Prepare for a v0.7.x release

.github/workflows/testing.yml

@@ -9,40 +9,38 @@ on:
     # '*' is a special character in YAML, so string must be quoted
     - cron: "0 1 * * *"
 env:
-  PETSC_ARCH: linux-gnu-real-32
+  PETSC_ARCH: linux-gnu-real64-32
 jobs:
   build:
-    if: "!(contains(github.event.head_commit.message, '[ci skip]') || contains(github.event.head_commit.message, '[skip ci]'))"
     runs-on:
       ubuntu-latest
-    container: fenicsproject/test-env:nightly-mpich
-
+    container: ghcr.io/fenics/test-env:v0.7.2-mpich
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
 
       - name: Get Basix
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: ./basix
           repository: FEniCS/basix
-          ref: main
+          ref: v0.7.0
 
       - name: Install UFL, Basix, FFCx
         run: |
           cmake -G Ninja -B build-basix -DCMAKE_BUILD_TYPE="Release" -S ./basix/cpp/
           cmake --build build-basix --parallel 3
           cmake --install build-basix
           BUILD_TYPE="Release" pip3 install ./basix/python
-          python3 -m pip install git+https://github.com/FEniCS/ufl.git
-          python3 -m pip install git+https://github.com/FEniCS/ffcx.git
+          python3 -m pip install git+https://github.com/FEniCS/ufl.git@2023.2.0
+          python3 -m pip install git+https://github.com/FEniCS/ffcx.git@v0.7.0
 
       - name: Get DOLFINx
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: ./dolfinx
           repository: FEniCS/dolfinx
-          ref: main
+          ref: v0.7.2
 
       - name: Configure C++ (dolfinx)
         run: |

.gitignore

@@ -0,0 +1,4 @@
+**/*build-dir*/**
+__pycache__
+*.egg-info
+*.bp

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Joseph P. Dean
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+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.

convergence.py

@@ -13,7 +13,7 @@
 # Problem
 create_problem = problems.create_problem_0
 # Characteristic element size
-hs = [1 / 4, 1 / 8]
+hs = [1 / 2, 1 / 4, 1 / 8]
 # Polynomial orders
 ks = [1, 2, 3, 4]
 # Coefficients

cpp/README.md

@@ -2,15 +2,49 @@
 ## Muelu Trilinos Demo
 
 To compile, first install FEniCS-X dolfinx (real or complex)
-and Trilinos (an example build script is in builder.sh)
+and [Trilinos](https://github.com/trilinos/Trilinos.git)  (an example build script is in builder.sh)
 
+1. Clone trilinos from their github and checkout the correct version:
+```bash
+git clone https://github.com/trilinos/Trilinos.git
+cd Trilinos
+git checkout trilinos-release-13-4-1
+```
+2. Buld trilinos
+```bash
+cmake -G Ninja -B build-dir-trilinos \
+      -DTPL_ENABLE_MPI=ON \
+      -DMPI_BASE_DIR=/usr/x86_64-linux/ \
+      -DTrilinos_ENABLE_COMPLEX_DOUBLE=ON \
+      -DTrilinos_ENABLE_MueLu=ON \
+      -DTrilinos_ENABLE_TrilinosCouplings=ON \
+      -DTrilinos_ENABLE_Teko=OFF \
+      -DTpetra_INST_INT_LONG=ON \
+      -DTpetra_INST_INT_LONG_LONG=OFF \
+      -DBUILD_SHARED_LIBS=ON \
+      -DTrilinos_ENABLE_PyTrilinos=OFF \
+      -DTPL_ENABLE_Netcdf=OFF \
+      .
+ninja -j8 -C build-dir-trilinos
+
+```
+
+3. Compile integration kernels
 For real
 
