuals_file.write(f"{nevals:6d},{elapsed_t:12.4e}") - for xj in x: - residuals_file.write(f",{xj:24.16e}") - residuals_file.write(f",{objective_val:24.16e}") - for fj in residuals: - residuals_file.write(f",{fj:24.16e}") - residuals_file.write("\n") - residuals_file.flush() + if save_residuals: + residuals_file.write(f"{nevals:6d},{elapsed_t:12.4e}") + for xj in x: + residuals_file.write(f",{xj:24.16e}") + residuals_file.write(f",{objective_val:24.16e}") + for fj in residuals: + residuals_file.write(f",{fj:24.16e}") + residuals_file.write("\n") + residuals_file.flush() nevals += 1 return residuals @@ -154,7 +160,8 @@ def objective(x): datalogging_started = False objective_file.close() - residuals_file.close() + if save_residuals: + residuals_file.close() logger.info("Completed solve.") prob.x = result.x diff --git a/tests/mhd/test_integrated_mpi.py b/tests/mhd/test_integrated_mpi.py index d00448154..40dc773c4 100644 --- a/tests/mhd/test_integrated_mpi.py +++ b/tests/mhd/test_integrated_mpi.py @@ -190,7 +190,7 @@ def test_Residue_parallelization(self): (residue2.J, 0, 1)]) # Solve for two nfevs to test if runs - least_squares_mpi_solve(prob, mpi=mpi, grad=grad, max_nfev=2) + least_squares_mpi_solve(prob, mpi=mpi, grad=grad, save_residuals=True, max_nfev=2) # No assertions, run is too short to complete, just testing if it does run diff --git a/tests/solve/test_least_squares.py b/tests/solve/test_least_squares.py index a2a04d77f..4896e1903 100755 --- a/tests/solve/test_least_squares.py +++ b/tests/solve/test_least_squares.py @@ -72,11 +72,12 @@ def test_solve_rosenbrock(self): """ with ScratchDir("."): for solver in solvers: - #for grad in [True, False]: - r = Rosenbrock() - prob = LeastSquaresProblem(0, 1, depends_on=r) - solver(prob) # , grad=grad) - self.assertAlmostEqual(prob.objective(), 0) + for save_residuals in [True, False]: + #for grad in [True, False]: + r = Rosenbrock() + prob = LeastSquaresProblem(0, 1, depends_on=r) + solver(prob, save_residuals=save_residuals) # , grad=grad) + self.assertAlmostEqual(prob.objective(), 0) if __name__ == "__main__": From 58b9bf71320482fafd473a7306a584cad9881741 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 3 May 2024 10:45:41 -0400 Subject: [PATCH 091/176] merge with master [skip ci] --- examples/2_Intermediate/boozerQA_ls_mpi.py | 7 +- .../inputs/input_ncsx/ncsx_init.json | 32 +- src/simsopt/geo/boozersurface.py | 43 +- src/simsoptpp/boozerresidual.cpp | 703 ------------------ src/simsoptpp/boozerresidual.h | 14 - tests/geo/test_boozersurface.py | 83 +-- 6 files changed, 50 insertions(+), 832 deletions(-) delete mode 100644 src/simsoptpp/boozerresidual.cpp delete mode 100644 src/simsoptpp/boozerresidual.h diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 104f09764..ec5c62d5c 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -24,6 +24,7 @@ def pprint(*args, **kwargs): comm = None size = 1 pprint = print + rank = 0 """ This example optimizes the NCSX coils and currents for QA on potentially multiple surfaces using the BoozerLS approach. @@ -59,7 +60,6 @@ def pprint(*args, **kwargs): surfaces = surfaces[:nsurfaces] boozer_surfaces = boozer_surfaces[:nsurfaces] ress = ress[:nsurfaces] - for boozer_surface, res in zip(boozer_surfaces, ress): boozer_surface.run_code('ls', res['iota'], res['G'], verbose=False) @@ -115,7 +115,6 @@ def pprint(*args, **kwargs): prevs = {'sdofs': [surface.x.copy() for surface in mpi_surfaces], 'iota': [boozer_surface.res['iota'] for boozer_surface in mpi_boozer_surfaces], 'G': [boozer_surface.res['G'] for boozer_surface in mpi_boozer_surfaces], 'J': JF.J(), 'dJ': JF.dJ().copy(), 'it': 0} - def fun(dofs): # initialize to last accepted surface values for idx, surface in enumerate(mpi_surfaces): @@ -124,8 +123,8 @@ def fun(dofs): boozer_surface.res['iota'] = prevs['iota'][idx] boozer_surface.res['G'] = prevs['G'][idx] - alldofs = MPI.COMM_WORLD.allgather(dofs) - assert np.all(np.norm(alldofs[0]-d) == 0 for d in alldofs) + #alldofs = MPI.COMM_WORLD.allgather(dofs) + #assert np.all(np.norm(alldofs[0]-d) == 0 for d in alldofs) JF.x = dofs J = JF.J() diff --git a/examples/2_Intermediate/inputs/input_ncsx/ncsx_init.json b/examples/2_Intermediate/inputs/input_ncsx/ncsx_init.json index 40adef205..557585731 100644 --- a/examples/2_Intermediate/inputs/input_ncsx/ncsx_init.json +++ b/examples/2_Intermediate/inputs/input_ncsx/ncsx_init.json @@ -19639,8 +19639,7 @@ "value": "Volume2" }, "targetlabel": -0.2960004452246598, - "constraint_weight": 100.0, - "reg": null + "constraint_weight": 100.0 }, "BiotSavart2": { "@module": "simsopt.field.biotsavart", @@ -21380,8 +21379,7 @@ "value": "Volume3" }, "targetlabel": -0.6985426179774754, - "constraint_weight": 100.0, - "reg": null + "constraint_weight": 100.0 }, "BiotSavart3": { "@module": "simsopt.field.biotsavart", @@ -23121,8 +23119,7 @@ "value": "Volume4" }, "targetlabel": -1.101084790730291, - "constraint_weight": 100.0, - "reg": null + "constraint_weight": 100.0 }, "BiotSavart4": { "@module": "simsopt.field.biotsavart", @@ -24862,8 +24859,7 @@ "value": "Volume5" }, "targetlabel": -1.5036269634831068, - "constraint_weight": 100.0, - "reg": null + "constraint_weight": 100.0 }, "BiotSavart5": { "@module": "simsopt.field.biotsavart", @@ -26603,8 +26599,7 @@ "value": "Volume6" }, "targetlabel": -1.9061691362359223, - "constraint_weight": 100.0, - "reg": null + "constraint_weight": 100.0 }, "BiotSavart6": { "@module": "simsopt.field.biotsavart", @@ -28344,8 +28339,7 @@ "value": "Volume7" }, "targetlabel": -2.308711308988738, - "constraint_weight": 100.0, - "reg": null + "constraint_weight": 100.0 }, "BiotSavart7": { "@module": "simsopt.field.biotsavart", @@ -30085,8 +30079,7 @@ "value": "Volume8" }, "targetlabel": -2.7112534817415535, - "constraint_weight": 100.0, - "reg": null + "constraint_weight": 100.0 }, "BiotSavart8": { "@module": "simsopt.field.biotsavart", @@ -31826,8 +31819,7 @@ "value": "Volume9" }, "targetlabel": -3.113795654494369, - "constraint_weight": 100.0, - "reg": null + "constraint_weight": 100.0 }, "BiotSavart9": { "@module": "simsopt.field.biotsavart", @@ -33567,8 +33559,7 @@ "value": "Volume10" }, "targetlabel": -3.5163378272471846, - "constraint_weight": 100.0, - "reg": null + "constraint_weight": 100.0 }, "BiotSavart10": { "@module": "simsopt.field.biotsavart", @@ -35308,8 +35299,7 @@ "value": "Volume11" }, "targetlabel": -3.91888, - "constraint_weight": 100.0, - "reg": null + "constraint_weight": 100.0 } } -} \ No newline at end of file +} diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 79496aef7..d9f1e22e7 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -1,6 +1,7 @@ import numpy as np from scipy.linalg import lu from scipy.optimize import minimize, least_squares +import simsoptpp as sopp from .surfaceobjectives import boozer_surface_residual, boozer_surface_dexactresidual_dcoils_dcurrents_vjp, boozer_surface_dlsqgrad_dcoils_vjp from .._core.optimizable import Optimizable @@ -65,13 +66,12 @@ def run_code(self, boozer_type, iota, G=None, verbose=True): elif boozer_type == 'ls': # first try BFGS - #res = self.minimize_boozer_penalty_constraints_ls(tol=1e-10, maxiter=100, constraint_weight=self.constraint_weight, iota=iota, G=G, method='manual') - res = self.compute_boozerls_BFGS(tol=1e-10, maxiter=1500, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) + res = self.minimize_boozer_penalty_constraints_LBFGS(tol=1e-10, maxiter=1500, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose, limited_memory=False) iota, G = res['iota'], res['G'] ## polish off using Newton's method self.need_to_run_code = True - res = self.compute_boozerls_newton(tol=1e-11, maxiter=40, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) + res = self.minimize_boozer_penalty_constraints_newton(tol=1e-11, maxiter=40, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) return res else: raise Exception(f"boozer_type not supported: {boozer_type}") @@ -111,17 +111,17 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca sdofs = x[:-1] iota = x[-1] G = None - nsurfdofs = sdofs.size s = self.surface + num_res = 3 * s.quadpoints_phi.size * s.quadpoints_theta.size biotsavart = self.biotsavart s.set_dofs(sdofs) boozer = boozer_surface_residual(s, iota, G, biotsavart, derivatives=derivatives, weight_inv_modB=weight_inv_modB) + boozer = tuple([b/np.sqrt(num_res) for b in boozer]) r = boozer[0] - l = self.label.J() rl = (l-self.targetlabel) rz = (s.gamma()[0, 0, 2] - 0.) @@ -216,6 +216,7 @@ def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_ if derivatives == 2: d2B_by_dXdX = biotsavart.d2B_by_dXdX().reshape((nphi, ntheta, 3, 3, 3)) + num_res = 3 * s.quadpoints_phi.size * s.quadpoints_theta.size if derivatives == 0: val = sopp.boozer_residual(G, iota, xphi, xtheta, B, weight_inv_modB) boozer = val, @@ -225,6 +226,8 @@ def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_ elif derivatives == 2: val, dval, d2val = sopp.boozer_residual_ds2(G, iota, B, dB_dx, d2B_by_dXdX, xphi, xtheta, dx_dc, dxphi_dc, dxtheta_dc, weight_inv_modB) boozer = val, dval, d2val + + boozer = tuple([b/num_res for b in boozer]) lab = self.label.J() @@ -328,7 +331,7 @@ def boozer_exact_constraints(self, xl, derivatives=0, optimize_G=True): dres[-1, :-2] = drz return res, dres - def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, vectorize=False): + def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, vectorize=True, limited_memory=True, verbose=False): r""" This function tries to find the surface that approximately solves @@ -353,9 +356,15 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons fun_name = self.boozer_penalty_constraints_vectorized if vectorize else self.boozer_penalty_constraints fun = lambda x: fun_name(x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) + method = 'L-BFGS-B' if limited_memory else 'BFGS' + options = {'maxiter': maxiter, 'gtol': tol} + if limited_memory: + options['maxcor'] = 200 + options['ftol'] = tol + res = minimize( - fun, x, jac=True, method='L-BFGS-B', - options={'maxiter': maxiter, 'ftol': tol, 'gtol': tol, 'maxcor': 200}) + fun, x, jac=True, method=method, + options=options) resdict = { "fun": res.fun, "gradient": res.jac, "iter": res.nit, "info": res, "success": res.success, "G": None, @@ -373,9 +382,13 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons self.res = resdict self.need_to_run_code = False + + if verbose: + print(f"{method} solve - {resdict['success']} iter={resdict['iter']}, iota={resdict['iota']:.16f}, ||grad||_inf = {np.linalg.norm(resdict['gradient'], ord=np.inf):.3e}", flush=True) + return resdict - def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0., vectorize=False): + def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0., vectorize=True, verbose=False): """ This function does the same as :mod:`minimize_boozer_penalty_constraints_LBFGS`, but instead of LBFGS it uses Newton's method. @@ -403,11 +416,14 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons val, dval, d2val = fun_name(x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) norm = np.linalg.norm(dval) i = i+1 - + r = self.boozer_penalty_constraints( x, derivatives=0, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) + + P, L, U = lu(d2val) res = { - "residual": r, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "G": None, + "residual": r, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "G": None, + "PLU" : (P, L, U), "vjp": boozer_surface_dlsqgrad_dcoils_vjp, "type": "ls" } if G is None: s.set_dofs(x[:-1]) @@ -417,11 +433,14 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons iota = x[-2] G = x[-1] res['G'] = G - res['s'] = s res['iota'] = iota self.res = res self.need_to_run_code = False + + if verbose: + print(f"NEWTON solve - {res['success']} iter={res['iter']}, iota={res['iota']:.16f}, ||grad||_inf = {np.linalg.norm(res['jacobian'], ord=np.inf):.3e}", flush=True) + return res def minimize_boozer_penalty_constraints_ls(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, method='lm'): diff --git a/src/simsoptpp/boozerresidual.cpp b/src/simsoptpp/boozerresidual.cpp deleted file mode 100644 index 821e02e96..000000000 --- a/src/simsoptpp/boozerresidual.cpp +++ /dev/null @@ -1,703 +0,0 @@ -#include "boozerresidual.h" - -#include "xsimd/xsimd.hpp" -#include "simdhelpers.h" -#include "vec3dsimd.h" -#include "xtensor/xarray.hpp" -#include "xtensor/xview.hpp" -#include "xtensor/xstrided_view.hpp" -#include -#include "xtensor/xadapt.hpp" - -double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B){ - int nphi = B.shape(0); - int ntheta = B.shape(1); - Array res = xt::zeros({nphi, ntheta, 3}); - int num_points = 3 * nphi * ntheta; - for(int i=0; i -void boozer_residual_ds_impl(double G, double iota, T& B, T& dB_dx, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres){ - int nphi = xphi.shape(0); - int ntheta = xtheta.shape(1); - size_t ndofs = dx_ds.shape(3); - int num_points = 3 * nphi * ntheta; - - constexpr size_t simd_size = xsimd::simd_type::size; - auto dx_ds_ij0 = AlignedPaddedVec(ndofs, 0); - auto dx_ds_ij1 = AlignedPaddedVec(ndofs, 0); - auto dx_ds_ij2 = AlignedPaddedVec(ndofs, 0); - auto dxphi_ds_ij0 = AlignedPaddedVec(ndofs, 0); - auto dxphi_ds_ij1 = AlignedPaddedVec(ndofs, 0); - auto dxphi_ds_ij2 = AlignedPaddedVec(ndofs, 0); - auto dxtheta_ds_ij0 = AlignedPaddedVec(ndofs, 0); - auto dxtheta_ds_ij1 = AlignedPaddedVec(ndofs, 0); - auto dxtheta_ds_ij2 = AlignedPaddedVec(ndofs, 0); - - simd_t it(iota); - simd_t GG(G); - for(int i=0; i boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds){ - // flatten the quadrature points - int nphi = xphi.shape(0); - int ntheta = xtheta.shape(1); - size_t ndofs = dx_ds.shape(3); - int num_points = nphi * ntheta; - - int num_threads= 0; - #pragma omp parallel reduction(+:num_threads) - num_threads += 1; - - int batch_size = num_points / num_threads; - if(num_points % num_threads != 0) - batch_size++; - - vector res_list(num_threads, 0.); - vector> dres_list; - - for(int idx = 0; idx < num_threads; idx++){ - dres_list.push_back(xt::zeros({ndofs+2})); - } - - double res =0.; - xt::xarray dres =xt::zeros({ndofs+2}); - - - #pragma omp parallel for - for (int idx = 0; idx < num_threads; ++idx) { - int idx_start = batch_size * idx; - int idx_end = batch_size * (idx+1) > num_points ? num_points : batch_size*(idx+1); - size_t diff = idx_end-idx_start; - - size_t size_B = 3; - size_t size_dB_dx = 3 * 3; - size_t size_d2B_dx2 = 3 * 3 * 3; - size_t size_xphi = 3; - size_t size_xtheta = 3; - size_t size_dx_ds = 3 * ndofs; - size_t size_dxphi_ds = 3 * ndofs; - size_t size_dxtheta_ds = 3 * ndofs; - - vector shape_B = {diff, 1, 3}; - vector shape_dB_dx = {diff, 1, 3, 3}; - vector shape_d2B_dx2 = {diff, 1, 3, 3, 3}; - vector shape_xphi = {diff, 1, 3}; - vector shape_xtheta = {diff, 1, 3}; - vector shape_dx_ds = {diff, 1, 3, ndofs}; - vector shape_dxphi_ds = {diff, 1, 3, ndofs}; - vector shape_dxtheta_ds = {diff, 1, 3, ndofs}; - - xt::xarray bB = xt::adapt(B.data() + idx_start*size_B , diff*size_B , xt::no_ownership(), shape_B ); - xt::xarray bdB_dx = xt::adapt(dB_dx.data() + idx_start*size_dB_dx , diff*size_dB_dx , xt::no_ownership(), shape_dB_dx ); - xt::xarray bxphi = xt::adapt(xphi.data() + idx_start*size_xphi , diff*size_xphi , xt::no_ownership(), shape_xphi ); - xt::xarray bxtheta = xt::adapt(xtheta.data() + idx_start*size_xtheta , diff*size_xtheta , xt::no_ownership(), shape_xtheta ); - xt::xarray bdx_ds = xt::adapt(dx_ds.data() + idx_start*size_dx_ds , diff*size_dx_ds , xt::no_ownership(), shape_dx_ds ); - xt::xarray bdxphi_ds = xt::adapt(dxphi_ds.data() + idx_start*size_dxphi_ds , diff*size_dxphi_ds , xt::no_ownership(), shape_dxphi_ds ); - xt::xarray bdxtheta_ds = xt::adapt(dxtheta_ds.data()+ idx_start*size_dxtheta_ds, diff*size_dxtheta_ds, xt::no_ownership(), shape_dxtheta_ds); - - boozer_residual_ds_impl>(G, iota, bB, bdB_dx, bxphi, bxtheta, bdx_ds, bdxphi_ds, bdxtheta_ds, res_list[idx], dres_list[idx]); - res_list[idx] *= (idx_end-idx_start)*3; - dres_list[idx] *= (idx_end-idx_start)*3; - } - - for(int i=0; i < num_threads; i++){ - res+=res_list[i]/num_points/3.; - dres+=dres_list[i]/num_points/3.; - } - - auto tup = std::make_tuple(res, dres); - return tup; -} - - - - -template -void boozer_residual_ds2_impl(double G, double iota, T& B, T& dB_dx, T& d2B_dx2, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres, T& d2res){ - int nphi = xphi.shape(0); - int ntheta = xtheta.shape(1); - size_t ndofs = dx_ds.shape(3); - int num_points = 3 * nphi * ntheta; - - constexpr size_t simd_size = xsimd::simd_type::size; - auto dx_ds_ij0 = AlignedPaddedVec(ndofs, 0); - auto dx_ds_ij1 = AlignedPaddedVec(ndofs, 0); - auto dx_ds_ij2 = AlignedPaddedVec(ndofs, 0); - auto dxphi_ds_ij0 = AlignedPaddedVec(ndofs, 0); - auto dxphi_ds_ij1 = AlignedPaddedVec(ndofs, 0); - auto dxphi_ds_ij2 = AlignedPaddedVec(ndofs, 0); - auto dxtheta_ds_ij0 = AlignedPaddedVec(ndofs, 0); - auto dxtheta_ds_ij1 = AlignedPaddedVec(ndofs, 0); - auto dxtheta_ds_ij2 = AlignedPaddedVec(ndofs, 0); - - auto drtilij0 = AlignedPaddedVec(ndofs+2, 0); - auto drtilij1 = AlignedPaddedVec(ndofs+2, 0); - auto drtilij2 = AlignedPaddedVec(ndofs+2, 0); - - auto dresij0 = AlignedPaddedVec(ndofs+2, 0); - auto dresij1 = AlignedPaddedVec(ndofs+2, 0); - auto dresij2 = AlignedPaddedVec(ndofs+2, 0); - - auto dw_ij = AlignedPaddedVec(ndofs+2, 0); - - auto dtang_ij0 = AlignedPaddedVec(ndofs+2, 0); - auto dtang_ij1 = AlignedPaddedVec(ndofs+2, 0); - auto dtang_ij2 = AlignedPaddedVec(ndofs+2, 0); - - auto dB2_ij = AlignedPaddedVec(ndofs+2, 0); - auto dBij0 = AlignedPaddedVec(ndofs+2, 0); - auto dBij1 = AlignedPaddedVec(ndofs+2, 0); - auto dBij2 = AlignedPaddedVec(ndofs+2, 0); - auto dmodB_ij = AlignedPaddedVec(ndofs+2, 0); - - simd_t it(iota); - simd_t GG(G); - - for(int i=0; i boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds){ - // flatten the quadrature points - int nphi = xphi.shape(0); - int ntheta = xtheta.shape(1); - size_t ndofs = dx_ds.shape(3); - int num_points = nphi * ntheta; - - int num_threads= 0; - #pragma omp parallel reduction(+:num_threads) - num_threads += 1; - - int batch_size = num_points / num_threads; - if(num_points % num_threads != 0) - batch_size++; - - vector res_list(num_threads, 0.); - vector> dres_list; - vector> d2res_list; - - for(int idx = 0; idx < num_threads; idx++){ - dres_list.push_back(xt::zeros({ndofs+2})); - d2res_list.push_back(xt::zeros({ndofs+2, ndofs+2})); - } - - double res =0.; - xt::xarray dres =xt::zeros({ndofs+2}); - xt::xarray d2res=xt::zeros({ndofs+2, ndofs+2}); - - - #pragma omp parallel for - for (int idx = 0; idx < num_threads; ++idx) { - int idx_start = batch_size * idx; - int idx_end = batch_size * (idx+1) > num_points ? num_points : batch_size*(idx+1); - size_t diff = idx_end-idx_start; - - size_t size_B = 3; - size_t size_dB_dx = 3 * 3; - size_t size_d2B_dx2 = 3 * 3 * 3; - size_t size_xphi = 3; - size_t size_xtheta = 3; - size_t size_dx_ds = 3 * ndofs; - size_t size_dxphi_ds = 3 * ndofs; - size_t size_dxtheta_ds = 3 * ndofs; - - vector shape_B = {diff, 1, 3}; - vector shape_dB_dx = {diff, 1, 3, 3}; - vector shape_d2B_dx2 = {diff, 1, 3, 3, 3}; - vector shape_xphi = {diff, 1, 3}; - vector shape_xtheta = {diff, 1, 3}; - vector shape_dx_ds = {diff, 1, 3, ndofs}; - vector shape_dxphi_ds = {diff, 1, 3, ndofs}; - vector shape_dxtheta_ds = {diff, 1, 3, ndofs}; - - xt::xarray bB = xt::adapt(B.data() + idx_start*size_B , diff*size_B , xt::no_ownership(), shape_B ); - xt::xarray bdB_dx = xt::adapt(dB_dx.data() + idx_start*size_dB_dx , diff*size_dB_dx , xt::no_ownership(), shape_dB_dx ); - xt::xarray bdB2_dx2 = xt::adapt(d2B_dx2.data() + idx_start*size_d2B_dx2 , diff*size_d2B_dx2 , xt::no_ownership(), shape_d2B_dx2 ); - xt::xarray bxphi = xt::adapt(xphi.data() + idx_start*size_xphi , diff*size_xphi , xt::no_ownership(), shape_xphi ); - xt::xarray bxtheta = xt::adapt(xtheta.data() + idx_start*size_xtheta , diff*size_xtheta , xt::no_ownership(), shape_xtheta ); - xt::xarray bdx_ds = xt::adapt(dx_ds.data() + idx_start*size_dx_ds , diff*size_dx_ds , xt::no_ownership(), shape_dx_ds ); - xt::xarray bdxphi_ds = xt::adapt(dxphi_ds.data() + idx_start*size_dxphi_ds , diff*size_dxphi_ds , xt::no_ownership(), shape_dxphi_ds ); - xt::xarray bdxtheta_ds = xt::adapt(dxtheta_ds.data()+ idx_start*size_dxtheta_ds, diff*size_dxtheta_ds, xt::no_ownership(), shape_dxtheta_ds); - - boozer_residual_ds2_impl>(G, iota, bB, bdB_dx, bdB2_dx2, bxphi, bxtheta, bdx_ds, bdxphi_ds, bdxtheta_ds, res_list[idx], dres_list[idx], d2res_list[idx]); - res_list[idx] *= (idx_end-idx_start)*3; - dres_list[idx] *= (idx_end-idx_start)*3; - d2res_list[idx] *= (idx_end-idx_start)*3; - } - - for(int i=0; i < num_threads; i++){ - res+=res_list[i]/num_points/3.; - dres+=dres_list[i]/num_points/3.; - d2res+=d2res_list[i]/num_points/3.; - } - - auto tup = std::make_tuple(res, dres, d2res); - return tup; -} - -Array boozer_residual_dc(double G, Array& dB_dc, Array& B, Array& tang, Array& B2, Array& dxphi_dc, double iota, Array& dxtheta_dc){ - int nphi = dB_dc.shape(0); - int ntheta = dB_dc.shape(1); - int ndofs = dB_dc.shape(3); - Array res = xt::zeros({nphi, ntheta, 3, ndofs}); - double* B_dB_dc = new double[ndofs]; - for(int i=0; i Array; -using std::vector; - -double boozer_residual(double G, double iota, Array& xphi, Array& xtheta, Array& B); -std::tuple boozer_residual_ds(double G, double iota, Array& B, Array& dB_dx, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds); -std::tuple boozer_residual_ds2(double G, double iota, Array& B, Array& dB_dx, Array& d2B_dx2, Array& xphi, Array& xtheta, Array& dx_ds, Array& dxphi_ds, Array& dxtheta_ds); - - -Array boozer_residual_dc(double G, Array& dB_dc, Array& B, Array& tang, Array& B2, Array& dxphi_dc, double iota, Array& dxtheta_dc); diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 3c40f6d69..8851f6a29 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -281,21 +281,22 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, G = 2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi)) else: G = None - + + cw = (s.quadpoints_phi.size * s.quadpoints_theta.size * 3) # compute surface first using LBFGS exact and an area constraint res = boozer_surface.minimize_boozer_penalty_constraints_LBFGS( - tol=1e-11, maxiter=700, constraint_weight=100., iota=iota, G=G, + tol=1e-11, maxiter=700, constraint_weight=100/cw, iota=iota, G=G, vectorize=vectorize) print('Residual norm after LBFGS', res['iter'], np.sqrt(2*res['fun'])) boozer_surface.recompute_bell() if second_stage == 'ls': res = boozer_surface.minimize_boozer_penalty_constraints_ls( - tol=1e-11, maxiter=100, constraint_weight=1000., + tol=1e-11, maxiter=100, constraint_weight=1000./cw, iota=res['iota'], G=res['G']) elif second_stage == 'newton': res = boozer_surface.minimize_boozer_penalty_constraints_newton( - tol=1e-10, maxiter=20, constraint_weight=100., + tol=1e-10, maxiter=20, constraint_weight=100./cw, iota=res['iota'], G=res['G'], stab=1e-4, vectorize=vectorize) elif second_stage == 'newton_exact': res = boozer_surface.minimize_boozer_exact_constraints_newton( @@ -500,80 +501,6 @@ def compute_differences(Ha, Hb): print(f'max err ({i1:03}, {j1:03}): {np.max(diff):.6e}, {Ha[i1, j1]:.6e}\nmax rel err ({i2:03}, {j2:03}): {np.max(rel_diff):.6e}, {Ha[i2,j2]:.6e}\n') compute_differences(H0, H1) - def test_boozer_penalty_constraints_cpp_notcpp(self): - """ - Test to verify cpp and python implementations of the BoozerLS objective return the same thing. - """ - for surfacetype in surfacetypes_list: - for stellsym in stellsym_list: - for (optimize_G, nphi, ntheta) in [(True, 10, 17), (False, 13, 21)]: - with self.subTest(surfacetype=surfacetype, - stellsym=stellsym, - optimize_G=optimize_G): - self.subtest_boozer_penalty_constraints_cpp_notcpp(surfacetype, stellsym, optimize_G, nphi, ntheta) - - def subtest_boozer_penalty_constraints_cpp_notcpp(self, surfacetype, stellsym, optimize_G, nphi, ntheta): - - np.random.seed(1) - curves, currents, ma = get_ncsx_data() - coils = coils_via_symmetries(curves, currents, 3, stellsym) - bs = BiotSavart(coils) - bs_tf = BiotSavart(coils) - current_sum = sum(abs(c.current.get_value()) for c in coils) - - s = get_surface(surfacetype, stellsym, nphi=nphi, ntheta=ntheta) - s.fit_to_curve(ma, 0.1) - s.x = s.x + np.random.rand(s.x.size)*1e-6 - - tf = ToroidalFlux(s, bs_tf, nphi=51, ntheta=51) - - tf_target = 0.1 - boozer_surface = BoozerSurface(bs, s, tf, tf_target) - - iota = -0.3 - x = np.concatenate((s.get_dofs(), [iota])) - if optimize_G: - x = np.concatenate( - (x, [2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi))])) - - w = 1e2 - f0, J0, H0 = boozer_surface.boozer_penalty_constraints( - x, derivatives=2, constraint_weight=w, optimize_G=optimize_G, weight_inv_modB=True) - f1, J1, H1 = boozer_surface.boozerls_penalty( - x, derivatives=2, constraint_weight=w, optimize_G=optimize_G) - - # f1, and J1 scale the quadratic residual terms by 1/(number of residuals), while f0 and J0 do not. - # rescale below so that both quantities are comparable. - diff1 = (boozer_surface.label.J() - boozer_surface.targetlabel) - diff2 = s.gamma()[0, 0, 2] - f1 -= 0.5 * w * (diff1**2 + diff2**2) - f1 *= (3 * len(s.quadpoints_phi)*len(s.quadpoints_theta)) - f1 += 0.5 * w * (diff1**2 + diff2**2) - - to_add = [0] - if optimize_G: - to_add = [0, 0] - - dl = np.append(boozer_surface.label.dJ(partials=True)(s), to_add) - drz = np.append(s.dgamma_by_dcoeff()[0, 0, 2, :], to_add) - J1 -= w * (diff1 * dl + diff2 * drz) - J1 *= (3*len(s.quadpoints_phi)*len(s.quadpoints_theta)) - J1 += w * (diff1 * dl + diff2 * drz) - - nsurfdofs = s.x.size - d2l = np.zeros((x.size, x.size)) - d2l[:nsurfdofs, :nsurfdofs] = boozer_surface.label.d2J_by_dsurfacecoefficientsdsurfacecoefficients() - H1 -= w * dl[:, None] * dl[None, :] + w * diff1 * d2l - H1 -= w * drz[:, None] * drz[None, :] - H1 *= (3*len(s.quadpoints_phi)*len(s.quadpoints_theta)) - H1 += w * dl[:, None] * dl[None, :] + w * diff1 * d2l - H1 += w * drz[:, None] * drz[None, :] - - self.assertAlmostEqual(f0, f1) - np.testing.assert_allclose(J0, J1) - norm = np.max(np.abs(H0)) - assert np.all(np.abs((H0-H1)/norm) < 1e-13) - if __name__ == "__main__": unittest.main() From 1df2242745b59c5e1c7565674315e6d79bde0e21 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 3 May 2024 13:07:36 -0400 Subject: [PATCH 092/176] added unit test for BoozerResidual objective --- src/simsopt/geo/boozersurface.py | 2 ++ src/simsopt/geo/surfaceobjectives.py | 14 +------------ tests/geo/surface_test_helpers.py | 31 +++++++++++++++++++--------- tests/geo/test_surface_objectives.py | 30 +++++++++++++++++++++++++-- 4 files changed, 52 insertions(+), 25 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index d9f1e22e7..ecfcd3581 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -119,6 +119,7 @@ def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., sca s.set_dofs(sdofs) boozer = boozer_surface_residual(s, iota, G, biotsavart, derivatives=derivatives, weight_inv_modB=weight_inv_modB) + # normalizing the residuals here boozer = tuple([b/np.sqrt(num_res) for b in boozer]) r = boozer[0] @@ -227,6 +228,7 @@ def boozer_penalty_constraints_vectorized(self, dofs, derivatives=0, constraint_ val, dval, d2val = sopp.boozer_residual_ds2(G, iota, B, dB_dx, d2B_by_dXdX, xphi, xtheta, dx_dc, dxphi_dc, dxtheta_dc, weight_inv_modB) boozer = val, dval, d2val + # normalizing the residuals here boozer = tuple([b/num_res for b in boozer]) lab = self.label.J() diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index aa7cb1afc..f3e3b162b 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -1016,12 +1016,6 @@ def compute(self): Jtil = np.concatenate((J/np.sqrt(num_points), np.sqrt(self.constraint_weight) * dl[None, :]), axis=0) dJ_ds = Jtil.T@rtil - if booz_surf.res['type'] == 'lscons': - if booz_surf.surface.stellsym: - dJ_ds = np.concatenate((dJ_ds, [0.])) - else: - dJ_ds = np.concatenate((dJ_ds, [0., 0.])) - adj = forward_backward(P, L, U, dJ_ds) adj_times_dg_dcoil = dconstraint_dcoils_vjp(adj, booz_surf, iota, G) @@ -1096,13 +1090,7 @@ def boozer_surface_dlsqgrad_dcoils_vjp(lm, booz_surf, iota, G): G is known for exact boozer surfaces, so if G=None is passed, then that value is used instead. """ - - if booz_surf.res['type'] == 'lscons': - if booz_surf.surface.stellsym: - lm = lm[:-1] - else: - lm = lm[:-2] - + surface = booz_surf.surface biotsavart = booz_surf.biotsavart nphi = surface.quadpoints_phi.size diff --git a/tests/geo/surface_test_helpers.py b/tests/geo/surface_test_helpers.py index 6effa0e37..1aa40586d 100644 --- a/tests/geo/surface_test_helpers.py +++ b/tests/geo/surface_test_helpers.py @@ -3,7 +3,7 @@ import numpy as np from simsopt.configs import get_ncsx_data from simsopt.field import coils_via_symmetries, BiotSavart -from simsopt.geo import Volume, Area, ToroidalFlux, SurfaceXYZFourier, SurfaceRZFourier, SurfaceXYZTensorFourier, BoozerSurface +from simsopt.geo import Volume, Area, ToroidalFlux, SurfaceXYZFourier, SurfaceRZFourier, SurfaceXYZTensorFourier, BoozerSurface, AspectRatio TEST_DIR = Path(__file__).parent / ".." / "test_files" @@ -74,12 +74,12 @@ def get_exact_surface(surface_type='SurfaceXYZFourier'): return s -def get_boozer_surface(label="Volume", nphi=None, ntheta=None): +def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exact'): """ Returns a boozer surface that will be used in unit tests. """ - assert label == "Volume" or label == "ToroidalFlux" or label == "Area" + assert label == "Volume" or label == "ToroidalFlux" or label == "Area" or label == "AspectRatio" base_curves, base_currents, ma = get_ncsx_data() coils = coils_via_symmetries(base_curves, base_currents, 3, True) @@ -88,13 +88,18 @@ def get_boozer_surface(label="Volume", nphi=None, ntheta=None): G0 = 2. * np.pi * current_sum * (4 * np.pi * 10**(-7) / (2 * np.pi)) ## RESOLUTION DETAILS OF SURFACE ON WHICH WE OPTIMIZE FOR QA - mpol = 6 - ntor = 6 + mpol = 6 if boozer_type == 'exact' else 3 + ntor = 6 if boozer_type == 'exact' else 3 stellsym = True nfp = 3 + + if boozer_type == 'exact': + phis = np.linspace(0, 1/nfp, 2*ntor+1, endpoint=False) + thetas = np.linspace(0, 1, 2*mpol+1, endpoint=False) + elif boozer_type == 'ls': + phis = np.linspace(0, 1/nfp, 20, endpoint=False) + thetas = np.linspace(0, 1, 20, endpoint=False) - phis = np.linspace(0, 1/nfp, 2*ntor+1, endpoint=False) - thetas = np.linspace(0, 1, 2*mpol+1, endpoint=False) s = SurfaceXYZTensorFourier( mpol=mpol, ntor=ntor, stellsym=stellsym, nfp=nfp, quadpoints_phi=phis, quadpoints_theta=thetas) s.fit_to_curve(ma, 0.1, flip_theta=True) @@ -110,10 +115,16 @@ def get_boozer_surface(label="Volume", nphi=None, ntheta=None): elif label == "Area": lab = Area(s, nphi=nphi, ntheta=ntheta) lab_target = lab.J() + elif label == "AspectRatio": + lab = AspectRatio(s, nphi=nphi, ntheta=ntheta) + lab_target = lab.J()*0.9 ## COMPUTE THE SURFACE - boozer_surface = BoozerSurface(bs, s, lab, lab_target) - res = boozer_surface.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=iota, G=G0) - print(f"NEWTON {res['success']}: iter={res['iter']}, iota={res['iota']:.3f}, vol={s.volume():.3f}") + cw = None if boozer_type == 'exact' else 100. + boozer_surface = BoozerSurface(bs, s, lab, lab_target, constraint_weight=cw) + boozer_surface.run_code(boozer_type, iota, G=G0, verbose=True) + + #res = boozer_surface.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=iota, G=G0) + #print(f"NEWTON {res['success']}: iter={res['iter']}, iota={res['iota']:.3f}, vol={s.volume():.3f}") return bs, boozer_surface diff --git a/tests/geo/test_surface_objectives.py b/tests/geo/test_surface_objectives.py index 759d3ccaf..895df1bf6 100644 --- a/tests/geo/test_surface_objectives.py +++ b/tests/geo/test_surface_objectives.py @@ -2,7 +2,7 @@ import numpy as np from simsopt.field.biotsavart import BiotSavart from simsopt.field.coil import coils_via_symmetries -from simsopt.geo.surfaceobjectives import ToroidalFlux, QfmResidual, parameter_derivatives, Volume, PrincipalCurvature, MajorRadius, Iotas, NonQuasiSymmetricRatio +from simsopt.geo.surfaceobjectives import ToroidalFlux, QfmResidual, parameter_derivatives, Volume, PrincipalCurvature, MajorRadius, Iotas, NonQuasiSymmetricRatio, AspectRatio, BoozerResidual from simsopt.configs.zoo import get_ncsx_data from .surface_test_helpers import get_surface, get_exact_surface, get_boozer_surface @@ -338,9 +338,35 @@ def df(dofs): epsilons=np.power(2., -np.asarray(range(13, 19)))) +class BoozerResidualTests(unittest.TestCase): + def test_boozerresidual_derivative(self): + """ + Taylor test for derivative of surface non QS ratio wrt coil parameters + """ + for label in ["Volume"]: + with self.subTest(label=label): + self.subtest_boozerresidual_derivative(label) + + def subtest_boozerresidual_derivative(self, label): + bs, boozer_surface = get_boozer_surface(label=label, boozer_type='ls') + coeffs = bs.x + br = BoozerResidual(boozer_surface, bs) + + def f(dofs): + bs.x = dofs + return br.J() + + def df(dofs): + bs.x = dofs + return br.dJ() + + taylor_test1(f, df, coeffs, + epsilons=np.power(2., -np.asarray(range(13, 19)))) + + class LabelTests(unittest.TestCase): def test_label_surface_derivative1(self): - for label in ["Volume", "ToroidalFlux", "Area"]: + for label in ["Volume", "ToroidalFlux", "Area", "AspectRatio"]: with self.subTest(label=label): self.subtest_label_derivative1(label) From b6e0b66abcc61a81b7b1e0f4c92049fdd78b1790 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 3 May 2024 13:16:40 -0400 Subject: [PATCH 093/176] added more unit tests --- examples/2_Intermediate/boozerQA_ls_mpi.py | 7 ++-- tests/geo/test_surface_objectives.py | 46 +++++++++++++--------- 2 files changed, 30 insertions(+), 23 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index ec5c62d5c..fa0fdb7f9 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -1,10 +1,9 @@ #!/usr/bin/env python3 -from simsopt.geo import SurfaceXYZTensorFourier, SurfaceRZFourier, BoozerSurface, curves_to_vtk, boozer_surface_residual, \ - ToroidalFlux, Volume, MajorRadius, CurveLength, CurveCurveDistance, NonQuasiSymmetricRatio, Iotas, BoozerResidual, \ - LpCurveCurvature, MeanSquaredCurvature, ArclengthVariation +from simsopt.geo import curves_to_vtk, MajorRadius, CurveLength, CurveCurveDistance, NonQuasiSymmetricRatio, Iotas,\ + BoozerResidual, LpCurveCurvature, MeanSquaredCurvature, ArclengthVariation from simsopt._core import load from simsopt.objectives import MPIObjective, MPIOptimizable -from simsopt.field import BiotSavart, coils_via_symmetries +from simsopt.field import BiotSavart from simsopt.configs import get_ncsx_data from simsopt.objectives import QuadraticPenalty from scipy.optimize import minimize diff --git a/tests/geo/test_surface_objectives.py b/tests/geo/test_surface_objectives.py index 895df1bf6..146dd20a2 100644 --- a/tests/geo/test_surface_objectives.py +++ b/tests/geo/test_surface_objectives.py @@ -259,13 +259,15 @@ def test_major_radius_derivative(self): """ Taylor test for derivative of surface major radius wrt coil parameters """ - - for label in ["Volume", "ToroidalFlux"]: - with self.subTest(label=label): - self.subtest_major_radius_surface_derivative(label) - - def subtest_major_radius_surface_derivative(self, label): - bs, boozer_surface = get_boozer_surface(label=label, nphi=51, ntheta=51) + for boozer_type in ['exact', 'ls']: + for label in ["Volume", "ToroidalFlux"]: + with self.subTest(label=label, boozer_type=boozer_type): + if boozer_type == 'ls' and label == 'ToroidalFlux': + continue + self.subtest_major_radius_surface_derivative(label, boozer_type) + + def subtest_major_radius_surface_derivative(self, label, boozer_type): + bs, boozer_surface = get_boozer_surface(label=label, nphi=51, ntheta=51, boozer_type=boozer_type) coeffs = bs.x mr = MajorRadius(boozer_surface) @@ -286,16 +288,19 @@ def test_iotas_derivative(self): Taylor test for derivative of surface rotational transform wrt coil parameters """ - for label in ["Volume", "ToroidalFlux"]: - with self.subTest(label=label): - self.subtest_iotas_derivative(label) + for boozer_type in ['exact', 'ls']: + for label in ["Volume", "ToroidalFlux"]: + if boozer_type == 'ls' and label == 'ToroidalFlux': + continue + with self.subTest(label=label, boozer_type=boozer_type): + self.subtest_iotas_derivative(label, boozer_type) - def subtest_iotas_derivative(self, label): + def subtest_iotas_derivative(self, label, boozer_type): """ Taylor test for derivative of surface rotational transform wrt coil parameters """ - bs, boozer_surface = get_boozer_surface(label=label) + bs, boozer_surface = get_boozer_surface(label=label, boozer_type=boozer_type) coeffs = bs.x io = Iotas(boozer_surface) @@ -316,13 +321,16 @@ def test_nonQSratio_derivative(self): """ Taylor test for derivative of surface non QS ratio wrt coil parameters """ - for label in ["Volume", "ToroidalFlux"]: - for axis in [False, True]: - with self.subTest(label=label, axis=axis): - self.subtest_nonQSratio_derivative(label, axis) - - def subtest_nonQSratio_derivative(self, label, axis): - bs, boozer_surface = get_boozer_surface(label=label) + for boozer_type in ['exact', 'ls']: + for label in ["Volume", "ToroidalFlux"]: + if boozer_type == 'ls' and label == 'ToroidalFlux': + continue + for axis in [False, True]: + with self.subTest(label=label, axis=axis, boozer_type=boozer_type): + self.subtest_nonQSratio_derivative(label, axis, boozer_type) + + def subtest_nonQSratio_derivative(self, label, axis, boozer_type): + bs, boozer_surface = get_boozer_surface(label=label, boozer_type=boozer_type) coeffs = bs.x io = NonQuasiSymmetricRatio(boozer_surface, bs, quasi_poloidal=axis) From 251fadef7ad0d30c282a23182feb23909171bfca Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 3 May 2024 13:25:20 -0400 Subject: [PATCH 094/176] changed to pprint to proc0_print --- examples/2_Intermediate/boozerQA_ls_mpi.py | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index fa0fdb7f9..66334000c 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -7,6 +7,7 @@ from simsopt.configs import get_ncsx_data from simsopt.objectives import QuadraticPenalty from scipy.optimize import minimize +from simsopt.util import proc0_print import numpy as np import os try: @@ -15,14 +16,9 @@ rank = comm.rank size = comm.size - def pprint(*args, **kwargs): - if comm.rank == 0: # only print on rank 0 - print(*args, **kwargs) - except ImportError: comm = None size = 1 - pprint = print rank = 0 """ @@ -51,8 +47,8 @@ def pprint(*args, **kwargs): OUT_DIR = "./output/" os.makedirs(OUT_DIR, exist_ok=True) -pprint("Running 2_Intermediate/boozerQA_ls_mpi.py") -pprint("================================") +proc0_print("Running 2_Intermediate/boozerQA_ls_mpi.py") +proc0_print("================================") base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress = load(IN_DIR + f"ncsx_init.json") nsurfaces = 2 @@ -171,14 +167,14 @@ def callback(x): outstr += f"{'āˆ« Īŗ^2 dl / āˆ« dl':{width}}" + ', '.join([f'{Jmsc.J():.6f}' for Jmsc in msc_list]) + "\n" outstr += "\n\n" - pprint(outstr) + proc0_print(outstr) prevs['it'] += 1 dofs = JF.x callback(dofs) -pprint(""" +proc0_print(""" ################################################################################ ### Run the optimization ####################################################### ################################################################################ @@ -191,5 +187,5 @@ def callback(x): curves_to_vtk(curves, OUT_DIR + f"curves_opt") boozer_surface.surface.to_vtk(OUT_DIR + "surf_opt") -pprint("End of 2_Intermediate/boozerQA_ls.py") -pprint("================================") +proc0_print("End of 2_Intermediate/boozerQA_ls.py") +proc0_print("================================") From 205cc7d77718512e4fb9551f18e5caaabe235c37 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 3 May 2024 14:01:55 -0400 Subject: [PATCH 095/176] added unit test for MPIOptimizable class [skip ci] --- tests/objectives/test_utilities.py | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/tests/objectives/test_utilities.py b/tests/objectives/test_utilities.py index 5357cd6cd..59b09c8a3 100644 --- a/tests/objectives/test_utilities.py +++ b/tests/objectives/test_utilities.py @@ -3,9 +3,10 @@ import numpy as np +from simsopt.geo import SurfaceXYZTensorFourier from simsopt.geo.curvexyzfourier import CurveXYZFourier from simsopt.geo.curveobjectives import CurveLength, LpCurveTorsion -from simsopt.objectives.utilities import MPIObjective, QuadraticPenalty +from simsopt.objectives.utilities import MPIObjective, QuadraticPenalty, MPIOptimizable from simsopt.geo import parameters from simsopt._core.json import GSONDecoder, GSONEncoder, SIMSON parameters['jit'] = False @@ -84,3 +85,26 @@ def test_mpi_objective(self): Jmpi1 = MPIObjective(Js1subset, comm, needs_splitting=False) assert abs(Jmpi1.J() - sum(J.J() for J in Js)/n) < 1e-14 assert np.sum(np.abs(Jmpi1.dJ() - sum(J.dJ() for J in Js)/n)) < 1e-14 + + def test_mpi_optimizable(self): + """ + This test checks that the `x` attribute of the surfaces is correctly communicated across the ranks. + """ + if MPI is None: + print("skip test_mpi_optimizable") + return + + comm = MPI.COMM_WORLD + surfaces = [SurfaceXYZTensorFourier(mpol=1, ntor=1, stellsym=True) for i in range(comm.size)] + + equal_to = [] + for i in range(comm.size): + x = np.zeros(surfaces[i].x.size) + x[:] = i + equal_to.append(x) + if comm.rank == i: + surfaces[i].x = x.copy() + + mpi_surfaces = MPIOptimizable(surfaces, ["x"], comm) + for s, sx in zip(mpi_surfaces, equal_to): + np.testing.assert_allclose(s.x, sx, atol=1e-14) From e9522cd700a85b8c6b5e79da89c2054d1ecae7e5 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 3 May 2024 14:19:34 -0400 Subject: [PATCH 096/176] edit to test_mpi_optimizable --- tests/objectives/test_utilities.py | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/tests/objectives/test_utilities.py b/tests/objectives/test_utilities.py index 59b09c8a3..8060d0cba 100644 --- a/tests/objectives/test_utilities.py +++ b/tests/objectives/test_utilities.py @@ -9,6 +9,7 @@ from simsopt.objectives.utilities import MPIObjective, QuadraticPenalty, MPIOptimizable from simsopt.geo import parameters from simsopt._core.json import GSONDecoder, GSONEncoder, SIMSON +from simsopt._core.util import parallel_loop_bounds parameters['jit'] = False try: from mpi4py import MPI @@ -95,16 +96,19 @@ def test_mpi_optimizable(self): return comm = MPI.COMM_WORLD - surfaces = [SurfaceXYZTensorFourier(mpol=1, ntor=1, stellsym=True) for i in range(comm.size)] + for size in [1, 2, 3, 4, 5]: + surfaces = [SurfaceXYZTensorFourier(mpol=1, ntor=1, stellsym=True) for i in range(size)] - equal_to = [] - for i in range(comm.size): - x = np.zeros(surfaces[i].x.size) - x[:] = i - equal_to.append(x) - if comm.rank == i: - surfaces[i].x = x.copy() + equal_to = [] + for i in range(size): + x = np.zeros(surfaces[i].x.size) + x[:] = i + equal_to.append(x) + + startidx, endidx = parallel_loop_bounds(comm, len(surfaces)) + for idx in range(startidx, endidx): + surfaces[idx].x = equal_to[idx] - mpi_surfaces = MPIOptimizable(surfaces, ["x"], comm) - for s, sx in zip(mpi_surfaces, equal_to): - np.testing.assert_allclose(s.x, sx, atol=1e-14) + mpi_surfaces = MPIOptimizable(surfaces, ["x"], comm) + for s, sx in zip(mpi_surfaces, equal_to): + np.testing.assert_allclose(s.x, sx, atol=1e-14) From a65680e20be866ce3db8534d97ea342c4264dd38 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 3 May 2024 14:28:53 -0400 Subject: [PATCH 097/176] fixing a unit test --- examples/2_Intermediate/boozerQA_ls_mpi.py | 4 ++-- tests/geo/test_boozersurface.py | 7 ++++--- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 66334000c..ba38b3f15 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -118,8 +118,8 @@ def fun(dofs): boozer_surface.res['iota'] = prevs['iota'][idx] boozer_surface.res['G'] = prevs['G'][idx] - #alldofs = MPI.COMM_WORLD.allgather(dofs) - #assert np.all(np.norm(alldofs[0]-d) == 0 for d in alldofs) + alldofs = MPI.COMM_WORLD.allgather(dofs) + assert np.all(np.norm(alldofs[0]-d) == 0 for d in alldofs) JF.x = dofs J = JF.J() diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 8851f6a29..c23995a09 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -382,16 +382,17 @@ def subtest_convergence_cpp_and_notcpp_same(self, vectorize): G = 2.*np.pi*current_sum*(4*np.pi*10**(-7)/(2 * np.pi)) + cw = 3*s.quadpoints_phi.size * s.quadpoints_theta.size # vectorized solution first res = boozer_surface.minimize_boozer_penalty_constraints_LBFGS( - tol=1e-10, maxiter=600, constraint_weight=100., iota=iota, G=G, + tol=1e-10, maxiter=600, constraint_weight=100./cw, iota=iota, G=G, vectorize=vectorize) print('Residual norm after LBFGS', np.sqrt(2*res['fun'])) boozer_surface.recompute_bell() res = boozer_surface.minimize_boozer_penalty_constraints_newton( - tol=1e-10, maxiter=20, constraint_weight=100., - iota=res['iota'], G=res['G'], stab=1e-4, vectorize=vectorize) + tol=1e-10, maxiter=20, constraint_weight=100./cw, + iota=res['iota'], G=res['G'], stab=0., vectorize=vectorize) assert res['success'] x = boozer_surface.surface.x.copy() From 7b0e7724054fc3591a95e9b1b52461d7fe05c053 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 3 May 2024 15:58:40 -0400 Subject: [PATCH 098/176] linting fix [skip ci] --- examples/2_Intermediate/boozerQA_ls_mpi.