unit KronMult methods

Add a CI test for Hypre Big Int [testing/bernede1/hypre-bigint]

.github/workflows/builds-and-tests.yml

@@ -47,26 +47,36 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-18.04, macos-10.15]
-        target: [debug, optim]
-        mpi: [sequential, parallel]
+        target: [dbg, opt]
+        mpi: [seq, par]
         build-system: [make]
-        # 'include' allows us to
-        # - add a variable without creating a new matrix dimension.
-        # - add a new combination ('build-system: cmake' case here)
+        hypre-target: [int32]
+        # 'include' allows us to:
+        # - Add a variable to all jobs without creating a new matrix dimension.
+        #   Codecov is defined that way.
+        # - Add a new combination.
+        #   'build-system: cmake' and 'hypre-target: int64'
         #
         # note: we will gather coverage info for any non-debug run except the
         # CMake build.
         include:
-          - target: debug
+          - target: dbg
             codecov: NO
-          - target: optim
+          - target: opt
             codecov: YES
           - os: ubuntu-18.04
-            target: optim
+            target: opt
             codecov: NO
-            mpi: parallel
+            mpi: par
             build-system: cmake
-    name: ${{ matrix.os }}-${{ matrix.target }}-${{ matrix.mpi }}-${{ matrix.build-system }}
+            hypre-target: int32
+          - os: ubuntu-18.04
+            target: opt
+            codecov: NO
+            mpi: par
+            build-system: make
+            hypre-target: int64
+    name: ${{ matrix.os }}-${{ matrix.build-system }}-${{ matrix.target }}-${{ matrix.mpi }}-${{ matrix.hypre-target }}
 
     runs-on: ${{ matrix.os }}
 
@@ -92,7 +102,7 @@ jobs:
     # TODO: It would be nice to have only one step, e.g. with a dedicated
     # action, but I (@adrienbernede) don't see how at the moment.
     - name: get MPI (Linux)
-      if: matrix.mpi == 'parallel' && matrix.os == 'ubuntu-18.04'
+      if: matrix.mpi == 'par' && matrix.os == 'ubuntu-18.04'
       run: |
         sudo apt-get install mpich libmpich-dev
         export MAKE_CXX_FLAG="MPICXX=mpic++"
@@ -103,11 +113,11 @@ jobs:
         sudo apt-get install lcov
 
     - name: Set up Homebrew
-      if: ( matrix.mpi == 'parallel' || matrix.codecov == 'YES' ) && matrix.os == 'macos-10.15'
+      if: ( matrix.mpi == 'par' || matrix.codecov == 'YES' ) && matrix.os == 'macos-10.15'
       uses: Homebrew/actions/setup-homebrew@c4aafe8c4620bf08883dd4679c374f11e73329d3
 
     - name: get MPI (MacOS)
-      if: matrix.mpi == 'parallel' && matrix.os == 'macos-10.15'
+      if: matrix.mpi == 'par' && matrix.os == 'macos-10.15'
       run: |
         export HOMEBREW_NO_INSTALL_CLEANUP=1
         brew install openmpi
@@ -123,39 +133,40 @@ jobs:
     # Install will only run on cache miss.
     - name: cache hypre
       id: hypre-cache
-      if: matrix.mpi == 'parallel'
+      if: matrix.mpi == 'par'
       uses: actions/cache@v2
       with:
         path: ${{ env.HYPRE_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-v2
+        key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-${{ matrix.hypre-target }}-v2.0
 
     - name: get hypre
-      if: matrix.mpi == 'parallel' && steps.hypre-cache.outputs.cache-hit != 'true'
-      uses: mfem/github-actions/build-hypre@v1.0
+      if: matrix.mpi == 'par' && steps.hypre-cache.outputs.cache-hit != 'true'
+      uses: mfem/github-actions/build-hypre@v2.0
       with:
-        hypre-archive: ${{ env.HYPRE_ARCHIVE }}
-        hypre-dir: ${{ env.HYPRE_TOP_DIR }}
+        archive: ${{ env.HYPRE_ARCHIVE }}
+        dir: ${{ env.HYPRE_TOP_DIR }}
+        target: ${{ matrix.hypre-target }}
 
     # Get Metis through cache, or build it.
     # Install will only run on cache miss.
     - name: cache metis
       id: metis-cache
-      if: matrix.mpi == 'parallel'
+      if: matrix.mpi == 'par'
       uses: actions/cache@v2
       with:
         path: ${{ env.METIS_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2
+        key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.0
 
     - name: install metis
-      if: matrix.mpi == 'parallel' && steps.metis-cache.outputs.cache-hit != 'true'
-      uses: mfem/github-actions/build-metis@v1.0
+      if: matrix.mpi == 'par' && steps.metis-cache.outputs.cache-hit != 'true'
+      uses: mfem/github-actions/build-metis@v2.0
       with:
-        metis-archive: ${{ env.METIS_ARCHIVE }}
-        metis-dir: ${{ env.METIS_TOP_DIR }}
+        archive: ${{ env.METIS_ARCHIVE }}
+        dir: ${{ env.METIS_TOP_DIR }}
 
     # MFEM build and test
     - name: build
-      uses: mfem/github-actions/build-mfem@v1.0
+      uses: mfem/github-actions/build-mfem@v2.0
       with:
         os: ${{ matrix.os }}
         target: ${{ matrix.target }}
@@ -168,17 +179,17 @@ jobs:
 
     # Run checks (and only checks) on debug targets
     - name: checks
-      if: matrix.build-system == 'make' && matrix.target == 'debug'
+      if: matrix.build-system == 'make' && matrix.target == 'dbg'
       run: |
         cd ${{ env.MFEM_TOP_DIR }}  && make check
 
     - name: unit tests
-      if: matrix.build-system == 'make' && matrix.target == 'optim'
+      if: matrix.build-system == 'make' && matrix.target == 'opt'
       run: |
         cd ${{ env.MFEM_TOP_DIR }} && make unittest
 
     - name: tests
-      if: matrix.build-system == 'make' && matrix.target == 'optim'
+      if: matrix.build-system == 'make' && matrix.target == 'opt'
       run: |
         cd ${{ env.MFEM_TOP_DIR }} && make test
 
@@ -190,8 +201,8 @@ jobs:
     # Code coverage (process and upload reports)
     - name: codecov
       if: matrix.codecov == 'YES'
-      uses: mfem/github-actions/upload-coverage@v1.0
+      uses: mfem/github-actions/upload-coverage@v2.0
       with:
-        name: ${{ matrix.os }}-${{ matrix.mpi }}
+        name: ${{ matrix.os }}-${{ matrix.build-system }}-${{ matrix.target }}-${{ matrix.mpi }}-${{ matrix.hypre-target }}
         project_dir: ${{ env.MFEM_TOP_DIR }}
         directories: "fem general linalg mesh"

.github/workflows/mfem-analysis.yml

@@ -53,32 +53,33 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ${{ env.HYPRE_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-v2
+        key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-v2.0
 
     - name: Get Hypre
       if: steps.hypre-cache.outputs.cache-hit != 'true'
-      uses: mfem/github-actions/build-hypre@master
+      uses: mfem/github-actions/build-hypre@v2.0
       with:
-        hypre-archive: ${{ env.HYPRE_ARCHIVE }}
-        hypre-dir: ${{ env.HYPRE_TOP_DIR }}
+        archive: ${{ env.HYPRE_ARCHIVE }}
+        dir: ${{ env.HYPRE_TOP_DIR }}
+        target: int32
 
     - name: Cache Metis Install
       id: metis-cache
       uses: actions/cache@v2
       with:
         path: ${{ env.METIS_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2
+        key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.0
 
     - name: Install Metis
       if: steps.metis-cache.outputs.cache-hit != 'true'
-      uses: mfem/github-actions/build-metis@master
+      uses: mfem/github-actions/build-metis@v2.0
       with:
-        metis-archive: ${{ env.METIS_ARCHIVE }}
-        metis-dir: ${{ env.METIS_TOP_DIR }}
+        archive: ${{ env.METIS_ARCHIVE }}
+        dir: ${{ env.METIS_TOP_DIR }}
 
     # MFEM build and test
     - name: build-mfem
-      uses: mfem/github-actions/build-mfem@master
+      uses: mfem/github-actions/build-mfem@v2.0
       with:
         os: ${{ runner.os }}
         target: optim

.github/workflows/repo-check.yml

@@ -28,49 +28,24 @@ jobs:
         access_token: ${{ github.token }}
     - name: checkout mfem
       uses: actions/checkout@v2
-      with:
-        path: mfem
 
     - name: copyright check
       id: copyright
       run: |
-        cd mfem
-        if git grep -l "^\(#\|//\).*\(\-2020\|\ 2010,\)" > matches.txt
-        then
-          echo "Please update the following files to Copyright (c) 2010-2021:"
-          cat matches.txt
-          exit 1
-        else
-          echo "No outdated copyright found."
-        fi
+        ./config/githooks/pre-push --copyright
+
       continue-on-error: true
 
     - name: license check
       id: license
       run: |
-        cd mfem
-        if git grep -li "^\(#\|//\).*GNU\ Lesser\ General\ Public\ License" > matches.txt
-        then
-          echo "Please update the following files to the BSD-3 license:"
-          cat matches.txt
-          exit 1
-        else
-          echo "No GNU GPL license found."
-        fi
+        ./config/githooks/pre-push --license
       continue-on-error: true
 
     - name: release check
       id: release
       run: |
-        cd mfem
-        if git grep -l "^\(#\|//\).*LLNL\-CODE\-443211" > matches.txt
-        then
-          echo "Please update the following files to LLNL-CODE-806117:"
-          cat matches.txt
-          exit 1
-        else
-          echo "No outdated release number found."
-        fi
+        ./config/githooks/pre-push --release
       continue-on-error: true
 
     - name: wrap-up
@@ -100,8 +75,7 @@ jobs:
 
     - name: style check
       run: |
-        cd tests/scripts
-        ./runtest code-style
+        ./config/githooks/pre-push --style
 
   documentation:
     runs-on: ubuntu-18.04
@@ -133,5 +107,4 @@ jobs:
       run: |
         git fetch origin master:master
         git checkout -b gh-actions-branch-history
-        cd tests/scripts
-        ./runtest branch-history
+        ./config/githooks/pre-push --history

.gitignore

@@ -26,6 +26,7 @@ CMakeFiles/
 config/_config.hpp
 config/config.mk
 config/sample-runs-build.log
+config/user.mk
 doc/CodeDocumentation.conf
 doc/CodeDocumentation.html
 doc/CodeDocumentation

.gitlab-ci.yml

@@ -48,39 +48,58 @@ variables:
   TPLS_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/tpls.git
   TESTS_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/tests.git
   AUTOTEST_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/autotest.git
+  MFEM_DATA_REPO: https://github.com/mfem/data.git
   ARTIFACTS_DIR: artifacts
 
 # The pipeline is divided into stages. Usually, these are also synchronization
 # points, however, we use "needs" keyword to express the DAG of jobs for more
 # efficiency.
-# - We use setup phase to download content outside of mfem directory.
+# - We use setup and setup_baseline phases to download content outside of mfem
+#   directory.
 # - Allocate/Release is where quartz resources are allocated/released once for all.
 # - Build and Test is where we build and MFEM for multiple toolchains.
 # - Baseline_checks gathers baseline-type test suites execution
 # - Baseline_publish, only available on master, allows to update baseline
 #   results
 stages:
+  - setup
   - q_allocate_resources
   - q_build_and_test
   - q_release_resources
   - l_build_and_test
   - c_build_and_test
-  - setup
+  - setup_baseline
   - baseline_check
   - baseline_to_autotest
   - baseline_publish
 
-# The setup job in setup stage don't rely on MFEM git repo. It prepares a
-# pipeline-wide working directory downloading/updating external repos.
-# TODO: updating tests and tpls is not necessary anymore since pipelines are
-# now using unique directories so repo are never shared with another pipeline.
-# This is not memory efficient (we keep a lot of data), hence this reminder.
-# Setup
+# setup clones the mfem/data repo in ${BUILD_ROOT}. The build_and_test script
+# then symlinks the repo to the parent directory of the MFEM source directory.
+# Unit tests that depend on the mfem/data repo will then detect that this
+# directory is present and be enabled.
 setup:
   tags:
     - shell
     - quartz
   stage: setup
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - mkdir -p ${BUILD_ROOT} && cd ${BUILD_ROOT}
+    - if [ ! -d data ]; then git clone ${MFEM_DATA_REPO}; fi
+  needs: []
+
+# The setup_baseline job in setup stage_baseline doesn't rely on MFEM git repo.
+# It prepares a pipeline-wide working directory downloading/updating external
+# repos. TODO: updating tests and tpls is not necessary anymore since pipelines
+# are now using unique directories so repo are never shared with another
+# pipeline. This is not memory efficient (we keep a lot of data), hence this
+# reminder.
+setup_baseline:
+  tags:
+    - shell
+    - quartz
+  stage: setup_baseline
   variables:
     GIT_STRATEGY: none
   script:

.gitlab/lassen.yml

@@ -25,7 +25,7 @@
 .build_and_test_on_lassen:
   extends: [.build_blueos_3_ppc64le_ib_script, .on_lassen]
   stage: l_build_and_test
-  needs: []
+  needs: [setup]
 
 opt_mpi_cuda_xl_16_1_1_8:
   variables:

.gitlab/quartz.yml

@@ -94,6 +94,7 @@ q_report_failure:
 .build_and_test_on_quartz:
   extends: [.build_toss_3_x86_64_ib_script, .on_quartz]
   stage: q_build_and_test
+  needs: [setup]
 
 # Build MFEM
 debug_ser_gcc_4_9_3:
@@ -139,7 +140,7 @@ opt_par_gcc_6_1_0_pumi:
 # Baseline
 baselinecheck_mfem_intel_quartz:
   extends: [.baselinecheck_mfem, .on_quartz]
-  needs: [setup]
+  needs: [setup_baseline]
 
 update_autotest:
   extends: [.on_quartz]

.travis.yml

@@ -1,469 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-language: cpp
-
-os: linux
-dist: bionic
-
-stages:
-  - checks
-  - tests
-  - optional
-
-env:
-  global:
-    - HYPRE_ARCHIVE=v2.19.0.tar.gz
-      HYPRE_URL=https://github.com/hypre-space/hypre/archive/$HYPRE_ARCHIVE
-      HYPRE_TOP_DIR=hypre-2.19.0
-
-jobs:
-  include:
-
-    # ========================
-    #         Checks
-    # ========================
-    # - code-style
-    # - documentation
-    # - gitignore
-
-    - stage: checks
-      os: linux
-      dist: xenial
-      name: "code-style"
-      addons:
-        apt:
-          packages:
-            - astyle=2.05.1-0ubuntu1
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - cd tests/scripts
-        - ./runtest code-style
-
-    - stage: checks
-      os: linux
-      name: "documentation"
-      addons:
-        apt:
-          packages:
-            - doxygen
-            - graphviz
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - cd tests/scripts
-        - ./runtest documentation
-
-    - stage: checks
-      os: linux
-      name: "gitignore"
-      addons:
-        apt:
-          packages:
-            - mpich
-            - libmpich-dev
-      env: MPI=YES
-      before_script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - mpicxx -v
-        - make config MFEM_USE_MPI=YES MFEM_MPI_NP=2
-        - make all -j3
-        - make test-noclean
-      script:
-        - cd tests/scripts
-        - ./runtest gitignore
-      cache:
-        ccache: true
-        directories:
-          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
-          - $TRAVIS_BUILD_DIR/../metis-4.0
-      before_cache:
-        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
-
-    # ========================
-    #  Optional Checks/Tests
-    # ========================
-    # - branch-history
-
-    - stage: optional
-      name: "branch-history"
-      if: branch != next
-      # need full git history for the binary/big files check
-      git:
-        depth: false
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        # update master
-        - git fetch origin master:master
-        # checkout a branch (otherwise Travis works in detached head)
-        - git checkout -b travis_tests
-        - cd tests/scripts
-        - ./runtest branch-history
-
-    # ========================
-    #       Linux tests
-    # ========================
-    # - serial + debug
-    # - serial
-    # - parallel + debug
-    # - parallel
-
-    - stage: tests
-      os: linux
-      compiler: gcc
-      name: "Linux: Serial + Debug"
-      env: DEBUG=YES
-           MPI=NO
-           CODECOV=NO
-           MFEM_TEST_TARGET=check
-      cache:
-        ccache: true
-
-    - os: linux
-      compiler: gcc
-      name: "Linux: Serial"
-      env: DEBUG=NO
-           MPI=NO
-           CODECOV=NO
-           MFEM_TEST_TARGET=test
-      cache:
-        ccache: true
-
-    - os: linux
-      compiler: gcc
-      name: "Linux: Parallel + Debug"
-      addons:
-        apt:
-          # sources:
-            # - ubuntu-toolchain-r-test
-          packages:
-            # GCC 4.9
-            # - g++-4.9
-            # MPICH
-            - mpich
-            - libmpich-dev
-            # OpenMPI
-            # - openmpi-bin
-            # - libopenmpi-dev
-      env: DEBUG=YES
-           MPI=YES
-           CODECOV=NO
-           MFEM_TEST_TARGET=check
-           NPROCS=2
-      cache:
-        ccache: true
-        directories:
-          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
-          - $TRAVIS_BUILD_DIR/../metis-4.0
-      before_cache:
-        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
-
-    - os: linux
-      compiler: gcc
-      name: "Linux: Parallel"
-      addons:
-        apt:
-          # sources:
-            # - ubuntu-toolchain-r-test
-          packages:
-            # GCC 4.9
-            # - g++-4.9
-            # MPICH
-            - mpich
-            - libmpich-dev
-            # OpenMPI
-            # - openmpi-bin
-            # - libopenmpi-dev
-      env: DEBUG=NO
-           MPI=YES
-           CODECOV=YES
-           MFEM_TEST_TARGET=test
-           NPROCS=2
-      cache:
-        ccache: true
-        directories:
-          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
-          - $TRAVIS_BUILD_DIR/../metis-4.0
-      before_cache:
-        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
-
-    - os: linux
-      compiler: gcc
-      name: "Linux: Parallel (cmake)"
-      addons:
-        apt:
-          packages:
-            - mpich
-            - libmpich-dev
-      env: MPI=YES
-           NPROCS=2
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - mkdir ${TRAVIS_BUILD_DIR}/build
-        - cd ${TRAVIS_BUILD_DIR}/build
-        - cmake ..
-             -DMFEM_USE_MPI=ON
-             -DHYPRE_DIR=${TRAVIS_BUILD_DIR}/../$HYPRE_TOP_DIR/src/hypre
-             -DMFEM_MPI_NP=$NPROCS
-        - make -j3 mfem examples
-        - cd ${TRAVIS_BUILD_DIR}/build/tests/unit
-        - make -j3
-        - ctest --output-on-failure
-      cache:
-        ccache: true
-        directories:
-          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
-          - $TRAVIS_BUILD_DIR/../metis-4.0
-      before_cache:
-        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
-
-    # ========================
-    #      Mac OS X tests
-    # ========================
-    # - serial + debug
-    # - serial
-    # - parallel + debug
-    # - parallel
-
-    - os: osx
-      osx_image: xcode11.2
-      compiler: clang
-      name: "Mac: Serial + Debug"
-      addons:
-        homebrew:
-          packages:
-            - ccache
-      env: DEBUG=YES
-           MPI=NO
-           CODECOV=NO
-           MFEM_TEST_TARGET=check
-      cache:
-        ccache: true
-
-    - os: osx
-      osx_image: xcode11.2
-      compiler: clang
-      name: "Mac: Serial"
-      addons:
-        homebrew:
-          packages:
-            - ccache
-      env: DEBUG=NO
-           MPI=NO
-           CODECOV=NO
-           MFEM_TEST_TARGET=test
-      cache:
-        ccache: true
-
-    - os: osx
-      osx_image: xcode11.2
-      compiler: clang
-      name: "Mac: Parallel + Debug"
-      addons:
-        homebrew:
-          packages:
-            - ccache
-      env: DEBUG=YES
-           MPI=YES
-           CODECOV=NO
-           MFEM_TEST_TARGET=check
-           NPROCS=4
-           TMPDIR=/tmp
-      cache:
-        ccache: true
-        directories:
-          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
-          - $TRAVIS_BUILD_DIR/../metis-4.0
-          - $HOME/local-cached
-      before_cache:
-        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
-
-    - os: osx
-      osx_image: xcode11.2
-      compiler: clang
-      name: "Mac: Parallel"
-      addons:
-        homebrew:
-          packages:
-            - ccache
-      env: DEBUG=NO
-           MPI=YES
-           CODECOV=YES
-           MFEM_TEST_TARGET=test
-           NPROCS=4
-           TMPDIR=/tmp
-      cache:
-        ccache: true
-        directories:
-          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
-          - $TRAVIS_BUILD_DIR/../metis-4.0
-          - $HOME/local-cached
-      before_cache:
-        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
-
-before_install:
-   # No addon for brew yet, have to install OSX packages this way.
-   # - if [ $TRAVIS_OS_NAME == "osx" ] && [ $MPI == "YES" ]; then
-   #      brew install open-mpi;
-   #   fi
-
-   # Disable ccache while building dependencies that are cached:
-   - echo "before \$PATH = $PATH";
-     export PATH=${PATH//\/usr\/lib\/ccache:/};
-     echo "after  \$PATH = $PATH"
-
-   # On Mac OS X, build and cache OpenMPI 2.1.6:
-   - if [ $TRAVIS_OS_NAME == "osx" ] && [ $MPI == "YES" ]; then
-        if [ ! -e $HOME/local-cached/bin/mpicc ]; then
-           mkdir -p $HOME/builds && cd $HOME/builds &&
-           wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.6.tar.bz2 &&
-           tar jxf openmpi-2.1.6.tar.bz2 &&
-           mkdir openmpi-build && cd openmpi-build &&
-           ../openmpi-2.1.6/configure --prefix=$HOME/local-cached &&
-           make -j3 all && make install;
-        fi;
-        PATH=$HOME/local-cached/bin:$PATH;
-        cd $TRAVIS_BUILD_DIR;
-     fi
-
-   # Update environment to find g++ 4.9 installation first.
-   # - if [ $TRAVIS_OS_NAME == "linux" ]; then
-   #      mkdir -p latest-gcc-symlinks;
-   #      ln -s /usr/bin/g++-4.9 latest-gcc-symlinks/g++;
-   #      ln -s /usr/bin/gcc-4.9 latest-gcc-symlinks/gcc;
-   #      ln -s /usr/bin/gcov-4.9 latest-gcc-symlinks/gcov;
-   #      export PATH=$PWD/latest-gcc-symlinks:$PATH;
-   #   fi
-
-   # Install tool to upload code coverage reports to coveralls.io
-   - if [ "$CODECOV" == "YES" ]; then
-        export PYTHONUSERBASE=$HOME/local;
-        pip install --user cpp-coveralls;
-        pip install --user pyyaml;
-        PATH=$HOME/local/bin:$PATH;
-     fi
-
-install:
-   # Set MPI compilers, print compiler version
-   - if [ $MPI == "YES" ]; then
-        if [ "$TRAVIS_OS_NAME" == "linux" ]; then
-           export MPICH_CC="$CC";
-           export MPICH_CXX="$CXX";
-        else
-           export OMPI_CC="$CC";
-           export OMPI_CXX="$CXX";
-           mpic++ --showme:version;
-        fi;
-        mpic++ -v;
-     else
-        $CXX -v;
-     fi
-
-   # Back out of the mfem directory to install the libraries
-   - cd ..
-
-   # hypre
-   - if [ $MPI == "YES" ]; then
-        if [ ! -e $HYPRE_TOP_DIR/src/hypre/lib/libHYPRE.a ]; then
-           wget $HYPRE_URL;
-           rm -rf $HYPRE_TOP_DIR;
-           tar xvzf $HYPRE_ARCHIVE;
-           cd $HYPRE_TOP_DIR/src;
-           ./configure --disable-fortran CC=mpicc CXX=mpic++;
-           make -j3;
-           cd ../..;
-        else
-            echo "Reusing cached $HYPRE_TOP_DIR/";
-        fi;
-        ln -s $HYPRE_TOP_DIR hypre;
-     else
-        echo "Serial build, not using hypre";
-     fi
-
-   # METIS, use a mirror because the original source server is not always up.
-   # Original url:
-   #    http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.3.tar.gz
-   - if [ $MPI == "YES" ]; then
-        if [ ! -e metis-4.0/libmetis.a ]; then
-           wget https://mfem.github.io/tpls/metis-4.0.3.tar.gz;
-           tar xvzf metis-4.0.3.tar.gz;
-           make -j3 -C metis-4.0.3/Lib CC="$CC" OPTFLAGS="-O2";
-           rm -rf metis-4.0;
-           mv metis-4.0.3 metis-4.0;
-        else
-           echo "Reusing cached metis-4.0/";
-        fi;
-     fi
-
-   # Re-enable ccache on linux; enable ccache on mac os:
-   - if [ $TRAVIS_OS_NAME == "linux" ]; then
-        export PATH="/usr/lib/ccache:$PATH";
-     else
-        if [ $TRAVIS_OS_NAME == "osx" ]; then
-           export PATH="/usr/local/opt/ccache/libexec:$PATH";
-        fi;
-     fi
-
-   - printf "which \$CC  = "; which $CC;
-     printf "which \$CXX = "; which $CXX
-
-script:
-   # Compiler
-   - if [ $MPI == "YES" ]; then
-        export MYCXX=mpic++;
-        export MAKE_CXX_FLAG=MPICXX=$MYCXX;
-     else
-        export MYCXX="$CXX";
-        export MAKE_CXX_FLAG=CXX=$MYCXX;
-     fi
-
-   # Print the compiler version
-   - $MYCXX -v
-
-   # Set some variables
-   - cd $TRAVIS_BUILD_DIR;
-     CPPFLAGS="";
-     SKIP_TEST_DIRS="";
-     if [ "$CODECOV" == "YES" ]; then
-        CPPFLAGS="--coverage -g";
-     fi;
-     if [ "$TRAVIS_OS_NAME" != "linux" ] || [ "$DEBUG" == "YES" ]; then
-        CPPFLAGS+=" -pedantic -Wall -Werror";
-     fi
-
-   # Configure the library
-   - make config MFEM_USE_MPI=$MPI MFEM_DEBUG=$DEBUG $MAKE_CXX_FLAG
-        MFEM_MPI_NP=$NPROCS CPPFLAGS="$CPPFLAGS"
-   # Show the configuration
-   - make info
-   # Build the library
-   - make -j3
-   # Build the examples and the miniapps
-   - make -j3 all
-   # Run tests
-   - make $MFEM_TEST_TARGET SKIP_TEST_DIRS="$SKIP_TEST_DIRS"
-
-after_success:
-   - if [ "$CODECOV" == "YES" ]; then
-        coveralls --include fem --include general --include linalg --include
-           mesh --exclude /usr --gcov-options '\-lp' --root $TRAVIS_BUILD_DIR;
-     fi

CHANGELOG

@@ -173,7 +173,11 @@ Version 4.2.1 (development)
   mixed meshes. The LOR Transfer miniapp (miniapps/tools/lor-transfer.cpp) now
   supports meshes with any element geometry.
 
-- Gitlab CI: use Spack (and Uberenv) to automate the build of TPLs.
+- Testing improvements:
+  * Transitioned from Travis to GitHub Action for testing/CI on GitHub.
+  * Effectively remove Travis from CI.
+  * Use Spack (and Uberenv) to automate TPL building in LLNL GitLab tests.
+  * Added a set of suggested git hooks for developers in config/githooks.
 
 - Added new miniapps demonstrating: 1) the use of GSLIB for overlapping grids,
   see gslib/schwarz_ex1, and 2) coupling different physics in different domains,
@@ -231,6 +235,15 @@ Version 4.2.1 (development)
 
 - Added makefile rule to generate TAGS table for vi or Emacs users.
 
+API changes
+-----------
+- Added an abstract interface `mfem::FaceRestriction` for `H1FaceRestriction`
+  and `L2FaceRestriction`.
+  In order to conform with the semantic of `MultTranspose` in `mfem::Operator`,
+  `mfem::FaceRestriction::MultTranspose` now sets instead of adding values, and
+  `mfem::FaceRestriction::AddMultTranspose` should replace previous calls to
+  `mfem::FaceRestriction::MultTranspose`.
+
 libCEED integration improvements
 --------------------------------
 - Refactor the libCEED integration