-`ffcx --scalar_type=double maxwell.ufl`
+```bash
+python3 -m ffcx --scalar_type=double maxwell.py
+```
 
 or for complex
 
-`ffcx --scalar_type="double complex" maxwell.ufl`
+```bash
+python3 -m ffcx --scalar_type="double complex" maxwell.py
+```
+
+4. Compile demo
 
-cmake .
-make
+```bash
+cmake -G Ninja -B build-dir -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="-fmax-errors=1"
+ninja -j8 -C build-dir
+```

cpp/builder.sh

@@ -1,15 +1,16 @@
 #!/bin/bash
-rm -r build
-mkdir -p build
-cd build
-cmake -DTPL_ENABLE_MPI=ON \
+# Based on trilinos released: trilinos-release-13.4.1
+cmake -B build-dir-trilinos \
+      -DTPL_ENABLE_MPI=ON \
       -DMPI_BASE_DIR=/usr/x86_64-linux/ \
       -DTrilinos_ENABLE_COMPLEX_DOUBLE=ON \
       -DTrilinos_ENABLE_MueLu=ON \
       -DTrilinos_ENABLE_TrilinosCouplings=ON \
-      -DTpetra_INST_INT_LONG_LONG=OFF \
+      -DTrilinos_ENABLE_Teko=OFF \
       -DTpetra_INST_INT_LONG=ON \
+      -DTpetra_INST_INT_LONG_LONG=OFF \
       -DBUILD_SHARED_LIBS=ON \
       -DTrilinos_ENABLE_PyTrilinos=OFF \
       -DTPL_ENABLE_Netcdf=OFF \
       -DCMAKE_INSTALL_PREFIX=/home/chris/packages/trilinos ..
+      .

cpp/main.cpp

@@ -1,9 +1,7 @@
 
 #include "lumping.h"
 #include "maxwell.h"
-#include "tpetra_util.h"
-
-#include <MatrixMarket_Tpetra.hpp>
+#include "tpetra_util.h" #include < MatrixMarket_Tpetra.hpp>
 #include <MueLu_CreateTpetraPreconditioner.hpp>
 #include <MueLu_RefMaxwell.hpp>
 #include <Tpetra_Core.hpp>
@@ -28,7 +26,8 @@
 void tpetra_assemble(Teuchos::RCP<Tpetra::CrsMatrix<PetscScalar, std::int32_t,
                                                     std::int64_t, Node>>
                          A_Tpetra,
-                     const fem::Form<PetscScalar> &form) {
+                     const fem::Form<PetscScalar> &form)
+{
 