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index ba38b3f15..73e6ed019 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -4,7 +4,6 @@ from simsopt._core import load from simsopt.objectives import MPIObjective, MPIOptimizable from simsopt.field import BiotSavart -from simsopt.configs import get_ncsx_data from simsopt.objectives import QuadraticPenalty from scipy.optimize import minimize from simsopt.util import proc0_print @@ -50,7 +49,7 @@ proc0_print("Running 2_Intermediate/boozerQA_ls_mpi.py") proc0_print("================================") -base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress = load(IN_DIR + f"ncsx_init.json") +base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress = load(IN_DIR + "ncsx_init.json") nsurfaces = 2 surfaces = surfaces[:nsurfaces] boozer_surfaces = boozer_surfaces[:nsurfaces] @@ -104,7 +103,7 @@ boozer_surface.surface.to_vtk(OUT_DIR + f"surf_init_{rank}") if comm is None or comm.rank == 0: - curves_to_vtk(curves, OUT_DIR + f"curves_init") + curves_to_vtk(curves, OUT_DIR + "curves_init") # dictionary used to save the last accepted surface dofs in the line search, in case Newton's method fails prevs = {'sdofs': [surface.x.copy() for surface in mpi_surfaces], 'iota': [boozer_surface.res['iota'] for boozer_surface in mpi_boozer_surfaces], From 3ca3fc1571e13a1ae98d7e070390c2772ad89971 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 6 May 2024 14:14:10 -0400 Subject: [PATCH 099/176] edits to example --- examples/2_Intermediate/boozerQA_ls_mpi.py | 24 ++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 73e6ed019..8dc921b22 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -38,6 +38,11 @@ Surface solves using the BoozerLS approach can be costly, so this script supports distributing the solves across multiple MPI ranks. +You can change the value of nsurfaces below to optimize for nested surfaces and QS on up to 7 surfaces. The BoozerSurface +solves can be distributed to Nranks ranks using: + mpirun -n Nranks ./boozerQA_ls_mpi.py +where nsurfaces is the number of surfaces your optimizing on. + More details on this work can be found at or doi:10.1063/5.0129716 arxiv:2210.03248. """ @@ -50,7 +55,11 @@ proc0_print("================================") base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress = load(IN_DIR + "ncsx_init.json") -nsurfaces = 2 + +# you can optimize for QA on up to 10 surfaces, by changing nsurfaces below. +nsurfaces = 3 +assert nsurfaces <=10 + surfaces = surfaces[:nsurfaces] boozer_surfaces = boozer_surfaces[:nsurfaces] ress = ress[:nsurfaces] @@ -117,15 +126,18 @@ def fun(dofs): boozer_surface.res['iota'] = prevs['iota'][idx] boozer_surface.res['G'] = prevs['G'][idx] - alldofs = MPI.COMM_WORLD.allgather(dofs) - assert np.all(np.norm(alldofs[0]-d) == 0 for d in alldofs) - + #alldofs = MPI.COMM_WORLD.allgather(dofs) + #assert np.all(np.norm(alldofs[0]-d) == 0 for d in alldofs) + JF.x = dofs J = JF.J() grad = JF.dJ() - success = np.all([boozer_surface.res['success'] for boozer_surface in mpi_boozer_surfaces]) - if not success: + # check to make sure that all the surface solves succeeded + success1 = np.all([boozer_surface.res['success'] for boozer_surface in mpi_boozer_surfaces]) + # check to make sure that the surfaces are not self-intersecting + success2 = np.all([not surface.is_self_intersecting() for surface in mpi_surfaces]) + if not (success1 and success2): J = prevs['J'] grad = -prevs['dJ'] for idx, boozer_surface in enumerate(mpi_boozer_surfaces): From f8ae885d2799d8ab697d273799a45fb39574185a Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 6 May 2024 14:22:52 -0400 Subject: [PATCH 100/176] linting fix --- examples/2_Intermediate/boozerQA_ls_mpi.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 8dc921b22..878661f3a 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -38,7 +38,7 @@ Surface solves using the BoozerLS approach can be costly, so this script supports distributing the solves across multiple MPI ranks. -You can change the value of nsurfaces below to optimize for nested surfaces and QS on up to 7 surfaces. The BoozerSurface +You can change the value of nsurfaces below to optimize for nested surfaces and QS on up to 10 surfaces. The BoozerSurface solves can be distributed to Nranks ranks using: mpirun -n Nranks ./boozerQA_ls_mpi.py where nsurfaces is the number of surfaces your optimizing on. @@ -195,7 +195,7 @@ def callback(x): MAXITER = 50 if ci else 1e3 res = minimize(fun, dofs, jac=True, method='BFGS', options={'maxiter': MAXITER}, tol=1e-15, callback=callback) -curves_to_vtk(curves, OUT_DIR + f"curves_opt") +curves_to_vtk(curves, OUT_DIR + "curves_opt") boozer_surface.surface.to_vtk(OUT_DIR + "surf_opt") proc0_print("End of 2_Intermediate/boozerQA_ls.py") From d8884a74c9ffb8e536b5728bad1013d477650d19 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 6 May 2024 14:33:03 -0400 Subject: [PATCH 101/176] linting fix --- tests/geo/test_surface_objectives.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/geo/test_surface_objectives.py b/tests/geo/test_surface_objectives.py index 146dd20a2..3b0e63b2b 100644 --- a/tests/geo/test_surface_objectives.py +++ b/tests/geo/test_surface_objectives.py @@ -2,7 +2,7 @@ import numpy as np from simsopt.field.biotsavart import BiotSavart from simsopt.field.coil import coils_via_symmetries -from simsopt.geo.surfaceobjectives import ToroidalFlux, QfmResidual, parameter_derivatives, Volume, PrincipalCurvature, MajorRadius, Iotas, NonQuasiSymmetricRatio, AspectRatio, BoozerResidual +from simsopt.geo.surfaceobjectives import ToroidalFlux, QfmResidual, parameter_derivatives, Volume, PrincipalCurvature, MajorRadius, Iotas, NonQuasiSymmetricRatio, BoozerResidual from simsopt.configs.zoo import get_ncsx_data from .surface_test_helpers import get_surface, get_exact_surface, get_boozer_surface From 069c5f780b7fbd69802a3c21bea475904c030471 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 6 May 2024 15:55:25 -0400 Subject: [PATCH 102/176] tightening tolerances for unit tests --- tests/geo/test_boozersurface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index c23995a09..7c40997b3 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -285,7 +285,7 @@ def subtest_boozer_surface_optimisation_convergence(self, surfacetype, cw = (s.quadpoints_phi.size * s.quadpoints_theta.size * 3) # compute surface first using LBFGS exact and an area constraint res = boozer_surface.minimize_boozer_penalty_constraints_LBFGS( - tol=1e-11, maxiter=700, constraint_weight=100/cw, iota=iota, G=G, + tol=1e-12, maxiter=700, constraint_weight=100/cw, iota=iota, G=G, vectorize=vectorize) print('Residual norm after LBFGS', res['iter'], np.sqrt(2*res['fun'])) From c9d729b17df41908759998675ac80053114a3531 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 6 May 2024 17:28:11 -0400 Subject: [PATCH 103/176] more unit tests for code coverage --- tests/geo/test_boozersurface.py | 21 +++++++++++++++++++++ tests/objectives/test_utilities.py | 5 +++++ 2 files changed, 26 insertions(+) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 7c40997b3..6c6ea421b 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -354,6 +354,27 @@ def subtest_boozer_serialization(self, label): # check that BoozerSurface.surface and label.surface are the same surfaces assert bs_regen.label.surface is bs_regen.surface + def test_run_code(self): + """ + This unit test verifies that the run_code portion of the BoozerSurface class is working as expected + """ + bs, boozer_surface = get_boozer_surface(boozer_type='ls') + boozer_surface.run_code('ls', boozer_surface.res['iota'], boozer_surface.res['G'], verbose=False) + + # this second time should not actually run + boozer_surface.run_code('ls', boozer_surface.res['iota'], boozer_surface.res['G'], verbose=False) + + bs, boozer_surface = get_boozer_surface(boozer_type='exact') + boozer_surface.run_code('exact', boozer_surface.res['iota'], boozer_surface.res['G'], verbose=False) + + # this second time should not actually run + boozer_surface.run_code('exact', boozer_surface.res['iota'], boozer_surface.res['G'], verbose=False) + + boozer_surface.need_to_run_code=True + # this should raise an exception + with self.assertRaises(Exception): + boozer_surface.run_code('', boozer_surface.res['iota'], boozer_surface.res['G'], verbose=False) + def test_convergence_cpp_and_notcpp_same(self): """ This unit test verifies that that the cpp and not cpp implementations converge to diff --git a/tests/objectives/test_utilities.py b/tests/objectives/test_utilities.py index 8060d0cba..2989523f9 100644 --- a/tests/objectives/test_utilities.py +++ b/tests/objectives/test_utilities.py @@ -112,3 +112,8 @@ def test_mpi_optimizable(self): mpi_surfaces = MPIOptimizable(surfaces, ["x"], comm) for s, sx in zip(mpi_surfaces, equal_to): np.testing.assert_allclose(s.x, sx, atol=1e-14) + + # this should raise an exception + mpi_surfaces = [SurfaceXYZTensorFourier(mpol=1, ntor=1, stellsym=True) for i in range(size)] + with self.assertRaises(Exception): + _ = MPIOptimizable(surfaces, ["y"], comm) From 29be21abc817223e9fb0db781daa517da3cb609c Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 6 May 2024 14:31:36 -0700 Subject: [PATCH 104/176] minor changes to the example --- examples/2_Intermediate/boozerQA_ls_mpi.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 878661f3a..4366ae65c 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -57,7 +57,7 @@ base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress = load(IN_DIR + "ncsx_init.json") # you can optimize for QA on up to 10 surfaces, by changing nsurfaces below. -nsurfaces = 3 +nsurfaces = 10 assert nsurfaces <=10 surfaces = surfaces[:nsurfaces] @@ -110,9 +110,10 @@ # let's fix the coil current base_currents[0].fix_all() -boozer_surface.surface.to_vtk(OUT_DIR + f"surf_init_{rank}") if comm is None or comm.rank == 0: curves_to_vtk(curves, OUT_DIR + "curves_init") + for idx, surface in enumerate(mpi_surfaces): + surface.to_vtk(OUT_DIR + f"surf_init_{idx}") # dictionary used to save the last accepted surface dofs in the line search, in case Newton's method fails prevs = {'sdofs': [surface.x.copy() for surface in mpi_surfaces], 'iota': [boozer_surface.res['iota'] for boozer_surface in mpi_boozer_surfaces], @@ -195,8 +196,10 @@ def callback(x): MAXITER = 50 if ci else 1e3 res = minimize(fun, dofs, jac=True, method='BFGS', options={'maxiter': MAXITER}, tol=1e-15, callback=callback) -curves_to_vtk(curves, OUT_DIR + "curves_opt") -boozer_surface.surface.to_vtk(OUT_DIR + "surf_opt") +if comm is None or comm.rank == 0: + curves_to_vtk(curves, OUT_DIR + "curves_opt") + for idx, surface in enumerate(mpi_surfaces): + surface.to_vtk(OUT_DIR + f"surf_opt_{idx}") proc0_print("End of 2_Intermediate/boozerQA_ls.py") proc0_print("================================") From ca116816396fa298ef18338b1795c6e4c268d240 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 7 May 2024 11:23:12 -0400 Subject: [PATCH 105/176] small change to unit tests for code coverage --- tests/geo/test_surface_objectives.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/geo/test_surface_objectives.py b/tests/geo/test_surface_objectives.py index 3b0e63b2b..7fea67dec 100644 --- a/tests/geo/test_surface_objectives.py +++ b/tests/geo/test_surface_objectives.py @@ -379,7 +379,7 @@ def test_label_surface_derivative1(self): self.subtest_label_derivative1(label) def subtest_label_derivative1(self, label): - bs, boozer_surface = get_boozer_surface(label=label) + bs, boozer_surface = get_boozer_surface(label=label, nphi=13, ntheta=14) surface = boozer_surface.surface label = boozer_surface.label coeffs = surface.x From d872fcf1c96ad35bb4a575c87ca7d14122c48afd Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 7 May 2024 11:49:39 -0400 Subject: [PATCH 106/176] more edits to the text in the example --- examples/2_Intermediate/boozerQA_ls_mpi.py | 46 +++++++++++++--------- 1 file changed, 28 insertions(+), 18 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 4366ae65c..b7239c69c 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -25,23 +25,32 @@ For a single surface, the objective is: J = ( \int_S B_nonQA**2 dS )/(\int_S B_QA dS) + + \int \int BoozerResidual(varphi, theta)^2 d\varphi d\theta + 0.5*(iota - iota_0)**2 + 0.5*(major_radius - target_major_radius)**2 + 0.5*max(\sum_{coils} CurveLength - CurveLengthTarget, 0)**2 - -We first load a surface close to the magnetic axis, then optimize for QA on that surface. -The objective also includes penalty terms on the rotational transform, major radius, -and total coil length. The rotational transform and major radius penalty ensures that the surface's -rotational transform and aspect ratio do not stray too far from the value in the initial configuration. -There is also a penalty on the total coil length as a regularizer to prevent the coils from becoming -too complex. The BFGS optimizer is used, and quasisymmetry is improved substantially on the surface. -Surface solves using the BoozerLS approach can be costly, so this script supports distributing the solves -across multiple MPI ranks. - -You can change the value of nsurfaces below to optimize for nested surfaces and QS on up to 10 surfaces. The BoozerSurface -solves can be distributed to Nranks ranks using: - mpirun -n Nranks ./boozerQA_ls_mpi.py -where nsurfaces is the number of surfaces your optimizing on. + + other coil regularization penalties on curvature, mean squared curvature, + coil-to-coil distance, and coil arclength. + +We first load surfaces in the NCSX equilibrium, then optimize for QA on them. +The first term the objective minimizes the deviation from quasi-axisymmetry on the loaded surfaces. +The second term minimizes the Boozer residual on the surfaces, which pushes the optimizer to heal +islands and generalized chaos. It is typically a good idea to weight this penalty term to be ~ the +same order of magnitude of the first term in the objective. + +The objective also includes penalty terms on the rotational transform, major radius, total coil length, curvature, +mean squared curvature, and coil arclength. The rotational transform and major radius penalty ensures +that the surfaces' rotational transform and aspect ratio do not stray too far from the value in the initial configuration. +There are also a few coil regularization penalties to prevent the coils from becoming too complex. The BFGS +optimizer is used, and quasisymmetry is improved substantially on the surface. Surface solves using the BoozerLS +approach can be costly, so this script supports distributing the solves across multiple MPI ranks. + +You can change the value of the variable `nsurfaces` below to optimize for nested surfaces and QS on up to 10 surfaces. +The BoozerSurface solves can be distributed to Nranks ranks using: + mpirun -np Nranks ./boozerQA_ls_mpi.py +where `nsurfaces` is the number of surfaces your optimizing on. For example, if you want one surface solve per rank, +and nsurfaces=Nranks=2, then the proper call is: + mpirun -np 2 ./boozerQA_ls_mpi.py More details on this work can be found at or doi:10.1063/5.0129716 arxiv:2210.03248. """ @@ -57,7 +66,7 @@ base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress = load(IN_DIR + "ncsx_init.json") # you can optimize for QA on up to 10 surfaces, by changing nsurfaces below. -nsurfaces = 10 +nsurfaces = 2 assert nsurfaces <=10 surfaces = surfaces[:nsurfaces] @@ -70,6 +79,7 @@ mpi_boozer_surfaces = MPIOptimizable(boozer_surfaces, ["res", "need_to_run_code"], comm) mrs = [MajorRadius(boozer_surface) for boozer_surface in boozer_surfaces] +mrs_equality = [len(mrs)*QuadraticPenalty(mr, mr.J(), 'identity') if idx == len(mrs)-1 else 0*QuadraticPenalty(mr, mr.J(), 'identity') for idx, mr in enumerate(mrs)] iotas = [Iotas(boozer_surface) for boozer_surface in boozer_surfaces] nonQSs = [NonQuasiSymmetricRatio(boozer_surface, BiotSavart(coils)) for boozer_surface in boozer_surfaces] brs = [BoozerResidual(boozer_surface, BiotSavart(coils)) for boozer_surface in boozer_surfaces] @@ -92,7 +102,7 @@ Jiotas = QuadraticPenalty(mean_iota, IOTAS_TARGET, 'identity') JnonQSRatio = MPIObjective(nonQSs, comm, needs_splitting=True) JBoozerResidual = MPIObjective(brs, comm, needs_splitting=True) -Jmajor_radius = MPIObjective([len(mrs)*QuadraticPenalty(mr, mr.J(), 'identity') if idx == 0 else 0*QuadraticPenalty(mr, mr.J(), 'identity') for idx, mr in enumerate(mrs)], comm, needs_splitting=True) +Jmajor_radius = MPIObjective(mrs_equality, comm, needs_splitting=True) ls = [CurveLength(c) for c in base_curves] Jls = QuadraticPenalty(sum(ls), float(sum(ls).J()), 'max') @@ -110,7 +120,7 @@ # let's fix the coil current base_currents[0].fix_all() -if comm is None or comm.rank == 0: +if comm is None or rank == 0: curves_to_vtk(curves, OUT_DIR + "curves_init") for idx, surface in enumerate(mpi_surfaces): surface.to_vtk(OUT_DIR + f"surf_init_{idx}") @@ -196,7 +206,7 @@ def callback(x): MAXITER = 50 if ci else 1e3 res = minimize(fun, dofs, jac=True, method='BFGS', options={'maxiter': MAXITER}, tol=1e-15, callback=callback) -if comm is None or comm.rank == 0: +if comm is None or rank == 0: curves_to_vtk(curves, OUT_DIR + "curves_opt") for idx, surface in enumerate(mpi_surfaces): surface.to_vtk(OUT_DIR + f"surf_opt_{idx}") From 4e6fca10343a89441319af50e7a7e1444249f9ce Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 7 May 2024 12:52:53 -0400 Subject: [PATCH 107/176] changes for code coverage --- src/simsopt/geo/boozersurface.py | 17 +++++--- src/simsopt/geo/surfaceobjectives.py | 28 ++++++++----- tests/geo/surface_test_helpers.py | 4 +- tests/geo/test_boozersurface.py | 14 ++++--- tests/geo/test_surface_objectives.py | 60 ++++++++++++++++------------ 5 files changed, 75 insertions(+), 48 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index ecfcd3581..6bebde08f 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -55,17 +55,24 @@ def recompute_bell(self, parent=None): def run_code(self, boozer_type, iota, G=None, verbose=True): """ - Run the default solvers. + Run the default solvers, i.e., run Newton's method directly if you are computing a BoozerExact surface, + and run BFGS followed by Newton if you are computing a BoozerLS surface. """ if not self.need_to_run_code: return - + + # BoozerExact default solver if boozer_type == 'exact': res = self.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=40, iota=iota, G=G, verbose=verbose) return res - + + # BoozerLS default solver elif boozer_type == 'ls': - # first try BFGS + # you need a label constraint for a BoozerLS surface + assert self.constraint_weight is not None + + # first try BFGS. You could also try L-BFGS by setting limited_memory=True, which might be faster. However, BFGS appears + # to generally result in solutions closer to optimality. res = self.minimize_boozer_penalty_constraints_LBFGS(tol=1e-10, maxiter=1500, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose, limited_memory=False) iota, G = res['iota'], res['G'] @@ -679,7 +686,7 @@ def solve_residual_equation_exactly_newton(self, tol=1e-10, maxiter=10, iota=0., label = self.label if G is None: - G = 2. * np.pi * np.sum(np.abs(self.biotsavart.coil_currents)) * (4 * np.pi * 10**(-7) / (2 * np.pi)) + G = 2. * np.pi * np.sum(np.abs([c.current.get_value() for c in self.biotsavart.coils])) * (4 * np.pi * 10**(-7) / (2 * np.pi)) x = np.concatenate((s.get_dofs(), [iota, G])) i = 0 r, J = boozer_surface_residual(s, iota, G, self.biotsavart, derivatives=1) diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index f3e3b162b..d62ec574a 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -782,9 +782,11 @@ def compute(self): dJ_by_dB = self.dJ_by_dB().reshape((-1, 3)) dJ_by_dcoils = self.biotsavart.B_vjp(dJ_by_dB) - + # tack on dJ_diota = dJ_dG = 0 to the end of dJ_ds - dJ_ds = np.concatenate((self.dJ_by_dsurfacecoefficients(), [0., 0.])) + dJ_ds = np.zeros(L.shape[0]) + dj_ds = self.dJ_by_dsurfacecoefficients() + dJ_ds[:dj_ds.size] = dj_ds adj = forward_backward(P, L, U, dJ_ds) adj_times_dg_dcoil = dconstraint_dcoils_vjp(adj, booz_surf, iota, G) @@ -919,9 +921,14 @@ def compute(self): P, L, U = booz_surf.res['PLU'] dconstraint_dcoils_vjp = self.boozer_surface.res['vjp'] - # tack on dJ_diota = dJ_dG = 0 to the end of dJ_ds dJ_ds = np.zeros(L.shape[0]) - dJ_ds[-2] = 1. + if G is not None: + # tack on dJ_diota = 1, and dJ_dG = 0 to the end of dJ_ds + dJ_ds[-2] = 1. + else: + # tack on dJ_diota = 1 to the end of dJ_ds + dJ_ds[-1] = 1. + adj = forward_backward(P, L, U, dJ_ds) adj_times_dg_dcoil = dconstraint_dcoils_vjp(adj, booz_surf, iota, G) @@ -1012,7 +1019,8 @@ def compute(self): # dJ_diota, dJ_dG to the end of dJ_ds are on the end dl = np.zeros((J.shape[1],)) - dl[:-2] = self.boozer_surface.label.dJ_by_dsurfacecoefficients() + dlabel_dsurface = self.boozer_surface.label.dJ_by_dsurfacecoefficients() + dl[:dlabel_dsurface.size] = dlabel_dsurface Jtil = np.concatenate((J/np.sqrt(num_points), np.sqrt(self.constraint_weight) * dl[None, :]), axis=0) dJ_ds = Jtil.T@rtil @@ -1050,8 +1058,6 @@ def boozer_surface_dexactresidual_dcoils_dcurrents_vjp(lm, booz_surf, iota, G): \lambda^T \frac{d\mathbf{r}}{d\text{currents}} &= [G\lambda - 2\lambda\|\mathbf B(\mathbf x)\| (\mathbf{x}_\varphi + \iota \mathbf{x}_\theta) ]^T \frac{d\mathbf B}{d\text{currents}} where :math:`\mathbf{r}` is the Boozer residual. - G is known for exact boozer surfaces, so if G=None is passed, then that - value is used instead. Args: lm: adjoint variable, @@ -1061,9 +1067,9 @@ def boozer_surface_dexactresidual_dcoils_dcurrents_vjp(lm, booz_surf, iota, G): """ surface = booz_surf.surface biotsavart = booz_surf.biotsavart - user_provided_G = G is not None - if not user_provided_G: - G = 2. * np.pi * np.sum(np.abs(biotsavart.coil_currents)) * (4 * np.pi * 10**(-7) / (2 * np.pi)) + + # G must be provided here + assert G is not None res, dres_dB = boozer_surface_residual_dB(surface, iota, G, biotsavart) dres_dB = dres_dB.reshape((-1, 3, 3)) @@ -1124,7 +1130,7 @@ def boozer_surface_residual_dB(surface, iota, G, biotsavart, derivatives=0, weig user_provided_G = G is not None if not user_provided_G: - G = 2. * np.pi * np.sum(np.abs(biotsavart.coil_currents)) * (4 * np.pi * 10**(-7) / (2 * np.pi)) + G = 2. * np.pi * np.sum(np.abs([c.current.get_value() for c in biotsavart.coils])) * (4 * np.pi * 10**(-7) / (2 * np.pi)) x = surface.gamma() xphi = surface.gammadash1() diff --git a/tests/geo/surface_test_helpers.py b/tests/geo/surface_test_helpers.py index 1aa40586d..fe9c12933 100644 --- a/tests/geo/surface_test_helpers.py +++ b/tests/geo/surface_test_helpers.py @@ -74,7 +74,7 @@ def get_exact_surface(surface_type='SurfaceXYZFourier'): return s -def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exact'): +def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exact', optimize_G=True): """ Returns a boozer surface that will be used in unit tests. """ @@ -85,7 +85,7 @@ def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exac coils = coils_via_symmetries(base_curves, base_currents, 3, True) bs = BiotSavart(coils) current_sum = sum(abs(c.current.get_value()) for c in coils) - G0 = 2. * np.pi * current_sum * (4 * np.pi * 10**(-7) / (2 * np.pi)) + G0 = 2. * np.pi * current_sum * (4 * np.pi * 10**(-7) / (2 * np.pi)) if optimize_G else None ## RESOLUTION DETAILS OF SURFACE ON WHICH WE OPTIMIZE FOR QA mpol = 6 if boozer_type == 'exact' else 3 diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 6c6ea421b..3e599451c 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -359,21 +359,25 @@ def test_run_code(self): This unit test verifies that the run_code portion of the BoozerSurface class is working as expected """ bs, boozer_surface = get_boozer_surface(boozer_type='ls') - boozer_surface.run_code('ls', boozer_surface.res['iota'], boozer_surface.res['G'], verbose=False) + boozer_surface.run_code('ls', boozer_surface.res['iota'], G=boozer_surface.res['G'], verbose=False) # this second time should not actually run - boozer_surface.run_code('ls', boozer_surface.res['iota'], boozer_surface.res['G'], verbose=False) + boozer_surface.run_code('ls', boozer_surface.res['iota'], G=boozer_surface.res['G'], verbose=False) bs, boozer_surface = get_boozer_surface(boozer_type='exact') - boozer_surface.run_code('exact', boozer_surface.res['iota'], boozer_surface.res['G'], verbose=False) + boozer_surface.run_code('exact', boozer_surface.res['iota'], G=boozer_surface.res['G'], verbose=False) # this second time should not actually run - boozer_surface.run_code('exact', boozer_surface.res['iota'], boozer_surface.res['G'], verbose=False) + boozer_surface.run_code('exact', boozer_surface.res['iota'], G=boozer_surface.res['G'], verbose=False) + boozer_surface.need_to_run_code=True + # run without providing value of G + boozer_surface.run_code('exact', boozer_surface.res['iota'], verbose=True) + boozer_surface.need_to_run_code=True # this should raise an exception with self.assertRaises(Exception): - boozer_surface.run_code('', boozer_surface.res['iota'], boozer_surface.res['G'], verbose=False) + boozer_surface.run_code('', boozer_surface.res['iota'], G=boozer_surface.res['G'], verbose=False) def test_convergence_cpp_and_notcpp_same(self): """ diff --git a/tests/geo/test_surface_objectives.py b/tests/geo/test_surface_objectives.py index 7fea67dec..5e3d184b7 100644 --- a/tests/geo/test_surface_objectives.py +++ b/tests/geo/test_surface_objectives.py @@ -261,13 +261,16 @@ def test_major_radius_derivative(self): """ for boozer_type in ['exact', 'ls']: for label in ["Volume", "ToroidalFlux"]: - with self.subTest(label=label, boozer_type=boozer_type): - if boozer_type == 'ls' and label == 'ToroidalFlux': - continue - self.subtest_major_radius_surface_derivative(label, boozer_type) - - def subtest_major_radius_surface_derivative(self, label, boozer_type): - bs, boozer_surface = get_boozer_surface(label=label, nphi=51, ntheta=51, boozer_type=boozer_type) + for optimize_G in [True, False]: + with self.subTest(label=label, boozer_type=boozer_type, optimize_G=optimize_G): + if boozer_type == 'ls' and label == 'ToroidalFlux': + continue + if boozer_type == 'exact' and optimize_G is False: + continue + self.subtest_major_radius_surface_derivative(label, boozer_type, optimize_G) + + def subtest_major_radius_surface_derivative(self, label, boozer_type, optimize_G): + bs, boozer_surface = get_boozer_surface(label=label, nphi=51, ntheta=51, boozer_type=boozer_type, optimize_G=optimize_G) coeffs = bs.x mr = MajorRadius(boozer_surface) @@ -290,17 +293,20 @@ def test_iotas_derivative(self): for boozer_type in ['exact', 'ls']: for label in ["Volume", "ToroidalFlux"]: - if boozer_type == 'ls' and label == 'ToroidalFlux': - continue - with self.subTest(label=label, boozer_type=boozer_type): - self.subtest_iotas_derivative(label, boozer_type) + for optimize_G in [True, False]: + if boozer_type == 'ls' and label == 'ToroidalFlux': + continue + if boozer_type == 'exact' and optimize_G is False: + continue + with self.subTest(label=label, boozer_type=boozer_type, optimize_G=optimize_G): + self.subtest_iotas_derivative(label, boozer_type, optimize_G) - def subtest_iotas_derivative(self, label, boozer_type): + def subtest_iotas_derivative(self, label, boozer_type, optimize_G): """ Taylor test for derivative of surface rotational transform wrt coil parameters """ - bs, boozer_surface = get_boozer_surface(label=label, boozer_type=boozer_type) + bs, boozer_surface = get_boozer_surface(label=label, boozer_type=boozer_type, optimize_G=optimize_G) coeffs = bs.x io = Iotas(boozer_surface) @@ -323,14 +329,17 @@ def test_nonQSratio_derivative(self): """ for boozer_type in ['exact', 'ls']: for label in ["Volume", "ToroidalFlux"]: - if boozer_type == 'ls' and label == 'ToroidalFlux': - continue - for axis in [False, True]: - with self.subTest(label=label, axis=axis, boozer_type=boozer_type): - self.subtest_nonQSratio_derivative(label, axis, boozer_type) - - def subtest_nonQSratio_derivative(self, label, axis, boozer_type): - bs, boozer_surface = get_boozer_surface(label=label, boozer_type=boozer_type) + for optimize_G in [True, False]: + if boozer_type == 'ls' and label == 'ToroidalFlux': + continue + if boozer_type == 'exact' and optimize_G is False: + continue + for axis in [False, True]: + with self.subTest(label=label, axis=axis, boozer_type=boozer_type, optimize_G=optimize_G): + self.subtest_nonQSratio_derivative(label, axis, boozer_type, optimize_G) + + def subtest_nonQSratio_derivative(self, label, axis, boozer_type, optimize_G): + bs, boozer_surface = get_boozer_surface(label=label, boozer_type=boozer_type, optimize_G=optimize_G) coeffs = bs.x io = NonQuasiSymmetricRatio(boozer_surface, bs, quasi_poloidal=axis) @@ -352,11 +361,12 @@ def test_boozerresidual_derivative(self): Taylor test for derivative of surface non QS ratio wrt coil parameters """ for label in ["Volume"]: - with self.subTest(label=label): - self.subtest_boozerresidual_derivative(label) + for optimize_G in [True, False]: + with self.subTest(label=label, optimize_G=optimize_G): + self.subtest_boozerresidual_derivative(label, optimize_G) - def subtest_boozerresidual_derivative(self, label): - bs, boozer_surface = get_boozer_surface(label=label, boozer_type='ls') + def subtest_boozerresidual_derivative(self, label, optimize_G): + bs, boozer_surface = get_boozer_surface(label=label, boozer_type='ls', optimize_G=optimize_G) coeffs = bs.x br = BoozerResidual(boozer_surface, bs) From 31cdd2251b5da594ce935341ef5ffbd4a3800a37 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 7 May 2024 15:46:10 -0400 Subject: [PATCH 108/176] fix to example --- examples/2_Intermediate/boozerQA_ls_mpi.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index b7239c69c..1299283ca 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -122,7 +122,8 @@ if comm is None or rank == 0: curves_to_vtk(curves, OUT_DIR + "curves_init") - for idx, surface in enumerate(mpi_surfaces): +for idx, surface in enumerate(mpi_surfaces): + if comm is None or rank == 0: surface.to_vtk(OUT_DIR + f"surf_init_{idx}") # dictionary used to save the last accepted surface dofs in the line search, in case Newton's method fails @@ -137,8 +138,10 @@ def fun(dofs): boozer_surface.res['iota'] = prevs['iota'][idx] boozer_surface.res['G'] = prevs['G'][idx] - #alldofs = MPI.COMM_WORLD.allgather(dofs) - #assert np.all(np.norm(alldofs[0]-d) == 0 for d in alldofs) + # this check makes sure that all ranks have exactly the same dofs + if comm is not None: + alldofs = comm.allgather(dofs) + assert np.all(np.all(alldofs[0]-d == 0) for d in alldofs) JF.x = dofs J = JF.J() @@ -208,7 +211,8 @@ def callback(x): res = minimize(fun, dofs, jac=True, method='BFGS', options={'maxiter': MAXITER}, tol=1e-15, callback=callback) if comm is None or rank == 0: curves_to_vtk(curves, OUT_DIR + "curves_opt") - for idx, surface in enumerate(mpi_surfaces): +for idx, surface in enumerate(mpi_surfaces): + if comm is None or rank == 0: surface.to_vtk(OUT_DIR + f"surf_opt_{idx}") proc0_print("End of 2_Intermediate/boozerQA_ls.py") From d68dec92bfd757afe449e2dcdf82e7ba81d330b4 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 8 May 2024 12:21:40 -0400 Subject: [PATCH 109/176] changes for code coverage --- tests/geo/surface_test_helpers.py | 9 +++------ tests/geo/test_surface_objectives.py | 16 ++++++++++------ 2 files changed, 13 insertions(+), 12 deletions(-) diff --git a/tests/geo/surface_test_helpers.py b/tests/geo/surface_test_helpers.py index fe9c12933..6b0d6205b 100644 --- a/tests/geo/surface_test_helpers.py +++ b/tests/geo/surface_test_helpers.py @@ -74,7 +74,7 @@ def get_exact_surface(surface_type='SurfaceXYZFourier'): return s -def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exact', optimize_G=True): +def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exact', optimize_G=True, converge=True, stellsym=True): """ Returns a boozer surface that will be used in unit tests. """ @@ -90,7 +90,6 @@ def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exac ## RESOLUTION DETAILS OF SURFACE ON WHICH WE OPTIMIZE FOR QA mpol = 6 if boozer_type == 'exact' else 3 ntor = 6 if boozer_type == 'exact' else 3 - stellsym = True nfp = 3 if boozer_type == 'exact': @@ -122,9 +121,7 @@ def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exac ## COMPUTE THE SURFACE cw = None if boozer_type == 'exact' else 100. boozer_surface = BoozerSurface(bs, s, lab, lab_target, constraint_weight=cw) - boozer_surface.run_code(boozer_type, iota, G=G0, verbose=True) - - #res = boozer_surface.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=20, iota=iota, G=G0) - #print(f"NEWTON {res['success']}: iter={res['iter']}, iota={res['iota']:.3f}, vol={s.volume():.3f}") + if converge: + boozer_surface.run_code(boozer_type, iota, G=G0, verbose=True) return bs, boozer_surface diff --git a/tests/geo/test_surface_objectives.py b/tests/geo/test_surface_objectives.py index 5e3d184b7..42d8545d0 100644 --- a/tests/geo/test_surface_objectives.py +++ b/tests/geo/test_surface_objectives.py @@ -385,11 +385,15 @@ def df(dofs): class LabelTests(unittest.TestCase): def test_label_surface_derivative1(self): for label in ["Volume", "ToroidalFlux", "Area", "AspectRatio"]: - with self.subTest(label=label): - self.subtest_label_derivative1(label) - - def subtest_label_derivative1(self, label): - bs, boozer_surface = get_boozer_surface(label=label, nphi=13, ntheta=14) + for stellsym in stellsym_list: + for nphi, ntheta in [(13, 14), (None, None), (13, None), (None, 14)]: + with self.subTest(label=label, stellsym=stellsym, converge=stellsym): + # don't converge the BoozerSurface when stellsym=False because it takes a long time + # for a unit test + self.subtest_label_derivative1(label, stellsym=stellsym, converge=stellsym, nphi=nphi, ntheta=ntheta) + + def subtest_label_derivative1(self, label, stellsym, converge, nphi, ntheta): + bs, boozer_surface = get_boozer_surface(label=label, nphi=nphi, ntheta=ntheta, converge=converge, stellsym=stellsym) surface = boozer_surface.surface label = boozer_surface.label coeffs = surface.x @@ -406,7 +410,7 @@ def df(dofs): epsilons=np.power(2., -np.asarray(range(13, 19)))) def test_label_surface_derivative2(self): - for label in ["Volume", "ToroidalFlux", "Area"]: + for label in ["Volume", "ToroidalFlux", "Area", "AspectRatio"]: with self.subTest(label=label): self.subtest_label_derivative2(label) From a9953c7da4b1e917aa921d0f12884a1a0a5cb66d Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 8 May 2024 13:33:55 -0400 Subject: [PATCH 110/176] small change in finite difference test --- tests/geo/test_surface_objectives.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/geo/test_surface_objectives.py b/tests/geo/test_surface_objectives.py index 42d8545d0..e146a7849 100644 --- a/tests/geo/test_surface_objectives.py +++ b/tests/geo/test_surface_objectives.py @@ -407,7 +407,7 @@ def df(dofs): return label.dJ(partials=True)(surface) taylor_test1(f, df, coeffs, - epsilons=np.power(2., -np.asarray(range(13, 19)))) + epsilons=np.power(2., -np.asarray(range(12, 18)))) def test_label_surface_derivative2(self): for label in ["Volume", "ToroidalFlux", "Area", "AspectRatio"]: From df64329ef5c81d750c82b4978bce964b51dc781a Mon Sep 17 00:00:00 2001 From: Stefan Buller Date: Tue, 14 May 2024 13:32:10 -0400 Subject: [PATCH 111/176] Added support for stellarator non-symmetric configurations in vmec_splines. --- src/simsopt/mhd/vmec_diagnostics.py | 85 ++++++++++++++++++++++++++--- 1 file changed, 78 insertions(+), 7 deletions(-) diff --git a/src/simsopt/mhd/vmec_diagnostics.py b/src/simsopt/mhd/vmec_diagnostics.py index 716524595..357c945fa 100644 --- a/src/simsopt/mhd/vmec_diagnostics.py +++ b/src/simsopt/mhd/vmec_diagnostics.py @@ -720,15 +720,22 @@ def vmec_splines(vmec): """ vmec.run() results = Struct() - if vmec.wout.lasym: - raise ValueError("vmec_splines is not yet set up for non-stellarator-symmetric cases.") - rmnc = [] zmns = [] lmns = [] d_rmnc_d_s = [] d_zmns_d_s = [] d_lmns_d_s = [] + + # for stellarator non-symmetric configs + rmns = [] + zmnc = [] + lmnc = [] + d_rmns_d_s = [] + d_zmnc_d_s = [] + d_lmnc_d_s = [] + + for jmn in range(vmec.wout.mnmax): rmnc.append(InterpolatedUnivariateSpline(vmec.s_full_grid, vmec.wout.rmnc[jmn, :])) zmns.append(InterpolatedUnivariateSpline(vmec.s_full_grid, vmec.wout.zmns[jmn, :])) @@ -736,7 +743,24 @@ def vmec_splines(vmec): d_rmnc_d_s.append(rmnc[-1].derivative()) d_zmns_d_s.append(zmns[-1].derivative()) d_lmns_d_s.append(lmns[-1].derivative()) - + if vmec.wout.lasym: + # stellarator non-symmetric + rmns.append(InterpolatedUnivariateSpline(vmec.s_full_grid, vmec.wout.rmns[jmn, :])) + zmnc.append(InterpolatedUnivariateSpline(vmec.s_full_grid, vmec.wout.zmnc[jmn, :])) + lmnc.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.lmnc[jmn, 1:])) + d_rmns_d_s.append(rmns[-1].derivative()) + d_zmnc_d_s.append(zmnc[-1].derivative()) + d_lmnc_d_s.append(lmnc[-1].derivative()) + else: + # if stellarator symmetric, set modes to zero + rmns.append(InterpolatedUnivariateSpline([0,1], [0, 0], k=1)) + zmnc.append(InterpolatedUnivariateSpline([0,1], [0, 0], k=1)) + lmnc.append(InterpolatedUnivariateSpline([0,1], [0, 0], k=1)) + d_rmns_d_s.append(rmns[-1].derivative()) + d_zmnc_d_s.append(zmnc[-1].derivative()) + d_lmnc_d_s.append(lmnc[-1].derivative()) + + # nyquist quantities gmnc = [] bmnc = [] bsupumnc = [] @@ -747,6 +771,20 @@ def vmec_splines(vmec): d_bmnc_d_s = [] d_bsupumnc_d_s = [] d_bsupvmnc_d_s = [] + + # for stellarator non-symmetric configs + gmns = [] + bmns = [] + bsupumns = [] + bsupvmns = [] + bsubsmnc = [] + bsubumns = [] + bsubvmns = [] + d_bmns_d_s = [] + d_bsupumns_d_s = [] + d_bsupvmns_d_s = [] + + for jmn in range(vmec.wout.mnmax_nyq): gmnc.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.gmnc[jmn, 1:])) bmnc.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.bmnc[jmn, 1:])) @@ -759,7 +797,34 @@ def vmec_splines(vmec): d_bmnc_d_s.append(bmnc[-1].derivative()) d_bsupumnc_d_s.append(bsupumnc[-1].derivative()) d_bsupvmnc_d_s.append(bsupvmnc[-1].derivative()) - + if vmec.wout.lasym: + # stellarator non-symmetric + gmns.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.gmns[jmn, 1:])) + bmns.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.bmns[jmn, 1:])) + bsupumns.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.bsupumns[jmn, 1:])) + bsupvmns.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.bsupvmns[jmn, 1:])) + # Note that bsubsmns is on the full mesh, unlike the other components: + bsubsmnc.append(InterpolatedUnivariateSpline(vmec.s_full_grid, vmec.wout.bsubsmnc[jmn, :])) + bsubumns.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.bsubumns[jmn, 1:])) + bsubvmns.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.bsubvmns[jmn, 1:])) + d_bmns_d_s.append(bmns[-1].derivative()) + d_bsupumns_d_s.append(bsupumns[-1].derivative()) + d_bsupvmns_d_s.append(bsupvmns[-1].derivative()) + else: + # if stellarator symmetric, set modes to zero + gmns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) + bmns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) + bsupumns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) + bsupvmns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) + # Note that bsubsmns is on the full mesh, unlike the other components: + bsubsmnc.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) + bsubumns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) + bsubvmns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) + d_bmns_d_s.append(bmns[-1].derivative()) + d_bsupumns_d_s.append(bsupumns[-1].derivative()) + d_bsupvmns_d_s.append(bsupvmns[-1].derivative()) + + # Handle 1d profiles: results.pressure = InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.pres[1:]) results.d_pressure_d_s = results.pressure.derivative() @@ -775,6 +840,11 @@ def vmec_splines(vmec): variables = ['rmnc', 'zmns', 'lmns', 'd_rmnc_d_s', 'd_zmns_d_s', 'd_lmns_d_s', 'gmnc', 'bmnc', 'd_bmnc_d_s', 'bsupumnc', 'bsupvmnc', 'd_bsupumnc_d_s', 'd_bsupvmnc_d_s', 'bsubsmns', 'bsubumnc', 'bsubvmnc'] + # stellarator non-symmetric + variables = variables + \ + ['rmns', 'zmnc', 'lmnc', 'd_rmns_d_s', 'd_zmnc_d_s', 'd_lmnc_d_s', + 'gmns', 'bmns', 'd_bmns_d_s', 'bsupumns', 'bsupvmns', 'd_bsupumns_d_s', 'd_bsupvmns_d_s', + 'bsubsmnc', 'bsubumns', 'bsubvmns'] for v in variables: results.__setattr__(v, eval(v)) @@ -983,7 +1053,8 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): d_R_d_s = np.einsum('ij,jikl->ikl', d_rmnc_d_s, cosangle) d_R_d_theta_vmec = -np.einsum('ij,jikl->ikl', rmnc, msinangle) d_R_d_phi = np.einsum('ij,jikl->ikl', rmnc, nsinangle) - + + Z = np.einsum('ij,jikl->ikl', zmns, sinangle) d_Z_d_s = np.einsum('ij,jikl->ikl', d_zmns_d_s, sinangle) d_Z_d_theta_vmec = np.einsum('ij,jikl->ikl', zmns, mcosangle) @@ -1332,7 +1403,7 @@ def residual(theta_v, phi0, theta_p_target, jradius): variables = ['modB', 'B_sup_theta_pest', 'B_sup_phi', 'B_cross_grad_B_dot_grad_alpha', 'B_cross_grad_B_dot_grad_psi', 'B_cross_kappa_dot_grad_alpha', 'B_cross_kappa_dot_grad_psi', 'grad_alpha_dot_grad_alpha', 'grad_alpha_dot_grad_psi', 'grad_psi_dot_grad_psi', - 'bmag', 'gradpar_theta_pest', 'gradpar_phi', 'gbdrift', 'gbdrift0', 'cvdrift', 'cvdrift0', 'gds2', 'gds21', 'gds22'] + 'bmag', 'gradpar_theta_pest', 'gradpar_phi', 'gbdrift', 'gbdrift0', 'cvdrift', 'cvdrift0', 'gds2', 'gds21', 'gds22', 'X', 'Y', 'Z', 'grad_s_X', 'grad_s_Y', 'grad_s_Z'] for j, variable in enumerate(variables): plt.subplot(nrows, ncols, j + 1) plt.plot(phi[0, 0, :], eval("results." + variable + '[0, 0, :]')) From fb235f05437238d872da4eeb47c695bc45f81029 Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Wed, 15 May 2024 08:53:20 -0400 Subject: [PATCH 112/176] Eliminated duplicated code in vmec_splines; fixed broken test for vmec_fieldlines --- src/simsopt/mhd/vmec_diagnostics.py | 48 ++++++++++++++--------------- 1 file changed, 23 insertions(+), 25 deletions(-) diff --git a/src/simsopt/mhd/vmec_diagnostics.py b/src/simsopt/mhd/vmec_diagnostics.py index 357c945fa..5632d2dcf 100644 --- a/src/simsopt/mhd/vmec_diagnostics.py +++ b/src/simsopt/mhd/vmec_diagnostics.py @@ -720,6 +720,7 @@ def vmec_splines(vmec): """ vmec.run() results = Struct() + stellsym = not vmec.wout.lasym rmnc = [] zmns = [] lmns = [] @@ -748,17 +749,15 @@ def vmec_splines(vmec): rmns.append(InterpolatedUnivariateSpline(vmec.s_full_grid, vmec.wout.rmns[jmn, :])) zmnc.append(InterpolatedUnivariateSpline(vmec.s_full_grid, vmec.wout.zmnc[jmn, :])) lmnc.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.lmnc[jmn, 1:])) - d_rmns_d_s.append(rmns[-1].derivative()) - d_zmnc_d_s.append(zmnc[-1].derivative()) - d_lmnc_d_s.append(lmnc[-1].derivative()) else: # if stellarator symmetric, set modes to zero - rmns.append(InterpolatedUnivariateSpline([0,1], [0, 0], k=1)) - zmnc.append(InterpolatedUnivariateSpline([0,1], [0, 0], k=1)) - lmnc.append(InterpolatedUnivariateSpline([0,1], [0, 0], k=1)) - d_rmns_d_s.append(rmns[-1].derivative()) - d_zmnc_d_s.append(zmnc[-1].derivative()) - d_lmnc_d_s.append(lmnc[-1].derivative()) + rmns.append(InterpolatedUnivariateSpline([0, 1], [0, 0], k=1)) + zmnc.append(InterpolatedUnivariateSpline([0, 1], [0, 0], k=1)) + lmnc.append(InterpolatedUnivariateSpline([0, 1], [0, 0], k=1)) + + d_rmns_d_s.append(rmns[-1].derivative()) + d_zmnc_d_s.append(zmnc[-1].derivative()) + d_lmnc_d_s.append(lmnc[-1].derivative()) # nyquist quantities gmnc = [] @@ -807,22 +806,19 @@ def vmec_splines(vmec): bsubsmnc.append(InterpolatedUnivariateSpline(vmec.s_full_grid, vmec.wout.bsubsmnc[jmn, :])) bsubumns.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.bsubumns[jmn, 1:])) bsubvmns.append(InterpolatedUnivariateSpline(vmec.s_half_grid, vmec.wout.bsubvmns[jmn, 1:])) - d_bmns_d_s.append(bmns[-1].derivative()) - d_bsupumns_d_s.append(bsupumns[-1].derivative()) - d_bsupvmns_d_s.append(bsupvmns[-1].derivative()) else: # if stellarator symmetric, set modes to zero - gmns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) - bmns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) - bsupumns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) - bsupvmns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) - # Note that bsubsmns is on the full mesh, unlike the other components: - bsubsmnc.