CONTRIBUTING.md

@@ -4,7 +4,9 @@
 
 <p align="center">
 <a href="https://github.com/mfem/mfem/blob/master/LICENSE"><img alt="License" src="https://img.shields.io/badge/License-BSD-brightgreen.svg"></a>
-<a href="https://travis-ci.org/mfem/mfem"><img alt="Build Status" src="https://travis-ci.org/mfem/mfem.svg?branch=master"></a>
+<a href="https://github.com/mfem/mfem/actions?query=workflow%3Arepo-check+branch%3Amaster"><img alt="Repo check" src="https://github.com/mfem/mfem/actions/workflows/repo-check.yml/badge.svg?branch=master"></a>
+<a href="https://github.com/mfem/mfem/actions?query=workflow%3Abuild-analysis+branch%3Amaster"><img alt="Build Analysis" src="https://github.com/mfem/mfem/actions/workflows/mfem-analysis.yml/badge.svg?branch=master"></a>
+<a href="https://github.com/mfem/mfem/actions?query=workflow%3Abuilds-and-tests+branch%3Amaster"><img alt="Builds and Tests" src="https://github.com/mfem/mfem/actions/workflows/builds-and-tests.yml/badge.svg?branch=master"></a>
 <a href="https://ci.appveyor.com/project/mfem/mfem"><img alt="Build Status" src="https://ci.appveyor.com/api/projects/status/19non9sqm6msi2wy?svg=true"></a>
 <a href="https://mfem.github.io/doxygen/html/index.html"><img alt="Doxygen" src="https://img.shields.io/badge/code-documented-brightgreen.svg"></a>
 </p>
@@ -63,6 +65,8 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
   development branches off `mfem:master`.
 - Please follow the [developer guidelines](#developer-guidelines), in particular
   with regards to documentation and code styling.
+- Please do not commit large/binary files to the central repository (use a fork
+  instead).
 - Pull requests  should be issued toward `mfem:master`. Make sure
   to check the items off the [Pull Request Checklist](#pull-request-checklist).
 - When your contribution is fully working and ready to be reviewed, add
@@ -71,6 +75,7 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
   reviewers to evaluate the changes.
 - The reviewers have 3 weeks to evaluate the PR and work with the author to
   fix issues and implement improvements.
+- During review there should be no force pushes/rewriting history in the branch.
 - After approval, MFEM developers merge the PR manually in the [mfem:next branch](#masternext-workflow).
 - After a week of testing in `mfem:next`, the original PR is merged in `mfem:master`.
 - We use [milestones](https://github.com/mfem/mfem/milestones) to coordinate the
@@ -91,8 +96,9 @@ The MFEM source code has the following structure:
 ```
   .
   ├── config
-  │   └── cmake
-  │       └── ...
+  │   ├── cmake
+  │   │    └── ...
+  │   └── githooks
   ├── data
   ├── doc
   ├── examples
@@ -363,6 +369,10 @@ Before you can start, you need a GitHub account, here are a few suggestions:
   two reviewers to evaluate the changes. The reviewers have 3 weeks to evaluate
   the PR and work with the author to implement improvements and fix issues.
 
+- Once the `ready-for-review` label has been applied and reviewers have been
+  assigned, the PR is considered under review. To help with the review process
+  there should be no force pushes/rewriting history in the branch.
+
 - After approval, the PR is [tested](#masternext-workflow) for a week with
   other approved PRs in the `mfem:next` branch.
 
@@ -370,16 +380,20 @@ Before you can start, you need a GitHub account, here are a few suggestions:
   `mfem:next`, see the [README](tests/scripts/README) file in that directory
   for more details.
 
-- Track the Travis CI, Github Actions and Appveyor [continuous integration](#automated-testing)
+- Track the GitHub Actions and Appveyor [continuous integration](#automated-testing)
   builds at the end of the PR. These should generally run clean, so address any
   errors as soon as possible. Please ask if you are unsure how to do that.
 
-- Note that some tests, such as the `branch-history` check in Travis and Github
-  Actions are safeguards that are allowed to fail in certain cases.
+- Note that some tests, such as the `branch-history` check in GitHub Actions
+  are safeguards that are allowed to fail in certain cases.
 
 - Other tests, such as the `code-style`, `documentation` and `gitignore`
-  checks in Travis and Github Actions enforce MFEM-specific rules which are
-  explained in the error messages and the `tests/scripts` directory.
+  checks in GitHub Actions enforce MFEM-specific rules which are explained in
+  the error messages and the `tests/scripts` directory.
+
+- Also note that the tests `branch-history` and `repos-checks` found in GitHub
+  Actions can be triggered automatically before each push using git hooks. See
+  the [git hooks README](config/githooks/README.md) for a detailed explanation.
 
 - If triggered, track the status of the LLNL GitLab tests. If failing, ask
   one of the _LLNL developers_ for details.
@@ -399,7 +413,7 @@ Before a PR can be merged, it should satisfy the following:
     - [ ] Does `make` or `cmake` have a new target?
     - [ ] Did the requirements or the installation process change? *(rare)*
 - [ ] Update continuous integration server configurations if necessary (e.g. with new version requirements for each of MFEM's dependencies)
-    - [ ] `.travis.yml`
+    - [ ] `.github`
     - [ ] `.appveyor.yml`
 - [ ] Update `.gitignore`:
     - [ ] Check if `make distclean; git status` shows any files that were generated from the source by the project (not an IDE) but we don't want to track in the repository.
@@ -516,7 +530,7 @@ MFEM uses a `master`/`next`-branch workflow as described below:
     - [ ] `doc/CodeDocumentation.conf.in`
 - [ ] Check that version requirements for each of MFEM's dependencies are documented in `INSTALL` and up-to-date
 - [ ] Check that continuous integration server configurations reflect the dependency version requirements of the new release
-    - [ ] `.travis.yml`
+    - [ ] `.github`
     - [ ] `.appveyor.yml`
 - [ ] Update the `CHANGELOG` to organize all release contributions
 - [ ] Review the whole source code once over
@@ -578,14 +592,17 @@ MFEM uses a `master`/`next`-branch workflow as described below:
 MFEM has several levels of automated testing running on GitHub, as well as on
 local Mac and Linux workstations, and Livermore Computing clusters at LLNL.
 
-### Linux and Mac smoke tests
-We use Travis CI and Github Actions to drive the default tests on the `master`
-and `next` branches. See the `.travis` file and the logs at
-[https://travis-ci.org/mfem/mfem](https://travis-ci.org/mfem/mfem).
+In addition, developers can set local git hooks to run some quick checks on
+commit or push, see the [README](config/githooks/README.md) in the `config/githooks`
+directory.
 
-Testing using Travis CI and Github Actions should be kept lightweight, as there
-is a time constraint on jobs. Two virtual machines are configured - Mac (OS X)
-and Linux.
+### Linux and Mac smoke tests
+We use GitHub Actions to drive the default tests on the `master` and `next`
+branches. See the `.github/workflows` files and the logs at
+[https://github.com/mfem/mfem/actions](https://github.com/mfem/mfem/actions).
+
+Testing using GitHub Actions should be kept lightweight, as there is a time
+constraint on jobs. Two virtual machines are configured - Mac (OS X) and Linux.
 
 - Tests on the `master` branch are triggered whenever a PR is issued on this branch.
 - Tests on the `next` branch are currently scheduled to run each night.

config/githooks/README.md

@@ -0,0 +1,41 @@
+                    Finite Element Discretization Library
+                                   __
+                       _ __ ___   / _|  ___  _ __ ___
+                      | '_ ` _ \ | |_  / _ \| '_ ` _ \
+                      | | | | | ||  _||  __/| | | | | |
+                      |_| |_| |_||_|   \___||_| |_| |_|
+
+                               https://mfem.org
+
+
+This directory contains recommended git hooks, which are scripts that can be
+used to improve your development experience with MFEM:
+
+### The hooks
+
+* `pre-commit` is a hook that will be applied before each commit and run
+`astyle` on the code. This will ensure that your changes comply with the MFEM
+code styling guidelines.
+
+* `pre-push` is a hook that will be applied before each push to run a quick set
+of tests that verify that your files headers are in compliance, and that you did
+not add any large files to the repo.
+
+### Setup
+
+To setup the git hooks, run `make hooks`, which creates symlinks to the hooks in
+the `.git/hooks` directory. Individual hooks can be enabled by manually creating
+symlinks.
+
+(You may also copy the scripts directly and customize them further, but this way
+you may miss additional updates in the future.)
+
+### Failures
+
+The `branch-history` check can fail in some cases when the history is OK. For
+example, when a large number of files were modified for a legitimate reason, or
+when a picture was added for documentation.
+
+If that is the case, make sure the failure is indeed justified, and rerun the
+push command with the `--no-verify` option. This will skip the hooks, allowing
+you to push those changes.

config/githooks/pre-commit

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+# Apply automated code formatting
+make -C $(git rev-parse --show-toplevel) style

config/githooks/pre-push

@@ -0,0 +1,107 @@
+#!/bin/bash
+
+# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+# LICENSE and NOTICE for details. LLNL-CODE-806117.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability visit https://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the BSD-3 license. We welcome feedback and contributions, see file
+# CONTRIBUTING.md for details.
+
+option=${1:-""}
+
+if [[ "${option}" == "--help" ]]; then
+  echo "This script runs checks on the repository."
+  echo "It has 2 modes: with and without an option."
+  echo ""
+  echo "Options are used in GitHub Actions and can be:"
+  echo "  --copyright"
+  echo "  --license"
+  echo "  --release"
+  echo "  --style"
+  echo "  --history"
+  echo ""
+  echo "As a githook, the script is used without options."
+  echo "In that case, it will run all the checks except style."
+  echo ""
+  echo "Use --help to print this help message."
+fi
+
+cd $(git rev-parse --show-toplevel)
+
+# copyright check
+copyright=true
+if [[ "${option}" == "--copyright" || "${option}" == "" ]]; then
+  if git grep -l "^\(#\|//\).*\(\-2020\|\ 2010,\)" > matches.txt; then
+    echo "Please update the following files to Copyright (c) 2010-2021:"
+    cat matches.txt
+    copyright=false
+  fi
+fi
+
+# license check
+license=true
+if [[ "${option}" == "--license" || "${option}" == "" ]]; then
+  if git grep -li "^\(#\|//\).*GNU\ Lesser\ General\ Public\ License" > matches.txt; then
+    echo "Please update the following files to the BSD-3 license:"
+    cat matches.txt
+    license=false
+  fi
+fi
+
+# release check
+release=true
+if [[ "${option}" == "--release" || "${option}" == "" ]]; then
+  if git grep -l "^\(#\|//\).*LLNL\-CODE\-443211" > matches.txt
+  then
+    echo "Please update the following files to LLNL-CODE-806117:"
+    cat matches.txt
+    release=false
+  fi
+fi
+
+# wrap-up
+code=0
+if ! $copyright ; then
+  echo "copyright check failed, unroll log for details"
+  code=1
+fi
+if ! $license ; then
+  echo "license check failed, unroll log for details"
+  code=1
+fi
+if ! $release ; then
+  echo "release check failed, unroll log for details"
+  code=1
+fi
+
+# `code-style` is not just a check, it will actually reformat the code if
+# necessary. This means that if one pushes while the repo is in dirty state
+# (changes not staged), those changes may be mixed with format changes.
+# To activate this, you will need to hard-copy this hook script in the hook
+# directory and uncomment only then. (See README.md)
+#
+## style check
+#if [[ "${option}" == "--style" || "${option}" == "" ]]; then
+if [[ "${option}" == "--style" ]]; then
+  if which astyle && [[ "$(astyle --version)" == "Artistic Style Version 2.05.1" ]]; then
+    cd tests/scripts
+    if ! ./runtest code-style; then code=1; fi
+    cd -
+  else
+    echo "Warning: astyle not found or version is not 2.05.1"
+  fi
+fi
+
+# branch-history
+if [[ "${option}" == "--history" || "${option}" == "" ]]; then
+  git fetch origin master:master
+  cd tests/scripts
+  if ! ./runtest branch-history; then code=1; fi
+  cd -
+fi
+
+exit $code

examples/ex26.cpp

@@ -105,7 +105,7 @@ private:
       Vector diag(fespace.GetTrueVSize());
       bfs.Last()->AssembleDiagonal(diag);
 
-      Solver* smoother = new OperatorChebyshevSmoother(opr.Ptr(), diag,
+      Solver* smoother = new OperatorChebyshevSmoother(*opr, diag,
                                                        *essentialTrueDofs.Last(), 2);
       AddLevel(opr.Ptr(), smoother, true, true);
    }

examples/ex26p.cpp

@@ -115,7 +115,7 @@ private:
       Vector diag(fespace.GetTrueVSize());
       bfs.Last()->AssembleDiagonal(diag);
 
-      Solver* smoother = new OperatorChebyshevSmoother(opr.Ptr(), diag,
+      Solver* smoother = new OperatorChebyshevSmoother(*opr, diag,
                                                        *essentialTrueDofs.Last(), 2, fespace.GetParMesh()->GetComm());
 
       AddLevel(opr.Ptr(), smoother, true, true);

examples/maxwell-solver-dev/ParDST/DofMapsDST.cpp

@@ -1,960 +0,0 @@
-#include "DofMapsDST.hpp"
-
-double testcoeff(const Vector & x)
-{
-   return sin(3*M_PI*(x.Sum()));
-}
-
-int get_rank(int tdof, std::vector<int> & tdof_offsets)
-{
-   int size = tdof_offsets.size();
-   if (size == 1) { return 0; }
-   std::vector<int>::iterator up;
-   up=std::upper_bound(tdof_offsets.begin(), tdof_offsets.end(),tdof); // 
-   return std::distance(tdof_offsets.begin(),up)-1;
-}
-
-void ComputeTdofOffsets(const MPI_Comm & comm, const ParFiniteElementSpace * pfes, 
-                        std::vector<int> & tdof_offsets)
-{
-   int num_procs;
-   MPI_Comm_size(comm, &num_procs);
-   tdof_offsets.resize(num_procs);
-   int mytoffset = pfes->GetMyTDofOffset();
-   MPI_Allgather(&mytoffset,1,MPI_INT,&tdof_offsets[0],1,MPI_INT,comm);
-}
-
-void GetSubdomainijk(int ip, const Array<int> nxyz, Array<int> & ijk)
-{
-   ijk.SetSize(3);
-   ijk[2] = ip/(nxyz[0]*nxyz[1]);
-   ijk[1] = (ip-ijk[2]*nxyz[0]*nxyz[1])/nxyz[0];
-   ijk[0] = (ip-ijk[2]*nxyz[0]*nxyz[1])%nxyz[0];
-}
-void GetDirectionijk(int id, Array<int> & ijk)
-{
-   ijk.SetSize(3);
-   int n = 3;
-   ijk[2] = id/(n*n) - 1;
-   ijk[1] = (id-(ijk[2]+1)*n*n)/n - 1;
-   ijk[0] = (id-(ijk[2]+1)*n*n)%n - 1;
-}
-
-int GetSubdomainId(const Array<int> nxyz, Array<int> & ijk)
-{
-   int dim=ijk.Size();
-   int k = (dim==2)? 0 : ijk[2];
-   return k*nxyz[1]*nxyz[0] + ijk[1]*nxyz[0] + ijk[0];
-}
-
-int GetDirectionId(const Array<int> & ijk)
-{
-   int n = 3;
-   int dim = ijk.Size();
-   int k = (dim == 2) ? -1 : ijk[2];
-   return (k+1)*n*n + (ijk[1]+1)*n + ijk[0]+1; 
-}
-
-void DofMaps::Init()
-{
-   comm = pfes->GetComm();
-   MPI_Comm_size(comm, &num_procs);
-   MPI_Comm_rank(comm, &myid);
-
-   dim = pfes->GetParMesh()->Dimension();
-   ComputeTdofOffsets(comm, pfes, tdof_offsets);
-   myelemoffset = part->myelem_offset;
-   mytoffset = pfes->GetMyTDofOffset();
-   subdomain_rank = part->subdomain_rank;
-   nrsubdomains = part->nrsubdomains;
-   nxyz.SetSize(3);
-   for (int i = 0; i<3; i++) { nxyz[i] = part->nxyz[i]; }
-
-   //compute sign factors for tdofs
-   int lsize = pfes->GetVSize();
-   int tsize = pfes->GetTrueVSize();
-   tdof_sign.SetSize(tsize); 
-   for (int i = 0; i<lsize; i++)
-   {
-      int j = pfes->GetGlobalTDofNumber(i);
-      if (j<mytoffset || j>=mytoffset+tsize) continue;
-      tdof_sign[j-mytoffset] = pfes->GetDofSign(i);
-   }
-}
-
-DofMaps::DofMaps(ParFiniteElementSpace *pfes_, ParMeshPartition * part_, bool CompFlag_)
-: pfes(pfes_), part(part_), CompFlag(CompFlag_)
-{
-   Init();
-   Setup();
-}
-
-void DofMaps::Setup()
-{
-   // Setup the local FiniteElementSpaces
-   const FiniteElementCollection * fec = pfes->FEColl();
-   fes.SetSize(nrsubdomains);
-   for (int i = 0; i<nrsubdomains; i++)
-   {
-      fes[i] = nullptr; // initialize with null on all procs
-      if (myid == subdomain_rank[i])
-      {
-         fes[i] = new FiniteElementSpace(part->subdomain_mesh[i],fec);
-      }
-   }
-   // cout << "Computing Overlap Tdofs" << endl;
-   SubdomainToSubdomainMapsSetup();
-   // TestSubdomainToSubdomainMaps();
-
-   SubdomainToGlobalMapsSetup();
-   // TestSubdomainToGlobalMaps();
-}
-
-void DofMaps::SubdomainToSubdomainMapsSetup()
-{
-   ComputeOvlpElems();
-   ComputeOvlpTdofs();
-}
-
-void DofMaps::AddElementToOvlpLists(int l, int iel, 
-                            const Array<bool> & neg, const Array<bool> & pos)
-{
-   int kbeg = (dim == 2) ? 0 : -1;
-   int kend = (dim == 2) ? 0 :  1;
-   Array<int> dijk(3);
-   for (int k = kbeg; k<=kend; k++)
-   {
-      if (dim == 3)
-      {
-         if (k == -1 && !neg[2]) continue;   
-         if (k ==  1 && !pos[2]) continue;   
-      }   
-
-      for (int j = -1; j<=1; j++)
-      {
-         if (j== -1 && !neg[1]) continue;   
-         if (j==  1 && !pos[1]) continue;   
-         for (int i = -1; i<=1; i++)
-         {
-            // cases to skip 
-            if (i==-1 && !neg[0]) continue;   
-            if (i== 1 && !pos[0]) continue;   
-
-            if (i==0 && j==0 && k == 0) continue;
-            dijk[0] = i; dijk[1] = j; dijk[2] = (dim==2)?-1 : k;  
-            int DirId = GetDirectionId(dijk);
-            OvlpElems[l][DirId].Append(iel);
-         }
-      }
-   }
-}
-
-void DofMaps::ComputeOvlpElems()
-{
-   // first compute the element in the overlaps
-   OvlpElems.resize(nrsubdomains);
-   int nlayers = 2*part->OvlpNlayers; 
-   // loop through subdomains
-   for (int l = 0; l<nrsubdomains; l++)
-   {
-      if (myid == subdomain_rank[l])
-      {
-         Array<int> ijk;
-         GetSubdomainijk(l,nxyz,ijk);
-         Mesh * mesh = part->subdomain_mesh[l];
-         OvlpElems[l].resize(pow(3,dim)); 
-         Vector pmin, pmax;
-         mesh->GetBoundingBox(pmin,pmax);
-         double h = part->MeshSize;
-         // loop through the elements in the mesh and assign them to the 
-         // appropriate lists of overlaps
-         for (int iel=0; iel< mesh->GetNE(); iel++)
-         {
-            // Get element center
-            Vector center(dim);
-            int geom = mesh->GetElementBaseGeometry(iel);
-            ElementTransformation * tr = mesh->GetElementTransformation(iel);
-            tr->Transform(Geometries.GetCenter(geom),center);
-
-            Array<bool> pos(dim); pos = false;
-            Array<bool> neg(dim); neg = false;
-            // loop through dimensions   
-            for (int d=0;d<dim; d++)
-            {
-               if (ijk[d]>0 && center[d] < pmin[d]+h*nlayers)
-               {
-                  neg[d] = true;
-               }
-
-               if (ijk[d]<nxyz[d]-1 && center[d] > pmax[d]-h*nlayers) 
-               {
-                  pos[d] = true;
-               }
-            }
-            // Add the element to the appropriate lists
-            AddElementToOvlpLists(l,iel,neg,pos);        
-         }   
-      }
-   }
-}
-
-void DofMaps::ComputeOvlpTdofs()
-{
-   OvlpTDofs.resize(nrsubdomains);
-   int nrneighbors = pow(3,dim); // including its self
-
-   // loop through subdomains
-   for (int l = 0; l<nrsubdomains; l++)
-   {
-      if (myid != subdomain_rank[l]) continue;
-      int ntdofs = fes[l]->GetTrueVSize();
-      Array<int> tdof_marker(ntdofs); 
-      OvlpTDofs[l].resize(nrneighbors);
-      // loop through neighboring directions/neighbors
-      for (int d=0; d<nrneighbors; d++)
-      {
-         tdof_marker = 0;
-         Array<int> tdoflist;
-         // Get the direction
-         Array<int> dijk;
-         GetDirectionijk(l,dijk);
-         int nel = OvlpElems[l][d].Size();
-         Array<int>Elems = OvlpElems[l][d];
-         for (int iel = 0; iel<nel; ++iel)
-         {
-            int jel = Elems[iel];   
-            Array<int> ElemDofs;
-
-            fes[l]->GetElementDofs(jel,ElemDofs);
-            int ndof = ElemDofs.Size();
-            for (int i = 0; i<ndof; ++i)
-            {
-               int dof_ = ElemDofs[i];
-               int dof = (dof_ >= 0) ? dof_ : abs(dof_) - 1;
-               if (!tdof_marker[dof])
-               {
-                  tdoflist.Append(dof); // dofs of ip0 in ovlp
-                  tdof_marker[dof] = 1;
-               }
-            }
-         }
-         OvlpTDofs[l][d] = tdoflist; 
-         if (CompFlag)
-         {
-            for (int i=0; i<tdoflist.Size(); i++)
-            {
-               tdoflist[i] += fes[l]->GetTrueVSize();
-            }
-            OvlpTDofs[l][d].Append(tdoflist);
-         }
-      }
-   }
-}
-
-void DofMaps::PrintOvlpTdofs()
-{
-   int nrneighbors = pow(3,dim); // including its self
-   if (myid == 0)
-   {
-      for (int i = 0; i<nrsubdomains; i++)
-      {
-         if (myid != subdomain_rank[i]) continue;
-         Array<int> ijk;
-         GetSubdomainijk(i,nxyz,ijk);
-         cout << "subdomain = " ; ijk.Print();
-         cout << "myid = " << myid << endl;
-         cout << "ip   = " << i << endl;
-         for (int d = 0; d<nrneighbors; d++)
-         {
-            Array<int> dijk;
-            GetDirectionijk(d,dijk);
-            cout << "direction = " ; dijk.Print();
-
-            if (OvlpTDofs[i][d].Size())
-            {
-               cout << "OvlpTdofs = " ; 
-               OvlpTDofs[i][d].Print(cout,OvlpTDofs[i][d].Size() );
-            }
-         }
-      }
-   }
-}
-
-void DofMaps::TransferToNeighbors(const Array<int> & SubdomainIds, const Array<Vector *> & x,
-std::vector<std::vector<Vector * >> & OvlpSol)
-{
-   // 2D for now....
-   MFEM_VERIFY(SubdomainIds.Size() == x.Size(), "TransferToNeighbors: Size inconsistency");
-   int nrsendIds = SubdomainIds.Size();
-   int nrneighbors = pow(3,dim);
-   MPI_Request *recv_requests = new MPI_Request[nrsendIds*nrneighbors];
-   MPI_Request *send_requests = new MPI_Request[nrsendIds*nrneighbors];
-   MPI_Status  *recv_statuses = new MPI_Status[nrsendIds*nrneighbors];
-   MPI_Status  *send_statuses = new MPI_Status[nrsendIds*nrneighbors];
-   Array<Vector * > send_buffer(nrsendIds*nrneighbors);
-   Array<Vector * > recv_buffer(nrsendIds*nrneighbors);
-   int send_counter = 0;
-   int recv_counter = 0;
-   for (int is = 0; is<nrsendIds; is++)
-   {
-      int i0 = SubdomainIds[is];
-      Array<int> ijk;
-      GetSubdomainijk(i0,nxyz,ijk);
-      for (int d=0;d<nrneighbors; d++)
-      {
-         Array<int>directions;
-         GetDirectionijk(d,directions);
-
-         if (dim == 2 && directions[0] == 0 && directions[1] == 0) continue;
-         if (dim == 3 && directions[0] == 0 
-                      && directions[1] == 0 
-                      && directions[2] == 0) continue;
-         int i = ijk[0] + directions[0];
-         if (i<0 || i>=nxyz[0]) continue;
-         int j = ijk[1] + directions[1];
-         if (j<0 || j>=nxyz[1]) continue;
-         int k = (dim ==3 ) ? ijk[2] + directions[2] : 0;
-         if (k<0 || k>=nxyz[2]) continue;
-         Array<int>ijk1(3);
-         ijk1[0] = i;
-         ijk1[1] = j;
-         ijk1[2] = k;
-         int i1 = GetSubdomainId(nxyz,ijk1);
-         if (myid == subdomain_rank[i0])
-         {
-            Array<int> tdofs0 = OvlpTDofs[i0][d]; // map of dofs in the overlap
-            send_buffer[send_counter] = new Vector(tdofs0.Size());
-            x[is]->GetSubVector(tdofs0,*send_buffer[send_counter]);
-            // Destination rank
-            int dest = subdomain_rank[i1];
-            int tag = i0 * nrneighbors + d;
-
-            int count = tdofs0.Size();
-            MPI_Isend(send_buffer[send_counter]->GetData(),count,MPI_DOUBLE,dest,
-                      tag,comm,&send_requests[send_counter]);
-            send_counter++;
-
-         }
-         if (myid == subdomain_rank[i1])
-         {
-            Array<int> direction1(3); direction1 = -1;
-            for (int dd=0;dd<dim;dd++) 
-            { 
-               direction1[dd] = -directions[dd];
-            }
-            int d1 = GetDirectionId(direction1);
-
-            int count = OvlpTDofs[i1][d1].Size();
-            recv_buffer[recv_counter] = new Vector(count); 
-            int src = subdomain_rank[i0];
-            int tag = i0 * nrneighbors + d;
-            MPI_Irecv(recv_buffer[recv_counter]->GetData(), count,MPI_DOUBLE,src,
-                      tag,comm, &recv_requests[recv_counter]);
-            recv_counter++;
-         }
-      }   
-   }
-   MPI_Waitall(send_counter, send_requests, send_statuses);
-   MPI_Waitall(recv_counter, recv_requests, recv_statuses);
-
-   delete [] send_statuses;
-   delete [] send_requests;
-   delete [] recv_statuses;
-   delete [] recv_requests;
-
-   for (int i = 0; i<send_counter; i++)
-   {
-      delete send_buffer[i];
-   }
-   send_buffer.DeleteAll();
-
-
-   // Extract the transfered solutions
-   recv_counter = 0;
-   for (int is = 0; is<nrsendIds; is++)
-   {
-      int i0 = SubdomainIds[is];
-      Array<int> ijk;
-      GetSubdomainijk(i0,nxyz,ijk);
-      for (int d=0;d<nrneighbors; d++)
-      {
-         Array<int>directions;
-         GetDirectionijk(d,directions);
-         if (dim == 2 && directions[0] == 0 && directions[1] == 0) continue;
-         if (dim == 3 && directions[0] == 0 
-                      && directions[1] == 0 
-                      && directions[2] == 0) continue;
-         int i = ijk[0] + directions[0];
-         if (i<0 || i>=nxyz[0]) continue;
-         int j = ijk[1] + directions[1];
-         if (j<0 || j>=nxyz[1]) continue;
-         int k = (dim ==3 ) ? ijk[2] + directions[2] : 0;
-         if (k<0 || k>=nxyz[2]) continue;
-
-         Array<int>ijk1(3);
-         ijk1[0] = i;
-         ijk1[1] = j;
-         ijk1[2] = k;
-         int i1 = GetSubdomainId(nxyz,ijk1);
-         if (myid == subdomain_rank[i1])
-         {
-            Array<int> direction1(3); direction1 = -1;
-            for (int d=0;d<dim;d++) 
-            { 
-               direction1[d] = -directions[d];
-            }
-            int d1 = GetDirectionId(direction1);
-            Array<int> tdofs1 = OvlpTDofs[i1][d1];
-            if (!OvlpSol[i1][d1])
-            {
-               OvlpSol[i1][d1] = new Vector(2*fes[i1]->GetTrueVSize());
-            }
-            *OvlpSol[i1][d1] = 0.0;
-            OvlpSol[i1][d1]->SetSubVector(tdofs1,*recv_buffer[recv_counter]);
-            recv_counter++;
-         }
-      }   
-   }
-   for (int i = 0; i<recv_counter; i++)
-   {
-      delete recv_buffer[i];
-   }
-   recv_buffer.DeleteAll();
-}
-
-void DofMaps::TestSubdomainToSubdomainMaps()
-{
-      // testing inter-subdomain communication
-   FunctionCoefficient c1(testcoeff);
-   int nrsub = nrsubdomains;
-   Array<int> subdomain_ids(nrsub);
-   Array<Vector*> x(nrsub);
-   for (int i = 0; i<nrsub; i++)
-   {
-      x[i] = nullptr;
-      subdomain_ids[i] = i;
-      if (fes[i])
-      {
-         ComplexGridFunction gf(fes[i]);
-         gf = 0.0;
-         gf.ProjectCoefficient(c1,c1);
-         x[i] = new Vector(2*fes[i]->GetTrueVSize());
-         *x[i] = gf;
-      }
-   }
-
-   std::vector<std::vector<Vector * >> OvlpSol;
-
-   OvlpSol.resize(nrsubdomains);
-   int nrneighbors = pow(3,dim);
-   for (int ip = 0; ip<nrsubdomains; ip++)
-   {
-      if (myid == subdomain_rank[ip])
-      {
-         OvlpSol[ip].resize(nrneighbors);
-      }
-   }
-
-
-   TransferToNeighbors(subdomain_ids,x,OvlpSol);
-
-   string keys = "keys amrRljc\n";
-   for (int i0 = 0 ; i0< nrsubdomains; i0++)
-   {
-      if (fes[i0])
-      {
-         ComplexGridFunction gf0(fes[i0]);
-         for (int d = 0; d<nrneighbors; d++)
-         {
-            if(OvlpSol[i0][d])
-            {
-               Array<int>dijk;
-               GetDirectionijk(d,dijk);
-               Array<int>ijk;
-               GetSubdomainijk(i0,nxyz,ijk);
-               ostringstream oss;
-               oss << "myid: " << myid 
-                     << ", subdomain: (" << ijk[0] << "," << ijk[1] <<")"
-                     << ", direction: (" << dijk[0] << "," << dijk[1] <<")";
-
-               gf0 = 0.0;
-               gf0.real().SetVector(*OvlpSol[i0][d],0);
-               gf0.imag().SetVector(*OvlpSol[i0][d],fes[i0]->GetTrueVSize());
-               char vishost[] = "localhost";