   std::vector<std::int64_t> global_cols; // temp for columns
   const std::shared_ptr<const fem::FunctionSpace> V = form.function_spaces()[0];
@@ -41,36 +40,42 @@ void tpetra_assemble(Teuchos::RCP<Tpetra::CrsMatrix<PetscScalar, std::int32_t,
       tpetra_insert = [&A_Tpetra, &global_indices, &global_cols, &nlocalrows](
                           std::int32_t nr, const std::int32_t *rows,
                           const std::int32_t nc, const std::int32_t *cols,
-                          const PetscScalar *data) {
-        for (std::int32_t i = 0; i < nr; ++i) {
-          Teuchos::ArrayView<const PetscScalar> data_view(data + i * nc, nc);
-          if (rows[i] < nlocalrows) {
-            Teuchos::ArrayView<const int> col_view(cols, nc);
-            int nvalid =
-                A_Tpetra->sumIntoLocalValues(rows[i], col_view, data_view);
-            if (nvalid != nc)
-              throw std::runtime_error("Inserted " + std::to_string(nvalid) +
-                                       "/" + std::to_string(nc) + " on row:" +
-                                       std::to_string(global_indices[rows[i]]));
-          } else {
-            global_cols.resize(nc);
-            for (int j = 0; j < nc; ++j)
-              global_cols[j] = global_indices[cols[j]];
-            int nvalid = A_Tpetra->sumIntoGlobalValues(global_indices[rows[i]],
-                                                       global_cols, data_view);
-            if (nvalid != nc)
-              throw std::runtime_error("Inserted " + std::to_string(nvalid) +
-                                       "/" + std::to_string(nc) + " on row:" +
-                                       std::to_string(global_indices[rows[i]]));
-          }
-        }
-        return 0;
-      };
+                          const PetscScalar *data)
+  {
+    for (std::int32_t i = 0; i < nr; ++i)
+    {
+      Teuchos::ArrayView<const PetscScalar> data_view(data + i * nc, nc);
+      if (rows[i] < nlocalrows)
+      {
+        Teuchos::ArrayView<const int> col_view(cols, nc);
+        int nvalid =
+            A_Tpetra->sumIntoLocalValues(rows[i], col_view, data_view);
+        if (nvalid != nc)
+          throw std::runtime_error("Inserted " + std::to_string(nvalid) +
+                                   "/" + std::to_string(nc) + " on row:" +
+                                   std::to_string(global_indices[rows[i]]));
+      }
+      else
+      {
+        global_cols.resize(nc);
+        for (int j = 0; j < nc; ++j)
+          global_cols[j] = global_indices[cols[j]];
+        int nvalid = A_Tpetra->sumIntoGlobalValues(global_indices[rows[i]],
+                                                   global_cols, data_view);
+        if (nvalid != nc)
+          throw std::runtime_error("Inserted " + std::to_string(nvalid) +
+                                   "/" + std::to_string(nc) + " on row:" +
+                                   std::to_string(global_indices[rows[i]]));
+      }
+    }
+    return 0;
+  };
 
   fem::assemble_matrix(tpetra_insert, form, {});
 }
 
-int main(int argc, char **argv) {
+int main(int argc, char **argv)
+{
   common::subsystem::init_mpi(argc, argv);
   common::subsystem::init_logging(argc, argv);
 
@@ -121,7 +126,8 @@ int main(int argc, char **argv) {
       create_tpetra_diagonal_matrix<PetscScalar>(Q->dofmap()->index_map);
   std::vector<std::int32_t> col(1);
   std::vector<PetscScalar> val(1);
-  for (int i = 0; i < Q->dofmap()->index_map->size_local(); ++i) {
+  for (int i = 0; i < Q->dofmap()->index_map->size_local(); ++i)
+  {
     col[0] = i;
     val[0] = 1.0 / vals[i];
     Mg_mat->replaceLocalValues(i, col, val);
@@ -135,14 +141,16 @@ int main(int argc, char **argv) {
   std::function<int(std::int32_t, const std::int32_t *, std::int32_t,
                     const std::int32_t *, const PetscScalar *)>
       mat_set_dg = [&D0_mat](int nr, const int *rows, int nc, const int *cols,
-                             const PetscScalar *data) {
-        for (int i = 0; i < nr; ++i) {
-          Teuchos::ArrayView<const PetscScalar> data_view(data + i * nc, nc);
-          Teuchos::ArrayView<const int> col_view(cols, nc);
-          D0_mat->replaceLocalValues(rows[i], col_view, data_view);
-        }
-        return 0;
-      };
+                             const PetscScalar *data)
+  {
+    for (int i = 0; i < nr; ++i)
+    {
+      Teuchos::ArrayView<const PetscScalar> data_view(data + i * nc, nc);
+      Teuchos::ArrayView<const int> col_view(cols, nc);
+      D0_mat->replaceLocalValues(rows[i], col_view, data_view);
+    }
+    return 0;
+  };
 
   fem::assemble_discrete_gradient(mat_set_dg, *V, *Q);
   D0_mat->fillComplete();
@@ -153,10 +161,12 @@ int main(int argc, char **argv) {
           new Tpetra::MultiVector<double, std::int32_t, std::int64_t, Node>(
               Mg_mat->getRowMap(), 3));
   fem::Function<double> xcoord(Q);
-  for (int j = 0; j < 3; ++j) {
+  for (int j = 0; j < 3; ++j)
+  {
     common::Timer time_interpolate("Interpolate x");
     xcoord.interpolate(
-        [&j](const xt::xtensor<double, 2> &x) -> xt::xarray<double> {
+        [&j](const xt::xtensor<double, 2> &x) -> xt::xarray<double>
+        {
           return xt::row(x, j);
         });
     time_interpolate.stop();
@@ -168,7 +178,8 @@ int main(int argc, char **argv) {
 
   bool write_files = false;
 