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) - bsubumns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) - bsubvmns.append(InterpolatedUnivariateSpline([0,1],[0, 0], k=1)) - d_bmns_d_s.append(bmns[-1].derivative()) - d_bsupumns_d_s.append(bsupumns[-1].derivative()) - d_bsupvmns_d_s.append(bsupvmns[-1].derivative()) + gmns.append(InterpolatedUnivariateSpline([0, 1], [0, 0], k=1)) + bmns.append(InterpolatedUnivariateSpline([0, 1], [0, 0], k=1)) + bsupumns.append(InterpolatedUnivariateSpline([0, 1], [0, 0], k=1)) + bsupvmns.append(InterpolatedUnivariateSpline([0, 1], [0, 0], k=1)) + bsubsmnc.append(InterpolatedUnivariateSpline([0, 1], [0, 0], k=1)) + bsubumns.append(InterpolatedUnivariateSpline([0, 1], [0, 0], k=1)) + bsubvmns.append(InterpolatedUnivariateSpline([0, 1], [0, 0], k=1)) + + d_bmns_d_s.append(bmns[-1].derivative()) + d_bsupumns_d_s.append(bsupumns[-1].derivative()) + d_bsupvmns_d_s.append(bsupvmns[-1].derivative()) # Handle 1d profiles: @@ -839,7 +835,7 @@ def vmec_splines(vmec): variables = ['rmnc', 'zmns', 'lmns', 'd_rmnc_d_s', 'd_zmns_d_s', 'd_lmns_d_s', 'gmnc', 'bmnc', 'd_bmnc_d_s', 'bsupumnc', 'bsupvmnc', 'd_bsupumnc_d_s', 'd_bsupvmnc_d_s', - 'bsubsmns', 'bsubumnc', 'bsubvmnc'] + 'bsubsmns', 'bsubumnc', 'bsubvmnc', 'stellsym'] # stellarator non-symmetric variables = variables + \ ['rmns', 'zmnc', 'lmnc', 'd_rmns_d_s', 'd_zmnc_d_s', 'd_lmnc_d_s', @@ -950,6 +946,8 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): # If given a Vmec object, convert it to vmec_splines: if isinstance(vs, Vmec): vs = vmec_splines(vs) + if not vs.stellsym: + raise NotImplementedError("vmec_compute_geometry() does not yet support non-stellarator-symmetric configurations.") # Make sure s is an array: try: @@ -1403,7 +1401,7 @@ def residual(theta_v, phi0, theta_p_target, jradius): variables = ['modB', 'B_sup_theta_pest', 'B_sup_phi', 'B_cross_grad_B_dot_grad_alpha', 'B_cross_grad_B_dot_grad_psi', 'B_cross_kappa_dot_grad_alpha', 'B_cross_kappa_dot_grad_psi', 'grad_alpha_dot_grad_alpha', 'grad_alpha_dot_grad_psi', 'grad_psi_dot_grad_psi', - 'bmag', 'gradpar_theta_pest', 'gradpar_phi', 'gbdrift', 'gbdrift0', 'cvdrift', 'cvdrift0', 'gds2', 'gds21', 'gds22', 'X', 'Y', 'Z', 'grad_s_X', 'grad_s_Y', 'grad_s_Z'] + 'bmag', 'gradpar_theta_pest', 'gradpar_phi', 'gbdrift', 'gbdrift0', 'cvdrift', 'cvdrift0', 'gds2', 'gds21', 'gds22'] for j, variable in enumerate(variables): plt.subplot(nrows, ncols, j + 1) plt.plot(phi[0, 0, :], eval("results." + variable + '[0, 0, :]')) From 2ee3b39d86ada165965b34fb0262a8ff5bccd5c5 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 15 May 2024 17:40:58 -0400 Subject: [PATCH 113/176] adding support for solver options, more changes for code coverage --- examples/2_Intermediate/boozerQA_ls_mpi.py | 2 +- src/simsopt/geo/boozersurface.py | 120 +++++++++++++++++---- src/simsopt/geo/surfaceobjectives.py | 20 ++-- src/simsopt/geo/surfacexyztensorfourier.py | 6 +- tests/geo/surface_test_helpers.py | 9 +- tests/geo/test_boozersurface.py | 15 +-- tests/geo/test_surface_objectives.py | 76 +++++++------ 7 files changed, 168 insertions(+), 80 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 1299283ca..63f01b52e 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -73,7 +73,7 @@ boozer_surfaces = boozer_surfaces[:nsurfaces] ress = ress[:nsurfaces] for boozer_surface, res in zip(boozer_surfaces, ress): - boozer_surface.run_code('ls', res['iota'], res['G'], verbose=False) + boozer_surface.run_code(res['iota'], res['G']) mpi_surfaces = MPIOptimizable(surfaces, ["x"], comm) mpi_boozer_surfaces = MPIOptimizable(boozer_surfaces, ["res", "need_to_run_code"], comm) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 6bebde08f..32a447023 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -5,6 +5,7 @@ from .surfaceobjectives import boozer_surface_residual, boozer_surface_dexactresidual_dcoils_dcurrents_vjp, boozer_surface_dlsqgrad_dcoils_vjp from .._core.optimizable import Optimizable +from functools import partial __all__ = ['BoozerSurface'] @@ -23,10 +24,13 @@ class BoozerSurface(Optimizable): to a magnetic surface of the field and :math:`(\phi,\theta)` that parametrize the surface correspond to Boozer angles, and the constraints are satisfied. - The surface label can be area, volume, or toroidal flux. The label on the computed surface will be equal or close - to the user-provided ``targetlabel``, depending on how the label constraint is imposed. This - constrained least squares problem can be solved by scalarizing and adding the constraint as - an additional penalty term to the objective. This is done in + There are two approaches for computing these surfaces, called BoozerLS or BoozerExact surfaces. + + For BoozerLS surfaces, the objective mentioned above is minimized :math:`J(x)`, subject to + the surface label constraint. The surface label can be area, volume, or toroidal flux. The label + on the computed surface will be equal or close to the user-provided ``targetlabel``, depending on + how the label constraint is imposed. This constrained least squares problem can be solved by + scalarizing and adding the constraint as an additional penalty term to the objective. This is done in #. :mod:`minimize_boozer_penalty_constraints_LBFGS` #. :mod:`minimize_boozer_penalty_constraints_newton` @@ -39,49 +43,120 @@ class BoozerSurface(Optimizable): #. :mod:`minimize_boozer_exact_constraints_newton` where Newton is used to solve the first order necessary conditions for optimality. + + For BoozerExact surfaces, we try to find surfaces such that the residual :math:`\mathbf r(x)` + is exactly equal to zero at a specific set of colocation points on the surface. The colocation + points are chosen such that the number of colocation points is equal to the number of unknowns + in on the surface, so that the resulting nonlinear system of equations can be solved using + Newton's method. This is done in: + + #. :mod:`solve_residual_equation_exactly_newton` + + Note that there are specific requirements on the set of colocation points, i.e. + :mod:`surface.quadpoints_phi` and :mod:`surface.quadpoints_theta`, for stellarator + symmetric BoozerExact surfaces, see `solve_residual_equation_exactly_newton` + and `SurfaceXYZTensorFourier.get_stellsym_mask()` for more information. + + Alternatively, the user can use the default solvers in + + #. :mod:`run_code(iota_guess, G=G_guess)` + + for BoozerExact or BoozerLS surfaces. """ - def __init__(self, biotsavart, surface, label, targetlabel, constraint_weight=None): + def __init__(self, biotsavart, surface, label, targetlabel, constraint_weight=None, options=None): super().__init__(depends_on=[biotsavart]) + + from simsopt.geo import SurfaceXYZFourier, SurfaceXYZTensorFourier + if not isinstance(surface, SurfaceXYZTensorFourier) and not isinstance(surface, SurfaceXYZFourier): + raise Exception("The input surface must be a SurfaceXYZTensorFourier or SurfaceXYZFourier.") + self.biotsavart = biotsavart self.surface = surface self.label = label self.targetlabel = targetlabel self.constraint_weight = constraint_weight + self.boozer_type = 'ls' if constraint_weight else 'exact' self.need_to_run_code = True + + if options is None: + options={} + + # set the default options now + if 'verbose' not in options: + options['verbose'] = True + if 'G' not in options: + options['G'] = None + + # default solver options for the BoozerExact and BoozerLS solvers + if self.boozer_type == 'exact': + if 'newton_tol' not in options: + options['newton_tol'] = 1e-13 + if 'newton_maxiter' not in options: + options['newton_maxiter'] = 40 + elif self.boozer_type == 'ls': + if 'bfgs_tol' not in options: + options['bfgs_tol'] = 1e-10 + if 'newton_tol' not in options: + options['newton_tol'] = 1e-11 + if 'newton_maxiter' not in options: + options['newton_maxiter'] = 40 + if 'bfgs_maxiter' not in options: + options['bfgs_maxiter'] = 1500 + if 'limited_memory' not in options: + options['limited_memory'] = False + if 'weight_inv_modB' not in options: + options['weight_inv_modB'] = True + self.options = options def recompute_bell(self, parent=None): self.need_to_run_code = True - def run_code(self, boozer_type, iota, G=None, verbose=True): + def run_code(self, iota, G=None): """ Run the default solvers, i.e., run Newton's method directly if you are computing a BoozerExact surface, and run BFGS followed by Newton if you are computing a BoozerLS surface. + + Args: + boozer_type: either 'exact' or 'ls', to indicate whether a BoozerExact or a BoozerLS surface is to be computed. + iota: guess for value of rotational transform on the surface, + G: guess for value of G on surface, defaults to None. + options: dictionary of solver options. If keyword is not specified, then a default + value is used. Possible keywords are: + `verbose`: display convergence information + `newton_tol`: tolerance for newton solver + `bfgs_tol`: tolerance for bfgs solver + `newton_maxiter`: maximum number of iterations for Newton solver + `bfgs_maxiter`: maximum number of iterations for BFGS solver + `limited_memory`: True if L-BFGS solver is desired, False if the BFGS solver otherwise. + `weight_inv_modB`: for BoozerLS surfaces, weight the residual by modB so that it does not scale with coil currents. Defaults to True. """ if not self.need_to_run_code: return # BoozerExact default solver - if boozer_type == 'exact': - res = self.solve_residual_equation_exactly_newton(tol=1e-13, maxiter=40, iota=iota, G=G, verbose=verbose) + if self.boozer_type == 'exact': + res = self.solve_residual_equation_exactly_newton(iota=iota, G=G, tol=self.options['newton_tol'], maxiter=self.options['newton_maxiter'], verbose=self.options['verbose']) return res # BoozerLS default solver - elif boozer_type == 'ls': + elif self.boozer_type == 'ls': # you need a label constraint for a BoozerLS surface assert self.constraint_weight is not None - # first try BFGS. You could also try L-BFGS by setting limited_memory=True, which might be faster. However, BFGS appears + # first try BFGS. You could also try L-BFGS by setting limited_memory=True in the options dictionary, which might be faster. However, BFGS appears # to generally result in solutions closer to optimality. - res = self.minimize_boozer_penalty_constraints_LBFGS(tol=1e-10, maxiter=1500, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose, limited_memory=False) + res = self.minimize_boozer_penalty_constraints_LBFGS(constraint_weight=self.constraint_weight, iota=iota, G=G, \ + tol=self.options['bfgs_tol'], maxiter=self.options['bfgs_maxiter'], verbose=self.options['verbose'], limited_memory=self.options['limited_memory'],\ + weight_inv_modB=self.options['weight_inv_modB']) iota, G = res['iota'], res['G'] ## polish off using Newton's method self.need_to_run_code = True - res = self.minimize_boozer_penalty_constraints_newton(tol=1e-11, maxiter=40, constraint_weight=self.constraint_weight, iota=iota, G=G, verbose=verbose) + res = self.minimize_boozer_penalty_constraints_newton(constraint_weight=self.constraint_weight, iota=iota, G=G, \ + verbose=self.options['verbose'], tol=self.options['newton_tol'], maxiter=self.options['newton_maxiter'],\ + weight_inv_modB=self.options['weight_inv_modB']) return res - else: - raise Exception(f"boozer_type not supported: {boozer_type}") def boozer_penalty_constraints(self, x, derivatives=0, constraint_weight=1., scalarize=True, optimize_G=False, weight_inv_modB=True): r""" @@ -340,7 +415,7 @@ def boozer_exact_constraints(self, xl, derivatives=0, optimize_G=True): dres[-1, :-2] = drz return res, dres - def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, vectorize=True, limited_memory=True, verbose=False): + def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, constraint_weight=1., iota=0., G=None, vectorize=True, limited_memory=True, weight_inv_modB=True, verbose=False): r""" This function tries to find the surface that approximately solves @@ -363,7 +438,7 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons x = np.concatenate((s.get_dofs(), [iota, G])) fun_name = self.boozer_penalty_constraints_vectorized if vectorize else self.boozer_penalty_constraints - fun = lambda x: fun_name(x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None) + fun = lambda x: fun_name(x, derivatives=1, constraint_weight=constraint_weight, optimize_G=G is not None, weight_inv_modB=weight_inv_modB) method = 'L-BFGS-B' if limited_memory else 'BFGS' options = {'maxiter': maxiter, 'gtol': tol} @@ -376,7 +451,7 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons options=options) resdict = { - "fun": res.fun, "gradient": res.jac, "iter": res.nit, "info": res, "success": res.success, "G": None, + "fun": res.fun, "gradient": res.jac, "iter": res.nit, "info": res, "success": res.success, "G": None, 'weight_inv_modB':weight_inv_modB, 'type':'ls' } if G is None: s.set_dofs(res.x[:-1]) @@ -397,7 +472,7 @@ def minimize_boozer_penalty_constraints_LBFGS(self, tol=1e-3, maxiter=1000, cons return resdict - def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0., vectorize=True, verbose=False): + def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, constraint_weight=1., iota=0., G=None, stab=0., vectorize=True, weight_inv_modB=True, verbose=False): """ This function does the same as :mod:`minimize_boozer_penalty_constraints_LBFGS`, but instead of LBFGS it uses Newton's method. @@ -413,7 +488,7 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons i = 0 fun_name = self.boozer_penalty_constraints_vectorized if vectorize else self.boozer_penalty_constraints - val, dval, d2val = fun_name(x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + val, dval, d2val = fun_name(x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None, weight_inv_modB=weight_inv_modB) norm = np.linalg.norm(dval) while i < maxiter and norm > tol: @@ -422,17 +497,18 @@ def minimize_boozer_penalty_constraints_newton(self, tol=1e-12, maxiter=10, cons if norm < 1e-9: dx += np.linalg.solve(d2val, dval - d2val@dx) x = x - dx - val, dval, d2val = fun_name(x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None) + val, dval, d2val = fun_name(x, derivatives=2, constraint_weight=constraint_weight, optimize_G=G is not None, weight_inv_modB=weight_inv_modB) norm = np.linalg.norm(dval) i = i+1 r = self.boozer_penalty_constraints( - x, derivatives=0, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None) + x, derivatives=0, constraint_weight=constraint_weight, scalarize=False, optimize_G=G is not None, weight_inv_modB=weight_inv_modB) P, L, U = lu(d2val) res = { "residual": r, "jacobian": dval, "hessian": d2val, "iter": i, "success": norm <= tol, "G": None, - "PLU" : (P, L, U), "vjp": boozer_surface_dlsqgrad_dcoils_vjp, "type": "ls" + "PLU" : (P, L, U), "vjp": partial(boozer_surface_dlsqgrad_dcoils_vjp, weight_inv_modB=weight_inv_modB),\ + "type": "ls", "weight_inv_modB": weight_inv_modB } if G is None: s.set_dofs(x[:-1]) diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index d62ec574a..63a676675 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -659,7 +659,7 @@ def recompute_bell(self, parent=None): def compute(self): if self.boozer_surface.need_to_run_code: res = self.boozer_surface.res - res = self.boozer_surface.run_code(res['type'], res['iota'], G=res['G']) + res = self.boozer_surface.run_code(res['iota'], G=res['G']) surface = self.surface self._J = surface.major_radius() @@ -747,7 +747,7 @@ def dJ(self): def compute(self): if self.boozer_surface.need_to_run_code: res = self.boozer_surface.res - res = self.boozer_surface.run_code(res['type'], res['iota'], G=res['G']) + res = self.boozer_surface.run_code(res['iota'], G=res['G']) self.biotsavart.set_points(self.surface.gamma().reshape((-1, 3))) axis = self.axis @@ -905,13 +905,14 @@ def dJ(self): def recompute_bell(self, parent=None): self._J = None + self._dJ = None self._dJ_by_dcoefficients = None self._dJ_by_dcoilcurrents = None def compute(self): if self.boozer_surface.need_to_run_code: res = self.boozer_surface.res - res = self.boozer_surface.run_code(res['type'], res['iota'], G=res['G']) + res = self.boozer_surface.run_code(res['iota'], G=res['G']) self._J = self.boozer_surface.res['iota'] @@ -993,7 +994,7 @@ def recompute_bell(self, parent=None): def compute(self): if self.boozer_surface.need_to_run_code: res = self.boozer_surface.res - res = self.boozer_surface.run_code(res['type'], res['iota'], G=res['G']) + res = self.boozer_surface.run_code(res['iota'], G=res['G']) self.surface.set_dofs(self.in_surface.get_dofs()) self.biotsavart.set_points(self.surface.gamma().reshape((-1, 3))) @@ -1006,7 +1007,7 @@ def compute(self): surface = self.surface iota = self.boozer_surface.res['iota'] G = self.boozer_surface.res['G'] - r, J = boozer_surface_residual(surface, iota, G, self.biotsavart, derivatives=1, weight_inv_modB=True) + r, J = boozer_surface_residual(surface, iota, G, self.biotsavart, derivatives=1, weight_inv_modB=res['weight_inv_modB']) rtil = np.concatenate((r/np.sqrt(num_points), [np.sqrt(self.constraint_weight)*(self.boozer_surface.label.J()-self.boozer_surface.targetlabel)])) self._J = 0.5*np.sum(rtil**2) @@ -1035,10 +1036,11 @@ def dJ_by_dB(self): """ surface = self.surface + res = self.boozer_surface.res nphi = self.surface.quadpoints_phi.size ntheta = self.surface.quadpoints_theta.size num_points = 3 * nphi * ntheta - r, r_dB = boozer_surface_residual_dB(surface, self.boozer_surface.res['iota'], self.boozer_surface.res['G'], self.biotsavart, derivatives=0, weight_inv_modB=True) + r, r_dB = boozer_surface_residual_dB(surface, self.boozer_surface.res['iota'], self.boozer_surface.res['G'], self.biotsavart, derivatives=0, weight_inv_modB=res['weight_inv_modB']) r /= np.sqrt(num_points) r_dB /= np.sqrt(num_points) @@ -1086,7 +1088,7 @@ def boozer_surface_dexactresidual_dcoils_dcurrents_vjp(lm, booz_surf, iota, G): return lm_times_dres_dcoils+lm_times_dlabel_dcoils -def boozer_surface_dlsqgrad_dcoils_vjp(lm, booz_surf, iota, G): +def boozer_surface_dlsqgrad_dcoils_vjp(lm, booz_surf, iota, G, weight_inv_modB=True): """ For a given surface with points x on it, this function computes the vector-Jacobian product of \lm^T * dlsqgrad_dcoils, \lm^T * dlsqgrad_dcurrents: @@ -1096,14 +1098,14 @@ def boozer_surface_dlsqgrad_dcoils_vjp(lm, booz_surf, iota, G): G is known for exact boozer surfaces, so if G=None is passed, then that value is used instead. """ - + surface = booz_surf.surface biotsavart = booz_surf.biotsavart nphi = surface.quadpoints_phi.size ntheta = surface.quadpoints_theta.size num_points = 3 * nphi * ntheta # r, dr_dB, J, d2residual_dsurfacedB, d2residual_dsurfacedgradB - boozer = boozer_surface_residual_dB(surface, iota, G, biotsavart, derivatives=1, weight_inv_modB=True) + boozer = boozer_surface_residual_dB(surface, iota, G, biotsavart, derivatives=1, weight_inv_modB=weight_inv_modB) r = boozer[0]/np.sqrt(num_points) dr_dB = boozer[1].reshape((-1, 3, 3))/np.sqrt(num_points) dr_ds = boozer[2]/np.sqrt(num_points) diff --git a/src/simsopt/geo/surfacexyztensorfourier.py b/src/simsopt/geo/surfacexyztensorfourier.py index a6e2197aa..8244d2f04 100644 --- a/src/simsopt/geo/surfacexyztensorfourier.py +++ b/src/simsopt/geo/surfacexyztensorfourier.py @@ -159,10 +159,12 @@ def npsame(a, b): npsame(thetas, np.linspace(0, 1, 2*mpol+1, endpoint=False)): mask[:, mpol+1:] = False mask[ntor+1:, 0] = False - if npsame(phis, np.linspace(0, 1/self.nfp, 2*ntor+1, endpoint=False)) and \ + elif npsame(phis, np.linspace(0, 1/self.nfp, 2*ntor+1, endpoint=False)) and \ npsame(thetas, np.linspace(0, 0.5, mpol+1, endpoint=False)): mask[ntor+1:, 0] = False - if npsame(phis, np.linspace(0, 1/(2*self.nfp), ntor+1, endpoint=False)) and \ + elif npsame(phis, np.linspace(0, 1/(2*self.nfp), ntor+1, endpoint=False)) and \ npsame(thetas, np.linspace(0, 1, 2*mpol+1, endpoint=False)): mask[0, mpol+1:] = False + else: + raise Exception('Stellarator symmetric BoozerExact surfaces require a specific set of quadrature points on the surface. See the SurfaceXYZTensorFourier.get_stellsym_mask() docstring for more information.') return mask diff --git a/tests/geo/surface_test_helpers.py b/tests/geo/surface_test_helpers.py index 6b0d6205b..1a1a6b559 100644 --- a/tests/geo/surface_test_helpers.py +++ b/tests/geo/surface_test_helpers.py @@ -74,12 +74,15 @@ def get_exact_surface(surface_type='SurfaceXYZFourier'): return s -def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exact', optimize_G=True, converge=True, stellsym=True): +def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exact', optimize_G=True, converge=True, stellsym=True, weight_inv_modB=False): """ Returns a boozer surface that will be used in unit tests. """ assert label == "Volume" or label == "ToroidalFlux" or label == "Area" or label == "AspectRatio" + + if boozer_type == 'exact': + assert weight_inv_modB == False base_curves, base_currents, ma = get_ncsx_data() coils = coils_via_symmetries(base_curves, base_currents, 3, True) @@ -120,8 +123,8 @@ def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exac ## COMPUTE THE SURFACE cw = None if boozer_type == 'exact' else 100. - boozer_surface = BoozerSurface(bs, s, lab, lab_target, constraint_weight=cw) + boozer_surface = BoozerSurface(bs, s, lab, lab_target, constraint_weight=cw, options={'weight_inv_modB':weight_inv_modB}) if converge: - boozer_surface.run_code(boozer_type, iota, G=G0, verbose=True) + boozer_surface.run_code(iota, G=G0) return bs, boozer_surface diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 3e599451c..c90118345 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -359,26 +359,21 @@ def test_run_code(self): This unit test verifies that the run_code portion of the BoozerSurface class is working as expected """ bs, boozer_surface = get_boozer_surface(boozer_type='ls') - boozer_surface.run_code('ls', boozer_surface.res['iota'], G=boozer_surface.res['G'], verbose=False) + boozer_surface.run_code(boozer_surface.res['iota'], G=boozer_surface.res['G']) # this second time should not actually run - boozer_surface.run_code('ls', boozer_surface.res['iota'], G=boozer_surface.res['G'], verbose=False) + boozer_surface.run_code(boozer_surface.res['iota'], G=boozer_surface.res['G']) bs, boozer_surface = get_boozer_surface(boozer_type='exact') - boozer_surface.run_code('exact', boozer_surface.res['iota'], G=boozer_surface.res['G'], verbose=False) + boozer_surface.run_code(boozer_surface.res['iota'], G=boozer_surface.res['G']) # this second time should not actually run - boozer_surface.run_code('exact', boozer_surface.res['iota'], G=boozer_surface.res['G'], verbose=False) + boozer_surface.run_code(boozer_surface.res['iota'], G=boozer_surface.res['G']) boozer_surface.need_to_run_code=True # run without providing value of G - boozer_surface.run_code('exact', boozer_surface.res['iota'], verbose=True) + boozer_surface.run_code(boozer_surface.res['iota']) - boozer_surface.need_to_run_code=True - # this should raise an exception - with self.assertRaises(Exception): - boozer_surface.run_code('', boozer_surface.res['iota'], G=boozer_surface.res['G'], verbose=False) - def test_convergence_cpp_and_notcpp_same(self): """ This unit test verifies that that the cpp and not cpp implementations converge to diff --git a/tests/geo/test_surface_objectives.py b/tests/geo/test_surface_objectives.py index e146a7849..29dcf0511 100644 --- a/tests/geo/test_surface_objectives.py +++ b/tests/geo/test_surface_objectives.py @@ -262,15 +262,18 @@ def test_major_radius_derivative(self): for boozer_type in ['exact', 'ls']: for label in ["Volume", "ToroidalFlux"]: for optimize_G in [True, False]: - with self.subTest(label=label, boozer_type=boozer_type, optimize_G=optimize_G): - if boozer_type == 'ls' and label == 'ToroidalFlux': - continue - if boozer_type == 'exact' and optimize_G is False: - continue - self.subtest_major_radius_surface_derivative(label, boozer_type, optimize_G) - - def subtest_major_radius_surface_derivative(self, label, boozer_type, optimize_G): - bs, boozer_surface = get_boozer_surface(label=label, nphi=51, ntheta=51, boozer_type=boozer_type, optimize_G=optimize_G) + for weight_inv_modB in [True, False]: + with self.subTest(label=label, boozer_type=boozer_type, optimize_G=optimize_G): + if boozer_type == 'ls' and label == 'ToroidalFlux': + continue + if boozer_type == 'exact' and optimize_G is False: + continue + if boozer_type == 'exact' and weight_inv_modB: + continue + self.subtest_major_radius_surface_derivative(label, boozer_type, optimize_G, weight_inv_modB) + + def subtest_major_radius_surface_derivative(self, label, boozer_type, optimize_G, weight_inv_modB): + bs, boozer_surface = get_boozer_surface(label=label, nphi=51, ntheta=51, boozer_type=boozer_type, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) coeffs = bs.x mr = MajorRadius(boozer_surface) @@ -294,19 +297,22 @@ def test_iotas_derivative(self): for boozer_type in ['exact', 'ls']: for label in ["Volume", "ToroidalFlux"]: for optimize_G in [True, False]: - if boozer_type == 'ls' and label == 'ToroidalFlux': - continue - if boozer_type == 'exact' and optimize_G is False: - continue - with self.subTest(label=label, boozer_type=boozer_type, optimize_G=optimize_G): - self.subtest_iotas_derivative(label, boozer_type, optimize_G) - - def subtest_iotas_derivative(self, label, boozer_type, optimize_G): + for weight_inv_modB in [True, False]: + if boozer_type == 'ls' and label == 'ToroidalFlux': + continue + if boozer_type == 'exact' and optimize_G is False: + continue + if boozer_type == 'exact' and weight_inv_modB: + continue + with self.subTest(label=label, boozer_type=boozer_type, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB): + self.subtest_iotas_derivative(label, boozer_type, optimize_G, weight_inv_modB) + + def subtest_iotas_derivative(self, label, boozer_type, optimize_G, weight_inv_modB): """ Taylor test for derivative of surface rotational transform wrt coil parameters """ - bs, boozer_surface = get_boozer_surface(label=label, boozer_type=boozer_type, optimize_G=optimize_G) + bs, boozer_surface = get_boozer_surface(label=label, boozer_type=boozer_type, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) coeffs = bs.x io = Iotas(boozer_surface) @@ -329,17 +335,20 @@ def test_nonQSratio_derivative(self): """ for boozer_type in ['exact', 'ls']: for label in ["Volume", "ToroidalFlux"]: - for optimize_G in [True, False]: - if boozer_type == 'ls' and label == 'ToroidalFlux': - continue - if boozer_type == 'exact' and optimize_G is False: - continue - for axis in [False, True]: - with self.subTest(label=label, axis=axis, boozer_type=boozer_type, optimize_G=optimize_G): - self.subtest_nonQSratio_derivative(label, axis, boozer_type, optimize_G) - - def subtest_nonQSratio_derivative(self, label, axis, boozer_type, optimize_G): - bs, boozer_surface = get_boozer_surface(label=label, boozer_type=boozer_type, optimize_G=optimize_G) + for weight_inv_modB in [True, False]: + for optimize_G in [True, False]: + if boozer_type == 'ls' and label == 'ToroidalFlux': + continue + if boozer_type == 'exact' and optimize_G is False: + continue + if boozer_type == 'exact' and weight_inv_modB: + continue + for axis in [False, True]: + with self.subTest(label=label, axis=axis, boozer_type=boozer_type, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB): + self.subtest_nonQSratio_derivative(label, axis, boozer_type, optimize_G, weight_inv_modB) + + def subtest_nonQSratio_derivative(self, label, axis, boozer_type, optimize_G, weight_inv_modB): + bs, boozer_surface = get_boozer_surface(label=label, boozer_type=boozer_type, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) coeffs = bs.x io = NonQuasiSymmetricRatio(boozer_surface, bs, quasi_poloidal=axis) @@ -362,11 +371,12 @@ def test_boozerresidual_derivative(self): """ for label in ["Volume"]: for optimize_G in [True, False]: - with self.subTest(label=label, optimize_G=optimize_G): - self.subtest_boozerresidual_derivative(label, optimize_G) + for weight_inv_modB in [True, False]: + with self.subTest(label=label, optimize_G=optimize_G, weight_inv_modB=weight_inv_modB): + self.subtest_boozerresidual_derivative(label, optimize_G, weight_inv_modB) - def subtest_boozerresidual_derivative(self, label, optimize_G): - bs, boozer_surface = get_boozer_surface(label=label, boozer_type='ls', optimize_G=optimize_G) + def subtest_boozerresidual_derivative(self, label, optimize_G, weight_inv_modB): + bs, boozer_surface = get_boozer_surface(label=label, boozer_type='ls', optimize_G=optimize_G, weight_inv_modB=weight_inv_modB) coeffs = bs.x br = BoozerResidual(boozer_surface, bs) From 0401b8baf3c32a1b9226c24e2aad132b40dfe915 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Thu, 16 May 2024 11:06:51 -0400 Subject: [PATCH 114/176] changes for code coverage --- tests/geo/surface_test_helpers.py | 6 ++- tests/geo/test_boozersurface.py | 64 +++++++++++++++++++++++++++++++ 2 files changed, 69 insertions(+), 1 deletion(-) diff --git a/tests/geo/surface_test_helpers.py b/tests/geo/surface_test_helpers.py index 1a1a6b559..dfd981568 100644 --- a/tests/geo/surface_test_helpers.py +++ b/tests/geo/surface_test_helpers.py @@ -123,7 +123,11 @@ def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exac ## COMPUTE THE SURFACE cw = None if boozer_type == 'exact' else 100. - boozer_surface = BoozerSurface(bs, s, lab, lab_target, constraint_weight=cw, options={'weight_inv_modB':weight_inv_modB}) + if weight_inv_modB: + boozer_surface = BoozerSurface(bs, s, lab, lab_target, constraint_weight=cw) + else: + boozer_surface = BoozerSurface(bs, s, lab, lab_target, constraint_weight=cw, options={'weight_inv_modB':False}) + if converge: boozer_surface.run_code(iota, G=G0) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index c90118345..b307bd4af 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -4,6 +4,7 @@ from simsopt.field.coil import coils_via_symmetries from simsopt.geo.boozersurface import BoozerSurface from simsopt.field.biotsavart import BiotSavart +from simsopt.geo import SurfaceXYZTensorFourier, SurfaceRZFourier from simsopt.geo.surfaceobjectives import ToroidalFlux, Area from simsopt.configs.zoo import get_ncsx_data, get_hsx_data, get_giuliani_data from .surface_test_helpers import get_surface, get_exact_surface, get_boozer_surface @@ -522,6 +523,69 @@ def compute_differences(Ha, Hb): print(f'max err ({i1:03}, {j1:03}): {np.max(diff):.6e}, {Ha[i1, j1]:.6e}\nmax rel err ({i2:03}, {j2:03}): {np.max(rel_diff):.6e}, {Ha[i2,j2]:.6e}\n') compute_differences(H0, H1) + def test_boozer_surface_quadpoints(self): + """ + this unit test checks that the quadpoints mask for stellarator symmetric Boozer Surfaces are correctly initialized + """ + for idx in range(4): + with self.subTest(idx=idx): + self.subtest_boozer_surface_quadpoints(idx) + + def subtest_boozer_surface_quadpoints(self, idx): + mpol = 6 + ntor = 6 + nfp = 3 + + if idx == 0: + phis = np.linspace(0, 1/nfp, 2*ntor+1, endpoint=False) + thetas = np.linspace(0, 1, 2*mpol+1, endpoint=False) + mask_true = np.ones((phis.size, thetas.size), dtype=bool) + mask_true[:, mpol+1:] = False + mask_true[ntor+1:, 0] = False + elif idx == 1: + phis = np.linspace(0, 1/nfp, 2*ntor+1, endpoint=False) + thetas = np.linspace(0, 0.5, mpol+1, endpoint=False) + mask_true = np.ones((phis.size, thetas.size), dtype=bool) + mask_true[ntor+1:, 0] = False + elif idx == 2: + phis = np.linspace(0, 1/(2*nfp), ntor+1, endpoint=False) + thetas = np.linspace(0, 1, 2*mpol+1, endpoint=False) + mask_true = np.ones((phis.size, thetas.size), dtype=bool) + mask_true[0, mpol+1:] = False + elif idx == 3: + phis = np.linspace(0, 1., 2*ntor+1, endpoint=False) + thetas = np.linspace(0, 1., 2*mpol+1, endpoint=False) + + s = SurfaceXYZTensorFourier(mpol=mpol, ntor=ntor, stellsym=True, nfp=nfp, quadpoints_phi=phis, quadpoints_theta=thetas) + + if idx < 3: # the first three quadrature point sets should pass without issue. + mask = s.get_stellsym_mask() + assert np.all(mask == mask_true) + else: + with self.assertRaises(Exception): + mask = s.get_stellsym_mask() + + def test_boozer_surface_type_assert(self): + """ + this unit test checks that an exception is raised if a SurfaceRZFourier is passed to a BoozerSurface + """ + mpol = 6 + ntor = 6 + nfp = 3 + phis = np.linspace(0, 1/nfp, 2*ntor+1, endpoint=False) + thetas = np.linspace(0, 1, 2*mpol+1, endpoint=False) + s = SurfaceRZFourier(mpol=mpol, ntor=ntor, stellsym=True, nfp=nfp, quadpoints_phi=phis, quadpoints_theta=thetas) + + base_curves, base_currents, ma = get_ncsx_data() + coils = coils_via_symmetries(base_curves, base_currents, 3, True) + bs = BiotSavart(coils) + + lab = Area(s) + lab_target = 0.1 + + with self.assertRaises(Exception): + boozer_surface = BoozerSurface(bs, s, lab, lab_target) + if __name__ == "__main__": unittest.main() From 47666b52716a33fce2b132ee14fc402d9d1a3689 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Thu, 16 May 2024 11:09:41 -0400 Subject: [PATCH 115/176] linting fix --- tests/geo/test_boozersurface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index b307bd4af..1cb199073 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -584,7 +584,7 @@ def test_boozer_surface_type_assert(self): lab_target = 0.1 with self.assertRaises(Exception): - boozer_surface = BoozerSurface(bs, s, lab, lab_target) + _ = BoozerSurface(bs, s, lab, lab_target) if __name__ == "__main__": From 8a5101e0443a577fdc0f31aee9629e622cd6362b Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Thu, 16 May 2024 11:21:34 -0400 Subject: [PATCH 116/176] fix to example --- examples/2_Intermediate/boozerQA_ls_mpi.py | 4 ++-- src/simsopt/geo/surfaceobjectives.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 63f01b52e..6c0bf5ea0 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -61,7 +61,7 @@ os.makedirs(OUT_DIR, exist_ok=True) proc0_print("Running 2_Intermediate/boozerQA_ls_mpi.py") -proc0_print("================================") +proc0_print("=========================================") base_curves, base_currents, coils, curves, surfaces, boozer_surfaces, ress = load(IN_DIR + "ncsx_init.json") @@ -216,4 +216,4 @@ def callback(x): surface.to_vtk(OUT_DIR + f"surf_opt_{idx}") proc0_print("End of 2_Intermediate/boozerQA_ls.py") -proc0_print("================================") +proc0_print("====================================") diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 63a676675..188b49d24 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -1007,7 +1007,7 @@ def compute(self): surface = self.surface iota = self.boozer_surface.res['iota'] G = self.boozer_surface.res['G'] - r, J = boozer_surface_residual(surface, iota, G, self.biotsavart, derivatives=1, weight_inv_modB=res['weight_inv_modB']) + r, J = boozer_surface_residual(surface, iota, G, self.biotsavart, derivatives=1, weight_inv_modB=self.boozer_surface.res['weight_inv_modB']) rtil = np.concatenate((r/np.sqrt(num_points), [np.sqrt(self.constraint_weight)*(self.boozer_surface.label.J()-self.boozer_surface.targetlabel)])) self._J = 0.5*np.sum(rtil**2) From 44e56c4ac4af5436a42582c569497068c345df00 Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Fri, 17 May 2024 09:25:20 -0400 Subject: [PATCH 117/176] Fix area -> aspect ratio in AspectRatio, tidy up boozerQA_ls_mpi.py and test_mpi_optimizable --- examples/2_Intermediate/boozerQA_ls_mpi.py | 59 ++++++++++++---------- src/simsopt/geo/surfaceobjectives.py | 4 +- tests/geo/surface_test_helpers.py | 2 +- tests/objectives/test_utilities.py | 8 +-- 4 files changed, 36 insertions(+), 37 deletions(-) diff --git a/examples/2_Intermediate/boozerQA_ls_mpi.py b/examples/2_Intermediate/boozerQA_ls_mpi.py index 6c0bf5ea0..f754fb170 100755 --- a/examples/2_Intermediate/boozerQA_ls_mpi.py +++ b/examples/2_Intermediate/boozerQA_ls_mpi.py @@ -1,26 +1,6 @@ -#!/usr/bin/env python3 -from simsopt.geo import curves_to_vtk, MajorRadius, CurveLength, CurveCurveDistance, NonQuasiSymmetricRatio, Iotas,\ - BoozerResidual, LpCurveCurvature, MeanSquaredCurvature, ArclengthVariation -from simsopt._core import load -from simsopt.objectives import MPIObjective, MPIOptimizable -from simsopt.field import BiotSavart -from simsopt.objectives import QuadraticPenalty -from scipy.optimize import minimize -from simsopt.util import proc0_print -import numpy as np -import os -try: - from mpi4py import MPI - comm = MPI.COMM_WORLD - rank = comm.rank - size = comm.size - -except ImportError: - comm = None - size = 1 - rank = 0 +#!/usr/bin/env python -""" +r""" This example optimizes the NCSX coils and currents for QA on potentially multiple surfaces using the BoozerLS approach. For a single surface, the objective is: @@ -52,9 +32,33 @@ and nsurfaces=Nranks=2, then the proper call is: mpirun -np 2 ./boozerQA_ls_mpi.py -More details on this work can be found at or doi:10.1063/5.0129716 arxiv:2210.03248. +More details on this work can be found at +A Giuliani et al, "Direct stellarator coil optimization for nested magnetic surfaces with precise +quasi-symmetry", Physics of Plasmas 30, 042511 (2023) doi:10.1063/5.0129716 +or arxiv:2210.03248. """ +import os +import numpy as np +from scipy.optimize import minimize +from simsopt.geo import curves_to_vtk, MajorRadius, CurveLength, CurveCurveDistance, NonQuasiSymmetricRatio, Iotas,\ + BoozerResidual, LpCurveCurvature, MeanSquaredCurvature, ArclengthVariation +from simsopt._core import load +from simsopt.objectives import MPIObjective, MPIOptimizable +from simsopt.field import BiotSavart +from simsopt.objectives import QuadraticPenalty +from simsopt.util import proc0_print, in_github_actions +try: + from mpi4py import MPI + comm = MPI.COMM_WORLD + rank = comm.rank + size = comm.size + +except ImportError: + comm = None + size = 1 + rank = 0 + # Directory for output IN_DIR = "./inputs/input_ncsx/" OUT_DIR = "./output/" @@ -67,7 +71,7 @@ # you can optimize for QA on up to 10 surfaces, by changing nsurfaces below. nsurfaces = 2 -assert nsurfaces <=10 +assert nsurfaces <= 10 surfaces = surfaces[:nsurfaces] boozer_surfaces = boozer_surfaces[:nsurfaces] @@ -205,8 +209,7 @@ def callback(x): ################################################################################ """) # Number of iterations to perform: -ci = "CI" in os.environ and os.environ['CI'].lower() in ['1', 'true'] -MAXITER = 50 if ci else 1e3 +MAXITER = 50 if in_github_actions else 1e3 res = minimize(fun, dofs, jac=True, method='BFGS', options={'maxiter': MAXITER}, tol=1e-15, callback=callback) if comm is None or rank == 0: @@ -215,5 +218,5 @@ def callback(x): if comm is None or rank == 0: surface.to_vtk(OUT_DIR + f"surf_opt_{idx}") -proc0_print("End of 2_Intermediate/boozerQA_ls.py") -proc0_print("====================================") +proc0_print("End of 2_Intermediate/boozerQA_ls_mpi.py") +proc0_print("========================================") diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 188b49d24..e743af500 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -18,7 +18,7 @@ class AspectRatio(Optimizable): """ - Wrapper class for surface area label. + Wrapper class for surface aspect ratio. """ def __init__(self, surface, range=None, nphi=None, ntheta=None): @@ -46,7 +46,7 @@ def __init__(self, surface, range=None, nphi=None, ntheta=None): def J(self): """ - Compute the area of a surface. + Compute the aspect ratio of a surface. """ return self.surface.aspect_ratio() diff --git a/tests/geo/surface_test_helpers.py b/tests/geo/surface_test_helpers.py index dfd981568..3e9490ba6 100644 --- a/tests/geo/surface_test_helpers.py +++ b/tests/geo/surface_test_helpers.py @@ -79,7 +79,7 @@ def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exac Returns a boozer surface that will be used in unit tests. """ - assert label == "Volume" or label == "ToroidalFlux" or label == "Area" or label == "AspectRatio" + assert label in ["Volume", "ToroidalFlux", "Area", "AspectRatio"] if boozer_type == 'exact': assert weight_inv_modB == False diff --git a/tests/objectives/test_utilities.py b/tests/objectives/test_utilities.py index 2989523f9..1c6414dd2 100644 --- a/tests/objectives/test_utilities.py +++ b/tests/objectives/test_utilities.py @@ -63,10 +63,8 @@ def test_quadratic_penalty(self): with self.assertRaises(Exception): self.subtest_quadratic_penalty(curve, J.J()+0.1, 'NotInList') + @unittest.skipIf(MPI is None, "mpi4py not found") def test_mpi_objective(self): - if MPI is None: - print("skip test_mpi_objective") - return comm = MPI.COMM_WORLD c = self.create_curve() @@ -87,13 +85,11 @@ def test_mpi_objective(self): assert abs(Jmpi1.J() - sum(J.J() for J in Js)/n) < 1e-14 assert np.sum(np.abs(Jmpi1.dJ() - sum(J.dJ() for J in Js)/n)) < 1e-14 + @unittest.skipIf(MPI is None, "mpi4py not found") def test_mpi_optimizable(self): """ This test checks that the `x` attribute of the surfaces is correctly communicated across the ranks. """ - if MPI is None: - print("skip test_mpi_optimizable") - return comm = MPI.COMM_WORLD for size in [1, 2, 3, 4, 5]: From 6890be81b4341d0a997ba84194638e228fd50698 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 17 May 2024 16:17:58 -0400 Subject: [PATCH 118/176] clarifying documentation and fixing unit test --- src/simsopt/geo/boozersurface.py | 8 +++++--- tests/geo/surface_test_helpers.py | 5 +++++ 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/src/simsopt/geo/boozersurface.py b/src/simsopt/geo/boozersurface.py index 32a447023..ba0fc3a87 100644 --- a/src/simsopt/geo/boozersurface.py +++ b/src/simsopt/geo/boozersurface.py @@ -85,8 +85,6 @@ def __init__(self, biotsavart, surface, label, targetlabel, constraint_weight=No # set the default options now if 'verbose' not in options: options['verbose'] = True - if 'G' not in options: - options['G'] = None # default solver options for the BoozerExact and BoozerLS solvers if self.boozer_type == 'exact': @@ -120,7 +118,7 @@ def run_code(self, iota, G=None): Args: boozer_type: either 'exact' or 'ls', to indicate whether a BoozerExact or a BoozerLS surface is to be computed. iota: guess for value of rotational transform on the surface, - G: guess for value of G on surface, defaults to None. + G: guess for value of G on surface, defaults to None. Note that if None is used, then the coil currents must be fixed. options: dictionary of solver options. If keyword is not specified, then a default value is used. Possible keywords are: `verbose`: display convergence information @@ -134,6 +132,10 @@ def run_code(self, iota, G=None): if not self.need_to_run_code: return + # for coil optimizations, the gradient calculations of the objective assume that the coil currents are fixed when G is None. + if G is None: + assert np.all([c.current.dofs.all_fixed() for c in self.biotsavart.coils]) + # BoozerExact default solver if self.boozer_type == 'exact': res = self.solve_residual_equation_exactly_newton(iota=iota, G=G, tol=self.options['newton_tol'], maxiter=self.options['newton_maxiter'], verbose=self.options['verbose']) diff --git a/tests/geo/surface_test_helpers.py b/tests/geo/surface_test_helpers.py index 3e9490ba6..12d9fcfdd 100644 --- a/tests/geo/surface_test_helpers.py +++ b/tests/geo/surface_test_helpers.py @@ -90,6 +90,11 @@ def get_boozer_surface(label="Volume", nphi=None, ntheta=None, boozer_type='exac current_sum = sum(abs(c.current.get_value()) for c in coils) G0 = 2. * np.pi * current_sum * (4 * np.pi * 10**(-7) / (2 * np.pi)) if optimize_G else None + # currents need to be fixed if optimize_G is None + if optimize_G is False: + for c in bs.coils: + c.current.fix_all() + ## RESOLUTION DETAILS OF SURFACE ON WHICH WE OPTIMIZE FOR QA mpol = 6 if boozer_type == 'exact' else 3 ntor = 6 if boozer_type == 'exact' else 3 From 8be1c500dbf466eecaea36794521a1baba4e02f0 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 17 May 2024 17:36:26 -0400 Subject: [PATCH 119/176] edit to unit test --- tests/geo/test_boozersurface.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 1cb199073..461437cc1 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -365,15 +365,18 @@ def test_run_code(self): # this second time should not actually run boozer_surface.run_code(boozer_surface.res['iota'], G=boozer_surface.res['G']) + for c in bs.coils: + c.current.fix_all() + + boozer_surface.need_to_run_code=True + # run without providing value of G + boozer_surface.run_code(boozer_surface.res['iota']) + bs, boozer_surface = get_boozer_surface(boozer_type='exact') boozer_surface.run_code(boozer_surface.res['iota'], G=boozer_surface.res['G']) # this second time should not actually run boozer_surface.run_code(boozer_surface.res['iota'], G=boozer_surface.res['G']) - - boozer_surface.need_to_run_code=True - # run without providing value of G - boozer_surface.run_code(boozer_surface.res['iota']) def test_convergence_cpp_and_notcpp_same(self): """ From 11f176b7125cf4b097be899441ea6aea573c05c7 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 17 May 2024 17:59:28 -0400 Subject: [PATCH 120/176] another edit to unit test --- tests/geo/test_boozersurface.