-               int  visport   = 19916;
-               socketstream sol_sock(vishost, visport);
-               sol_sock.precision(8);
-               sol_sock << "solution\n" << *(part->subdomain_mesh[i0]) << gf0.real() 
-               << keys
-               << "window_title '" << oss.str() << "'" << flush;
-            }
-         }
-      }
-   }
-   for (int i = 0; i<nrsub; i++)
-   {
-      delete x[i];
-   }
-}
-
-void DofMaps::SubdomainToGlobalMapsSetup()
-{
-   // workspace for MPI_AlltoAll
-   send_count.SetSize(num_procs);  send_count = 0;
-   send_displ.SetSize(num_procs);  send_displ = 0; 
-   recv_count.SetSize(num_procs);  recv_count = 0;
-   recv_displ.SetSize(num_procs);  recv_displ = 0;
-
-   // 1. Communicate to the subdomain rank the list of tdofs 
-   // a. Compute send count
-   for (int ip = 0; ip<nrsubdomains; ++ip)
-   {
-      // avoid any communication if on subdomain rank
-      int nel = part->local_element_map[ip].Size();
-
-      for (int iel = 0; iel<nel; iel++)
-      {
-         int elem_idx = part->local_element_map[ip][iel] - myelemoffset;
-         // int ndofs = local_tdofs[ip].Size();
-         int ndofs = pfes->GetFE(elem_idx)->GetDof();
-
-         send_count[subdomain_rank[ip]] += 2 + ndofs; 
-      }
-   }
-   // b. Compute receive count
-   MPI_Alltoall(send_count,1,MPI_INT,recv_count,1,MPI_INT,comm);
-   for (int k=0; k<num_procs-1; k++)
-   {
-      send_displ[k+1] = send_displ[k] + send_count[k];
-      recv_displ[k+1] = recv_displ[k] + recv_count[k];
-   }
-   sbuff_size = send_count.Sum();
-   rbuff_size = recv_count.Sum();
-   // c. Allocate and fill the send buffer
-   Array<int> sendbuf(sbuff_size);  sendbuf = 0;
-   Array<int> soffs(num_procs); soffs = 0;
-   for (int ip = 0; ip<nrsubdomains; ++ip)
-   {
-      int nel = part->local_element_map[ip].Size();
-      for (int iel = 0; iel<nel; iel++)
-      {
-         int elem_idx = part->local_element_map[ip][iel] - myelemoffset;
-         Array<int>ElemDofs;
-         pfes->GetElementDofs(elem_idx,ElemDofs);
-         int ndofs = ElemDofs.Size();
-
-         int j = send_displ[subdomain_rank[ip]] + soffs[subdomain_rank[ip]];
-         sendbuf[j] = ip;
-         sendbuf[j+1] = ndofs;
-
-         for (int k = 0; k < ndofs ; ++k)
-         {
-            int edof_ = ElemDofs[k];
-            int edof = (edof_ >= 0) ? edof_ : abs(edof_) - 1;
-            sendbuf[j+2+k] = pfes->GetGlobalTDofNumber(edof);
-         }
-         soffs[subdomain_rank[ip]] +=  2 + ndofs;
-      }
-   }
-
-   // d. Communication
-   Array<int> recvbuf(rbuff_size);
-   MPI_Alltoallv(sendbuf, send_count, send_displ, MPI_INT, recvbuf,
-                 recv_count, recv_displ, MPI_INT, comm);
-
-   // 3. Extract from recv_buffer
-   std::vector<Array<int>> global_tdofs(nrsubdomains);
-   int k=0;
-   while (k<rbuff_size)
-   {
-      int ip = recvbuf[k++]; 
-      int ndofs = recvbuf[k++];
-      for (int i = 0; i < ndofs; ++i)
-      {
-         global_tdofs[ip].Append(recvbuf[i+k]); 
-      }
-      k += ndofs;
-   }
-
-   SubdomainGTrueDofs.resize(nrsubdomains);
-   // 4. Construct SubdomainTdof to Global mesh tdof maps
-   for (int ip=0; ip<nrsubdomains; ++ip)
-   {
-      if (myid != subdomain_rank[ip]) continue;
-      int nrdof = fes[ip]->GetTrueVSize();
-
-      SubdomainGTrueDofs[ip].SetSize(nrdof);
-      int nel = part->element_map[ip].Size();
-      int k = 0;
-      for (int iel = 0; iel<nel; ++iel)
-      {
-         Array<int> elem_dofs;
-         fes[ip]->GetElementDofs(iel,elem_dofs);
-         int ndof = elem_dofs.Size();
-         for (int i = 0; i<ndof; ++i)
-         {
-            int edof_ = elem_dofs[i];
-            int edof = (edof_ >= 0) ? edof_ : abs(edof_) - 1;
-            // rearranging dofs from serial fespace to pfes ordering
-            SubdomainGTrueDofs[ip][edof] = global_tdofs[ip][k++];
-         }
-      }
-   }
-
-   // 5. Communicate SubdomainGTrueDofs to participating ranks 
-   send_count = 0;  send_displ = 0;
-   recv_count = 0;  recv_displ = 0;
-
-   for (int ip = 0; ip < nrsubdomains; ++ip)
-   {
-      if (myid != subdomain_rank[ip]) continue;
-      int ndofs = SubdomainGTrueDofs[ip].Size();
-      for (int i = 0; i<ndofs; ++i)
-      {
-         int tdof = SubdomainGTrueDofs[ip][i];
-         int rank = get_rank(tdof,tdof_offsets);
-         if (rank == subdomain_rank[ip]) continue; // <--------------
-         send_count[rank] += 2; // 1 for the dof and 1 for the ip that goes to 
-      }
-   }
-
-   // communicate so that recv_count is constructed
-   MPI_Alltoall(send_count,1,MPI_INT,recv_count,1,MPI_INT,comm);
-   //
-   for (int k=0; k<num_procs-1; k++)
-   {
-      send_displ[k+1] = send_displ[k] + send_count[k];
-      recv_displ[k+1] = recv_displ[k] + recv_count[k];
-   }
-   sbuff_size = send_count.Sum();
-   rbuff_size = recv_count.Sum();
-
-   sendbuf.SetSize(sbuff_size);  
-   sendbuf = 0; soffs = 0;
-
-   for (int ip = 0; ip < nrsubdomains; ip++)
-   {
-      if (myid != subdomain_rank[ip]) continue;
-      int ndofs = SubdomainGTrueDofs[ip].Size();
-      // loop through dofs
-      for (int i = 0; i<ndofs; ++i)
-      {
-         int tdof = SubdomainGTrueDofs[ip][i];
-         int irank = get_rank(tdof,tdof_offsets);
-         if (irank == subdomain_rank[ip]) continue; // <--------------
-         int j = send_displ[irank] + soffs[irank];
-         sendbuf[j] = ip;
-         sendbuf[j+1] = SubdomainGTrueDofs[ip][i];
-         soffs[irank] +=  2 ;
-      }
-   }
-
-   recvbuf.SetSize(rbuff_size);
-   MPI_Alltoallv(sendbuf, send_count, send_displ, MPI_INT, recvbuf,
-                 recv_count, recv_displ, MPI_INT, comm);
-
-   // List of tdofs owned by the processor for subdomains not owned
-   SubdomainLTrueDofs.resize(nrsubdomains); 
-   for (int k=0; k<rbuff_size/2; k++)
-   {
-      int ip = recvbuf[2*k];
-      int tdof = recvbuf[2*k+1];
-      SubdomainLTrueDofs[ip].Append(tdof);
-   }    
-}
-
-// Restriction of global residual to subdomain residuals
-void DofMaps::GlobalToSubdomains(const Vector & y, Array<Vector*> & x)
-{
-   send_count = 0; send_displ = 0;
-   recv_count = 0; recv_displ = 0;
-
-   // Compute send_counts
-   int m = (CompFlag) ? 2 : 1 ;
-   for (int ip = 0; ip < nrsubdomains; ip++)
-   {
-      if (myid == subdomain_rank[ip]) continue;  // <---------------
-      int ndofs = SubdomainLTrueDofs[ip].Size();
-      send_count[subdomain_rank[ip]] += m * ndofs;
-   }
-
-    // communicate so that recv_count is constructed
-   MPI_Alltoall(send_count,1,MPI_INT,recv_count,1,MPI_INT,comm);
-
-   for (int k=0; k<num_procs-1; k++)
-   {
-      send_displ[k+1] = send_displ[k] + send_count[k];
-      recv_displ[k+1] = recv_displ[k] + recv_count[k];
-   }
-   sbuff_size = send_count.Sum();
-   rbuff_size = recv_count.Sum();
-
-   Array<double> sendbuf(sbuff_size); sendbuf = 0;
-   Array<int> soffs(num_procs); soffs = 0;
-
-   for (int ip = 0; ip < nrsubdomains; ip++)
-   {
-      if (myid == subdomain_rank[ip]) continue;  // <---------------
-      int ndofs = SubdomainLTrueDofs[ip].Size();
-      for (int i = 0; i<ndofs; i++)
-      {
-         int tdof = SubdomainLTrueDofs[ip][i];
-         int j = send_displ[subdomain_rank[ip]] + soffs[subdomain_rank[ip]];
-         soffs[subdomain_rank[ip]] +=m;
-         int k = tdof - mytoffset;
-         // sendbuf[j] = y[k];
-         sendbuf[j] = tdof_sign[k]*y[k];
-         if (CompFlag)
-         {  // if complex valued 
-            int tsize = pfes->GetTrueVSize();
-            // sendbuf[j+1] = y[k+tsize];
-            sendbuf[j+1] = tdof_sign[k]*y[k+tsize];
-         }
-      }
-   }
-
-   // communication
-   Array<double> recvbuf(rbuff_size);
-   MPI_Alltoallv(sendbuf, send_count, send_displ, MPI_DOUBLE, recvbuf,
-                 recv_count, recv_displ, MPI_DOUBLE, comm);
-   Array<int> roffs(num_procs);
-   roffs = 0;
-   // Now each process will construct the res vector
-   x.SetSize(nrsubdomains);
-   for (int ip = 0; ip < nrsubdomains; ip++)
-   {
-      if (myid != subdomain_rank[ip]) continue;
-      int ndof = SubdomainGTrueDofs[ip].Size();
-      if (!x[ip]) x[ip] = new Vector(m*ndof); 
-      *x[ip] = 0.0;
-      // extract the data from receiv buffer
-      for (int i=0; i<ndof; i++)
-      {
-         // pick up the tdof and find its rank
-         int tdof = SubdomainGTrueDofs[ip][i];
-         int tdof_rank = get_rank(tdof,tdof_offsets);
-         if (tdof_rank != subdomain_rank[ip])  // <---------------
-         {
-            int k = recv_displ[tdof_rank] + roffs[tdof_rank];
-            roffs[tdof_rank] += m;
-            (*x[ip])[i] = recvbuf[k];
-            if (CompFlag)
-            {  
-               (*x[ip])[i+ndof] = recvbuf[k+1];
-            }
-         }
-         else
-         {
-            int k = tdof - mytoffset;
-            // (*x[ip])[i] = y[k];
-            (*x[ip])[i] = tdof_sign[k]*y[k];
-            if (CompFlag)
-            {  
-               int gtsize = pfes->GetTrueVSize();
-               (*x[ip])[i+ndof] = tdof_sign[k]*y[k+gtsize];
-            }
-         }
-      }
-   }
-}
-
-// Prolongation of subdomain solutions to the global solution
-void DofMaps::SubdomainsToGlobal(const Array<Vector*> & x, Vector & y)
-{
-   send_count = 0; send_displ = 0;
-   recv_count = 0; recv_displ = 0;
-
-   // Compute send_counts
-   int m = (CompFlag) ? 2 : 1 ;
-   for (int ip = 0; ip < nrsubdomains; ip++)
-   {
-      if (myid != subdomain_rank[ip]) continue;
-      int ndofs = SubdomainGTrueDofs[ip].Size();
-      for (int i=0; i<ndofs; i++)
-      {
-         // pick up the tdof and find its rank
-         int tdof = SubdomainGTrueDofs[ip][i];
-         int tdof_rank = get_rank(tdof,tdof_offsets);
-         if (tdof_rank == subdomain_rank[ip]) continue;
-         send_count[tdof_rank] +=m;
-      }
-   }
-
-   MPI_Alltoall(send_count,1,MPI_INT,recv_count,1,MPI_INT,comm);
-
-   for (int k=0; k<num_procs-1; k++)
-   {
-      send_displ[k+1] = send_displ[k] + send_count[k];
-      recv_displ[k+1] = recv_displ[k] + recv_count[k];
-   }
-   sbuff_size = send_count.Sum();
-   rbuff_size = recv_count.Sum();
-
-   Array<double> sendbuf(sbuff_size); sendbuf = 0;
-   Array<int> soffs(num_procs); soffs = 0;
-
-   for (int ip = 0; ip < nrsubdomains; ip++)
-   {
-      if (myid != subdomain_rank[ip]) continue;
-      int ndofs = SubdomainGTrueDofs[ip].Size();
-      // loop through dofs
-      for (int i=0; i<ndofs; i++)
-      {
-         //  pick up the dof and find its tdof_rank
-         int tdof = SubdomainGTrueDofs[ip][i];
-         int tdof_rank = get_rank(tdof,tdof_offsets);
-         // offset
-         if (tdof_rank == subdomain_rank[ip]) continue;
-         int k = send_displ[tdof_rank] + soffs[tdof_rank];
-         soffs[tdof_rank] +=m;
-         sendbuf[k] = (*x[ip])[i];
-         if (CompFlag)
-         {
-            sendbuf[k+1] = (*x[ip])[i+ndofs];
-         }
-      }
-   }
-
-   Array<double> recvbuf(rbuff_size);
-   Array<int> roffs(num_procs); roffs = 0;
-   MPI_Alltoallv(sendbuf, send_count, send_displ, MPI_DOUBLE, recvbuf,
-                 recv_count, recv_displ, MPI_DOUBLE, comm);
-
-   for (int ip = 0; ip < nrsubdomains; ip++)
-   {
-      if (myid == subdomain_rank[ip]) 
-      {
-         int ndofs = SubdomainGTrueDofs[ip].Size();
-         for (int i = 0; i<ndofs; i++)
-         {
-            int tdof = SubdomainGTrueDofs[ip][i];
-            int k = tdof - mytoffset;
-            if (k<0 || k>=pfes->GetTrueVSize()) continue;
-            y[k] += tdof_sign[k] * (*x[ip])[i];
-            if (CompFlag)
-            {  
-               int gtsize = pfes->GetTrueVSize();
-               y[k+gtsize] += tdof_sign[k]*(*x[ip])[i+ndofs];
-            }
-         }
-      }
-      else
-      {
-         int ndofs = SubdomainLTrueDofs[ip].Size();
-         for (int i = 0; i<ndofs; i++)
-         {
-            int tdof = SubdomainLTrueDofs[ip][i];
-            int k = tdof - mytoffset;
-            int j = recv_displ[subdomain_rank[ip]] + roffs[subdomain_rank[ip]];
-            roffs[subdomain_rank[ip]] +=m;
-            y[k] += tdof_sign[k] * recvbuf[j];
-            if (CompFlag)
-            {
-               int tsize = pfes->GetTrueVSize();
-               y[k+tsize] += tdof_sign[k]*recvbuf[j+1];
-            }
-         }
-      }
-   }              
-}
-
-void DofMaps::TestSubdomainToGlobalMaps()
-{
-   cout << "Testing Subdomain To Global Maps" << endl;
-   FunctionCoefficient c1(testcoeff);
-   Array<Vector*> x(nrsubdomains);
-   Vector y(pfes->GetTrueVSize()); y = 0.0;
-   for (int i = 0 ; i<nrsubdomains; i++)
-   {
-      if (myid != subdomain_rank[i]) continue;
-      x[i] = new Vector(fes[i]->GetTrueVSize());
-      GridFunction gf(fes[i]);
-      gf = 0.0;
-
-      if (i==3) gf.ProjectCoefficient(c1);
-      *x[i] = gf;
-   }
-
-   SubdomainsToGlobal(x,y);
-
-   // cout << "1: myid = " <<  myid << ", y = "; y.Print();
-
-   string keys = (dim==2) ? "keys amrRljc\n": "keys m\n";
-   ParGridFunction pgf(pfes);
-
-   const Operator &P = *pfes->GetProlongationMatrix();
-   P.Mult(y, pgf);
-   
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock(vishost, visport);
-   sol_sock.precision(8);
-   sol_sock << "parallel " << num_procs << " " << myid << "\n"
-               << "solution\n" << *pfes->GetParMesh() << pgf 
-               << keys << flush;
-
-   ParGridFunction pgf1(pfes);
-   pgf1.ProjectCoefficient(c1);
-   Vector y1(pfes->GetTrueVSize());
-   const SparseMatrix * R = pfes->GetRestrictionMatrix();
-
-   R->Mult(pgf1,y1);
-   // P.MultTranspose(pgf1,y1);
-   Array<Vector*> x1;
-   GlobalToSubdomains(y1,x1);
-
-
-   // for (int i = 0 ; i<nrsubdomains; i++)
-   // {
-   //    if (myid != subdomain_rank[i]) continue;
-   //    ostringstream mesh_name;
-   //    mesh_name << "output/mesh." << setfill('0') << setw(6) << i;
-   //    ofstream mesh_ofs(mesh_name.str().c_str());
-   //    mesh_ofs.precision(8);
-   //    fes[i]->GetMesh()->Print(mesh_ofs);
-   //    GridFunction gf(fes[i]);
-   //    gf = x1[i];
-   //    ostringstream gf_name;
-   //    gf_name << "output/gf." << setfill('0') << setw(6) << i;
-   //    ofstream gf_ofs(gf_name.str().c_str());
-   //    gf_ofs.precision(8);
-   //    gf.Save(gf_ofs);
-   // }
-
-
-
-   int nrsub = nrsubdomains;
-   for (int i = 0 ; i<nrsub; i++)
-   {
-      if (myid == subdomain_rank[i])
-      {
-         socketstream sol_sock1(vishost, visport);
-         sol_sock1.precision(8);
-         sol_sock1 << "parallel " << nrsub << " " << i << "\n";
-         GridFunction gf(fes[i]);
-         GridFunction gf1(fes[i]);
-         gf1.ProjectCoefficient(c1);
-         gf = *x1[i];
-         gf1-=gf;
-         cout << "ip, Diff norm = " <<i<<", " << gf1.Norml2() << endl;
-         sol_sock1 << "solution\n" << *fes[i]->GetMesh() << gf
-                   << keys << flush;
-      }
-      MPI_Barrier(MPI_COMM_WORLD);
-   }
-
-   socketstream gf_sock(vishost, visport);
-   gf_sock.precision(8);
-   gf_sock << "parallel " << num_procs << " " << myid << "\n"
-           << "solution\n" << *pfes->GetParMesh() << pgf1 
-           << keys << flush;
-}
-
-
-DofMaps::~DofMaps()
-{
-   for (int i = 0; i<nrsubdomains; i++)
-   {
-      delete fes[i];
-   }
-}

examples/maxwell-solver-dev/ParDST/DofMapsDST.hpp

@@ -1,109 +0,0 @@
-#pragma once
-#include "../common/Utilities.hpp"
-#include "../common/PML.hpp"
-using namespace std;
-using namespace mfem;
-
-double testcoeff(const Vector & x);
-int get_rank(int tdof, std::vector<int> & tdof_offsets);
-
-
-void ComputeTdofOffsets(const MPI_Comm & comm, const ParFiniteElementSpace * pfes, 
-                        std::vector<int> & tdof_offsets);
-
-void GetSubdomainijk(int ip, const Array<int> nxyz, Array<int> & ijk);
-void GetDirectionijk(int id, Array<int> & ijk);
-int GetSubdomainId(const Array<int> nxyz, Array<int> & ijk);
-int GetDirectionId(const Array<int> & ijk);
-
-
-// class handling two types of dof maps
-// 1. Subdomain truedofs ---> Global truedofs
-// 2. Subdomain truedofs ---> Neighbor truedofs 
-class DofMaps
-{
-private:
-   // The FE space of the problem (H1/Hcurl)
-   ParFiniteElementSpace *pfes = nullptr;
-
-   // The given partition of the parmesh
-   ParMeshPartition *part = nullptr;
-   // partition in x-y-z
-   Array<int> nxyz;
-
-   // MPI parameters
-   MPI_Comm comm = MPI_COMM_WORLD;
-   int num_procs, myid;
-
-   // true dof offset and element offset of the processor
-   vector<int> tdof_offsets;
-   int mytoffset;
-   int myelemoffset;
-   
-   int dim;
-   // Total number of subdomains
-   int nrsubdomains;
-   
-   // Array specifying the subdomain rank
-   Array<int> subdomain_rank;
-
-   // Complex flag
-   bool CompFlag;
-
-   // sign factors
-   Array<int> tdof_sign;
-   // Initializing mpi and helper parameters
-   void Init();
-
-   // 1. Setting up the subdomains FE spaces
-   // 2. Setting up the subdomains-to-subdomains maps
-   // 3. Setting up the subdomain-to-global maps
-   void Setup();
-
-   // -----------------------------------------------
-   //           Subdomain to Subdomain maps
-   // -----------------------------------------------
-   std::vector<std::vector<Array<int>>> OvlpElems;
-   void AddElementToOvlpLists(int l, int iel, 
-                            const Array<bool> & neg, 
-                            const Array<bool> & pos);
-   std::vector<std::vector<Array<int>>> OvlpTDofs;
-   void SubdomainToSubdomainMapsSetup();
-   void ComputeOvlpElems();
-   void ComputeOvlpTdofs();
-   void PrintOvlpTdofs();
-
-   // -----------------------------------------------
-   //           Subdomain to Global maps
-   // -----------------------------------------------
-   std::vector<Array<int>> SubdomainGTrueDofs; // Subdomain Tdofs to Global Tdofs
-   std::vector<Array<int>> SubdomainLTrueDofs; // Subdomain Tdofs to Local (on rank) Tdofs
-
-   Array<int> send_count, send_displ;  
-   Array<int> recv_count, recv_displ;  
-   int sbuff_size = 0;
-   int rbuff_size = 0;
-   void SubdomainToGlobalMapsSetup();
-
-   // Testing
-   void TestSubdomainToGlobalMaps();
-   void TestSubdomainToSubdomainMaps();
-
-public:
-   // constructor
-
-   // FiniteElementSpaces of the subdomains
-   Array<FiniteElementSpace *> fes;
-
-   DofMaps(ParFiniteElementSpace *fespace_, ParMeshPartition * part_, bool CompFlag_ = false);
-   ~DofMaps();
-   // Transfering from subdomains SubdomainIds to all their neighbors
-   void TransferToNeighbors(const Array<int> & SubdomainIds, const Array<Vector *> & x, 
-   std::vector<std::vector<Vector * >> & OvlpSol);
-
-   // Prolongation of subdomain solutions to the global solution
-   void SubdomainsToGlobal(const Array<Vector*> & x, Vector & y);
-   // Restriction of global residual to subdomain residuals
-   // bool comp: true for complex valued problems
-   void GlobalToSubdomains(const Vector & y, Array<Vector*> & x);
-};

examples/maxwell-solver-dev/ParDST/ParDST.cpp

@@ -1,849 +0,0 @@
-//Parallel Diagonal Source Transfer Preconditioner
-
-#include "ParDST.hpp"
-
-ParDST::ParDST(ParSesquilinearForm * bf_, Array2D<double> & Pmllength_, 
-         double omega_, Coefficient * Q_,  int nrlayers_ , int nx_, int ny_, int nz_)
-   : Solver(2*bf_->ParFESpace()->GetTrueVSize(), 2*bf_->ParFESpace()->GetTrueVSize()), 
-     bf(bf_), Pmllength(Pmllength_), omega(omega_), 
-     Q(Q_), nrlayers(nrlayers_)
-{
-   nx = nx_; ny = ny_; nz = nz_;
-   Init();
-}
-ParDST::ParDST(ParSesquilinearForm * bf_, Array2D<double> & Pmllength_, 
-         double omega_, VectorCoefficient * VQ_,  int nrlayers_ , int nx_, int ny_, int nz_)
-   : Solver(2*bf_->ParFESpace()->GetTrueVSize(), 2*bf_->ParFESpace()->GetTrueVSize()), 
-     bf(bf_), Pmllength(Pmllength_), omega(omega_), 
-     VQ(VQ_), nrlayers(nrlayers_)
-{
-   nx = nx_; ny = ny_; nz = nz_;
-   Init();
-}
-ParDST::ParDST(ParSesquilinearForm * bf_, Array2D<double> & Pmllength_, 
-         double omega_, MatrixCoefficient * MQ_,  int nrlayers_ , int nx_, int ny_, int nz_)
-   : Solver(2*bf_->ParFESpace()->GetTrueVSize(), 2*bf_->ParFESpace()->GetTrueVSize()), 
-     bf(bf_), Pmllength(Pmllength_), omega(omega_), 
-     MQ(MQ_), nrlayers(nrlayers_)
-{
-   nx = nx_; ny = ny_; nz = nz_;
-   Init();
-}
-
-void ParDST::Init()
-{
-   pfes = bf->ParFESpace();
-   fec = pfes->FEColl();
- 
-   comm = pfes->GetComm();
-   MPI_Comm_size(comm, &num_procs);
-   MPI_Comm_rank(comm, &myid);
-
-   //1. Indentify problem ... Helmholtz or Maxwell
-   prob_kind = fec->GetContType();
-   if (myid == 0)
-   {
-      cout << " 1. Indentify problem to be solved ... " << endl;
-      if (prob_kind == 0) cout << "    Helmholtz" << endl;
-      if (prob_kind == 1) cout << "    Maxwell" << endl; 
-   }
-
-   //2. Create the parallel mesh partition
-   pmesh = pfes->GetParMesh();
-   dim = pmesh->Dimension();
-   if (myid == 0)
-   {
-      cout << "\n 2. Generating ParMesh partitioning ... " << endl;
-   }
-   ovlpnrlayers = nrlayers+1;
-   part = new ParMeshPartition(pmesh,nx,ny,nz,ovlpnrlayers);
-   nxyz.SetSize(3);
-   nxyz[0] = nx = part->nxyz[0]; 
-   nxyz[1] = ny = part->nxyz[1];  
-   nxyz[2] = nz = part->nxyz[2];
-
-   nrsubdomains = part->nrsubdomains;
-   SubdomainRank = part->subdomain_rank;
-
-   for (int ip = 0; ip<nrsubdomains; ip++)
-   {
-      if (myid == SubdomainRank[ip])
-      {
-         RankSubdomains.Append(ip);
-      }
-   }
-
-   cout << " myid: " << myid 
-        << ", nrsubdomains: " << RankSubdomains.Size() << endl;
-
-   MPI_Barrier(comm);
-
-   if (myid == 0)
-   {
-      cout << "    Done ! " << endl;
-   }
-   //3. Setup info for sweeps
-   if (myid == 0)
-   {
-      cout << "\n 3. Computing sweeps info ..." << endl; 
-   }
-   sweeps = new Sweep(dim);
-   if (myid == 0)
-   {
-      cout << "    Done ! " << endl;
-   }
-   //4. Create LocalToGlobal maps 
-   //   (local GridFunctions/Vector to Global ParGridFunction/Vector) 
-   if (myid == 0)
-   {
-      cout << "\n 4. Computing true dofs maps ..." << endl; 
-   }
-
-   // if (myid == SubdomainRank[0])
-   // {
-   //    cout << "myid = " << myid << endl;
-   //    char vishost[] = "localhost";
-   //    int visport = 19916;
-   //    socketstream mesh_sock1(vishost, visport);
-   //    mesh_sock1.precision(8);
-   //    mesh_sock1 << "mesh\n"
-   //               << *part->subdomain_mesh[0] << "window_title 'Subdomain'" << flush;
-   //    part->subdomain_mesh[0]->Print();
-   
-   // }
-   bool comp = true;
-
-   dmaps = new DofMaps(pfes,part, comp);
-   
-   if (myid == 0)
-   {
-      cout << "    Done ! " << endl;
-   }
-   // 4. Setting up the local problems 
-   if (myid == 0)
-   {
-      cout << "\n 5. Setting up the subdomain problems ..." << endl; 
-   }
-
-   SetupSubdomainProblems();
-   
-   if (myid == 0)
-   {
-      cout << "    Done ! " << endl;
-   }
-   if (myid == 0)
-   {
-      cout << "\n 6. Mark subdomain overlap truedofs ..." << endl; 
-   }
-   MarkSubdomainOverlapDofs(comp);
-   if (myid == 0)
-   {
-      cout << "    Done ! " << endl;
-   }
-}
-
-void ParDST::Mult(const Vector &r, Vector &z) const
-{
-   // Initialize transfered residuals to 0.0;
-   for (int ip=0; ip<nrsubdomains; ip++)
-   {
-      if (myid != SubdomainRank[ip]) continue;
-      for (int i=0;i<sweeps->nsweeps; i++)
-      {
-         *f_transf[ip][i] = 0.0;
-      }
-   }
-
-   // restrict given residual to subdomains
-   dmaps->GlobalToSubdomains(r,f_orig);
-
-   for (int ip=0; ip<nrsubdomains; ip++)
-   {
-      if (myid != SubdomainRank[ip]) continue;
-      Array<int> ijk(3);
-      GetSubdomainijk(ip,nxyz,ijk);
-      Array2D<int> direct(dim,2); direct = 0;
-      for (int d=0;d<dim; d++)
-      {
-         if (ijk[d] > 0) direct[d][0] = 1; 
-         if (ijk[d] < part->nxyz[d]-1) direct[d][1] = 1; 
-      }
-      GetChiRes(*f_orig[ip],ip,direct);
-   }
-
-   z = 0.0; 
-   int nsteps;
-   switch(dim)
-   {
-      case 1: nsteps = nx; break;
-      case 2: nsteps = nx+ny-1; break;
-      default: nsteps = nx+ny+nz-2; break;
-   }
-   int nsweeps = sweeps->nsweeps;
-   // 1. Loop through sweeps
-   if (dim == 3 && nz == 1) { nsweeps = 4; } // x-y partition only;
-   for (int l=0; l<nsweeps; l++)
-   {  
-      // 2. loop through diagonals/steps of each sweep   
-      for (int s = 0; s<nsteps; s++)
-      {
-         Array2D<int> subdomains;
-         GetStepSubdomains(l,s,subdomains);
-         int nsubdomains = subdomains.NumRows();
-
-         // 3. Loop through the subdomains on the diagonal
-         Array<int> subdomain_ids;
-         for (int sb=0; sb < nsubdomains; sb++)
-         {
-            Array<int> ijk(dim); ijk = 0;
-            for (int d=0; d<dim; d++) ijk[d] = subdomains[sb][d]; 
-            int ip = GetSubdomainId(nxyz,ijk);
-            subdomain_ids.Append(ip);
-            if (myid != SubdomainRank[ip]) continue;
-
-            int n = dmaps->fes[ip]->GetTrueVSize();
-            Vector res_local(2*n); res_local = 0.0;
-
-            if (l==0)  { res_local += *f_orig[ip]; }
-            res_local += *f_transf[ip][l];
-            if (res_local.Norml2() < 1e-12) 
-            {
-               *subdomain_sol[ip] = 0.0;
-               continue;
-            }
-            PmlMatInv[ip]->Mult(res_local, *subdomain_sol[ip]);
-         }
-         // 4. Transfer solutions to neighbors so that the subdomain
-         // residuals are updated
-         TransferSources(l,subdomain_ids);
-      }
-      // 5. Update the global solution 
-      dmaps->SubdomainsToGlobal(subdomain_sol,z);
-   }
-}
-
-void ParDST::SetupSubdomainProblems()
-{
-   sqf.SetSize(nrsubdomains);
-   Optr.SetSize(nrsubdomains);
-   PmlMat.SetSize(nrsubdomains);
-   PmlMatInv.SetSize(nrsubdomains);
-   f_orig.SetSize(nrsubdomains);
-   f_transf.SetSize(nrsubdomains);
-   subdomain_sol.SetSize(nrsubdomains);
-   for (int ip=0; ip<nrsubdomains; ip++)
-   {
-      sqf[ip] = nullptr;
-      f_orig[ip] = nullptr;
-      subdomain_sol[ip] = nullptr;
-      PmlMat[ip] = nullptr;
-      PmlMatInv[ip] = nullptr;
-      Optr[ip] = nullptr;
-
-      if (myid != SubdomainRank[ip]) continue;
-      subdomain_sol[ip] = new Vector(2*dmaps->fes[ip]->GetTrueVSize());
-      if (prob_kind == 0)
-      {
-         SetHelmholtzPmlSystemMatrix(ip);
-      }
-      else if (prob_kind == 1)
-      {
-         SetMaxwellPmlSystemMatrix(ip);
-      }
-      PmlMat[ip] = Optr[ip]->As<ComplexSparseMatrix>();
-
-      PmlMatInv[ip] = new ComplexUMFPackSolver;
-      PmlMatInv[ip]->Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-      PmlMatInv[ip]->SetOperator(*PmlMat[ip]);
-
-      // HYPRE_Int rowstarts[2]; rowstarts[0] = 0;
-      // rowstarts[1] = dmaps->fes[ip]->GetTrueVSize();
-      // HypreParMatrix * HypreMat_r =
-      //    new HypreParMatrix(MPI_COMM_SELF,rowstarts[1],rowstarts,
-      //                       &(PmlMat[ip]->real()));
-      // HypreParMatrix * HypreMat_i =
-      //    new HypreParMatrix(MPI_COMM_SELF,rowstarts[1],rowstarts,
-      //                       &(PmlMat[ip]->imag()));
-      // ComplexHypreParMatrix * HypreMat =
-      //    new ComplexHypreParMatrix(HypreMat_r,HypreMat_i,true,true);
-      // PmlMatInv[ip] = new ComplexMUMPSSolver;
-      // PmlMatInv[ip]->SetOperator(*HypreMat);
-      // delete HypreMat;
-      int ndofs = dmaps->fes[ip]->GetTrueVSize();
-      f_transf[ip].SetSize(sweeps->nsweeps);
-      for (int i=0;i<sweeps->nsweeps; i++)
-      {
-         f_transf[ip][i] = new Vector(2*ndofs);
-      }
-   }
-}
-
-
-
-void ParDST::SetHelmholtzPmlSystemMatrix(int ip)
-{
-   MFEM_VERIFY(part->subdomain_mesh[ip], "Null mesh pointer");
-   Mesh * mesh = part->subdomain_mesh[ip];
-   double h = part->MeshSize;
-   Array2D<double> length(dim,2);
-   length = h*(nrlayers);
-
-   Array<int> ijk;
-   GetSubdomainijk(ip,nxyz,ijk);
-   int i = ijk[0];
-   int j = ijk[1];
-   int k = ijk[2];
-
-   if (i == 0 )    length[0][0] = Pmllength[0][0];
-   if (i == nx-1 ) length[0][1] = Pmllength[0][1];
-   if (dim  > 1)
-   {
-      if (j == 0 )    length[1][0] = Pmllength[1][0];
-      if (j == ny-1 ) length[1][1] = Pmllength[1][1];
-   }
-   if (dim  == 3)
-   {
-      if (k == 0 )    length[2][0] = Pmllength[2][0];
-      if (k == nz-1 ) length[2][1] = Pmllength[2][1];
-   }
-   
-   CartesianPML pml(mesh, length);
-   pml.SetOmega(omega);
-
-   Array <int> ess_tdof_list;
-   if (mesh->bdr_attributes.Size())
-   {
-      Array<int> ess_bdr(mesh->bdr_attributes.Max());
-      ess_bdr = 1;
