Implemented support for solving the Poisson problem in 2D

.cmake/mito-config.cmake.in

@@ -7,8 +7,8 @@
 include(${CMAKE_CURRENT_LIST_DIR}/mito-targets.cmake)
 check_required_components(mito)
 
-# request c++20
-set(CMAKE_CXX_STANDARD 20)
+# request c++23
+set(CMAKE_CXX_STANDARD 23)
 
 # adjust the include path
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})

.cmake/mito_benchmarks_mito_lib.cmake

@@ -20,5 +20,9 @@ mito_benchmark_driver(benchmarks/mito.lib/integration/integration.cc)
 # fields
 mito_benchmark_driver(benchmarks/mito.lib/fields/laplacian.cc)
 
+if(WITH_PETSC)
+    # poisson boundary value problem
+    mito_benchmark_driver(benchmarks/mito.lib/pdes/poisson.cc)
+endif()
 
 # end of file

.cmake/mito_init.cmake

@@ -30,12 +30,12 @@ function(mito_cxxInit)
     # set C++ standard
     include(CheckCXXCompilerFlag)
 
-    # request c++20
-    set(CMAKE_CXX_STANDARD 20 PARENT_SCOPE)
+    # request c++23
+    set(CMAKE_CXX_STANDARD 23 PARENT_SCOPE)
     set(CMAKE_CXX_STANDARD_REQUIRED True PARENT_SCOPE)
 
     # additional compilation flags
-    set(CMAKE_CXX_FLAGS "-fdiagnostics-color=always -Wall -Wextra -pedantic -Werror" PARENT_SCOPE)
+    set(CMAKE_CXX_FLAGS "-fdiagnostics-color=always -Wall -Wextra -pedantic -Werror -Wno-psabi" PARENT_SCOPE)
 
     # all done
 endfunction(mito_cxxInit)

.cmake/mito_sources.cmake

@@ -10,7 +10,8 @@ set(MITO_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/lib/mito/version.cc)
 # the mito petsc backend
 if (WITH_PETSC)
 set(MITO_SOURCES ${MITO_SOURCES}
-    lib/mito/solvers/backend/petsc/PETScKrylovSolver.cc
+lib/mito/matrix_solvers/backend/petsc/PETScLinearSystem.cc
+lib/mito/matrix_solvers/backend/petsc/PETScKrylovSolver.cc
 )
 endif()
 

.cmake/mito_tests_mito_lib.cmake

@@ -10,9 +10,11 @@ mito_test_driver(tests/mito.lib/functions/derivative_constants.cc)
 mito_test_driver(tests/mito.lib/functions/derivative_chain_rule.cc)
 mito_test_driver(tests/mito.lib/functions/derivative_higher_order.cc)
 mito_test_driver(tests/mito.lib/functions/derivative_sum.cc)
+mito_test_driver(tests/mito.lib/functions/derivative_subscript.cc)
 mito_test_driver(tests/mito.lib/functions/derivative_product.cc)
 mito_test_driver(tests/mito.lib/functions/derivative_inverse.cc)
 mito_test_driver(tests/mito.lib/functions/partial_derivatives.cc)
+mito_test_driver(tests/mito.lib/functions/tensor_derivatives.cc)
 
 #  geometry
 mito_test_driver(tests/mito.lib/geometry/coordinates.cc)
@@ -35,9 +37,20 @@ mito_test_driver(tests/mito.lib/geometry/euclidean_metric_space.cc)
 mito_test_driver(tests/mito.lib/geometry/polar_metric_space.cc)
 mito_test_driver(tests/mito.lib/geometry/spherical_metric_space.cc)
 
-# discretization
-mito_test_driver(tests/mito.lib/discretization/quadrature_field.cc)
-mito_test_driver(tests/mito.lib/discretization/nodal_field.cc)
+# constraints
+mito_test_driver(tests/mito.lib/constraints/dirichlet.cc)
+
+# discrete
+mito_test_driver(tests/mito.lib/discrete/quadrature_field.cc)
+mito_test_driver(tests/mito.lib/discrete/mesh_field.cc)
+
+# fem
+mito_test_driver(tests/mito.lib/fem/block_grad_grad.cc)
+mito_test_driver(tests/mito.lib/fem/block_mass.cc)
+mito_test_driver(tests/mito.lib/fem/shape_functions_triangle_construction.cc)
+mito_test_driver(tests/mito.lib/fem/shape_functions_triangle_p1.cc)
+mito_test_driver(tests/mito.lib/fem/shape_functions_triangle_p2.cc)
+mito_test_driver(tests/mito.lib/fem/isoparametric_triangle.cc)
 
 # io
 mito_test_driver(tests/mito.lib/io/summit_mesh_reader_2D.cc)
@@ -64,9 +77,8 @@ endif()
 
 # solvers
 if(WITH_PETSC)
-    mito_test_driver(tests/mito.lib/solvers/petsc_external_initialize.cc)
-    mito_test_driver(tests/mito.lib/solvers/petsc_internal_initialize.cc)
-    mito_test_driver(tests/mito.lib/solvers/petsc_solve_linear_system.cc)
+    mito_test_driver(tests/mito.lib/matrix_solvers/petsc_initialize_finalize.cc)
+    mito_test_driver(tests/mito.lib/matrix_solvers/petsc_ksp.cc)
 endif()
 