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/geo/test_boozersurface.py b/tests/geo/test_boozersurface.py index 461437cc1..badd5b34e 100644 --- a/tests/geo/test_boozersurface.py +++ b/tests/geo/test_boozersurface.py @@ -378,6 +378,10 @@ def test_run_code(self): # this second time should not actually run boozer_surface.run_code(boozer_surface.res['iota'], G=boozer_surface.res['G']) + # run the BoozerExact algorithm without a guess for G + boozer_surface.need_to_run_code = True + boozer_surface.solve_residual_equation_exactly_newton(iota=boozer_surface.res['iota']) + def test_convergence_cpp_and_notcpp_same(self): """ This unit test verifies that that the cpp and not cpp implementations converge to From e076915ecbdb981be0c3402fe0496be30957f7e8 Mon Sep 17 00:00:00 2001 From: Chris Date: Thu, 23 May 2024 17:13:20 +0200 Subject: [PATCH 121/176] re-factor normal_field and spec, add FT fn to surface --- src/simsopt/field/normal_field.py | 257 +++++++++++-- src/simsopt/geo/surface.py | 125 +++++++ src/simsopt/mhd/spec.py | 598 +++++++++++++++++++++--------- 3 files changed, 782 insertions(+), 198 deletions(-) diff --git a/src/simsopt/field/normal_field.py b/src/simsopt/field/normal_field.py index 8c14d3398..52e75daf4 100644 --- a/src/simsopt/field/normal_field.py +++ b/src/simsopt/field/normal_field.py @@ -14,12 +14,18 @@ __all__ = ['NormalField'] - class NormalField(Optimizable): r""" ``NormalField`` represents the magnetic field normal to a toroidal surface, for example the computational boundary of SPEC free-boundary. + It consists a surface (the computational boundary), and a set of Fourier harmonics that describe + the normal component of an externally provided field. + + The Fourier harmonics are the degees of freedom, the computational boundary is kept fixed. + The normal field should not be normalized to unit area, i.e. it is the + fourier components of B.(\grad\theta \times \nabla\zeta) on the surface. + Args: nfp: The number of field period stellsym: Whether (=True) or not (=False) stellarator symmetry is enforced. @@ -37,7 +43,7 @@ class NormalField(Optimizable): """ def __init__(self, nfp=1, stellsym=True, mpol=1, ntor=0, - vns=None, vnc=None): + vns=None, vnc=None, computational_boundary=None): self.nfp = nfp self.stellsym = stellsym @@ -47,44 +53,51 @@ def __init__(self, nfp=1, stellsym=True, mpol=1, ntor=0, if vns is None: vns = np.zeros((self.mpol + 1, 2 * self.ntor + 1)) - if vnc is None and not stellsym: + if not self.stellsym and vnc is None: vnc = np.zeros((self.mpol + 1, 2 * self.ntor + 1)) + + if computational_boundary is None: + computational_boundary = SurfaceRZFourier(nfp=nfp, stellsym=stellsym, mpol=mpol, ntor=ntor) + computational_boundary.fix_all() + self.computational_boundary = computational_boundary if self.stellsym: self.ndof = self.ntor + self.mpol * (2 * self.ntor + 1) else: self.ndof = 2 * (self.ntor + self.mpol * (2 * self.ntor + 1)) + 1 - - # Pack in a single array - dofs = np.zeros((self.ndof,)) - - # Populate dofs array - vns_shape = vns.shape - input_mpol = int(vns_shape[0]-1) - input_ntor = int((vns_shape[1]-1)/2) - for mm in range(0, self.mpol+1): - for nn in range(-self.ntor, self.ntor+1): - if mm == 0 and nn < 0: continue - if mm > input_mpol: continue - if nn > input_ntor: continue - - if not (mm == 0 and nn == 0): - ii = self.get_index_in_dofs(mm, nn, even=False) - dofs[ii] = vns[mm, input_ntor+nn] - - if not self.stellsym: - ii = self.get_index_in_dofs(mm, nn, even=True) - dofs[ii] = vnc[mm, input_ntor+nn] + + self._vns = vns + self._vnc = vnc + + dofs = self.get_dofs() Optimizable.__init__( self, x0=dofs, names=self._make_names()) + + @property + def vns(self): + return self._vns + + @vns.setter + def vns(self): + raise AttributeError('change Vns using set_vns() or set_vns_asarray()') + + @property + def vnc(self): + return self._vnc + + @vnc.setter + def vnc(self): + raise AttributeError('change Vnc using set_vnc() or set_vnc_asarray()') @classmethod def from_spec(cls, filename): """ Initialize using the harmonics in SPEC input file + WARNING: A normal field initialized with this method will + not have a computational boundary """ # Test if py_spec is available @@ -114,6 +127,60 @@ def from_spec(cls, filename): return normal_field + @classmethod + def from_spec_object(cls, spec): + """ + Initialize using the simsopt SPEC object's attributes + """ + if not spec.freebound: + raise ValueError('The given SPEC object is not free-boundary') + boundary_dict = {'specrc': spec.inputlist.rbc, + 'speczs': spec.inputlist.zbs} + if not spec.stellsym: + boundary_dict.append({'specrs': spec.inputlist.rbs, + 'speczc': spec.inputlist.zbc}) + computational_boundary = spec._specarrays_to_surfRZFourier(boundary_dict) + + # Grab all the attributes from the SPEC object into an input dictionary + input_dict = {'nfp': spec.nfp, + 'stellsym': spec.stellsym, + 'mpol': spec.mpol, + 'ntor': spec.ntor, + 'vns': spec.inputlist.vns, + 'computational_boundary': computational_boundary} + if not spec.stellsym: + input_dict.append({'vnc': spec.inputlist.vnc}) + + normal_field = cls(**input_dict) + + return normal_field + + def get_dofs(self): + """ + get DOFs from vns and vnc + """ + # Pack in a single array + dofs = np.zeros((self.ndof,)) + + # Populate dofs array + vns_shape = self.vns.shape + input_mpol = int(vns_shape[0]-1) + input_ntor = int((vns_shape[1]-1)/2) + for mm in range(0, self.mpol+1): + for nn in range(-self.ntor, self.ntor+1): + if mm == 0 and nn < 0: continue + if mm > input_mpol: continue + if nn > input_ntor: continue + + if not (mm == 0 and nn == 0): + ii = self.get_index_in_dofs(mm, nn, even=False) + dofs[ii] = self.vns[mm, input_ntor+nn] + + if not self.stellsym: + ii = self.get_index_in_dofs(mm, nn, even=True) + dofs[ii] = self.vnc[mm, input_ntor+nn] + return dofs + def get_index_in_dofs(self, m, n, mpol=None, ntor=None, even=False): """ Returns position of mode (m,n) in dofs array @@ -162,7 +229,9 @@ def get_vns(self, m, n): def set_vns(self, m, n, value): self.check_mn(m, n) ii = self.get_index_in_dofs(m, n) - self.local_full_x[ii] = value + tmp = self.local_full_x + tmp[ii] = value + self.local_full_x = tmp def get_vnc(self, m, n): self.check_mn(m, n) @@ -178,7 +247,9 @@ def set_vnc(self, m, n, value): if self.stellsym: raise ValueError('Stellarator symmetric has no vnc') else: - self.local_full_x[ii] = value + tmp = self.local_full_x + tmp[ii] = value + self.local_full_x = tmp def check_mn(self, m, n): if m < 0 or m > self.mpol: @@ -193,10 +264,10 @@ def _make_names(self): Form a list of names of the ``vns``, ``vnc`` """ if self.stellsym: - names = self._make_names_helper(False) + names = self._make_names_helper(even=False) else: - names = np.append(self._make_names_helper(False), - self._make_names_helper(True)) + names = np.append(self._make_names_helper(even=False), + self._make_names_helper(even=True)) return names @@ -287,3 +358,131 @@ def fixed_range(self, mmin, mmax, nmin, nmax, fixed=True): fn(f'vns({m},{n})') if not self.stellsym: fn(f'vnc({m},{n})') + + def get_vns_asarray(self, mpol=None, ntor=None): + """ + Return the vns as a single array + """ + if mpol == None: + mpol = self.mpol + elif mpol > self.mpol: + raise ValueError('mpol out of bound') + + if ntor == None: + ntor = self.ntor + elif ntor > self.ntor: + raise ValueError('ntor out of bound') + + vns = np.zeros((mpol + 1, 2 * ntor + 1)) + for mm in range(0, mpol + 1): + for nn in range(-ntor, ntor + 1): + if mm == 0 and nn <= 0: continue + vns[mm, ntor + nn] = self.get_vns(mm, nn) + + return vns + + def get_vnc_asarray(self, mpol=None, ntor=None): + """ + Return the vnc as a single array + """ + if mpol == None: + mpol = self.mpol + elif mpol > self.mpol: + raise ValueError('mpol out of bound') + + if ntor == None: + ntor = self.ntor + elif ntor > self.ntor: + raise ValueError('ntor out of bound') + + vnc = np.zeros((mpol + 1, 2 * ntor + 1)) + for mm in range(0, mpol + 1): + for nn in range(-ntor, ntor + 1): + if mm == 0 and nn < 0: continue + vnc[mm, ntor + nn] = self.get_vnc(mm, nn) + + return vnc + + def get_vns_vnc_asarray(self, mpol, ntor): + """ + Return the vns and vnc as two arrays single array + """ + if mpol == None: + mpol = self.mpol + elif mpol > self.mpol: + raise ValueError('mpol out of bound') + + if ntor == None: + ntor = self.ntor + elif ntor > self.ntor: + raise ValueError('ntor out of bound') + + vns = self.get_vns_asarray(mpol, ntor) + vnc = self.get_vnc_asarray(mpol, ntor) + return vns, vnc + + def set_vns_asarray(self, vns, mpol=None, ntor=None): + """ + Set the vns from a single array + """ + if mpol == None: + mpol = self.mpol + elif mpol > self.mpol: + raise ValueError('mpol out of bound') + + if ntor == None: + ntor = self.ntor + elif ntor > self.ntor: + raise ValueError('ntor out of bound') + + for mm in range(0, mpol + 1): + for nn in range(-ntor, ntor + 1): + if mm == 0 and nn <= 0: continue + self.set_vns(mm, nn, vns[mm, ntor + nn]) + + def set_vnc_asarray(self, vnc, mpol=None, ntor=None): + """ + Set the vnc from a single array + """ + if mpol == None: + mpol = self.mpol + elif mpol > self.mpol: + raise ValueError('mpol out of bound') + + if ntor == None: + ntor = self.ntor + elif ntor > self.ntor: + raise ValueError('ntor out of bound') + + for mm in range(0, mpol + 1): + for nn in range(-ntor, ntor + 1): + if mm == 0 and nn < 0: continue + self.set_vnc(mm, nn, vnc[mm, ntor + nn]) + + def set_vns_vnc_asarray(self, vns, vnc, mpol=None, ntor=None): + """ + Set the vns and vnc from two single arrays + """ + if mpol == None: + mpol = self.mpol + elif mpol > self.mpol: + raise ValueError('mpol out of bound') + + if ntor == None: + ntor = self.ntor + elif ntor > self.ntor: + raise ValueError('ntor out of bound') + + self.set_vns_asarray(vns, mpol, ntor) + + def get_real_space_field(self): + """ + Fourier transform the field and get the real-space values of the normal component of the externally + provided field on the computational boundary. + The returned array will be of size specified by the computational boudary's SurfaceRZFourier quadpoints. + """ + vns, vnc = self.get_vns_vnc_asarray(mpol=self.mpol, ntor=self.ntor) + BdotN_unnormalized = self.computational_boundary.inverse_fourier_transform_field(vns, vnc, normalization=(2*np.pi)**2, stellsym=self.stellsym) + normal_field_real_space = -1 * BdotN_unnormalized / np.linalg.norm(self.computational_boundary.normal(), axis=-1) + return normal_field_real_space + diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index 9da6fba97..f51f44a35 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -839,6 +839,131 @@ def interpolate_on_arclength_grid(self, function, theta_evaluate): return function_interpolated + def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=None, **kwargs): + r""" + Compute the Fourier components of a field on the surface. The field + is evaluated at the quadrature points on the surface. + The Fourier uses the conventions of the FourierRZSurface series, + with `npol` going from `-ntor` to `ntor` and `mpol` from 0 to `mpol` + i.e.: + :math:`f(\theta, \phi) = \Sum_{m=0}^{mpol} \Sum_{n=-npol}^{npol} A^{mn}_s \sin(m\theta - n*Nfp*\phi)\\ + + A^{mn}_c \cos(m\theta - n*Nfp*\phi)` + Where the cosine series is only evaluated if the surface is not stellarator + symmetric (if the field does not adhere to the symmetry of the surface, + request the cosine series by setting the kwarg stellsym=False) + *Arguments*: + - field: 2D array of shape (numquadpoints_phi, numquadpoints_theta). + - mpol: maximum poloidal mode number of the transform, if None, + the mpol attribute of the surface is used. + - ntor: maximum toroidal mode number of the transform if None, + the ntor attribute of the surface is used. + *Optional keyword arguments*: + - normalization: Fourier transform normalization. Can be: + None: forward and back transform are not normalized + float: forward transform is divided by this number + - stellsym: boolean to override the stellsym attribute + of the surface if you want to force the calculation of the cosine series + *Returns*: + - A_mns: 2D array of shape (mpol+1, 2*ntor+1) containing the sine coefficients + - A_mnc: 2D array of shape (mpol+1, 2*ntor+1) containing the cosine coefficients + (these are zero if the surface is stellarator symmetric) + """ + assert (field.shape == [self.quadpoints_phi.size, self.quadpoints_theta.size], + "Field must be evaluated at the quadrature points on the surface. \ + the field you passed in has shape {}".format(field.shape)) + stellsym = kwargs.pop('stellsym', self.stellsym) + if mpol is None: + try: mpol = self.mpol + except AttributeError: raise ValueError("mpol must be specified") + if ntor is None: + try: ntor = self.ntor + except AttributeError: raise ValueError("ntor must be specified") + A_mns = np.zeros((int(mpol + 1), int(2 * ntor + 1))) # sine coefficients + A_mnc = np.zeros((int(mpol + 1), int(2 * ntor + 1))) # cosine coefficients + ntheta_grid = len(self.quadpoints_theta) + nphi_grid = len(self.quadpoints_phi) + + factor = 2.0 / (ntheta_grid * nphi_grid) + + phi2d, theta2d = np.meshgrid(2 * np.pi * self.quadpoints_phi, + 2 * np.pi * self.quadpoints_theta, + indexing="ij") + + for m in range(mpol + 1): + nmin = -ntor + if m == 0: nmin = 1 + for n in range(nmin, ntor+1): + angle = m * theta2d - n * self.nfp * phi2d + sinangle = np.sin(angle) + if not stellsym: + cosangle = np.cos(angle) + factor2 = factor + # The next 2 lines ensure inverse Fourier transform(Fourier transform) = identity + if np.mod(ntheta_grid, 2) == 0 and m == (ntheta_grid/2): factor2 = factor2 / 2 + if np.mod(nphi_grid, 2) == 0 and abs(n) == (nphi_grid/2): factor2 = factor2 / 2 + A_mns[m, n + ntor] = np.sum(field * sinangle * factor2) + if not stellsym: + A_mnc[m, n + ntor] = np.sum(field * cosangle * factor2) + + if not stellsym: + A_mnc[0, ntor] = np.sum(field) / (ntheta_grid * nphi_grid) + if normalization is not None: + if type(normalization) is not float: + raise ValueError("normalization must be a float") + A_mns = A_mns / normalization + A_mnc = A_mnc / normalization + + return A_mns, A_mnc + + def inverse_fourier_transform_field(self, A_mns, A_mnc, normalization=None, **kwargs): + r""" + Compute the inverse Fourier transform of a field on the surface. The field + is evaluated at the quadrature points on the surface. The Fourier + transform is defined as + :math:`f(\theta, \phi) = \Sum_{m=0}^{mpol} \Sum_{n=-npol}^{npol} A^{mn}_s \sin(m\theta - n*Nfp*\phi)\\ + + A^{mn}_c \cos(m\theta - n*Nfp*\phi)` + Where the cosine series is only evaluated if the surface is not stellarator + symmetric. + *Arguments*: + - A_mns: 2D array of shape (mpol+1, 2*ntor+1) containing the sine coefficients + - A_mnc: 2D array of shape (mpol+1, 2*ntor+1) containing the cosine coefficients + (these are zero if the surface is stellarator symmetric) + *Optional keyword arguments*: + - normalization: Fourier transform normalization. Can be: + None: forward and back transform are not normalized + float: inverse transform is multiplied by this number + - stellsym: boolean to override the stellsym attribute of the surface + """ + mpol = A_mns.shape[0] - 1 + ntor = int((A_mns.shape[1] - 1) / 2) + stellsym = kwargs.pop('stellsym', self.stellsym) + ntheta_grid = len(self.quadpoints_theta) + nphi_grid = len(self.quadpoints_phi) + + phi2d, theta2d = np.meshgrid(2 * np.pi * self.quadpoints_phi, + 2 * np.pi * self.quadpoints_theta, + indexing="ij") + + field = np.zeros((nphi_grid, ntheta_grid)) + for m in range(mpol + 1): + nmin = -ntor + if m == 0: nmin = 1 + for n in range(nmin, ntor+1): + angle = m * theta2d - n * self.nfp * phi2d + sinangle = np.sin(angle) + if not stellsym: + cosangle = np.cos(angle) + field = field + A_mns[m, n + ntor] * sinangle + if not stellsym: + field = field + A_mnc[m, n + ntor] * cosangle + + if not stellsym: + field = field + A_mnc[0, ntor] + if normalization is not None: + if type(normalization) is not float: + raise ValueError("normalization must be a float") + field = field * normalization + return field def signed_distance_from_surface(xyz, surface): """ diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index 05e304a52..e9a7d8118 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -1,4 +1,3 @@ -# coding: utf-8 # Copyright (c) HiddenSymmetries Development Team. # Distributed under the terms of the MIT License @@ -11,6 +10,7 @@ import os.path import traceback from typing import Optional +from scipy.constants import mu_0 import numpy as np @@ -80,7 +80,7 @@ class Spec(Optimizable): mpi: A :obj:`simsopt.util.mpi.MpiPartition` instance, from which the worker groups will be used for SPEC calculations. If ``None``, each MPI process will run SPEC independently. - verbose: Whether to print SPEC output to stdout. + verbose: Whether to print SPEC output to stdout (and also a few other statements) keep_all_files: If ``False``, all output files will be deleted except for the first and most recent ones from worker group 0. If ``True``, all output files will be kept. @@ -102,26 +102,24 @@ def __init__(self, if py_spec is None: raise RuntimeError( "Using Spec requires py_spec to be installed.") + if tolerance <= 0: + raise ValueError( + 'tolerance should be greater than zero' + ) + self.tolerance = tolerance self.lib = spec # For the most commonly accessed fortran modules, provide a - # shorthand so ".lib" is not needed: - modules = [ - "inputlist", - "allglobal", - ] - for key in modules: - setattr(self, key, getattr(spec, key)) + # shorthand: + setattr(self, "inputlist", getattr(spec, "inputlist")) + setattr(self, "allglobal", getattr(spec, "allglobal")) self.verbose = verbose # mute screen output if necessary - # TODO: relies on /dev/null being accessible (Windows!) + # TODO: mute SPEC in windows, currently relies on /dev/null being accessible if not self.verbose: self.lib.fileunits.mute(1) - # python wrapper does not need to write files along the run - #self.lib.allglobal.skip_write = True - # If mpi is not specified, use a single worker group: if mpi is None: self.mpi = MpiPartition(ngroups=1) @@ -134,77 +132,47 @@ def __init__(self, # Read default input file, which should be in the same # directory as this file: filename = os.path.join(os.path.dirname(__file__), 'defaults.sp') - logger.info( - f"Initializing a SPEC object from defaults in {filename}") + if self.mpi.proc0_groups: + logger.info( + f"Initializing a SPEC object from defaults in {filename}") else: if not filename.endswith('.sp'): filename = f"{filename}.sp" - logger.info(f"Initializing a SPEC object from file: {filename}") - - if tolerance <= 0: - raise ValueError( - 'tolerance should be greater than zero' - ) - self.tolerance = tolerance + if self.mpi.proc0_groups: + logger.info(f"Group {self.mpi.group}: Initializing a SPEC object from file: {filename}") - self.init(filename) + # Initialize the FORTRAN state with values in the input file: + self._init_fortran_state(filename) si = spec.inputlist # Shorthand - # Read number of (plasma) volumes + # Copy useful and commonly used values from SPEC inputlist to + self.stellsym = bool(si.istellsym) + self.freebound = bool(si.lfreebound) + self.nfp = si.nfp + self.mpol = si.mpol + self.ntor = si.ntor self.nvol = si.nvol - - # Read number of (plasma+vacuum) volumes - if si.lfreebound: - self.mvol = self.nvol + 1 - else: - self.mvol = self.nvol + if self.freebound: + self.mvol = si.nvol + 1 + else: + self.mvol = si.nvol # Store initial guess data # The initial guess is a collection of SurfaceRZFourier instances, # stored in a list of size Mvol-1 (the number of inner interfaces) - nmodes = self.allglobal.num_modes - stellsym = bool(si.istellsym) - if nmodes > 0 and self.nvol > 1: - self.initial_guess = [ - SurfaceRZFourier(nfp=si.nfp, stellsym=stellsym, mpol=si.mpol, ntor=si.ntor) for n in range(0, self.mvol-1) - ] - for imode in range(0, nmodes): - mm = self.allglobal.mmrzrz[imode] - nn = self.allglobal.nnrzrz[imode] - if mm > si.mpol: - continue - if abs(nn) > si.ntor: - continue - - # Populate SurfaceRZFourier instances, except plasma boundary - for lvol in range(0, self.nvol-1): - self.initial_guess[lvol].set_rc(mm, nn, self.allglobal.allrzrz[0, lvol, imode]) - self.initial_guess[lvol].set_zs(mm, nn, self.allglobal.allrzrz[1, lvol, imode]) - - if not si.istellsym: - self.initial_guess[lvol].set_rs(mm, nn, self.allglobal.allrzrz[2, lvol, imode]) - self.initial_guess[lvol].set_zc(mm, nn, self.allglobal.allrzrz[3, lvol, imode]) - - if si.lfreebound: # Populate plasma boundary as well - self.initial_guess[self.nvol-1].set_rc(mm, nn, si.rbc[si.mntor+nn, si.mmpol+mm]) - self.initial_guess[self.nvol-1].set_zs(mm, nn, si.zbs[si.mntor+nn, si.mmpol+mm]) - - if not si.istellsym: - self.initial_guess[self.nvol-1].set_rs(mm, nn, si.rbs[si.mntor+nn, si.mmpol+mm]) - self.initial_guess[self.nvol-1].set_zc(mm, nn, si.zbc[si.mntor+nn, si.mmpol+mm]) - + initial_guess_present = bool(self.allglobal.num_modes > 0 and self.nvol > 1) + if initial_guess_present: + self.initial_guess = self._read_initial_guess() # In general, initial guess is NOT a degree of freedom for the # optimization - we thus fix them. - for lvol in range(0, self.mvol-1): - self.initial_guess[lvol].fix_all() - + for surface in self.initial_guess: + surface.fix_all() else: # There is no initial guess - in this case, we let SPEC handle # the construction of the initial guess. This generally means # that the geometry of the inner interfaces will be constructed # by interpolation between the plasma (or computational) boundary # and the magnetic axis - self.initial_guess = None # Store axis data @@ -220,31 +188,28 @@ def __init__(self, self.files_to_delete = [] # Create a surface object for the boundary: - logger.debug(f"In __init__, si.istellsym={si.istellsym} stellsym={stellsym}") - self._boundary = SurfaceRZFourier(nfp=si.nfp, - stellsym=stellsym, - mpol=si.mpol, - ntor=si.ntor) - - # Transfer the boundary shape from fortran to the boundary - # surface object: - for m in range(si.mpol + 1): - for n in range(-si.ntor, si.ntor + 1): - self._boundary.rc[m, - n + si.ntor] = si.rbc[n + si.mntor, - m + si.mmpol] - self._boundary.zs[m, - n + si.ntor] = si.zbs[n + si.mntor, - m + si.mmpol] - if not stellsym: - self._boundary.rs[m, - n + si.ntor] = si.rbs[n + si.mntor, - m + si.mmpol] - self._boundary.zc[m, - n + si.ntor] = si.zbc[n + si.mntor, - m + si.mmpol] + self._boundary = SurfaceRZFourier(nfp=self.nfp, stellsym=self.stellsym, + mpol=self.mpol, ntor=self.ntor) + self._boundary.rc[:] = self.array_translator(si.rbc, style='spec').as_simsopt + self._boundary.zs[:] = self.array_translator(si.zbs, style='spec').as_simsopt + if not self.freebound: + self._boundary.rs[:] = self.array_translator(si.rbs, style='spec').as_simsopt + self._boundary.zc[:] = self.array_translator(si.zbc, style='spec').as_simsopt self._boundary.local_full_x = self._boundary.get_dofs() + # If the equilibrium is freeboundary, we need to read the computational + # boundary as well. Otherwise set the outermost boundary as the + # computational boundary. + if self.freebound: + self._computational_boundary = SurfaceRZFourier(nfp=self.nfp, stellsym=self.stellsym, + mpol=self.mpol, ntor=self.ntor) + self._computational_boundary.rc[:] = self.array_translator(si.rwc, style='spec').as_simsopt + self._computational_boundary.zs[:] = self.array_translator(si.zws, style='spec').as_simsopt + if not self.stellsym: + self._computational_boundary.rs[:] = self.array_translator(si.rws, style='spec').as_simsopt + self._computational_boundary.zc[:] = self.array_translator(si.zwc, style='spec').as_simsopt + self._computational_boundary.local_full_x = self._computational_boundary.get_dofs() + self.need_to_run_code = True self.counter = -1 @@ -262,24 +227,125 @@ def __init__(self, # Define normal field - these are the Vns, Vnc harmonics. Can be used as # dofs in an optimization - if si.lfreebound: - self.normal_field = NormalField.from_spec(filename) + if self.freebound: + vns = self.array_translator(si.vns) + vnc = self.array_translator(si.vnc) + self._normal_field = NormalField(nfp=self.nfp, stellsym=self.stellsym, + mpol=self.mpol, ntor=self.ntor, + vns=vns.as_simsopt, vnc=vnc.as_simsopt, + computational_boundary=self._computational_boundary) else: - self.normal_field: Optional[NormalField] = None + self._normal_field: Optional[NormalField] = None # By default, all dofs owned by SPEC directly, as opposed to # dofs owned by the boundary surface object, are fixed. x0 = self.get_dofs() fixed = np.full(len(x0), True) names = ['phiedge', 'curtor'] - if si.lfreebound: - depends_on = [self.normal_field] + if self.freebound: + depends_on = [self._normal_field] else: depends_on = [self._boundary] super().__init__(x0=x0, fixed=fixed, names=names, depends_on=depends_on, external_dof_setter=Spec.set_dofs) + + @classmethod + def default_freeboundary(cls): + """ + Create a default freeboundary SPEC object + """ + return cls(filename=os.path.join(os.path.dirname(__file__), 'defaults_freebound.sp')) + + @classmethod + def default_fixedboundary(cls): + """ + Create a default fixedboundary SPEC object (same as calling class empty) + """ + return cls() + + def _read_initial_guess(self): + """ + Read initial guesses from SPEC and return a list of surfaceRZFourier objects. + """ + nmodes = self.allglobal.num_modes + interfaces = [] # initialize list + n_guess_surfs = self.nvol if self.freebound else self.nvol - 1 # if freeboundary, plasma boundary is also a guess surface + for lvol in range(0, n_guess_surfs): # loop over volumes + # the fourier comonents of the initial guess are stored in the allrzrz array + thissurf_rc = self.allglobal.allrzrz[0, lvol, :nmodes] + thissurf_zs = self.allglobal.allrzrz[1, lvol, :nmodes] + if not self.stellsym: + thissurf_rs = self.allglobal.allrzrz[2, lvol, :nmodes] + thissurf_zc = self.allglobal.allrzrz[3, lvol, :nmodes] + thissurf = SurfaceRZFourier(nfp=self.nfp, stellsym=self.stellsym, + mpol=self.mpol, ntor=self.ntor) + # the mode number convention is different in SPEC. Best to use the + # in-built array mmrzrz to get the numbers for each fourier component: + for imode in range(0, nmodes): + mm = self.allglobal.mmrzrz[imode] # helper arrays to get index for each mode + nn = self.allglobal.nnrzrz[imode] + # The guess surface could have more modes than we are running SPEC with, skip if case + if mm > self.mpol or abs(nn) > self.ntor: + continue + thissurf.set_rc(mm, nn, thissurf_rc[imode]) + thissurf.set_zs(mm, nn, thissurf_zs[imode]) + if not self.stellsym: + thissurf.set_rs(mm, nn, thissurf_rs[imode]) + thissurf.set_zc(mm, nn, thissurf_zc[imode]) + interfaces.append(thissurf) + return interfaces + + def _set_spec_initial_guess(self): + """ + Set initial guesses in SPEC from a list of surfaceRZFourier objects. + """ + # Set all modes to zero + spec.allglobal.mmrzrz[:] = 0 + spec.allglobal.nnrzrz[:] = 0 + spec.allglobal.allrzrz[:] = 0 + + # transform to SurfaceRZFourier if necessary + initial_guess = [s.to_RZFourier() for s in self.initial_guess] + + # Loop on modes + imn = -1 # counter + for mm in range(0, self.mpol+1): + for nn in range(-self.ntor, self.ntor+1): + if mm == 0 and nn < 0: + continue + + imn += 1 + + spec.allglobal.mmrzrz[imn] = mm + spec.allglobal.nnrzrz[imn] = nn + + # Populate inner plasma boundaries + for lvol in range(0, self.nvol-1): + spec.allglobal.allrzrz[0, lvol, imn] = initial_guess[lvol].get_rc(mm, nn) + spec.allglobal.allrzrz[1, lvol, imn] = initial_guess[lvol].get_zs(mm, nn) + + if not self.stellsym: + spec.allglobal.allrzrz[2, lvol, imn] = initial_guess[lvol].get_rs(mm, nn) + spec.allglobal.allrzrz[3, lvol, imn] = initial_guess[lvol].get_zc(mm, nn) + spec.allglobal.num_modes = imn + 1 + # possibly cleaner way to do this (tested to work Chris Smiet 11/9/2023): +# n_indices, m_values = np.indices([2*si.ntor+1, si.mpol+1]) #get indices for array +# n_values = n_indices - si.ntor # offset indices to correspond with mode numbers +# index_mask = ~np.logical_and(m_values==0, n_values < 0) # twiddle ~ NOT, pick elements +# numel = np.sum(index_mask) # number of trues in mask, i.e. chosen elements +# spec.allglobal.mmrzrz[:numel] = m_values[index_mask] # skip elements, make 1 +# spec.allglobal.nnrzrz[:numel] = n_values[index_mask] # skip m==0 n<0 elements +# +# initial_guess = [s.to_RZFourier() for s in self.initial_guess] +# for lvol, surface in enumerate(initial_guess): +# # EXPLAIN: surface.rc is m,n indexed, transpose, apply above mask which unravels to 1d +# spec.allglobal.allrzrz[0, lvol, :numel] = surface.rc.transpose()[index_mask] +# spec.allglobal.allrzrz[1, lvol, :numel] = surface.zs.transpose()[index_mask] +# if not self.stellsym: +# spec.allglobal.allrzrz[2, lvol, :numel] = surface.rs.transpose()[index_mask] +# spec.allglobal.allrzrz[3, lvol, :numel] = surface.zc.transpose()[index_mask] @property def boundary(self): @@ -291,6 +357,56 @@ def boundary(self): """ return self._boundary + @boundary.setter + def boundary(self, boundary): + """ + Setter for the geometry of the plasma boundary + """ + if not self.freebound: + if self._boundary is not boundary: + self.remove_parent(self._boundary) + self._boundary = boundary + self.append_parent(boundary) + return + else: # in freeboundary case, plasma boundary is is not a parent + self._boundary = boundary + + @property + def normal_field(self): + """ + Getter for the normal field + """ + return self._normal_field + + @normal_field.setter + def normal_field(self, normal_field): + """ + Setter for the normal field + """ + if not self.freebound: + raise ValueError('Normal field can only be set in freeboundary case') + if not isinstance(normal_field, NormalField) or not isinstance(normal_field): + raise ValueError('Input should be a NormalField or CoilNormalField') + if self._normal_field is not normal_field: + self.remove_parent(self._normal_field) + if self._computational_boundary is not normal_field.computational_boundary: + normal_field.computational_boundary = self._computational_boundary + self._normal_field = normal_field + self.append_parent(normal_field) + return + + @property + def computational_boundary(self): + """ + Getter for the computational boundary. + Same as the plasma boundary in the non-free-boundary case, + gives the surface on which Vns and Vnc are defined in the free-boundary case. + + Returns: + SurfaceRZFourier instance representing the plasma boundary + """ + return self._computational_boundary + @property def pressure_profile(self): """ @@ -617,6 +733,39 @@ def helicity_profile(self, helicity_profile): self.append_parent(helicity_profile) self.need_to_run_code = True + def activate_profile(self, longname): + """ + Take a profile from the inputlist, and make it optimizable in + simsopt. + Args: + longname: string, either + - 'pressure' + - 'volume_current' + - 'surface_current' + - 'iota' + - 'oita' + - 'mu' + - 'pflux' + - 'tflux' + - 'helicity' + """ + profile_dict = { + 'pressure': {'specname': 'pressure', 'cumulative': False, 'length': self.nvol}, + 'volume_current': {'specname': 'ivolume', 'cumulative': True, 'length': self.nvol}, + 'interface_current': {'specname': 'isurf', 'cumulative': False, 'length': self.nvol-1}, + 'helicity': {'specname': 'helicity', 'cumulative': False, 'length': self.mvol}, + 'iota': {'specname': 'iota', 'cumulative': False, 'length': self.mvol}, + 'oita': {'specname': 'oita', 'cumulative': False, 'length': self.mvol}, + 'mu': {'specname': 'mu', 'cumulative': False, 'length': self.mvol}, + 'pflux': {'specname': 'pflux', 'cumulative': True, 'length': self.mvol}, + 'tflux': {'specname': 'tflux', 'cumulative': True, 'length': self.mvol} + } + + profile_data = self.inputlist.__getattribute__(profile_dict[longname]['specname'])[0:profile_dict[longname]['length']] + profile = ProfileSpec(profile_data, cumulative=profile_dict[longname]['cumulative'], psi_edge=self.inputlist.phiedge) + profile.unfix_all() + self.__setattr__(longname + '_profile', profile) + def set_profile(self, longname, lvol, value): """ This function is used to set the pressure, currents, iota, oita, @@ -678,17 +827,6 @@ def get_profile(self, longname, lvol): return profile.f(lvol) - @boundary.setter - def boundary(self, boundary): - """ - Setter for the geometry of the plasma boundary - """ - - if self._boundary is not boundary: - self.remove_parent(self._boundary) - self._boundary = boundary - self.append_parent(boundary) - def recompute_bell(self, parent=None): self.need_to_run_code = True @@ -714,9 +852,18 @@ def set_dofs(self, x): ] for p in profiles: if p is not None: - p.phiedge = x[0] + p.psi_edge = x[0] - def init(self, filename: str): + @property + def poloidal_current_amperes(self): + """ + return the total poloidal current in Amperes, + i.e. the current that must be carried by the coils that link the plasma + poloidally + """ + return self.inputlist.curpol/(mu_0) + + def _init_fortran_state(self, filename: str): """ Initialize SPEC fortran state from an input file. @@ -742,6 +889,11 @@ def init(self, filename: str): def run(self, update_guess: bool = True): """ Run SPEC, if needed. + The FORTRAN state has been created in the __init__ method (there can be only one for one python kernel), and the values in the FORTRAN memory are updated by python. + + The most important values are in inputlist and allglobal. + + Note: Since all calls to fortran memory access the same memory, there is no difference between spec.inputlist and self.inputlist (or even my_other_spec2.inputlist). Args: - update_guess: boolean. If True, initial guess will be updated with @@ -751,11 +903,17 @@ def run(self, update_guess: bool = True): if not self.need_to_run_code: logger.info("run() called but no need to re-run SPEC.") return - logger.info("Preparing to run SPEC.") + if self.mpi.proc0_groups: + logger.info(f"Group {self.mpi.group}: Preparing to run SPEC.") self.counter += 1 si = self.inputlist # Shorthand + # if freeboundary, store plasma-caused boundary field to re-set if run does not converge + if self.freebound: + initial_bns = np.copy(si.bns) + initial_bnc = np.copy(si.bnc) + # Check that number of volumes in internal memory is consistent with # the input file if self.nvol != si.nvol: @@ -770,21 +928,19 @@ def run(self, update_guess: bool = True): boundary_RZFourier = self.boundary.to_RZFourier() # Transfer boundary data to fortran: - si.rbc[:, :] = 0.0 - si.zbs[:, :] = 0.0 + si.rbc[:, :] = self.array_translator(boundary_RZFourier.rc, style='simsopt').as_spec + si.zbs[:, :] = self.array_translator(boundary_RZFourier.zs, style='simsopt').as_spec si.rbs[:, :] = 0.0 si.zbc[:, :] = 0.0 - mpol_capped = np.min([boundary_RZFourier.mpol, si.mmpol]) - ntor_capped = np.min([boundary_RZFourier.ntor, si.mntor]) - stellsym = bool(si.istellsym) - logger.debug(f"In run, si.istellsym = {si.istellsym} stellsym = {stellsym}") - for m in range(mpol_capped + 1): - for n in range(-ntor_capped, ntor_capped + 1): - si.rbc[n + si.mntor, m + si.mmpol] = boundary_RZFourier.get_rc(m, n) - si.zbs[n + si.mntor, m + si.mmpol] = boundary_RZFourier.get_zs(m, n) - if not stellsym: - si.rbs[n + si.mntor, m + si.mmpol] = boundary_RZFourier.get_rs(m, n) - si.zbc[n + si.mntor, m + si.mmpol] = boundary_RZFourier.get_zc(m, n) + if not self.stellsym: + si.rbs[:, :] = self.array_translator(boundary_RZFourier.rs, style='simsopt').as_spec + si.zbc[:, :] = self.array_translator(boundary_RZFourier.zc, style='simsopt').as_spec + + # transfer normal field to fortran: + if self.freebound: + si.vns[:, :] = self.array_translator(self.normal_field.get_vns_asarray(), style='simsopt').as_spec + if not self.stellsym: + si.vnc[:, :] = self.array_translator(self.normal_field.get_vnc_asarray(), style='simsopt').as_spec # Set the coordinate axis using the lrzaxis=2 feature: si.lrzaxis = 2 @@ -798,46 +954,17 @@ def run(self, update_guess: bool = True): si.zac[0:mn] = self.axis['zac'] # Set initial guess - if self.initial_guess is not None: - # Set all modes to zero - spec.allglobal.mmrzrz[:] = 0 - spec.allglobal.nnrzrz[:] = 0 - spec.allglobal.allrzrz[:] = 0 - - # transform to SurfaceRZFourier if necessary - initial_guess = [s.to_RZFourier() for s in self.initial_guess] - - # Loop on modes - imn = -1 # counter - for mm in range(0, si.mpol+1): - for nn in range(-si.ntor, si.ntor+1): - if mm == 0 and nn < 0: - continue - - imn += 1 - - spec.allglobal.mmrzrz[imn] = mm - spec.allglobal.nnrzrz[imn] = nn - - # Populate inner plasma boundaries - for lvol in range(0, self.nvol-1): - spec.allglobal.allrzrz[0, lvol, imn] = initial_guess[lvol].get_rc(mm, nn) - spec.allglobal.allrzrz[1, lvol, imn] = initial_guess[lvol].get_zs(mm, nn) - - if not si.istellsym: - spec.allglobal.allrzrz[2, lvol, imn] = initial_guess[lvol].get_rs(mm, nn) - spec.allglobal.allrzrz[3, lvol, imn] = initial_guess[lvol].get_zc(mm, nn) - - # Populate plasma boundary - if si.lfreebound: - si.rbc[si.mntor+nn, si.mmpol+mm] = initial_guess[self.nvol-1].get_rc(mm, nn) - si.zbs[si.mntor+nn, si.mmpol+mm] = initial_guess[self.nvol-1].get_zs(mm, nn) - - if not si.istellsym: - si.rbs[si.mntor+nn, si.mmpol+mm] = initial_guess[self.nvol-1].get_rs(mm, nn) - si.zbc[si.mntor+nn, si.mmpol+mm] = initial_guess[self.nvol-1].get_zc(mm, nn) - - spec.allglobal.num_modes = imn + 1 + if self.initial_guess is not None: # note: self.initial_guess is None for workers!! only leaders read and do_stuff with initial_guess + self._set_spec_initial_guess() # workers get the info through a broadcast. this line fails if workers get a guess set + + # write the boundary which is a guess in freeboundary + if self.freebound: + boundaryguess = self.initial_guess[-1].to_RZFourier() + si.rbc[:] = self.array_translator(boundaryguess.rc, style='simsopt').as_spec + si.zbs[:] = self.array_translator(boundaryguess.zs, style='simsopt').as_spec + if not self.stellsym: + si.rbs[:] = self.array_translator(boundaryguess.rs, style='simsopt').as_spec + si.zbc[:] = self.array_translator(boundaryguess.zc, style='simsopt').as_spec # Set profiles from dofs if self.pressure_profile is not None: @@ -936,6 +1063,7 @@ def run(self, update_guess: bool = True): logger.debug('About to call check_inputs') spec.allglobal.check_inputs() logger.debug('About to call broadcast_inputs') + self.mpi.comm_groups.Barrier() # wait for spec.allglobal.broadcast_inputs() logger.debug('About to call preset') spec.preset() @@ -968,8 +1096,8 @@ def run(self, update_guess: bool = True): if self.verbose: traceback.print_exc() raise ObjectiveFailure("SPEC did not run successfully.") - - logger.info("SPEC run complete.") + if self.mpi.proc0_groups: + logger.info(f"{filename}: SPEC run complete.") # Barrier so workers do not try to read the .h5 file before it # is finished: self.mpi.comm_groups.Barrier() @@ -983,16 +1111,35 @@ def run(self, update_guess: bool = True): raise ObjectiveFailure( "Unable to read results following SPEC execution") - logger.info("Successfully loaded SPEC results.") + if self.mpi.proc0_groups: + logger.info("Successfully loaded SPEC results.") self.need_to_run_code = False # Deal with unconverged equilibria - these are excluded by # the optimizer, and the objective function is set to a large number if self.results.output.ForceErr > self.tolerance: + # re-set the boundary field guess before failing, so the next run does not start unconverged. + if self.freebound: + logger.info(f"run {filename}: Force balance unconverged, re-setting boundary field guess and raising ObjectiveFailure") + si.bns, si.bnc = initial_bns, initial_bnc raise ObjectiveFailure( 'SPEC could not find force balance' ) - + + # check for picard convergence once SPEC is updated + if self.freebound: + try: + if self.results.output.BnsErr > self.inputlist.gbntol: + if self.mpi.proc0_groups: + logger.info(f"run {filename}: Picard iteration unconverged, re-setting boundary field guess and raising ObjectiveFailure") + si.bns, si.bnc = initial_bns, initial_bnc + raise ObjectiveFailure( + 'Picard iteration failed to reach convergence, increase mfreeits or gbntol' + ) + except AttributeError: + logger.info('Picard convergence not checked, please update SPEC version 3.22 or higher') + print("Picard convergence not checked, please update SPEC version 3.22 or higher") + # Save geometry as initial guess for next iterations if update_guess: new_guess = None @@ -1002,7 +1149,7 @@ def run(self, update_guess: bool = True): ] for ii, (mm, nn) in enumerate(zip(self.results.output.im, self.results.output.in_)): - nnorm = (nn / si.nfp).astype('int') + nnorm = (nn / si.nfp).astype('int') # results.output.in_ is fourier number for 1 field period for reasons... for lvol in range(0, self.mvol-1): new_guess[lvol].set_rc(mm, nnorm, self.results.output.Rbc[lvol+1, ii]) new_guess[lvol].set_zs(mm, nnorm, self.results.output.Zbs[lvol+1, ii]) @@ -1016,8 +1163,9 @@ def run(self, update_guess: bool = True): axis['zas'] = self.results.output.Zbs[0, 0:si.ntor+1] self.axis = copy.copy(axis) - # Enforce SPEC to use initial guess - self.initial_guess = new_guess + # Enforce SPEC to use initial guess, but only group leaders have the necessary arrays + if self.mpi.proc0_groups: + self.initial_guess = new_guess # set this here? or make whole above monster proc0-exclusive self.inputlist.linitialize = 0 # Group leaders handle deletion of files: @@ -1027,6 +1175,8 @@ def run(self, update_guess: bool = True): if (not self.keep_all_files) and (self.mpi.group > 0): os.remove(filename + '.sp.h5') os.remove(filename + '.sp.end') + if os.path.exists('.' + filename + '.sp.DF'): + os.remove('.' + filename + '.sp.DF') # Delete the previous output file, if desired: for file_to_delete in self.files_to_delete: @@ -1038,6 +1188,8 @@ def run(self, update_guess: bool = True): self.counter > 0) and (not self.keep_all_files): self.files_to_delete.append(filename + '.sp.h5') self.files_to_delete.append(filename + '.sp.end') + if self.mpi.proc0_groups: + logger.info(f"file {filename} completed run sucessfully") def volume(self): """ @@ -1052,6 +1204,113 @@ def iota(self): """ self.run() return self.results.transform.fiota[1, 0] + + def replace_normal_field_with_coils(self, filename=None, TARGET_LENGTH=3000): + """ + replace the daddy normal_field with a CoilNormalField instance that + inherits its' degrees of freedom from a CoilSet. + + A filename can be given in which the coils are specified (standard + JSON format used by calling Optimizable.to_json() on a CoilSet instance) + [NOT IMPLEMENTED YET] + """ + if filename is not None: + raise NotImplementedError('filename not supported yet') + + coil_normal_field = CoilNormalField.from_spec_object(self, optimize_coils=True, TARGET_LENGTH=TARGET_LENGTH) + self.normal_field = coil_normal_field + + def array_translator(self, array=None, style='spec'): + """ + Returns a SpecFourierArray object to help transforming between + arrays using SPEC conventions and simsopt conventions. + + create from an array of either style by setting style='spec' or + style='simsopt' upon creation. + + The created class will have properties: + - as_spec: returns the SPEC style array + - as_simsopt: returns the simsopt style array + and setters to set the arrays from either convention after creation. + + SPEC arrays are zero-padded and indexed with Fortran conventions, + in python that means the m=0,n=0 component is at [nmtor,mmpol]. + + use: + vnc = myspec.array_translator(myspec.inputlist.rbc) + mysurf.rc = vnc.as_simsopt + """ + if style == 'spec': + return Spec.SpecFourierArray(self, array) + elif style == 'simsopt': + obj = Spec.SpecFourierArray(self) + obj.as_simsopt = array # setter function + return obj + else: + raise ValueError(f'array style:{style} not supported, options: [simsopt, spec]') + + # Inner class of Spec + class SpecFourierArray: + """ + Helper class to make index-jangling easier and hide away + strange SPEC array sizing and indexing conventions. + + SPEC stores Fourier series in a very large zero-padded + array with Fortran variable indexing and 'n,m' indexing + convention. + In python this means the m=0,n=0 component is at [nmtor,mmpol]. + + + """ + def __init__(self, outer_spec, array=None): + self._outer_spec = outer_spec + self._mmpol = outer_spec.inputlist.mmpol + self._mntor = outer_spec.inputlist.mntor + if array is None: + array = np.zeros((2*self._mntor+1, 2*self._mmpol+1)) + self._array = np.array(array) + + @property + def as_spec(self): + return self._array + + @as_spec.setter + def as_spec(self, array): + if array.shape != [2*self.mntor+1, 2*self.mmpol+1]: + raise ValueError('Array size is not consistent witn mmpol and mntor') + self._array = array + + @property + def as_simsopt(self, ntor=None, mpol=None): + """ + get a simsopt style 'n,m' intexed non-padded array + from the SpecFourierArray. + """ + if ntor is None: + ntor = self._outer_spec.ntor + if mpol is None: + mpol = self._outer_spec.mpol + n_start = self._mntor - ntor + n_end = self._mntor + ntor + 1 + m_start = self._mmpol + m_end = self._mmpol + mpol + 1 + return self._array[n_start:n_end, m_start:m_end].transpose() # switch n and m + + @as_simsopt.setter + def as_simsopt(self, array, ntor=None, mpol=None): + """ + set the SpecFourierArray from a simsopt style 'm,n' intexed non-padded array + """ + if mpol is None: + mpol = array.shape[0]-1 + if ntor is None: + ntor = int((array.shape[1]-1)/2) + n_start = self._mntor - ntor + n_end = self._mntor + ntor + 1 + m_start = self._mmpol + m_end = self._mmpol + mpol + 1 + self._array = np.zeros((2*self._mntor+1, 2*self._mmpol+1)) + self._array[n_start:n_end, m_start:m_end] = array.transpose() class Residue(Optimizable): @@ -1069,7 +1328,7 @@ class Residue(Optimizable): rtol: the relative tolerance of the integrator """ - def __init__(self, spec, pp, qq, vol=1, theta=0, s_guess=None, s_min=-1.0, + def __init__(self, spec, pp, qq, vol=1, theta=0., s_guess=None, s_min=-1.0, s_max=1.0, rtol=1e-9): # if not spec_found: if spec is None: @@ -1113,7 +1372,7 @@ def J(self): self.spec.run() if not self.mpi.proc0_groups: - logger.info( + logger.debug( "This proc is skipping Residue.J() since it is not a group leader.") return 0.0 else: @@ -1133,5 +1392,6 @@ def J(self): if self.fixed_point is None: raise ObjectiveFailure("Residue calculation failed") + logger.info(f"group {self.mpi.group} found residue {self.fixed_point.GreenesResidue} for {self.pp}/{self.qq} in {self.spec.allglobal.ext}") return self.fixed_point.GreenesResidue From 498338269b81f678ed3b3bd9deb012560f8162b5 Mon Sep 17 00:00:00 2001 From: Chris Date: Thu, 23 May 2024 17:33:39 +0200 Subject: [PATCH 122/176] fix linting --- src/simsopt/field/normal_field.py | 25 ++++++++--------- src/simsopt/geo/surface.py | 9 +++---- src/simsopt/mhd/spec.py | 15 ----------- tests/geo/test_surface_rzfourier.py | 42 +++++++++++++++++++++++++++++ 4 files changed, 59 insertions(+), 32 deletions(-) diff --git a/src/simsopt/field/normal_field.py b/src/simsopt/field/normal_field.py index 52e75daf4..9adb3f18e 100644 --- a/src/simsopt/field/normal_field.py +++ b/src/simsopt/field/normal_field.py @@ -57,6 +57,7 @@ def __init__(self, nfp=1, stellsym=True, mpol=1, ntor=0, vnc = np.zeros((self.mpol + 1, 2 * self.ntor + 1)) if computational_boundary is None: + from simsopt.geo import SurfaceRZFourier computational_boundary = SurfaceRZFourier(nfp=nfp, stellsym=stellsym, mpol=mpol, ntor=ntor) computational_boundary.fix_all() self.computational_boundary = computational_boundary @@ -363,12 +364,12 @@ def get_vns_asarray(self, mpol=None, ntor=None): """ Return the vns as a single array """ - if mpol == None: + if mpol is None: mpol = self.mpol elif mpol > self.mpol: raise ValueError('mpol out of bound') - if ntor == None: + if ntor is None: ntor = self.ntor elif ntor > self.ntor: raise ValueError('ntor out of bound') @@ -385,12 +386,12 @@ def get_vnc_asarray(self, mpol=None, ntor=None): """ Return the vnc as a single array """ - if mpol == None: + if mpol is None: mpol = self.mpol elif mpol > self.mpol: raise ValueError('mpol out of bound') - if ntor == None: + if ntor is None: ntor = self.ntor elif ntor > self.ntor: raise ValueError('ntor out of bound') @@ -407,12 +408,12 @@ def get_vns_vnc_asarray(self, mpol, ntor): """ Return the vns and vnc as two arrays single array """ - if mpol == None: + if mpol is None: mpol = self.mpol elif mpol > self.mpol: raise ValueError('mpol out of bound') - if ntor == None: + if ntor is None: ntor = self.ntor elif ntor > self.ntor: raise ValueError('ntor out of bound') @@ -425,12 +426,12 @@ def set_vns_asarray(self, vns, mpol=None, ntor=None): """ Set the vns from a single array """ - if mpol == None: + if mpol is None: mpol = self.mpol elif mpol > self.mpol: raise ValueError('mpol out of bound') - if ntor == None: + if ntor is None: ntor = self.ntor elif ntor > self.ntor: raise ValueError('ntor out of bound') @@ -444,12 +445,12 @@ def set_vnc_asarray(self, vnc, mpol=None, ntor=None): """ Set the vnc from a single array """ - if mpol == None: + if mpol is None: mpol = self.mpol elif mpol > self.mpol: raise ValueError('mpol out of bound') - if ntor == None: + if ntor is None: ntor = self.ntor elif ntor > self.ntor: raise ValueError('ntor out of bound') @@ -463,12 +464,12 @@ def set_vns_vnc_asarray(self, vns, vnc, mpol=None, ntor=None): """ Set the vns and vnc from two single arrays """ - if mpol == None: + if mpol is None: mpol = self.mpol elif mpol > self.mpol: raise ValueError('mpol out of bound') - if ntor == None: + if ntor is None: ntor = self.ntor elif ntor > self.ntor: raise ValueError('ntor out of bound') diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index f51f44a35..4a6d0eb09 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -868,9 +868,8 @@ def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=Non - A_mnc: 2D array of shape (mpol+1, 2*ntor+1) containing the cosine coefficients (these are zero if the surface is stellarator symmetric) """ - assert (field.shape == [self.quadpoints_phi.size, self.quadpoints_theta.size], - "Field must be evaluated at the quadrature points on the surface. \ - the field you passed in has shape {}".format(field.shape)) + assert field.shape[0]!