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NGSolve · Nov 8, 2024 · 9168553 · 9168553
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diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ If you already have NGSolve (with MPI support) and PETSc installed, you can inst
 git clone https://github.com/UZerbinati/ngsPETSc.git
 pip install ./ngsPETSc
 ```
-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).
 
 ### Testing
 To test the installation, you can run the tests in the `tests` folder, via the Makefile in the root directory of the repository:

diff --git a/docs/src/install.rst b/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"

diff --git a/ngsPETSc/utils/fenicsx.py b/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.
 

diff --git a/paper/paper.bib b/paper/paper.bib
@@ -24,6 +24,23 @@ @article{Firedrake
   year={2023},
   doi= {10.25561/104839}
 }
+@article{TETGEN,
+author = {Si, Hang},
+title = {TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator},
+year = {2015},
+issue_date = {January 2015},
+publisher = {Association for Computing Machinery},
+address = {New York, NY, USA},
+volume = {41},
+number = {2},
+issn = {0098-3500},
+url = {https://doi.org/10.1145/2629697},
+doi = {10.1145/2629697},
+journal = {ACM Trans. Math. Softw.},
+month = feb,
+articleno = {11},
+numpages = {36}
+}
 @techreport{PETSc,
   author={Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed
           Brown and Peter Brune and Kris Buschelman and Emil Constantinescu and Lisandro
@@ -181,3 +198,67 @@ @article{stevenson2006
  R.},
  year={2006},
  pages={245--269} }
+@article{FreeFEM,
+  title={FreeFem++ manual},
+  author={Hecht, Fr{\'e}d{\'e}ric and Pironneau, Olivier and Le Hyaric, A and Ohtsuka, K},
+  journal={Laboratoire Jacques Louis Lions},
+  year={2005}
+}
+@Article{DUNE,
+author={Dedner, Andreas
+and Kl{\"o}fkorn, Robert
+and Nolte, Martin
+and Ohlberger, Mario},
+title={A generic interface for parallel and adaptive discretization schemes: abstraction principles and the Dune-Fem module},
+journal={Computing},
+year={2010},
+month={Nov},
+day={01},
+volume={90},
+number={3},
+pages={165-196},
+issn={1436-5057},
+doi={10.1007/s00607-010-0110-3},
+url={https://doi.org/10.1007/s00607-010-0110-3}
+}
+@Article{dealII,
+  title   = {The \texttt{deal.II} Library, Version 9.5},
+  author  = {Daniel Arndt and Wolfgang Bangerth and Maximilian Bergbauer and
+             Marco Feder and Marc Fehling and Johannes Heinz and
+             Timo Heister and Luca Heltai and Martin Kronbichler and
+             Matthias Maier and Peter Munch and Jean-Paul Pelteret and
+             Bruno Turcksin and David Wells and Stefano Zampini},
+  journal = {Journal of Numerical Mathematics},
+  year    = {2023},
+  doi     = {10.1515/jnma-2023-0089},
+  pages   = {231--246},
+  volume  = {31},
+  number  = {3},
+  url     = {https://dealii.org/deal95-preprint.pdf}
+}
+@misc{dolfinX,
+  author       = {Baratta, Igor A. and
+                  Dean, Joseph P. and
+                  Dokken, Jørgen S. and
+                  Habera, Michal and
+                  Hale, Jack S. and
+                  Richardson, Chris N. and
+                  Rognes, Marie E. and
+                  Scroggs, Matthew W. and
+                  Sime, Nathan and
+                  Wells, Garth N.},
+  title        = {{DOLFINx: The next generation FEniCS problem solving environment}},
+  month        = dec,
+  year         = 2023,
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.10447666},
+  url          = {https://doi.org/10.5281/zenodo.10447666}
+}
+@article{GMSH,
+  title={A three-dimensional finite element mesh generator with built-in pre-and post-processing facilities},
+  author={Geuzaine, Christophe and Remacle, Jean-Fran{\c{c}}ois},
+  journal={International Journal for Numerical Methods in Engineering},
+  volume={11},
+  pages={79},
+  year={2020}
+}
diff --git a/paper/paper.md b/paper/paper.md
@@ -12,15 +12,23 @@ authors:
   - name: Patrick E. Farrell
     orcid: 0000-0002-1241-7060
     equal-contrib: true
+    affiliation: 3
+  - name: Matthias Hochsteger
+    orcid: 0009-0001-8842-3221
+    equal-contrib: true
+    affiliation: 2
+  - name: Christopher Lackner
+    orcid: 0009-0000-3448-3002
+    equal-contrib: true
     affiliation: 2
   - name: Joachim Schöberl
-    affiliation: 3
+    affiliation: 2,4
     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
@@ -29,19 +37,21 @@ authors:
 affiliations:
  - name: Imperial College London, United Kingdom
    index: 1
- - name: University of Oxford, United Kingdom
+ - name: CERBSim GmbH, Austria
    index: 2
- - name: TU Wien, Austria
+ - 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
 ---
 
 # Summary
 
-Combining advanced meshing techniques with robust solver capabilities is essential for solving difficult problems in computational science and engineering. This paper introduces ngsPETSc, software built with petsc4py [@petsc4py] that seamlessly integrates the NETGEN mesher [@Netgen], the NGSolve finite element library [@NGSolve], and the PETSc toolkit [@PETSc]. ngsPETSc enables the use of NETGEN meshes and geometries in PETSc-based solvers, and provides NGSolve users access to the wide array of linear, nonlinear solvers, and time-steppers available in PETSc.
+Combining advanced meshing techniques with robust solver capabilities is essential for solving difficult problems in computational science and engineering. In recent years, various software packages have been developed to support the integration of meshing tools with finite element solvers. To mention a few, FreeFEM [@FreeFEM] includes built-in support for mesh generation, allowing users to create and manipulate meshes directly within the software. Similarly, deal.II [@dealII] provides a GridGenerator class for generating standard mesh geometries like grids and cylinders. Furthermore, deal.II can interface with OpenCASCADE [@OpenCASCADE] to refine existing grids while conforming to the geometry provided. Other finite element libraries, such as Firedrake [@Firedrake], DUNE-FEM [@DUNE], and FEniCSx [@dolfinX], rely on external tools like Gmsh [@GMSH] and Tetgen [@TETGEN] for mesh generation. This paper introduces ngsPETSc, software built with petsc4py [@petsc4py] that seamlessly integrates the NETGEN mesher [@Netgen], the NGSolve finite element library [@NGSolve], and the PETSc toolkit [@PETSc]. ngsPETSc enables the use of NETGEN meshes and geometries in PETSc-based solvers, and provides NGSolve users access to the wide array of linear, nonlinear solvers, and time-steppers available in PETSc.
 
 # Statement of Need