-      dmaps->fes[ip]->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   ConstantCoefficient one(1.0);
-   ConstantCoefficient sigma(-pow(omega, 2));
-   PmlMatrixCoefficient c1_re(dim,pml_detJ_JT_J_inv_Re,&pml);
-   PmlMatrixCoefficient c1_im(dim,pml_detJ_JT_J_inv_Im,&pml);
-   PmlCoefficient detJ_re(pml_detJ_Re,&pml);
-   PmlCoefficient detJ_im(pml_detJ_Im,&pml);
-   ProductCoefficient c2_re0(sigma, detJ_re);
-   ProductCoefficient c2_im0(sigma, detJ_im);
-   ProductCoefficient c2_re(c2_re0, *Q);
-   ProductCoefficient c2_im(c2_im0, *Q);
-   sqf[ip] = new SesquilinearForm (dmaps->fes[ip],bf->GetConvention());
-
-   sqf[ip]->AddDomainIntegrator(new DiffusionIntegrator(c1_re),
-                         new DiffusionIntegrator(c1_im));
-   sqf[ip]->AddDomainIntegrator(new MassIntegrator(c2_re),
-                         new MassIntegrator(c2_im));
-   sqf[ip]->Assemble(0);
-
-   Optr[ip] = new OperatorPtr;
-   sqf[ip]->FormSystemMatrix(ess_tdof_list,*Optr[ip]);
-}
-
-void ParDST::SetMaxwellPmlSystemMatrix(int ip)
-{
-   MFEM_VERIFY(part->subdomain_mesh[ip], "Null mesh pointer");
-   Mesh * mesh = part->subdomain_mesh[ip];
-   double h = part->MeshSize;
-   Array2D<double> length(dim,2);
-   length = h*(nrlayers);
-
-   Array<int> ijk;
-   GetSubdomainijk(ip,nxyz,ijk);
-   int i = ijk[0];
-   int j = ijk[1];
-   int k = ijk[2];
-
-   if (i == 0 )    length[0][0] = Pmllength[0][0];
-   if (i == nx-1 ) length[0][1] = Pmllength[0][1];
-   if (dim  > 1)
-   {
-      if (j == 0 )    length[1][0] = Pmllength[1][0];
-      if (j == ny-1 ) length[1][1] = Pmllength[1][1];
-   }
-   if (dim  == 3)
-   {
-      if (k == 0 )    length[2][0] = Pmllength[2][0];
-      if (k == nz-1 ) length[2][1] = Pmllength[2][1];
-   }
-   
-   CartesianPML pml(mesh, length);
-   pml.SetOmega(omega);
-   Array <int> ess_tdof_list;
-   if (mesh->bdr_attributes.Size())
-   {
-      Array<int> ess_bdr(mesh->bdr_attributes.Max());
-      ess_bdr = 1;
-      dmaps->fes[ip]->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   ConstantCoefficient omeg(-pow(omega, 2));
-   int cdim = (dim == 2) ? 1 : dim;
-
-   PmlMatrixCoefficient pml_c1_Re(cdim,detJ_inv_JT_J_Re, &pml);
-   PmlMatrixCoefficient pml_c1_Im(cdim,detJ_inv_JT_J_Im, &pml);
-
-   PmlMatrixCoefficient pml_c2_Re(dim, detJ_JT_J_inv_Re,&pml);
-   PmlMatrixCoefficient pml_c2_Im(dim, detJ_JT_J_inv_Im,&pml);
-   ScalarMatrixProductCoefficient c2_Re0(omeg,pml_c2_Re);
-   ScalarMatrixProductCoefficient c2_Im0(omeg,pml_c2_Im);
-
-   MatrixCoefficient * c2_Re=nullptr;
-   MatrixCoefficient * c2_Im=nullptr;
-
-   if (Q)
-   {
-      c2_Re = new ScalarMatrixProductCoefficient(*Q,c2_Re0);
-      c2_Im = new ScalarMatrixProductCoefficient(*Q,c2_Im0);
-   }
-   else if (VQ)
-   {
-      MFEM_ABORT("Vector Coeffiecient not supported ");
-   }
-   else if (MQ)
-   {
-      c2_Re = new MatrixMatrixProductCoefficient(c2_Re0,*MQ);
-      c2_Im = new MatrixMatrixProductCoefficient(c2_Im0,*MQ);
-   }
-   
-   sqf[ip] = new SesquilinearForm(dmaps->fes[ip],bf->GetConvention());
-
-   sqf[ip]->AddDomainIntegrator(new CurlCurlIntegrator(pml_c1_Re),
-                         new CurlCurlIntegrator(pml_c1_Im));
-   sqf[ip]->AddDomainIntegrator(new VectorFEMassIntegrator(*c2_Re),
-                         new VectorFEMassIntegrator(*c2_Im));
-   sqf[ip]->Assemble(0);
-
-   Optr[ip] = new OperatorPtr;
-   sqf[ip]->FormSystemMatrix(ess_tdof_list,*Optr[ip]);
-   delete c2_Re;
-   delete c2_Im;
-}
-
-
-void ParDST::MarkSubdomainOverlapDofs(const bool comp)
-{
-   // First mark the elements
-         // cout<< "Compute Overlap Elements (in each possible direction) " << endl;
-      // Lists of elements
-      // x,y,z = +/- 1 ovlp 
-   NovlpElems.resize(nrsubdomains);
-
-   for (int ip = 0; ip<nrsubdomains; ip++)
-   {
-      if (myid != SubdomainRank[ip]) continue;
-      Array<int> ijk;
-      GetSubdomainijk(ip,nxyz,ijk);
-
-      Mesh * mesh = dmaps->fes[ip]->GetMesh();
-      NovlpElems[ip].resize(2*dim);
-
-      Vector pmin, pmax;
-      mesh->GetBoundingBox(pmin,pmax);
-      double h = part->MeshSize;
-      // Loop through elements
-      for (int iel=0; iel<mesh->GetNE(); iel++)
-      {
-         // Get element center
-         Vector center(dim);
-         int geom = mesh->GetElementBaseGeometry(iel);
-         ElementTransformation * tr = mesh->GetElementTransformation(iel);
-         tr->Transform(Geometries.GetCenter(geom),center);
-
-         // Assign elements to the appropriate lists
-         for (int d=0;d<dim; d++)
-         {
-            if (ijk[d]>0)
-            {
-               if (center[d] >= pmin[d]+h*ovlpnrlayers) 
-               {
-                  NovlpElems[ip][d].Append(iel);
-               }
-            }
-            else
-            {
-               NovlpElems[ip][d].Append(iel);
-            }
-               
-            if (ijk[d]<nxyz[d]-1)
-            {
-               if (center[d] <= pmax[d]-h*ovlpnrlayers) 
-               {
-                  NovlpElems[ip][dim+d].Append(iel);
-               }
-            }
-            else
-            {
-               NovlpElems[ip][dim+d].Append(iel);
-            }
-         }
-      }
-   }
-
-      // mark dofs
-   NovlpDofs.resize(nrsubdomains);
-   int mm = (comp) ? 2 : 1; // complex or real valued
-   for (int ip = 0; ip<nrsubdomains; ip++)
-   {
-      if (myid != SubdomainRank[ip]) continue;
-      FiniteElementSpace * fes = dmaps->fes[ip];
-      // Loop through the marked elements
-      NovlpDofs[ip].resize(2*dim);
-      int n = fes->GetTrueVSize();
-      Array<int> marker(n);
-      for (int d=0;d<2*dim; d++)
-      {
-         marker = 0;
-         int m = 0;
-         int melems = NovlpElems[ip][d].Size(); 
-         for (int iel=0; iel<melems; iel++)
-         {
-            Array<int> ElemDofs;
-            int el =  NovlpElems[ip][d][iel];
-            fes->GetElementDofs(el,ElemDofs);
-            int ndof = ElemDofs.Size();
-            for (int i = 0; i<ndof; ++i)
-            {
-               int eldof = ElemDofs[i];
-               int tdof = (eldof >= 0) ? eldof : abs(eldof) - 1; 
-               if (marker[tdof] == 1) continue;
-               marker[tdof] = 1;
-               m++;
-            }
-         }
-         int k = mm*(n-m);
-         NovlpDofs[ip][d].SetSize(k);
-         int l = 0;
-         for (int i = 0; i<n; i++)
-         {
-            if (marker[i]==0) 
-            {
-               NovlpDofs[ip][d][l] = i;  // real dofs
-               if (comp) 
-               {
-                  NovlpDofs[ip][d][l+k/2] = i+fes->GetTrueVSize();
-               }
-               l++;
-            }
-         }
-      }
-   }
-}
-
-void ParDST::GetChiRes(Vector & res, int ip, Array2D<int> direct) const
-{
-   for (int d=0; d<dim; d++)
-   {
-      // negative direction
-      if (direct[d][0]==1) res.SetSubVector(NovlpDofs[ip][d],0.0);
-      // possitive direction
-      if (direct[d][1]==1) res.SetSubVector(NovlpDofs[ip][d+dim],0.0);
-   }
-}
-
-
-
-void ParDST::PlotLocal(Vector & sol, socketstream & sol_sock, int ip) const
-{
-   FiniteElementSpace * fes = dmaps->fes[ip];
-   Mesh * mesh = fes->GetMesh();
-   GridFunction gf(fes);
-   double * data = sol.GetData();
-   gf.SetData(data);
-   
-   string keys;
-   keys = "keys mrRljc\n";
-   sol_sock << "solution\n" << *mesh << gf << keys << flush;
-}
-
-
-void ParDST::GetStepSubdomains(const int sweep, const int step, Array2D<int> & subdomains) const
-{
-   Array<int> aux;
-   switch(dim)
-   {
-      case 2: 
-      for (int i=nx-1;i>=0; i--)
-      {  
-         int j;
-         switch (sweep)
-         {
-            case 0:  j = step-i;         break;
-            case 1:  j = step-nx+i+1;    break;
-            case 2:  j = nx+i-step-1;    break;
-            default: j = nx+ny-i-step-2; break;
-         }
-         if (j<0 || j>=ny) continue;
-         aux.Append(i); aux.Append(j);
-      }
-      break; 
-      default:
-      for (int i=nx-1;i>=0; i--)
-      {  
-         for (int j=ny-1;j>=0; j--)
-         {
-            int k;
-            switch (sweep)
-            {
-               case 0:  k = step-i-j;            break;
-               case 1:  k = step-nx+i+1-j;       break;
-               case 2:  k = step-ny+j+1-i;       break;
-               case 3:  k = step-nx-ny+i+j+2;    break;
-               case 4:  k = i+j+nz-1-step;       break;
-               case 5:  k = nx+nz-i+j-step-2;    break;
-               case 6:  k = ny+nz+i-j-step-2;    break;
-               default: k = nx+ny+nz-i-j-step-3; break;
-            }
-            if (k<0 || k>=nz) continue;   
-            aux.Append(i); aux.Append(j); aux.Append(k); 
-         }
-      }
-      break;
-   }
-
-   int nrows = aux.Size()/dim;
-   int ncols = dim;
-
-   subdomains.SetSize(nrows,ncols);
-   for (int r=0;r<nrows; r++)
-   {
-      for (int c=0; c<ncols; c++)
-      {
-         int k = r*ncols + c;
-         subdomains[r][c] = aux[k];
-      }
-   }
-}
-
-
-void ParDST::TransferSources(int sweep, const Array<int> & subdomain_ids) const
-{
-   OvlpSol.resize(nrsubdomains);
-   int nrneighbors = pow(3,dim);
-   for (int ip = 0; ip<nrsubdomains; ip++)
-   {
-      if (myid == SubdomainRank[ip])
-      {
-         OvlpSol[ip].resize(nrneighbors);
-      }
-   }
-   int m = subdomain_ids.Size();
-   Array<Vector *> x(m);
-   for (int i = 0; i<m; i++)
-   {
-      x[i] = nullptr;
-      int ip = subdomain_ids[i];
-      if (myid != SubdomainRank[ip]) continue;
-      x[i] = new Vector(subdomain_sol[ip]->GetData(),subdomain_sol[ip]->Size());
-   }
-   dmaps->TransferToNeighbors(subdomain_ids,x,OvlpSol);
-   for (int i = 0; i<m; i++)
-   {
-      delete x[i]; x[i] = nullptr;
-   }
-   // Update residuals
-//   Find all neighbors of patch ip0
-   for (int is = 0; is<m; is++)
-   {
-      int ip0 = subdomain_ids[is];
-      Array<int> ijk;
-      Array<int> ijk1(3);
-      GetSubdomainijk(ip0,nxyz,ijk);
-      Array<int> directions(3);   
-      for (int i=-1; i<2; i++)
-      {
-         int i1 = ijk[0] + i;
-         if (i1 <0 || i1>=nx) continue;
-         directions[0] = i;
-         ijk1[0] = i1;
-         for (int j=-1; j<2; j++)
-         {
-            int j1 = ijk[1] + j;
-            if (j1 <0 || j1>=ny) continue;
-            directions[1] = j;
-            ijk1[1] = j1;
-            int kbeg = (dim == 2) ? 0 : -1;
-            int kend = (dim == 2) ? 1 :  2;
-            for (int k=kbeg; k<kend; k++)
-            {
-               int k1 = ijk[2] + k;
-               if (k1 <0 || k1>=nz) continue;
-               directions[2] = (dim == 3) ? k : -1 ;
-               if (i==0 && j==0 && k==0) continue;
-
-               int l = GetSweepToTransfer(sweep,directions);
-               if (l == -1) continue;
-               ijk1[2] = k1;
-               int ip1 = GetSubdomainId(nxyz,ijk1);
-
-               if (myid != SubdomainRank[ip1]) continue;
-               Array<int>directions1(3); directions1 = -1;
-               for (int i = 0; i<dim; i++) directions1[i] = -directions[i];
-               int dir = GetDirectionId(directions1);
-               int n = dmaps->fes[ip1]->GetTrueVSize();
-               Vector res(2*n);
-               PmlMat[ip1]->Mult(*OvlpSol[ip1][dir],res);
-
-               Array2D<int> direct(dim,2); direct = 0;
-               for (int d = 0; d<dim; d++)
-               {
-                  if (directions[d]==1)  direct[d][0] = 1;
-                  if (directions[d]==-1) direct[d][1] = 1;
-               }   
-               GetChiRes(res,ip1,direct);
-               *f_transf[ip1][l] -= res;
-            }
-         }  
-      }
-   }
-
-   for (int ip = 0; ip<nrsubdomains; ip++)
-   {
-      if (myid == SubdomainRank[ip])
-      {
-         for (int i = 0; i<nrneighbors; i++)
-         {
-            if (OvlpSol[ip][i])
-            {
-               delete OvlpSol[ip][i];
-            }
-         }
-         OvlpSol[ip].clear();
-      }
-   }
-}
-
-int ParDST::GetSweepToTransfer(const int s, Array<int> directions) const
-{
-   int l1=-1;
-   int nsweeps = sweeps->nsweeps;
-   Array<int> sweep0;   
-   sweeps->GetSweep(s,sweep0);
-   switch (dim)
-   {
-      case 2:
-      for (int l=s; l<nsweeps; l++)
-      {
-         // Rule 1: the transfer source direction has to be similar with 
-         // the sweep direction
-         Array<int> sweep1;   
-         sweeps->GetSweep(l,sweep1);
-         int ddot = 0;
-         for (int d=0; d<dim; d++) ddot+= sweep1[d] * directions[d];
-         if (ddot <= 0) continue;
-
-         // Rule 2: The horizontal or vertical transfer source cannot be used
-         // Case of horizontal or vertical transfer source 
-         // (it can't be both 0 cause it's skipped)
-         if (directions[0]==0 || directions[1] == 0) 
-         {
-            if (sweep0[0] == -sweep1[0] && sweep0[1] == -sweep1[1]) continue;
-         }
-         l1 = l;
-         break;
-      }
-      break;
-      default:
-      for (int l=s; l<nsweeps; l++)
-      {
-         // Rule 1: (similar directions) the transfer source direction has to be similar with 
-         // the sweep direction
-         Array<int> sweep1;   
-         sweeps->GetSweep(l,sweep1);
-         int ddot = 0;
-         bool similar = true;
-         for (int d=0; d<dim; d++) 
-         {
-            if (sweep1[d] * directions[d] < 0) similar = false;
-            ddot+= sweep1[d] * directions[d];
-         }
-         if (!similar || ddot<=0) continue; // not similar
-
-         // Rule 2: (oposite directions) the transfer source direction has to be similar with 
-         // the sweep direction
-         // 
-         // check any of the projections onto the planes
-         // (xy, xz, yz)
-
-         if ( (directions[0]==0 && directions[1] != 0) || 
-              (directions[0]!=0 && directions[1] == 0) ||
-              (directions[0]==0 && directions[2] != 0) || 
-              (directions[0]!=0 && directions[2] == 0) ||
-              (directions[2]==0 && directions[1] != 0) || 
-              (directions[2]!=0 && directions[1] == 0) ) 
-         {
-            if (sweep0[0] == -sweep1[0] && 
-                sweep0[1] == -sweep1[1] && 
-                sweep0[2] == -sweep1[2]) continue;
-         }
-         l1 = l;
-         break;
-      }
-      break;
-   }
-
-   return l1;   
-}
-
-void ParDST::CorrectOrientation(int ip,Vector &x) const
-{
-   FiniteElementSpace * fespace = dmaps->fes[ip];
-   Mesh * mesh = fespace->GetMesh();
-   int nrelems = mesh->GetNE();
-   // GridFunction test; 
-   // test.SetFromTrueDofs(x)
-   Array<int> signs(fespace->GetTrueVSize()); signs = 0;
-   for (int iel=0; iel<nrelems; iel++)
-   {
-      Array<int> ElemDofs;
-      fespace->GetElementDofs(iel,ElemDofs);
-      int ndofs = ElemDofs.Size();
-      ElemDofs.Print();
-      for (int i = 0; i< ndofs; i++)
-      {
-         int pdof_ = ElemDofs[i];
-         if (pdof_ < 0) 
-         {
-            signs[abs(pdof_)-1] += 1.0 ; 
-         }
-         else
-         {
-            signs[pdof_] -= 1.0 ; 
-         }
-      }
-   }
-
-   cout << "signs = " ; signs.Print();
-   for (int i = 0; i<fespace->GetTrueVSize(); i++)
-   {
-      if (signs[i]<0) 
-      {
-         x(i) *= -1.0;
-         x(i+fespace->GetTrueVSize()) *= -1.0;
-      }
-   }
-}
-
-
-ParDST::~ParDST()
-{
-
-   for (int ip=0; ip<nrsubdomains; ip++)
-   {
-      delete Optr[ip];
-      delete subdomain_sol[ip];
-      delete PmlMatInv[ip];
-      delete sqf[ip];
-      if (myid != SubdomainRank[ip]) continue;
-      for (int i=0;i<sweeps->nsweeps; i++)
-      {
-         delete f_transf[ip][i];
-      }
-      delete f_orig[ip];
-   }
-   f_orig.DeleteAll();
-   delete dmaps;
-   delete sweeps;
-   delete part;
-
-}

examples/maxwell-solver-dev/ParDST/ParDST.hpp

@@ -1,70 +0,0 @@
-#pragma once
-#include "../common/Utilities.hpp"
-#include "../common/PML.hpp"
-#include "DofMapsDST.hpp"
-using namespace std;
-using namespace mfem;
-
-
-class ParDST : public Solver//
-{
-private:
-   MPI_Comm comm = MPI_COMM_WORLD;
-   int num_procs, myid;
-   // Constructor inputs
-   int prob_kind;
-   ParSesquilinearForm *bf=nullptr;
-   ParFiniteElementSpace * pfes = nullptr;
-   ParMesh * pmesh = nullptr;
-   ParMeshPartition * part = nullptr;
-   Array<int> SubdomainRank;
-   Array<int> RankSubdomains;
-   const FiniteElementCollection * fec = nullptr;
-   Array2D<double> Pmllength;
-   int dim = 2;
-   double omega = 0.5;
-   Coefficient * Q=nullptr;
-   VectorCoefficient * VQ=nullptr;
-   MatrixCoefficient * MQ=nullptr;
-   int nrlayers;
-   int ovlpnrlayers;
-   int nrsubdomains = 0;
-   int nx,ny,nz;
-   Array<int> nxyz;
-   Sweep * sweeps = nullptr;
-   DofMaps * dmaps = nullptr;
-   Array< SesquilinearForm * > sqf;
-   Array< OperatorPtr * > Optr;
-   Array<ComplexSparseMatrix *> PmlMat;
-   Array<ComplexUMFPackSolver *> PmlMatInv;
-//    Array<ComplexMUMPSSolver *> PmlMatInv;
-   mutable Array<Vector *> f_orig;
-   mutable Array<Array<Vector * >> f_transf;
-   mutable Array<Vector * > subdomain_sol;
-   mutable std::vector<std::vector<Vector * >> OvlpSol;
-   void SetupSubdomainProblems();
-   std::vector<std::vector<Array<int>>> NovlpElems;
-   std::vector<std::vector<Array<int>>> NovlpDofs;
-   void MarkSubdomainOverlapDofs(const bool comp = false);
-   void SetHelmholtzPmlSystemMatrix(int ip);   
-   void SetMaxwellPmlSystemMatrix(int ip);
-   void GetChiRes(Vector & res, int ip, Array2D<int> direct) const;
-   void PlotLocal(Vector & sol, socketstream & sol_sock, int ip) const;
-   void GetStepSubdomains(const int sweep, const int step, Array2D<int> & subdomains) const;
-   void TransferSources(int sweep, const Array<int> & subdomain_ids) const;
-   int GetSweepToTransfer(const int s, Array<int> directions) const;
-   void CorrectOrientation(int ip, Vector & x) const;
-   void Init();
-public:
-   ParDST(ParSesquilinearForm * bf_, Array2D<double> & Pmllength_, 
-       double omega_, Coefficient * Q_, int nrlayers_, int nx_=2, int ny_=2, int nz_=2);
-   ParDST(ParSesquilinearForm * bf_, Array2D<double> & Pmllength_, 
-       double omega_, VectorCoefficient * VQ_, int nrlayers_, int nx_=2, int ny_=2, int nz_=2);
-   ParDST(ParSesquilinearForm * bf_, Array2D<double> & Pmllength_, 
-       double omega_, MatrixCoefficient * MQ_, int nrlayers_, int nx_=2, int ny_=2, int nz_=2);              
-   virtual void SetOperator(const Operator &op) {}
-   virtual void Mult(const Vector &r, Vector &z) const;
-   virtual ~ParDST();
-};
-
-

examples/maxwell-solver-dev/common/MeshPartition.hpp

@@ -1,151 +0,0 @@
-#pragma once
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-using namespace std;
-using namespace mfem;
-
-
-struct UniqueIndexGenerator
-{
-   int counter = 0;
-   std::unordered_map<int,int> idx;
-   int Get(int i)
-   {
-      std::unordered_map<int,int>::iterator f = idx.find(i);
-      if (f == idx.end())
-      {
-         idx[i] = counter;
-         return counter++;
-      }
-      else
-      {
-         return (*f).second;
-      }
-   }
-   void Reset()
-   {
-      counter = 0;
-      idx.clear();
-   }
-};
-
-
-double GetUniformMeshElementSize(Mesh * mesh);
-Mesh * ExtendMesh(Mesh * mesh, const Array<int> & directions);
-
-class CartesianMeshPartition 
-{
-private:
-   Mesh *mesh=nullptr;
-public:
-   int nrpatch;
-   int nxyz[3];
-   double MeshSize;
-   std::vector<Array<int>> element_map;
-   Array3D<int>subdomains;
-   // constructor
-   CartesianMeshPartition(Mesh * mesh_,int & nx, int & ny, int & nz);
-   ~CartesianMeshPartition() {};
-};
-
-class OverlappingCartesianMeshPartition 
-{
-private:
-   Mesh *mesh=nullptr;
-public:
-   int nrpatch;
-   double MeshSize;
-   int nxyz[3];
-   std::vector<Array<int>> element_map;
-   Array3D<int> subdomains;
-   // constructor
-   OverlappingCartesianMeshPartition(Mesh * mesh_,int & nx, int & ny, int & nz);
-   OverlappingCartesianMeshPartition(Mesh * mesh_,int & nx, int & ny, int & nz, int ovlp_nlayers);
-   ~OverlappingCartesianMeshPartition() {};
-};
-
-class STPOverlappingCartesianMeshPartition // Special layered partition for STP
-{
-private:
-   Mesh *mesh=nullptr;
-public:
-   int nrpatch;
-   int nx, ny, nz;
-   std::vector<Array<int>> element_map;
-   // constructor
-   STPOverlappingCartesianMeshPartition(Mesh * mesh_);
-   ~STPOverlappingCartesianMeshPartition() {};
-};
-
-class MeshPartition
-{
-private:
-   Mesh *mesh=nullptr;
-   void AddElementToMesh(Mesh * mesh,mfem::Element::Type elem_type,int * ind);
-   void GetNumVertices(int type, mfem::Element::Type & elem_type, int & nrvert);
-   void PrintElementMap();
-public:
-   int nrpatch;
-   double MeshSize;
-   std::vector<Array<int>> element_map;
-   Array3D<int> subdomains;
-   Array<Mesh *> patch_mesh;
-   int partition_kind;
-   int nxyz[3];
-   // constructor
-   MeshPartition(Mesh * mesh_, int part, int mx=1, int my=1, int mz=1, int ovl_nlayers=0);
-   ~MeshPartition();
-};
-
-void SaveMeshPartition(Array<Mesh * > meshes, 
-                       string mfilename="output/mesh.",
-                       string sfilename="output/sol.");
-
-
-#ifdef MFEM_USE_MPI
-
-class CartesianParMeshPartition 
-{
-private:
-   ParMesh *pmesh=nullptr;
-public:
-   int nrsubdomains;
-   int nxyz[3];
-   double MeshSize;
-   std::vector<Array<int>> local_element_map;
-   Array<int> subdomain_rank;
-   Array3D<int>subdomains;
-   // constructor
-   CartesianParMeshPartition(ParMesh * pmesh_,int & nx, int & ny, int & nz, 
-                             int ovlp_nlayers);
-   ~CartesianParMeshPartition() {};
-};
-
-class ParMeshPartition
-{
-private:
-   MPI_Comm comm;
-   ParMesh *pmesh=nullptr;
-   void AddElementToMesh(Mesh * mesh,mfem::Element::Type elem_type,int * ind);
-   void GetNumVertices(int type, mfem::Element::Type & elem_type, int & nrvert);
-   void PrintElementMap();
-public:
-   int nrsubdomains;
-   int OvlpNlayers;
-   int myelem_offset = 0;
-   double MeshSize;
-   std::vector<Array<int>> element_map;
-   std::vector<Array<int>> local_element_map;
-   Array3D<int> subdomains;
-   Array<Mesh *> subdomain_mesh;
-   Array<int> subdomain_rank;
-   int partition_kind;
-   int nxyz[3];
-   // constructor
-   ParMeshPartition(ParMesh * pmesh_, int mx=1, int my=1, int mz=1, int ovl_nlayers=0);
-   void SaveMeshPartition();
-   ~ParMeshPartition();
-};
-
-#endif

examples/maxwell-solver-dev/common/PML.cpp

@@ -1,570 +0,0 @@
-#include "PML.hpp"
-
-CartesianPML::CartesianPML(Mesh *mesh_, Array2D<double> length_)
-   : mesh(mesh_), length(length_)
-{
-   dim = mesh->Dimension();
-   SetBoundaries();
-}
-
-void CartesianPML::SetBoundaries()
-{
-   comp_dom_bdr.SetSize(dim, 2);
-   dom_bdr.SetSize(dim, 2);
-   // initialize
-   for (int i = 0; i < dim; i++)
-   {
-      dom_bdr(i, 0) = infinity();
-      dom_bdr(i, 1) = -infinity();
-   }
-
-   for (int i = 0; i < mesh->GetNBE(); i++)
-   {
-      Array<int> bdr_vertices;
-      mesh->GetBdrElementVertices(i, bdr_vertices);
-      for (int j = 0; j < bdr_vertices.Size(); j++)
-      {
-         for (int k = 0; k < dim; k++)
-         {
-            dom_bdr(k, 0) = min(dom_bdr(k, 0), mesh->GetVertex(bdr_vertices[j])[k]);
-            dom_bdr(k, 1) = max(dom_bdr(k, 1), mesh->GetVertex(bdr_vertices[j])[k]);
-         }
-      }
-   }
-
-#ifdef MFEM_USE_MPI
-   ParMesh * pmesh = dynamic_cast<ParMesh *>(mesh);
-   if (pmesh)
-   {
-      for (int d=0; d<dim; d++)
-      {
-         MPI_Allreduce(MPI_IN_PLACE,&dom_bdr(d,0),1,MPI_DOUBLE,MPI_MIN,pmesh->GetComm());
-         MPI_Allreduce(MPI_IN_PLACE,&dom_bdr(d,1),1,MPI_DOUBLE,MPI_MAX,pmesh->GetComm());
-      }
-   }
-#endif
-
-   for (int i = 0; i < dim; i++)
-   {
-      comp_dom_bdr(i, 0) = dom_bdr(i, 0) + length(i, 0);
-      comp_dom_bdr(i, 1) = dom_bdr(i, 1) - length(i, 1);
-   }
-}
-
-void CartesianPML::SetAttributes(Mesh *mesh_)
-{
-   int nrelem = mesh_->GetNE();
-   elems.SetSize(nrelem);
-
-   for (int i = 0; i < nrelem; ++i)
-   {
-      elems[i] = 1;
-      bool in_pml = false;
-      Element *el = mesh_->GetElement(i);
-      Array<int> vertices;
-      // Initialize Attribute
-      el->SetAttribute(1);
-      el->GetVertices(vertices);
-      int nrvert = vertices.Size();
-      // Check if any vertex is in the pml
-      for (int iv = 0; iv < nrvert; ++iv)
-      {
-         int vert_idx = vertices[iv];
-         double *coords = mesh_->GetVertex(vert_idx);
-         for (int comp = 0; comp < dim; ++comp)
-         {
-            if (coords[comp] > comp_dom_bdr(comp, 1) ||
-                coords[comp] < comp_dom_bdr(comp, 0))
-            {
-               in_pml = true;
-               break;
-            }
-         }
-      }
-      if (in_pml)
-      {
-         elems[i] = 0;
-         el->SetAttribute(2);
-      }
-   }
-   mesh_->SetAttributes();
-}
-
-void CartesianPML::StretchFunction(const Vector &x,
-                                   vector<complex<double>> &dxs, double omega)
-{
-   complex<double> zi = complex<double>(0., 1.);
-
-   double n = 2.0;
-   double c = 10.0;
-   // double c = log(omega);
-   double coeff;
-   // Stretch in each direction independently
-   for (int i = 0; i < dim; ++i)
-   {
-      dxs[i] = 1.0;
-      if (x(i) >= comp_dom_bdr(i, 1))
-      {
-         coeff = n * c / omega / pow(length(i, 1), n);
-         dxs[i] = 1.0 + zi * coeff * abs(pow(x(i) - comp_dom_bdr(i, 1), n - 1.0));
-      }
-      if (x(i) <= comp_dom_bdr(i, 0))
-      {
-         coeff = n * c / omega / pow(length(i, 0), n);
-         dxs[i] = 1.0 + zi * coeff * abs(pow(x(i) - comp_dom_bdr(i, 0), n - 1.0));
-      }
-   }
-}
-
-ToroidPML::ToroidPML(Mesh *mesh_)
-   : mesh(mesh_)
-{
-   dim = mesh->Dimension();
-   zlim.SetSize(2);
-   rlim.SetSize(2);
-   alim.SetSize(2);
-   zpml_thickness.SetSize(2);
-   rpml_thickness.SetSize(2);
-   apml_thickness.SetSize(2);
-   SetBoundaries();
-}
-
-void ToroidPML::SetBoundaries()
-{
-   mesh->EnsureNodes();
-   int nrnodes = mesh->GetNodalFESpace()->GetTrueVSize()/dim;
-   double zmin = infinity();
-   double zmax = -infinity();
-   double rmin = infinity();
-   double rmax = -infinity();
-   double amin = infinity(); // in degrees
-   double amax = -infinity(); // in degrees
-   for (int i = 0; i<nrnodes; i++)
-   {
-      Vector coord(dim);
-      mesh->GetNode(i,coord);
-      for (int d = 0; d<dim; d++)
-      {
-         if (abs(coord[d])<1e-13) coord[d] = 0.0;
-      }
-      // Find r and a for this point
-      double x = coord[0];
-      double y = coord[1];
-      double z = 0.0;
-      if (dim == 3) z = coord[2];
-      double a = GetAngle(x,y);
-      double r = sqrt(x*x + y*y);
-      
-      zmin = min(zmin,z);
-      zmax = max(zmax,z);
-      rmin = min(rmin,r);
-      rmax = max(rmax,r);
-      amin = min(amin,a);
-      amax = max(amax,a);
-   }
-
-   zlim[0] = zmin;
-   zlim[1] = zmax;
-   rlim[0] = rmin;
-   rlim[1] = rmax;
-   alim[0] = amin;
-   alim[1] = amax;
-
-
-#ifdef MFEM_USE_MPI
-   ParMesh * pmesh = dynamic_cast<ParMesh *>(mesh);
-   if (pmesh)
-   {
-      MPI_Allreduce(MPI_IN_PLACE,&zlim[0],1,MPI_DOUBLE,MPI_MIN,pmesh->GetComm());
-      MPI_Allreduce(MPI_IN_PLACE,&zlim[1],1,MPI_DOUBLE,MPI_MAX,pmesh->GetComm());
-      MPI_Allreduce(MPI_IN_PLACE,&rlim[0],1,MPI_DOUBLE,MPI_MIN,pmesh->GetComm());
-      MPI_Allreduce(MPI_IN_PLACE,&rlim[1],1,MPI_DOUBLE,MPI_MAX,pmesh->GetComm());
-      MPI_Allreduce(MPI_IN_PLACE,&alim[0],1,MPI_DOUBLE,MPI_MIN,pmesh->GetComm());
-      MPI_Allreduce(MPI_IN_PLACE,&alim[1],1,MPI_DOUBLE,MPI_MAX,pmesh->GetComm());
-   }
-#endif
-}
-
-void ToroidPML::SetAttributes(Mesh *mesh_)
-{
-   int nrelem = mesh_->GetNE();
-   elems.SetSize(nrelem);
-
-   // Loop through the elements and identify which of them are in the PML
-   for (int i = 0; i < nrelem; ++i)
-   {
-      // initialize with 1
-      elems[i] = 1;
-      Element *el = mesh_->GetElement(i);
-      // Initialize attribute
-      el->SetAttribute(1);
-
-      Array<int> vertices;
-      el->GetVertices(vertices);
-      int nrvert = vertices.Size();
-      // Check if any vertex is in the pml
-      bool in_pml = false;
-      for (int iv = 0; iv < nrvert; ++iv)
-      {
-         int vert_idx = vertices[iv];
-         double *coords = mesh_->GetVertex(vert_idx);
-         double x = coords[0];
-         double y = coords[1];
-         double a = GetAngle(x,y);
-         double r = sqrt(x*x + y*y);
-
-         if (astretch)
-         {
-            if ( (a <= alim[0]+apml_thickness[0]) ||