= self.quadpoints_phi.size,"Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) + assert field.shape[1] != self.quadpoints_theta.size,"Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) stellsym = kwargs.pop('stellsym', self.stellsym) if mpol is None: try: mpol = self.mpol @@ -908,7 +907,7 @@ def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=Non if not stellsym: A_mnc[0, ntor] = np.sum(field) / (ntheta_grid * nphi_grid) if normalization is not None: - if type(normalization) is not float: + if isinstance(normalization, float): raise ValueError("normalization must be a float") A_mns = A_mns / normalization A_mnc = A_mnc / normalization @@ -960,7 +959,7 @@ def inverse_fourier_transform_field(self, A_mns, A_mnc, normalization=None, **kw if not stellsym: field = field + A_mnc[0, ntor] if normalization is not None: - if type(normalization) is not float: + if isinstance(normalization, float): raise ValueError("normalization must be a float") field = field * normalization return field diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index e9a7d8118..9e2b07695 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -1205,21 +1205,6 @@ def iota(self): self.run() return self.results.transform.fiota[1, 0] - def replace_normal_field_with_coils(self, filename=None, TARGET_LENGTH=3000): - """ - replace the daddy normal_field with a CoilNormalField instance that - inherits its' degrees of freedom from a CoilSet. - - A filename can be given in which the coils are specified (standard - JSON format used by calling Optimizable.to_json() on a CoilSet instance) - [NOT IMPLEMENTED YET] - """ - if filename is not None: - raise NotImplementedError('filename not supported yet') - - coil_normal_field = CoilNormalField.from_spec_object(self, optimize_coils=True, TARGET_LENGTH=TARGET_LENGTH) - self.normal_field = coil_normal_field - def array_translator(self, array=None, style='spec'): """ Returns a SpecFourierArray object to help transforming between diff --git a/tests/geo/test_surface_rzfourier.py b/tests/geo/test_surface_rzfourier.py index 538cf17d2..ba1ab871d 100755 --- a/tests/geo/test_surface_rzfourier.py +++ b/tests/geo/test_surface_rzfourier.py @@ -732,6 +732,48 @@ def test_make_rotating_ellipse_iota(self): np.testing.assert_array_less(0, eq.wout.iotaf) np.testing.assert_allclose(eq.mean_iota(), 0.4291137962772453, rtol=1e-6) + def test_fourier_transform_field(self): + """ + Test the Fourier transform of a field on a surface. + """ + s = SurfaceRZFourier(mpol=4, ntor=5) + s.rc[0, 0] = 1.3 + s.rc[1, 0] = 0.4 + s.zs[1, 0] = 0.2 + + # Create the grid of quadpoints: + phi2d, theta2d = np.meshgrid(2 * np.pi * s.quadpoints_phi, + 2 * np.pi * s.quadpoints_theta, + indexing='ij') + + # create a test field where only Fourier elements [m=2, n=3] + # and [m=4,n=5] are nonzero: + field = [] + for phi, theta in zip(phi2d.flatten(), theta2d.flatten()): + field.append(0.8 * np.sin(2*theta - 3*s.nfp*phi) + 0.2*np.sin(4*theta - 5*s.nfp*phi) + + 0.7*np.cos(3*theta - 3*s.nfp*phi)) + field = np.array(field).reshape(phi2d.shape) + + # Transform the field to Fourier space: + ft_sines, ft_cosines = s.fourier_transform_field(field, stellsym=False) + self.assertAlmostEqual(ft_sines[2, 3+s.ntor], 0.8) + self.assertAlmostEqual(ft_sines[4, 5+s.ntor], 0.2) + self.assertAlmostEqual(ft_cosines[3, 3+s.ntor], 0.7) + + # Test that all other elements are close to zero + sines_mask = np.ones_like(ft_sines, dtype=bool) + cosines_mask = sines_mask + sines_mask[2, 3 + s.ntor] = False + sines_mask[4, 5 + s.ntor] = False + cosines_mask[3, 3 + s.ntor] = False + self.assertEqual(np.all(np.abs(ft_sines[sines_mask]) < 1e-10), True) + self.assertEqual(np.all(np.abs(ft_cosines[cosines_mask]) < 1e-10), True) + + # Transform back to real space: + field2 = s.inverse_fourier_transform_field(ft_sines, ft_cosines, stellsym=False) + + # Check that the result is the same as the original field: + np.testing.assert_allclose(field, field2) class SurfaceRZPseudospectralTests(unittest.TestCase): def test_names(self): From 06cfbce707fbbb4ce07d52ceae51dc87e5938b85 Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 24 May 2024 09:21:33 +0200 Subject: [PATCH 123/176] fix assertion logic in surface FT --- src/simsopt/geo/surface.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index 4a6d0eb09..be0a40640 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -868,8 +868,8 @@ def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=Non - A_mnc: 2D array of shape (mpol+1, 2*ntor+1) containing the cosine coefficients (these are zero if the surface is stellarator symmetric) """ - assert field.shape[0]!= self.quadpoints_phi.size,"Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) - assert field.shape[1] != self.quadpoints_theta.size,"Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) + assert field.shape[0] == self.quadpoints_phi.size,"Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) + assert field.shape[1] == self.quadpoints_theta.size,"Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) stellsym = kwargs.pop('stellsym', self.stellsym) if mpol is None: try: mpol = self.mpol From da35cd0c0e80338ec36cf9f3219f002628db44b7 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 29 May 2024 15:45:42 -0400 Subject: [PATCH 124/176] cleaning up unit test --- tests/core/test_optimizable.py | 18 +++--------------- 1 file changed, 3 insertions(+), 15 deletions(-) diff --git a/tests/core/test_optimizable.py b/tests/core/test_optimizable.py index a035d7154..caa63a293 100755 --- a/tests/core/test_optimizable.py +++ b/tests/core/test_optimizable.py @@ -1365,18 +1365,6 @@ def dJ(self): return Derivative({self: self.local_full_x}) -class OptClassSharedDOFsQuadratic(Optimizable): - def __init__(self, **kwargs): - super().__init__(**kwargs) - - def J(self): - return sum(self.x) - - @derivative_dec - def dJ(self): - return Derivative({self: self.local_full_x}) - - class TestOptimizableSharedDOFs(unittest.TestCase): """ Test the DOFs sharing for the Optimizable classes @@ -1435,11 +1423,11 @@ def test_derivative(self): self.assertTrue((sum_obj.dJ(partials=True)(adder_shared_dofs) == sum_obj.dJ()).all()) def test_shared_dofs_as_derivative(self): - quadA = OptClassSharedDOFsQuadratic(x0=[1, 2, 3], names=["x", "y", "z"], + quadA = OptClassSharedDOFs(x0=[1, 2, 3], names=["x", "y", "z"], fixed=[False, False, True]) - quadA_shared_dofs = OptClassSharedDOFsQuadratic(dofs=quadA.dofs) + quadA_shared_dofs = OptClassSharedDOFs(dofs=quadA.dofs) - quadB = OptClassSharedDOFsQuadratic(x0=[np.pi, 1, 1.21], names=["xx", "yy", "zz"], + quadB = OptClassSharedDOFs(x0=[np.pi, 1, 1.21], names=["xx", "yy", "zz"], fixed=[False, False, True]) sum_quad = quadA + quadA_shared_dofs + quadB deriv = sum_quad.dJ(partials=True)(sum_quad, as_derivative=True) From b1350c2ebf7fc34f280268dc486e54cfda915956 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Wed, 29 May 2024 16:01:33 -0400 Subject: [PATCH 125/176] adding another unit test --- tests/core/test_optimizable.py | 33 ++++++++++++++++++++++++--------- 1 file changed, 24 insertions(+), 9 deletions(-) diff --git a/tests/core/test_optimizable.py b/tests/core/test_optimizable.py index caa63a293..222c94ec1 100755 --- a/tests/core/test_optimizable.py +++ b/tests/core/test_optimizable.py @@ -1422,19 +1422,34 @@ def test_derivative(self): self.assertTrue((sum_obj.dJ(partials=True)(adder_orig) == sum_obj.dJ()).all()) self.assertTrue((sum_obj.dJ(partials=True)(adder_shared_dofs) == sum_obj.dJ()).all()) - def test_shared_dofs_as_derivative(self): - quadA = OptClassSharedDOFs(x0=[1, 2, 3], names=["x", "y", "z"], + def test_as_derivative1(self): + # this test checks that you can restrict the Derivative dictionary + # to the proper subset of Optimizables when as_derivative=True + + optA = OptClassSharedDOFs(x0=[1, 2, 3], names=["x", "y", "z"], fixed=[False, False, True]) - quadA_shared_dofs = OptClassSharedDOFs(dofs=quadA.dofs) + optA_shared_dofs = OptClassSharedDOFs(dofs=optA.dofs) - quadB = OptClassSharedDOFs(x0=[np.pi, 1, 1.21], names=["xx", "yy", "zz"], + optB = OptClassSharedDOFs(x0=[np.pi, 1, 1.21], names=["xx", "yy", "zz"], fixed=[False, False, True]) - sum_quad = quadA + quadA_shared_dofs + quadB - deriv = sum_quad.dJ(partials=True)(sum_quad, as_derivative=True) + sum_opt = optA + optA_shared_dofs + optB + deriv = sum_opt.dJ(partials=True)(sum_opt, as_derivative=True) - np.testing.assert_allclose(deriv(quadA), quadA.dJ()*2, atol=1e-14) - np.testing.assert_allclose(deriv(quadA_shared_dofs), quadA.dJ()*2, atol=1e-14) - np.testing.assert_allclose(deriv(sum_quad), np.concatenate((quadA.dJ()*2, quadB.dJ())), atol=1e-14) + # restrict to optA + np.testing.assert_allclose(deriv(optA), optA.dJ()*2, atol=1e-14) + # restrict to optA_shared_dofs + np.testing.assert_allclose(deriv(optA_shared_dofs), optA.dJ()*2, atol=1e-14) + # restrict to sum_opt + np.testing.assert_allclose(deriv(sum_opt), np.concatenate((optA.dJ()*2, optB.dJ())), atol=1e-14) + + def test_as_derivative2(self): + # this test checks that when you sum a Derivative dictionary generated using as_derivative=True, + # to another that things work as expected when some DOFs are fixed. + + opt = OptClassSharedDOFs(x0=[1, 2, 3], names=["x", "y", "z"], + fixed=[False, False, True]) + deriv = opt.dJ(partials=True)(opt, as_derivative=True) + opt.dJ(partials=True) + np.testing.assert_allclose(deriv(opt), opt.dJ()*2, atol=1e-14) def test_load_save(self): import tempfile From 0b2ef408f09e27a24ff0cbecd2cc71276c74f53d Mon Sep 17 00:00:00 2001 From: daringli Date: Wed, 29 May 2024 22:06:52 +0200 Subject: [PATCH 126/176] Added a file not found exception handling. --- src/simsopt/mhd/vmec.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/simsopt/mhd/vmec.py b/src/simsopt/mhd/vmec.py index beef7c96e..822815fdb 100644 --- a/src/simsopt/mhd/vmec.py +++ b/src/simsopt/mhd/vmec.py @@ -755,7 +755,11 @@ def run(self): # Delete the previous output file, if desired: for filename in self.files_to_delete: - os.remove(filename) + try: + os.remove(filename) + except FileNotFoundError: + logger.debug('Tried to delete the file {filename} but it was not found') + self.files_to_delete = [] # Record the latest output file to delete if we run again: From a715c0f41579efc982aaf8b4a94fb352ebc199cc Mon Sep 17 00:00:00 2001 From: daringli <731405+daringli@users.noreply.github.com> Date: Wed, 29 May 2024 21:38:33 -0400 Subject: [PATCH 127/176] Fixed missing f in the f-string Thanks to VascoSch92! --- src/simsopt/mhd/vmec.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/simsopt/mhd/vmec.py b/src/simsopt/mhd/vmec.py index a2e0ce4f9..507c8c9a7 100644 --- a/src/simsopt/mhd/vmec.py +++ b/src/simsopt/mhd/vmec.py @@ -755,7 +755,7 @@ def run(self): try: os.remove(filename) except FileNotFoundError: - logger.debug('Tried to delete the file {filename} but it was not found') + logger.debug(f"Tried to delete the file {filename} but it was not found") self.files_to_delete = [] From 9c2db063cd94fb1ca96b935f030bacd1ca242986 Mon Sep 17 00:00:00 2001 From: Chris Date: Thu, 30 May 2024 15:42:40 +0200 Subject: [PATCH 128/176] test array translator and default_freeboundary spec --- src/simsopt/mhd/defaults_freebound.sp | 210 ++++++++++++++++++++++++++ src/simsopt/mhd/spec.py | 14 +- tests/mhd/test_spec.py | 48 ++++++ 3 files changed, 269 insertions(+), 3 deletions(-) create mode 100644 src/simsopt/mhd/defaults_freebound.sp diff --git a/src/simsopt/mhd/defaults_freebound.sp b/src/simsopt/mhd/defaults_freebound.sp new file mode 100644 index 000000000..b7fa02917 --- /dev/null +++ b/src/simsopt/mhd/defaults_freebound.sp @@ -0,0 +1,210 @@ +&physicslist + Igeometry = 3 + Istellsym = 1 + Lfreebound = 1 + phiedge = 2.000000000000000E+00 + curtor = 0.000000000000000E+00 + curpol = 4.000000000000000E+01 + gamma = 0.000000000000000E+00 + Nfp = 5 + Nvol = 1 + Mpol = 3 + Ntor = 3 + Lrad = 6 2 + tflux = 1.000000000000000E+00 6.218040116397460E+00 + pflux = 0.000000000000000E+00 3.816883073688957E+00 + helicity = 6.443366715051990E-02 1.116525236095663E+00 + pscale = 1.000000000000000E+02 + Ladiabatic = 0 + pressure = 0.000000000000000E+00 0.000000000000000E+00 + adiabatic = 0.000000000000000E+00 0.000000000000000E+00 + mu = 0.000000000000000E+00 0.000000000000000E+00 + Ivolume = 0.000000000000000E+00 0.000000000000000E+00 + Isurf = 0.000000000000000E+00 0.000000000000000E+00 + Lconstraint = 3 + pl = 0 0 0 + ql = 0 0 0 + pr = 0 0 0 + qr = 0 0 0 + iota = 0.000000000000000E+00 2.809417939338480E-01 3.050000000000000E-01 + lp = 0 0 0 + lq = 0 0 0 + rp = 0 0 0 + rq = 0 0 0 + oita = 0.000000000000000E+00 2.809417939338480E-01 3.050000000000000E-01 + mupftol = 1.000000000000000E-12 + mupfits = 128 + Lreflect = 0 + rpol = 1.000000000000000E+00 + rtor = 1.000000000000000E+00 + Rac = 9.645091076834294E+00 -1.273000100134322E-01 7.227734995841448E-04 2.901752615147871E-05 + Zas = 0.000000000000000E+00 -1.201876846458274E-01 1.210937745192939E-03 8.101291120903119E-05 + Ras = 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 + Zac = 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 +Rbc(0,0) = 9.704610460216003E+00 Zbs(0,0) = 0.000000000000000E+00 Rbs(0,0) = 0.000000000000000E+00 Zbc(0,0) = 0.000000000000000E+00 +Rbc(1,0) = -1.045848541227035E-01 Zbs(1,0) = -1.034983900846667E-01 Rbs(1,0) = 0.000000000000000E+00 Zbc(1,0) = 0.000000000000000E+00 +Rbc(2,0) = 5.496924456881049E-04 Zbs(2,0) = 8.105754421674023E-04 Rbs(2,0) = 0.000000000000000E+00 Zbc(2,0) = 0.000000000000000E+00 +Rbc(3,0) = -2.605852916338383E-05 Zbs(3,0) = 2.595333996994953E-06 Rbs(3,0) = 0.000000000000000E+00 Zbc(3,0) = 0.000000000000000E+00 +Rbc(-3,1) = -1.195463633068680E-05 Zbs(-3,1) = 2.841919864618188E-05 Rbs(-3,1) = 0.000000000000000E+00 Zbc(-3,1) = 0.000000000000000E+00 +Rbc(-2,1) = -3.394450906670391E-04 Zbs(-2,1) = 3.596274021066687E-04 Rbs(-2,1) = 0.000000000000000E+00 Zbc(-2,1) = 0.000000000000000E+00 +Rbc(-1,1) = -4.931651888369649E-03 Zbs(-1,1) = 6.963549886130800E-03 Rbs(-1,1) = 0.000000000000000E+00 Zbc(-1,1) = 0.000000000000000E+00 +Rbc(0,1) = 9.918678713491879E-01 Zbs(0,1) = -9.772386678651404E-01 Rbs(0,1) = 0.000000000000000E+00 Zbc(0,1) = 0.000000000000000E+00 +Rbc(1,1) = 8.640027952833292E-02 Zbs(1,1) = 9.241036581289261E-02 Rbs(1,1) = 0.000000000000000E+00 Zbc(1,1) = 0.000000000000000E+00 +Rbc(2,1) = 1.964242130996640E-03 Zbs(2,1) = 2.153208475198715E-03 Rbs(2,1) = 0.000000000000000E+00 Zbc(2,1) = 0.000000000000000E+00 +Rbc(3,1) = 7.998671801673742E-05 Zbs(3,1) = 1.161062030463278E-04 Rbs(3,1) = 0.000000000000000E+00 Zbc(3,1) = 0.000000000000000E+00 +Rbc(-3,2) = -2.762152103889883E-06 Zbs(-3,2) = 4.166379371076043E-06 Rbs(-3,2) = 0.000000000000000E+00 Zbc(-3,2) = 0.000000000000000E+00 +Rbc(-2,2) = -1.726514233457863E-05 Zbs(-2,2) = 1.983462874964590E-05 Rbs(-2,2) = 0.000000000000000E+00 Zbc(-2,2) = 0.000000000000000E+00 +Rbc(-1,2) = -6.283360944862572E-04 Zbs(-1,2) = 7.379659477847013E-04 Rbs(-1,2) = 0.000000000000000E+00 Zbc(-1,2) = 0.000000000000000E+00 +Rbc(0,2) = -2.706714444329093E-02 Zbs(0,2) = 2.833946442940345E-02 Rbs(0,2) = 0.000000000000000E+00 Zbc(0,2) = 0.000000000000000E+00 +Rbc(1,2) = -1.663136766639212E-02 Zbs(1,2) = -2.612324295966568E-03 Rbs(1,2) = 0.000000000000000E+00 Zbc(1,2) = 0.000000000000000E+00 +Rbc(2,2) = -4.482002741556905E-03 Zbs(2,2) = -5.025208765858588E-03 Rbs(2,2) = 0.000000000000000E+00 Zbc(2,2) = 0.000000000000000E+00 +Rbc(3,2) = 6.068006959746730E-05 Zbs(3,2) = -1.030827848856039E-05 Rbs(3,2) = 0.000000000000000E+00 Zbc(3,2) = 0.000000000000000E+00 +Rbc(-3,3) = 4.496337386676320E-06 Zbs(-3,3) = -2.281597748539077E-06 Rbs(-3,3) = 0.000000000000000E+00 Zbc(-3,3) = 0.000000000000000E+00 +Rbc(-2,3) = -1.615850297435840E-05 Zbs(-2,3) = -3.695652852901507E-05 Rbs(-2,3) = 0.000000000000000E+00 Zbc(-2,3) = 0.000000000000000E+00 +Rbc(-1,3) = 1.492859671801447E-04 Zbs(-1,3) = -2.388623508824467E-04 Rbs(-1,3) = 0.000000000000000E+00 Zbc(-1,3) = 0.000000000000000E+00 +Rbc(0,3) = 3.539712137494496E-03 Zbs(0,3) = -4.998079213999107E-03 Rbs(0,3) = 0.000000000000000E+00 Zbc(0,3) = 0.000000000000000E+00 +Rbc(1,3) = -3.845595274173447E-02 Zbs(1,3) = -2.589386621604443E-02 Rbs(1,3) = 0.000000000000000E+00 Zbc(1,3) = 0.000000000000000E+00 +Rbc(2,3) = -4.164306359043766E-02 Zbs(2,3) = -4.284945955446148E-02 Rbs(2,3) = 0.000000000000000E+00 Zbc(2,3) = 0.000000000000000E+00 +Rbc(3,3) = -1.242620719798954E-03 Zbs(3,3) = -1.354757246649995E-03 Rbs(3,3) = 0.000000000000000E+00 Zbc(3,3) = 0.000000000000000E+00 +Rwc(0,0) = 1.000000000000000E+01 Zws(0,0) = 0.000000000000000E+00 Rws(0,0) = 0.000000000000000E+00 Zwc(0,0) = 0.000000000000000E+00 +Rwc(1,0) = 0.000000000000000E+00 Zws(1,0) = 0.000000000000000E+00 Rws(1,0) = 0.000000000000000E+00 Zwc(1,0) = 0.000000000000000E+00 +Rwc(2,0) = 0.000000000000000E+00 Zws(2,0) = 0.000000000000000E+00 Rws(2,0) = 0.000000000000000E+00 Zwc(2,0) = 0.000000000000000E+00 +Rwc(3,0) = 0.000000000000000E+00 Zws(3,0) = 0.000000000000000E+00 Rws(3,0) = 0.000000000000000E+00 Zwc(3,0) = 0.000000000000000E+00 +Rwc(-3,1) = 0.000000000000000E+00 Zws(-3,1) = 0.000000000000000E+00 Rws(-3,1) = 0.000000000000000E+00 Zwc(-3,1) = 0.000000000000000E+00 +Rwc(-2,1) = 0.000000000000000E+00 Zws(-2,1) = 0.000000000000000E+00 Rws(-2,1) = 0.000000000000000E+00 Zwc(-2,1) = 0.000000000000000E+00 +Rwc(-1,1) = 0.000000000000000E+00 Zws(-1,1) = 0.000000000000000E+00 Rws(-1,1) = 0.000000000000000E+00 Zwc(-1,1) = 0.000000000000000E+00 +Rwc(0,1) = 3.000000000000000E+00 Zws(0,1) = -3.000000000000000E+00 Rws(0,1) = 0.000000000000000E+00 Zwc(0,1) = 0.000000000000000E+00 +Rwc(1,1) = 1.250000000000000E+00 Zws(1,1) = 1.250000000000000E+00 Rws(1,1) = 0.000000000000000E+00 Zwc(1,1) = 0.000000000000000E+00 +Rwc(2,1) = 0.000000000000000E+00 Zws(2,1) = 0.000000000000000E+00 Rws(2,1) = 0.000000000000000E+00 Zwc(2,1) = 0.000000000000000E+00 +Rwc(3,1) = 0.000000000000000E+00 Zws(3,1) = 0.000000000000000E+00 Rws(3,1) = 0.000000000000000E+00 Zwc(3,1) = 0.000000000000000E+00 +Rwc(-3,2) = 0.000000000000000E+00 Zws(-3,2) = 0.000000000000000E+00 Rws(-3,2) = 0.000000000000000E+00 Zwc(-3,2) = 0.000000000000000E+00 +Rwc(-2,2) = 0.000000000000000E+00 Zws(-2,2) = 0.000000000000000E+00 Rws(-2,2) = 0.000000000000000E+00 Zwc(-2,2) = 0.000000000000000E+00 +Rwc(-1,2) = 0.000000000000000E+00 Zws(-1,2) = 0.000000000000000E+00 Rws(-1,2) = 0.000000000000000E+00 Zwc(-1,2) = 0.000000000000000E+00 +Rwc(0,2) = 0.000000000000000E+00 Zws(0,2) = 0.000000000000000E+00 Rws(0,2) = 0.000000000000000E+00 Zwc(0,2) = 0.000000000000000E+00 +Rwc(1,2) = 0.000000000000000E+00 Zws(1,2) = 0.000000000000000E+00 Rws(1,2) = 0.000000000000000E+00 Zwc(1,2) = 0.000000000000000E+00 +Rwc(2,2) = 0.000000000000000E+00 Zws(2,2) = 0.000000000000000E+00 Rws(2,2) = 0.000000000000000E+00 Zwc(2,2) = 0.000000000000000E+00 +Rwc(3,2) = 0.000000000000000E+00 Zws(3,2) = 0.000000000000000E+00 Rws(3,2) = 0.000000000000000E+00 Zwc(3,2) = 0.000000000000000E+00 +Rwc(-3,3) = 0.000000000000000E+00 Zws(-3,3) = 0.000000000000000E+00 Rws(-3,3) = 0.000000000000000E+00 Zwc(-3,3) = 0.000000000000000E+00 +Rwc(-2,3) = 0.000000000000000E+00 Zws(-2,3) = 0.000000000000000E+00 Rws(-2,3) = 0.000000000000000E+00 Zwc(-2,3) = 0.000000000000000E+00 +Rwc(-1,3) = 0.000000000000000E+00 Zws(-1,3) = 0.000000000000000E+00 Rws(-1,3) = 0.000000000000000E+00 Zwc(-1,3) = 0.000000000000000E+00 +Rwc(0,3) = 0.000000000000000E+00 Zws(0,3) = 0.000000000000000E+00 Rws(0,3) = 0.000000000000000E+00 Zwc(0,3) = 0.000000000000000E+00 +Rwc(1,3) = 0.000000000000000E+00 Zws(1,3) = 0.000000000000000E+00 Rws(1,3) = 0.000000000000000E+00 Zwc(1,3) = 0.000000000000000E+00 +Rwc(2,3) = 0.000000000000000E+00 Zws(2,3) = 0.000000000000000E+00 Rws(2,3) = 0.000000000000000E+00 Zwc(2,3) = 0.000000000000000E+00 +Rwc(3,3) = 0.000000000000000E+00 Zws(3,3) = 0.000000000000000E+00 Rws(3,3) = 0.000000000000000E+00 Zwc(3,3) = 0.000000000000000E+00 +Vns(0,0) = 0.000000000000000E+00 Bns(0,0) = 0.000000000000000E+00 Vnc(0,0) = 0.000000000000000E+00 Bnc(0,0) = 0.000000000000000E+00 +Vns(1,0) = 0.000000000000000E+00 Bns(1,0) = -2.098314067166154E-02 Vnc(1,0) = 0.000000000000000E+00 Bnc(1,0) = 0.000000000000000E+00 +Vns(2,0) = 0.000000000000000E+00 Bns(2,0) = -8.308195552233343E-04 Vnc(2,0) = 0.000000000000000E+00 Bnc(2,0) = 0.000000000000000E+00 +Vns(3,0) = 0.000000000000000E+00 Bns(3,0) = -1.000049567085383E-05 Vnc(3,0) = 0.000000000000000E+00 Bnc(3,0) = 0.000000000000000E+00 +Vns(-3,1) = 0.000000000000000E+00 Bns(-3,1) = 1.025035236011660E-05 Vnc(-3,1) = 0.000000000000000E+00 Bnc(-3,1) = 0.000000000000000E+00 +Vns(-2,1) = 0.000000000000000E+00 Bns(-2,1) = 6.972200102040577E-05 Vnc(-2,1) = 0.000000000000000E+00 Bnc(-2,1) = 0.000000000000000E+00 +Vns(-1,1) = 0.000000000000000E+00 Bns(-1,1) = -8.857899561787283E-04 Vnc(-1,1) = 0.000000000000000E+00 Bnc(-1,1) = 0.000000000000000E+00 +Vns(0,1) = 0.000000000000000E+00 Bns(0,1) = 1.268794075038921E-02 Vnc(0,1) = 0.000000000000000E+00 Bnc(0,1) = 0.000000000000000E+00 +Vns(1,1) = 0.000000000000000E+00 Bns(1,1) = 5.235427842411160E-03 Vnc(1,1) = 0.000000000000000E+00 Bnc(1,1) = 0.000000000000000E+00 +Vns(2,1) = 0.000000000000000E+00 Bns(2,1) = -1.115762206996049E-03 Vnc(2,1) = 0.000000000000000E+00 Bnc(2,1) = 0.000000000000000E+00 +Vns(3,1) = 0.000000000000000E+00 Bns(3,1) = -4.424638432480133E-06 Vnc(3,1) = 0.000000000000000E+00 Bnc(3,1) = 0.000000000000000E+00 +Vns(-3,2) = 0.000000000000000E+00 Bns(-3,2) = -2.420544046309371E-06 Vnc(-3,2) = 0.000000000000000E+00 Bnc(-3,2) = 0.000000000000000E+00 +Vns(-2,2) = 0.000000000000000E+00 Bns(-2,2) = -1.127639127865856E-05 Vnc(-2,2) = 0.000000000000000E+00 Bnc(-2,2) = 0.000000000000000E+00 +Vns(-1,2) = 0.000000000000000E+00 Bns(-1,2) = -6.680730994641753E-04 Vnc(-1,2) = 0.000000000000000E+00 Bnc(-1,2) = 0.000000000000000E+00 +Vns(0,2) = 0.000000000000000E+00 Bns(0,2) = -2.105169513847248E-02 Vnc(0,2) = 0.000000000000000E+00 Bnc(0,2) = 0.000000000000000E+00 +Vns(1,2) = 0.000000000000000E+00 Bns(1,2) = -3.458317607829524E-02 Vnc(1,2) = 0.000000000000000E+00 Bnc(1,2) = 0.000000000000000E+00 +Vns(2,2) = 0.000000000000000E+00 Bns(2,2) = 7.025733332835698E-03 Vnc(2,2) = 0.000000000000000E+00 Bnc(2,2) = 0.000000000000000E+00 +Vns(3,2) = 0.000000000000000E+00 Bns(3,2) = 1.097429331303196E-03 Vnc(3,2) = 0.000000000000000E+00 Bnc(3,2) = 0.000000000000000E+00 +Vns(-3,3) = 0.000000000000000E+00 Bns(-3,3) = 2.012582723897679E-06 Vnc(-3,3) = 0.000000000000000E+00 Bnc(-3,3) = 0.000000000000000E+00 +Vns(-2,3) = 0.000000000000000E+00 Bns(-2,3) = -1.738204711861772E-06 Vnc(-2,3) = 0.000000000000000E+00 Bnc(-2,3) = 0.000000000000000E+00 +Vns(-1,3) = 0.000000000000000E+00 Bns(-1,3) = 5.534246820790295E-05 Vnc(-1,3) = 0.000000000000000E+00 Bnc(-1,3) = 0.000000000000000E+00 +Vns(0,3) = 0.000000000000000E+00 Bns(0,3) = 1.008641123981896E-03 Vnc(0,3) = 0.000000000000000E+00 Bnc(0,3) = 0.000000000000000E+00 +Vns(1,3) = 0.000000000000000E+00 Bns(1,3) = -8.786509679612788E-03 Vnc(1,3) = 0.000000000000000E+00 Bnc(1,3) = 0.000000000000000E+00 +Vns(2,3) = 0.000000000000000E+00 Bns(2,3) = -1.503823116287205E-02 Vnc(2,3) = 0.000000000000000E+00 Bnc(2,3) = 0.000000000000000E+00 +Vns(3,3) = 0.000000000000000E+00 Bns(3,3) = -9.987559625167259E-04 Vnc(3,3) = 0.000000000000000E+00 Bnc(3,3) = 0.000000000000000E+00 +/ +&numericlist + Linitialize = 0 + LautoinitBn = 0 + Lzerovac = 0 + Ndiscrete = 2 + Nquad = -1 + iMpol = -4 + iNtor = -4 + Lsparse = 0 + Lsvdiota = 0 + imethod = 3 + iorder = 2 + iprecon = 1 + iotatol = -1.000000000000000E+00 + Lextrap = 0 + Mregular = -1 + Lrzaxis = 2 + Ntoraxis = 3 +/ +&locallist + LBeltrami = 4 + Linitgues = 1 + Lmatsolver = 3 + NiterGMRES = 200 + LGMRESprec = 1 + epsGMRES = 1.000000000000000E-14 + epsILU = 1.000000000000000E-12 +/ +&globallist + Lfindzero = 2 + escale = 0.000000000000000E+00 + opsilon = 1.000000000000000E+00 + pcondense = 4.000000000000000E+00 + epsilon = 1.000000000000000E+00 + wpoloidal = 1.000000000000000E+00 + upsilon = 1.000000000000000E+00 + forcetol = 1.000000000000000E-12 + c05xmax = 1.000000000000000E-06 + c05xtol = 1.000000000000000E-12 + c05factor = 1.000000000000000E-04 + LreadGF = F + mfreeits = 1 + gBntol = 1.000000000000000E-04 + gBnbld = 1.000000000000000E-01 + vcasingeps = 1.000000000000000E-10 + vcasingtol = 1.000000000000000E-04 + vcasingits = 8 + vcasingper = 1 +/ +&diagnosticslist + odetol = 1.000000000000000E-07 + nPpts = -1 + Ppts = 0.000000000000000E+00 + nPtrj = 1 1 + LHevalues = F + LHevectors = F + LHmatrix = F + Lperturbed = 0 + dpp = -1 + dqq = -1 + dRZ = 1.000000000000000E-05 + Lcheck = 0 + Ltiming = F +/ +&screenlist +/ + 0 0 9.704610460216003E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 + 0 1 -1.045848541227035E-01 -1.034983900846667E-01 0.000000000000000E+00 0.000000000000000E+00 + 0 2 5.496924456881049E-04 8.105754421674023E-04 0.000000000000000E+00 0.000000000000000E+00 + 0 3 -2.605852916338383E-05 2.595333996994953E-06 0.000000000000000E+00 0.000000000000000E+00 + 1 -3 -1.195463633068680E-05 2.841919864618188E-05 0.000000000000000E+00 0.000000000000000E+00 + 1 -2 -3.394450906670391E-04 3.596274021066687E-04 0.000000000000000E+00 0.000000000000000E+00 + 1 -1 -4.931651888369649E-03 6.963549886130800E-03 0.000000000000000E+00 0.000000000000000E+00 + 1 0 9.918678713491879E-01 -9.772386678651404E-01 0.000000000000000E+00 0.000000000000000E+00 + 1 1 8.640027952833292E-02 9.241036581289261E-02 0.000000000000000E+00 0.000000000000000E+00 + 1 2 1.964242130996640E-03 2.153208475198715E-03 0.000000000000000E+00 0.000000000000000E+00 + 1 3 7.998671801673742E-05 1.161062030463278E-04 0.000000000000000E+00 0.000000000000000E+00 + 2 -3 -2.762152103889883E-06 4.166379371076043E-06 0.000000000000000E+00 0.000000000000000E+00 + 2 -2 -1.726514233457863E-05 1.983462874964590E-05 0.000000000000000E+00 0.000000000000000E+00 + 2 -1 -6.283360944862572E-04 7.379659477847013E-04 0.000000000000000E+00 0.000000000000000E+00 + 2 0 -2.706714444329093E-02 2.833946442940345E-02 0.000000000000000E+00 0.000000000000000E+00 + 2 1 -1.663136766639212E-02 -2.612324295966568E-03 0.000000000000000E+00 0.000000000000000E+00 + 2 2 -4.482002741556905E-03 -5.025208765858588E-03 0.000000000000000E+00 0.000000000000000E+00 + 2 3 6.068006959746730E-05 -1.030827848856039E-05 0.000000000000000E+00 0.000000000000000E+00 + 3 -3 4.496337386676320E-06 -2.281597748539077E-06 0.000000000000000E+00 0.000000000000000E+00 + 3 -2 -1.615850297435840E-05 -3.695652852901507E-05 0.000000000000000E+00 0.000000000000000E+00 + 3 -1 1.492859671801447E-04 -2.388623508824467E-04 0.000000000000000E+00 0.000000000000000E+00 + 3 0 3.539712137494496E-03 -4.998079213999107E-03 0.000000000000000E+00 0.000000000000000E+00 + 3 1 -3.845595274173447E-02 -2.589386621604443E-02 0.000000000000000E+00 0.000000000000000E+00 + 3 2 -4.164306359043766E-02 -4.284945955446148E-02 0.000000000000000E+00 0.000000000000000E+00 + 3 3 -1.242620719798954E-03 -1.354757246649995E-03 0.000000000000000E+00 0.000000000000000E+00 diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index 9e2b07695..73ad8c714 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -252,12 +252,20 @@ def __init__(self, external_dof_setter=Spec.set_dofs) @classmethod - def default_freeboundary(cls): + def default_freeboundary(cls, copy_to_pwd, verbose=True): """ Create a default freeboundary SPEC object + Args: + copy_to_pwd: boolean, if True, the default input file will be copied to the current working directory. Has to be set True as free-boundary SPEC can only handle files in the current working directory. + verbose: boolean, if True, print statements will be printed """ - return cls(filename=os.path.join(os.path.dirname(__file__), 'defaults_freebound.sp')) - + import shutil, os + filename = 'defaults_freebound.sp' + if verbose: + print(f'Copying {os.path.join(os.path.dirname(__file__), filename)} to {os.getcwd()}/{filename}') + shutil.copy(os.path.join(os.path.dirname(__file__), filename), os.getcwd()) + return cls(filename=filename, verbose=verbose) + @classmethod def default_fixedboundary(cls): """ diff --git a/tests/mhd/test_spec.py b/tests/mhd/test_spec.py index 0ab5fb536..97afee740 100755 --- a/tests/mhd/test_spec.py +++ b/tests/mhd/test_spec.py @@ -195,6 +195,54 @@ def test_set_profile_cumulative(self): self.assertEqual(s.get_profile('volume_current', lvol), 0) else: self.assertEqual(s.get_profile('volume_current', lvol), 1) + + def test_freeboundary_default(self): + """ + test the default freeboundary file, and re-set if Picard + iteration fails + """ + from simsopt._core.util import ObjectiveFailure + + with ScratchDir("."): + s = Spec.default_freeboundary(copy_to_pwd=True) + startingboundary = np.copy(s.inputlist.bns) + # run sucessfully as default should be converged + s.run() + # ask to generate guess, not enough freeboundary iterations + s.inputlist.linitialize = 2 + s.inputlist.lautoinitbn = 1 + s.inputlist.mfreeits = 2 + s.recompute_bell() + try: + s.run() + except ObjectiveFailure: + self.assertTrue(np.alltrue(s.inputlist.bns == startingboundary)) + else: + raise ValueError("ObjectiveFailure not raised") + # give enough freeboundary iterations, let ir run successfully + s.inputlist.mfreeits = 10 + s.recompute_bell() + s.run() + + def test_array_translator(self): + """ + Test the array_translator method to convert a SPEC style array to simsopt style array. + """ + spec = Spec() + array = spec.inputlist.rbc + translator = spec.array_translator(array) + translator2 = spec.array_translator(array, style='spec') + translator3 = spec.array_translator(translator.as_simsopt, style='simsopt') + #assert that translator.as_spec i + + self.assertTrue(np.alltrue(array == translator.as_spec)) + self.assertTrue(np.alltrue(array == translator2.as_spec)) + self.assertTrue(np.alltrue(array == translator3.as_spec)) + self.assertTrue(np.alltrue(translator.as_simsopt == translator2.as_simsopt)) + self.assertTrue(np.alltrue(translator2.as_simsopt == translator3.as_simsopt)) + # test that the shape of the array is correct: + self.assertEqual(translator2.as_simsopt.shape, (spec.inputlist.ntor+1, (2*spec.inputlist.mpol)+1)) + def test_integrated_stellopt_scenarios_1dof(self): """ From 903914142de065c70aa7a86c976d8c29aaa2ea25 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Thu, 30 May 2024 11:30:53 -0400 Subject: [PATCH 129/176] cleaning up docstring --- src/simsopt/_core/derivative.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/simsopt/_core/derivative.py b/src/simsopt/_core/derivative.py index 01b3baca7..6b62d848a 100644 --- a/src/simsopt/_core/derivative.py +++ b/src/simsopt/_core/derivative.py @@ -173,9 +173,12 @@ def __call__(self, optim, as_derivative=False): Args: optim: An Optimizable object - as_derivative: if True return as a Derivative object, else return as an numpy array. The keys + as_derivative: if True return as a Derivative object. The keys of the returned Derivative dictionary can include `optim`, the ancestors of `optim` - or Optimizables that share DOFs with ancestors of `optim`. + or Optimizables that share DOFs with ancestors of `optim`. The values are numpy arrays + corresponding to the derivatives with respect to all degrees of freedom, both free and fixed. + If False, return as a numpy array. The entries of the array correspond only to free + DOFs, and fixed ones are removed out. """ from .optimizable import Optimizable # Import here to avoid circular import assert isinstance(optim, Optimizable) @@ -186,11 +189,9 @@ def __call__(self, optim, as_derivative=False): for k in optim.unique_dof_lineage: for opt in k.dofs.dep_opts(): - # the next if-statament is there to avoid the dictionary from accumulating # empty values e.g. if there are no local DOFs to opt, then self.data[opt] # returns np.array([]). - if opt.local_full_dof_size > 0: derivs.append(self.data[opt]) keys.append(opt) From 389389c9f8c6ac53360785c8286f8361d20a992b Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Sun, 2 Jun 2024 06:47:11 -0400 Subject: [PATCH 130/176] Implemented L_{grad B} and tests for it --- src/simsopt/mhd/vmec_diagnostics.py | 158 +++++++++++++++++- tests/mhd/test_vmec_diagnostics.py | 136 +++++++++++++++ tests/test_files/input.purely_toroidal_field | 37 ++++ .../wout_purely_toroidal_field_reference.nc | Bin 0 -> 124068 bytes 4 files changed, 325 insertions(+), 6 deletions(-) create mode 100644 tests/test_files/input.purely_toroidal_field create mode 100644 tests/test_files/wout_purely_toroidal_field_reference.nc diff --git a/src/simsopt/mhd/vmec_diagnostics.py b/src/simsopt/mhd/vmec_diagnostics.py index 5632d2dcf..4f4e640b1 100644 --- a/src/simsopt/mhd/vmec_diagnostics.py +++ b/src/simsopt/mhd/vmec_diagnostics.py @@ -899,6 +899,7 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): - ``grad_alpha_dot_grad_alpha``: :math:`|\nabla\alpha|^2 = \nabla\alpha\cdot\nabla\alpha`. - ``grad_alpha_dot_grad_psi``: :math:`\nabla\alpha\cdot\nabla\psi`. - ``grad_psi_dot_grad_psi``: :math:`|\nabla\psi|^2 = \nabla\psi\cdot\nabla\psi`. + - ``L_grad_B``: The scale length of the magnetic field, from Kappel et al, PPCF 66 025018 (2024). - ``iota``: The rotational transform :math:`\iota`. This array has shape ``(ns,)``. - ``shat``: The magnetic shear :math:`\hat s= (x/q) (d q / d x)` where :math:`x = \mathrm{Aminor_p} \, \sqrt{s}` and :math:`q=1/\iota`. This array has shape ``(ns,)``. @@ -1027,6 +1028,8 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): bsubsmns = np.zeros((ns, mnmax_nyq)) bsubumnc = np.zeros((ns, mnmax_nyq)) bsubvmnc = np.zeros((ns, mnmax_nyq)) + d_bsupumnc_d_s = np.zeros((ns, mnmax_nyq)) + d_bsupvmnc_d_s = np.zeros((ns, mnmax_nyq)) for jmn in range(mnmax_nyq): gmnc[:, jmn] = vs.gmnc[jmn](s) bmnc[:, jmn] = vs.bmnc[jmn](s) @@ -1036,6 +1039,8 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): bsubsmns[:, jmn] = vs.bsubsmns[jmn](s) bsubumnc[:, jmn] = vs.bsubumnc[jmn](s) bsubvmnc[:, jmn] = vs.bsubvmnc[jmn](s) + d_bsupumnc_d_s[:, jmn] = vs.d_bsupumnc_d_s[jmn](s) + d_bsupvmnc_d_s[:, jmn] = vs.d_bsupvmnc_d_s[jmn](s) # Now that we know theta_vmec, compute all the geometric quantities angle = xm[:, None, None, None] * theta_vmec[None, :, :, :] - xn[:, None, None, None] * phi[None, :, :, :] @@ -1043,25 +1048,40 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): sinangle = np.sin(angle) mcosangle = xm[:, None, None, None] * cosangle ncosangle = xn[:, None, None, None] * cosangle + mncosangle = xm[:, None, None, None] * xn[:, None, None, None] * cosangle + m2cosangle = xm[:, None, None, None]**2 * cosangle + n2cosangle = xn[:, None, None, None]**2 * cosangle msinangle = xm[:, None, None, None] * sinangle nsinangle = xn[:, None, None, None] * sinangle + mnsinangle = xm[:, None, None, None] * xn[:, None, None, None] * sinangle + m2sinangle = xm[:, None, None, None]**2 * sinangle + n2sinangle = xn[:, None, None, None]**2 * sinangle # Order of indices in cosangle and sinangle: mn, s, theta, phi # Order of indices in rmnc, bmnc, etc: s, mn R = np.einsum('ij,jikl->ikl', rmnc, cosangle) d_R_d_s = np.einsum('ij,jikl->ikl', d_rmnc_d_s, cosangle) - d_R_d_theta_vmec = -np.einsum('ij,jikl->ikl', rmnc, msinangle) + d_R_d_theta_vmec = np.einsum('ij,jikl->ikl', -rmnc, msinangle) d_R_d_phi = np.einsum('ij,jikl->ikl', rmnc, nsinangle) - + d2_R_d_phi2 = np.einsum('ij,jikl->ikl', -rmnc, n2cosangle) + d2_R_d_theta_vmec2 = np.einsum('ij,jikl->ikl', -rmnc, m2cosangle) + d2_R_d_theta_vmec_d_phi = np.einsum('ij,jikl->ikl', rmnc, mncosangle) + d2_R_d_s_d_theta_vmec = np.einsum('ij,jikl->ikl', -d_rmnc_d_s, msinangle) + d2_R_d_s_d_phi = np.einsum('ij,jikl->ikl', d_rmnc_d_s, nsinangle) Z = np.einsum('ij,jikl->ikl', zmns, sinangle) d_Z_d_s = np.einsum('ij,jikl->ikl', d_zmns_d_s, sinangle) d_Z_d_theta_vmec = np.einsum('ij,jikl->ikl', zmns, mcosangle) - d_Z_d_phi = -np.einsum('ij,jikl->ikl', zmns, ncosangle) + d_Z_d_phi = np.einsum('ij,jikl->ikl', -zmns, ncosangle) + d2_Z_d_theta_vmec2 = np.einsum('ij,jikl->ikl', -zmns, m2sinangle) + d2_Z_d_phi2 = np.einsum('ij,jikl->ikl', -zmns, n2sinangle) + d2_Z_d_theta_vmec_d_phi = np.einsum('ij,jikl->ikl', zmns, mnsinangle) + d2_Z_d_s_d_theta_vmec = np.einsum('ij,jikl->ikl', d_zmns_d_s, mcosangle) + d2_Z_d_s_d_phi = np.einsum('ij,jikl->ikl', -d_zmns_d_s, ncosangle) lambd = np.einsum('ij,jikl->ikl', lmns, sinangle) d_lambda_d_s = np.einsum('ij,jikl->ikl', d_lmns_d_s, sinangle) d_lambda_d_theta_vmec = np.einsum('ij,jikl->ikl', lmns, mcosangle) - d_lambda_d_phi = -np.einsum('ij,jikl->ikl', lmns, ncosangle) + d_lambda_d_phi = np.einsum('ij,jikl->ikl', -lmns, ncosangle) theta_pest = theta_vmec + lambd # Now handle the Nyquist quantities: @@ -1076,7 +1096,7 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): sqrt_g_vmec = np.einsum('ij,jikl->ikl', gmnc, cosangle) modB = np.einsum('ij,jikl->ikl', bmnc, cosangle) d_B_d_s = np.einsum('ij,jikl->ikl', d_bmnc_d_s, cosangle) - d_B_d_theta_vmec = -np.einsum('ij,jikl->ikl', bmnc, msinangle) + d_B_d_theta_vmec = np.einsum('ij,jikl->ikl', -bmnc, msinangle) d_B_d_phi = np.einsum('ij,jikl->ikl', bmnc, nsinangle) B_sup_theta_vmec = np.einsum('ij,jikl->ikl', bsupumnc, cosangle) @@ -1085,6 +1105,12 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): B_sub_theta_vmec = np.einsum('ij,jikl->ikl', bsubumnc, cosangle) B_sub_phi = np.einsum('ij,jikl->ikl', bsubvmnc, cosangle) B_sup_theta_pest = iota[:, None, None] * B_sup_phi + d_B_sup_phi_d_theta_vmec = np.einsum('ij,jikl->ikl', -bsupvmnc, msinangle) + d_B_sup_phi_d_phi = np.einsum('ij,jikl->ikl', bsupvmnc, nsinangle) + d_B_sup_theta_vmec_d_theta_vmec = np.einsum('ij,jikl->ikl', -bsupumnc, msinangle) + d_B_sup_theta_vmec_d_phi = np.einsum('ij,jikl->ikl', bsupumnc, nsinangle) + d_B_sup_theta_vmec_d_s = np.einsum('ij,jikl->ikl', d_bsupumnc_d_s, cosangle) + d_B_sup_phi_d_s = np.einsum('ij,jikl->ikl', d_bsupvmnc_d_s, cosangle) sqrt_g_vmec_alt = R * (d_Z_d_s * d_R_d_theta_vmec - d_R_d_s * d_Z_d_theta_vmec) @@ -1223,6 +1249,119 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): cvdrift0 = gbdrift0 + # Quantities related to the grad \vec{B} tensor. + # See Appendix C of Kappel et al, "The Magnetic Gradient Scale Length + # Explains Why Certain Plasmas Require Close External Magnetic Coils" + # Plasma Phys. Control. Fusion 66 (2024) 025018 + # https://doi.org/10.1088/1361-6587/ad1a3e + + d_B_X_d_s = ( + d_B_sup_theta_vmec_d_s * d_R_d_theta_vmec * cosphi + + B_sup_theta_vmec * d2_R_d_s_d_theta_vmec * cosphi + + d_B_sup_phi_d_s * d_R_d_phi * cosphi + + B_sup_phi * d2_R_d_s_d_phi * cosphi + - d_B_sup_phi_d_s * R * sinphi + - B_sup_phi * d_R_d_s * sinphi + ) + + d_B_X_d_theta = ( + d_B_sup_theta_vmec_d_theta_vmec * d_R_d_theta_vmec * cosphi + + B_sup_theta_vmec * d2_R_d_theta_vmec2 * cosphi + + d_B_sup_phi_d_theta_vmec * d_R_d_phi * cosphi + + B_sup_phi * d2_R_d_theta_vmec_d_phi * cosphi + - d_B_sup_phi_d_theta_vmec * R * sinphi + - B_sup_phi * d_R_d_theta_vmec * sinphi + ) + + d_B_X_d_phi = ( + d_B_sup_theta_vmec_d_phi * d_R_d_theta_vmec * cosphi + + B_sup_theta_vmec * d2_R_d_theta_vmec_d_phi * cosphi + - B_sup_theta_vmec * d_R_d_theta_vmec * sinphi + + d_B_sup_phi_d_phi * d_R_d_phi * cosphi + + B_sup_phi * d2_R_d_phi2 * cosphi + - B_sup_phi * d_R_d_phi * sinphi + - d_B_sup_phi_d_phi * R * sinphi + - B_sup_phi * d_R_d_phi * sinphi + - B_sup_phi * R * cosphi + ) + + d_B_Y_d_s = ( + d_B_sup_theta_vmec_d_s * d_R_d_theta_vmec * sinphi + + B_sup_theta_vmec * d2_R_d_s_d_theta_vmec * sinphi + + d_B_sup_phi_d_s * d_R_d_phi * sinphi + + B_sup_phi * d2_R_d_s_d_phi * sinphi + + d_B_sup_phi_d_s * R * cosphi + + B_sup_phi * d_R_d_s * cosphi + ) + + d_B_Y_d_theta = ( + d_B_sup_theta_vmec_d_theta_vmec * d_R_d_theta_vmec * sinphi + + B_sup_theta_vmec * d2_R_d_theta_vmec2 * sinphi + + d_B_sup_phi_d_theta_vmec * d_R_d_phi * sinphi + + B_sup_phi * d2_R_d_theta_vmec_d_phi * sinphi + + d_B_sup_phi_d_theta_vmec * R * cosphi + + B_sup_phi * d_R_d_theta_vmec * cosphi + ) + + d_B_Y_d_phi = ( + d_B_sup_theta_vmec_d_phi * d_R_d_theta_vmec * sinphi + + B_sup_theta_vmec * d2_R_d_theta_vmec_d_phi * sinphi + + B_sup_theta_vmec * d_R_d_theta_vmec * cosphi + + d_B_sup_phi_d_phi * d_R_d_phi * sinphi + + B_sup_phi * d2_R_d_phi2 * sinphi + + B_sup_phi * d_R_d_phi * cosphi + + d_B_sup_phi_d_phi * R * cosphi + + B_sup_phi * d_R_d_phi * cosphi + - B_sup_phi * R * sinphi + ) + + d_B_Z_d_s = ( + d_B_sup_theta_vmec_d_s * d_Z_d_theta_vmec + + B_sup_theta_vmec * d2_Z_d_s_d_theta_vmec + + d_B_sup_phi_d_s * d_Z_d_phi + + B_sup_phi * d2_Z_d_s_d_phi + ) + + d_B_Z_d_theta = ( + d_B_sup_theta_vmec_d_theta_vmec * d_Z_d_theta_vmec + + B_sup_theta_vmec * d2_Z_d_theta_vmec2 + + d_B_sup_phi_d_theta_vmec * d_Z_d_phi + + B_sup_phi * d2_Z_d_theta_vmec_d_phi + ) + + d_B_Z_d_phi = ( + d_B_sup_theta_vmec_d_phi * d_Z_d_theta_vmec + + B_sup_theta_vmec * d2_Z_d_theta_vmec_d_phi + + d_B_sup_phi_d_phi * d_Z_d_phi + + B_sup_phi * d2_Z_d_phi2 + ) + + grad_B__XX = d_B_X_d_s * grad_s_X + d_B_X_d_theta * grad_theta_vmec_X + d_B_X_d_phi * grad_phi_X + grad_B__XY = d_B_X_d_s * grad_s_Y + d_B_X_d_theta * grad_theta_vmec_Y + d_B_X_d_phi * grad_phi_Y + grad_B__XZ = d_B_X_d_s * grad_s_Z + d_B_X_d_theta * grad_theta_vmec_Z + d_B_X_d_phi * grad_phi_Z + + grad_B__YX = d_B_Y_d_s * grad_s_X + d_B_Y_d_theta * grad_theta_vmec_X + d_B_Y_d_phi * grad_phi_X + grad_B__YY = d_B_Y_d_s * grad_s_Y + d_B_Y_d_theta * grad_theta_vmec_Y + d_B_Y_d_phi * grad_phi_Y + grad_B__YZ = d_B_Y_d_s * grad_s_Z + d_B_Y_d_theta * grad_theta_vmec_Z + d_B_Y_d_phi * grad_phi_Z + + grad_B__ZX = d_B_Z_d_s * grad_s_X + d_B_Z_d_theta * grad_theta_vmec_X + d_B_Z_d_phi * grad_phi_X + grad_B__ZY = d_B_Z_d_s * grad_s_Y + d_B_Z_d_theta * grad_theta_vmec_Y + d_B_Z_d_phi * grad_phi_Y + grad_B__ZZ = d_B_Z_d_s * grad_s_Z + d_B_Z_d_theta * grad_theta_vmec_Z + d_B_Z_d_phi * grad_phi_Z + + grad_B_double_dot_grad_B = ( + grad_B__XX * grad_B__XX + + grad_B__XY * grad_B__XY + + grad_B__XZ * grad_B__XZ + + grad_B__YX * grad_B__YX + + grad_B__YY * grad_B__YY + + grad_B__YZ * grad_B__YZ + + grad_B__ZX * grad_B__ZX + + grad_B__ZY * grad_B__ZY + + grad_B__ZZ * grad_B__ZZ + ) + norm_grad_B = np.sqrt(grad_B_double_dot_grad_B) + L_grad_B = modB * np.sqrt(2 / grad_B_double_dot_grad_B) + # Package results into a structure to return: results = Struct() variables = ['ns', 'ntheta', 'nphi', 's', 'iota', 'd_iota_d_s', 'd_pressure_d_s', 'shat', @@ -1230,6 +1369,10 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): 'd_lambda_d_s', 'd_lambda_d_theta_vmec', 'd_lambda_d_phi', 'sqrt_g_vmec', 'sqrt_g_vmec_alt', 'modB', 'd_B_d_s', 'd_B_d_theta_vmec', 'd_B_d_phi', 'B_sup_theta_vmec', 'B_sup_theta_pest', 'B_sup_phi', 'B_sub_s', 'B_sub_theta_vmec', 'B_sub_phi', 'edge_toroidal_flux_over_2pi', 'sinphi', 'cosphi', + 'd2_R_d_phi2', 'd2_R_d_theta_vmec2', 'd2_R_d_theta_vmec_d_phi', 'd2_R_d_s_d_theta_vmec', 'd2_R_d_s_d_phi', + 'd2_Z_d_theta_vmec2', 'd2_Z_d_phi2', 'd2_Z_d_theta_vmec_d_phi', 'd2_Z_d_s_d_theta_vmec', 'd2_Z_d_s_d_phi', + 'd_B_sup_phi_d_theta_vmec', 'd_B_sup_phi_d_phi', 'd_B_sup_theta_vmec_d_theta_vmec', + 'd_B_sup_theta_vmec_d_phi', 'd_B_sup_theta_vmec_d_s', 'd_B_sup_phi_d_s', 'R', 'd_R_d_s', 'd_R_d_theta_vmec', 'd_R_d_phi', 'X', 'Y', 'Z', 'd_Z_d_s', 'd_Z_d_theta_vmec', 'd_Z_d_phi', 'd_X_d_theta_vmec', 'd_X_d_phi', 'd_X_d_s', 'd_Y_d_theta_vmec', 'd_Y_d_phi', 'd_Y_d_s', 'grad_s_X', 'grad_s_Y', 'grad_s_Z', 'grad_theta_vmec_X', 'grad_theta_vmec_Y', 'grad_theta_vmec_Z', @@ -1241,7 +1384,10 @@ def vmec_compute_geometry(vs, s, theta, phi, phi_center=0): 'B_cross_grad_B_dot_grad_psi', 'B_cross_kappa_dot_grad_psi', 'B_cross_kappa_dot_grad_alpha', 'grad_alpha_dot_grad_alpha', 'grad_alpha_dot_grad_psi', 'grad_psi_dot_grad_psi', 'L_reference', 'B_reference', 'toroidal_flux_sign', - 'bmag', 'gradpar_theta_pest', 'gradpar_phi', 'gds2', 'gds21', 'gds22', 'gbdrift', 'gbdrift0', 'cvdrift', 'cvdrift0'] + 'bmag', 'gradpar_theta_pest', 'gradpar_phi', 'gds2', 'gds21', 'gds22', 'gbdrift', 'gbdrift0', 'cvdrift', 'cvdrift0', + 'grad_B__XX', 'grad_B__XY', 'grad_B__XZ', 'grad_B__YX', 'grad_B__YY', 'grad_B__YZ', 'grad_B__ZX', 'grad_B__ZY', 'grad_B__ZZ', + 'grad_B_double_dot_grad_B', 'norm_grad_B', 'L_grad_B', + ] for v in variables: results.