Merge branch 'main' into uzerbinati/paper

NGSolve · Mar 1, 2024 · df50ad6 · df50ad6
2 parents 0039bdb + e0f9628
commit df50ad6
Show file tree

Hide file tree

Showing 10 changed files with 277 additions and 71 deletions.
diff --git a/.github/workflows/Docker.yml b/.github/workflows/Docker.yml
@@ -4,6 +4,8 @@ on:
     schedule:
     - cron:  '30 10 7,14,21,28 * *'
 
+    workflow_dispatch:
+
     push:
         paths:
         - Dockerfile
@@ -14,8 +16,9 @@ jobs:
     timeout-minutes: 360
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Login to Docker Hub
+        if: github.repository == 'NGSolve/ngsPETSc'
         uses: docker/login-action@v1
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
@@ -24,6 +27,7 @@ jobs:
         run: |
           docker build -t ngspetsc:latest .
       - name: Push Docker image
+        if: github.repository == 'NGSolve/ngsPETSc'
         run: |
           docker tag ngspetsc:latest urzerbinati/ngspetsc:latest
           docker push urzerbinati/ngspetsc:latest
diff --git a/.github/workflows/ngsPETSc.yml b/.github/workflows/ngsPETSc.yml
@@ -1,8 +1,8 @@
 # .github/workflows/app.yaml
 name: ngsPETSc tests
-on: 
+on:
     push:
-      branches-ignore:    
+      branches-ignore:
       - 'no-ci/*'
 
     schedule:
@@ -16,7 +16,7 @@ jobs:
 
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Install ngsPETSc
         run: |
@@ -51,20 +51,20 @@ jobs:
 
   fenicsx:
     runs-on: ubuntu-latest
-    container: dolfinx/dolfinx:latest
-    timeout-minutes: 30
+    container: dolfinx/dolfinx:nightly
+    timeout-minutes: 50
 
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Install Netgen and ngsPETSc
         run: |
-          pip3 install netgen-mesher \
-          && pip3 install pylint \
-          && export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python3.10/site-packages \
-          && echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV \
-          && NGSPETSC_NO_INSTALL_REQUIRED=ON pip install .
+          pip install netgen-mesher
+          pip install pylint
+          export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python3.10/site-packages
+          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+          NGSPETSC_NO_INSTALL_REQUIRED=ON pip install .
 
       - name: Check formatting
         run: |
@@ -73,4 +73,4 @@ jobs:
 
       - name: Run test suite in serial
         run: |
-          pytest -v tests/test_fenicsx.py
+          pytest -v tests/test_fenicsx.py
diff --git a/Makefile b/Makefile
@@ -1,9 +1,9 @@
 MPI_EXEC = ${PETSC_DIR}/${PETSC_ARCH}/bin/mpiexec
 lint:
-	pylint --disable=C0412,C0103,C0415,C0321,E0401,E1101,E0611,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc
-	pylint --disable=C0412,C0103,C0415,C0321,C3001,E0401,E1101,E0611,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,W0406,W0212,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc/utils
+	pylint --disable=C0412,C0103,C0415,C0321,E0401,E1101,E0611,R1728,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc
+	pylint --disable=C0412,C0103,C0415,C0321,C3001,E0401,E1101,E0611,R1728,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,W0406,W0212,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc/utils
 lint_test:
-	pylint --disable=C0412,C0103,C0415,C0321,E0401,E1101,E0611,R1736,R0401,R0914,R0801,R0902,R1702,R0913,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase tests
+	pylint --disable=C0412,C0103,C0415,C0321,E0401,E1101,E0611,R1728,R1736,R0401,R0914,R0801,R0902,R1702,R0913,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase tests
 test:
 	pytest tests/test_env.py
 	pytest tests/test_vec.py

diff --git a/docs/src/Tutorials.rst b/docs/src/Tutorials.rst
@@ -9,3 +9,4 @@ How to use ngsPETSc
    notebooks/Meshes
    notebooks/Krylov Solver and Preconditioners
    notebooks/Eigenvalue Problems
+   Firedrake-Netgen interface via ngsPETSc <https://www.firedrakeproject.org/demos/netgen_mesh.py.html>
diff --git a/ngsPETSc/plex.py b/ngsPETSc/plex.py
@@ -33,8 +33,9 @@ class MeshMapping:
 