 # tensor
@@ -78,7 +90,10 @@ mito_test_driver(tests/mito.lib/tensor/tensor_product_forms.cc)
 # fields
 mito_test_driver(tests/mito.lib/fields/fields.cc)
 mito_test_driver(tests/mito.lib/fields/fields_traits.cc)
+mito_test_driver(tests/mito.lib/fields/calculus_identities.cc)
 mito_test_driver(tests/mito.lib/fields/calculus_scalar_field.cc)
+mito_test_driver(tests/mito.lib/fields/calculus_vector_field.cc)
+mito_test_driver(tests/mito.lib/fields/gradient_non_square.cc)
 mito_test_driver(tests/mito.lib/fields/polar_metric_field.cc)
 mito_test_driver(tests/mito.lib/fields/spherical_metric_field.cc)
 
@@ -152,6 +167,7 @@ mito_test_driver(tests/mito.lib/utilities/segmented_vector_iterator.cc)
 mito_test_driver(tests/mito.lib/utilities/segmented_vector_subscript.cc)
 mito_test_driver(tests/mito.lib/utilities/segmented_vector_print.cc)
 mito_test_driver(tests/mito.lib/utilities/shared_pointer.cc)
+mito_test_driver(tests/mito.lib/utilities/named_class.cc)
 
 # quadrature
 mito_test_driver(tests/mito.lib/quadrature/quadrature_parametric_segment.cc)

.devcontainer/Dockerfile

@@ -0,0 +1,84 @@
+# global args
+ARG user=user
+ARG homedir=/home/${user}
+ARG nprocs=4
+
+FROM ubuntu:latest
+
+# to avoid user interaction with tzdata asking for timezone
+ARG DEBIAN_FRONTEND=noninteractive
+
+#
+ARG user
+ARG homedir
+ARG nprocs
+
+# environment
+# colorize the terminal
+ENV TERM=xterm-256color
+# openmpi
+ENV OMPI_ALLOW_RUN_AS_ROOT=1
+ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+ENV OMPI_MCA_rmaps_base_oversubscribe=1
+
+# get the latest
+RUN apt dist-upgrade -y
+
+# update the package repository
+RUN apt update -y
+
+# install multipurpose packages
+RUN apt install -y cmake-curses-gui
+RUN apt install -y git
+RUN apt install -y git-core
+RUN apt install -y bash-completion
+RUN apt install -y make
+RUN apt install -y vim
+RUN apt install -y sudo
+
+# install mito dependencies
+RUN apt install -y libgtest-dev
+RUN apt install -y libbenchmark-dev
+RUN apt install -y libopenmpi-dev
+RUN apt install -y libmetis-dev
+RUN apt install -y libvtk9-dev
+RUN apt install -y petsc-dev
+RUN apt install -y valgrind
+RUN apt install -y libpython3-dev
+RUN apt install -y python3-pytest
+
+# install pyre dependencies
+RUN apt install -y pybind11-dev
+
+# install pyre
+WORKDIR ${homedir}
+RUN git clone https://github.com/pyre/pyre \
+    && cd pyre \
+    && git checkout tensor \
+    && mkdir build \
+    && cd build \
+    && cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local/pyre .. \
+    && make -j ${nprocs} \
+    && make install \
+    && cd .. \
+    && rm -rf build
+
+# setup {user} user
+ENV USER=${user}
+ENV HOME=${homedir}
+RUN useradd -s /bin/bash --create-home --home-dir $HOME $USER \
+    && usermod -aG sudo $USER \
+    && chown -R $USER:$USER $HOME
+RUN echo "$USER:password" | chpasswd
+# copy the bashrc
+COPY --chown=${user}:${user} bashrc .bashrc
+
+# default user and work directory when running the container
+USER ${user}
+WORKDIR ${homedir}
+# remove annoying message on how to run a sudo command
+RUN touch ~/.sudo_as_admin_successful
+# configure git
+RUN git config --global pull.ff only
+
+# end of file

.devcontainer/bashrc

@@ -0,0 +1,6 @@
+# enable bash completion
+if [ -f /etc/bash_completion ]; then
+    . /etc/bash_completion
+elif [ -f /usr/share/bash-completion/bash_completion ]; then
+    . /usr/share/bash-completion/bash_completion
+fi

.devcontainer/devcontainer.json

@@ -0,0 +1,16 @@
+// .devcontainer/devcontainer.json
+{
+    "name": "mito",
+    "build": {
+        "dockerfile": "Dockerfile"
+    },
+    "mounts": [
+        "source=${localWorkspaceFolder},target=/home/user/mito,type=bind"
+    ],
+    "extensions": [
+        "ms-vscode.cpptools-extension-pack",
+        "eamodio.gitlens",
+        "med-h.git-graph-revamped",
+    ],
+    "remoteUser": "user"
+}