-                 (a >= alim[1]-apml_thickness[1]) )
-            {
-               in_pml = true;
-               break;  
-            }
-         }
-
-         if (rstretch)
-         {
-            if ( (r <= rlim[0]+rpml_thickness[0]) ||
-                 (r >= rlim[1]-rpml_thickness[1]) )
-            {
-               in_pml = true;
-               break;  
-            }
-         }
-      }
-      if (in_pml)
-      {
-         elems[i] = 0;
-         el->SetAttribute(2);
-      }
-
-      // Vector center;
-      // mesh_->GetElementCenter(i,center);
-      // double x = center[0];
-      // double y = center[1];
-      // double a = GetAngle(x,y);
-      // double r = sqrt(x*x + y*y);
-      // // check upper and lower bound
-      // if (astretch)
-      // {
-      //    if ( (a <= alim[0]+apml_thickness[0]) ||
-      //      (a >= alim[1]-apml_thickness[1]) )
-      //    {
-      //       elems[i] = 0;
-      //       el->SetAttribute(2);
-      //    }
-      // }
-      // if (rstretch)
-      // {
-      //    if ( (r <= rlim[0]+rpml_thickness[0]) ||
-      //         (r >= rlim[1]-rpml_thickness[1]) )
-      //    {
-      //       elems[i] = 0;
-      //       el->SetAttribute(2);
-      //    }
-      // }
-   }
-   mesh_->SetAttributes();
-}
-
-
-double ToroidPML::GetAngle(const double x, const double y)
-{
-   // Find r and a for this point
-   double arad;
-   if (x == 0.0)
-   {
-      arad = (y > 0.0)? M_PI/2.0 : 3.0 * M_PI/2.0;
-   }
-   else
-   {
-      arad = atan(y/x);
-      int k = 0;
-      if (x<0)
-      {
-         k = 1;
-      }
-      else if (y<0)
-      {
-         k = 2;
-      }
-      arad += k*M_PI;
-   }
-   return arad * 180.0/M_PI;
-}
-
-// void ToroidPML::StretchFunction(const Vector &X,
-//                                    vector<complex<double>> &dxs, double omega)
-void ToroidPML::StretchFunction(const Vector &X, ComplexDenseMatrix & J, double omega)
-
-{
-   complex<double> zi = complex<double>(0., 1.);
-
-   double n = 2.0;
-   double c = 10.0;
-   // double c = log(omega);
-   // Stretch in the azimuthal direction
-   double x = X[0];
-   double y = X[1];
-   if (abs(x) < 1e-12) x = 0.0;
-   if (abs(y) < 1e-12) y = 0.0;
-   double a = GetAngle(x,y);
-   double r = sqrt(x*x + y*y);
-   // dxs[0] = 1.0;
-   // dxs[1] = 1.0;
-   J = 0.0;
-   J(0,0) = 1.0;
-   J(1,1) = 1.0;
-   if (dim == 3) J(2,2) = 1.0;
-
-   if (astretch)
-   {
-      double th = a * M_PI/180.0;
-      double thl, thL, thH;
-      bool in_pml = false;
-      // negative direction 
-      if (a <= alim[0]+apml_thickness[0])
-      {
-         in_pml = true;
-         thL = alim[1] * M_PI/180.0;
-         thH = apml_thickness[1] * M_PI/180.0;
-         thl = thL + thH;
-      }
-      // positive direction 
-      if (a >= alim[1]-apml_thickness[1])
-      {
-         in_pml = true;
-         thL = alim[1] * M_PI/180.0;
-         thH = apml_thickness[1] * M_PI/180.0;
-         thl = thL - thH;
-      }
-      // double c1 = min(20.0*M_PI/180.0,thH);
-      if (in_pml)
-      {
-         double c1 = thH;
-         double coeff = n * c / omega / pow(c1,n);
-         double f_th = pow(th - thl,n-1);
-         double th_x = - y / (r * r);
-         double th_y =   x / (r * r);
-
-         J(0,0) = 1.0 + zi * coeff * abs(f_th * th_x);
-         J(0,1) = zi * f_th * th_y;
-         J(1,0) = zi * f_th * th_x;
-         J(1,1) = 1.0 + zi * coeff * abs(f_th * th_y);
-      }
-   }
-   // Stretch in the radial direction
-   if (rstretch)
-   {  // negative
-      double rl, rL, rH;
-      bool in_pml = false;
-      if (r <= rlim[0]+rpml_thickness[0])
-      {
-         in_pml = true;
-         rL = rlim[0];     
-         rH = rpml_thickness[0];
-         rl = rL + rH;
-      }
-      // positive direction 
-      if (r >= rlim[1]-rpml_thickness[1])
-      {
-         in_pml = true;
-         rL = rlim[1];     
-         rH = rpml_thickness[1];
-         rl = rL - rH;
-      }
-
-      if (in_pml)
-      {
-         double coeff = n * c / omega / pow (rH,n);
-         double f_r =  pow(r-rl,n-1.0);
-         double r_x = x / r;
-         double r_y = y / r;
-
-         J(0,0) = 1.0 + zi * coeff * abs(f_r*r_x);
-         J(0,1) = zi * f_r * r_y;
-         J(1,0) = zi * f_r * r_x;
-         J(1,1) = 1.0 + zi * coeff * abs(f_r*r_y);
-      }
-   }
-}
-
-double pml_detJ_Re(const Vector & x, CartesianPML * pml)
-{
-   int dim = pml->dim;
-   double omega = pml->omega;
-   std::vector<std::complex<double>> dxs(dim);
-   complex<double> det(1.0,0.0);
-   pml->StretchFunction(x, dxs, omega);
-   for (int i=0; i<dim; ++i) det *= dxs[i];
-   return det.real();
-}
-
-double pml_detJ_Im(const Vector & x, CartesianPML * pml)
-{
-   int dim = pml->dim;
-   double omega = pml->omega;
-   std::vector<std::complex<double>> dxs(dim);
-   complex<double> det(1.0,0.0);
-   pml->StretchFunction(x, dxs, omega);
-   for (int i=0; i<dim; ++i) det *= dxs[i];
-   return det.imag();
-}
-
-void pml_detJ_JT_J_inv_Re(const Vector & x, CartesianPML * pml , DenseMatrix & M)
-{
-   int dim = pml->dim;
-   double omega = pml->omega;
-   std::vector<std::complex<double>> dxs(dim);
-   complex<double> det(1.0,0.0);
-   pml->StretchFunction(x, dxs, omega);
-
-   for (int i = 0; i<dim; ++i)
-   {
-      det *= dxs[i];
-   }
-
-   M=0.0;
-   for (int i = 0; i<dim; ++i)
-   {
-      M(i,i) = (det / pow(dxs[i],2)).real();
-   }
-}
-
-void pml_detJ_JT_J_inv_Im(const Vector & x, CartesianPML * pml , DenseMatrix & M)
-{
-   int dim = pml->dim;
-   double omega = pml->omega;
-
-   std::vector<std::complex<double>> dxs(dim);
-   complex<double> det = 1.0;
-   pml->StretchFunction(x, dxs, omega);
-
-   for (int i = 0; i<dim; ++i)
-   {
-      det *= dxs[i];
-   }
-
-   M=0.0;
-   for (int i = 0; i<dim; ++i)
-   {
-      M(i,i) = (det / pow(dxs[i],2)).imag();
-   }
-}
-
-
-void detJ_JT_J_inv_Re(const Vector &x, CartesianPML * pml, DenseMatrix &M)
-{
-   int dim = pml->dim;
-   double omega = pml->omega;
-   vector<complex<double>> dxs(dim);
-   complex<double> det(1.0, 0.0);
-   pml->StretchFunction(x, dxs, omega);
-
-   for (int i = 0; i < dim; ++i)
-   {
-      det *= dxs[i];
-   }
-
-   M = 0.0;
-   for (int i = 0; i < dim; ++i)
-   {
-      M(i, i) = (det / pow(dxs[i], 2)).real();
-   }
-}
-
-void detJ_JT_J_inv_Im(const Vector &x, CartesianPML * pml, DenseMatrix &M)
-{
-   int dim = pml->dim;
-   double omega = pml->omega;
-   vector<complex<double>> dxs(dim);
-   complex<double> det = 1.0;
-   pml->StretchFunction(x, dxs, omega);
-
-   for (int i = 0; i < dim; ++i)
-   {
-      det *= dxs[i];
-   }
-
-   M = 0.0;
-   for (int i = 0; i < dim; ++i)
-   {
-      M(i, i) = (det / pow(dxs[i], 2)).imag();
-   }
-}
-
-void detJ_JT_J_inv_abs(const Vector &x, CartesianPML * pml, DenseMatrix &M)
-{
-   int dim = pml->dim;
-   double omega = pml->omega;
-   vector<complex<double>> dxs(dim);
-   complex<double> det = 1.0;
-   pml->StretchFunction(x, dxs, omega);
-
-   for (int i = 0; i < dim; ++i)
-   {
-      det *= dxs[i];
-   }
-
-   M = 0.0;
-   for (int i = 0; i < dim; ++i)
-   {
-      M(i, i) = abs(det / pow(dxs[i], 2));
-   }
-}
-
-void detJ_inv_JT_J_Re(const Vector &x, CartesianPML * pml, DenseMatrix &M)
-{
-   int dim = pml->dim;
-   double omega = pml->omega;
-   vector<complex<double>> dxs(dim);
-   complex<double> det(1.0, 0.0);
-   pml->StretchFunction(x, dxs, omega);
-
-   for (int i = 0; i < dim; ++i)
-   {
-      det *= dxs[i];
-   }
-
-   // in the 2D case the coefficient is scalar 1/det(J)
-   if (dim == 2)
-   {
-      M = (1.0 / det).real();
-   }
-   else
-   {
-      M = 0.0;
-      for (int i = 0; i < dim; ++i)
-      {
-         M(i, i) = (pow(dxs[i], 2) / det).real();
-      }
-   }
-}
-
-void detJ_inv_JT_J_Im(const Vector &x, CartesianPML * pml, DenseMatrix &M)
-{
-   int dim = pml->dim;
-   double omega = pml->omega;
-   vector<complex<double>> dxs(dim);
-   complex<double> det = 1.0;
-   pml->StretchFunction(x, dxs, omega);
-
-   for (int i = 0; i < dim; ++i)
-   {
-      det *= dxs[i];
-   }
-
-   if (dim == 2)
-   {
-      M = (1.0 / det).imag();
-   }
-   else
-   {
-      M = 0.0;
-      for (int i = 0; i < dim; ++i)
-      {
-         M(i, i) = (pow(dxs[i], 2) / det).imag();
-      }
-   }
-}

examples/maxwell-solver-dev/common/PML.hpp

@@ -1,179 +0,0 @@
-#pragma once
-#include "mfem.hpp"
-#include "complex_linalg.hpp"
-#include <fstream>
-#include <iostream>
-using namespace std;
-using namespace mfem;
-
-
-// Class for setting up a simple Cartesian PML region
-class CartesianPML
-{
-private:
-   Mesh *mesh;
-
-   // Length of the PML Region in each direction
-   Array2D<double> length;
-
-   // Computational Domain Boundary
-   Array2D<double> comp_dom_bdr;
-
-   // Domain Boundary
-   Array2D<double> dom_bdr;
-
-   // Integer Array identifying elements in the pml
-   // 0: in the pml, 1: not in the pml
-   Array<int> elems;
-
-   // Compute Domain and Computational Domain Boundaries
-   void SetBoundaries();
-
-public:
-   // Constructor
-   CartesianPML(Mesh *mesh_,Array2D<double> length_);
-
-   int dim;
-   double omega;
-   // Return Computational Domain Boundary
-   Array2D<double> GetCompDomainBdr() {return comp_dom_bdr;}
-
-   // Return Domain Boundary
-   Array2D<double> GetDomainBdr() {return dom_bdr;}
-
-   // Return Marker list for elements
-   Array<int> * GetMarkedPMLElements() {return &elems;}
-
-   // Mark element in the PML region
-   void SetAttributes(Mesh *mesh_);
-
-   void SetOmega(double omega_) {omega = omega_;}
-
-   // PML complex stretching function
-   void StretchFunction(const Vector &x, vector<complex<double>> &dxs, double omega);
-};
-
-class ToroidPML
-{
-private:
-   Mesh *mesh;
-
-   Vector zlim, zpml_thickness; // range in axial direction
-   Vector rlim, rpml_thickness; // range in radial direction
-   Vector alim, apml_thickness; // range in azimuthal direction
-
-   // Integer Array identifying elements in the pml
-   // 0: in the pml, 1: not in the pml
-   Array<int> elems;
-
-   double GetAngle(const double x, const double y);
-
-   // Compute Domain and Computational Domain Boundaries
-   void SetBoundaries();
-
-   bool zstretch = false;
-   bool rstretch = false;
-   bool astretch = false;
-
-public:
-   // Constructor
-   ToroidPML(Mesh *mesh_);
-
-   int dim;
-   double omega;
-   // Return Computational Domain Boundary
-
-   // Return Domain Boundary
-   void GetDomainBdrs(Vector & zlim_, Vector & rlim_, Vector & alim_)
-   {
-      zlim_.SetSize(2); zlim_ = zlim;
-      rlim_.SetSize(2); rlim_ = rlim;
-      alim_.SetSize(2); alim_ = alim;
-   }
-
-   void SetPmlWidth(const Vector & zpml, const Vector & rpml, const Vector & apml)
-   {
-      MFEM_VERIFY(zpml.Size() == 2 , "Check zpml size");
-      MFEM_VERIFY(rpml.Size() == 2 , "Check rpml size");
-      MFEM_VERIFY(apml.Size() == 2 , "Check apml size");
-      zpml_thickness = zpml;
-      rpml_thickness = rpml;
-      apml_thickness = apml;
-   }
-
-   void SetPmlAxes(const bool zstretch_, 
-                   const bool rstretch_, 
-                   const bool astretch_ )
-   {
-      zstretch = zstretch_;
-      rstretch = rstretch_;
-      astretch = astretch_;
-   }
-
-   // // Return Marker list for elements
-   Array<int> * GetMarkedPMLElements() {return &elems;}
-
-   // Mark element in the PML region
-   void SetAttributes(Mesh *mesh_);
-
-   void SetOmega(double omega_) {omega = omega_;}
-
-   // PML complex stretching function
-   // void StretchFunction(const Vector &X, vector<complex<double>> &dxs, double omega);
-   void StretchFunction(const Vector &X, ComplexDenseMatrix & J, double omega);
-};
-
-class PmlCoefficient : public Coefficient
-{
-private:
-   CartesianPML * pml = nullptr;
-   double (*Function)(const Vector &, CartesianPML * );
-public:
-   PmlCoefficient(double (*F)(const Vector &, CartesianPML *), CartesianPML * pml_)
-      : pml(pml_), Function(F)
-   {}
-   virtual double Eval(ElementTransformation &T, const IntegrationPoint &ip)
-   {
-      double x[3];
-      Vector transip(x, 3);
-      T.Transform(ip, transip);
-      return ((*Function)(transip, pml));
-   }
-};
-
-
-// This includes scalar coefficients
-class PmlMatrixCoefficient : public MatrixCoefficient
-{
-private:
-   CartesianPML * pml = nullptr;
-   void (*Function)(const Vector &, CartesianPML * , DenseMatrix &);
-public:
-   PmlMatrixCoefficient(int dim, void(*F)(const Vector &, CartesianPML *,
-                                          DenseMatrix &),
-                        CartesianPML * pml_)
-      : MatrixCoefficient(dim), pml(pml_), Function(F)
-   {}
-   virtual void Eval(DenseMatrix &K, ElementTransformation &T,
-                     const IntegrationPoint &ip)
-   {
-      double x[3];
-      Vector transip(x, 3);
-      T.Transform(ip, transip);
-      K.SetSize(height, width);
-      (*Function)(transip, pml, K);
-   }
-};
-
-// Helmholtz pml Functions
-double pml_detJ_Re(const Vector & x, CartesianPML * pml);
-double pml_detJ_Im(const Vector & x, CartesianPML * pml);
-void pml_detJ_JT_J_inv_Re(const Vector & x, CartesianPML * pml , DenseMatrix & M);
-void pml_detJ_JT_J_inv_Im(const Vector & x, CartesianPML * pml , DenseMatrix & M);
-
-// Maxwell Pml functions
-void detJ_JT_J_inv_Re(const Vector &x, CartesianPML * pml, DenseMatrix &M);
-void detJ_JT_J_inv_Im(const Vector &x, CartesianPML * pml, DenseMatrix &M);
-void detJ_JT_J_inv_abs(const Vector &x, CartesianPML * pml, DenseMatrix &M);
-void detJ_inv_JT_J_Re(const Vector &x, CartesianPML * pml, DenseMatrix &M);
-void detJ_inv_JT_J_Im(const Vector &x, CartesianPML * pml, DenseMatrix &M);

examples/maxwell-solver-dev/common/Utilities.cpp

@@ -1,619 +0,0 @@
-#include "Utilities.hpp"
-
-Sweep::Sweep(int dim_) : dim(dim_)
-{
-   nsweeps = pow(2,dim);
-   sweeps.resize(nsweeps);
-
-   for (int is = 0; is<nsweeps; is++)
-   {
-      sweeps[is].SetSize(dim);
-   }
-
-   switch(dim)
-   {
-      case 1: 
-         sweeps[0][0] =  1; 
-         sweeps[1][0] = -1; 
-         break;
-      case 2: 
-         sweeps[0][0] =  1; sweeps[0][1] =  1; 
-         sweeps[1][0] = -1; sweeps[1][1] =  1; 
-         sweeps[2][0] =  1; sweeps[2][1] = -1; 
-         sweeps[3][0] = -1; sweeps[3][1] = -1;
-         break;
-      default:
-         sweeps[0][0] =  1; sweeps[0][1] =  1; sweeps[0][2] =  1; 
-         sweeps[1][0] = -1; sweeps[1][1] =  1; sweeps[1][2] =  1; 
-         sweeps[2][0] =  1; sweeps[2][1] = -1; sweeps[2][2] =  1; 
-         sweeps[3][0] = -1; sweeps[3][1] = -1; sweeps[3][2] =  1;
-         sweeps[4][0] =  1; sweeps[4][1] =  1; sweeps[4][2] = -1; 
-         sweeps[5][0] = -1; sweeps[5][1] =  1; sweeps[5][2] = -1; 
-         sweeps[6][0] =  1; sweeps[6][1] = -1; sweeps[6][2] = -1; 
-         sweeps[7][0] = -1; sweeps[7][1] = -1; sweeps[7][2] = -1;
-         break;
-   }
-}
-
-Sweep::~Sweep()
-{
-   for (int i = 0; i<nsweeps; i++)
-   {
-      sweeps[i].DeleteAll();
-   }
-}
-
-
-double CutOffFncn(const Vector &x, const Vector & pmin, const Vector & pmax, const Array2D<double> & h_)
-{
-   int dim = pmin.Size();
-   Vector h0(dim);
-   Vector h1(dim);
-   for (int i=0; i<dim; i++)
-   {
-      h0(i) = h_[i][0];
-      h1(i) = h_[i][1];
-   }
-   Vector x0(dim);
-   Vector x1(dim);
-   x0 = pmin; x0+=h0;
-   x1 = pmax; x1-=h1;
-
-   double f = 1.0;
-   for (int i = 0; i<dim; i++)
-   {
-      double val = 1.0;
-      if( x(i) >= pmax(i) || x(i) <= pmin(i))
-      {
-         val = 0.0;
-      }  
-      else if (x(i) < pmax(i) && x(i) >= x1(i))
-      {
-         if(h1(i) != 0.0)
-            // val = (x(i)-pmax(i))/(x1(i)-pmax(i)); 
-            val = pow((x(i)-pmax(i))/(x1(i)-pmax(i)),1.0); 
-      }
-      else if (x(i) > pmin(i) && x(i) <= x0(i))
-      {
-         if (h0(i) != 0.0)
-            // val = (x(i)-pmin(i))/(x0(i)-pmin(i)); 
-            val = pow((x(i)-pmin(i))/(x0(i)-pmin(i)),1.0); 
-      }
-
-      if (h0(i) == 0 && x(i) <= x1(i))
-      {
-         val = 1.0;
-      }
-      if (h1(i) == 0 && x(i) >= x0(i))
-      {
-         val = 1.0;
-      }
-      f *= val;
-   }
-   return f;
-}
-
-double ChiFncn(const Vector &x, const Vector & pmin, const Vector & pmax, const Array2D<double> & h_)
-{
-   int dim = pmin.Size();
-   Vector h0(dim);
-   Vector h1(dim);
-   for (int i=0; i<dim; i++)
-   {
-      h0(i) = h_[i][0];
-      h1(i) = h_[i][1];
-   }
-   Vector x0(dim);
-   Vector x1(dim);
-   x0 = pmin; x0+=h0;
-   x1 = pmax; x1-=h1;
-
-   double f = 1.0;
-   for (int i = 0; i<dim; i++)
-   {
-      double val = 1.0;
-      if( x(i) >= pmax(i) || x(i) <= pmin(i))
-      {
-         val = 0.0;
-      }  
-      else if (x(i) < pmax(i) && x(i) >= x1(i))
-      {
-         if(h1(i) != 0.0)
-            val = (x(i)-pmax(i))/(x1(i)-pmax(i)); 
-            // This function has to be changed to smth more reasonable
-            // val = pow((x(i)-pmax(i))/(x1(i)-pmax(i)),100.0); 
-      }
-      else if (x(i) > pmin(i) && x(i) <= x0(i))
-      {
-         if (h0(i) != 0.0)
-            val = (x(i)-pmin(i))/(x0(i)-pmin(i)); 
-            // val = pow((x(i)-pmin(i))/(x0(i)-pmin(i)),100.0); 
-      }
-
-      if (h0(i) == 0 && x(i) <= x1(i))
-      {
-         val = 1.0;
-      }
-      if (h1(i) == 0 && x(i) >= x0(i))
-      {
-         val = 1.0;
-      }
-      f *= val;
-   }
-   return f;
-}
-
-
-DofMap::DofMap(FiniteElementSpace * fes , MeshPartition * partition) 
-{
-   const FiniteElementCollection * fec = fes->FEColl();
-   nrpatch = partition->nrpatch;
-
-   fespaces.SetSize(nrpatch);
-
-   Dof2GlobalDof.resize(nrpatch);
-
-   for (int ip=0; ip<nrpatch; ++ip)
-   {
-      // create finite element spaces for each patch 
-      fespaces[ip] = new FiniteElementSpace(partition->patch_mesh[ip],fec);
-
-      // construct the patch tdof to global tdof map
-      int nrdof = fespaces[ip]->GetTrueVSize();
-      Dof2GlobalDof[ip].SetSize(2*nrdof);
-
-      // loop through the elements in the patch
-      for (int iel = 0; iel<partition->element_map[ip].Size(); ++iel)
-      {
-         // index in the global mesh
-         int iel_idx = partition->element_map[ip][iel];
-         // get the dofs of this element
-         Array<int> ElemDofs;
-         Array<int> GlobalElemDofs;
-         fespaces[ip]->GetElementDofs(iel,ElemDofs);
-         fes->GetElementDofs(iel_idx,GlobalElemDofs);
-         // the sizes have to match
-         MFEM_VERIFY(ElemDofs.Size() == GlobalElemDofs.Size(),
-                     "Size inconsistency");
-         // loop through the dofs and take into account the signs;
-         int ndof = ElemDofs.Size();
-         for (int i = 0; i<ndof; ++i)
-         {
-            int pdof_ = ElemDofs[i];
-            int gdof_ = GlobalElemDofs[i];
-            int pdof = (pdof_ >= 0) ? pdof_ : abs(pdof_) - 1;
-            int gdof = (gdof_ >= 0) ? gdof_ : abs(gdof_) - 1;
-            Dof2GlobalDof[ip][pdof] = gdof;
-            Dof2GlobalDof[ip][pdof+nrdof] = gdof+fes->GetTrueVSize();
-         }
-      }
-   }
-}
-
-DofMap::DofMap(FiniteElementSpace * fes , MeshPartition * partition, int nrlayers) 
-{
-
-   nx = partition->nxyz[0];
-   ny = partition->nxyz[1];
-   nz = partition->nxyz[2];
-
-   int partition_kind = partition->partition_kind;
-   // Mesh * mesh = fespace->GetMesh();
-   const FiniteElementCollection * fec = fes->FEColl();
-   nrpatch = partition->nrpatch;
-
-   fespaces.SetSize(nrpatch);
-   PmlMeshes.SetSize(nrpatch);
-   // Extend patch meshes to include pml
-
-   for  (int ip = 0; ip<nrpatch; ip++)
-   {
-      int k = ip/(nx*ny);
-      int j = (ip-k*nx*ny)/nx;
-      int i = (ip-k*nx*ny)%nx;
-      
-      Array<int> directions;
-      if (i > 0)
-      {
-         for (int i=0; i<nrlayers; i++)
-         {
-            directions.Append(-1);
-         }
-      }
-      if (j > 0)
-      {
-         for (int i=0; i<nrlayers; i++)
-         {
-            directions.Append(-2);
-         }
-      }
-      if (k > 0)
-      {
-         for (int i=0; i<nrlayers; i++)
-         {
-            directions.Append(-3);
-         }
-      }
-      if (i < nx-1)
-      {
-         for (int i=0; i<nrlayers; i++)
-         {
-            if (partition_kind == 3 || partition_kind == 2) directions.Append(1);
-         }
-      }
-      if (j < ny-1)
-      {
-         for (int i=0; i<nrlayers; i++)
-         {
-            if (partition_kind == 3 || partition_kind == 2) directions.Append(2);
-         }
-      }
-      if (k < nz-1)
-      {
-         for (int i=0; i<nrlayers; i++)
-         {
-            if (partition_kind == 3 || partition_kind == 2) directions.Append(1);
-         }
-      }
-      PmlMeshes[ip] = ExtendMesh(partition->patch_mesh[ip],directions);
-   }
-
-   // Save PML_meshes
-   string meshpath;
-   string solpath;
-   if (partition_kind == 3 || partition_kind == 2) 
-   {
-      meshpath = "output/mesh_ovlp_pml.";
-      solpath = "output/sol_ovlp_pml.";
-   }
-   else if (partition_kind == 4)
-   {
-      meshpath = "output/mesh_novlp_pml.";
-      solpath = "output/sol_novlp_pml.";
-   }
-   else
-   {
-      MFEM_ABORT("This partition kind not supported yet");
-   }
-   
-   // SaveMeshPartition(PmlMeshes, meshpath, solpath);
-
-   PmlFespaces.SetSize(nrpatch);
-   Dof2GlobalDof.resize(nrpatch);
-   Dof2PmlDof.resize(nrpatch);
-
-   for (int ip=0; ip<nrpatch; ++ip)
-   {
-      // create finite element spaces for each patch 
-      fespaces[ip] = new FiniteElementSpace(partition->patch_mesh[ip],fec);
-      PmlFespaces[ip] = new FiniteElementSpace(PmlMeshes[ip],fec);
-
-      // construct the patch tdof to global tdof map
-      int nrdof = fespaces[ip]->GetTrueVSize();
-      Dof2GlobalDof[ip].SetSize(2*nrdof);
-      Dof2PmlDof[ip].SetSize(2*nrdof);
-
-      // build dof maps between patch and extended patch
-      // loop through the patch elements and constract the dof map
-      // The same elements in the extended mesh have the same ordering (but not the dofs)
-
-      // loop through the elements in the patch
-      for (int iel = 0; iel<partition->element_map[ip].Size(); ++iel)
-      {
-         // index in the global mesh
-         int iel_idx = partition->element_map[ip][iel];
-         // get the dofs of this element
-         Array<int> ElemDofs;
-         Array<int> PmlElemDofs;
-         Array<int> GlobalElemDofs;
-         fespaces[ip]->GetElementDofs(iel,ElemDofs);
-         PmlFespaces[ip]->GetElementDofs(iel,PmlElemDofs);
-         fes->GetElementDofs(iel_idx,GlobalElemDofs);
-         // the sizes have to match
-         MFEM_VERIFY(ElemDofs.Size() == GlobalElemDofs.Size(),
-                     "Size inconsistency");
-         MFEM_VERIFY(ElemDofs.Size() == PmlElemDofs.Size(),
-                     "Size inconsistency");            
-         // loop through the dofs and take into account the signs;
-         int ndof = ElemDofs.Size();
-         for (int i = 0; i<ndof; ++i)
-         {
-            int pdof_ = ElemDofs[i];
-            int gdof_ = GlobalElemDofs[i];
-            int pmldof_ = PmlElemDofs[i];
-            int pdof = (pdof_ >= 0) ? pdof_ : abs(pdof_) - 1;
-            int gdof = (gdof_ >= 0) ? gdof_ : abs(gdof_) - 1;
-            int pmldof = (pmldof_ >= 0) ? pmldof_ : abs(pmldof_) - 1;
-
-            Dof2GlobalDof[ip][pdof] = gdof;
-            Dof2GlobalDof[ip][pdof+nrdof] = gdof+fes->GetTrueVSize();
-            Dof2PmlDof[ip][pdof] = pmldof;
-            Dof2PmlDof[ip][pdof+nrdof] = pmldof+PmlFespaces[ip]->GetTrueVSize();
-         }
-      }
-   }
-}
-
-
-LocalDofMap::LocalDofMap(const FiniteElementCollection * fec_, MeshPartition * part1_, 
-               MeshPartition * part2_):fec(fec_), part1(part1_), part2(part2_)
-{
-   // Each overlapping patch has 2 non-overlapping subdomains
-   // Thre are n non-overlapping and and n-1 overlapping subdomains
-   int nrpatch = part2->nrpatch;
-   MFEM_VERIFY(part1->nrpatch-1 == part2->nrpatch, "Check number of subdomains");
-
-   cout << "Constructing local dof maps" << endl; 
-   map1.resize(nrpatch);
-   map2.resize(nrpatch);
-   for (int ip=0; ip<nrpatch; ip++)
-   {
-      // Get the 3 meshes involved
-      Mesh * mesh = part2->patch_mesh[ip];
-      Mesh * mesh1 = part1->patch_mesh[ip];
-      Mesh * mesh2 = part1->patch_mesh[ip+1];
-
-      // Define the fespaces
-      FiniteElementSpace fespace(mesh, fec);
-      FiniteElementSpace fespace1(mesh1, fec);
-      FiniteElementSpace fespace2(mesh2, fec);
-
-      int ndof1 = fespace1.GetTrueVSize();
-      int ndof2 = fespace2.GetTrueVSize();
-
-      map1[ip].SetSize(2*ndof1); // times 2 because it's complex
-      map2[ip].SetSize(2*ndof2); // times 2 because it's complex
-
-      // loop through the elements in the patches
-      // map 1 is constructed by the first half of elements
-      // map 2 is constructed by the second half of elements
-
-      for (int iel = 0; iel<part1->element_map[ip].Size(); ++iel)
-      {
-         // index in the overlapping mesh
-         int iel_idx = iel;
-         Array<int> ElemDofs;
-         Array<int> GlobalElemDofs;
-         fespace1.GetElementDofs(iel,ElemDofs);
-         fespace.GetElementDofs(iel_idx,GlobalElemDofs);
-         // the sizes have to match
-         MFEM_VERIFY(ElemDofs.Size() == GlobalElemDofs.Size(),
-                     "Size inconsistency");
-         // loop through the dofs and take into account the signs;
-         int ndof = ElemDofs.Size();
-         for (int i = 0; i<ndof; ++i)
-         {
-            int pdof_ = ElemDofs[i];
-            int gdof_ = GlobalElemDofs[i];
-            int pdof = (pdof_ >= 0) ? pdof_ : abs(pdof_) - 1;
-            int gdof = (gdof_ >= 0) ? gdof_ : abs(gdof_) - 1;
-            map1[ip][pdof] = gdof;
-            map1[ip][pdof+ndof1] = gdof+fespace.GetTrueVSize();
-         }
-      }
-      for (int iel = 0; iel<part1->element_map[ip+1].Size(); ++iel)
-      {
-         // index in the overlapping mesh
-         int k = part1->element_map[ip].Size();
-         int iel_idx = iel+k;
-         Array<int> ElemDofs;
-         Array<int> GlobalElemDofs;
-         fespace2.GetElementDofs(iel,ElemDofs);
-         fespace.GetElementDofs(iel_idx,GlobalElemDofs);
-         // the sizes have to match
-         MFEM_VERIFY(ElemDofs.Size() == GlobalElemDofs.Size(),
-                     "Size inconsistency");
-         // loop through the dofs and take into account the signs;
-         int ndof = ElemDofs.Size();
-         for (int i = 0; i<ndof; ++i)
-         {
-            int pdof_ = ElemDofs[i];
-            int gdof_ = GlobalElemDofs[i];
-            int pdof = (pdof_ >= 0) ? pdof_ : abs(pdof_) - 1;
-            int gdof = (gdof_ >= 0) ? gdof_ : abs(gdof_) - 1;
-            map2[ip][pdof] = gdof;
-            map2[ip][pdof+ndof2] = gdof+fespace.GetTrueVSize();
-         }
-      }
-   }
-};
-
-
-NeighborDofMaps::NeighborDofMaps(MeshPartition * part_, FiniteElementSpace * fes_,
-                                DofMap * dmap_, 
-                                int ovlp_layers_) : part(part_), fes(fes_), 
-                                dmap(dmap_),
-                                ovlp_layers(ovlp_layers_)
-{
-
-   nrsubdomains = part->nrpatch;
-   nxyz.SetSize(3);
-   mesh = fes->GetMesh();
-   dim = mesh->Dimension();
-   for (int d=0; d<3; d++)  nxyz[d] = part->nxyz[d];
-   MarkOvlpElements();
-   ComputeNeighborDofMaps();
-}
-
-void NeighborDofMaps::MarkOvlpElements()
-{
-   // Lists of elements
-   // x,y,z = +/- 1 ovlp 
-   OvlpElems.resize(nrsubdomains);
-
-   for (int ip = 0; ip<nrsubdomains; ip++)
-   {
-      int i0,j0,k0;
-      Getijk(ip,i0,j0,k0);
-      int ijk[dim]; ijk[0] = i0; ijk[1]=j0;
-      if (dim==3) ijk[2] = k0;
-
-      FiniteElementSpace * sub_fes = dmap->fespaces[ip];
-      Mesh * sub_mesh = sub_fes->GetMesh();
-      // OvlpElems[ip].resize(2*dim);
-      OvlpElems[ip].resize(pow(3,dim)); 
-
-      Vector pmin, pmax;
-      sub_mesh->GetBoundingBox(pmin,pmax);
-      double h = part->MeshSize;
-      // Loop through elements
-      for (int iel=0; iel<sub_mesh->GetNE(); iel++)
-      {
-         // Get element center
-         Vector center(dim);
-         int geom = sub_mesh->GetElementBaseGeometry(iel);
-         ElementTransformation * tr = sub_mesh->GetElementTransformation(iel);
-         tr->Transform(Geometries.GetCenter(geom),center);
-
-         // loop through dimensions   
-         Array<bool> pos(dim); pos = 0;
-         Array<bool> neg(dim); neg = 0;
-
-         for (int d=0;d<dim; d++)
-         {