-  if (write_files) {
+  if (write_files)
+  {
     common::Timer tw("Tpetra: write files");
     Tpetra::MatrixMarket::Writer<
         Tpetra::CrsMatrix<PetscScalar, std::int32_t, std::int64_t, Node>>::

cpp/maxwell.ufl → cpp/maxwell.py

@@ -1,3 +1,19 @@
+from ufl import (
+    VectorElement,
+    FiniteElement,
+    Mesh,
+    SpatialCoordinate,
+    as_vector,
+    TrialFunction,
+    TestFunction,
+    inner,
+    curl,
+    dx,
+    FunctionSpace,
+    tetrahedron,
+    pi,
+    cos,
+)
 
 coord_element = VectorElement("Lagrange", tetrahedron, 1)
 mesh = Mesh(coord_element)
@@ -9,15 +25,15 @@
 # T_0 = Coefficient(element)
 
 x = SpatialCoordinate(mesh)
-T_0 = as_vector((- pi * cos(x[2] * pi) / mu,
-                 - pi * cos(x[0] * pi) / mu,
-                 - pi * cos(x[1] * pi) / mu))
+T_0 = as_vector(
+    (-pi * cos(x[2] * pi) / mu, -pi * cos(x[0] * pi) / mu, -pi * cos(x[1] * pi) / mu)
+)
 
 A = TrialFunction(Q)
 v = TestFunction(Q)
 
-Kc = inner(1 / mu * curl(A), curl(v)) * dx + 1e-8 * inner(A, v)*dx
-Mc = inner(A, v)*dx
+Kc = inner(1 / mu * curl(A), curl(v)) * dx + 1e-8 * inner(A, v) * dx
+Mc = inner(A, v) * dx
 L = inner(T_0, curl(v)) * dx
 
 Hgrad_element = FiniteElement("Lagrange", tetrahedron, 1)
@@ -26,4 +42,4 @@
 v = TestFunction(V)
 Mg = inner(u, v) * dx
 
-forms = [Kc, Mc, Mg, L]
+forms = [Kc, Mc, Mg, L]

pyproject.toml

@@ -0,0 +1,32 @@
+[build-system] # Require setuptool version due to https://github.com/pypa/setuptools/issues/2938
+requires = ["setuptools>=64.4.0", "wheel", "pip>=22.3"]
+
+[project]
+name = "maxwell_problems"
+version = "0.7.0"
+description = "Implementation for solving Maxwell-problems with DOLFINx"
+authors = [
+      { name = "Joseph P. Dean", email="jpd62@eng.cam.ac.uk"},
+      { name = "Jørgen S. Dokken", email = "dokken@simula.no" }]
+license = { file = "LICENSE" }
+readme = "README.md"
+dependencies = ["fenics-dolfinx>=0.7.0"]
+
+[tool.setuptools]
+packages = []
+
+[project.optional-dependencies]
+test = ["pytest", "coverage"]
+dev = ["pdbpp", "ipython", "mypy", "flake8"]
+all = ["adios4dolfinx[test,dev]"]
+
+[tool.pytest.ini_options]
+addopts = ["--import-mode=importlib"]
+testpaths = ["tests"]
+
+[tool.mypy]
+ignore_missing_imports = true
+# Folders to exclude
+exclude = ["build/"]
+# Folder to check with mypy
+files = ["src", "tests"]