Merge with master

.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 }}

.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')

.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<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

.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:

.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<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

.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

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:
@@ -119,6 +119,7 @@ set(XTENSOR_USE_TBB 0)
 
 pybind11_add_module(${PROJECT_NAME}
     src/simsoptpp/python.cpp src/simsoptpp/python_surfaces.cpp src/simsoptpp/python_curves.cpp
+    src/simsoptpp/boozerresidual_py.cpp
     src/simsoptpp/python_magneticfield.cpp src/simsoptpp/python_tracing.cpp src/simsoptpp/python_distance.cpp
     src/simsoptpp/biot_savart_py.cpp
     src/simsoptpp/biot_savart_vjp_py.cpp
@@ -127,7 +128,7 @@ pybind11_add_module(${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
     )

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.
+

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
@@ -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 desc-opt toml
-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 desc-opt
 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

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
@@ -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

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
-<https://github.com/hiddenSymmetries/simsopt/wiki/NERSC-Cori>`_.
+<https://github.com/hiddenSymmetries/simsopt/wiki/NERSC-Perlmutter>`_.
 
 
 .. _singularity_doc:

docs/source/simsopt.geo.rst

@@ -76,6 +76,14 @@ simsopt.geo.curvexyzfourier module
    :undoc-members:
    :show-inheritance:
 
+simsopt.geo.curvexyzfouriersymmetries module
+--------------------------------------------
+
+.. automodule:: simsopt.geo.curvexyzfouriersymmetries
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 simsopt.geo.finitebuild module
 ------------------------------
 

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}")