     '''
 
-    def __init__(self, mesh=None, name="Default"):
+    def __init__(self, mesh=None, comm=MPI.COMM_WORLD, name="Default"):
         self.name = name
+        self.comm = comm
         if isinstance(mesh,(ngs.comp.Mesh,ngm.Mesh)):
             self.createPETScDMPlex(mesh)
         elif isinstance(mesh,PETSc.DMPlex):
@@ -157,7 +158,7 @@ def createPETScDMPlex(self, mesh):
             self.ngMesh = mesh.ngmesh
         else:
             self.ngMesh = mesh
-        comm = MPI.COMM_WORLD
+        comm = self.comm
         if self.ngMesh.dim == 3:
             if comm.rank == 0:
                 V = self.ngMesh.Coordinates()
@@ -168,7 +169,7 @@ def createPETScDMPlex(self, mesh):
                     surfMesh, dim = True, 2
                     T = self.ngMesh.Elements2D().NumPy()["nodes"]
                     T = np.array([list(np.trim_zeros(a, 'b')) for a in list(T)])-1
-                plex = PETSc.DMPlex().createFromCellList(dim, T, V)
+                plex = PETSc.DMPlex().createFromCellList(dim, T, V, comm=comm)
                 plex.setName(self.name)
                 vStart, _ = plex.getDepthStratum(0)
                 if surfMesh:
@@ -186,14 +187,15 @@ def createPETScDMPlex(self, mesh):
             else:
                 plex = PETSc.DMPlex().createFromCellList(3,
                                                         np.zeros((0, 4), dtype=np.int32),
-                                                        np.zeros((0, 3), dtype=np.double))
+                                                        np.zeros((0, 3), dtype=np.double),
+                                                        comm=comm)
                 self.petscPlex = plex
         elif self.ngMesh.dim == 2:
             if comm.rank == 0:
                 V = self.ngMesh.Coordinates()
                 T = self.ngMesh.Elements2D().NumPy()["nodes"]
                 T = np.array([list(np.trim_zeros(a, 'b')) for a in list(T)])-1
-                plex = PETSc.DMPlex().createFromCellList(2, T, V)
+                plex = PETSc.DMPlex().createFromCellList(2, T, V, comm=comm)
                 plex.setName(self.name)
                 vStart, _ = plex.getDepthStratum(0)   # vertices
                 for e in self.ngMesh.Elements1D():
@@ -208,5 +210,6 @@ def createPETScDMPlex(self, mesh):
             else:
                 plex = PETSc.DMPlex().createFromCellList(2,
                                                         np.zeros((0, 3), dtype=np.int32),
-                                                        np.zeros((0, 2), dtype=np.double))
+                                                        np.zeros((0, 2), dtype=np.double),
+                                                        comm=comm)
                 self.petscPlex = plex
diff --git a/ngsPETSc/utils/fenicsx.py b/ngsPETSc/utils/fenicsx.py
@@ -34,7 +34,7 @@ def model_to_mesh(self, hmax: float, gdim: int = 2,
         dolfinx.cpp.mesh.MeshTags_int32,dolfinx.cpp.mesh.MeshTags_int32]:
         """Given a NetGen model, take all physical entities of the highest
         topological dimension and create the corresponding DOLFINx mesh.
-        
+
         This function only works in serial, at the moment.
 
         Args:
@@ -73,9 +73,10 @@ def model_to_mesh(self, hmax: float, gdim: int = 2,
             V = ngmesh.Coordinates()
             T = ngmesh.Elements3D().NumPy()["nodes"]
             T = np.array([list(np.trim_zeros(a, 'b')) for a in list(T)])-1
-        ufl_domain = dolfinx.io.gmshio.ufl_mesh(_ngs_to_cells[(gdim,T.shape[1])],gdim)
+        ufl_domain = dolfinx.io.gmshio.ufl_mesh(
+            _ngs_to_cells[(gdim,T.shape[1])], gdim, dolfinx.default_real_type)
         cell_perm = dolfinx.cpp.io.perm_gmsh(dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())),
                                              T.shape[1])
-        T = T[:, cell_perm]
+        T = np.ascontiguousarray(T[:, cell_perm])
         mesh = dolfinx.mesh.create_mesh(self.comm, T, V, ufl_domain, partitioner)
         return mesh