-            if (ijk[d]>0 && center[d] < pmin[d]+2.0*h*ovlp_layers)
-            {
-               neg[d] = true;
-            }
-
-            if (ijk[d]<nxyz[d]-1 && center[d] > pmax[d]-2.0*h*ovlp_layers) 
-            {
-               pos[d] = true;
-            }
-         }
-         SetElementToOverlap(ip,iel,neg,pos);        
-      }   
-   }
-}
-
-void NeighborDofMaps::ComputeNeighborDofMaps()
-{
-   OvlpDofMaps.resize(nrsubdomains);
-
-   // Array<UniqueIndexGen * > Gen(nrsubdomains);
-   // // construct unique number generator for the elements of a patch
-   // for (int ip = 0; ip<nrsubdomains; ip++)
-   // {
-   //    Gen[ip] = new UniqueIndexGen;
-   //    // register the elements
-   //    int nel = part->element_map[ip].Size();
-   //    for (int iel=0; iel<nel; iel++)
-   //    {
-   //       int iel_idx = part->element_map[ip][iel];
-   //       Gen[ip]->Set(iel_idx);
-   //    }
-   // }
-
-   // construct dof maps
-   int nrneighbors = pow(3,dim); // including its self
-
-   for (int ip0 = 0; ip0<nrsubdomains; ip0++)
-   {
-      OvlpDofMaps[ip0].resize(nrneighbors);
-
-      FiniteElementSpace * fes0 = dmap->fespaces[ip0];
-      int tdofs0 = fes0->GetTrueVSize();
-      Array<int> marker0(tdofs0); marker0 = 0;
-      int i0, j0, k0;
-      Array<int> ijk(dim);
-      Getijk(ip0, i0,j0,k0);
-
-      int kbeg = (dim == 2) ? 0 : -1;
-      int kend = (dim == 2) ? 1 :  2;
-      for (int k=kbeg; k<kend; k++)
-      {
-         int k1 = k0 + k;
-         if (k1 <0 || k1>=nxyz[2]) continue;
-         int kk = (dim == 2) ? -1 : k;
-         for (int j=-1; j<2; j++)
-         {
-            int j1 = j0 + j;
-            if (j1 <0 || j1>=nxyz[1]) continue;
-            for (int i=-1; i<2; i++)
-            {
-               int i1 = i0 + i;
-               if (i1 <0 || i1>=nxyz[0]) continue;
-     
-               Array<int> ip0list;  marker0 = 0;
-               int directionId = GetDirectionId(i,j,kk);
-
-               Array<int> Elems = OvlpElems[ip0][directionId];
-               int nel = Elems.Size();
-
-               for (int iel = 0; iel<nel; ++iel)
-               {
-                  int iel0 = Elems[iel];   
-                  Array<int> ElemDofs0;
-
-                  fes0->GetElementDofs(iel0,ElemDofs0);
-                  int ndof = ElemDofs0.Size();
-                  // since the elements are added to the subdomain meshes 
-                  // in the same ordered fashion (as they come from the
-                  // original mesh) then the ordering of elements in each 
-                  // subdomain is the same. Hence the dof ovlp lists
-                  // can be computed for each subdomain independendly
-                  for (int l = 0; l<ndof; ++l)
-                  {
-                     int dof0_ = ElemDofs0[l];
-                     int dof0 = (dof0_ >= 0) ? dof0_ : abs(dof0_) - 1;
-                     if (!marker0[dof0])
-                     {
-                        ip0list.Append(dof0); // dofs of ip0 in ovlp
-                        marker0[dof0] = 1;
-                     }
-                  }
-               }
-               
-               OvlpDofMaps[ip0][directionId].Append(ip0list);
-               int tsize = fes0->GetTrueVSize();
-               // Imaginary part
-               for (int l=0;l<ip0list.Size(); l++) { ip0list[l] += tsize; }
-               OvlpDofMaps[ip0][directionId].Append(ip0list);
-            }
-         }
-      }
-   }
-}
-
-
-void NeighborDofMaps::GetNeighborDofMap(const int ip,
-                                        const Array<int> & directions, 
-                                        Array<int> & dofmap)
-{
-   int k = (dim == 2) ? -1 : directions[2];
-   int directionid = GetDirectionId(directions[0],directions[1],k);
-   dofmap = OvlpDofMaps[ip][directionid];
-}
-
-
-void NeighborDofMaps::SetElementToOverlap(int ip, int iel,
-                        const Array<bool> & neg, 
-                        const Array<bool> & pos)
-{
-   int kbeg = (dim == 2) ? 0 : -1;
-   int kend = (dim == 2) ? 0 :  1;
-   for (int k = kbeg; k<=kend; k++)
-   {
-      if (dim == 3)
-      {
-         if (k == -1 && !neg[2]) continue;   
-         if (k ==  1 && !pos[2]) continue;   
-      }   
-      for (int j = -1; j<=1; j++)
-      {
-         if (j== -1 && !neg[1]) continue;   
-         if (j==  1 && !pos[1]) continue;   
-         for (int i = -1; i<=1; i++)
-         {
-            // cases to skip 
-            if (i==-1 && !neg[0]) continue;   
-            if (i== 1 && !pos[0]) continue;   
-
-            if (i==0 && j==0 && k == 0) continue;
-            int kk  = (dim==2)?-1 : k;  
-            int DirId = GetDirectionId(i,j,kk);
-            OvlpElems[ip][DirId].Append(iel);
-         }
-      }
-   }
-}

examples/maxwell-solver-dev/common/Utilities.hpp

@@ -1,179 +0,0 @@
-#pragma once
-#include "MeshPartition.hpp"
-#include "complex_linalg.hpp"
-
-struct UniqueIndexGen
-{
-   int counter = 0;
-   std::unordered_map<int,int> idx;
-
-   void Set(int i)
-   {
-      std::unordered_map<int,int>::iterator f = idx.find(i);
-      if (f == idx.end())
-      {
-         idx[i] = counter;
-         counter++;
-      }
-   }
-
-   int Get(int i)
-   {
-      std::unordered_map<int,int>::iterator f = idx.find(i);
-      if (f == idx.end())
-      {
-         return -1;
-      }
-      else
-      {
-         return (*f).second;
-      }
-   }
-   void Reset()
-   {
-      counter = 0;
-      idx.clear();
-   }
-};
-
-
-struct Sweep
-{
-private:
-   int dim;
-   std::vector<Array<int>> sweeps;
-public:   
-   int nsweeps;
-   Sweep(int dim_);
-   ~Sweep();
-   void GetSweep(const int i, Array<int> & sweep)
-   {
-      MFEM_VERIFY(i<nsweeps, "Sweep number out of bounds");
-      sweep.SetSize(dim);
-      sweep = sweeps[i];
-   }
-
-
-};
-
-
-
-// Function coefficient that takes the bounding box of the mesh as an input
-class CutOffFnCoefficient : public Coefficient
-{
-private:
-   double (*Function)(const Vector &, const Vector &, const Vector &, const Array2D<double> &);
-   Vector pmin, pmax;
-   Array2D<double> h; // specify the with of the cutoff function (h in each direction)
-   
-
-public:
-   CutOffFnCoefficient(double (*F)(const Vector &, const Vector &, const Vector &, const Array2D<double> &), 
-                             const Vector & pmin_, const Vector & pmax_, Array2D<double> & h_)
-      : Function(F), pmin(pmin_), pmax(pmax_), h(h_)
-   {}
-   virtual double Eval(ElementTransformation &T, const IntegrationPoint &ip)
-   {
-      double x[3];
-      Vector transip(x, 3);
-      T.Transform(ip, transip);
-      return ((*Function)(transip, pmin, pmax, h));
-   }
-};
-
-double CutOffFncn(const Vector &x, const Vector & pmin, 
-const Vector & pmax, const Array2D<double> & h_);
-double ChiFncn(const Vector &x, const Vector & pmin, 
-const Vector & pmax, const Array2D<double> & h_);
-
-class DofMap // Constructs dof maps for a given partition
-{
-public:
-   int nrpatch, nx, ny, nz;
-   vector<Array<int>> Dof2GlobalDof;
-   vector<Array<int>> Dof2PmlDof;
-   Array<Mesh *> PmlMeshes;
-   Array<FiniteElementSpace *> fespaces;
-   Array<FiniteElementSpace *> PmlFespaces;
-   // constructor
-   // Non PML constructor dof map
-   DofMap(FiniteElementSpace * fes, MeshPartition * partition);
-   // PML
-   DofMap(FiniteElementSpace * fes , MeshPartition * partition, int nrlayers);
-   ~DofMap(){};
-};
-
-
-
-class LocalDofMap // Constructs dof mapbetween two partitions
-{
-   const FiniteElementCollection *fec=nullptr;
-   MeshPartition * part1=nullptr;
-   MeshPartition * part2=nullptr;
-public:
-   int nrpatch, nx, ny, nz;
-   vector<Array<int>> map1;
-   vector<Array<int>> map2;
-   // constructor
-   LocalDofMap(const FiniteElementCollection * fec_, MeshPartition * part1_, 
-               MeshPartition * part2_);
-   ~LocalDofMap();
-};
-
-
-struct NeighborDofMaps
-{
-private:
-   int dim;
-   MeshPartition * part = nullptr;
-   FiniteElementSpace * fes = nullptr;
-   Mesh * mesh = nullptr;
-   std::vector<std::vector<Array<int>>> OvlpElems;
-   std::vector<std::vector<Array<int>>> OvlpDofMaps;
-
-   DofMap * dmap = nullptr;
-   int nrsubdomains = 0;
-   int ovlp_layers = 0;
-   Array<int> nxyz;
-   void SetElementToOverlap(int ip, int iel, 
-                           const Array<bool> & neg, 
-                           const Array<bool> & pos);
-
-   void MarkOvlpElements();
-   void ComputeNeighborDofMaps();
-
-   void Getijk(int ip, int & i, int & j, int & k) const
-   {
-      k = ip/(nxyz[0]*nxyz[1]);
-      j = (ip-k*nxyz[0]*nxyz[1])/nxyz[0];
-      i = (ip-k*nxyz[0]*nxyz[1])%nxyz[0];
-   }
-
-   int GetPatchId(const Array<int> & ijk) const
-   {
-      int d=ijk.Size();
-      int z = (d==2)? 0 : ijk[2];
-      return part->subdomains(ijk[0],ijk[1],z);
-   }
-      int GetDirectionId(int i, int j, int k=-1) 
-   {
-      int n = 3;
-      return (k+1)*n*n + (j+1)*n + i+1; 
-   }
-   void GetDirections(const int id, int & i, int & j, int & k) 
-   {
-      int n = 3;
-      k = id/(n*n) - 1;
-      j = (id-(k+1)*n*n)/n - 1;
-      i = (id-(k+1)*n*n)%n - 1;
-   }
-
-public:   
-   NeighborDofMaps(MeshPartition * part_, 
-                   FiniteElementSpace * fes_, 
-                   DofMap * dmap_,
-                   int ovlp_layers_);
-
-   void GetNeighborDofMap(const int ip, const Array<int> & directions,
-                          Array<int> & dofmap);
-};

examples/maxwell-solver-dev/common/complex_linalg.cpp

@@ -1,358 +0,0 @@
-
-#include "../../../linalg/kernels.hpp"
-#include "complex_linalg.hpp"
-
-
-ComplexDenseMatrix::ComplexDenseMatrix(){}
-
-ComplexDenseMatrix::ComplexDenseMatrix(int s) 
-{
-   MFEM_ASSERT(s >= 0, "invalid ComplexDenseMatrix size: " << s);
-   height = s;
-   width  = s;
-   if (s > 0)
-   {
-      data = new complex<double>[s*s];
-      *this = 0.0; // init with zeroes
-   }
-}
-
-
-ComplexDenseMatrix::ComplexDenseMatrix(int m, int n) 
-{
-   MFEM_VERIFY(m >= 0 && n >= 0,
-               "invalid DenseMatrix size: " << m << " x " << n);
-   const int s = m*n;
-   height = m;
-   width  = n;
-   if (s > 0)
-   {
-      data = new complex<double>[s];
-      *this = 0.0; // init with zeroes
-   }
-}
-
-void ComplexDenseMatrix::SetSize(int h, int w)
-{
-   MFEM_VERIFY(h >= 0 && w >= 0,
-               "invalid ComplexDenseMatrix size: " << h << " x " << w);
-   if (Height() == h && Width() == w)
-   {
-      return;
-   }
-   height = h;
-   width = w;
-   const int hw = h*w;
-   delete data;
-   data = new complex<double>[hw];
-   *this = 0.0; // init with zeroes
-}
-
-ComplexDenseMatrix &ComplexDenseMatrix::operator=(double c)
-{
-   const int s = Height()*Width();
-   for (int i = 0; i < s; i++)
-   {
-      data[i] = c;
-   }
-   return *this;
-}
-
-ComplexDenseMatrix &ComplexDenseMatrix::operator=(complex<double> c)
-{
-   const int s = Height()*Width();
-   for (int i = 0; i < s; i++)
-   {
-      data[i] = c;
-   }
-   return *this;
-}
-
-
-std::complex<double> ComplexDenseMatrix::Det() const
-{
-   MFEM_ASSERT(Height() == Width() && Height() > 0,
-               "The matrix must be square and "
-               << "sized larger than zero to compute the determinant."
-               << "  Height() = " << Height()
-               << ", Width() = " << Width());
-
-   switch (Height())
-   {
-      case 1:
-         return data[0];
-
-      case 2:
-         return data[0] * data[3] - data[1] * data[2];
-
-      case 3:
-      {
-         const complex<double> *d = data;
-         return
-            d[0] * (d[4] * d[8] - d[5] * d[7]) +
-            d[3] * (d[2] * d[7] - d[1] * d[8]) +
-            d[6] * (d[1] * d[5] - d[2] * d[4]);
-      }
-      default:
-      {
-         MFEM_ABORT("dim>3 not supported yet");         
-         return 0;
-      }
-   }
-}
-
-DenseMatrix * ComplexDenseMatrix::real() const
-{
-   DenseMatrix * Ar = new DenseMatrix(height,width);
-   double * data = Ar->Data();
-   complex<double> * zdata = this->data;
-   for (int s = 0; s<height*width; s++)
-   {
-         data[s] = zdata[s].real();
-   }
-   return Ar;
-}
-DenseMatrix * ComplexDenseMatrix::imag() const
-{
-   DenseMatrix * Ai = new DenseMatrix(height,width);
-   double * data = Ai->Data();
-   complex<double> * zdata = this->data;
-   for (int s = 0; s<height*width; s++)
-   {
-         data[s] = zdata[s].imag();
-   }
-   return Ai;
-}
-
-void ComplexDenseMatrix::GetReal(DenseMatrix & Ar) 
-{
-   MFEM_ASSERT(Ar.Height() == height && Ar.Width() == width, "Incompatible dimensions");
-   double * data = Ar.Data();
-   complex<double> * zdata = this->data;
-   for (int s = 0; s<height*width; s++)
-   {
-         data[s] = zdata[s].real();
-   }
-}
-
-void ComplexDenseMatrix::GetImag(DenseMatrix & Ai) 
-{
-   double * data = Ai.Data();
-   complex<double> * zdata = this->data;
-   for (int s = 0; s<height*width; s++)
-   {
-         data[s] = zdata[s].imag();
-   }
-}
-
-ComplexDenseMatrix &ComplexDenseMatrix::operator=(const ComplexDenseMatrix &m)
-{
-   SetSize(m.height, m.width);
-
-   const int hw = height * width;
-   for (int i = 0; i < hw; i++)
-   {
-      data[i] = m.data[i];
-   }
-   return *this;
-}
-
-ComplexDenseMatrix &ComplexDenseMatrix::operator+=(const complex<double> *m)
-{
-   const int hw = Height()*Width();
-   for (int i = 0; i < hw; i++)
-   {
-      data[i] += m[i];
-   }
-   return *this;
-}
-
-ComplexDenseMatrix &ComplexDenseMatrix::operator+=(const ComplexDenseMatrix &m)
-{
-   MFEM_ASSERT(Height() == m.Height() && Width() == m.Width(),
-               "incompatible matrix sizes.");
-   return *this += m.GetData();
-}
-
-ComplexDenseMatrix &ComplexDenseMatrix::operator-=(const ComplexDenseMatrix &m)
-{
-   int s = Height()*Width();
-   complex<double> * mdata = m.GetData();
-   for (int i = 0; i < s; i++)
-   {
-      data[i] -= mdata[s];
-   }
-   return *this;
-}
-
-ComplexDenseMatrix &ComplexDenseMatrix::operator*=(complex<double> c)
-{
-   int s = Height()*Width();
-   for (int i = 0; i < s; i++)
-   {
-      data[i] *= c;
-   }
-   return *this;
-}
-
-
-void ComplexDenseMatrix::Print(std::ostream &out, int width_) const
-{
-   // save current output flags
-   ios::fmtflags old_flags = out.flags();
-   // output flags = scientific + show sign
-   out << setiosflags(ios::scientific | ios::showpos);
-   for (int i = 0; i < height; i++)
-   {
-      out << "[row " << i << "]\n";
-      for (int j = 0; j < width; j++)
-      {
-         out << (*this)(i,j);
-         if (j+1 == width || (j+1) % width_ == 0)
-         {
-            out << '\n';
-         }
-         else
-         {
-            out << ' ';
-         }
-      }
-   }
-   // reset output flags to original values
-   out.flags(old_flags);
-}
-
-void ComplexDenseMatrix::PrintMatlab(std::ostream &out) const
-{
-   // save current output flags
-   // ios::fmtflags old_flags = out.flags();
-   // output flags = scientific + show sign
-   // out << setiosflags(ios::scientific | ios::showpos);
-   for (int i = 0; i < height; i++)
-   {
-      for (int j = 0; j < width; j++)
-      {
-         out << (*this)(i,j);
-         out << ' ';
-      }
-      out << "\n";
-   }
-   // reset output flags to original values
-   // out.flags(old_flags);
-}
-
-ComplexDenseMatrixInverse::ComplexDenseMatrixInverse(const ComplexDenseMatrix & A) : ComplexDenseMatrix(A.Height())
-{
-   MFEM_VERIFY(A.Height() == A.Width(), "The matrix is not square");
-   MFEM_VERIFY(A.Height() < 4, "dim > 3 is not supported yet");
-
-   std::complex<double> detA = A.Det();
-   MFEM_VERIFY(abs(A.Det())>1e-14, "The given matrix is singular");
-
-   std::complex<double> * d = this->Data();
-   std::complex<double> *dA = A.GetData();
-   switch (A.Height())
-   {
-   case 1:
-      d[0] = 1.0/dA[0];
-      break;
-   case 2:
-      d[0] =  1.0/detA * dA[3];
-      d[1] = -1.0/detA * dA[1];
-      d[2] = -1.0/detA * dA[2];
-      d[3] =  1.0/detA * dA[0];
-      break;   
-   case 3:
-      d[0] =   1.0/detA*(dA[4]*dA[8] - dA[5]*dA[7]);
-      d[1] =  -1.0/detA*(dA[1]*dA[8] - dA[2]*dA[7]);
-      d[2] =   1.0/detA*(dA[1]*dA[5] - dA[2]*dA[4]);
-      d[3] =  -1.0/detA*(dA[3]*dA[8] - dA[5]*dA[6]);
-      d[4] =   1.0/detA*(dA[0]*dA[8] - dA[2]*dA[6]);
-      d[5] =  -1.0/detA*(dA[0]*dA[5] - dA[2]*dA[3]);
-      d[6] =   1.0/detA*(dA[3]*dA[7] - dA[4]*dA[6]);
-      d[7] =  -1.0/detA*(dA[0]*dA[7] - dA[1]*dA[6]);
-      d[8] =   1.0/detA*(dA[0]*dA[4] - dA[1]*dA[3]);
-      break;      
-   default:
-      // Should be unreachable 
-      break;
-   }
-}
-
-
-
-/// Matrix matrix multiplication.  A = B * C.
-void Mult(const ComplexDenseMatrix &b, const ComplexDenseMatrix &c, ComplexDenseMatrix &a)
-{
-   MFEM_ASSERT(a.Height() == b.Height() && a.Width() == c.Width() &&
-               b.Width() == c.Height(), "incompatible dimensions");
-
-   const int ah = a.Height();
-   const int aw = a.Width();
-   const int bw = b.Width();
-   complex<double> *ad = a.Data();
-   const complex<double> *bd = b.Data();
-   const complex<double> *cd = c.Data();
-   kernels::Mult(ah,aw,bw,bd,cd,ad);               
-}
-
-/// Multiply the transpose of a matrix A with a matrix B:   At*B
-void MultAtB(const ComplexDenseMatrix &A, const ComplexDenseMatrix &B, ComplexDenseMatrix &AtB)
-{
-   MFEM_ASSERT(A.Width() == AtB.Height() && B.Width() == AtB.Width() &&
-               A.Height() == B.Height(), "incompatible dimensions");
-   const int ah = A.Height();
-   const int aw = A.Width();
-   const int bw = B.Width();
-   const complex<double> *ad = A.Data();
-   const complex<double> *bd = B.Data();
-   complex<double> *cd = AtB.Data();
-
-   for (int j = 0; j < bw; j++)
-   {
-      const complex<double> *ap = ad;
-      for (int i = 0; i < aw; i++)
-      {
-         complex<double> d = 0.0;
-         for (int k = 0; k < ah; k++)
-         {
-            d += ap[k] * bd[k];
-         }
-         *(cd++) = d;
-         ap += ah;
-      }
-      bd += ah;
-   }            
-}
-
-/// Multiply the conjugate transpose of a matrix A with a matrix B:   At*B
-void MultAhB(const ComplexDenseMatrix &A, const ComplexDenseMatrix &B, ComplexDenseMatrix &AtB)
-{
-   MFEM_ASSERT(A.Width() == AtB.Height() && B.Width() == AtB.Width() &&
-               A.Height() == B.Height(), "incompatible dimensions");
-      MFEM_ASSERT(A.Width() == AtB.Height() && B.Width() == AtB.Width() &&
-               A.Height() == B.Height(), "incompatible dimensions");
-   const int ah = A.Height();
-   const int aw = A.Width();
-   const int bw = B.Width();
-   const complex<double> *ad = A.Data();
-   const complex<double> *bd = B.Data();
-   complex<double> *cd = AtB.Data();
-
-   for (int j = 0; j < bw; j++)
-   {
-      const complex<double> *ap = ad;
-      for (int i = 0; i < aw; i++)
-      {
-         complex<double> d = 0.0;
-         for (int k = 0; k < ah; k++)
-         {
-            d += conj(ap[k]) * bd[k];
-         }
-         *(cd++) = d;
-         ap += ah;
-      }
-      bd += ah;
-   }                    
-
-}

examples/maxwell-solver-dev/common/complex_linalg.hpp

@@ -1,98 +0,0 @@
-#pragma once
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-class ComplexDenseMatrix 
-{
-private:
-   std::complex<double> * data = nullptr;
-   int height = 0;
-   int width  = 0;
-public:
-   ComplexDenseMatrix();
-   
-   /// Creates square matrix of size s.
-   explicit ComplexDenseMatrix(int s);
-
-   /// Creates rectangular matrix of size m x n.
-   ComplexDenseMatrix(int m, int n);
-
-   /// Change the size of the DenseMatrix to s x s.
-   void SetSize(int s) { SetSize(s, s); }
-
-   /// Change the size of the DenseMatrix to h x w.
-   void SetSize(int h, int w);
-
-   /// Returns the matrix data array.
-   inline complex<double> *Data() const
-   { return const_cast<complex<double>*>((const complex<double>*)data);}
-
-   /// Returns the matrix data array.
-   inline complex<double> *GetData() const { return Data(); }
-
-   /// Returns reference to a_{ij}.
-   inline complex<double> &operator()(int i, int j);
-   inline const complex<double> &operator()(int i, int j) const;
-
-   inline int Height() const { return height; }
-   inline int Width() const { return width; }
-
-   /// Sets the matrix elements equal to constant c
-   ComplexDenseMatrix &operator=(std::complex<double> c);
-   ComplexDenseMatrix &operator=(double c);
-
-   /// Sets the matrix size and elements equal to those of m
-   ComplexDenseMatrix &operator=(const ComplexDenseMatrix &m);
-   ComplexDenseMatrix &operator+=(const complex<double> *m);
-   ComplexDenseMatrix &operator+=(const ComplexDenseMatrix &m);
-   ComplexDenseMatrix &operator-=(const ComplexDenseMatrix &m);
-   ComplexDenseMatrix &operator*=(complex<double> c);
-
-   /// Calculates the determinant of the matrix
-   /// (for 2x2, 3x3)
-   std::complex<double> Det() const;
-
-   virtual void Print(std::ostream &out = mfem::out, int width_ = 4) const;
-   virtual void PrintMatlab(std::ostream &out = mfem::out) const;
-
-   DenseMatrix * real() const;
-   DenseMatrix * imag() const;
-
-   void GetReal(DenseMatrix & Ar);
-   void GetImag(DenseMatrix & Ai);
-};
-
-inline complex<double> &ComplexDenseMatrix::operator()(int i, int j)
-{
-   MFEM_VERIFY(data && i >= 0 && i < height && j >= 0 && j < width, "");
-   // return data[i*width+j];
-   return data[j*height+i];
-}
-
-inline const complex<double> &ComplexDenseMatrix::operator()(int i, int j) const
-{
-   MFEM_VERIFY(data && i >= 0 && i < height && j >= 0 && j < width, "");
-   // return data[i*width+j];
-   return data[j*height+i];
-}
-
-
-class ComplexDenseMatrixInverse : public ComplexDenseMatrix
-{
-private:
-public:
-   ComplexDenseMatrixInverse(const ComplexDenseMatrix & );   
-};
-
-/// Matrix matrix multiplication.  A = B * C.
-void Mult(const ComplexDenseMatrix &b, const ComplexDenseMatrix &c, ComplexDenseMatrix &a);
-
-/// Multiply the transpose of a matrix A with a matrix B:   At*B
-void MultAtB(const ComplexDenseMatrix &A, const ComplexDenseMatrix &B, ComplexDenseMatrix &AtB);
-
-/// Multiply the conjugate transpose of a matrix A with a matrix B:   At*B
-void MultAhB(const ComplexDenseMatrix &A, const ComplexDenseMatrix &B, ComplexDenseMatrix &AtB);

examples/maxwell-solver-dev/helmholtzp.cpp

@@ -1,404 +0,0 @@
-//
-// Compile with: make helmholtzp
-//
-// Sample runs:   mpirun -np 4 ./helmholtzp -nd 2 -nx 4 -ny 4 -sr 3 -pr 3 -k 16.0 -o 2
-//                mpirun -np 4 ./helmholtzp -nd 3 -nx 2 -ny 2 -nz 2 -sr 3 -pr 1 -k 2.0 -o 2
-//
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-#include "ParDST/ParDST.hpp"
-
-using namespace std;
-using namespace mfem;
-
-// Exact solution and r.h.s., see below for implementation.
-double f_exact_Re(const Vector &x);
-double f_exact_Im(const Vector &x);
-
-double wavespeed(const Vector &x);
-
-double funccoeff_re(const Vector & x);
-double funccoeff_im(const Vector & x);
-
-
-int dim;
-double omega;
-int sol = 1;
-double length = 1.0;
-double pml_length = 0.25;
-Array2D<double>comp_bdr;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-   // 2. Parse command-line options.
-   // finite element order of approximation
-   int order = 1;
-   bool visualization = 1;
-   // number of wavelengths
-   double k = 0.5;
-   // number of serial refinements
-   int ser_ref_levels = 1;
-   // number of parallel refinements
-   int par_ref_levels = 2;
-   // dimension
-   int nd = 2;
-   int nx=2;
-   int ny=2;
-   int nz=2;
-   bool herm_conv = true;
-
-   // optional command line inputs
-   OptionsParser args(argc, argv);
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree) or -1 for"
-                  " isoparametric space.");
-   args.AddOption(&nd, "-nd", "--dim","Problem space dimension");
-   args.AddOption(&nx, "-nx", "--nx","Number of subdomains in x direction");
-   args.AddOption(&ny, "-ny", "--ny","Number of subdomains in y direction");
-   args.AddOption(&nz, "-nz", "--nz","Number of subdomains in z direction");
-   args.AddOption(&sol, "-sol", "--exact",
-                  "Exact solution flag - 0:polynomial, 1: plane wave, -1: unknown exact");
-   args.AddOption(&k, "-k", "--wavelengths",
-                  "Number of wavelengths.");
-   args.AddOption(&pml_length, "-pml_length", "--pml_length",
-                  "Length of the PML region in each direction");
-   args.AddOption(&length, "-length", "--length",
-                  "length of the domain in each direction.");
-   args.AddOption(&ser_ref_levels, "-sr", "--ser_ref_levels",
-                  "Number of Serial Refinements.");
-   args.AddOption(&par_ref_levels, "-pr", "--par_ref_levels",
-                  "Number of Parallel Refinements.");                  
-   args.AddOption(&herm_conv, "-herm", "--hermitian", "-no-herm",
-                  "--no-hermitian", "Use convention for Hermitian operators.");                  
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   // check if the inputs are correct
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-   // Angular frequency
-   omega = 2.0 * M_PI * k;
-
-   // 3. Read the mesh from the given mesh file.
-   Mesh *mesh;
-
-   if (nd == 2)
-   {
-      mesh = new Mesh(1, 1, Element::QUADRILATERAL, true, length, length, false);
-   }
-   else
-   {
-      mesh = new Mesh(1, 1, 1, Element::HEXAHEDRON, true, length, length, length,false);
-   }
-
-   // 3. Executing uniform h-refinement
-   dim = mesh->Dimension();
-   for (int i = 0; i < ser_ref_levels; i++ )
-   {
-      mesh->UniformRefinement();
-   }
-
-   // 4. Define a parallel mesh by a partitioning of the serial mesh.
-   // ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
-   int nprocs;
-   int nprocsx;
-   int nprocsy;
-   int nprocsz;
-   if (dim == 2)
-   {
-      nprocs = sqrt(num_procs); 
-      // nprocsx = nprocs;
-      // nprocsy = nprocs;
-      nprocsx = 1;
-      nprocsy = num_procs;
-      nprocsz = 1;
-   }    
-   else
-   {
-      nprocs = cbrt(num_procs); 
-      // nprocsx = nprocs;
-      // nprocsy = nprocs;
-      // nprocsz = nprocs;
-      nprocsx = 1;
-      if (nz != 1)
-      {
-         nprocsy = sqrt(num_procs);
-         nprocsz = nprocsy;
-      }
-      else
-      {
-         nprocsy = num_procs;
-         nprocsz = 1;
-      }
-   }
-   // MFEM_VERIFY(nprocs*nprocs == num_procs, "Check MPI partitioning");
-   // int nxyz[3] = {num_procs,1,1};
-   // int nxyz[3] = {nprocs,nprocs,1};
-   // int nxyz[3] = {1,num_procs,1};
-   
-   int nxyz[3] = {nprocsx,nprocsy,nprocsz};
-   // int nxyz[3] = {num_procs,1,1};
-   int * part = mesh->CartesianPartitioning(nxyz);
-   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD,*mesh,part);
-   // ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD,*mesh);
-   delete [] part;
-   delete mesh;
-
-   for (int l = 0; l < par_ref_levels; l++)
-   {
-      pmesh->UniformRefinement();
-   }
-
-
-   double hl = GetUniformMeshElementSize(pmesh);
-   int nrlayers = 3;
-
-   Array2D<double> lengths(dim,2);
-   lengths = hl*nrlayers;
-   // lengths[0][1] = 0.0;
-   // lengths[1][1] = 0.0;
-   // lengths[1][0] = 0.0;
-   // lengths[0][0] = 0.0;
-   CartesianPML pml(pmesh,lengths);
-   pml.SetOmega(omega);
-   comp_bdr.SetSize(dim,2);
-   comp_bdr = pml.GetCompDomainBdr(); 
-
-   // 6. Define a finite element space on the mesh.
-   FiniteElementCollection *fec = new H1_FECollection(order, dim);
-   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
-   HYPRE_Int size = fespace->GlobalTrueVSize();
-
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-   // 6. Set up the linear form (Real and Imaginary part)
-   FunctionCoefficient f_Re(f_exact_Re);
-   FunctionCoefficient f_Im(f_exact_Im);
-
-   // 8. Setup Complex Operator convention
-   ComplexOperator::Convention conv =
-      herm_conv ? ComplexOperator::HERMITIAN : ComplexOperator::BLOCK_SYMMETRIC;
-
-   // ParLinearForm *b_Re(new ParLinearForm);
-   ParComplexLinearForm b(fespace, conv);
-   b.AddDomainIntegrator(new DomainLFIntegrator(f_Re),
-                         new DomainLFIntegrator(f_Im));
-   b.real().Vector::operator=(0.0);
-   b.imag().Vector::operator=(0.0);
-   b.Assemble();
-
-   // 7. Set up the bilinear form (Real and Imaginary part)
-   ConstantCoefficient one(1.0);
-   ConstantCoefficient sigma(-pow(omega, 2));
-
-   FunctionCoefficient ws(wavespeed);
-
-   PmlMatrixCoefficient c1_re(dim,pml_detJ_JT_J_inv_Re,&pml);
-   PmlMatrixCoefficient c1_im(dim,pml_detJ_JT_J_inv_Im,&pml);
-
-   PmlCoefficient detJ_re(pml_detJ_Re,&pml);
