Add tests for ml modules

abipy/data/refs/al_eph/_runflow.py

@@ -109,12 +109,14 @@ def main(options):
 
     rename_table = [
         #  src, dest
+        ("_runflow/w1/outdata/out_DDB",  "out_444q_DDB"),
         ("_runflow/w2/t0/outdata/out_A2F.nc", "al_888k_161616q_A2F.nc"),
         ("_runflow/w2/t1/outdata/out_A2F.nc", "al_888k_161616q_vinterp_A2F.nc"),
-	("_runflow/w2/t2/outdata/out_PHDOS.nc", "al_161616q_PHDOS.nc"),
+        ("_runflow/w2/t2/outdata/out_PHDOS.nc", "al_161616q_PHDOS.nc"),
     ]
     import shutil
     for old, new in rename_table:
+        #print(old, new)
         shutil.copyfile(old, new)
     #shutil.rmtree("_runflow")
     sys.exit(0)

abipy/dynamics/hist.py

@@ -742,9 +742,9 @@ def get_dataframe(self, with_geo=True, index=None, abspath=False,
 
         kwargs:
             attrs:
-                List of additional attributes of the |GsrFile| to add to the |pandas-DataFrame|.
+                List of additional attributes of the |HistFile| to add to the |pandas-DataFrame|.
             funcs: Function or list of functions to execute to add more data to the DataFrame.
-                Each function receives a |GsrFile| object and returns a tuple (key, value)
+                Each function receives a |HistFile| object and returns a tuple (key, value)
                 where key is a string with the name of column and value is the value to be inserted.
         """
         # Add attributes specified by the users

abipy/eph/tests/test_varpeq.py

@@ -0,0 +1,61 @@
+"""Tests for varpeq module."""
+import abipy.data as abidata
+
+from abipy.core.testing import AbipyTest
+from abipy.eph.varpeq import VarpeqFile
+
+
+#class VarpeqTest(AbipyTest):
+#
+#    def test_varpeq_file(self):
+#        """Testing VarpeqFile."""
+#        with VarpeqFile(abidata.ref_file("abinitio_qpath_V1QAVG.nc")) as varpeq:
+#            repr(varpeq)
+#            str(varpeq)
+#            assert varpeq.to_string(verbose=2)
+#            assert not varpeq.params
+#            assert varpeq.structure.formula == "Ga1 P1" and len(varpeq.structure) == 2
+#
+#            #print(varpeq.ebands.kpoints.ksampling)
+#            for polaron in varpeq.polaron_spin:
+#                #print(polaron)
+#                #polaron.plot_bz_sampling()
+#                #polaron.plot_bqnu_with_phbands(phbands)
+#                polaron.plot_ank_with_ebands(ebands)
+#
+#                if self.has_matplotlib():
+#
+#            # Test jupyter notebook creation
+#            if self.has_nbformat():
+#                varpeq.write_notebook(nbpath=self.get_tmpname(text=True))
+
+
+#class VarpeqRobotTest(AbipyTest):
+#
+#    def test_varpeq_robot(self):
+#        """Testing VarpeqRobot."""
+#        files = abidata.ref_files(
+#            "abinitio_qpath_V1QAVG.nc",
+#            "interpolated_qpath_V1QAVG.nc",
+#        )
+#
+#        with VarpeqRobot.from_files(files[0]) as robot:
+#            robot.add_file("interpolated_v1qavg", files[1])
+#            assert len(robot) == 2
+#            repr(robot); str(robot)
+#            robot.to_string(verbose=2)
+#
+#            interp_ncfile = robot.abifiles[1]
+#            assert interp_ncfile.interpolated
+#            assert interp_ncfile.has_maxw
+#
+#            # Test matplotlib methods
+#            if self.has_matplotlib():
+#                assert robot.plot(ispden=0, vname="v1scf_avg", show=False)
+#                assert robot.plot_maxw(show=False) is None
+#                assert interp_ncfile.plot_maxw(show=False)
+#                assert interp_ncfile.plot_maxw_perts(scale="semilogy", sharey=False, fontsize=8, show=False)
+#
+#            # Test jupyter notebook creation
+#            if self.has_nbformat():
+#                robot.write_notebook(nbpath=self.get_tmpname(text=True))

abipy/flowtk/vzsisa.py

@@ -199,7 +199,7 @@ def on_all_ok(self):
             ph_work = PhononWork.from_scf_input(scf_input, self.ngqpt, is_ngqpt=True, tolerance=None,
                                                 with_becs=self.with_becs, with_quad=self.with_quad,
                                                 ndivsm=0 if bo_scale != 1.0 else self.ndivsm)
-            ph_work.set_name(f"PH for {bo_scale=}"
+            ph_work.set_name(f"PH for {bo_scale=}")
 