__setattr__(v, eval(v)) diff --git a/tests/mhd/test_vmec_diagnostics.py b/tests/mhd/test_vmec_diagnostics.py index 82a5c545e..a65400e0b 100755 --- a/tests/mhd/test_vmec_diagnostics.py +++ b/tests/mhd/test_vmec_diagnostics.py @@ -490,6 +490,142 @@ def test_compare_to_desc(self): np.testing.assert_allclose(simsopt_data.grad_psi_dot_grad_psi, desc_data, rtol=0.005, atol=0.0005) + def test_derivatives(self): + """ + Compare some of the derivatives to finite differences. + """ + vmec = Vmec(os.path.join(TEST_DIR, "wout_LandremanPaul2021_QA_lowres.nc")) + + ds = 0.01 + s = [1.0 - ds, 1.0] + ntheta = 100 + nphi = 102 + theta = np.linspace(0, 2 * np.pi, ntheta, endpoint=False) + phi = np.linspace(0, 2 * np.pi / vmec.wout.nfp, nphi, endpoint=False) + dtheta = theta[1] - theta[0] + dphi = phi[1] - phi[0] + + def d_d_theta(f): + return (np.roll(f, -1, axis=1) - np.roll(f, 1, axis=1)) / (2 * dtheta) + + def d_d_phi(f): + return (np.roll(f, -1, axis=2) - np.roll(f, 1, axis=2)) / (2 * dphi) + + def d2_d_theta2(f): + return (np.roll(f, -1, axis=1) - 2 * f + np.roll(f, 1, axis=1)) / (dtheta**2) + + def d2_d_phi2(f): + return (np.roll(f, -1, axis=2) - 2 * f + np.roll(f, 1, axis=2)) / (dphi**2) + + def d_d_s(f): + return (f[1, :, :] - f[0, :, :]) / ds + + def s_mean(f): + # Average over the two surfaces + return 0.5 * (f[0, :, :] + f[1, :, :]) + + data = vmec_compute_geometry(vmec, s, theta, phi) + + np.testing.assert_allclose(data.d_R_d_theta_vmec, d_d_theta(data.R), atol=3e-3) + np.testing.assert_allclose(data.d2_R_d_theta_vmec_d_phi, d_d_theta(d_d_phi(data.R)), atol=2e-3) + np.testing.assert_allclose(data.d2_Z_d_theta_vmec_d_phi, d_d_theta(d_d_phi(data.Z)), atol=2e-3) + np.testing.assert_allclose(data.d2_R_d_theta_vmec2, d2_d_theta2(data.R), atol=4e-4) + np.testing.assert_allclose(data.d2_Z_d_theta_vmec2, d2_d_theta2(data.Z), atol=3e-4) + np.testing.assert_allclose(data.d2_R_d_phi2, d2_d_phi2(data.R), atol=2e-3) + np.testing.assert_allclose(data.d2_Z_d_phi2, d2_d_phi2(data.Z), atol=2e-3) + np.testing.assert_allclose(s_mean(data.d2_R_d_s_d_phi), d_d_s(data.d_R_d_phi), atol=3e-6) + np.testing.assert_allclose(s_mean(data.d2_Z_d_s_d_phi), d_d_s(data.d_Z_d_phi), atol=2e-6) + np.testing.assert_allclose(s_mean(data.d2_R_d_s_d_theta_vmec), d_d_s(data.d_R_d_theta_vmec), atol=2e-6) + np.testing.assert_allclose(s_mean(data.d2_Z_d_s_d_theta_vmec), d_d_s(data.d_Z_d_theta_vmec), atol=2e-6) + + np.testing.assert_allclose(data.d_B_sup_theta_vmec_d_theta_vmec, d_d_theta(data.B_sup_theta_vmec), atol=2e-2) + np.testing.assert_allclose(data.d_B_sup_theta_vmec_d_phi, d_d_phi(data.B_sup_theta_vmec), atol=4e-3) + np.testing.assert_allclose(data.d_B_sup_phi_d_theta_vmec, d_d_theta(data.B_sup_phi), atol=8e-3) + np.testing.assert_allclose(data.d_B_sup_phi_d_phi, d_d_phi(data.B_sup_phi), atol=8e-4) + np.testing.assert_allclose(s_mean(data.d_B_sup_phi_d_s), d_d_s(data.B_sup_phi), atol=6e-6) + np.testing.assert_allclose(s_mean(data.d_B_sup_theta_vmec_d_s), d_d_s(data.B_sup_theta_vmec), atol=4e-5) + + if False: + # f_an = np.squeeze(data.d2_R_d_phi2)[1, :, :] + # f_fd = np.squeeze(d2_d_phi2(data.R))[1, :, :] + f_an = s_mean(data.d2_R_d_s_d_theta_vmec) + f_fd = d_d_s(data.d_R_d_theta_vmec) + import matplotlib.pyplot as plt + plt.figure(figsize=(14, 7)) + nrows = 1 + ncols = 3 + ncontours = 25 + + plt.subplot(nrows, ncols, 1) + plt.contour(phi, theta, f_an, ncontours) + plt.colorbar() + plt.title("analytic") + + plt.subplot(nrows, ncols, 2) + plt.contour(phi, theta, f_fd, ncontours) + plt.colorbar() + plt.title("finite diff") + + plt.subplot(nrows, ncols, 3) + plt.contour(phi, theta, f_an - f_fd, ncontours) + plt.colorbar() + plt.title("diff") + + plt.tight_layout() + plt.show() + + def test_L_grad_B_regression(self): + """ + Compare L_{grad B} to an indepedent calculation in Matt Landreman's + Matlab code m20240601_01_gradBTensorComplexityMetricForVMEC.m + """ + vmec = Vmec(os.path.join(TEST_DIR, "wout_LandremanPaul2021_QA_lowres.nc")) + + s = 1.0 + ntheta = 9 + nphi = 7 + theta = np.linspace(0, 2 * np.pi, ntheta, endpoint=True) + phi = np.linspace(0, 2 * np.pi / vmec.wout.nfp, nphi, endpoint=True) + + data = vmec_compute_geometry(vmec, s, theta, phi) + + matlab_data = np.array([ + [0.777048118791033, 0.850059335051267, 1.058251880937882, 1.238755906102585, 1.058251880937882, 0.850059335051267, 0.777048118791033], + [0.732357468770512, 0.887635027604753, 1.100038034467113, 1.149372447382607, 0.914652536061020, 0.732423846297739, 0.732357468770512], + [0.642772279126891, 0.810075234122540, 1.009506601358511, 1.036192879128092, 0.822941521630497, 0.638233465781766, 0.642772279126891], + [0.561114055795734, 0.718502389029629, 0.920071594222606, 0.997769685332234, 0.817986738735225, 0.595098001722719, 0.561114055795734], + [0.520891960189527, 0.633214068787356, 0.866980355399107, 0.967856711826989, 0.866980355399108, 0.633214068787355, 0.520891960189527], + [0.561114055795734, 0.595098001722719, 0.817986738735225, 0.997769685332234, 0.920071594222606, 0.718502389029630, 0.561114055795734], + [0.642772279126891, 0.638233465781766, 0.822941521630497, 1.036192879128092, 1.009506601358511, 0.810075234122540, 0.642772279126891], + [0.732357468770512, 0.732423846297739, 0.914652536061019, 1.149372447382608, 1.100038034467113, 0.887635027604753, 0.732357468770512], + [0.777048118791033, 0.850059335051268, 1.058251880937882, 1.238755906102585, 1.058251880937882, 0.850059335051267, 0.777048118791033], + ]) + + np.testing.assert_allclose(np.squeeze(data.L_grad_B), matlab_data, rtol=7e-3) + + # Trace of the grad \vec{B} tensor is div(B), which should be 0. + div_B = data.grad_B__XX + data.grad_B__YY + data.grad_B__ZZ + np.testing.assert_allclose(div_B, 0, atol=4e-4) + + def test_L_grad_B_axisymmetry(self): + """ + For a purely toroidal magnetic field, L_{grad B} should equal the major radius. + """ + vmec = Vmec(os.path.join(TEST_DIR, "wout_purely_toroidal_field_reference.nc")) + + s = 1.0 + ntheta = 50 + nphi = 4 + theta = np.linspace(0, 2 * np.pi, ntheta, endpoint=True) + phi = np.linspace(0, 2 * np.pi / vmec.wout.nfp, nphi, endpoint=True) + + data = vmec_compute_geometry(vmec, s, theta, phi) + np.testing.assert_allclose(data.L_grad_B, data.R, rtol=1e-5) + + # Trace of the grad \vec{B} tensor is div(B), which should be 0. + div_B = data.grad_B__XX + data.grad_B__YY + data.grad_B__ZZ + np.testing.assert_allclose(div_B, 0, atol=3e-11) + class VmecFieldlinesTests(unittest.TestCase): def test_fieldline_grids(self): diff --git a/tests/test_files/input.purely_toroidal_field b/tests/test_files/input.purely_toroidal_field new file mode 100644 index 000000000..343d885d3 --- /dev/null +++ b/tests/test_files/input.purely_toroidal_field @@ -0,0 +1,37 @@ +! DSHAPE tokamak boundary shape from Hirshman and Whitson 1983, but with no pressure and iota ~ 0. +&INDATA + MGRID_FILE = 'NONE ' + LOPTIM = F + LSPECTRUM_DUMP = F + DELT = 0.9 + TCON0 = 2. + NFP = 1 + MPOL = 6 + NTOR = 0 + +! NS_ARRAY = 13 25 51 +! FTOL_ARRAY = 1e-20 1e-20 1e-11 +! NITER_ARRAY = 1000 1500 2000 + + NS_ARRAY = 13 25 51 101 + FTOL_ARRAY = 1e-20 1e-20 1e-20 1e-15 + NITER_ARRAY = 1000 1500 2000 30000 + +! NS_ARRAY = 13 25 51 101 150 201 +! FTOL_ARRAY = 1e-20 1e-20 1e-20 1e-20 1e-20 1e-14 +! NITER_ARRAY = 1000 1500 2000 2500 3000 30000 + + NSTEP = 200 + NVACSKIP = 3 + GAMMA = 0.00000000E+00 + PHIEDGE = 5.0 + CURTOR = 1.0 + SPRES_PED = 1.0000E+00 + NCURR = 0 + AM = 0.0 + AI = 1.0e-6 ! 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a/docs/source/containers.rst b/docs/source/containers.rst index a9f28effd..9bc0043f0 100644 --- a/docs/source/containers.rst +++ b/docs/source/containers.rst @@ -130,7 +130,7 @@ issues associated with Docker containers. Shifter allows to you use the simsopt Docker image files hosted on Docker Hub. Detailed instructions for using Shifter can be found at the `NERSC page on the simsopt wiki -`_. +`_. .. _singularity_doc: From 504af282da2969bb944569824b380e2ad141486e Mon Sep 17 00:00:00 2001 From: Chris Date: Wed, 12 Jun 2024 16:57:27 +0200 Subject: [PATCH 132/176] updated test coverage and getter-setters in NormalField --- src/simsopt/field/normal_field.py | 129 +++++++++++++++++++----------- src/simsopt/geo/surface.py | 2 +- src/simsopt/mhd/spec.py | 2 +- tests/field/test_normal_field.py | 48 +++++++++++ 4 files changed, 133 insertions(+), 48 deletions(-) diff --git a/src/simsopt/field/normal_field.py b/src/simsopt/field/normal_field.py index 9adb3f18e..5a52427ba 100644 --- a/src/simsopt/field/normal_field.py +++ b/src/simsopt/field/normal_field.py @@ -14,6 +14,7 @@ __all__ = ['NormalField'] + class NormalField(Optimizable): r""" ``NormalField`` represents the magnetic field normal to a toroidal surface, for example the @@ -23,8 +24,10 @@ class NormalField(Optimizable): the normal component of an externally provided field. The Fourier harmonics are the degees of freedom, the computational boundary is kept fixed. - The normal field should not be normalized to unit area, i.e. it is the - fourier components of B.(\grad\theta \times \nabla\zeta) on the surface. + The Fourier harmonics are stored in the SPEC convention, + i.e. it is the + fourier components of B.(\partial\vec{r}/ \partial\theta \times \partial\vec{r}/ \partial\zeta) on the surface with a 1/(2\pi)^2 + Fourier normalization factor. Args: nfp: The number of field period @@ -43,7 +46,7 @@ class NormalField(Optimizable): """ def __init__(self, nfp=1, stellsym=True, mpol=1, ntor=0, - vns=None, vnc=None, computational_boundary=None): + vns=None, vnc=None, surface=None): self.nfp = nfp self.stellsym = stellsym @@ -56,11 +59,11 @@ def __init__(self, nfp=1, stellsym=True, mpol=1, ntor=0, if not self.stellsym and vnc is None: vnc = np.zeros((self.mpol + 1, 2 * self.ntor + 1)) - if computational_boundary is None: + if surface is None: from simsopt.geo import SurfaceRZFourier - computational_boundary = SurfaceRZFourier(nfp=nfp, stellsym=stellsym, mpol=mpol, ntor=ntor) - computational_boundary.fix_all() - self.computational_boundary = computational_boundary + surface = SurfaceRZFourier(nfp=nfp, stellsym=stellsym, mpol=mpol, ntor=ntor) + surface.fix_all() + self.surface = surface if self.stellsym: self.ndof = self.ntor + self.mpol * (2 * self.ntor + 1) @@ -105,6 +108,7 @@ def from_spec(cls, filename): if py_spec is None: raise RuntimeError( "Initialization from Spec requires py_spec to be installed.") + from simsopt.geo import SurfaceRZFourier # Read Namelist nm = py_spec.SPECNamelist(filename) @@ -116,6 +120,15 @@ def from_spec(cls, filename): vnc = None else: vnc = np.asarray(ph['vnc']) + mpol = ph['Mpol'] + ntor = ph['Ntor'] + surface = SurfaceRZFourier(nfp=ph['nfp'], stellsym=bool(ph['istellsym']), mpol=mpol, ntor=ntor) + old_mpol = np.array(ph['rbc']).shape[1]//2 + surface.rc[:] = np.array(ph['rbc'])[:ntor+1, old_mpol-mpol:old_mpol+mpol+1] + surface.zs[:] = np.array(ph['zbs'])[:ntor+1, old_mpol-mpol:old_mpol+mpol+1] + if not ph['istellsym']: + surface.zc[:] = np.array(ph['zbc'])[:ntor+1, old_mpol-mpol:old_mpol+mpol+1] + surface.rs[:] = np.array(ph['rbs'])[:ntor+1, old_mpol-mpol:old_mpol+mpol+1] normal_field = cls( nfp=ph['nfp'], @@ -123,7 +136,8 @@ def from_spec(cls, filename): mpol=ph['Mpol'], ntor=ph['Ntor'], vns=vns, - vnc=vnc + vnc=vnc, + surface=surface ) return normal_field @@ -135,22 +149,18 @@ def from_spec_object(cls, spec): """ if not spec.freebound: raise ValueError('The given SPEC object is not free-boundary') - boundary_dict = {'specrc': spec.inputlist.rbc, - 'speczs': spec.inputlist.zbs} - if not spec.stellsym: - boundary_dict.append({'specrs': spec.inputlist.rbs, - 'speczc': spec.inputlist.zbc}) - computational_boundary = spec._specarrays_to_surfRZFourier(boundary_dict) + + surface = spec.computational_boundary # Grab all the attributes from the SPEC object into an input dictionary input_dict = {'nfp': spec.nfp, 'stellsym': spec.stellsym, 'mpol': spec.mpol, 'ntor': spec.ntor, - 'vns': spec.inputlist.vns, - 'computational_boundary': computational_boundary} + 'vns': spec.array_translator(spec.inputlist.vns).as_simsopt, + 'surface': surface} if not spec.stellsym: - input_dict.append({'vnc': spec.inputlist.vnc}) + input_dict.append({'vnc': spec.array_translator(spec.inputlist.vnc).as_simsopt}) normal_field = cls(**input_dict) @@ -181,7 +191,36 @@ def get_dofs(self): ii = self.get_index_in_dofs(mm, nn, even=True) dofs[ii] = self.vnc[mm, input_ntor+nn] return dofs - + + def get_index_in_array(self, m, n, mpol=None, ntor=None, even=False): + """ + Returns position of mode (m,n) in vns or vnc array + + Args: + - m: poloidal mode number + - n: toroidal mode number (normalized by Nfp) + - mpol: resolution of dofs array. If None (by default), use self.mpol + - ntor: resolution of dofs array. If None (by default), use self.ntor + - even: set to True to get vnc. Default is False + """ + + if mpol is None: + mpol = self.mpol + if ntor is None: + ntor = self.ntor + + if m < 0 or m > mpol: + raise ValueError('m out of bound') + if abs(n) > ntor: + raise ValueError('n out of bound') + if m == 0 and n < 0: + raise ValueError('n has to be positive if m==0') + if not even and m == 0 and n == 0: + raise ValueError('m=n=0 not supported for odd series') + + return [m, n+ntor] + + def get_index_in_dofs(self, m, n, mpol=None, ntor=None, even=False): """ Returns position of mode (m,n) in dofs array @@ -229,10 +268,10 @@ def get_vns(self, m, n): def set_vns(self, m, n, value): self.check_mn(m, n) - ii = self.get_index_in_dofs(m, n) - tmp = self.local_full_x - tmp[ii] = value - self.local_full_x = tmp + i,j = self.get_index_in_array(m, n) + self._vns[i,j] = value + dofs = self.get_dofs() + self.local_full_x = dofs def get_vnc(self, m, n): self.check_mn(m, n) @@ -244,13 +283,13 @@ def get_vnc(self, m, n): def set_vnc(self, m, n, value): self.check_mn(m, n) - ii = self.get_index_in_dofs(m, n, even=True) + i,j = self.get_index_in_array(m, n) if self.stellsym: raise ValueError('Stellarator symmetric has no vnc') else: - tmp = self.local_full_x - tmp[ii] = value - self.local_full_x = tmp + self._vnc[i,j] = value + dofs = self.get_dofs() + self.local_full_x = dofs def check_mn(self, m, n): if m < 0 or m > self.mpol: @@ -374,13 +413,9 @@ def get_vns_asarray(self, mpol=None, ntor=None): elif ntor > self.ntor: raise ValueError('ntor out of bound') - vns = np.zeros((mpol + 1, 2 * ntor + 1)) - for mm in range(0, mpol + 1): - for nn in range(-ntor, ntor + 1): - if mm == 0 and nn <= 0: continue - vns[mm, ntor + nn] = self.get_vns(mm, nn) + vns = self.vns - return vns + return vns[0:mpol, self.ntor-ntor:self.ntor+ntor+1] def get_vnc_asarray(self, mpol=None, ntor=None): """ @@ -396,15 +431,11 @@ def get_vnc_asarray(self, mpol=None, ntor=None): elif ntor > self.ntor: raise ValueError('ntor out of bound') - vnc = np.zeros((mpol + 1, 2 * ntor + 1)) - for mm in range(0, mpol + 1): - for nn in range(-ntor, ntor + 1): - if mm == 0 and nn < 0: continue - vnc[mm, ntor + nn] = self.get_vnc(mm, nn) + vnc = self.vns - return vnc + return vnc[0:mpol, self.ntor-ntor:self.ntor+ntor+1] - def get_vns_vnc_asarray(self, mpol, ntor): + def get_vns_vnc_asarray(self, mpol=None, ntor=None): """ Return the vns and vnc as two arrays single array """ @@ -435,11 +466,11 @@ def set_vns_asarray(self, vns, mpol=None, ntor=None): ntor = self.ntor elif ntor > self.ntor: raise ValueError('ntor out of bound') + + self._vns = vns[0:mpol, self.ntor-ntor:self.ntor+ntor+1] + dofs = self.get_dofs() + self.local_full_x = dofs - for mm in range(0, mpol + 1): - for nn in range(-ntor, ntor + 1): - if mm == 0 and nn <= 0: continue - self.set_vns(mm, nn, vns[mm, ntor + nn]) def set_vnc_asarray(self, vnc, mpol=None, ntor=None): """ @@ -454,6 +485,11 @@ def set_vnc_asarray(self, vnc, mpol=None, ntor=None): ntor = self.ntor elif ntor > self.ntor: raise ValueError('ntor out of bound') + + self._vnc = vnc[0:mpol, self.ntor-ntor:self.ntor+ntor+1] + dofs = self.get_dofs() + self.local_full_x = dofs + for mm in range(0, mpol + 1): for nn in range(-ntor, ntor + 1): @@ -475,15 +511,16 @@ def set_vns_vnc_asarray(self, vns, vnc, mpol=None, ntor=None): raise ValueError('ntor out of bound') self.set_vns_asarray(vns, mpol, ntor) + self.set_vnc_asarray(vnc, mpol, ntor) def get_real_space_field(self): """ Fourier transform the field and get the real-space values of the normal component of the externally provided field on the computational boundary. - The returned array will be of size specified by the computational boudary's SurfaceRZFourier quadpoints. + The returned array will be of size specified by the surfaces' quadpoints and located on the quadpoints. """ vns, vnc = self.get_vns_vnc_asarray(mpol=self.mpol, ntor=self.ntor) - BdotN_unnormalized = self.computational_boundary.inverse_fourier_transform_field(vns, vnc, normalization=(2*np.pi)**2, stellsym=self.stellsym) - normal_field_real_space = -1 * BdotN_unnormalized / np.linalg.norm(self.computational_boundary.normal(), axis=-1) + BdotN_unnormalized = self.surface.inverse_fourier_transform_field(vns, vnc, normalization=(2*np.pi)**2, stellsym=self.stellsym) + normal_field_real_space = -1 * BdotN_unnormalized / np.linalg.norm(self.surface.normal(), axis=-1) return normal_field_real_space diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index be0a40640..9665306d9 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -959,7 +959,7 @@ def inverse_fourier_transform_field(self, A_mns, A_mnc, normalization=None, **kw if not stellsym: field = field + A_mnc[0, ntor] if normalization is not None: - if isinstance(normalization, float): + if not isinstance(normalization, float): raise ValueError("normalization must be a float") field = field * normalization return field diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index 73ad8c714..524189a6f 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -233,7 +233,7 @@ def __init__(self, self._normal_field = NormalField(nfp=self.nfp, stellsym=self.stellsym, mpol=self.mpol, ntor=self.ntor, vns=vns.as_simsopt, vnc=vnc.as_simsopt, - computational_boundary=self._computational_boundary) + surface=self._computational_boundary) else: self._normal_field: Optional[NormalField] = None diff --git a/tests/field/test_normal_field.py b/tests/field/test_normal_field.py index ea639b563..b420c0b2c 100644 --- a/tests/field/test_normal_field.py +++ b/tests/field/test_normal_field.py @@ -93,9 +93,13 @@ def test_getter_setter(self): normal_field.set_vns(m=1, n=-1, value=1) self.assertEqual(normal_field.get_vns(m=1, n=-1), 1) + i, j = normal_field.get_index_in_array(m=1, n=-1) + self.assertEqual(normal_field.vns[i, j], 1) normal_field.set_vnc(m=2, n=1, value=0.5) self.assertEqual(normal_field.get_vnc(m=2, n=1), 0.5) + i, j = normal_field.get_index_in_array(m=2, n=1) + self.assertEqual(normal_field.vnc[i, j], 0.5) def test_check_mn(self): """ @@ -208,3 +212,47 @@ def test_fixed_range(self): self.assertTrue(normal_field.is_fixed(ii)) else: self.assertTrue(normal_field.is_free(ii)) + + @unittest.skipIf(py_spec is None, "py_spec not found") + def test_from_spec_object(self): + """ + test classmethod to instantiate from an existing SPEC object + """ + from simsopt.mhd import Spec + # Init from SPEC input file + filename = os.path.join(TEST_DIR, 'Dommaschk.sp') + spec = Spec(filename) + normal_field = NormalField.from_spec_object(spec) + normal_field_2 = NormalField.from_spec(filename) + + self.assertAlmostEqual(normal_field.get_vns(m=3, n=-1), 1.71466651E-03) + self.assertAlmostEqual(normal_field.get_vns(m=5, n=1), -3.56991494E-05) + + self.assertTrue(np.allclose(normal_field.local_full_x, normal_field_2.local_full_x)) + + @unittest.skipIf(py_spec is None, "py_spec not found") + def test_get_set_vns_vnc_asarray(self): + """ + test the array-wise getter and setter functions for the + Vns and Vnc arrays + """ + filename = os.path.join(TEST_DIR, 'Dommaschk.sp') + normal_field = NormalField.from_spec(filename) + vns = normal_field.get_vns_asarray() + vnc = normal_field.get_vnc_asarray() + vns2, vnc2 = normal_field.get_vns_vnc_asarray() + self.assertTrue(np.allclose(vns, vns2)) + self.assertTrue(np.allclose(vnc, vnc2)) + vns3 = np.copy(vnc) + + @unittest.skipIf(py_spec is None, "py_spec not found") + def test_get_real_space_field(self): + """ + test the conversion to real space + """ + filename = os.path.join(TEST_DIR, 'Dommaschk.sp') + + normal_field = NormalField.from_spec(filename) + real_space_field = normal_field.get_real_space_field() + self.assertTrue(real_space_field is not None) + self.assertTrue(real_space_field.shape == normal_field.surface.get_quadpoints().shape) \ No newline at end of file From 59877c146a37fe815480e62433b7342ddfac2c30 Mon Sep 17 00:00:00 2001 From: Chris Date: Thu, 13 Jun 2024 13:37:03 +0200 Subject: [PATCH 133/176] make Surface's get_quadpoints staticmethods --- src/simsopt/geo/surface.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index 9665306d9..182c687fe 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -75,7 +75,7 @@ def from_nphi_ntheta(cls, nphi=61, ntheta=62, range="full torus", nfp=1, nphi, ntheta, nfp=nfp, range=range) return cls(quadpoints_phi=quadpoints_phi, quadpoints_theta=quadpoints_theta, nfp=nfp, **kwargs) - + @staticmethod def get_quadpoints(nphi=None, ntheta=None, range=None, @@ -109,7 +109,7 @@ def get_quadpoints(nphi=None, """ return (Surface.get_phi_quadpoints(nphi=nphi, range=range, nfp=nfp), Surface.get_theta_quadpoints(ntheta=ntheta)) - + @staticmethod def get_theta_quadpoints(ntheta=None): r""" Sets the theta grid points for Surface subclasses. @@ -124,7 +124,7 @@ def get_theta_quadpoints(ntheta=None): if ntheta is None: ntheta = 62 return list(np.linspace(0.0, 1.0, ntheta, endpoint=False)) - + @staticmethod def get_phi_quadpoints(nphi=None, range=None, nfp=1): r""" Sets the phi grid points for Surface subclasses. From 9e4ab7d096225ae905cf1ec10314981d6874fb14 Mon Sep 17 00:00:00 2001 From: Chris Date: Thu, 13 Jun 2024 13:45:32 +0200 Subject: [PATCH 134/176] test transformation to real space --- tests/field/test_normal_field.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/field/test_normal_field.py b/tests/field/test_normal_field.py index b420c0b2c..3c596bf37 100644 --- a/tests/field/test_normal_field.py +++ b/tests/field/test_normal_field.py @@ -255,4 +255,4 @@ def test_get_real_space_field(self): normal_field = NormalField.from_spec(filename) real_space_field = normal_field.get_real_space_field() self.assertTrue(real_space_field is not None) - self.assertTrue(real_space_field.shape == normal_field.surface.get_quadpoints().shape) \ No newline at end of file + self.assertEqual(real_space_field.shape, (normal_field.surface.quadpoints_phi.size, normal_field.surface.quadpoints_theta.size)) \ No newline at end of file From 5b440ab0edd69205909132b9e7b076d86487ab0e Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 14 Jun 2024 10:06:09 +0200 Subject: [PATCH 135/176] move fourier transformation to surfaceRZFourier class --- src/simsopt/geo/surface.py | 8 +- src/simsopt/geo/surfacerzfourier.py | 126 ++++++++++++++++++++++++++++ 2 files changed, 132 insertions(+), 2 deletions(-) diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index 182c687fe..f60af1761 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -75,6 +75,7 @@ def from_nphi_ntheta(cls, nphi=61, ntheta=62, range="full torus", nfp=1, nphi, ntheta, nfp=nfp, range=range) return cls(quadpoints_phi=quadpoints_phi, quadpoints_theta=quadpoints_theta, nfp=nfp, **kwargs) + @staticmethod def get_quadpoints(nphi=None, ntheta=None, @@ -109,6 +110,7 @@ def get_quadpoints(nphi=None, """ return (Surface.get_phi_quadpoints(nphi=nphi, range=range, nfp=nfp), Surface.get_theta_quadpoints(ntheta=ntheta)) + @staticmethod def get_theta_quadpoints(ntheta=None): r""" @@ -124,6 +126,7 @@ def get_theta_quadpoints(ntheta=None): if ntheta is None: ntheta = 62 return list(np.linspace(0.0, 1.0, ntheta, endpoint=False)) + @staticmethod def get_phi_quadpoints(nphi=None, range=None, nfp=1): r""" @@ -868,8 +871,8 @@ def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=Non - A_mnc: 2D array of shape (mpol+1, 2*ntor+1) containing the cosine coefficients (these are zero if the surface is stellarator symmetric) """ - assert field.shape[0] == self.quadpoints_phi.size,"Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) - assert field.shape[1] == self.quadpoints_theta.size,"Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) + assert field.shape[0] == self.quadpoints_phi.size, "Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) + assert field.shape[1] == self.quadpoints_theta.size, "Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) stellsym = kwargs.pop('stellsym', self.stellsym) if mpol is None: try: mpol = self.mpol @@ -964,6 +967,7 @@ def inverse_fourier_transform_field(self, A_mns, A_mnc, normalization=None, **kw field = field * normalization return field + def signed_distance_from_surface(xyz, surface): """ Compute the signed distances from points ``xyz`` to a surface. The sign is diff --git a/src/simsopt/geo/surfacerzfourier.py b/src/simsopt/geo/surfacerzfourier.py index 391da4f47..ac5e6cb5f 100644 --- a/src/simsopt/geo/surfacerzfourier.py +++ b/src/simsopt/geo/surfacerzfourier.py @@ -637,6 +637,132 @@ def write_nml(self, filename: str): with open(filename, 'w') as f: f.write(self.get_nml()) + def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=None, **kwargs): + r""" + Compute the Fourier components of a field on the surface. The field + is evaluated at the quadrature points on the surface. + The Fourier uses the conventions of the FourierRZSurface series, + with `npol` going from `-ntor` to `ntor` and `mpol` from 0 to `mpol` + i.e.: + :math:`f(\theta, \phi) = \Sum_{m=0}^{mpol} \Sum_{n=-npol}^{npol} A^{mn}_s \sin(m\theta - n*Nfp*\phi)\\ + + A^{mn}_c \cos(m\theta - n*Nfp*\phi)` + Where the cosine series is only evaluated if the surface is not stellarator + symmetric (if the field does not adhere to the symmetry of the surface, + request the cosine series by setting the kwarg stellsym=False) + By default, the poloidal and toroidal resolution are the same as those of the surface, but different quantities can be specified in the kwargs. + *Arguments*: + - field: 2D array of shape (numquadpoints_phi, numquadpoints_theta). + - mpol: maximum poloidal mode number of the transform, if None, + the mpol attribute of the surface is used. + - ntor: maximum toroidal mode number of the transform if None, + the ntor attribute of the surface is used. + *Optional keyword arguments*: + - normalization: Fourier transform normalization. Can be: + None: forward and back transform are not normalized + float: forward transform is divided by this number + - stellsym: boolean to override the stellsym attribute + of the surface if you want to force the calculation of the cosine series + *Returns*: + - A_mns: 2D array of shape (mpol+1, 2*ntor+1) containing the sine coefficients + - A_mnc: 2D array of shape (mpol+1, 2*ntor+1) containing the cosine coefficients + (these are zero if the surface is stellarator symmetric) + """ + assert field.shape[0] == self.quadpoints_phi.size, "Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) + assert field.shape[1] == self.quadpoints_theta.size, "Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) + stellsym = kwargs.pop('stellsym', self.stellsym) + if mpol is None: + try: mpol = self.mpol + except AttributeError: raise ValueError("mpol must be specified") + if ntor is None: + try: ntor = self.ntor + except AttributeError: raise ValueError("ntor must be specified") + A_mns = np.zeros((int(mpol + 1), int(2 * ntor + 1))) # sine coefficients + A_mnc = np.zeros((int(mpol + 1), int(2 * ntor + 1))) # cosine coefficients + ntheta_grid = len(self.quadpoints_theta) + nphi_grid = len(self.quadpoints_phi) + + factor = 2.0 / (ntheta_grid * nphi_grid) + + phi2d, theta2d = np.meshgrid(2 * np.pi * self.quadpoints_phi, + 2 * np.pi * self.quadpoints_theta, + indexing="ij") + + for m in range(mpol + 1): + nmin = -ntor + if m == 0: nmin = 1 + for n in range(nmin, ntor+1): + angle = m * theta2d - n * self.nfp * phi2d + sinangle = np.sin(angle) + if not stellsym: + cosangle = np.cos(angle) + factor2 = factor + # The next 2 lines ensure inverse Fourier transform(Fourier transform) = identity + if np.mod(ntheta_grid, 2) == 0 and m == (ntheta_grid/2): factor2 = factor2 / 2 + if np.mod(nphi_grid, 2) == 0 and abs(n) == (nphi_grid/2): factor2 = factor2 / 2 + A_mns[m, n + ntor] = np.sum(field * sinangle * factor2) + if not stellsym: + A_mnc[m, n + ntor] = np.sum(field * cosangle * factor2) + + if not stellsym: + A_mnc[0, ntor] = np.sum(field) / (ntheta_grid * nphi_grid) + if normalization is not None: + if isinstance(normalization, float): + raise ValueError("normalization must be a float") + A_mns = A_mns / normalization + A_mnc = A_mnc / normalization + + return A_mns, A_mnc + + def inverse_fourier_transform_scalar(self, A_mns, A_mnc, normalization=None, **kwargs): + r""" + Compute the inverse Fourier transform of a scalar on the surface, specified by the Fourier coefficients. The quantity must be + is evaluated at the quadrature points on the surface. The Fourier + transform is defined as + :math:`f(\theta, \phi) = \Sum_{m=0}^{mpol} \Sum_{n=-npol}^{npol} A^{mn}_s \sin(m\theta - n*Nfp*\phi)\\ + + A^{mn}_c \cos(m\theta - n*Nfp*\phi)` + Where the cosine series is only evaluated if the surface is not stellarator + symmetric. + *Arguments*: + - A_mns: 2D array of shape (mpol+1, 2*ntor+1) containing the sine coefficients + - A_mnc: 2D array of shape (mpol+1, 2*ntor+1) containing the cosine coefficients + (these are zero if the surface is stellarator symmetric) + *Optional keyword arguments*: + - normalization: Fourier transform normalization. Can be: + None: forward and back transform are not normalized + float: inverse transform is multiplied by this number + - stellsym: boolean to override the stellsym attribute of the surface + """ + mpol = A_mns.shape[0] - 1 + ntor = int((A_mns.shape[1] - 1) / 2) + stellsym = kwargs.pop('stellsym', self.stellsym) + ntheta_grid = len(self.quadpoints_theta) + nphi_grid = len(self.quadpoints_phi) + + phi2d, theta2d = np.meshgrid(2 * np.pi * self.quadpoints_phi, + 2 * np.pi * self.quadpoints_theta, + indexing="ij") + + scalars = np.zeros((nphi_grid, ntheta_grid)) + for m in range(mpol + 1): + nmin = -ntor + if m == 0: nmin = 1 + for n in range(nmin, ntor+1): + angle = m * theta2d - n * self.nfp * phi2d + sinangle = np.sin(angle) + if not stellsym: + cosangle = np.cos(angle) + scalars = scalars + A_mns[m, n + ntor] * sinangle + if not stellsym: + scalars = scalars + A_mnc[m, n + ntor] * cosangle + + if not stellsym: + scalars = scalars + A_mnc[0, ntor] + if normalization is not None: + if not isinstance(normalization, float): + raise ValueError("normalization must be a float") + scalars = scalars * normalization + return scalars + def make_rotating_ellipse(self, major_radius, minor_radius, elongation, torsion=0): """ Set the surface shape to be a rotating ellipse with the given From 13967467855df906648e922a0f728d3a2ec73113 Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 14 Jun 2024 10:08:49 +0200 Subject: [PATCH 136/176] change name field to scalar in fourier transform --- src/simsopt/geo/surfacerzfourier.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/simsopt/geo/surfacerzfourier.py b/src/simsopt/geo/surfacerzfourier.py index ac5e6cb5f..c0d492f28 100644 --- a/src/simsopt/geo/surfacerzfourier.py +++ b/src/simsopt/geo/surfacerzfourier.py @@ -637,9 +637,9 @@ def write_nml(self, filename: str): with open(filename, 'w') as f: f.write(self.get_nml()) - def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=None, **kwargs): + def fourier_transform_scalar(self, scalar, mpol=None, ntor=None, normalization=None, **kwargs): r""" - Compute the Fourier components of a field on the surface. The field + Compute the Fourier components of a scalar on the surface. The scalar is evaluated at the quadrature points on the surface. The Fourier uses the conventions of the FourierRZSurface series, with `npol` going from `-ntor` to `ntor` and `mpol` from 0 to `mpol` @@ -647,11 +647,11 @@ def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=Non :math:`f(\theta, \phi) = \Sum_{m=0}^{mpol} \Sum_{n=-npol}^{npol} A^{mn}_s \sin(m\theta - n*Nfp*\phi)\\ + A^{mn}_c \cos(m\theta - n*Nfp*\phi)` Where the cosine series is only evaluated if the surface is not stellarator - symmetric (if the field does not adhere to the symmetry of the surface, + symmetric (if the scalar does not adhere to the symmetry of the surface, request the cosine series by setting the kwarg stellsym=False) By default, the poloidal and toroidal resolution are the same as those of the surface, but different quantities can be specified in the kwargs. *Arguments*: - - field: 2D array of shape (numquadpoints_phi, numquadpoints_theta). + - scalar: 2D array of shape (numquadpoints_phi, numquadpoints_theta). - mpol: maximum poloidal mode number of the transform, if None, the mpol attribute of the surface is used. - ntor: maximum toroidal mode number of the transform if None, @@ -667,8 +667,8 @@ def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=Non - A_mnc: 2D array of shape (mpol+1, 2*ntor+1) containing the cosine coefficients (these are zero if the surface is stellarator symmetric) """ - assert field.shape[0] == self.quadpoints_phi.size, "Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) - assert field.shape[1] == self.quadpoints_theta.size, "Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) + assert scalar.shape[0] == self.quadpoints_phi.size, "scalar must be evaluated at the quadrature points on the surface.\n the scalar you passed in has shape {}".format(scalar.shape) + assert scalar.shape[1] == self.quadpoints_theta.size, "scalar must be evaluated at the quadrature points on the surface.\n the scalar you passed in has shape {}".format(scalar.shape) stellsym = kwargs.pop('stellsym', self.stellsym) if mpol is None: try: mpol = self.mpol @@ -699,12 +699,12 @@ def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=Non # The next 2 lines ensure inverse Fourier transform(Fourier transform) = identity if np.mod(ntheta_grid, 2) == 0 and m == (ntheta_grid/2): factor2 = factor2 / 2 if np.mod(nphi_grid, 2) == 0 and abs(n) == (nphi_grid/2): factor2 = factor2 / 2 - A_mns[m, n + ntor] = np.sum(field * sinangle * factor2) + A_mns[m, n + ntor] = np.sum(scalar * sinangle * factor2) if not stellsym: - A_mnc[m, n + ntor] = np.sum(field * cosangle * factor2) + A_mnc[m, n + ntor] = np.sum(scalar * cosangle * factor2) if not stellsym: - A_mnc[0, ntor] = np.sum(field) / (ntheta_grid * nphi_grid) + A_mnc[0, ntor] = np.sum(scalar) / (ntheta_grid * nphi_grid) if normalization is not None: if isinstance(normalization, float): raise ValueError("normalization must be a float") From 9b3f626d4c5d8a66932e4f95873a092d52e1dd11 Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 14 Jun 2024 13:43:33 +0200 Subject: [PATCH 137/176] add tests and Matt's improvements --- src/simsopt/geo/surfacerzfourier.py | 6 ++-- src/simsopt/mhd/spec.py | 4 +-- tests/geo/test_surface_rzfourier.py | 6 +--- tests/mhd/test_spec.py | 46 +++++++++++++++++++++++++++-- 4 files changed, 49 insertions(+), 13 deletions(-) diff --git a/src/simsopt/geo/surfacerzfourier.py b/src/simsopt/geo/surfacerzfourier.py index c0d492f28..f66a5c304 100644 --- a/src/simsopt/geo/surfacerzfourier.py +++ b/src/simsopt/geo/surfacerzfourier.py @@ -693,14 +693,13 @@ def fourier_transform_scalar(self, scalar, mpol=None, ntor=None, normalization=N for n in range(nmin, ntor+1): angle = m * theta2d - n * self.nfp * phi2d sinangle = np.sin(angle) - if not stellsym: - cosangle = np.cos(angle) factor2 = factor # The next 2 lines ensure inverse Fourier transform(Fourier transform) = identity if np.mod(ntheta_grid, 2) == 0 and m == (ntheta_grid/2): factor2 = factor2 / 2 if np.mod(nphi_grid, 2) == 0 and abs(n) == (nphi_grid/2): factor2 = factor2 / 2 A_mns[m, n + ntor] = np.sum(scalar * sinangle * factor2) if not stellsym: + cosangle = np.cos(angle) A_mnc[m, n + ntor] = np.sum(scalar * cosangle * factor2) if not stellsym: @@ -749,10 +748,9 @@ def inverse_fourier_transform_scalar(self, A_mns, A_mnc, normalization=None, **k for n in range(nmin, ntor+1): angle = m * theta2d - n * self.nfp * phi2d sinangle = np.sin(angle) - if not stellsym: - cosangle = np.cos(angle) scalars = scalars + A_mns[m, n + ntor] * sinangle if not stellsym: + cosangle = np.cos(angle) scalars = scalars + A_mnc[m, n + ntor] * cosangle if not stellsym: diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index 524189a6f..53d0075da 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -749,7 +749,7 @@ def activate_profile(self, longname): longname: string, either - 'pressure' - 'volume_current' - - 'surface_current' + - 'interface_current' - 'iota' - 'oita' - 'mu' @@ -1071,7 +1071,7 @@ def run(self, update_guess: bool = True): logger.debug('About to call check_inputs') spec.allglobal.check_inputs() logger.debug('About to call broadcast_inputs') - self.mpi.comm_groups.Barrier() # wait for + self.mpi.comm_groups.Barrier() # Barrier to ensure all groups are ready to broadcast. spec.allglobal.broadcast_inputs() logger.debug('About to call preset') spec.preset() diff --git a/tests/geo/test_surface_rzfourier.py b/tests/geo/test_surface_rzfourier.py index ba1ab871d..237f26b16 100755 --- a/tests/geo/test_surface_rzfourier.py +++ b/tests/geo/test_surface_rzfourier.py @@ -748,11 +748,7 @@ def test_fourier_transform_field(self): # create a test field where only Fourier elements [m=2, n=3] # and [m=4,n=5] are nonzero: - field = [] - for phi, theta in zip(phi2d.flatten(), theta2d.flatten()): - field.append(0.8 * np.sin(2*theta - 3*s.nfp*phi) + 0.2*np.sin(4*theta - 5*s.nfp*phi) - + 0.7*np.cos(3*theta - 3*s.nfp*phi)) - field = np.array(field).reshape(phi2d.shape) + field = field = 0.8 * np.sin(2*theta2d - 3*s.nfp*phi2d) + 0.2*np.sin(4*theta2d - 5*s.nfp*phi2d)+ 0.7*np.cos(3*theta2d - 3*s.nfp*phi2d) # Transform the field to Fourier space: ft_sines, ft_cosines = s.fourier_transform_field(field, stellsym=False) diff --git a/tests/mhd/test_spec.py b/tests/mhd/test_spec.py index 97afee740..89ccb1a30 100755 --- a/tests/mhd/test_spec.py +++ b/tests/mhd/test_spec.py @@ -195,7 +195,42 @@ def test_set_profile_cumulative(self): self.assertEqual(s.get_profile('volume_current', lvol), 0) else: self.assertEqual(s.get_profile('volume_current', lvol), 1) - + + def test_activate_profiles(self): + """ + test activate all profiles and confirm that DOFs are + correctly added + """ + profiles = ['pressure', + 'volume_current', + 'interface_current', + 'iota', + 'oita', + 'mu', + 'pflux', + 'tflux', + 'helicity'] + + for profile in profiles: + with ScratchDir("."): + s = Spec.default_freeboundary(copy_to_pwd=True) + startdofs = len(s.x) + self.assertIsNone(s.__getattribute__(profile+'_profile')) + s.activate_profile(profile) + self.assertIsNotNone(s.__getattribute__(profile+'_profile')) + if profile in ['tflux', 'pflux', 'mu', 'oita', 'iota', 'helicity']: + # test that the 'mvol' length profiles have been increased by two + self.assertEqual(len(s.x), startdofs+2) + elif profile in ['volume_current', 'pressure']: + # test that the 'nvol' length profiles have been increased by one + self.assertEqual(len(s.x), startdofs+1) + elif profile in ['interface_current']: + # test that the surface current profile has not been increased + self.assertEqual(len(s.x), startdofs) + else: + raise ValueError(f"Profile {profile} not recognized") + + def test_freeboundary_default(self): """ test the default freeboundary file, and re-set if Picard @@ -233,7 +268,6 @@ def test_array_translator(self): translator = spec.array_translator(array) translator2 = spec.array_translator(array, style='spec') translator3 = spec.array_translator(translator.as_simsopt, style='simsopt') - #assert that translator.as_spec i self.assertTrue(np.alltrue(array == translator.as_spec)) self.assertTrue(np.alltrue(array == translator2.as_spec)) @@ -243,6 +277,14 @@ def test_array_translator(self): # test that the shape of the array is correct: self.assertEqual(translator2.as_simsopt.shape, (spec.inputlist.ntor+1, (2*spec.inputlist.mpol)+1)) + def test_poloidal_current_amperes(self): + """ + Test the poloidal current in amperes + """ + from scipy.constants import mu_0 + filename = os.path.join(TEST_DIR, 'RotatingEllipse_Nvol8.sp') + s = Spec(filename) + self.assertAlmostEqual(s.poloidal_current_amperes(), s.inputlist.curpol/mu_0) def test_integrated_stellopt_scenarios_1dof(self): """ From 9f28499619423f012579fc55a84f058afa62e2b2 Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 14 Jun 2024 13:45:39 +0200 Subject: [PATCH 138/176] read intial guess based on Linitialize not array presence (f90wrap persists in tests) --- src/simsopt/mhd/spec.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index 53d0075da..ba6567e2f 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -160,8 +160,8 @@ def __init__(self, # Store initial guess data # The initial guess is a collection of SurfaceRZFourier instances, # stored in a list of size Mvol-1 (the number of inner interfaces) - initial_guess_present = bool(self.allglobal.num_modes > 0 and self.nvol > 1) - if initial_guess_present: + read_initial_guess = self.inputlist.linitialize <= 0 + if read_initial_guess: self.initial_guess = self._read_initial_guess() # In general, initial guess is NOT a degree of freedom for the # optimization - we thus fix them. From b177ce8489346d5a1ac4415ac9f160d34a432e4a Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 14 Jun 2024 14:10:31 +0200 Subject: [PATCH 139/176] FIX SPORADIC SPEC FAIL --- src/simsopt/mhd/spec.py | 2 +- tests/mhd/test_spec.