-   PmlCoefficient detJ_im(pml_detJ_Im,&pml);
-
-   ProductCoefficient c2_re0(sigma, detJ_re);
-   ProductCoefficient c2_im0(sigma, detJ_im);
-
-   ProductCoefficient c2_re(c2_re0, ws);
-   ProductCoefficient c2_im(c2_im0, ws);
-
-   ParSesquilinearForm a(fespace,conv);
-   a.AddDomainIntegrator(new DiffusionIntegrator(c1_re),
-                         new DiffusionIntegrator(c1_im));
-   a.AddDomainIntegrator(new MassIntegrator(c2_re),
-                         new MassIntegrator(c2_im));
-   a.Assemble();
-   a.Finalize();
-
-   Array<int> ess_tdof_list;
-   Array<int> ess_bdr(pmesh->bdr_attributes.Max());
-   ess_bdr = 1;
-   fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-
-   // Solution grid function
-   ParComplexGridFunction p_gf(fespace); p_gf = 0.0;
-   OperatorHandle Ah;
-   Vector X, B;
-
-   a.FormLinearSystem(ess_tdof_list, p_gf, b, Ah, X, B);
-   {
-      StopWatch chrono;
-      chrono.Clear();
-      chrono.Start();
-      ParDST S(&a,lengths,omega, &ws,nrlayers,nx,ny,nz);
-      chrono.Stop();
-      double t1 = chrono.RealTime();
-
-      chrono.Clear();
-      chrono.Start();
-      // X = 0.0;
-      GMRESSolver gmres(MPI_COMM_WORLD);
-      gmres.SetPreconditioner(S);
-      gmres.SetOperator(*Ah);
-      gmres.SetRelTol(1e-6);
-      gmres.SetMaxIter(20);
-      gmres.SetPrintLevel(1);
-      gmres.Mult(B, X);
-      chrono.Stop();
-
-      double t2 = chrono.RealTime();
-      
-      MPI_Barrier(MPI_COMM_WORLD);
-
-
-      cout << " myid: " << myid 
-           << ", setup time: " << t1
-           << ", solution time: " << t2 << endl; 
-
-
-      a.RecoverFEMSolution(X,B,p_gf);
-      if (visualization)
-      {
-         char vishost[] = "localhost";
-         int  visport   = 19916;
-         string keys;
-         if (dim ==2 )
-         {
-            keys = "keys mrRljc\n";
-         }
-         else
-         {
-            keys = "keys mc\n";
-         }
-         socketstream sol_sock_re(vishost, visport);
-         sol_sock_re.precision(8);
-         sol_sock_re << "parallel " << num_procs << " " << myid << "\n"
-                     << "solution\n" << *pmesh << p_gf.real() << keys 
-                     << "window_title 'Numerical Pressure: Real Part' " << flush;                     
-
-         socketstream sol_sock_im(vishost, visport);
-         sol_sock_im.precision(8);
-         sol_sock_im << "parallel " << num_procs << " " << myid << "\n"
-                     << "solution\n" << *pmesh << p_gf.imag() << keys 
-                     << "window_title 'Numerical Pressure: Imag Part' " << flush;                     
-      }
-   }
-
-   delete fespace;
-   delete fec;
-	delete pmesh;
-   MPI_Finalize();
-   return 0;
-}
-
-
-double f_exact_Re(const Vector &x)
-{
-   
-   int nrsources = (dim == 2) ? 4 : 8;
-   Vector x0(nrsources);
-   Vector y0(nrsources);
-   Vector z0(nrsources);
-   x0(0) = 0.25; y0(0) = 0.25; z0(0) = 0.25;
-   x0(1) = 0.75; y0(1) = 0.25; z0(1) = 0.25;
-   x0(2) = 0.25; y0(2) = 0.75; z0(2) = 0.25;
-   x0(3) = 0.75; y0(3) = 0.75; z0(3) = 0.25;
-   if (dim == 3)
-   {
-      x0(4) = 0.25; y0(4) = 0.25; z0(4) = 0.75;
-      x0(5) = 0.75; y0(5) = 0.25; z0(5) = 0.75;
-      x0(6) = 0.25; y0(6) = 0.75; z0(6) = 0.75;
-      x0(7) = 0.75; y0(7) = 0.75; z0(7) = 0.75;
-   }
-  
-   double n = 4.0*omega/M_PI;
-   double coeff = 16.0*omega*omega/M_PI/M_PI/M_PI;
-
-   double f_re = 0.0;
-   // for (int i = 0; i<1; i++)
-   for (int i = 0; i<nrsources; i++)
-   {
-      double beta = pow(x0(i)-x(0),2) + pow(y0(i)-x(1),2);
-      if (dim == 3) { beta += pow(z0(i)-x(2),2); }
-      double alpha = -pow(n,2) * beta;
-      f_re += coeff*exp(alpha);
-   }
-
-   bool in_pml = false;
-   for (int i = 0; i<dim; i++)
-   {
-      if (x(i)<=comp_bdr(i,0) || x(i)>=comp_bdr(i,1))
-      {
-         in_pml = true;
-         break;
-      }
-   }
-   if (in_pml) f_re = 0.0;
-
-   return f_re;
-
-}
-double f_exact_Im(const Vector &x)
-{
-   double f_im;
-   f_im = 0.0;
-   return f_im;
-}
-
-double wavespeed(const Vector &x)
-{
-   double ws;
-   ws = 1.0;
-   return ws;
-}
-
-double funccoeff_re(const Vector & x)
-{
-   return sin(3*M_PI*(x.Sum()));
-}
-
-double funccoeff_im(const Vector & x)
-{
-   return cos(10*M_PI*(x.Sum()));
-}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-

examples/maxwell-solver-dev/makefile

@@ -1,67 +0,0 @@
-# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
-# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
-# See file COPYRIGHT for details.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability see http://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License (as published by the Free
-# Software Foundation) version 2.1 dated February 1999.
-
-# Use the MFEM build directory
-MFEM_DIR ?= ../..
-MFEM_BUILD_DIR ?= ../..
-SRC = $(if $(MFEM_DIR:../../..=),$(MFEM_DIR)/examples/maxwell-solver-dev/,)
-CONFIG_MK = $(MFEM_BUILD_DIR)/config/config.mk
-
-MFEM_LIB_FILE = mfem_is_not_built
--include $(CONFIG_MK)
-
-SEQ_EXAMPLES = 
-PAR_EXAMPLES = helmholtzp maxwellp
-ifeq ($(MFEM_USE_MPI),NO)
-   EXAMPLES = $(SEQ_EXAMPLES)
-else
-   EXAMPLES = $(PAR_EXAMPLES) $(SEQ_EXAMPLES)
-endif
-
-.SUFFIXES:
-.SUFFIXES: .o .cpp .mk
-.PHONY: all clean
-.PRECIOUS: %.o
-
-COMMON_O= common/PML.o common/MeshPartition.o \
-			 common/Utilities.o common/complex_linalg.o\
-			 ParDST/ParDST.o ParDST/DofMapsDST.o
-
-# Remove built-in rules
-%: %.cpp
-%.o: %.cpp
-
-all: $(EXAMPLES)
-
-# Rules for building the EXAMPLES
-
-%: $(SRC)%.cpp $(COMMON_O) $(MFEM_LIB_FILE) $(CONFIG_MK)
-	$(MFEM_CXX) $(MFEM_FLAGS) $< -o $@ $(COMMON_O) $(MFEM_LIBS)
-
-# Rules for compiling miniapp dependencies
-$(COMMON_O) $($(EXAMPLES)): \
-%.o: $(SRC)%.cpp $(SRC)%.hpp $(CONFIG_MK)
-	$(MFEM_CXX) $(MFEM_FLAGS) -c $(<) -o $(@)
-
-# Generate an error message if the MFEM library is not built and exit
-$(MFEM_LIB_FILE):
-	$(error The MFEM library is not built)
-
-clean:
-	rm -f *.o *~ $(SEQ_EXAMPLES) $(PAR_EXAMPLES)
-	rm -f DST/*.o
-	rm -f ParDST/*.o
-	rm -f common/*.o
-	rm -f DST2D/*.o
-	rm -rf *.dSYM *.TVD.*breakpoints
-	rm output/*
-
-

examples/maxwell-solver-dev/maxwellp.cpp

@@ -1,535 +0,0 @@
-//
-// Compile with: make maxwellp
-//
-// Sample runs:   mpirun -np 4 ./maxwellp -nd 2 -nx 4 -ny 4 -sr 3 -pr 3 -k 16.0 -o 2
-//                mpirun -np 4 ./maxwellp -nd 3 -nx 2 -ny 2 -nz 2 -sr 3 -pr 1 -k 2.0 -o 2
-//
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-#include "ParDST/ParDST.hpp"
-
-using namespace std;
-using namespace mfem;
-  
-void source_re(const Vector &x, Vector & f);
-void source_im(const Vector &x, Vector & f);
-void exact_re(const Vector & x, Vector & E);
-void exact_im(const Vector & x, Vector & E);
-void maxwell_solution(const Vector & x, double E[], double curl2E[]);
-double wavespeed(const Vector &x);
-void Mwavespeed(const Vector & x, DenseMatrix & M);
-
-void ess_data_func(const Vector & x, Vector & E);
-
-
-double mu = 1.0;
-double epsilon = 1.0;
-double omega;
-int dim;
-double length = 1.0;
-Array2D<double> comp_bdr;
-Array2D<double> domain_bdr;
-bool exact_known = false;
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-   int order = 1;
-   // number of serial refinements
-   int ser_ref_levels = 1;
-   // number of parallel refinements
-   int par_ref_levels = 2;
-   // number of wavelengths
-   double k = 5.0; // 
-   bool herm_conv = true;
-   bool visualization = 1;
-   int nd=2;
-   int nx=2;
-   int ny=2;
-   int nz=2;
-   OptionsParser args(argc, argv);
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&nd, "-nd", "--dim","Problem space dimension");
-   args.AddOption(&nx, "-nx", "--nx","Number of subdomains in x direction");
-   args.AddOption(&ny, "-ny", "--ny","Number of subdomains in y direction");
-   args.AddOption(&nz, "-nz", "--nz","Number of subdomains in z direction");               
-   args.AddOption(&ser_ref_levels, "-sr", "--ser_ref_levels",
-                  "Number of Serial Refinements.");
-   args.AddOption(&par_ref_levels, "-pr", "--par_ref_levels",
-                  "Number of Parallel Refinements."); 
-   args.AddOption(&mu, "-mu", "--permeability",
-                  "Permeability of free space (or 1/(spring constant)).");
-   args.AddOption(&epsilon, "-eps", "--permittivity",
-                  "Permittivity of free space (or mass constant).");
-   args.AddOption(&k, "-k", "--wavelengths",
-                  "Number of wavelengths.");
-   args.AddOption(&herm_conv, "-herm", "--hermitian", "-no-herm",
-                  "--no-hermitian", "Use convention for Hermitian operators.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-
-   // check if the inputs are correct
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // Angular frequency
-   omega = 2.0 * M_PI * k;
-
-   Mesh *mesh;
-
-
-   int nel = 1;
-   if (nd == 2)
-   {
-      mesh = new Mesh(nel, nel, Element::QUADRILATERAL, true, length, length, false);
-   }
-   else
-   {
-      mesh = new Mesh(nel, nel, nel, Element::HEXAHEDRON, true, length, length, length,false);
-   }
-
-   dim = mesh->Dimension();
-
-   // 4. Refine the mesh to increase the resolution.
-   for (int l = 0; l < ser_ref_levels; l++)
-   {
-      mesh->UniformRefinement();
-   }
-
-   // 4. Define a parallel mesh by a partitioning of the serial mesh.
-   // ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
-   int nprocs;
-   int nprocsx;
-   int nprocsy;
-   int nprocsz;
-   if (dim == 2)
-   {
-      nprocs = sqrt(num_procs); 
-      nprocsx = nprocs;
-      nprocsy = nprocs;
-      nprocsz = 1;
-   }    
-   else
-   {
-      nprocs = cbrt(num_procs); 
-      nprocsx = nprocs;
-      nprocsy = nprocs;
-      nprocsz = nprocs;
-   }
-   int nxyz[3] = {nprocsx,nprocsy,nprocsz};
-   int * part = mesh->CartesianPartitioning(nxyz);
-   // ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD,*mesh,part);
-   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD,*mesh);
-   delete [] part;
-
-   
-   delete mesh;
-
-   for (int l = 0; l < par_ref_levels; l++)
-   {
-      pmesh->UniformRefinement();
-   }
-
-
-   double hl = GetUniformMeshElementSize(pmesh);
-   int nrlayers = 3;
-   Array2D<double> lengths(dim,2);
-   lengths = hl*nrlayers;
-   // lengths[0][1] = 0.0;
-   // lengths[1][1] = 0.0;
-   // lengths[1][0] = 0.0;
-   // lengths[0][0] = 0.0;
-   if (exact_known) lengths = 0.0;
-   // CartesianPML pml(mesh,lengths);
-   CartesianPML pml(pmesh,lengths);
-   pml.SetOmega(omega);
-   comp_bdr.SetSize(dim,2);
-   comp_bdr = pml.GetCompDomainBdr(); 
-
-
-   // 6. Define a finite element space on the mesh. Here we use the Nedelec
-   //    finite elements of the specified order.
-   FiniteElementCollection *fec = new ND_FECollection(order, dim);
-   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
-   HYPRE_Int size = fespace->GlobalTrueVSize();
-
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 7. Determine the list of true essential boundary dofs. In this example,
-   //    the boundary conditions are defined based on the specific mesh and the
-   //    problem type.
-   Array<int> ess_tdof_list;
-   if (pmesh->bdr_attributes.Size())
-   {
-      Array<int> ess_bdr(pmesh->bdr_attributes.Max());
-      ess_bdr = 1;
-      fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   // 8. Setup Complex Operator convention
-   ComplexOperator::Convention conv =
-      herm_conv ? ComplexOperator::HERMITIAN : ComplexOperator::BLOCK_SYMMETRIC;
-
-   // 9. Set up the linear form b(.) which corresponds to the right-hand side of
-   //    the FEM linear system.
-   VectorFunctionCoefficient f_re(dim, source_re);
-   VectorFunctionCoefficient f_im(dim, source_re);
-   ParComplexLinearForm b(fespace, conv);
-   b.AddDomainIntegrator(new VectorFEDomainLFIntegrator(f_re),
-                         new VectorFEDomainLFIntegrator(f_im));
-   b.Vector::operator=(0.0);
-   b.Assemble();
-
-   // 10. Define the solution vector x as a complex finite element grid function
-   //     corresponding to fespace.
-   ParComplexGridFunction x(fespace);
-   x = 0.0;
-   // VectorFunctionCoefficient done(dim,ess_data_func);
-   // x.ProjectCoefficient(done,done);
-   VectorFunctionCoefficient E_re(dim,exact_re);
-   VectorFunctionCoefficient E_im(dim,exact_re);
-   if (exact_known)
-   {
-      x.ProjectCoefficient(E_re,E_re);
-   }
-   // 11. Set up the sesquilinear form a(.,.)
-   //
-   //       1/mu (1/det(J) J^T J Curl E, Curl F)
-   //        - omega^2 * epsilon (det(J) * (J^T J)^-1 * E, F)
-   //
-   FunctionCoefficient ws(wavespeed);
-
-   // MatrixFunctionCoefficient Mws(dim,Mwavespeed);
-
-   // DenseMatrix M(dim); M = 0.0;
-   // M(0,0) = -pow(omega, 2);
-   // M(1,1) = -pow(omega, 2);
-   // M(2,2) = -pow(omega, 2);
-   // MatrixConstantCoefficient Momeg(M);
-   MatrixFunctionCoefficient eps_func(dim,Mwavespeed);
-
-   ConstantCoefficient omeg(-pow(omega, 2));
-   int cdim = (dim == 2) ? 1 : dim;
-   PmlMatrixCoefficient pml_c1_Re(cdim,detJ_inv_JT_J_Re, &pml);
-   PmlMatrixCoefficient pml_c1_Im(cdim,detJ_inv_JT_J_Im, &pml);
-
-   PmlMatrixCoefficient pml_c2_Re(dim, detJ_JT_J_inv_Re,&pml);
-   PmlMatrixCoefficient pml_c2_Im(dim, detJ_JT_J_inv_Im,&pml);
-   ScalarMatrixProductCoefficient c2_Re0(omeg,pml_c2_Re);
-   ScalarMatrixProductCoefficient c2_Im0(omeg,pml_c2_Im);
-   // ScalarMatrixProductCoefficient c2_Re(ws,c2_Re0);
-   // ScalarMatrixProductCoefficient c2_Im(ws,c2_Im0);
-
-   MatrixMatrixProductCoefficient c2_Re(c2_Re0,eps_func);
-   MatrixMatrixProductCoefficient c2_Im(c2_Im0,eps_func);
-
-   // MatrixMatrixProductCoefficient c2_Re0(Momeg,pml_c2_Re);
-   // MatrixMatrixProductCoefficient c2_Im0(Momeg,pml_c2_Im);
-   // MatrixMatrixProductCoefficient c2_Re(Mws,c2_Re0);
-   // MatrixMatrixProductCoefficient c2_Im(Mws,c2_Im0);
-
-
-   ParSesquilinearForm a(fespace, conv);
-   a.AddDomainIntegrator(new CurlCurlIntegrator(pml_c1_Re),
-                         new CurlCurlIntegrator(pml_c1_Im));
-   a.AddDomainIntegrator(new VectorFEMassIntegrator(c2_Re),
-                         new VectorFEMassIntegrator(c2_Im));
-
-   a.Assemble(0);
-
-   OperatorHandle Ah;
-   Vector B, X;
-   a.FormLinearSystem(ess_tdof_list, x, b, Ah, X, B);
-
-   ComplexSparseMatrix * Ac = Ah.As<ComplexSparseMatrix>();
-   StopWatch chrono;
-
-
-   chrono.Clear();
-   chrono.Start();
-   ParDST * S = new ParDST(&a,lengths, omega, &ws, nrlayers, nx, ny, nz);
-   chrono.Stop();
-   double t1 = chrono.RealTime();
-
-   chrono.Clear();
-   chrono.Start();
-   // X = 0.0;
-	GMRESSolver gmres(MPI_COMM_WORLD);
-	// gmres.iterative_mode = true;
-   gmres.SetPreconditioner(*S);
-	gmres.SetOperator(*Ac);
-	gmres.SetRelTol(1e-8);
-	gmres.SetMaxIter(100);
-	gmres.SetPrintLevel(1);
-	gmres.Mult(B, X);
-   delete S;
-   chrono.Stop();
-   double t2 = chrono.RealTime();
-
-   MPI_Barrier(MPI_COMM_WORLD);
-
-
-   cout << " myid: " << myid 
-         << ", setup time: " << t1
-         << ", solution time: " << t2 << endl; 
-
-   a.RecoverFEMSolution(X, b, x);
-
-
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      string keys;
-      if (dim ==2 )
-      {
-         keys = "keys mrRljc\n";
-      }
-      else
-      {
-         keys = "keys mc\n";
-      }
-      socketstream sol_sock_re(vishost, visport);
-      sol_sock_re.precision(8);
-      sol_sock_re << "parallel " << num_procs << " " << myid << "\n"
-                  << "solution\n" << *pmesh << x.real() << keys 
-                  << "window_title 'E: Real Part' " << flush;                     
-
-      socketstream sol_sock_im(vishost, visport);
-      sol_sock_im.precision(8);
-      sol_sock_im << "parallel " << num_procs << " " << myid << "\n"
-                  << "solution\n" << *pmesh << x.imag() << keys 
-                  << "window_title 'E: Imag Part' " << flush;   
-
-      {
-         ParGridFunction x_t(fespace);
-         x_t = x.real();
-
-         socketstream sol_sock(vishost, visport);
-         sol_sock.precision(8);
-         sol_sock << "parallel " << num_procs << " " << myid << "\n"
-                  << "solution\n" << *pmesh << x_t << keys << "autoscale off\n"
-                  << "window_title 'Harmonic Solution (t = 0.0 T)'"
-                  << "pause\n" << flush;
-
-         if (myid == 0)
-         {
-            cout << "GLVis visualization paused."
-                 << " Press space (in the GLVis window) to resume it.\n";
-         }
-
-         int num_frames = 32;
-         int i = 0;
-         while (sol_sock)
-         {
-            double t = (double)(i % num_frames) / num_frames;
-            ostringstream oss;
-            oss << "Harmonic Solution (t = " << t << " T)";
-
-            add(cos(2.0*M_PI*t), x.real(), sin(2.0*M_PI*t), x.imag(), x_t);
-            sol_sock << "parallel " << num_procs << " " << myid << "\n";
-            sol_sock << "solution\n" << *pmesh << x_t
-                     << "window_title '" << oss.str() << "'" << flush;
-            i++;
-         }
-      }
-   }
-
-   // 18. Free the used memory.
-   delete fespace;
-   delete fec;
-   delete pmesh;
-   MPI_Finalize();
-   return 0;
-}
-
-void source_re(const Vector &x, Vector &f)
-{
-   f = 0.0;
-   if (exact_known)
-   {
-      double E[3], curl2E[3];
-      maxwell_solution(x, E, curl2E);
-      // curl ( curl E) +/- omega^2 E = f
-      double coeff = -omega * omega;
-      f(0) = curl2E[0] + coeff * E[0];
-      f(1) = curl2E[1] + coeff * E[1];
-      if (dim == 2)
-      {
-         if (x.Size() == 3) {f(2)=0.0;}
-      }
-      else
-      {
-         f(2) = curl2E[2] + coeff * E[2];
-      }
-   }
-   else
-   {
-      int nrsources = (dim == 2) ? 4 : 8;
-      Vector x0(nrsources);
-      Vector y0(nrsources);
-      Vector z0(nrsources);
-      x0(0) = 0.25; y0(0) = 0.25; z0(0) = 0.25;
-      x0(1) = 0.75; y0(1) = 0.25; z0(1) = 0.25;
-      x0(2) = 0.25; y0(2) = 0.75; z0(2) = 0.25;
-      x0(3) = 0.75; y0(3) = 0.75; z0(3) = 0.25;
-      if (dim == 3)
-      {
-         x0(4) = 0.25; y0(4) = 0.25; z0(4) = 0.75;
-         x0(5) = 0.75; y0(5) = 0.25; z0(5) = 0.75;
-         x0(6) = 0.25; y0(6) = 0.75; z0(6) = 0.75;
-         x0(7) = 0.75; y0(7) = 0.75; z0(7) = 0.75;
-      }
-  
-      double n = 4.0*omega/M_PI;
-      double coeff = 16.0*omega*omega/M_PI/M_PI/M_PI;
-
-      for (int i = 0; i<nrsources; i++)
-      {
-         double beta = pow(x0(i)-x(0),2) + pow(y0(i)-x(1),2);
-         if (dim == 3) { beta += pow(z0(i)-x(2),2); }
-         double alpha = -pow(n,2) * beta;
-         f[0] += coeff*exp(alpha);
-      }
-
-      bool in_pml = false;
-      for (int i = 0; i<dim; i++)
-      {
-         if (x(i)<=comp_bdr(i,0) || x(i)>=comp_bdr(i,1))
-         {
-            in_pml = true;
-            break;
-         }
-      }
-      if (in_pml) f = 0.0;
-   }
-}
-
-void source_im(const Vector &x, Vector &f)
-{
-   f = 0.0;
-}
-
-double wavespeed(const Vector &x)
-{
-   double ws;
-   ws = 1.0;
-   return ws;
-}
-
-void Mwavespeed(const Vector & x, DenseMatrix & M)
-{
-   M = 0.0;
-   M(0,0) = 1.0;
-   M(1,1) = 1.0;
-   // M(2,2) = 4.0*x(0)-1.0;
-   if (dim == 3) M(2,2) = 1.0;
-}
-
-
-void exact_re(const Vector & x, Vector & E)
-{
-   double curl2E[3];
-   maxwell_solution(x, E, curl2E);
-}
-void exact_im(const Vector & x, Vector & E)
-{
-   // double curl2E[3];
-   // maxwell_solution(x, E, curl2E);
-   E = 0.0;
-}
-void maxwell_solution(const Vector & x, double E[], double curl2E[])
-{
-   // point source
-   if (dim == 2)
-   {
-      // shift to avoid singularity
-      double x0 = x(0) + 0.1;
-      double x1 = x(1) + 0.1;
-      //
-      double r = sqrt(x0 * x0 + x1 * x1);
-
-      E[0] = cos(omega * r);
-      E[1] = 0.0;
-
-      double r_x = x0 / r;
-      double r_y = x1 / r;
-      double r_xy = -(r_x / r) * r_y;
-      double r_yx = r_xy;
-      double r_yy = (1.0 / r) * (1.0 - r_y * r_y);
-
-      curl2E[0] = omega * ((r_yy ) * sin(omega * r) + (omega * r_y * r_y) * cos(omega * r));
-      curl2E[1] = -omega * (r_yx * sin(omega * r) + omega * r_y * r_x * cos(omega * r));
-      curl2E[2] = 0.0;
-   }
-   else
-   {
-   // shift to avoid singularity
-      double x0 = x(0) + 0.1;
-      double x1 = x(1) + 0.1;
-      double x2 = x(2) + 0.1;
-      //
-      double r = sqrt(x0 * x0 + x1 * x1 + x2 * x2);
-
-      E[0] = cos(omega * r);
-      E[1] = 0.0;
-      E[2] = 0.0;
-
-      double r_x = x0 / r;
-      double r_y = x1 / r;
-      double r_z = x2 / r;
-      double r_xy = -(r_x / r) * r_y;
-      double r_xz = -(r_x / r) * r_z;
-      double r_yx = r_xy;
-      double r_yy = (1.0 / r) * (1.0 - r_y * r_y);
-      double r_zx = r_xz;
-      double r_zz = (1.0 / r) * (1.0 - r_z * r_z);
-
-      curl2E[0] = omega * ((r_yy + r_zz) * sin(omega * r) +
-                           (omega * r_y * r_y + omega * r_z * r_z) * cos(omega * r));
-      curl2E[1] = -omega * (r_yx * sin(omega * r) + omega * r_y * r_x * cos(omega * r));
-      curl2E[2] = -omega * (r_zx * sin(omega * r) + omega * r_z * r_x * cos(omega * r));
-   }
-}
-
-
-void ess_data_func(const Vector & x, Vector & E)
-{
-   E = 0.0;
-   if (x(1)==0.0) E[0] = sin(x(0)+x(1));
-
-   bool in_pml = false;
-   for (int i = 0; i<dim; i++)
-   {
-      if (x(i)<comp_bdr(i,0) || x(i)>comp_bdr(i,1))
-      {
-         in_pml = true;
-         break;
-      }
-   }
-   if (in_pml) E = 0.0;
-
-}

fem/bilinearform.cpp

@@ -31,7 +31,7 @@ void BilinearForm::AllocMat()
    const Table &elem_dof = fes->GetElementToDofTable();
    Table dof_dof;
 
-   if (fbfi.Size() > 0)
+   if (interior_face_integs.Size() > 0)
    {
       // the sparsity pattern is defined from the map: face->element->dof
       Table face_dof, dof_face;
@@ -99,15 +99,15 @@ BilinearForm::BilinearForm (FiniteElementSpace * f, BilinearForm * bf, int ps)
    ext = NULL;
 
    // Copy the pointers to the integrators
-   dbfi = bf->dbfi;
+   domain_integs = bf->domain_integs;
 
-   bbfi = bf->bbfi;
-   bbfi_marker = bf->bbfi_marker;
+   boundary_integs = bf->boundary_integs;
+   boundary_integs_marker = bf->boundary_integs_marker;
 
-   fbfi = bf->fbfi;
+   interior_face_integs = bf->interior_face_integs;
 
-   bfbfi = bf->bfbfi;
-   bfbfi_marker = bf->bfbfi_marker;
+   boundary_face_integs = bf->boundary_face_integs;
+   boundary_face_integs_marker = bf->boundary_face_integs_marker;
 
    AllocMat();
 }
@@ -234,46 +234,47 @@ void BilinearForm::Finalize (int skip_zeros)
 
 void BilinearForm::AddDomainIntegrator(BilinearFormIntegrator *bfi)
 {
-   dbfi.Append(bfi);
-   dbfi_marker.Append(NULL); // NULL marker means apply everywhere
+   domain_integs.Append(bfi);
+   domain_integs_marker.Append(NULL); // NULL marker means apply everywhere
 }
 
 void BilinearForm::AddDomainIntegrator(BilinearFormIntegrator *bfi,
                                        Array<int> &elem_marker)
 {
-   dbfi.Append(bfi);
-   dbfi_marker.Append(&elem_marker);
+   domain_integs.Append(bfi);
+   domain_integs_marker.Append(&elem_marker);
 }
 
 void BilinearForm::AddBoundaryIntegrator (BilinearFormIntegrator * bfi)
 {
-   bbfi.Append (bfi);
-   bbfi_marker.Append(NULL); // NULL marker means apply everywhere
+   boundary_integs.Append (bfi);
+   boundary_integs_marker.Append(NULL); // NULL marker means apply everywhere
 }
 
 void BilinearForm::AddBoundaryIntegrator (BilinearFormIntegrator * bfi,
                                           Array<int> &bdr_marker)
 {
-   bbfi.Append (bfi);
-   bbfi_marker.Append(&bdr_marker);
+   boundary_integs.Append (bfi);
+   boundary_integs_marker.Append(&bdr_marker);
 }
 
 void BilinearForm::AddInteriorFaceIntegrator(BilinearFormIntegrator * bfi)
 {
-   fbfi.Append (bfi);
+   interior_face_integs.Append (bfi);
 }
 
 void BilinearForm::AddBdrFaceIntegrator(BilinearFormIntegrator *bfi)
 {
-   bfbfi.Append(bfi);
-   bfbfi_marker.Append(NULL); // NULL marker means apply everywhere
+   boundary_face_integs.Append(bfi);
+   // NULL marker means apply everywhere
+   boundary_face_integs_marker.Append(NULL);
 }
 
 void BilinearForm::AddBdrFaceIntegrator(BilinearFormIntegrator *bfi,
                                         Array<int> &bdr_marker)
 {
-   bfbfi.Append(bfi);
-   bfbfi_marker.Append(&bdr_marker);
+   boundary_face_integs.Append(bfi);
+   boundary_face_integs_marker.Append(&bdr_marker);
 }
 
 void BilinearForm::ComputeElementMatrix(int i, DenseMatrix &elmat)
@@ -285,14 +286,14 @@ void BilinearForm::ComputeElementMatrix(int i, DenseMatrix &elmat)
       return;
    }
 
-   if (dbfi.Size())
+   if (domain_integs.Size())
    {
       const FiniteElement &fe = *fes->GetFE(i);
       ElementTransformation *eltrans = fes->GetElementTransformation(i);
-      dbfi[0]->AssembleElementMatrix(fe, *eltrans, elmat);
-      for (int k = 1; k < dbfi.Size(); k++)
+      domain_integs[0]->AssembleElementMatrix(fe, *eltrans, elmat);
+      for (int k = 1; k < domain_integs.Size(); k++)
       {
-         dbfi[k]->AssembleElementMatrix(fe, *eltrans, elemmat);
+         domain_integs[k]->AssembleElementMatrix(fe, *eltrans, elemmat);
          elmat += elemmat;
       }
    }
@@ -306,14 +307,14 @@ void BilinearForm::ComputeElementMatrix(int i, DenseMatrix &elmat)
 
 void BilinearForm::ComputeBdrElementMatrix(int i, DenseMatrix &elmat)
 {
-   if (bbfi.Size())
+   if (boundary_integs.Size())
    {
       const FiniteElement &be = *fes->GetBE(i);
       ElementTransformation *eltrans = fes->GetBdrElementTransformation(i);
-      bbfi[0]->AssembleElementMatrix(be, *eltrans, elmat);
-      for (int k = 1; k < bbfi.Size(); k++)
+      boundary_integs[0]->AssembleElementMatrix(be, *eltrans, elmat);
+      for (int k = 1; k < boundary_integs.Size(); k++)
       {
-         bbfi[k]->AssembleElementMatrix(be, *eltrans, elemmat);
+         boundary_integs[k]->AssembleElementMatrix(be, *eltrans, elemmat);
          elmat += elemmat;
       }
    }
@@ -407,13 +408,14 @@ void BilinearForm::Assemble(int skip_zeros)
    }
 #endif
 
-   if (dbfi.Size())
+   if (domain_integs.Size())
    {
-      for (int k = 0; k < dbfi.Size(); k++)
+      for (int k = 0; k < domain_integs.Size(); k++)
       {
-         if (dbfi_marker[k] != NULL)
+         if (domain_integs_marker[k] != NULL)
          {
-            MFEM_VERIFY(mesh->attributes.Size() == dbfi_marker[k]->Size(),
+            MFEM_VERIFY(mesh->attributes.Size() ==
+                        domain_integs_marker[k]->Size(),
                         "invalid element marker for domain integrator #"
                         << k << ", counting from zero");
          }
@@ -430,14 +432,14 @@ void BilinearForm::Assemble(int skip_zeros)
          else
          {
             elmat.SetSize(0);
-            for (int k = 0; k < dbfi.Size(); k++)
+            for (int k = 0; k < domain_integs.Size(); k++)
             {
-               if ( dbfi_marker[k] == NULL ||
-                    (*(dbfi_marker[k]))[elem_attr-1] == 1)
+               if ( domain_integs_marker[k] == NULL ||
+                    (*(domain_integs_marker[k]))[elem_attr-1] == 1)
                {
                   const FiniteElement &fe = *fes->GetFE(i);
                   eltrans = fes->GetElementTransformation(i);
-                  dbfi[k]->AssembleElementMatrix(fe, *eltrans, elemmat);
+                  domain_integs[k]->AssembleElementMatrix(fe, *eltrans, elemmat);
                   if (elmat.Size() == 0)
                   {
                      elmat = elemmat;
@@ -472,20 +474,20 @@ void BilinearForm::Assemble(int skip_zeros)
       }
    }
 
-   if (bbfi.Size())
+   if (boundary_integs.Size())
    {
       // Which boundary attributes need to be processed?
       Array<int> bdr_attr_marker(mesh->bdr_attributes.Size() ?
                                  mesh->bdr_attributes.Max() : 0);
       bdr_attr_marker = 0;
-      for (int k = 0; k < bbfi.Size(); k++)
+      for (int k = 0; k < boundary_integs.Size(); k++)
       {
-         if (bbfi_marker[k] == NULL)
+         if (boundary_integs_marker[k] == NULL)
          {
             bdr_attr_marker = 1;
             break;
          }
-         Array<int> &bdr_marker = *bbfi_marker[k];
+         Array<int> &bdr_marker = *boundary_integs_marker[k];
          MFEM_ASSERT(bdr_marker.Size() == bdr_attr_marker.Size(),
                      "invalid boundary marker for boundary integrator #"
                      << k << ", counting from zero");
@@ -504,21 +506,21 @@ void BilinearForm::Assemble(int skip_zeros)
          fes -> GetBdrElementVDofs (i, vdofs);
          eltrans = fes -> GetBdrElementTransformation (i);
          int k = 0;