             # Reduce the number of files produced in the DFPT tasks to avoid possible disk quota issues.
             for task in ph_work[1:]:

abipy/flowtk/zsisa.py

@@ -274,7 +274,7 @@ def _on_ok(self):
                 structure=relaxed_structure,
                 cart_therm_stress=cart_therm_stress,
                 cart_bo_stress=gsr.cart_stress_tensor,
-                converged=converged.
+                converged=converged,
             )
 
         mjson_write(thermal_hist, json_path, indent=4)

abipy/ml/aseml.py

@@ -754,7 +754,10 @@ def plot_energies(self, fontsize=8, **kwargs) -> Figure:
             ax.grid(True)
             ax.set_xlabel(f"{key1} energy", fontsize=fontsize)
             ax.set_ylabel(f"{key2} energy", fontsize=fontsize)
-            linear_fit_ax(ax, xs, ys, fontsize=fontsize, with_label=True)
+            try:
+                linear_fit_ax(ax, xs, ys, fontsize=fontsize, with_label=True)
+            except ValueError as exc:
+                print(exc)
             ax.legend(loc="best", shadow=True, fontsize=fontsize)
             if irow == 0:
                 ax.set_title(f"{key1}/{key2} MAE: {stats.MAE:.6f}", fontsize=fontsize)
@@ -787,7 +790,10 @@ def plot_forces(self, symbol=None, site_inds=None, fontsize=8, **kwargs) -> Figu
                 xs, ys = self.xy_forces_for_keys(key1, key2, direction, symbol=symbol, site_inds=site_inds)
                 stats = diff_stats(xs, ys)
                 ax.scatter(xs, ys, marker="o")
-                linear_fit_ax(ax, xs, ys, fontsize=fontsize, with_label=True)
+                try:
+                    linear_fit_ax(ax, xs, ys, fontsize=fontsize, with_label=True)
+                except ValueError as exc:
+                    print(exc)
 
                 ax.legend(loc="best", shadow=True, fontsize=fontsize)
                 f_tex = f"$F_{direction}$"
@@ -820,7 +826,11 @@ def plot_stresses(self, fontsize=6, **kwargs) -> Figure:
                 stats = diff_stats(xs, ys)
                 ax = ax_mat[irow, icol]
                 ax.scatter(xs, ys, marker="o")
-                linear_fit_ax(ax, xs, ys, fontsize=fontsize, with_label=True)
+                try:
+                    linear_fit_ax(ax, xs, ys, fontsize=fontsize, with_label=True)
+                except ValueError as exc:
+                    print(exc)
+
                 ax.legend(loc="best", shadow=True, fontsize=fontsize)
                 ax.grid(True)
                 s_tex = r"$\sigma_{%s}$" % voigt_comp
@@ -880,7 +890,7 @@ def plot_forces_traj(self, delta_mode=True, symbol=None, fontsize=6, markersize=
             delta_mode: True to plot differences instead of absolute values.
             symbol: If not None, select only forces for this atomic species
         """
-        # Fx,Fy,Fx along rows, pairs along columns.
+        # Fx, Fy, Fx along rows, pairs along columns.
         key_pairs = self.get_key_pairs()
         nrows, ncols = 3, len(key_pairs)
         ax_mat, fig, plt = get_axarray_fig_plt(None, nrows=nrows, ncols=ncols,
@@ -892,7 +902,7 @@ def plot_forces_traj(self, delta_mode=True, symbol=None, fontsize=6, markersize=
         atom2_cmap = plt.get_cmap("jet")
         marker_idir = {0: ">", 1: "<", 2: "^"}
 
