Merge branch 'main' into uz/papero

.github/workflows/ngsPETSc.yml

@@ -73,11 +73,11 @@ jobs:
     steps:
       - name: Check out repository code
         uses: actions/checkout@v4
-      
+
       - name: Install pytest
         run: |
           pip install pytest --break-system-packages
-      
+
       - name: Install Netgen and ngsPETSc
         run: |
           pip install netgen-mesher --break-system-packages
@@ -120,3 +120,29 @@ jobs:
           pytest tests/regression/test_poisson_strong_bcs.py
           pytest tests/multigrid/test_netgen_gmg.py
           pytest tests/regression/test_netgen.py
+
+  firedrake-complex:
+    runs-on: ubuntu-latest
+    container:
+      image: firedrakeproject/firedrake-complex:latest
+      options: --user root
+    timeout-minutes: 50
+
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v4
+
+      - name: Install Netgen and ngsPETSc
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          pip install netgen-mesher
+          pip install xdist pytest-timeout ipympl
+          NGSPETSC_NO_INSTALL_REQUIRED=ON pip install .
+
+      - name: Run part of the Firedrake test suite
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          cd $VIRTUAL_ENV/src/firedrake
+          pytest tests/regression/test_poisson_strong_bcs.py
+          pytest tests/multigrid/test_netgen_gmg.py
+          pytest tests/regression/test_netgen.py

README.md

@@ -13,12 +13,12 @@ If you already have NGSolve (with MPI support) and PETSc installed, you can inst
     cd ngsPETSc
     pip install .
 ```
-Alternatively, you can also build PETSc, SLEPc, and NGSolve from source following the instructions in the [documentation](https://ngspetsc.readthedocs.io/en/latest/installation.html).
+Alternatively, you can also build PETSc, SLEPc, and NGSolve from source following the instructions in the [documentation](https://ngspetsc.readthedocs.io/en/latest/install.html).
 
 ## Getting started
 
 To get started with ngsPETSc, check out the [documentation](https://ngspetsc.readthedocs.io/en/latest/).
 To test the installation, you can run the tests in the `tests` folder, via the Makefile in the root directory of the repository:
 ```bash
     make test
-```
+```

docs/src/install.rst

@@ -11,15 +11,13 @@ First we install all the needed packages using apt and pip or an equivalent pack
 ::
     apt-get update
     apt-get -y install git build-essential cmake python3 python3-distutils python3-tk libpython3-dev libxmu-dev tk-dev tcl-dev g++ libglu1-mesa-dev liblapacke-dev libblas-dev liblapack-dev
-    pip install numpy cython pytest pytest-mpi
+    pip install numpy cython pytest pytest-mpi netgen-occt
 
 We now install PETSc from scratch in a suitable folder, with OpenMPI, HYPRE, Metis, MUMPS, SuprLU, Scalapack and eigen.
 ::
     git clone https://gitlab.com/petsc/petsc.git
     cd petsc
-    python configure --download-chaco \
-    --download-cmake \
-    --download-eigen \
+    python configure --download-cmake \
     --download-openmpi \
     --download-hypre \
     --download-metis \
@@ -28,13 +26,13 @@ We now install PETSc from scratch in a suitable folder, with OpenMPI, HYPRE, Met
     --download-mumps \
     --download-scalapack \
     --download-superlu_dist \
+    --download-fblaslapack=1 \
     --with-c2html=0 \
-    --with-cxx-dialect=C++11 \
     --with-debugging=0 \
-    --download-fblaslapack=1 \
     --with-fortran-bindings=0 \
     --with-shared-libraries=1 \
-    --with-petsc4py=1 \
+    --with-petsc4py=1
+
 To build PETSc you need to run the Makefile as suggested at the end of the configuration script.
 We now need to set in the ``.bashrc`` (on OSX in ``.bash_profile``) file the ``PETSC_DIR``, ``PETSC_ARCH`` system variables as they appear when we finish build PETSc.
 You also need to add to your ``PYTHONPATH`` the ``PYTHONPATH`` that appears when we finished building PETSc.
@@ -68,12 +66,14 @@ Now we build NGSolve from source.
     mkdir $BASEDIR/ngsolve-build
     mkdir $BASEDIR/ngsolve-install
     cd $BASEDIR/ngsolve-build
-    cmake -DCMAKE_INSTALL_PREFIX=${BASEDIR}/ngsolve-install ${BASEDIR}/ngsolve-src -DUSE_MPI=ON
+    cmake -DCMAKE_INSTALL_PREFIX=${BASEDIR}/ngsolve-install ${BASEDIR}/ngsolve-src -DUSE_MPI=ON -DUSE_OCC=ON
     make
     make install
+
 You should add to your ``.bashrc`` the ``BASEDIR`` system variable:
 ::
-  echo "export $BASEDIR=${BASEDIR}" >> ~/.bashrc  
+    echo "export $BASEDIR=${BASEDIR}" >> ~/.bashrc  
+
 We suggest you add the following lines to your ``.bashrc``:
 ::
     export NETGENDIR="${BASEDIR}/ngsolve-install/bin"