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index ba6567e2f..d5e10ba18 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -160,7 +160,7 @@ def __init__(self, # Store initial guess data # The initial guess is a collection of SurfaceRZFourier instances, # stored in a list of size Mvol-1 (the number of inner interfaces) - read_initial_guess = self.inputlist.linitialize <= 0 + read_initial_guess = self.inputlist.linitialize == 0 and self.nvol > 1 if read_initial_guess: self.initial_guess = self._read_initial_guess() # In general, initial guess is NOT a degree of freedom for the diff --git a/tests/mhd/test_spec.py b/tests/mhd/test_spec.py index 89ccb1a30..8aab9e696 100755 --- a/tests/mhd/test_spec.py +++ b/tests/mhd/test_spec.py @@ -284,7 +284,7 @@ def test_poloidal_current_amperes(self): from scipy.constants import mu_0 filename = os.path.join(TEST_DIR, 'RotatingEllipse_Nvol8.sp') s = Spec(filename) - self.assertAlmostEqual(s.poloidal_current_amperes(), s.inputlist.curpol/mu_0) + self.assertAlmostEqual(s.poloidal_current_amperes, s.inputlist.curpol/mu_0) def test_integrated_stellopt_scenarios_1dof(self): """ From a45278bce3ebb5bfb64e68b09c945e309e88f212 Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 14 Jun 2024 14:50:36 +0200 Subject: [PATCH 140/176] fix lint and expand test --- tests/field/test_normal_field.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/tests/field/test_normal_field.py b/tests/field/test_normal_field.py index 3c596bf37..93350a996 100644 --- a/tests/field/test_normal_field.py +++ b/tests/field/test_normal_field.py @@ -244,6 +244,12 @@ def test_get_set_vns_vnc_asarray(self): self.assertTrue(np.allclose(vns, vns2)) self.assertTrue(np.allclose(vnc, vnc2)) vns3 = np.copy(vnc) + i, j = normal_field.get_index_in_array(m=3, n=-1) + vns3[i, j] = 0.5 + normal_field.set_vns_asarray(vns3) + self.assertEqual(normal_field.get_vns(m=3, n=-1), 0.5) + dof_index = normal_field.get_index_in_dofs(m=3, n=-1) + self.assertEqual(normal_field.local_full_x[dof_index], 0.5) @unittest.skipIf(py_spec is None, "py_spec not found") def test_get_real_space_field(self): From f8d8e5dcc5b6426448772a079ea8c40df3a966d8 Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Sun, 16 Jun 2024 07:35:55 -0400 Subject: [PATCH 141/176] Add libxrender1 to containers for mayavi --- .github/workflows/singularity.yml | 1 + ci/Dockerfile.ubuntu | 2 +- ci/singularity.def | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/singularity.yml b/.github/workflows/singularity.yml index 55f686e49..809197d44 100644 --- a/.github/workflows/singularity.yml +++ b/.github/workflows/singularity.yml @@ -12,6 +12,7 @@ on: # Do the builds on all pull requests (to test them) pull_request: [] + workflow_dispatch: jobs: build-containers: diff --git a/ci/Dockerfile.ubuntu b/ci/Dockerfile.ubuntu index ee7fbfbfa..4c8c7d06c 100644 --- a/ci/Dockerfile.ubuntu +++ b/ci/Dockerfile.ubuntu @@ -5,7 +5,7 @@ FROM --platform=linux/amd64 ubuntu:22.04 as intermediate RUN apt update && \ DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential gfortran git m4 wget cmake ninja-build \ libopenblas-dev libfftw3-dev libhdf5-dev libhdf5-serial-dev libnetcdf-dev libnetcdff-dev libgl1-mesa-dev \ - python3-dev python3-pip python3-venv + python3-dev python3-pip python3-venv libxrender1 # Install mpich manually WORKDIR /src diff --git a/ci/singularity.def b/ci/singularity.def index 03ddd49f5..c070fddb1 100644 --- a/ci/singularity.def +++ b/ci/singularity.def @@ -8,7 +8,7 @@ Stage: devel libfabric-dev libfabric-bin \ libhwloc-dev libpmix-dev libevent-dev \ libopenblas-dev libfftw3-dev libhdf5-dev libhdf5-serial-dev libnetcdf-dev libnetcdff-dev libgl1-mesa-dev \ - python3-dev python3-pip python3-venv + python3-dev python3-pip python3-venv libxrender1 %post From cac8b20c5786cb2e23b816a27a21bb429aafb284 Mon Sep 17 00:00:00 2001 From: Chris Date: Mon, 17 Jun 2024 15:54:56 +0200 Subject: [PATCH 142/176] test non-stellarator-symmetric-dof-setters --- src/simsopt/field/normal_field.py | 19 +++++-------------- tests/field/test_normal_field.py | 10 +++++++++- 2 files changed, 14 insertions(+), 15 deletions(-) diff --git a/src/simsopt/field/normal_field.py b/src/simsopt/field/normal_field.py index 5a52427ba..97369e75a 100644 --- a/src/simsopt/field/normal_field.py +++ b/src/simsopt/field/normal_field.py @@ -100,8 +100,6 @@ def vnc(self): def from_spec(cls, filename): """ Initialize using the harmonics in SPEC input file - WARNING: A normal field initialized with this method will - not have a computational boundary """ # Test if py_spec is available @@ -123,12 +121,12 @@ def from_spec(cls, filename): mpol = ph['Mpol'] ntor = ph['Ntor'] surface = SurfaceRZFourier(nfp=ph['nfp'], stellsym=bool(ph['istellsym']), mpol=mpol, ntor=ntor) - old_mpol = np.array(ph['rbc']).shape[1]//2 - surface.rc[:] = np.array(ph['rbc'])[:ntor+1, old_mpol-mpol:old_mpol+mpol+1] - surface.zs[:] = np.array(ph['zbs'])[:ntor+1, old_mpol-mpol:old_mpol+mpol+1] + old_ntor = np.array(ph['rbc']).shape[1]//2 + surface.rc[:] = np.array(ph['rbc'])[:mpol+1, old_ntor-ntor:old_ntor+ntor+1] + surface.zs[:] = np.array(ph['zbs'])[:mpol+1, old_ntor-ntor:old_ntor+ntor+1] if not ph['istellsym']: - surface.zc[:] = np.array(ph['zbc'])[:ntor+1, old_mpol-mpol:old_mpol+mpol+1] - surface.rs[:] = np.array(ph['rbs'])[:ntor+1, old_mpol-mpol:old_mpol+mpol+1] + surface.zc[:] = np.array(ph['zbc'])[:mpol+1, old_ntor-ntor:old_ntor+ntor+1] + surface.rs[:] = np.array(ph['rbs'])[:mpol+1, old_ntor-ntor:old_ntor+ntor+1] normal_field = cls( nfp=ph['nfp'], @@ -471,7 +469,6 @@ def set_vns_asarray(self, vns, mpol=None, ntor=None): dofs = self.get_dofs() self.local_full_x = dofs - def set_vnc_asarray(self, vnc, mpol=None, ntor=None): """ Set the vnc from a single array @@ -490,12 +487,6 @@ def set_vnc_asarray(self, vnc, mpol=None, ntor=None): dofs = self.get_dofs() self.local_full_x = dofs - - for mm in range(0, mpol + 1): - for nn in range(-ntor, ntor + 1): - if mm == 0 and nn < 0: continue - self.set_vnc(mm, nn, vnc[mm, ntor + nn]) - def set_vns_vnc_asarray(self, vns, vnc, mpol=None, ntor=None): """ Set the vns and vnc from two single arrays diff --git a/tests/field/test_normal_field.py b/tests/field/test_normal_field.py index 93350a996..bb98248f5 100644 --- a/tests/field/test_normal_field.py +++ b/tests/field/test_normal_field.py @@ -236,7 +236,7 @@ def test_get_set_vns_vnc_asarray(self): test the array-wise getter and setter functions for the Vns and Vnc arrays """ - filename = os.path.join(TEST_DIR, 'Dommaschk.sp') + filename = os.path.join(TEST_DIR, 'M16N08.sp') normal_field = NormalField.from_spec(filename) vns = normal_field.get_vns_asarray() vnc = normal_field.get_vnc_asarray() @@ -244,12 +244,20 @@ def test_get_set_vns_vnc_asarray(self): self.assertTrue(np.allclose(vns, vns2)) self.assertTrue(np.allclose(vnc, vnc2)) vns3 = np.copy(vnc) + vnc3 = np.copy(vnc) i, j = normal_field.get_index_in_array(m=3, n=-1) vns3[i, j] = 0.5 normal_field.set_vns_asarray(vns3) self.assertEqual(normal_field.get_vns(m=3, n=-1), 0.5) dof_index = normal_field.get_index_in_dofs(m=3, n=-1) self.assertEqual(normal_field.local_full_x[dof_index], 0.5) + i, j = normal_field.get_index_in_array(m=2, n=1) + vnc3[i, j] = 1.5 + normal_field.set_vnc_asarray(vnc3) + self.assertEqual(normal_field.get_vnc(m=2, n=1), 1.5) + dof_index = normal_field.get_index_in_dofs(m=2, n=1, even=True) + self.assertEqual(normal_field.local_full_x[dof_index], 1.5) + normal_field.set_vns_vnc_asarray(vns2, vnc2) @unittest.skipIf(py_spec is None, "py_spec not found") def test_get_real_space_field(self): From 4bd94feae9064f695022c4a98dc8f0108f0866a4 Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Tue, 18 Jun 2024 09:13:29 -0400 Subject: [PATCH 143/176] Try to get CIs working again following numpy 2.0 release --- .github/workflows/extensive_test.yml | 2 +- .github/workflows/tests.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/extensive_test.yml b/.github/workflows/extensive_test.yml index f60d2e15f..dc28d372e 100644 --- a/.github/workflows/extensive_test.yml +++ b/.github/workflows/extensive_test.yml @@ -98,7 +98,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann + pip install wheel numpy<2.0.0 scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann - name: Install booz_xform if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 269c9588d..54c6b70c5 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -93,7 +93,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install numpy cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec pyoculus h5py ground bentley_ottmann + pip install numpy<2.0.0 cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec pyoculus h5py ground bentley_ottmann - name: Install booz_xform run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform From 674db321d71c34e65e0310f0a03dc6f14da7f80e Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Tue, 18 Jun 2024 09:17:42 -0400 Subject: [PATCH 144/176] Quotes around version inequality --- .github/workflows/extensive_test.yml | 2 +- .github/workflows/tests.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/extensive_test.yml b/.github/workflows/extensive_test.yml index dc28d372e..b7e07749e 100644 --- a/.github/workflows/extensive_test.yml +++ b/.github/workflows/extensive_test.yml @@ -98,7 +98,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install wheel numpy<2.0.0 scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann + pip install wheel "numpy<2.0.0" scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann - name: Install booz_xform if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 54c6b70c5..f91910245 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -93,7 +93,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install numpy<2.0.0 cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec pyoculus h5py ground bentley_ottmann + pip install "numpy<2.0.0" cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec pyoculus h5py ground bentley_ottmann - name: Install booz_xform run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform From 3718a330187545851f34d4d233ba1a7d0d69c452 Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Sun, 23 Jun 2024 20:09:58 -0400 Subject: [PATCH 145/176] In CIs and containers, use the branch of vmec2000 that works with numpy 2.0 --- .github/workflows/extensive_test.yml | 2 +- .github/workflows/tests.yml | 2 +- ci/Dockerfile.ubuntu | 2 +- ci/singularity.def | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/extensive_test.yml b/.github/workflows/extensive_test.yml index f60d2e15f..47d8e20e9 100644 --- a/.github/workflows/extensive_test.yml +++ b/.github/workflows/extensive_test.yml @@ -71,7 +71,7 @@ jobs: # We must run actions/checkout before downloading and building VMEC, since checkout deletes the contents of the directory. - name: Download the VMEC2000 standalone repository if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') - run: git clone https://github.com/hiddensymmetries/VMEC2000.git + run: git clone https://github.com/hiddensymmetries/VMEC2000.git@ml/numpy2_fix_4 - name: ls -l again run: | diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 269c9588d..170ec713a 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -66,7 +66,7 @@ jobs: # We must run actions/checkout before downloading and building VMEC, since checkout deletes the contents of the directory. - name: Download the VMEC2000 standalone repository - run: git clone --depth=1 https://github.com/hiddensymmetries/VMEC2000.git + run: git clone --depth=1 https://github.com/hiddensymmetries/VMEC2000.git@ml/numpy2_fix_4 - name: ls -l again run: | diff --git a/ci/Dockerfile.ubuntu b/ci/Dockerfile.ubuntu index 4c8c7d06c..d9266e164 100644 --- a/ci/Dockerfile.ubuntu +++ b/ci/Dockerfile.ubuntu @@ -48,7 +48,7 @@ RUN git clone --depth 1 https://github.com/PrincetonUniversity/SPEC.git /src/SPE cd /src/SPEC && \ /venv/bin/pip install -v . 2>&1 | tee spec_build.log -RUN git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git /src/VMEC && \ +RUN git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git@ml/numpy2_fix_4 /src/VMEC && \ cd /src/VMEC && \ cp cmake/machines/ubuntu.json cmake_config_file.json && \ /venv/bin/pip install -v . 2>&1 | tee vmec_build.log diff --git a/ci/singularity.def b/ci/singularity.def index c070fddb1..ee74c32d3 100644 --- a/ci/singularity.def +++ b/ci/singularity.def @@ -63,7 +63,7 @@ Stage: devel cd .. && \ rm -rf SPEC - git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git && \ + git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git@ml/numpy2_fix_4 && \ cd VMEC2000 && \ cp cmake/machines/ubuntu.json cmake_config_file.json && \ /venv/bin/pip install . && \ From 53bf9fcc3f9cf43114f8ea88ba7be5134b634bb7 Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Sun, 23 Jun 2024 20:14:22 -0400 Subject: [PATCH 146/176] use the branch of vmec2000 that works with numpy 2.0 --- .github/workflows/extensive_test.yml | 2 +- .github/workflows/tests.yml | 2 +- ci/Dockerfile.ubuntu | 2 +- ci/singularity.def | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/extensive_test.yml b/.github/workflows/extensive_test.yml index 47d8e20e9..b3895e463 100644 --- a/.github/workflows/extensive_test.yml +++ b/.github/workflows/extensive_test.yml @@ -71,7 +71,7 @@ jobs: # We must run actions/checkout before downloading and building VMEC, since checkout deletes the contents of the directory. - name: Download the VMEC2000 standalone repository if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') - run: git clone https://github.com/hiddensymmetries/VMEC2000.git@ml/numpy2_fix_4 + run: git clone -b ml/numpy2_fix_4 https://github.com/hiddensymmetries/VMEC2000.git - name: ls -l again run: | diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 170ec713a..6ed8418b7 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -66,7 +66,7 @@ jobs: # We must run actions/checkout before downloading and building VMEC, since checkout deletes the contents of the directory. - name: Download the VMEC2000 standalone repository - run: git clone --depth=1 https://github.com/hiddensymmetries/VMEC2000.git@ml/numpy2_fix_4 + run: git clone -b ml/numpy2_fix_4 --depth=1 https://github.com/hiddensymmetries/VMEC2000.git - name: ls -l again run: | diff --git a/ci/Dockerfile.ubuntu b/ci/Dockerfile.ubuntu index d9266e164..e865b3f1c 100644 --- a/ci/Dockerfile.ubuntu +++ b/ci/Dockerfile.ubuntu @@ -48,7 +48,7 @@ RUN git clone --depth 1 https://github.com/PrincetonUniversity/SPEC.git /src/SPE cd /src/SPEC && \ /venv/bin/pip install -v . 2>&1 | tee spec_build.log -RUN git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git@ml/numpy2_fix_4 /src/VMEC && \ +RUN git clone -b ml/numpy2_fix_4 --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git /src/VMEC && \ cd /src/VMEC && \ cp cmake/machines/ubuntu.json cmake_config_file.json && \ /venv/bin/pip install -v . 2>&1 | tee vmec_build.log diff --git a/ci/singularity.def b/ci/singularity.def index ee74c32d3..297e8ceb6 100644 --- a/ci/singularity.def +++ b/ci/singularity.def @@ -63,7 +63,7 @@ Stage: devel cd .. && \ rm -rf SPEC - git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git@ml/numpy2_fix_4 && \ + git clone -b ml/numpy2_fix_4 --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git && \ cd VMEC2000 && \ cp cmake/machines/ubuntu.json cmake_config_file.json && \ /venv/bin/pip install . && \ From 98d9f20636ab1e28256aba858e81fc445f10eed4 Mon Sep 17 00:00:00 2001 From: Bharat Medasani Date: Mon, 24 Jun 2024 10:02:13 -0400 Subject: [PATCH 147/176] replace nptyping with numpy.typing --- pyproject.toml | 2 +- src/simsopt/_core/types.py | 11 +++++++---- src/simsopt/geo/surfaceobjectives.py | 7 ++++--- 3 files changed, 12 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f34cda10d..870f48767 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,7 +57,7 @@ dependencies = [ "jaxlib>=0.1.56", "scipy>=1.5.4", "Deprecated>=1.2.10", - "nptyping>=1.3.0", + # "nptyping>=1.3.0", "monty>=2021.6.10", "ruamel.yaml", "sympy", diff --git a/src/simsopt/_core/types.py b/src/simsopt/_core/types.py index ac473e5b3..21dc29010 100644 --- a/src/simsopt/_core/types.py +++ b/src/simsopt/_core/types.py @@ -9,11 +9,14 @@ from typing import Union, Sequence, Any from numbers import Integral, Real -from nptyping import NDArray, Float, Int, Bool +# from nptyping import NDArray, Float, Int, Bool +import numpy as np +from numpy.typing import NDArray -RealArray = Union[Sequence[Real], NDArray[Any, Float]] -IntArray = Union[Sequence[Integral], NDArray[Any, Int]] +# RealArray is a type alias for numpy double array or RealArray +RealArray = Union[Sequence[Real], NDArray[np.double]] +IntArray = Union[Sequence[Integral], NDArray[np.int_]] StrArray = Sequence[str] -BoolArray = Union[Sequence[bool], NDArray[Any, Bool]] +BoolArray = Union[Sequence[bool], NDArray[np.bool]] Key = Union[Integral, str] diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index e743af500..5a92408e9 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -1,11 +1,12 @@ from typing import Any import numpy as np -from nptyping import NDArray, Float +# from nptyping import NDArray, Float import simsoptpp as sopp from .._core.optimizable import Optimizable from .._core.derivative import Derivative, derivative_dec +from .._core.types import RealArray from .surface import Surface from .surfacexyztensorfourier import SurfaceXYZTensorFourier from ..objectives.utilities import forward_backward @@ -517,8 +518,8 @@ def boozer_surface_residual(surface, iota, G, biotsavart, derivatives=0, weight_ def parameter_derivatives(surface: Surface, - shape_gradient: NDArray[Any, Float] - ) -> NDArray[Any, Float]: + shape_gradient: RealArray + ) -> RealArray: r""" Converts the shape gradient of a given figure of merit, :math:`f`, to derivatives with respect to parameters defining a surface. For From a8dafae66c2af34b5fbed0dce61473b984b4c71c Mon Sep 17 00:00:00 2001 From: Bharat Medasani Date: Mon, 24 Jun 2024 11:07:13 -0400 Subject: [PATCH 148/176] Replacing np.bool with bool --- src/simsopt/_core/types.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/simsopt/_core/types.py b/src/simsopt/_core/types.py index 21dc29010..6ba9ff184 100644 --- a/src/simsopt/_core/types.py +++ b/src/simsopt/_core/types.py @@ -17,6 +17,6 @@ RealArray = Union[Sequence[Real], NDArray[np.double]] IntArray = Union[Sequence[Integral], NDArray[np.int_]] StrArray = Sequence[str] -BoolArray = Union[Sequence[bool], NDArray[np.bool]] +BoolArray = Union[Sequence[bool], NDArray[bool]] Key = Union[Integral, str] From 63fa27a2a19bb8062432fb89a4935ce1f9d09d69 Mon Sep 17 00:00:00 2001 From: Bharat Medasani Date: Mon, 24 Jun 2024 11:19:36 -0400 Subject: [PATCH 149/176] limit numpy to below 2.0 in non-simd-tests --- .github/workflows/non_simd_tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/non_simd_tests.yml b/.github/workflows/non_simd_tests.yml index b59209470..121cc36ee 100644 --- a/.github/workflows/non_simd_tests.yml +++ b/.github/workflows/non_simd_tests.yml @@ -84,7 +84,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann + pip install wheel "numpy<2.0.0" scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann - name: Install booz_xform run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform From acf037dd8fae16f70bed9f1cdde949f6f0b4dd44 Mon Sep 17 00:00:00 2001 From: Chris Date: Mon, 24 Jun 2024 17:23:52 +0200 Subject: [PATCH 150/176] imports to top where they belong --- src/simsopt/field/normal_field.py | 3 +-- src/simsopt/mhd/spec.py | 2 +- tests/geo/test_surface_rzfourier.py | 2 +- tests/mhd/test_spec.py | 6 +++--- 4 files changed, 6 insertions(+), 7 deletions(-) diff --git a/src/simsopt/field/normal_field.py b/src/simsopt/field/normal_field.py index 97369e75a..45363e87b 100644 --- a/src/simsopt/field/normal_field.py +++ b/src/simsopt/field/normal_field.py @@ -3,6 +3,7 @@ import numpy as np from .._core.optimizable import DOFs, Optimizable +from simsopt.geo import SurfaceRZFourier logger = logging.getLogger(__name__) @@ -60,7 +61,6 @@ def __init__(self, nfp=1, stellsym=True, mpol=1, ntor=0, vnc = np.zeros((self.mpol + 1, 2 * self.ntor + 1)) if surface is None: - from simsopt.geo import SurfaceRZFourier surface = SurfaceRZFourier(nfp=nfp, stellsym=stellsym, mpol=mpol, ntor=ntor) surface.fix_all() self.surface = surface @@ -106,7 +106,6 @@ def from_spec(cls, filename): if py_spec is None: raise RuntimeError( "Initialization from Spec requires py_spec to be installed.") - from simsopt.geo import SurfaceRZFourier # Read Namelist nm = py_spec.SPECNamelist(filename) diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index d5e10ba18..f4b0a1bb0 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -8,6 +8,7 @@ import copy import logging import os.path +import shutil, os import traceback from typing import Optional from scipy.constants import mu_0 @@ -259,7 +260,6 @@ def default_freeboundary(cls, copy_to_pwd, verbose=True): copy_to_pwd: boolean, if True, the default input file will be copied to the current working directory. Has to be set True as free-boundary SPEC can only handle files in the current working directory. verbose: boolean, if True, print statements will be printed """ - import shutil, os filename = 'defaults_freebound.sp' if verbose: print(f'Copying {os.path.join(os.path.dirname(__file__), filename)} to {os.getcwd()}/{filename}') diff --git a/tests/geo/test_surface_rzfourier.py b/tests/geo/test_surface_rzfourier.py index 237f26b16..0bcd09857 100755 --- a/tests/geo/test_surface_rzfourier.py +++ b/tests/geo/test_surface_rzfourier.py @@ -748,7 +748,7 @@ def test_fourier_transform_field(self): # create a test field where only Fourier elements [m=2, n=3] # and [m=4,n=5] are nonzero: - field = field = 0.8 * np.sin(2*theta2d - 3*s.nfp*phi2d) + 0.2*np.sin(4*theta2d - 5*s.nfp*phi2d)+ 0.7*np.cos(3*theta2d - 3*s.nfp*phi2d) + field = 0.8 * np.sin(2*theta2d - 3*s.nfp*phi2d) + 0.2*np.sin(4*theta2d - 5*s.nfp*phi2d)+ 0.7*np.cos(3*theta2d - 3*s.nfp*phi2d) # Transform the field to Fourier space: ft_sines, ft_cosines = s.fourier_transform_field(field, stellsym=False) diff --git a/tests/mhd/test_spec.py b/tests/mhd/test_spec.py index 8aab9e696..dba3164ab 100755 --- a/tests/mhd/test_spec.py +++ b/tests/mhd/test_spec.py @@ -2,8 +2,11 @@ import os import unittest + import numpy as np from monty.tempfile import ScratchDir +from scipy.constants import mu_0 +from simsopt._core.util import ObjectiveFailure try: import spec as spec_mod @@ -236,8 +239,6 @@ def test_freeboundary_default(self): test the default freeboundary file, and re-set if Picard iteration fails """ - from simsopt._core.util import ObjectiveFailure - with ScratchDir("."): s = Spec.default_freeboundary(copy_to_pwd=True) startingboundary = np.copy(s.inputlist.bns) @@ -281,7 +282,6 @@ def test_poloidal_current_amperes(self): """ Test the poloidal current in amperes """ - from scipy.constants import mu_0 filename = os.path.join(TEST_DIR, 'RotatingEllipse_Nvol8.sp') s = Spec(filename) self.assertAlmostEqual(s.poloidal_current_amperes, s.inputlist.curpol/mu_0) From b6e1fbd313dc597c885e49454550adc77d257dbb Mon Sep 17 00:00:00 2001 From: Chris Date: Mon, 24 Jun 2024 17:26:00 +0200 Subject: [PATCH 151/176] test_surface copy mistake fix --- tests/geo/test_surface_rzfourier.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/geo/test_surface_rzfourier.py b/tests/geo/test_surface_rzfourier.py index 0bcd09857..49bf70c9f 100755 --- a/tests/geo/test_surface_rzfourier.py +++ b/tests/geo/test_surface_rzfourier.py @@ -758,7 +758,7 @@ def test_fourier_transform_field(self): # Test that all other elements are close to zero sines_mask = np.ones_like(ft_sines, dtype=bool) - cosines_mask = sines_mask + cosines_mask = np.copy(sines_mask) sines_mask[2, 3 + s.ntor] = False sines_mask[4, 5 + s.ntor] = False cosines_mask[3, 3 + s.ntor] = False From 66b09f30fddd764458b4031393be1f54d59c1e21 Mon Sep 17 00:00:00 2001 From: Bharat Medasani Date: Mon, 24 Jun 2024 11:27:21 -0400 Subject: [PATCH 152/176] Cleanup code --- src/simsopt/_core/types.py | 4 +--- src/simsopt/geo/surfaceobjectives.py | 3 --- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/src/simsopt/_core/types.py b/src/simsopt/_core/types.py index 6ba9ff184..ad634f2a4 100644 --- a/src/simsopt/_core/types.py +++ b/src/simsopt/_core/types.py @@ -6,14 +6,12 @@ This module contains small utility functions and classes. """ -from typing import Union, Sequence, Any +from typing import Union, Sequence # , Any from numbers import Integral, Real -# from nptyping import NDArray, Float, Int, Bool import numpy as np from numpy.typing import NDArray -# RealArray is a type alias for numpy double array or RealArray RealArray = Union[Sequence[Real], NDArray[np.double]] IntArray = Union[Sequence[Integral], NDArray[np.int_]] StrArray = Sequence[str] diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 5a92408e9..d5db86f4b 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -1,7 +1,4 @@ -from typing import Any - import numpy as np -# from nptyping import NDArray, Float import simsoptpp as sopp from .._core.optimizable import Optimizable From a97db7b31df2cea494e628c8992db262b630aca6 Mon Sep 17 00:00:00 2001 From: Bharat Medasani Date: Mon, 24 Jun 2024 11:31:01 -0400 Subject: [PATCH 153/176] limit numpy version to less than 2.0.0 --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 870f48767..236e4c4cd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,12 +52,11 @@ keywords = [ "magnetostatics" ] dependencies = [ - "numpy>=1.21", + "numpy>=1.21,<2.0.0", "jax>=0.2.5", "jaxlib>=0.1.56", "scipy>=1.5.4", "Deprecated>=1.2.10", - # "nptyping>=1.3.0", "monty>=2021.6.10", "ruamel.yaml", "sympy", From 9dd34c5b0f7eab40f1fed3532983affb96061341 Mon Sep 17 00:00:00 2001 From: Bharat Medasani Date: Mon, 24 Jun 2024 13:37:35 -0400 Subject: [PATCH 154/176] update github runner for macos from 11 to 12 --- .github/workflows/conda.yml | 2 +- .github/workflows/wheel.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml index 48926a07f..b53322842 100644 --- a/.github/workflows/conda.yml +++ b/.github/workflows/conda.yml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: false matrix: - platform: [ubuntu-latest, macos-11] + platform: [ubuntu-latest, macos-12] python-version: ["3.9"] runs-on: ${{ matrix.platform }} diff --git a/.github/workflows/wheel.yml b/.github/workflows/wheel.yml index 8044ebfe4..159b78e8f 100644 --- a/.github/workflows/wheel.yml +++ b/.github/workflows/wheel.yml @@ -8,7 +8,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - os: [macos-11, ubuntu-20.04] + os: [macos-12, ubuntu-20.04] steps: - uses: actions/checkout@v4 From 96e840556972c73db3453f18d6bf71c594e5a910 Mon Sep 17 00:00:00 2001 From: Chris Date: Tue, 25 Jun 2024 11:52:34 +0200 Subject: [PATCH 155/176] pull numpy fix from SPEC repo and pyoculus repo --- .github/workflows/extensive_test.yml | 16 +++++----------- .github/workflows/non_simd_tests.yml | 2 +- .github/workflows/tests.yml | 17 +++++++---------- 3 files changed, 13 insertions(+), 22 deletions(-) diff --git a/.github/workflows/extensive_test.yml b/.github/workflows/extensive_test.yml index 251f39621..804c2c81c 100644 --- a/.github/workflows/extensive_test.yml +++ b/.github/workflows/extensive_test.yml @@ -98,7 +98,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install wheel "numpy<2.0.0" scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann + pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann - name: Install booz_xform if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') @@ -107,15 +107,8 @@ jobs: - name: Install virtual_casing run: pip install -v git+https://github.com/hiddenSymmetries/virtual-casing - # See https://github.community/t/best-way-to-clone-a-private-repo-during-script-run-of-private-github-action/16116/7 - # https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions - # https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token - - name: Check out SPEC - if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all') - uses: actions/checkout@v4 - with: - repository: PrincetonUniversity/SPEC - path: SPEC + - name: Download SPEC + run: git clone -b numpy2_fix --depth=1 https://github.com/PrincetonUniversity/SPEC # For some reason, installing py_spec does not install the dependencies f90nml and h5py. Therefore I installed these manually above. - name: Install py_spec @@ -167,7 +160,8 @@ jobs: if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all') run: | pip install -v . - pip install mpi4py py_spec pyoculus h5py + pip install mpi4py h5py + pip install -v git+https://github.com/zhisong/pyoculus@numpy2_fix - name: Install simsopt package if: contains(matrix.packages, 'none') diff --git a/.github/workflows/non_simd_tests.yml b/.github/workflows/non_simd_tests.yml index 121cc36ee..b59209470 100644 --- a/.github/workflows/non_simd_tests.yml +++ b/.github/workflows/non_simd_tests.yml @@ -84,7 +84,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install wheel "numpy<2.0.0" scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann + pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann - name: Install booz_xform run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 402fa82a3..5ba17fc55 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -93,7 +93,10 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install "numpy<2.0.0" cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec pyoculus h5py ground bentley_ottmann + pip install numpy cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py h5py ground bentley_ottmann + + - name: Install pyoculus numpy2_fix + run: pip install -v git+https://github.com/zhisong/pyoculus@numpy2_fix - name: Install booz_xform run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform @@ -101,14 +104,8 @@ jobs: - name: Install virtual_casing run: pip install -v git+https://github.com/hiddenSymmetries/virtual-casing - # See https://github.community/t/best-way-to-clone-a-private-repo-during-script-run-of-private-github-action/16116/7 - # https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions - # https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token - - name: Check out SPEC - uses: actions/checkout@v4 - with: - repository: PrincetonUniversity/SPEC - path: SPEC + - name: Download SPEC + run: git clone -b numpy2_fix --depth=1 https://github.com/PrincetonUniversity/SPEC - name: ls -l again run: | @@ -129,7 +126,7 @@ jobs: python -c "import py_spec; print('success')" - name: Install f90wrap - run: pip install -U git+https://github.com/zhucaoxiang/f90wrap + run: pip install git+https://github.com/zhucaoxiang/f90wrap@main_off - name: Build SPEC python wrapper. run: | From d1c1a31b7ad20ab1a36c23d436f01656cece8d68 Mon Sep 17 00:00:00 2001 From: Chris Date: Tue, 25 Jun 2024 13:38:38 +0200 Subject: [PATCH 156/176] install simsopt with python 2.0.0 (forgot to undo mkumbar fix) --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 236e4c4cd..dbc82b45c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,7 +52,7 @@ keywords = [ "magnetostatics" ] dependencies = [ - "numpy>=1.21,<2.0.0", + "numpy>=1.21", "jax>=0.2.5", "jaxlib>=0.1.56", "scipy>=1.5.4", From 2f139bc6fa28e49698619b743166de547b3198ba Mon Sep 17 00:00:00 2001 From: Chris Date: Tue, 25 Jun 2024 13:46:17 +0200 Subject: [PATCH 157/176] second time updating pyproject is the charm --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index dbc82b45c..060590467 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,7 +2,7 @@ requires = [ "scikit-build-core>=0.3.3", "pybind11", - "oldest-supported-numpy", + "numpy>=2.0", "setuptools_scm>=8.0", 'tomli; python_version < "3.11"',] build-backend = "scikit_build_core.build" From efebae15d33b5191b9044e57ee625acbbe7a8ffc Mon Sep 17 00:00:00 2001 From: Chris Date: Tue, 25 Jun 2024 14:02:18 +0200 Subject: [PATCH 158/176] test python3.8 support with oldest-supported-numpy --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 060590467..c26cfad26 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,7 +2,8 @@ requires = [ "scikit-build-core>=0.3.3", "pybind11", - "numpy>=2.0", + "oldest-supported-numpy; python_version=='3.8'", + "numpy>=2.0.0; python_version>='3.9'", "setuptools_scm>=8.0", 'tomli; python_version < "3.11"',] build-backend = "scikit_build_core.build" From ec8af3d9090bb6d4e152be8230e9a5d3c03e79d5 Mon Sep 17 00:00:00 2001 From: Chris Date: Tue, 25 Jun 2024 14:09:34 +0200 Subject: [PATCH 159/176] replace deprecated np.NINF with -np.inf --- src/simsopt/_core/optimizable.py | 4 ++-- tests/core/test_dofs.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/simsopt/_core/optimizable.py b/src/simsopt/_core/optimizable.py index e95228b1d..58a3d6ba7 100644 --- a/src/simsopt/_core/optimizable.py +++ b/src/simsopt/_core/optimizable.py @@ -87,7 +87,7 @@ def __init__(self, free: Array of boolean values denoting if the DOFs is are free. False values implies the corresponding DOFs are fixed lower_bounds: Lower bounds for the DOFs. Meaningful only if - DOF is not fixed. Default is np.NINF + DOF is not fixed. Default is -np.inf upper_bounds: Upper bounds for the DOFs. Meaningful only if DOF is not fixed. Default is np.inf """ @@ -106,7 +106,7 @@ def __init__(self, free = np.asarray(free, dtype=np.bool_) if lower_bounds is None: - lower_bounds = np.full(len(x), np.NINF) + lower_bounds = np.full(len(x), -np.inf) else: lower_bounds = np.asarray(lower_bounds, np.double) diff --git a/tests/core/test_dofs.py b/tests/core/test_dofs.py index 1c6c00c4a..452f7ffe7 100755 --- a/tests/core/test_dofs.py +++ b/tests/core/test_dofs.py @@ -168,7 +168,7 @@ def test_lower_bounds(self): names=np.array(['x', 'y', 'z']), free=np.array([True, True, False])) self.assertTrue(np.allclose(dofs.free_lower_bounds, - np.array([np.NINF, np.NINF]))) + np.array([-np.inf, -np.inf]))) with self.assertRaises(DofLengthMismatchError): dofs.free_lower_bounds = np.array([-1000.0, -1001.0, -1002.0]) @@ -180,7 +180,7 @@ def test_lower_bounds(self): dofs.unfix_all() self.assertTrue(np.allclose(dofs.free_lower_bounds, - np.array([-1000.0, -1001.0, np.NINF]))) + np.array([-1000.0, -1001.0, -np.inf]))) dofs.free_lower_bounds = np.array([-1000.0, -1001.0, -1002.]) self.assertTrue(np.allclose(dofs.free_lower_bounds, From 75a1ddfd6c234462744a1fc3d5c9517f2d76871b Mon Sep 17 00:00:00 2001 From: Chris Date: Tue, 25 Jun 2024 17:07:54 +0200 Subject: [PATCH 160/176] np.product -> np.prod --- tests/core/test_optimizable.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/core/test_optimizable.py b/tests/core/test_optimizable.py index 222c94ec1..079b245b5 100755 --- a/tests/core/test_optimizable.py +++ b/tests/core/test_optimizable.py @@ -97,7 +97,7 @@ def sum(self): return np.sum(self.local_full_x) def product(self): - return np.product(self.local_full_x) + return np.prod(self.local_full_x) return_fn_map = {'sum': sum, 'prod': product} From 7c2a1f956f11cd8d1903b00b3984190b85fea21c Mon Sep 17 00:00:00 2001 From: Chris Date: Wed, 26 Jun 2024 11:48:36 +0200 Subject: [PATCH 161/176] remove deprecated alltrue->all --- tests/mhd/test_spec.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/mhd/test_spec.py b/tests/mhd/test_spec.py index dba3164ab..cea494812 100755 --- a/tests/mhd/test_spec.py +++ b/tests/mhd/test_spec.py @@ -252,7 +252,7 @@ def test_freeboundary_default(self): try: s.run() except ObjectiveFailure: - self.assertTrue(np.alltrue(s.inputlist.bns == startingboundary)) + self.assertTrue(np.all(s.inputlist.bns == startingboundary)) else: raise ValueError("ObjectiveFailure not raised") # give enough freeboundary iterations, let ir run successfully @@ -270,11 +270,11 @@ def test_array_translator(self): translator2 = spec.array_translator(array, style='spec') translator3 = spec.array_translator(translator.as_simsopt, style='simsopt') - self.assertTrue(np.alltrue(array == translator.as_spec)) - self.assertTrue(np.alltrue(array == translator2.as_spec)) - self.assertTrue(np.alltrue(array == translator3.as_spec)) - self.assertTrue(np.alltrue(translator.as_simsopt == translator2.as_simsopt)) - self.assertTrue(np.alltrue(translator2.as_simsopt == translator3.as_simsopt)) + self.assertTrue(np.all(array == translator.as_spec)) + self.assertTrue(np.all(array == translator2.as_spec)) + self.assertTrue(np.all(array == translator3.as_spec)) + self.assertTrue(np.all(translator.as_simsopt == translator2.as_simsopt)) + self.assertTrue(np.all(translator2.as_simsopt == translator3.as_simsopt)) # test that the shape of the array is correct: self.assertEqual(translator2.as_simsopt.shape, (spec.inputlist.ntor+1, (2*spec.inputlist.mpol)+1)) From 7fb1729b56c2a64826d5f219d4d334b7d330b01c Mon Sep 17 00:00:00 2001 From: Chris Date: Wed, 26 Jun 2024 16:27:36 +0200 Subject: [PATCH 162/176] FIX SPEC SPORADIC FAIL FINALLY --- src/simsopt/mhd/spec.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index f4b0a1bb0..b4fddc139 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -141,6 +141,10 @@ def __init__(self, filename = f"{filename}.sp" if self.mpi.proc0_groups: logger.info(f"Group {self.mpi.group}: Initializing a SPEC object from file: {filename}") + + #If spec has run before, clear the f90wrap array caches. + if spec.allglobal._arrays: + self._clear_f90wrap_array_caches() # Initialize the FORTRAN state with values in the input file: self._init_fortran_state(filename) @@ -870,6 +874,13 @@ def poloidal_current_amperes(self): poloidally """ return self.inputlist.curpol/(mu_0) + + def _clear_f90wrap_array_caches(self): + """ + Clear the f90wrap array caches. This is necessary when a new file is read after SPEC has run before. + """ + spec.allglobal._arrays = {} + spec.inputlist._arrays = {} def _init_fortran_state(self, filename: str): """ From c68c10458e1c959e022c9b9d7d55b62de6e17d49 Mon Sep 17 00:00:00 2001 From: Chris Date: Wed, 26 Jun 2024 16:41:13 +0200 Subject: [PATCH 163/176] Revert "Merge remote-tracking branch 'origin/ml/vmec_update_for_numpy_2' into cbs/spec_update_rebase" This reverts commit a193adecc2a3717c49032e0a0f5c5351ddf09988, reversing changes made to 7c2a1f956f11cd8d1903b00b3984190b85fea21c. --- .github/workflows/extensive_test.yml | 18 ++++++++++++------ .github/workflows/non_simd_tests.yml | 2 +- .github/workflows/tests.yml | 19 +++++++++++-------- ci/Dockerfile.ubuntu | 2 +- ci/singularity.def | 2 +- pyproject.toml | 5 ++--- src/simsopt/_core/optimizable.py | 4 ++-- tests/core/test_dofs.py | 4 ++-- tests/core/test_optimizable.py | 2 +- 9 files changed, 33 insertions(+), 25 deletions(-) diff --git a/.github/workflows/extensive_test.yml b/.github/workflows/extensive_test.yml index 804c2c81c..b7e07749e 100644 --- a/.github/workflows/extensive_test.yml +++ b/.github/workflows/extensive_test.yml @@ -71,7 +71,7 @@ jobs: # We must run actions/checkout before downloading and building VMEC, since checkout deletes the contents of the directory. - name: Download the VMEC2000 standalone repository if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') - run: git clone -b ml/numpy2_fix_4 https://github.com/hiddensymmetries/VMEC2000.git + run: git clone https://github.com/hiddensymmetries/VMEC2000.git - name: ls -l again run: | @@ -98,7 +98,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann + pip install wheel "numpy<2.0.0" scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann - name: Install booz_xform if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all') @@ -107,8 +107,15 @@ jobs: - name: Install virtual_casing run: pip install -v git+https://github.com/hiddenSymmetries/virtual-casing - - name: Download SPEC - run: git clone -b numpy2_fix --depth=1 https://github.com/PrincetonUniversity/SPEC + # See https://github.community/t/best-way-to-clone-a-private-repo-during-script-run-of-private-github-action/16116/7 + # https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions + # https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token + - name: Check out SPEC + if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all') + uses: actions/checkout@v4 + with: + repository: PrincetonUniversity/SPEC + path: SPEC # For some reason, installing py_spec does not install the dependencies f90nml and h5py. Therefore I installed these manually above. - name: Install py_spec @@ -160,8 +167,7 @@ jobs: if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all') run: | pip install -v . - pip install mpi4py h5py - pip install -v git+https://github.com/zhisong/pyoculus@numpy2_fix + pip install mpi4py py_spec pyoculus h5py - name: Install simsopt package if: contains(matrix.packages, 'none') diff --git a/.github/workflows/non_simd_tests.yml b/.github/workflows/non_simd_tests.yml index b59209470..121cc36ee 100644 --- a/.github/workflows/non_simd_tests.yml +++ b/.github/workflows/non_simd_tests.yml @@ -84,7 +84,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann + pip install wheel "numpy<2.0.0" scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann - name: Install booz_xform run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 5ba17fc55..f91910245 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -66,7 +66,7 @@ jobs: # We must run actions/checkout before downloading and building VMEC, since checkout deletes the contents of the directory. - name: Download the VMEC2000 standalone repository - run: git clone -b ml/numpy2_fix_4 --depth=1 https://github.com/hiddensymmetries/VMEC2000.git + run: git clone --depth=1 https://github.com/hiddensymmetries/VMEC2000.git - name: ls -l again run: | @@ -93,10 +93,7 @@ jobs: - name: Install python dependencies run: | sudo apt-get install graphviz graphviz-dev - pip install numpy cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py h5py ground bentley_ottmann - - - name: Install pyoculus numpy2_fix - run: pip install -v git+https://github.com/zhisong/pyoculus@numpy2_fix + pip install "numpy<2.0.0" cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec pyoculus h5py ground bentley_ottmann - name: Install booz_xform run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform @@ -104,8 +101,14 @@ jobs: - name: Install virtual_casing run: pip install -v git+https://github.com/hiddenSymmetries/virtual-casing - - name: Download SPEC - run: git clone -b numpy2_fix --depth=1 https://github.com/PrincetonUniversity/SPEC + # See https://github.community/t/best-way-to-clone-a-private-repo-during-script-run-of-private-github-action/16116/7 + # https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions + # https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token + - name: Check out SPEC + uses: actions/checkout@v4 + with: + repository: PrincetonUniversity/SPEC + path: SPEC - name: ls -l again run: | @@ -126,7 +129,7 @@ jobs: python -c "import py_spec; print('success')" - name: Install f90wrap - run: pip install git+https://github.com/zhucaoxiang/f90wrap@main_off + run: pip install -U git+https://github.com/zhucaoxiang/f90wrap - name: Build SPEC python wrapper. run: | diff --git a/ci/Dockerfile.ubuntu b/ci/Dockerfile.ubuntu index e865b3f1c..4c8c7d06c 100644 --- a/ci/Dockerfile.ubuntu +++ b/ci/Dockerfile.ubuntu @@ -48,7 +48,7 @@ RUN git clone --depth 1 https://github.com/PrincetonUniversity/SPEC.git /src/SPE cd /src/SPEC && \ /venv/bin/pip install -v . 2>&1 | tee spec_build.log -RUN git clone -b ml/numpy2_fix_4 --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git /src/VMEC && \ +RUN git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git /src/VMEC && \ cd /src/VMEC && \ cp cmake/machines/ubuntu.json cmake_config_file.json && \ /venv/bin/pip install -v . 2>&1 | tee vmec_build.log diff --git a/ci/singularity.def b/ci/singularity.def index 297e8ceb6..c070fddb1 100644 --- a/ci/singularity.def +++ b/ci/singularity.def @@ -63,7 +63,7 @@ Stage: devel cd .. && \ rm -rf SPEC - git clone -b ml/numpy2_fix_4 --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git && \ + git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git && \ cd VMEC2000 && \ cp cmake/machines/ubuntu.json cmake_config_file.json && \ /venv/bin/pip install . && \ diff --git a/pyproject.toml b/pyproject.toml index c26cfad26..236e4c4cd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,8 +2,7 @@ requires = [ "scikit-build-core>=0.3.3", "pybind11", - "oldest-supported-numpy; python_version=='3.8'", - "numpy>=2.0.0; python_version>='3.9'", + "oldest-supported-numpy", "setuptools_scm>=8.0", 'tomli; python_version < "3.11"',] build-backend = "scikit_build_core.build" @@ -53,7 +52,7 @@ keywords = [ "magnetostatics" ] dependencies = [ - "numpy>=1.21", + "numpy>=1.21,<2.0.0", "jax>=0.2.5", "jaxlib>=0.1.56", "scipy>=1.5.4", diff --git a/src/simsopt/_core/optimizable.py b/src/simsopt/_core/optimizable.py index 58a3d6ba7..e95228b1d 100644 --- a/src/simsopt/_core/optimizable.py +++ b/src/simsopt/_core/optimizable.py @@ -87,7 +87,7 @@ def __init__(self, free: Array of boolean values denoting if the DOFs is are free. False values implies the corresponding DOFs are fixed lower_bounds: Lower bounds for the DOFs. Meaningful only if - DOF is not fixed. Default is -np.inf + DOF is not fixed. Default is np.NINF upper_bounds: Upper bounds for the DOFs. Meaningful only if DOF is not fixed. Default is np.inf """ @@ -106,7 +106,7 @@ def __init__(self, free = np.asarray(free, dtype=np.bool_) if lower_bounds is None: - lower_bounds = np.full(len(x), -np.inf) + lower_bounds = np.full(len(x), np.NINF) else: lower_bounds = np.asarray(lower_bounds, np.double) diff --git a/tests/core/test_dofs.py b/tests/core/test_dofs.py index 452f7ffe7..1c6c00c4a 100755 --- a/tests/core/test_dofs.py +++ b/tests/core/test_dofs.py @@ -168,7 +168,7 @@ def test_lower_bounds(self): names=np.array(['x', 'y', 'z']), free=np.array([True, True, False])) self.assertTrue(np.allclose(dofs.free_lower_bounds, - np.array([-np.inf, -np.inf]))) + np.array([np.NINF, np.NINF]))) with self.assertRaises(DofLengthMismatchError): dofs.free_lower_bounds = np.array([-1000.0, -1001.0, -1002.0]) @@ -180,7 +180,7 @@ def test_lower_bounds(self): dofs.unfix_all() self.assertTrue(np.allclose(dofs.free_lower_bounds, - np.array([-1000.0, -1001.0, -np.inf]))) + np.array([-1000.0, -1001.0, np.NINF]))) dofs.free_lower_bounds = np.array([-1000.0, -1001.0, -1002.]) self.assertTrue(np.allclose(dofs.free_lower_bounds, diff --git a/tests/core/test_optimizable.py b/tests/core/test_optimizable.py index 079b245b5..222c94ec1 100755 --- a/tests/core/test_optimizable.py +++ b/tests/core/test_optimizable.py @@ -97,7 +97,7 @@ def sum(self): return np.sum(self.local_full_x) def product(self): - return np.prod(self.local_full_x) + return np.product(self.local_full_x) return_fn_map = {'sum': sum, 'prod': product} From 8fba42ceb768f5623539794af81ea169190e3c77 Mon Sep 17 00:00:00 2001 From: Chris Date: Thu, 27 Jun 2024 10:20:42 +0200 Subject: [PATCH 164/176] clear spec cache to avoid sporadic mismatch --- src/simsopt/mhd/spec.