.github/workflows/cmake-macos.yaml

@@ -23,11 +23,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-13]
+        os: [macos-14]
         target: [Debug, Release]
         python: ["3.12"]
         suite: [gcc]
-        suiteVersion: ["13"]
+        suiteVersion: ["14"]
         include:
           - suite: gcc
             cc: gcc
@@ -39,9 +39,7 @@ jobs:
           echo " -- install our dependencies"
           brew install make cmake metis open-mpi
           # install {google-benchmark} from source to make sure it is built with the same compiler
-          brew install --build-from-source --cc=gcc-12 google-benchmark
-          curl https://raw.githubusercontent.com/Homebrew/homebrew-core/67b277e6d1faee20d2aa4fc8b2dc229a241fa807/Formula/vtk.rb > vtk.rb
-          HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 brew install vtk.rb
+          brew install --build-from-source --cc=gcc-14 google-benchmark
 
       - name: python ${{matrix.python}} setup
         uses: actions/setup-python@v4
@@ -51,7 +49,7 @@ jobs:
       - name: install dependencies
         run: |
           python3 -m pip install --upgrade pip
-          pip3 install distro 'numpy<2.0' pybind11 pytest vtk
+          pip3 install distro 'numpy<2.0' pybind11 pytest
 
       - name: checkout gtest
         uses: actions/checkout@v3
@@ -84,7 +82,7 @@ jobs:
           repository: pyre/pyre
           fetch-depth: 0
           path: ${{github.workspace}}/pyre
-          ref: main
+          ref: tensor
 
       - name: retrieve pyre commit SHA
         id: pyre-sha
@@ -155,8 +153,6 @@ jobs:
           find ${pythonLocation}/lib/python${pythonVersion}/site-packages/pybind11
           echo " -- pytest"
           pip3 show pytest
-          echo " -- vtk"
-          pip3 show vtk
         env:
           pythonVersion: ${{matrix.python}}
 
@@ -172,7 +168,7 @@ jobs:
           mkdir build
           cd build
           echo " -- configuring the build"
-          cmake -DCMAKE_INSTALL_PREFIX=${prefix} -DCMAKE_BUILD_TYPE=${target} -DCMAKE_CXX_COMPILER=${cxx} -DPython_EXECUTABLE=${pythonLocation}/bin/python${pythonVersion} -Dpybind11_DIR=${pythonLocation}/lib/python${pythonVersion}/site-packages/pybind11/share/cmake/pybind11 -DMITO_BUILD_TESTING=ON -DMITO_BUILD_BENCHMARKS=ON -Dpyre_DIR=${{runner.temp}}/pyre_install/share/cmake/pyre -DGTest_DIR=${{runner.temp}}/gtest_install/lib/cmake/GTest -DWITH_VTK=ON -DWITH_METIS=ON ${{github.workspace}}/mito
+          cmake -DCMAKE_INSTALL_PREFIX=${prefix} -DCMAKE_BUILD_TYPE=${target} -DCMAKE_CXX_COMPILER=${cxx} -DPython_EXECUTABLE=${pythonLocation}/bin/python${pythonVersion} -Dpybind11_DIR=${pythonLocation}/lib/python${pythonVersion}/site-packages/pybind11/share/cmake/pybind11 -DMITO_BUILD_TESTING=ON -DMITO_BUILD_BENCHMARKS=ON -Dpyre_DIR=${{runner.temp}}/pyre_install/share/cmake/pyre -DGTest_DIR=${{runner.temp}}/gtest_install/lib/cmake/GTest -DWITH_VTK=OFF -DWITH_METIS=ON ${{github.workspace}}/mito
           echo " -- building mito"
           make -j 2 install
         env:

.github/workflows/cmake-ubuntu.yaml

@@ -27,7 +27,7 @@ jobs:
         target: [Debug, Release]
         python: ["3.12"]
         suite: [gcc]
-        suiteVersion: ["13"]
+        suiteVersion: ["14"]
         include:
           - suite: gcc
             cc: gcc
@@ -38,10 +38,6 @@ jobs:
         run: |
           echo " -- update the package cache"
           sudo apt update
-          echo " -- upgradables"
-          sudo apt list --upgradable
-          echo " -- upgrade"
-          sudo apt dist-upgrade
           echo " -- install our dependencies"
           sudo apt install -y make cmake libgtest-dev libbenchmark-dev libvtk9-dev libopenmpi-dev libmetis-dev valgrind petsc-dev
 
@@ -61,7 +57,7 @@ jobs:
           repository: pyre/pyre
           fetch-depth: 0
           path: ${{github.workspace}}/pyre
-          ref: main
+          ref: tensor
 
       - name: retrieve pyre commit SHA
         id: pyre-sha

benchmarks/mito.lib/integration/integration.cc

@@ -76,7 +76,7 @@ main()
     auto integrator = mito::quadrature::integrator<mito::quadrature::GAUSS, 2>(manifold);
 
     auto result = integrator.integrate(f);
-    auto exact = mito::tensor::scalar_t(0.9460830607878437);
+    auto exact = mito::tensor::scalar_t{ 0.9460830607878437 };
     channel << "Integration of cos(x*y): Result = " << result
             << ", Error = " << std::fabs(result - exact) << journal::endl;