-        if symbol is None:
+        if symbol is not None:
             inds = np.array(self.structure.indices_from_symbol(symbol))
             if len(inds) == 0:
                 raise ValueError(f"Cannot find chemical {symbol=} in structure!")
@@ -1104,9 +1114,9 @@ def relax_atoms(atoms: Atoms,
     Args:
         atoms: ASE atoms.
         relax_mode: "ions" to relax ions only, "cell" for ions + cell, "no" for no relaxation.
-        optimizer: name of the ASE optimizer to use.
+        optimizer: name of the ASE optimizer to use for relaxation.
         fmax: tolerance for relaxation convergence. Here fmax is a sum of force and stress forces.
-        pressure: Target pressure.
+        pressure: Target pressure in GPa.
         verbose: whether to print stdout.
         steps: max number of steps for relaxation.
         opt_kwargs (dict): kwargs for the ASE optimizer class.
@@ -2101,7 +2111,7 @@ def __init__(self,
         """
         Args:
             atoms: ASE atoms to relax.
-            relax_mode: Relaxation mode.
+            relax_mode: "ions" to relax ions only, "cell" for ions + cell, "no" for no relaxation.
             fmax: tolerance for relaxation convergence. Here fmax is a sum of force and stress forces.
             pressure: Target pressure in GPa.
             steps: max number of steps for relaxation.
@@ -2309,7 +2319,7 @@ def __init__(self,
         Args:
             atoms: ASE atoms.
             temperature: Temperature in K
-            pressure:
+            pressure: Target pressure in GPa.
             timestep:
             steps: Number of steps.
             loginterval:
@@ -2427,9 +2437,9 @@ def __init__(self, traj_filepath, relax_mode, fmax, pressure, steps, optimizer,
         """
         Args:
             traj_filepath:
-            relax_mode:
+            relax_mode: "ions" to relax ions only, "cell" for ions + cell, "no" for no relaxation.
             fmax: tolerance for relaxation convergence. Here fmax is a sum of force and stress forces.
-            pressure: Target pressure.
+            pressure: Target pressure in GPa.
             steps: max number of steps for relaxation.
             optimizer: name of the ASE optimizer to use for relaxation.
             nn_name: String defining the NN potential. See also CalcBuilder.
@@ -2612,7 +2622,7 @@ def __init__(self,
             optimizer: name of the ASE optimizer to use for relaxation.
             relax_mode: "ions" to relax ions only, "cell" for ions + cell, "no" for no relaxation.
             fmax: tolerance for relaxation convergence. Here fmax is a sum of force and stress forces.
-            pressure: Target pressure
+            pressure: Target pressure in GPa.
             nn_name: String defining the NN potential. See also CalcBuilder.
             verbose: Verbosity level.
             workdir: Working directory.
@@ -2768,10 +2778,10 @@ def __init__(self,
             nimages: Number of NEB images.
             neb_method:
             climb:
-            optimizer:
+            optimizer: name of the ASE optimizer to use for relaxation.
             relax_mode: "ions" to relax ions only, "cell" for ions + cell, "no" for no relaxation.
             fmax: tolerance for relaxation convergence. Here fmax is a sum of force and stress forces.
-            pressure:
+            pressure: Target pressure in GPa.
             nn_name: String defining the NN potential. See also CalcBuilder.
             verbose: Verbosity level.
             workdir: Working directory.
@@ -2903,7 +2913,8 @@ def __init__(self,
                  max_ns,
                  optimizer,
                  relax_mode,
-                 fmax, pressure,
+                 fmax,
+                 pressure,
                  steps,
                  nn_name,
                  verbose,
@@ -2912,11 +2923,11 @@ def __init__(self,
         """
         Args:
             structure: Abipy Structure object or any object that can be converted to structure.
-            max_ns:
-            optimizer:
-            relax_mode:
-            fmax:
-            pressure:
+            max_ns: Maximum number of structures
+            optimizer: name of the ASE optimizer to use for relaxation.
+            relax_mode: "ions" to relax ions only, "cell" for ions + cell, "no" for no relaxation.
+            fmax: tolerance for relaxation convergence. Here fmax is a sum of force and stress forces.
+            pressure: Target pressure in GPa.
             steps:
             nn_name: String defining the NN potential. See also CalcBuilder.
             verbose: Verbosity level.
@@ -2964,10 +2975,10 @@ def run(self) -> None:
         Run MlOrderer.
         """
         workdir = self.workdir
-        from pymatgen.core import Lattice
-        specie = {"Cu0+": 0.5, "Au0+": 0.5}
-        structure = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.677), [specie], [[0, 0, 0]])
-        #structure = self.structure
+        #from pymatgen.core import Lattice
+        #specie = {"Cu0+": 0.5, "Au0+": 0.5}
+        #structure = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.677), [specie], [[0, 0, 0]])
+        structure = self.structure
         #print(structure)
 
         # Each dict in d_list contains the following entries:
@@ -3464,7 +3475,7 @@ def __init__(self,
             vol_scales: List of volumetric scaling factors.
             relax_mode:
             fmax: tolerance for relaxation convergence. Here fmax is a sum of force and stress forces.
-            pressure: Target pressure.
+            pressure: Target pressure in GPa.
             steps: max number of steps for relaxation.
             optimizer: name of the ASE optimizer to use for relaxation.
             nn_name: String defining the NN potential. See also CalcBuilder.