ngsPETSc/utils/fenicsx.py

@@ -30,8 +30,7 @@ def model_to_mesh(self, hmax: float, gdim: int = 2,
         [_MPI.Comm, int, int, dolfinx.cpp.graph.AdjacencyList_int32],
         dolfinx.cpp.graph.AdjacencyList_int32] =
         dolfinx.mesh.create_cell_partitioner(dolfinx.mesh.GhostMode.none),
-        transform: typing.Any = None, routine: typing.Any = None) -> typing.Tuple[dolfinx.mesh.Mesh,
-        dolfinx.cpp.mesh.MeshTags_int32,dolfinx.cpp.mesh.MeshTags_int32]:
+        transform: typing.Any = None, routine: typing.Any = None) -> dolfinx.mesh.Mesh:
         """Given a NetGen model, take all physical entities of the highest
         topological dimension and create the corresponding DOLFINx mesh.
 

paper/paper.md

@@ -5,40 +5,46 @@ tags:
   - FEM
   - Meshing
 authors:
+  - name: Jack Betteridge
+    orcid: 0000-0002-3919-8603
+    equal-contrib: true
+    affiliation: 1
   - name: Patrick E. Farrell
     orcid: 0000-0002-1241-7060
     equal-contrib: true
-    affiliation: 1
+    affiliation: 2
   - name: Matthias Hochsteger
     orcid: 0009-0001-8842-3221
     equal-contrib: true
-    affiliation: 2
+    affiliation: 3
   - name: Christopher Lackner
     orcid: 0009-0000-3448-3002
     equal-contrib: true
-    affiliation: 2
+    affiliation: 3
   - name: Joachim Schöberl
-    affiliation: 2,3
+    affiliation: 3,4
     equal-contrib: true 
     orcid: 0000-0002-1250-5087
   - name: Stefano Zampini
     orcid: 0000-0002-0435-0433
     equal-contrib: true 
-    affiliation: 4
+    affiliation: 5
   - name: Umberto Zerbinati
     orcid: 0000-0002-2577-1106
     corresponding: true
     equal-contrib: true 
-    affiliation: 1
+    affiliation: 2
 affiliations:
- - name: University of Oxford, United Kingdom
+ - name: Imperial College London, United Kingdom
    index: 1
  - name: CERBSim GmbH, Austria
-   index: 2
- - name: TU Wien, Austria
+ - index: 2
+ - name: University of Oxford, United Kingdom
    index: 3
- - name: King Abdullah University of Science and Technology, Saudi Arabia
+ - name: TU Wien, Austria
    index: 4
+ - name: King Abdullah University of Science and Technology, Saudi Arabia
+   index: 5
 date: 1 July 2024
 bibliography: paper.bib
 ---