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index 05e304a52..00501af93 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -141,6 +141,10 @@ def __init__(self, filename = f"{filename}.sp" logger.info(f"Initializing a SPEC object from file: {filename}") + #If spec has run before, clear the f90wrap array caches. + if spec.allglobal._arrays: + self._clear_f90wrap_array_caches() + if tolerance <= 0: raise ValueError( 'tolerance should be greater than zero' @@ -716,6 +720,13 @@ def set_dofs(self, x): if p is not None: p.phiedge = x[0] + def _clear_f90wrap_array_caches(self): + """ + Clear the f90wrap array caches. This is necessary when a new file is read after SPEC has run before. + """ + spec.allglobal._arrays = {} + spec.inputlist._arrays = {} logger.debug("Done with init") + def init(self, filename: str): """ Initialize SPEC fortran state from an input file. @@ -737,7 +748,6 @@ def init(self, filename: str): spec.allglobal.broadcast_inputs() logger.debug('About to call preset') spec.preset() - logger.debug("Done with init") def run(self, update_guess: bool = True): """ From d11685beac1d2e6096be9a2b74b008e352d6d0bc Mon Sep 17 00:00:00 2001 From: Chris Date: Thu, 27 Jun 2024 10:25:29 +0200 Subject: [PATCH 165/176] fix paste error --- src/simsopt/mhd/spec.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index 00501af93..27cfcd408 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -725,7 +725,7 @@ def _clear_f90wrap_array_caches(self): Clear the f90wrap array caches. This is necessary when a new file is read after SPEC has run before. """ spec.allglobal._arrays = {} - spec.inputlist._arrays = {} logger.debug("Done with init") + spec.inputlist._arrays = {} def init(self, filename: str): """ @@ -748,6 +748,7 @@ def init(self, filename: str): spec.allglobal.broadcast_inputs() logger.debug('About to call preset') spec.preset() + logger.debug("Done with init") def run(self, update_guess: bool = True): """ From 6ac3fa8485940519e0ce7eb118a4b07397c8fe7d Mon Sep 17 00:00:00 2001 From: Bharat Medasani Date: Thu, 27 Jun 2024 11:12:10 -0400 Subject: [PATCH 166/176] Fix for python 3.8 and numpy dependency --- pyproject.toml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 236e4c4cd..b89247f2c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,9 @@ [build-system] requires = [ - "scikit-build-core>=0.3.3", + "scikit-build-core", "pybind11", - "oldest-supported-numpy", + "numpy >= 2.0.0; python_version > '3.8'", + "oldest-supported-numpy; python_version <= '3.8'", "setuptools_scm>=8.0", 'tomli; python_version < "3.11"',] build-backend = "scikit_build_core.build" From bd5d9e9cdcb051fc287306ce66c200f6d5624c0b Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 28 Jun 2024 12:41:09 +0200 Subject: [PATCH 167/176] update containers --- ci/Dockerfile.ubuntu | 10 ++++++---- ci/singularity.def | 10 ++++++---- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/ci/Dockerfile.ubuntu b/ci/Dockerfile.ubuntu index 4c8c7d06c..39b11e23d 100644 --- a/ci/Dockerfile.ubuntu +++ b/ci/Dockerfile.ubuntu @@ -40,20 +40,22 @@ RUN python3 -m pip install wheel RUN python3 -m venv /venv/ RUN /venv/bin/pip install -U pip -RUN /venv/bin/python -m pip install numpy scipy jax jaxlib f90nml mpi4py jupyter notebook ipython qsc sympy scikit-build ninja "pybind11[global]" cmake -RUN /venv/bin/pip install git+https://github.com/zhucaoxiang/f90wrap +RUN /venv/bin/python -m pip install numpy scipy jax jaxlib f90nml mpi4py jupyter notebook ipython qsc sympy scikit-build ninja "pybind11[global]" cmake f90wrap h5py ENV PATH="/venv/bin:${PATH}" RUN git clone --depth 1 https://github.com/PrincetonUniversity/SPEC.git /src/SPEC && \ cd /src/SPEC && \ - /venv/bin/pip install -v . 2>&1 | tee spec_build.log + /venv/bin/pip install -v . 2>&1 | tee spec_build.log && \ + cd Utilities/pythontools && \ + /venv/bin/pip install -r requirements.txt + /venv/bin/pip install -v . RUN git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git /src/VMEC && \ cd /src/VMEC && \ cp cmake/machines/ubuntu.json cmake_config_file.json && \ /venv/bin/pip install -v . 2>&1 | tee vmec_build.log -RUN /venv/bin/pip install h5py pyoculus py_spec +RUN /venv/bin/pip install pyoculus RUN /venv/bin/pip install vtk==9.2.6 pyqt5 matplotlib pyevtk plotly RUN /venv/bin/pip install mayavi RUN /venv/bin/pip install git+https://github.com/hiddenSymmetries/booz_xform diff --git a/ci/singularity.def b/ci/singularity.def index c070fddb1..11a70ac81 100644 --- a/ci/singularity.def +++ b/ci/singularity.def @@ -44,8 +44,7 @@ Stage: devel python3 -m venv /venv/ . /venv/bin/activate /venv/bin/pip install -U pip - /venv/bin/pip install numpy scipy jax jaxlib f90nml jupyter notebook ipython qsc sympy scikit-build ninja "pybind11[global]" cmake - /venv/bin/pip install git+https://github.com/zhucaoxiang/f90wrap + /venv/bin/pip install numpy scipy jax jaxlib f90nml jupyter notebook ipython qsc sympy scikit-build ninja "pybind11[global]" cmake f90wrap h5py PATH="/usr/local/bin:/venv/bin:${PATH}" LD_LIBRARY_PATH="/usr/local/lib:${LD_LIBRARY_PATH}" @@ -60,7 +59,10 @@ Stage: devel cd SPEC && \ /venv/bin/python setup.py bdist_wheel && \ /venv/bin/pip install -v dist/*.whl && \ - cd .. && \ + cd Utilities/pythontools && \ + /venv/bin/pip install -r requirements.txt && \ + /venv/bin/pip install . && \ + cd ../../.. && \ rm -rf SPEC git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git && \ @@ -70,7 +72,7 @@ Stage: devel cd .. && \ rm -rf VMEC2000 - /venv/bin/pip install h5py pyoculus py_spec + /venv/bin/pip install pyoculus /venv/bin/pip install vtk==9.2.6 pyqt5 matplotlib pyevtk plotly /venv/bin/pip install mayavi /venv/bin/pip install git+https://github.com/hiddenSymmetries/booz_xform From ca972ce6c34a42ea3c416af039c233e014af6c5a Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 28 Jun 2024 12:58:02 +0200 Subject: [PATCH 168/176] fix line continuation --- ci/Dockerfile.ubuntu | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/Dockerfile.ubuntu b/ci/Dockerfile.ubuntu index 39b11e23d..afac3239d 100644 --- a/ci/Dockerfile.ubuntu +++ b/ci/Dockerfile.ubuntu @@ -47,7 +47,7 @@ RUN git clone --depth 1 https://github.com/PrincetonUniversity/SPEC.git /src/SPE cd /src/SPEC && \ /venv/bin/pip install -v . 2>&1 | tee spec_build.log && \ cd Utilities/pythontools && \ - /venv/bin/pip install -r requirements.txt + /venv/bin/pip install -r requirements.txt && \ /venv/bin/pip install -v . RUN git clone --depth 1 https://github.com/hiddenSymmetries/VMEC2000.git /src/VMEC && \ From 7bc1e4c175052713e1bfb09589f384c3273beb69 Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Wed, 3 Jul 2024 11:56:44 -0400 Subject: [PATCH 169/176] Mention github issue and PR in comments related to spec CI failures --- src/simsopt/mhd/spec.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index 27cfcd408..ec7444417 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -141,7 +141,9 @@ def __init__(self, filename = f"{filename}.sp" logger.info(f"Initializing a SPEC object from file: {filename}") - #If spec has run before, clear the f90wrap array caches. + # If spec has run before, clear the f90wrap array caches. + # See https://github.com/hiddenSymmetries/simsopt/pull/431 + # This addresses the issue https://github.com/hiddenSymmetries/simsopt/issues/357 if spec.allglobal._arrays: self._clear_f90wrap_array_caches() @@ -722,7 +724,12 @@ def set_dofs(self, x): def _clear_f90wrap_array_caches(self): """ - Clear the f90wrap array caches. This is necessary when a new file is read after SPEC has run before. + Clear the f90wrap array caches. This is necessary when a new file is + read after SPEC has run before. + + See https://github.com/hiddenSymmetries/simsopt/pull/431 + + This function is for addressing the issue https://github.com/hiddenSymmetries/simsopt/issues/357 """ spec.allglobal._arrays = {} spec.inputlist._arrays = {} From 03b64b5f60d288f5a213cb4384283519fbcc21f9 Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 5 Jul 2024 09:28:00 +0200 Subject: [PATCH 170/176] remove vestigial surface fourier transforms --- src/simsopt/geo/surface.py | 124 ------------------------------------- 1 file changed, 124 deletions(-) diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index f60af1761..081aa5633 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -842,130 +842,6 @@ def interpolate_on_arclength_grid(self, function, theta_evaluate): return function_interpolated - def fourier_transform_field(self, field, mpol=None, ntor=None, normalization=None, **kwargs): - r""" - Compute the Fourier components of a field on the surface. The field - is evaluated at the quadrature points on the surface. - The Fourier uses the conventions of the FourierRZSurface series, - with `npol` going from `-ntor` to `ntor` and `mpol` from 0 to `mpol` - i.e.: - :math:`f(\theta, \phi) = \Sum_{m=0}^{mpol} \Sum_{n=-npol}^{npol} A^{mn}_s \sin(m\theta - n*Nfp*\phi)\\ - + A^{mn}_c \cos(m\theta - n*Nfp*\phi)` - Where the cosine series is only evaluated if the surface is not stellarator - symmetric (if the field does not adhere to the symmetry of the surface, - request the cosine series by setting the kwarg stellsym=False) - *Arguments*: - - field: 2D array of shape (numquadpoints_phi, numquadpoints_theta). - - mpol: maximum poloidal mode number of the transform, if None, - the mpol attribute of the surface is used. - - ntor: maximum toroidal mode number of the transform if None, - the ntor attribute of the surface is used. - *Optional keyword arguments*: - - normalization: Fourier transform normalization. Can be: - None: forward and back transform are not normalized - float: forward transform is divided by this number - - stellsym: boolean to override the stellsym attribute - of the surface if you want to force the calculation of the cosine series - *Returns*: - - A_mns: 2D array of shape (mpol+1, 2*ntor+1) containing the sine coefficients - - A_mnc: 2D array of shape (mpol+1, 2*ntor+1) containing the cosine coefficients - (these are zero if the surface is stellarator symmetric) - """ - assert field.shape[0] == self.quadpoints_phi.size, "Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) - assert field.shape[1] == self.quadpoints_theta.size, "Field must be evaluated at the quadrature points on the surface.\n the field you passed in has shape {}".format(field.shape) - stellsym = kwargs.pop('stellsym', self.stellsym) - if mpol is None: - try: mpol = self.mpol - except AttributeError: raise ValueError("mpol must be specified") - if ntor is None: - try: ntor = self.ntor - except AttributeError: raise ValueError("ntor must be specified") - A_mns = np.zeros((int(mpol + 1), int(2 * ntor + 1))) # sine coefficients - A_mnc = np.zeros((int(mpol + 1), int(2 * ntor + 1))) # cosine coefficients - ntheta_grid = len(self.quadpoints_theta) - nphi_grid = len(self.quadpoints_phi) - - factor = 2.0 / (ntheta_grid * nphi_grid) - - phi2d, theta2d = np.meshgrid(2 * np.pi * self.quadpoints_phi, - 2 * np.pi * self.quadpoints_theta, - indexing="ij") - - for m in range(mpol + 1): - nmin = -ntor - if m == 0: nmin = 1 - for n in range(nmin, ntor+1): - angle = m * theta2d - n * self.nfp * phi2d - sinangle = np.sin(angle) - if not stellsym: - cosangle = np.cos(angle) - factor2 = factor - # The next 2 lines ensure inverse Fourier transform(Fourier transform) = identity - if np.mod(ntheta_grid, 2) == 0 and m == (ntheta_grid/2): factor2 = factor2 / 2 - if np.mod(nphi_grid, 2) == 0 and abs(n) == (nphi_grid/2): factor2 = factor2 / 2 - A_mns[m, n + ntor] = np.sum(field * sinangle * factor2) - if not stellsym: - A_mnc[m, n + ntor] = np.sum(field * cosangle * factor2) - - if not stellsym: - A_mnc[0, ntor] = np.sum(field) / (ntheta_grid * nphi_grid) - if normalization is not None: - if isinstance(normalization, float): - raise ValueError("normalization must be a float") - A_mns = A_mns / normalization - A_mnc = A_mnc / normalization - - return A_mns, A_mnc - - def inverse_fourier_transform_field(self, A_mns, A_mnc, normalization=None, **kwargs): - r""" - Compute the inverse Fourier transform of a field on the surface. The field - is evaluated at the quadrature points on the surface. The Fourier - transform is defined as - :math:`f(\theta, \phi) = \Sum_{m=0}^{mpol} \Sum_{n=-npol}^{npol} A^{mn}_s \sin(m\theta - n*Nfp*\phi)\\ - + A^{mn}_c \cos(m\theta - n*Nfp*\phi)` - Where the cosine series is only evaluated if the surface is not stellarator - symmetric. - *Arguments*: - - A_mns: 2D array of shape (mpol+1, 2*ntor+1) containing the sine coefficients - - A_mnc: 2D array of shape (mpol+1, 2*ntor+1) containing the cosine coefficients - (these are zero if the surface is stellarator symmetric) - *Optional keyword arguments*: - - normalization: Fourier transform normalization. Can be: - None: forward and back transform are not normalized - float: inverse transform is multiplied by this number - - stellsym: boolean to override the stellsym attribute of the surface - """ - mpol = A_mns.shape[0] - 1 - ntor = int((A_mns.shape[1] - 1) / 2) - stellsym = kwargs.pop('stellsym', self.stellsym) - ntheta_grid = len(self.quadpoints_theta) - nphi_grid = len(self.quadpoints_phi) - - phi2d, theta2d = np.meshgrid(2 * np.pi * self.quadpoints_phi, - 2 * np.pi * self.quadpoints_theta, - indexing="ij") - - field = np.zeros((nphi_grid, ntheta_grid)) - for m in range(mpol + 1): - nmin = -ntor - if m == 0: nmin = 1 - for n in range(nmin, ntor+1): - angle = m * theta2d - n * self.nfp * phi2d - sinangle = np.sin(angle) - if not stellsym: - cosangle = np.cos(angle) - field = field + A_mns[m, n + ntor] * sinangle - if not stellsym: - field = field + A_mnc[m, n + ntor] * cosangle - - if not stellsym: - field = field + A_mnc[0, ntor] - if normalization is not None: - if not isinstance(normalization, float): - raise ValueError("normalization must be a float") - field = field * normalization - return field def signed_distance_from_surface(xyz, surface): From 9d807fa84ba69816b8b72a1fe41e68f0285e705d Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 5 Jul 2024 09:53:40 +0200 Subject: [PATCH 171/176] change last occurences of transform_field->transform_scalar --- src/simsopt/field/normal_field.py | 2 +- tests/geo/test_surface_rzfourier.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/simsopt/field/normal_field.py b/src/simsopt/field/normal_field.py index 45363e87b..bc2b23487 100644 --- a/src/simsopt/field/normal_field.py +++ b/src/simsopt/field/normal_field.py @@ -510,7 +510,7 @@ def get_real_space_field(self): The returned array will be of size specified by the surfaces' quadpoints and located on the quadpoints. """ vns, vnc = self.get_vns_vnc_asarray(mpol=self.mpol, ntor=self.ntor) - BdotN_unnormalized = self.surface.inverse_fourier_transform_field(vns, vnc, normalization=(2*np.pi)**2, stellsym=self.stellsym) + BdotN_unnormalized = self.surface.inverse_fourier_transform_scalar(vns, vnc, normalization=(2*np.pi)**2, stellsym=self.stellsym) normal_field_real_space = -1 * BdotN_unnormalized / np.linalg.norm(self.surface.normal(), axis=-1) return normal_field_real_space diff --git a/tests/geo/test_surface_rzfourier.py b/tests/geo/test_surface_rzfourier.py index 49bf70c9f..39ceb6b53 100755 --- a/tests/geo/test_surface_rzfourier.py +++ b/tests/geo/test_surface_rzfourier.py @@ -732,7 +732,7 @@ def test_make_rotating_ellipse_iota(self): np.testing.assert_array_less(0, eq.wout.iotaf) np.testing.assert_allclose(eq.mean_iota(), 0.4291137962772453, rtol=1e-6) - def test_fourier_transform_field(self): + def test_fourier_transform_scalar(self): """ Test the Fourier transform of a field on a surface. """ @@ -751,7 +751,7 @@ def test_fourier_transform_field(self): field = 0.8 * np.sin(2*theta2d - 3*s.nfp*phi2d) + 0.2*np.sin(4*theta2d - 5*s.nfp*phi2d)+ 0.7*np.cos(3*theta2d - 3*s.nfp*phi2d) # Transform the field to Fourier space: - ft_sines, ft_cosines = s.fourier_transform_field(field, stellsym=False) + ft_sines, ft_cosines = s.fourier_transform_scalar(field, stellsym=False) self.assertAlmostEqual(ft_sines[2, 3+s.ntor], 0.8) self.assertAlmostEqual(ft_sines[4, 5+s.ntor], 0.2) self.assertAlmostEqual(ft_cosines[3, 3+s.ntor], 0.7) @@ -766,7 +766,7 @@ def test_fourier_transform_field(self): self.assertEqual(np.all(np.abs(ft_cosines[cosines_mask]) < 1e-10), True) # Transform back to real space: - field2 = s.inverse_fourier_transform_field(ft_sines, ft_cosines, stellsym=False) + field2 = s.inverse_fourier_transform_scalar(ft_sines, ft_cosines, stellsym=False) # Check that the result is the same as the original field: np.testing.assert_allclose(field, field2) From ac812243537003c71287cd12447ab0394b3d7066 Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 5 Jul 2024 13:44:13 +0200 Subject: [PATCH 172/176] cover normalization of ft surface_rzfourier --- tests/geo/test_surface_rzfourier.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/geo/test_surface_rzfourier.py b/tests/geo/test_surface_rzfourier.py index 39ceb6b53..fce6fec00 100755 --- a/tests/geo/test_surface_rzfourier.py +++ b/tests/geo/test_surface_rzfourier.py @@ -766,10 +766,10 @@ def test_fourier_transform_scalar(self): self.assertEqual(np.all(np.abs(ft_cosines[cosines_mask]) < 1e-10), True) # Transform back to real space: - field2 = s.inverse_fourier_transform_scalar(ft_sines, ft_cosines, stellsym=False) + field2 = s.inverse_fourier_transform_scalar(ft_sines, ft_cosines, stellsym=False, normalization=1/2*np.pi**2) # Check that the result is the same as the original field: - np.testing.assert_allclose(field, field2) + np.testing.assert_allclose(field/2*np.pi**2, field2) class SurfaceRZPseudospectralTests(unittest.TestCase): def test_names(self): From 800060fa4577daf32b39f8c97b59b2f8463df12f Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 5 Jul 2024 14:19:17 +0200 Subject: [PATCH 173/176] test normal field setter too --- src/simsopt/mhd/spec.py | 6 +++--- tests/mhd/test_spec.py | 22 ++++++++++++++++++++++ 2 files changed, 25 insertions(+), 3 deletions(-) diff --git a/src/simsopt/mhd/spec.py b/src/simsopt/mhd/spec.py index b42cabeb1..8a9655efc 100644 --- a/src/simsopt/mhd/spec.py +++ b/src/simsopt/mhd/spec.py @@ -399,12 +399,12 @@ def normal_field(self, normal_field): """ if not self.freebound: raise ValueError('Normal field can only be set in freeboundary case') - if not isinstance(normal_field, NormalField) or not isinstance(normal_field): + if not isinstance(normal_field, NormalField): raise ValueError('Input should be a NormalField or CoilNormalField') if self._normal_field is not normal_field: self.remove_parent(self._normal_field) - if self._computational_boundary is not normal_field.computational_boundary: - normal_field.computational_boundary = self._computational_boundary + if self._computational_boundary is not normal_field.surface: + normal_field.surface = self._computational_boundary self._normal_field = normal_field self.append_parent(normal_field) return diff --git a/tests/mhd/test_spec.py b/tests/mhd/test_spec.py index cea494812..179a7e2af 100755 --- a/tests/mhd/test_spec.py +++ b/tests/mhd/test_spec.py @@ -25,6 +25,7 @@ from simsopt.geo import SurfaceGarabedian from simsopt.mhd import ProfileSpec +from simsopt.field import NormalField from simsopt.objectives import LeastSquaresProblem from simsopt.solve import least_squares_serial_solve @@ -94,6 +95,27 @@ def test_init_freeboundary_nonstellsym(self): self.assertAlmostEqual(s.normal_field.get_vns(3, -1), -1.269776831212886e-04, places) self.assertAlmostEqual(s.normal_field.get_vnc(1, 0), 1.924871538367248e-04, places) self.assertAlmostEqual(s.normal_field.get_vnc(1, -2), 4.070523669489626e-04, places) + + def test_normal_field_setter(self): + """ + Try creating a Spec instance from a freeboundary file that is also + non-stellarator symmetric. + Check value of normal field + """ + + filename = os.path.join(TEST_DIR, 'M16N08.sp') + + with ScratchDir("."): + s = Spec(filename) + surface = s.boundary + old_normal = s.normal_field + new_normal = NormalField(s.nfp, stellsym=s.stellsym, mpol=s.mpol, ntor=s.ntor, surface=surface) + s.normal_field = new_normal + self.assertAlmostEqual(s.normal_field.get_vns(0,1), 0) # set to zeros + self.assertIs(s.normal_field.surface, s._computational_boundary) # normal field surface is set to spec computational boundary. + self.assertIsNot(old_normal, new_normal) + + def test_init_freeboundary(self): """ From a2a05ae0ddd0f4668cc0d22ca748ec22b49aeed1 Mon Sep 17 00:00:00 2001 From: Chris Date: Fri, 5 Jul 2024 17:24:23 +0200 Subject: [PATCH 174/176] Test raises in NormalField --- src/simsopt/field/normal_field.py | 8 ++-- tests/field/test_normal_field.py | 79 ++++++++++++++++++++++++++++++- 2 files changed, 82 insertions(+), 5 deletions(-) diff --git a/src/simsopt/field/normal_field.py b/src/simsopt/field/normal_field.py index bc2b23487..68f09cd3e 100644 --- a/src/simsopt/field/normal_field.py +++ b/src/simsopt/field/normal_field.py @@ -85,16 +85,16 @@ def vns(self): return self._vns @vns.setter - def vns(self): - raise AttributeError('change Vns using set_vns() or set_vns_asarray()') + def vns(self, value): + raise AttributeError('Change Vns using set_vns() or set_vns_asarray()') @property def vnc(self): return self._vnc @vnc.setter - def vnc(self): - raise AttributeError('change Vnc using set_vnc() or set_vnc_asarray()') + def vnc(self, value): + raise AttributeError('Change Vnc using set_vnc() or set_vnc_asarray()') @classmethod def from_spec(cls, filename): diff --git a/tests/field/test_normal_field.py b/tests/field/test_normal_field.py index bb98248f5..c17ee816b 100644 --- a/tests/field/test_normal_field.py +++ b/tests/field/test_normal_field.py @@ -230,6 +230,72 @@ def test_from_spec_object(self): self.assertTrue(np.allclose(normal_field.local_full_x, normal_field_2.local_full_x)) + @unittest.skipIf(py_spec is None, "py_spec not found") + def test_fail_for_fixedb(self): + """ + test if instantiation fails if spec is not freeboundary + """ + from simsopt.mhd import Spec + # Init from SPEC input file + spec = Spec() + with self.assertRaises(ValueError): + NormalField.from_spec_object(spec) + + def test_wrong_index(self): + """ + test if accessing a wrong m or n raises an error + """ + normal_field = NormalField(stellsym=False, mpol=3, ntor=2) + with self.assertRaises(ValueError): + normal_field.get_index_in_array(m=4, n=1) + with self.assertRaises(ValueError): + normal_field.get_index_in_array(m=4, n=1, even=True) + with self.assertRaises(ValueError): + normal_field.get_index_in_array(m=1, n=3) + with self.assertRaises(ValueError): + normal_field.get_index_in_array(m=1, n=3, even=True) + with self.assertRaises(ValueError): + normal_field.get_index_in_array(m=0, n=-1) + with self.assertRaises(ValueError): + normal_field.get_index_in_array(m=0, n=-1, even=True) + with self.assertRaises(ValueError): + normal_field.get_index_in_array(m=3, n=-3) + with self.assertRaises(ValueError): + normal_field.get_index_in_array(m=3, n=-3, even=True) + with self.assertRaises(ValueError): + normal_field.get_index_in_array(m=4, n=-3) + with self.assertRaises(ValueError): + normal_field.get_index_in_array(m=4, n=-3, even=True) + self.assertIsInstance(normal_field.get_index_in_array(m=0, n=0, even=True), list) + normal_field2 = NormalField(stellsym=True, mpol=3, ntor=2) + with self.assertRaises(ValueError): + normal_field2.get_index_in_array(m=0, n=0) + + def test_asarray_getter_setter_raises(self): + """ + test that if wrong bounds are given, an error is raised + """ + normal_field = NormalField(stellsym=False, mpol=3, ntor=2) + with self.assertRaises(ValueError): + normal_field.get_vns_asarray(mpol=4, ntor=5) + with self.assertRaises(ValueError): + normal_field.get_vns_asarray(mpol=3, ntor=4) + with self.assertRaises(ValueError): + normal_field.get_vnc_asarray(mpol=4, ntor=5) + with self.assertRaises(ValueError): + normal_field.get_vnc_asarray(mpol=3, ntor=4) + with self.assertRaises(ValueError): + normal_field.get_vns_vnc_asarray(mpol=4, ntor=5) + with self.assertRaises(ValueError): + normal_field.get_vns_vnc_asarray(mpol=3, ntor=4) + with self.assertRaises(ValueError): + normal_field.set_vns_asarray(np.zeros((3, 7)), mpol=2, ntor=3) + with self.assertRaises(ValueError): + normal_field.set_vnc_asarray(np.zeros((4, 7)), mpol=2, ntor=3) + with self.assertRaises(ValueError): + normal_field.set_vns_vnc_asarray(np.zeros((4, 7)), np.zeros((4, 7)), mpol=2, ntor=3) + + @unittest.skipIf(py_spec is None, "py_spec not found") def test_get_set_vns_vnc_asarray(self): """ @@ -269,4 +335,15 @@ def test_get_real_space_field(self): normal_field = NormalField.from_spec(filename) real_space_field = normal_field.get_real_space_field() self.assertTrue(real_space_field is not None) - self.assertEqual(real_space_field.shape, (normal_field.surface.quadpoints_phi.size, normal_field.surface.quadpoints_theta.size)) \ No newline at end of file + self.assertEqual(real_space_field.shape, (normal_field.surface.quadpoints_phi.size, normal_field.surface.quadpoints_theta.size)) + + def test_vns_vnc_setter(self): + normal_field = NormalField() + with self.assertRaises(AttributeError): + normal_field.vns = 1 + with self.assertRaises(AttributeError): + normal_field.vnc = 1 + + +if __name__ == '__main__': + unittest.main() \ No newline at end of file From b7efaf9a674d73ea7ddb77a3a40897db3a73cc05 Mon Sep 17 00:00:00 2001 From: Christopher Albert Date: Thu, 2 May 2024 18:37:55 +0000 Subject: [PATCH 175/176] Fix #411 compile flags --- CMakeLists.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 6a41b4654..92663e5d7 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -56,11 +56,11 @@ else() unset(COMPILER_SUPPORTS_MARCH_NATIVE CACHE) CHECK_CXX_COMPILER_FLAG(-march=native COMPILER_SUPPORTS_MARCH_NATIVE) if(COMPILER_SUPPORTS_MARCH_NATIVE) - set(CMAKE_CXX_FLAGS "-O3 -march=native -mfma -ffp-contract=fast") - elseif(${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "arm64") - set(CMAKE_CXX_FLAGS "-O3 -mcpu=apple-a14 -mfma -ffp-contract=fast") + set(CMAKE_CXX_FLAGS "-O3 -march=native -ffp-contract=fast") + elseif(${CMAKE_HOST_SYSTEM_PROCESSOR} STREQUAL "arm64") + set(CMAKE_CXX_FLAGS "-O3 -mcpu=apple-a14 -ffp-contract=fast") else() - set(CMAKE_CXX_FLAGS "-O3 -ffp-contract=fast") + set(CMAKE_CXX_FLAGS "-O3 -ffp-contract=fast") endif() endif() # Ensure all code used from Eigen does not have LGPL license: @@ -128,7 +128,7 @@ pybind11_add_module(${PROJECT_NAME} src/simsoptpp/surface.cpp src/simsoptpp/surfacerzfourier.cpp src/simsoptpp/surfacexyzfourier.cpp src/simsoptpp/integral_BdotN.cpp src/simsoptpp/dipole_field.cpp src/simsoptpp/permanent_magnet_optimization.cpp - src/simsoptpp/dommaschk.cpp src/simsoptpp/reiman.cpp src/simsoptpp/tracing.cpp + src/simsoptpp/dommaschk.cpp src/simsoptpp/reiman.cpp src/simsoptpp/tracing.cpp src/simsoptpp/magneticfield_biotsavart.cpp src/simsoptpp/python_boozermagneticfield.cpp src/simsoptpp/boozerradialinterpolant.cpp ) From 5f4509e6488d9d0d195ecdaf5371da2d19f87c00 Mon Sep 17 00:00:00 2001 From: Matt Landreman Date: Thu, 11 Jul 2024 11:34:47 -0400 Subject: [PATCH 176/176] Bugfix for logging error in boozer.py to address github issue #435 --- src/simsopt/mhd/boozer.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/simsopt/mhd/boozer.py b/src/simsopt/mhd/boozer.py index b7344c873..03b69bad4 100644 --- a/src/simsopt/mhd/boozer.py +++ b/src/simsopt/mhd/boozer.py @@ -33,7 +33,6 @@ __all__ = ['Boozer', 'Quasisymmetry'] - class Boozer(Optimizable): """ This class handles the transformation to Boozer coordinates. @@ -178,8 +177,8 @@ def run(self): self.bx.mnmax = wout.mnmax self.bx.xm = wout.xm self.bx.xn = wout.xn - logger.info('mnmax:', wout.mnmax, ' len(xm):', len(wout.xm), ' len(xn):', len(wout.xn)) - logger.info('mnmax_nyq:', wout.mnmax_nyq, ' len(xm_nyq):', len(wout.xm_nyq), ' len(xn_nyq):', len(wout.xn_nyq)) + logger.info(f'mnmax: {wout.mnmax} len(xm): {len(wout.xm)} len(xn): {len(wout.xn)}') + logger.info(f'mnmax_nyq: {wout.mnmax_nyq} len(xm_nyq): {len(wout.xm_nyq)} len(xn_nyq): {len(wout.xn_nyq)}') assert len(wout.xm) == wout.mnmax assert len(wout.xn) == wout.mnmax assert len(self.bx.xm) == self.bx.mnmax

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t=M=a}{KT^y{&}--7)iNp(TLQg+{;S*N6L-P|NjNf|8v7LxnO+X{{!m7zQ6zg literal 0 HcmV?d00001 diff --git a/src/simsoptpp/python.cpp b/src/simsoptpp/python.cpp index 3312fa891..ffc7d44db 100644 --- a/src/simsoptpp/python.cpp +++ b/src/simsoptpp/python.cpp @@ -18,9 +18,6 @@ typedef xt::pyarray PyArray; #include "boozerradialinterpolant.h" #include "boozerresidual.h" -#include "linking_number.hh" -typedef LK::LinkingNumber LK_class; - namespace py = pybind11; @@ -148,30 +145,6 @@ PYBIND11_MODULE(simsoptpp, m) { return 0.5 * res / (nphi*ntheta); }); - m.def("ln", [](PyArray& A, PyArray& B) { - LK_class lk(2); - int nseg1 = A.shape(0); - int nseg2 = B.shape(0); - - double c1[10000][3]; - double c2[10000][3]; - for(int i; i < nseg1; i++){ - c1[i][0] = A(i, 0); - c1[i][1] = A(i, 1); - c1[i][2] = A(i, 2); - } - - for(int i; i < nseg2; i++){ - c2[i][0] = B(i, 0); - c2[i][1] = B(i, 1); - c2[i][2] = B(i, 2); - } - - return lk.eval(c1, nseg1, c2, nseg2) ; - }); - - - #ifdef VERSION_INFO From c49aac286573a2b3940db126ea959d10c5706afe Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 9 Oct 2023 11:54:40 -0400 Subject: [PATCH 026/176] linting --- src/simsopt/geo/surface.py | 58 +++++++++++++--------------- src/simsopt/geo/surfaceobjectives.py | 3 +- tests/geo/test_surface_taylor.py | 3 -- 3 files changed, 27 insertions(+), 37 deletions(-) diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index 3d18bf7c1..23706d0d3 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -498,8 +498,7 @@ def d2aspect_ratio_by_dcoeff_dcoeff(self): dR_dt = self.dmajor_radius_by_dcoeff()[None, :] d2R_dsdt = self.d2major_radius_by_dcoeff_dcoeff() - return (2*R*dr_dt*dr_ds)/r**3 - (dR_dt*dr_ds)/r**2 - \ - (dr_dt*dR_ds)/r**2 - (R*d2r_dsdt)/r**2 + d2R_dsdt/r + return (2*R*dr_dt*dr_ds)/r**3 - (dR_dt*dr_ds)/r**2 - (dr_dt*dR_ds)/r**2 - (R*d2r_dsdt)/r**2 + d2R_dsdt/r def minor_radius(self): r""" @@ -576,7 +575,7 @@ def d2major_radius_by_dcoeff_dcoeff(self): return ((6*V*dr_dt*dr_ds)/r**4 - (2*dV_dt*dr_ds)/r**3 - \ (2*dr_dt*dV_ds)/r**3 - (2*V*d2r_dsdt)/r**3 + \ - d2V_dsdt/r**2)* np.sign(V)/(2*np.pi**2) + d2V_dsdt/r**2) * np.sign(V)/(2*np.pi**2) def mean_cross_sectional_area(self): r""" @@ -746,38 +745,33 @@ def d2mean_cross_sectional_area_by_dcoeff_dcoeff(self): dytheta_dt = dg2_ds[:, :, 1, None, :] dztheta_dt = dg2_ds[:, :, 2, None, :] - mean_area = np.mean((1/r) * (ztheta*(x*yvarphi-y*xvarphi)-zvarphi*(x*ytheta-y*xtheta)))/(2.*np.pi) - d2mean_area_ds2 = np.sign(mean_area)*np.mean( - (2*(-(xvarphi*y*ztheta) + xtheta*y*zvarphi + x*(yvarphi*ztheta - \ - ytheta*zvarphi))*dr_dt*dr_ds - r*((yvarphi*ztheta - \ - ytheta*zvarphi)*dx_dt + y*zvarphi*dxtheta_dt - y*ztheta*dxvarphi_dt - \ - xvarphi*ztheta*dy_dt + xtheta*zvarphi*dy_dt - xvarphi*y*dztheta_dt + \ - xtheta*y*dzvarphi_dt + x*(-(zvarphi*dytheta_dt) + ztheta*dyvarphi_dt \ - + yvarphi*dztheta_dt - ytheta*dzvarphi_dt))*dr_ds - \ - r*dr_dt*((yvarphi*ztheta - ytheta*zvarphi)*dx_ds + \ - y*zvarphi*dxtheta_ds - y*ztheta*dxvarphi_ds - xvarphi*ztheta*dy_ds + \ - xtheta*zvarphi*dy_ds - xvarphi*y*dztheta_ds + xtheta*y*dzvarphi_ds + \ - x*(-(zvarphi*dytheta_ds) + ztheta*dyvarphi_ds + yvarphi*dztheta_ds - \ - ytheta*dzvarphi_ds)) + r**2*((-(zvarphi*dytheta_dt) + \ - ztheta*dyvarphi_dt + yvarphi*dztheta_dt - ytheta*dzvarphi_dt)*dx_ds + \ - zvarphi*dy_dt*dxtheta_ds + y*dzvarphi_dt*dxtheta_ds - \ - ztheta*dy_dt*dxvarphi_ds - y*dztheta_dt*dxvarphi_ds + \ - zvarphi*dxtheta_dt*dy_ds - ztheta*dxvarphi_dt*dy_ds - \ - xvarphi*dztheta_dt*dy_ds + xtheta*dzvarphi_dt*dy_ds - \ - y*dxvarphi_dt*dztheta_ds - xvarphi*dy_dt*dztheta_ds + \ - y*dxtheta_dt*dzvarphi_ds + xtheta*dy_dt*dzvarphi_ds + \ - dx_dt*(-(zvarphi*dytheta_ds) + ztheta*dyvarphi_ds + \ - yvarphi*dztheta_ds - ytheta*dzvarphi_ds) + \ - x*(-(dzvarphi_dt*dytheta_ds) + dztheta_dt*dyvarphi_ds + \ - dyvarphi_dt*dztheta_ds - dytheta_dt*dzvarphi_ds)) + \ - r*(xvarphi*y*ztheta - xtheta*y*zvarphi + x*(-(yvarphi*ztheta) + \ - ytheta*zvarphi))*dr2_dsdt)/r**3 - , axis=(0, 1))/(2*np.pi) + d2mean_area_ds2 = np.sign(mean_area)*np.mean((2*(-(xvarphi*y*ztheta) + xtheta*y*zvarphi + x*(yvarphi*ztheta - \ # noqa + ytheta*zvarphi))*dr_dt*dr_ds - r*((yvarphi*ztheta - \ + ytheta*zvarphi)*dx_dt + y*zvarphi*dxtheta_dt - y*ztheta*dxvarphi_dt - \ + xvarphi*ztheta*dy_dt + xtheta*zvarphi*dy_dt - xvarphi*y*dztheta_dt + \ + xtheta*y*dzvarphi_dt + x*(-(zvarphi*dytheta_dt) + ztheta*dyvarphi_dt \ + + yvarphi*dztheta_dt - ytheta*dzvarphi_dt))*dr_ds - \ + r*dr_dt*((yvarphi*ztheta - ytheta*zvarphi)*dx_ds + \ + y*zvarphi*dxtheta_ds - y*ztheta*dxvarphi_ds - xvarphi*ztheta*dy_ds + \ + xtheta*zvarphi*dy_ds - xvarphi*y*dztheta_ds + xtheta*y*dzvarphi_ds + \ + x*(-(zvarphi*dytheta_ds) + ztheta*dyvarphi_ds + yvarphi*dztheta_ds - \ + ytheta*dzvarphi_ds)) + r**2*((-(zvarphi*dytheta_dt) + \ + ztheta*dyvarphi_dt + yvarphi*dztheta_dt - ytheta*dzvarphi_dt)*dx_ds + \ + zvarphi*dy_dt*dxtheta_ds + y*dzvarphi_dt*dxtheta_ds - \ + ztheta*dy_dt*dxvarphi_ds - y*dztheta_dt*dxvarphi_ds + \ + zvarphi*dxtheta_dt*dy_ds - ztheta*dxvarphi_dt*dy_ds - \ + xvarphi*dztheta_dt*dy_ds + xtheta*dzvarphi_dt*dy_ds - \ + y*dxvarphi_dt*dztheta_ds - xvarphi*dy_dt*dztheta_ds + \ + y*dxtheta_dt*dzvarphi_ds + xtheta*dy_dt*dzvarphi_ds + \ + dx_dt*(-(zvarphi*dytheta_ds) + ztheta*dyvarphi_ds + \ + yvarphi*dztheta_ds - ytheta*dzvarphi_ds) + \ + x*(-(dzvarphi_dt*dytheta_ds) + dztheta_dt*dyvarphi_ds + \ + dyvarphi_dt*dztheta_ds - dytheta_dt*dzvarphi_ds)) + \ + r*(xvarphi*y*ztheta - xtheta*y*zvarphi + x*(-(yvarphi*ztheta) + \ + ytheta*zvarphi))*dr2_dsdt)/r**3, axis=(0, 1))/(2*np.pi) return d2mean_area_ds2 - - def arclength_poloidal_angle(self): """ Computes poloidal angle based on arclenth along magnetic surface at diff --git a/src/simsopt/geo/surfaceobjectives.py b/src/simsopt/geo/surfaceobjectives.py index 13f896ba4..d167c0841 100644 --- a/src/simsopt/geo/surfaceobjectives.py +++ b/src/simsopt/geo/surfaceobjectives.py @@ -15,6 +15,7 @@ 'MajorRadius', 'NonQuasiSymmetricRatio', 'BoozerResidual', 'AspectRatio'] + class AspectRatio(Optimizable): """ Wrapper class for surface area label. @@ -66,8 +67,6 @@ def d2J_by_dsurfacecoefficientsdsurfacecoefficients(self): return self.surface.d2aspect_ratio_by_dcoeff_dcoeff() - - class Area(Optimizable): """ Wrapper class for surface area label. diff --git a/tests/geo/test_surface_taylor.py b/tests/geo/test_surface_taylor.py index a3594f1a0..3814fdd2f 100644 --- a/tests/geo/test_surface_taylor.py +++ b/tests/geo/test_surface_taylor.py @@ -483,9 +483,6 @@ def d2f(dofs): taylor_test2(f, df, d2f, coeffs, epsilons=np.power(2., -np.asarray(range(13, 20)))) - - - def subtest_surface_phi_derivative(self, surfacetype, stellsym): epss = [0.5**i for i in range(10, 15)] phis = np.asarray([0.6] + [0.6 + eps for eps in epss]) From 609143e4eda8148d4722c87b6a05fd6e539e33a7 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Mon, 9 Oct 2023 12:00:53 -0400 Subject: [PATCH 027/176] missing space --- tests/geo/test_surface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/geo/test_surface.py b/tests/geo/test_surface.py index aa47c9440..1c4e9a120 100755 --- a/tests/geo/test_surface.py +++ b/tests/geo/test_surface.py @@ -377,7 +377,7 @@ class isSelfIntersecting(unittest.TestCase): def test_is_self_intersecting(self): # dofs1 results in a surface that is self-intersecting # dofs2 results in a surface that is not self-intersecting - dofs1 = np.array([1., 0., 0., 0., 0., 0.1, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.1,\ + dofs1 = np.array([1., 0., 0., 0., 0., 0.1, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.1, \ 0., 0., 0., 0., 0., 0., 0.1]) s = get_surface('SurfaceRZFourier', True, full=True, nphi=200, ntheta=200, mpol=2, ntor=2) s.x = dofs1 From 643132c21c4bd3f21851c0c8c52998b5005e04f7 Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Tue, 10 Oct 2023 11:57:46 -0400 Subject: [PATCH 028/176] noqa for linting on a long formula --- src/simsopt/geo/surface.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/simsopt/geo/surface.py b/src/simsopt/geo/surface.py index 23706d0d3..04aaf54d4 100644 --- a/src/simsopt/geo/surface.py +++ b/src/simsopt/geo/surface.py @@ -746,7 +746,7 @@ def d2mean_cross_sectional_area_by_dcoeff_dcoeff(self): dztheta_dt = dg2_ds[:, :, 2, None, :] mean_area = np.mean((1/r) * (ztheta*(x*yvarphi-y*xvarphi)-zvarphi*(x*ytheta-y*xtheta)))/(2.*np.pi) - d2mean_area_ds2 = np.sign(mean_area)*np.mean((2*(-(xvarphi*y*ztheta) + xtheta*y*zvarphi + x*(yvarphi*ztheta - \ # noqa + d2mean_area_ds2 = np.sign(mean_area)*np.mean((2*(-(xvarphi*y*ztheta) + xtheta*y*zvarphi + x*(yvarphi*ztheta - \ ytheta*zvarphi))*dr_dt*dr_ds - r*((yvarphi*ztheta - \ ytheta*zvarphi)*dx_dt + y*zvarphi*dxtheta_dt - y*ztheta*dxvarphi_dt - \ xvarphi*ztheta*dy_dt + xtheta*zvarphi*dy_dt - xvarphi*y*dztheta_dt + \ @@ -769,7 +769,7 @@ def d2mean_cross_sectional_area_by_dcoeff_dcoeff(self): x*(-(dzvarphi_dt*dytheta_ds) + dztheta_dt*dyvarphi_ds + \ dyvarphi_dt*dztheta_ds - dytheta_dt*dzvarphi_ds)) + \ r*(xvarphi*y*ztheta - xtheta*y*zvarphi + x*(-(yvarphi*ztheta) + \ - ytheta*zvarphi))*dr2_dsdt)/r**3, axis=(0, 1))/(2*np.pi) + ytheta*zvarphi))*dr2_dsdt)/r**3, axis=(0, 1))/(2*np.pi) # noqa return d2mean_area_ds2 def arclength_poloidal_angle(self): From fe31f7b6b5d44bead58e103ac3ac32c294bb9c13 Mon Sep 17 00:00:00 2001 From: Elizabeth Date: Wed, 29 Nov 2023 20:58:42 -0500 Subject: [PATCH 029/176] Fix to cpp for clang compiler. --- src/simsoptpp/boozerresidual.cpp | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/simsoptpp/boozerresidual.cpp b/src/simsoptpp/boozerresidual.cpp index 13931d3c8..821e02e96 100644 --- a/src/simsoptpp/boozerresidual.cpp +++ b/src/simsoptpp/boozerresidual.cpp @@ -36,10 +36,10 @@ template void boozer_residual_ds_impl(double G, double iota, T& B, T& dB_dx, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres){ int nphi = xphi.shape(0); int ntheta = xtheta.shape(1); - int ndofs = dx_ds.shape(3); + size_t ndofs = dx_ds.shape(3); int num_points = 3 * nphi * ntheta; - constexpr int simd_size = xsimd::simd_type::size; + constexpr size_t simd_size = xsimd::simd_type::size; auto dx_ds_ij0 = AlignedPaddedVec(ndofs, 0); auto dx_ds_ij1 = AlignedPaddedVec(ndofs, 0); auto dx_ds_ij2 = AlignedPaddedVec(ndofs, 0); @@ -184,7 +184,7 @@ std::tuple boozer_residual_ds(double G, double iota, Array& B, Ar // flatten the quadrature points int nphi = xphi.shape(0); int ntheta = xtheta.shape(1); - int ndofs = dx_ds.shape(3); + size_t ndofs = dx_ds.shape(3); int num_points = nphi * ntheta; int num_threads= 0; @@ -259,10 +259,10 @@ template void boozer_residual_ds2_impl(double G, double iota, T& B, T& dB_dx, T& d2B_dx2, T& xphi, T& xtheta, T& dx_ds, T& dxphi_ds, T& dxtheta_ds, double& res, T& dres, T& d2res){ int nphi = xphi.shape(0); int ntheta = xtheta.shape(1); - int ndofs = dx_ds.shape(3); + size_t ndofs = dx_ds.shape(3); int num_points = 3 * nphi * ntheta; - constexpr int simd_size = xsimd::simd_type::size; + constexpr size_t simd_size = xsimd::simd_type::size; auto dx_ds_ij0 = AlignedPaddedVec(ndofs, 0); auto dx_ds_ij1 = AlignedPaddedVec(ndofs, 0); auto dx_ds_ij2 = AlignedPaddedVec(ndofs, 0); @@ -593,7 +593,7 @@ std::tuple boozer_residual_ds2(double G, double iota, Arra // flatten the quadrature points int nphi = xphi.shape(0); int ntheta = xtheta.shape(1); - int ndofs = dx_ds.shape(3); + size_t ndofs = dx_ds.shape(3); int num_points = nphi * ntheta; int num_threads= 0; From ee590e36e59faaa0bad315fff308bef3550deedd Mon Sep 17 00:00:00 2001 From: Bharat Medasani Date: Wed, 3 Apr 2024 16:45:03 -0400 Subject: [PATCH 030/176] Tmp commit to license --- LICENSE | 1 + 1 file changed, 1 insertion(+) diff --git a/LICENSE b/LICENSE index 47140c918..9c839b9b3 100644 --- a/LICENSE +++ b/LICENSE @@ -19,3 +19,4 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + From 3c6523ca5f0be1468474042497c03c0d24adcd0c Mon Sep 17 00:00:00 2001 From: Andrew Giuliani Date: Fri, 5 Apr 2024 12:57:09 -0400 Subject: [PATCH 031/176] cleaning up files --- .../inputs/input_ncsx/surface_0.json | 7022 ----------------- .../inputs/input_ncsx/surface_0.vts | Bin 31872 -> 0 bytes .../inputs/input_ncsx/surface_1.json | 7022 ----------------- .../inputs/input_ncsx/surface_1.vts | Bin 31872 -> 0 bytes .../inputs/input_ncsx/surface_2.json | 7022 ----------------- .../inputs/input_ncsx/surface_2.vts | Bin 31872 -> 0 bytes .../inputs/input_ncsx/surface_3.json | 7022 ----------------- .../inputs/input_ncsx/surface_3.vts | Bin 31872 -> 0 bytes .../inputs/input_ncsx/surface_4.json | 7022 ----------------- .../inputs/input_ncsx/surface_4.vts | Bin 31872 -> 0 bytes .../inputs/input_ncsx/surface_5.json | 7022 ----------------- .../inputs/input_ncsx/surface_5.vts | Bin 31872 -> 0 bytes .../inputs/input_ncsx/surface_6.json | 7022 ----------------- .../inputs/input_ncsx/surface_6.vts | Bin 31872 -> 0 bytes .../inputs/input_ncsx/surface_7.json | 7022 ----------------- .../inputs/input_ncsx/surface_7.vts | Bin 31872 -> 0 bytes .../inputs/input_ncsx/surface_8.json | 7022 ----------------- .../inputs/input_ncsx/surface_8.vts | Bin 31872 -> 0 bytes .../inputs/input_ncsx/surface_9.json | 7022 ----------------- .../inputs/input_ncsx/surface_9.vts | Bin 31872 -> 0 bytes 20 files changed, 70220 deletions(-) delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_0.json delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_0.vts delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_1.json delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_1.vts delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_2.json delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_2.vts delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_3.json delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_3.vts delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_4.json delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_4.vts delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_5.json delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_5.vts delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_6.json delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_6.vts delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_7.json delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_7.vts delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_8.json delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_8.vts delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_9.json delete mode 100644 examples/2_Intermediate/inputs/input_ncsx/surface_9.vts diff --git a/examples/2_Intermediate/inputs/input_ncsx/surface_0.json b/examples/2_Intermediate/inputs/input_ncsx/surface_0.json deleted file mode 100644 index 15dffe388..000000000 --- a/examples/2_Intermediate/inputs/input_ncsx/surface_0.json +++ /dev/null @@ -1,7022 +0,0 @@ -{ - "@module": "simsopt._core.json", - "@class": "SIMSON", - "@version": "0.13.0.post3+g0f8c1278.d20230501.dirty", - "graph": [ - { - "$type": "ref", - "value": "BoozerSurface1" - }, - { - "iota": -0.40631610013137615, - "G": 13.88747927294629 - } - ], - "simsopt_objs": { - "140342738246336": { - "@module": "simsopt._core.optimizable", - "@class": "DOFs", - "@name": "140342738246336", - "@version": "0.13.0.post3+g0f8c1278.d20230501.dirty", - "x": { - "@module": "numpy", - "@class": "array", - "dtype": "float64", - "data": [ - 1.506387961733893, - 0.1058930714809362, - 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