-         for (; k < bbfi.Size(); k++)
+         for (; k < boundary_integs.Size(); k++)
          {
-            if (bbfi_marker[k] &&
-                (*bbfi_marker[k])[bdr_attr-1] == 0) { continue; }
+            if (boundary_integs_marker[k] &&
+                (*boundary_integs_marker[k])[bdr_attr-1] == 0) { continue; }
 
-            bbfi[k]->AssembleElementMatrix(be, *eltrans, elmat);
+            boundary_integs[k]->AssembleElementMatrix(be, *eltrans, elmat);
             k++;
             break;
          }
-         for (; k < bbfi.Size(); k++)
+         for (; k < boundary_integs.Size(); k++)
          {
-            if (bbfi_marker[k] &&
-                (*bbfi_marker[k])[bdr_attr-1] == 0) { continue; }
+            if (boundary_integs_marker[k] &&
+                (*boundary_integs_marker[k])[bdr_attr-1] == 0) { continue; }
 
-            bbfi[k]->AssembleElementMatrix(be, *eltrans, elemmat);
+            boundary_integs[k]->AssembleElementMatrix(be, *eltrans, elemmat);
             elmat += elemmat;
          }
          if (!static_cond)
@@ -536,7 +538,7 @@ void BilinearForm::Assemble(int skip_zeros)
       }
    }
 
-   if (fbfi.Size())
+   if (interior_face_integs.Size())
    {
       FaceElementTransformations *tr;
       Array<int> vdofs2;
@@ -550,18 +552,19 @@ void BilinearForm::Assemble(int skip_zeros)
             fes -> GetElementVDofs (tr -> Elem1No, vdofs);
             fes -> GetElementVDofs (tr -> Elem2No, vdofs2);
             vdofs.Append (vdofs2);
-            for (int k = 0; k < fbfi.Size(); k++)
+            for (int k = 0; k < interior_face_integs.Size(); k++)
             {
-               fbfi[k] -> AssembleFaceMatrix (*fes -> GetFE (tr -> Elem1No),
-                                              *fes -> GetFE (tr -> Elem2No),
-                                              *tr, elemmat);
+               interior_face_integs[k]->
+               AssembleFaceMatrix(*fes->GetFE(tr->Elem1No),
+                                  *fes->GetFE(tr->Elem2No),
+                                  *tr, elemmat);
                mat -> AddSubMatrix (vdofs, vdofs, elemmat, skip_zeros);
             }
          }
       }
    }
 
-   if (bfbfi.Size())
+   if (boundary_face_integs.Size())
    {
       FaceElementTransformations *tr;
       const FiniteElement *fe1, *fe2;
@@ -570,14 +573,14 @@ void BilinearForm::Assemble(int skip_zeros)
       Array<int> bdr_attr_marker(mesh->bdr_attributes.Size() ?
                                  mesh->bdr_attributes.Max() : 0);
       bdr_attr_marker = 0;
-      for (int k = 0; k < bfbfi.Size(); k++)
+      for (int k = 0; k < boundary_face_integs.Size(); k++)
       {
-         if (bfbfi_marker[k] == NULL)
+         if (boundary_face_integs_marker[k] == NULL)
          {
             bdr_attr_marker = 1;
             break;
          }
-         Array<int> &bdr_marker = *bfbfi_marker[k];
+         Array<int> &bdr_marker = *boundary_face_integs_marker[k];
          MFEM_ASSERT(bdr_marker.Size() == bdr_attr_marker.Size(),
                      "invalid boundary marker for boundary face integrator #"
                      << k << ", counting from zero");
@@ -601,12 +604,14 @@ void BilinearForm::Assemble(int skip_zeros)
             // but we can't dereference a NULL pointer, and we don't want to
             // actually make a fake element.
             fe2 = fe1;
-            for (int k = 0; k < bfbfi.Size(); k++)
+            for (int k = 0; k < boundary_face_integs.Size(); k++)
             {
-               if (bfbfi_marker[k] &&
-                   (*bfbfi_marker[k])[bdr_attr-1] == 0) { continue; }
+               if (boundary_face_integs_marker[k] &&
+                   (*boundary_face_integs_marker[k])[bdr_attr-1] == 0)
+               { continue; }
 
-               bfbfi[k] -> AssembleFaceMatrix (*fe1, *fe2, *tr, elemmat);
+               boundary_face_integs[k] -> AssembleFaceMatrix (*fe1, *fe2, *tr,
+                                                              elemmat);
                mat -> AddSubMatrix (vdofs, vdofs, elemmat, skip_zeros);
             }
          }
@@ -857,7 +862,7 @@ void BilinearForm::RecoverFEMSolution(const Vector &X,
 
 void BilinearForm::ComputeElementMatrices()
 {
-   if (element_matrices || dbfi.Size() == 0 || fes->GetNE() == 0)
+   if (element_matrices || domain_integs.Size() == 0 || fes->GetNE() == 0)
    {
       return;
    }
@@ -886,11 +891,11 @@ void BilinearForm::ComputeElementMatrices()
 #endif
       fes->GetElementTransformation(i, &eltrans);
 
-      dbfi[0]->AssembleElementMatrix(fe, eltrans, elmat);
-      for (int k = 1; k < dbfi.Size(); k++)
+      domain_integs[0]->AssembleElementMatrix(fe, eltrans, elmat);
+      for (int k = 1; k < domain_integs.Size(); k++)
       {
          // note: some integrators may not be thread-safe
-         dbfi[k]->AssembleElementMatrix(fe, eltrans, tmp);
+         domain_integs[k]->AssembleElementMatrix(fe, eltrans, tmp);
          elmat += tmp;
       }
       elmat.ClearExternalData();
@@ -1105,10 +1110,12 @@ BilinearForm::~BilinearForm()
    if (!extern_bfs)
    {
       int k;
-      for (k=0; k < dbfi.Size(); k++) { delete dbfi[k]; }
-      for (k=0; k < bbfi.Size(); k++) { delete bbfi[k]; }
-      for (k=0; k < fbfi.Size(); k++) { delete fbfi[k]; }
-      for (k=0; k < bfbfi.Size(); k++) { delete bfbfi[k]; }
+      for (k=0; k < domain_integs.Size(); k++) { delete domain_integs[k]; }
+      for (k=0; k < boundary_integs.Size(); k++) { delete boundary_integs[k]; }
+      for (k=0; k < interior_face_integs.Size(); k++)
+      { delete interior_face_integs[k]; }
+      for (k=0; k < boundary_face_integs.Size(); k++)
+      { delete boundary_face_integs[k]; }
    }
 
    delete ext;
@@ -1141,13 +1148,13 @@ MixedBilinearForm::MixedBilinearForm (FiniteElementSpace *tr_fes,
    ext = NULL;
 
    // Copy the pointers to the integrators
-   dbfi = mbf->dbfi;
-   bbfi = mbf->bbfi;
-   tfbfi = mbf->tfbfi;
-   btfbfi = mbf->btfbfi;
+   domain_integs = mbf->domain_integs;
+   boundary_integs = mbf->boundary_integs;
+   trace_face_integs = mbf->trace_face_integs;
+   boundary_trace_face_integs = mbf->boundary_trace_face_integs;
 
-   bbfi_marker = mbf->bbfi_marker;
-   btfbfi_marker = mbf->btfbfi_marker;
+   boundary_integs_marker = mbf->boundary_integs_marker;
+   boundary_trace_face_integs_marker = mbf->boundary_trace_face_integs_marker;
 
    assembly = AssemblyLevel::LEGACY;
    ext = NULL;
@@ -1236,7 +1243,8 @@ MatrixInverse * MixedBilinearForm::Inverse() const
 {
    if (assembly != AssemblyLevel::LEGACY)
    {
-      MFEM_WARNING("MixedBilinearForm::Inverse not possible with this assembly level!");
+      MFEM_WARNING("MixedBilinearForm::Inverse not possible with this "
+                   "assembly level!");
       return NULL;
    }
    else
@@ -1267,38 +1275,39 @@ void MixedBilinearForm::GetBlocks(Array2D<SparseMatrix *> &blocks) const
 
 void MixedBilinearForm::AddDomainIntegrator (BilinearFormIntegrator * bfi)
 {
-   dbfi.Append (bfi);
+   domain_integs.Append (bfi);
 }
 
 void MixedBilinearForm::AddBoundaryIntegrator (BilinearFormIntegrator * bfi)
 {
-   bbfi.Append (bfi);
-   bbfi_marker.Append(NULL); // NULL marker means apply everywhere
+   boundary_integs.Append (bfi);
+   boundary_integs_marker.Append(NULL); // NULL marker means apply everywhere
 }
 
 void MixedBilinearForm::AddBoundaryIntegrator (BilinearFormIntegrator * bfi,
                                                Array<int> &bdr_marker)
 {
-   bbfi.Append (bfi);
-   bbfi_marker.Append(&bdr_marker);
+   boundary_integs.Append (bfi);
+   boundary_integs_marker.Append(&bdr_marker);
 }
 
 void MixedBilinearForm::AddTraceFaceIntegrator (BilinearFormIntegrator * bfi)
 {
-   tfbfi.Append (bfi);
+   trace_face_integs.Append (bfi);
 }
 
 void MixedBilinearForm::AddBdrTraceFaceIntegrator(BilinearFormIntegrator *bfi)
 {
-   btfbfi.Append(bfi);
-   btfbfi_marker.Append(NULL); // NULL marker means apply everywhere
+   boundary_trace_face_integs.Append(bfi);
+   // NULL marker means apply everywhere
+   boundary_trace_face_integs_marker.Append(NULL);
 }
 
 void MixedBilinearForm::AddBdrTraceFaceIntegrator(BilinearFormIntegrator *bfi,
                                                   Array<int> &bdr_marker)
 {
-   btfbfi.Append(bfi);
-   btfbfi_marker.Append(&bdr_marker);
+   boundary_trace_face_integs.Append(bfi);
+   boundary_trace_face_integs_marker.Append(&bdr_marker);
 }
 
 void MixedBilinearForm::Assemble (int skip_zeros)
@@ -1320,37 +1329,37 @@ void MixedBilinearForm::Assemble (int skip_zeros)
       mat = new SparseMatrix(height, width);
    }
 
-   if (dbfi.Size())
+   if (domain_integs.Size())
    {
       for (int i = 0; i < test_fes -> GetNE(); i++)
       {
          trial_fes -> GetElementVDofs (i, tr_vdofs);
          test_fes  -> GetElementVDofs (i, te_vdofs);
          eltrans = test_fes -> GetElementTransformation (i);
-         for (int k = 0; k < dbfi.Size(); k++)
+         for (int k = 0; k < domain_integs.Size(); k++)
          {
-            dbfi[k] -> AssembleElementMatrix2 (*trial_fes -> GetFE(i),
-                                               *test_fes  -> GetFE(i),
-                                               *eltrans, elemmat);
+            domain_integs[k] -> AssembleElementMatrix2 (*trial_fes -> GetFE(i),
+                                                        *test_fes  -> GetFE(i),
+                                                        *eltrans, elemmat);
             mat -> AddSubMatrix (te_vdofs, tr_vdofs, elemmat, skip_zeros);
          }
       }
    }
 
-   if (bbfi.Size())
+   if (boundary_integs.Size())
    {
       // Which boundary attributes need to be processed?
       Array<int> bdr_attr_marker(mesh->bdr_attributes.Size() ?
                                  mesh->bdr_attributes.Max() : 0);
       bdr_attr_marker = 0;
-      for (int k = 0; k < bbfi.Size(); k++)
+      for (int k = 0; k < boundary_integs.Size(); k++)
       {
-         if (bbfi_marker[k] == NULL)
+         if (boundary_integs_marker[k] == NULL)
          {
             bdr_attr_marker = 1;
             break;
          }
-         Array<int> &bdr_marker = *bbfi_marker[k];
+         Array<int> &bdr_marker = *boundary_integs_marker[k];
          MFEM_ASSERT(bdr_marker.Size() == bdr_attr_marker.Size(),
                      "invalid boundary marker for boundary integrator #"
                      << k << ", counting from zero");
@@ -1368,20 +1377,20 @@ void MixedBilinearForm::Assemble (int skip_zeros)
          trial_fes -> GetBdrElementVDofs (i, tr_vdofs);
          test_fes  -> GetBdrElementVDofs (i, te_vdofs);
          eltrans = test_fes -> GetBdrElementTransformation (i);
-         for (int k = 0; k < bbfi.Size(); k++)
+         for (int k = 0; k < boundary_integs.Size(); k++)
          {
-            if (bbfi_marker[k] &&
-                (*bbfi_marker[k])[bdr_attr-1] == 0) { continue; }
+            if (boundary_integs_marker[k] &&
+                (*boundary_integs_marker[k])[bdr_attr-1] == 0) { continue; }
 
-            bbfi[k] -> AssembleElementMatrix2 (*trial_fes -> GetBE(i),
-                                               *test_fes  -> GetBE(i),
-                                               *eltrans, elemmat);
+            boundary_integs[k]->AssembleElementMatrix2 (*trial_fes -> GetBE(i),
+                                                        *test_fes  -> GetBE(i),
+                                                        *eltrans, elemmat);
             mat -> AddSubMatrix (te_vdofs, tr_vdofs, elemmat, skip_zeros);
          }
       }
    }
 
-   if (tfbfi.Size())
+   if (trace_face_integs.Size())
    {
       FaceElementTransformations *ftr;
       Array<int> te_vdofs2;
@@ -1408,16 +1417,16 @@ void MixedBilinearForm::Assemble (int skip_zeros)
             // want to actually make a fake element.
             test_fe2 = test_fe1;
          }
-         for (int k = 0; k < tfbfi.Size(); k++)
+         for (int k = 0; k < trace_face_integs.Size(); k++)
          {
-            tfbfi[k]->AssembleFaceMatrix(*trial_face_fe, *test_fe1, *test_fe2,
-                                         *ftr, elemmat);
+            trace_face_integs[k]->AssembleFaceMatrix(*trial_face_fe, *test_fe1,
+                                                     *test_fe2, *ftr, elemmat);
             mat->AddSubMatrix(te_vdofs, tr_vdofs, elemmat, skip_zeros);
          }
       }
    }
 
-   if (btfbfi.Size())
+   if (boundary_trace_face_integs.Size())
    {
       FaceElementTransformations *ftr;
       Array<int> te_vdofs2;
@@ -1427,17 +1436,17 @@ void MixedBilinearForm::Assemble (int skip_zeros)
       Array<int> bdr_attr_marker(mesh->bdr_attributes.Size() ?
                                  mesh->bdr_attributes.Max() : 0);
       bdr_attr_marker = 0;
-      for (int k = 0; k < btfbfi.Size(); k++)
+      for (int k = 0; k < boundary_trace_face_integs.Size(); k++)
       {
-         if (btfbfi_marker[k] == NULL)
+         if (boundary_trace_face_integs_marker[k] == NULL)
          {
             bdr_attr_marker = 1;
             break;
          }
-         Array<int> &bdr_marker = *btfbfi_marker[k];
+         Array<int> &bdr_marker = *boundary_trace_face_integs_marker[k];
          MFEM_ASSERT(bdr_marker.Size() == bdr_attr_marker.Size(),
-                     "invalid boundary marker for boundary trace face integrator #"
-                     << k << ", counting from zero");
+                     "invalid boundary marker for boundary trace face"
+                     "integrator #" << k << ", counting from zero");
          for (int i = 0; i < bdr_attr_marker.Size(); i++)
          {
             bdr_attr_marker[i] |= bdr_marker[i];
@@ -1460,13 +1469,16 @@ void MixedBilinearForm::Assemble (int skip_zeros)
             // boundaries, but we can't dereference a NULL pointer, and we don't
             // want to actually make a fake element.
             test_fe2 = test_fe1;
-            for (int k = 0; k < btfbfi.Size(); k++)
+            for (int k = 0; k < boundary_trace_face_integs.Size(); k++)
             {
-               if (btfbfi_marker[k] &&
-                   (*btfbfi_marker[k])[bdr_attr-1] == 0) { continue; }
+               if (boundary_trace_face_integs_marker[k] &&
+                   (*boundary_trace_face_integs_marker[k])[bdr_attr-1] == 0)
+               { continue; }
 
-               btfbfi[k]->AssembleFaceMatrix(*trial_face_fe, *test_fe1, *test_fe2,
-                                             *ftr, elemmat);
+               boundary_trace_face_integs[k]->AssembleFaceMatrix(*trial_face_fe,
+                                                                 *test_fe1,
+                                                                 *test_fe2,
+                                                                 *ftr, elemmat);
                mat->AddSubMatrix(te_vdofs, tr_vdofs, elemmat, skip_zeros);
             }
          }
@@ -1557,15 +1569,17 @@ void MixedBilinearForm::ConformingAssemble()
 
 void MixedBilinearForm::ComputeElementMatrix(int i, DenseMatrix &elmat)
 {
-   if (dbfi.Size())
+   if (domain_integs.Size())
    {
       const FiniteElement &trial_fe = *trial_fes->GetFE(i);
       const FiniteElement &test_fe = *test_fes->GetFE(i);
       ElementTransformation *eltrans = test_fes->GetElementTransformation(i);
-      dbfi[0]->AssembleElementMatrix2(trial_fe, test_fe, *eltrans, elmat);
-      for (int k = 1; k < dbfi.Size(); k++)
+      domain_integs[0]->AssembleElementMatrix2(trial_fe, test_fe, *eltrans,
+                                               elmat);
+      for (int k = 1; k < domain_integs.Size(); k++)
       {
-         dbfi[k]->AssembleElementMatrix2(trial_fe, test_fe, *eltrans, elemmat);
+         domain_integs[k]->AssembleElementMatrix2(trial_fe, test_fe, *eltrans,
+                                                  elemmat);
          elmat += elemmat;
       }
    }
@@ -1580,15 +1594,17 @@ void MixedBilinearForm::ComputeElementMatrix(int i, DenseMatrix &elmat)
 
 void MixedBilinearForm::ComputeBdrElementMatrix(int i, DenseMatrix &elmat)
 {
-   if (bbfi.Size())
+   if (boundary_integs.Size())
    {
       const FiniteElement &trial_be = *trial_fes->GetBE(i);
       const FiniteElement &test_be = *test_fes->GetBE(i);
       ElementTransformation *eltrans = test_fes->GetBdrElementTransformation(i);
-      bbfi[0]->AssembleElementMatrix2(trial_be, test_be, *eltrans, elmat);
-      for (int k = 1; k < bbfi.Size(); k++)
+      boundary_integs[0]->AssembleElementMatrix2(trial_be, test_be, *eltrans,
+                                                 elmat);
+      for (int k = 1; k < boundary_integs.Size(); k++)
       {
-         bbfi[k]->AssembleElementMatrix2(trial_be, test_be, *eltrans, elemmat);
+         boundary_integs[k]->AssembleElementMatrix2(trial_be, test_be, *eltrans,
+                                                    elemmat);
          elmat += elemmat;
       }
    }
@@ -1688,10 +1704,10 @@ void MixedBilinearForm::EliminateTestDofs (const Array<int> &bdr_attr_is_ess)
       }
 }
 
-void MixedBilinearForm::FormRectangularSystemMatrix(const Array<int>
-                                                    &trial_tdof_list,
-                                                    const Array<int> &test_tdof_list,
-                                                    OperatorHandle &A)
+void MixedBilinearForm::FormRectangularSystemMatrix(
+   const Array<int> &trial_tdof_list,
+   const Array<int> &test_tdof_list,
+   OperatorHandle &A)
 
 {
    if (ext)
@@ -1729,17 +1745,17 @@ void MixedBilinearForm::FormRectangularSystemMatrix(const Array<int>
    A.Reset(mat, false);
 }
 
-void MixedBilinearForm::FormRectangularLinearSystem(const Array<int>
-                                                    &trial_tdof_list,
-                                                    const Array<int> &test_tdof_list,
-                                                    Vector &x, Vector &b,
-                                                    OperatorHandle &A,
-                                                    Vector &X, Vector &B)
+void MixedBilinearForm::FormRectangularLinearSystem(
+   const Array<int> &trial_tdof_list,
+   const Array<int> &test_tdof_list,
+   Vector &x, Vector &b,
+   OperatorHandle &A,
+   Vector &X, Vector &B)
 {
    if (ext)
    {
-      ext->FormRectangularLinearSystem(trial_tdof_list, test_tdof_list, x, b, A, X,
-                                       B);
+      ext->FormRectangularLinearSystem(trial_tdof_list, test_tdof_list,
+                                       x, b, A, X, B);
       return;
    }
 
@@ -1777,10 +1793,13 @@ MixedBilinearForm::~MixedBilinearForm()
    if (!extern_bfs)
    {
       int i;
-      for (i = 0; i < dbfi.Size(); i++) { delete dbfi[i]; }
-      for (i = 0; i < bbfi.Size(); i++) { delete bbfi[i]; }
-      for (i = 0; i < tfbfi.Size(); i++) { delete tfbfi[i]; }
-      for (i = 0; i < btfbfi.Size(); i++) { delete btfbfi[i]; }
+      for (i = 0; i < domain_integs.Size(); i++) { delete domain_integs[i]; }
+      for (i = 0; i < boundary_integs.Size(); i++)
+      { delete boundary_integs[i]; }
+      for (i = 0; i < trace_face_integs.Size(); i++)
+      { delete trace_face_integs[i]; }
+      for (i = 0; i < boundary_trace_face_integs.Size(); i++)
+      { delete boundary_trace_face_integs[i]; }
    }
    delete ext;
 }
@@ -1830,7 +1849,7 @@ void DiscreteLinearOperator::Assemble(int skip_zeros)
       mat = new SparseMatrix(height, width);
    }
 
-   if (dbfi.Size() > 0)
+   if (domain_integs.Size() > 0)
    {
       for (int i = 0; i < test_fes->GetNE(); i++)
       {
@@ -1840,17 +1859,19 @@ void DiscreteLinearOperator::Assemble(int skip_zeros)
          dom_fe = trial_fes->GetFE(i);
          ran_fe = test_fes->GetFE(i);
 
-         dbfi[0]->AssembleElementMatrix2(*dom_fe, *ran_fe, *T, totelmat);
-         for (int j = 1; j < dbfi.Size(); j++)
+         domain_integs[0]->AssembleElementMatrix2(*dom_fe, *ran_fe, *T,
+                                                  totelmat);
+         for (int j = 1; j < domain_integs.Size(); j++)
          {
-            dbfi[j]->AssembleElementMatrix2(*dom_fe, *ran_fe, *T, elmat);
+            domain_integs[j]->AssembleElementMatrix2(*dom_fe, *ran_fe, *T,
+                                                     elmat);
             totelmat += elmat;
          }
          mat->SetSubMatrix(ran_vdofs, dom_vdofs, totelmat, skip_zeros);
       }
    }
 
-   if (tfbfi.Size())
+   if (trace_face_integs.Size())
    {
       const int nfaces = test_fes->GetMesh()->GetNumFaces();
       for (int i = 0; i < nfaces; i++)
@@ -1861,10 +1882,12 @@ void DiscreteLinearOperator::Assemble(int skip_zeros)
          dom_fe = trial_fes->GetFaceElement(i);
          ran_fe = test_fes->GetFaceElement(i);
 
-         tfbfi[0]->AssembleElementMatrix2(*dom_fe, *ran_fe, *T, totelmat);
-         for (int j = 1; j < tfbfi.Size(); j++)
+         trace_face_integs[0]->AssembleElementMatrix2(*dom_fe, *ran_fe, *T,
+                                                      totelmat);
+         for (int j = 1; j < trace_face_integs.Size(); j++)
          {
-            tfbfi[j]->AssembleElementMatrix2(*dom_fe, *ran_fe, *T, elmat);
+            trace_face_integs[j]->AssembleElementMatrix2(*dom_fe, *ran_fe, *T,
+                                                         elmat);
             totelmat += elmat;
          }
          mat->SetSubMatrix(ran_vdofs, dom_vdofs, totelmat, skip_zeros);

fem/bilinearform.hpp

@@ -84,28 +84,29 @@ protected:
        the BilinearForm. */
    long sequence;
 
-   /** @brief Indicates the BilinearFormIntegrator%s stored in #dbfi, #bbfi,
-       #fbfi, and #bfbfi are owned by another BilinearForm. */
+   /** @brief Indicates the BilinearFormIntegrator%s stored in #domain_integs,
+       #boundary_integs, #interior_face_integs, and #boundary_face_integs are
+       owned by another BilinearForm. */
    int extern_bfs;
 
    /// Set of Domain Integrators to be applied.
-   Array<BilinearFormIntegrator*> dbfi;
+   Array<BilinearFormIntegrator*> domain_integs;
    /// Element attribute marker (should be of length mesh->attributes)
    /// Includes all by default.
    /// 0 - ignore attribute
    /// 1 - include attribute
-   Array<Array<int>*>             dbfi_marker;
+   Array<Array<int>*>             domain_integs_marker;
 
    /// Set of Boundary Integrators to be applied.
-   Array<BilinearFormIntegrator*> bbfi;
-   Array<Array<int>*>             bbfi_marker; ///< Entries are not owned.
+   Array<BilinearFormIntegrator*> boundary_integs;
+   Array<Array<int>*> boundary_integs_marker; ///< Entries are not owned.
 
    /// Set of interior face Integrators to be applied.
-   Array<BilinearFormIntegrator*> fbfi;
+   Array<BilinearFormIntegrator*> interior_face_integs;
 
    /// Set of boundary face Integrators to be applied.
-   Array<BilinearFormIntegrator*> bfbfi;
-   Array<Array<int>*>             bfbfi_marker; ///< Entries are not owned.
+   Array<BilinearFormIntegrator*> boundary_face_integs;
+   Array<Array<int>*> boundary_face_integs_marker; ///< Entries are not owned.
 
    DenseMatrix elemmat;
    Array<int>  vdofs;
@@ -231,24 +232,25 @@ public:
    void AllocateMatrix() { if (mat == NULL) { AllocMat(); } }
 
    /// Access all the integrators added with AddDomainIntegrator().
-   Array<BilinearFormIntegrator*> *GetDBFI() { return &dbfi; }
+   Array<BilinearFormIntegrator*> *GetDBFI() { return &domain_integs; }
 
    /// Access all the integrators added with AddBoundaryIntegrator().
-   Array<BilinearFormIntegrator*> *GetBBFI() { return &bbfi; }
+   Array<BilinearFormIntegrator*> *GetBBFI() { return &boundary_integs; }
    /** @brief Access all boundary markers added with AddBoundaryIntegrator().
        If no marker was specified when the integrator was added, the
        corresponding pointer (to Array<int>) will be NULL. */
-   Array<Array<int>*> *GetBBFI_Marker() { return &bbfi_marker; }
+   Array<Array<int>*> *GetBBFI_Marker() { return &boundary_integs_marker; }
 
    /// Access all integrators added with AddInteriorFaceIntegrator().
-   Array<BilinearFormIntegrator*> *GetFBFI() { return &fbfi; }
+   Array<BilinearFormIntegrator*> *GetFBFI() { return &interior_face_integs; }
 
    /// Access all integrators added with AddBdrFaceIntegrator().
-   Array<BilinearFormIntegrator*> *GetBFBFI() { return &bfbfi; }
+   Array<BilinearFormIntegrator*> *GetBFBFI() { return &boundary_face_integs; }
    /** @brief Access all boundary markers added with AddBdrFaceIntegrator().
        If no marker was specified when the integrator was added, the
        corresponding pointer (to Array<int>) will be NULL. */
-   Array<Array<int>*> *GetBFBFI_Marker() { return &bfbfi_marker; }
+   Array<Array<int>*> *GetBFBFI_Marker()
+   { return &boundary_face_integs_marker; }
 
    /// Returns a reference to: \f$ M_{ij} \f$
    const double &operator()(int i, int j) { return (*mat)(i,j); }
@@ -652,23 +654,25 @@ protected:
        Partial Assembly (PA), or Matrix Free assembly (MF). */
    MixedBilinearFormExtension *ext;
 
-   /** @brief Indicates the BilinearFormIntegrator%s stored in #dbfi, #bbfi,
-       #tfbfi and #btfbfi are owned by another MixedBilinearForm. */
+   /** @brief Indicates the BilinearFormIntegrator%s stored in #domain_integs,
+       #boundary_integs, #trace_face_integs and #boundary_trace_face_integs
+       are owned by another MixedBilinearForm. */
    int extern_bfs;
 
    /// Domain integrators.
-   Array<BilinearFormIntegrator*> dbfi;
+   Array<BilinearFormIntegrator*> domain_integs;
 
    /// Boundary integrators.
-   Array<BilinearFormIntegrator*> bbfi;
-   Array<Array<int>*>             bbfi_marker;///< Entries are not owned.
+   Array<BilinearFormIntegrator*> boundary_integs;
+   Array<Array<int>*> boundary_integs_marker; ///< Entries are not owned.
 
    /// Trace face (skeleton) integrators.
-   Array<BilinearFormIntegrator*> tfbfi;
+   Array<BilinearFormIntegrator*> trace_face_integs;
 
    /// Boundary trace face (skeleton) integrators.
-   Array<BilinearFormIntegrator*> btfbfi;
-   Array<Array<int>*>             btfbfi_marker;///< Entries are not owned.
+   Array<BilinearFormIntegrator*> boundary_trace_face_integs;
+   /// Entries are not owned.
+   Array<Array<int>*> boundary_trace_face_integs_marker;
 
    DenseMatrix elemmat;
    Array<int>  trial_vdofs, test_vdofs;
@@ -762,24 +766,26 @@ public:
                                    Array<int> &bdr_marker);
 
    /// Access all integrators added with AddDomainIntegrator().
-   Array<BilinearFormIntegrator*> *GetDBFI() { return &dbfi; }
+   Array<BilinearFormIntegrator*> *GetDBFI() { return &domain_integs; }
 
    /// Access all integrators added with AddBoundaryIntegrator().
-   Array<BilinearFormIntegrator*> *GetBBFI() { return &bbfi; }
+   Array<BilinearFormIntegrator*> *GetBBFI() { return &boundary_integs; }
    /** @brief Access all boundary markers added with AddBoundaryIntegrator().
        If no marker was specified when the integrator was added, the
        corresponding pointer (to Array<int>) will be NULL. */
-   Array<Array<int>*> *GetBBFI_Marker() { return &bbfi_marker; }
+   Array<Array<int>*> *GetBBFI_Marker() { return &boundary_integs_marker; }
 
    /// Access all integrators added with AddTraceFaceIntegrator().
-   Array<BilinearFormIntegrator*> *GetTFBFI() { return &tfbfi; }
+   Array<BilinearFormIntegrator*> *GetTFBFI() { return &trace_face_integs; }
 
    /// Access all integrators added with AddBdrTraceFaceIntegrator().
-   Array<BilinearFormIntegrator*> *GetBTFBFI() { return &btfbfi; }
+   Array<BilinearFormIntegrator*> *GetBTFBFI()
+   { return &boundary_trace_face_integs; }
    /** @brief Access all boundary markers added with AddBdrTraceFaceIntegrator().
        If no marker was specified when the integrator was added, the
        corresponding pointer (to Array<int>) will be NULL. */
-   Array<Array<int>*> *GetBTFBFI_Marker() { return &btfbfi_marker; }
+   Array<Array<int>*> *GetBTFBFI_Marker()
+   { return &boundary_trace_face_integs_marker; }
 
    /// Sets all sparse values of \f$ M \f$ to @a a.
    void operator=(const double a) { *mat = a; }
@@ -1004,7 +1010,7 @@ public:
    { AddTraceFaceIntegrator(di); }
 
    /// Access all interpolators added with AddDomainInterpolator().
-   Array<BilinearFormIntegrator*> *GetDI() { return &dbfi; }
+   Array<BilinearFormIntegrator*> *GetDI() { return &domain_integs; }
 
    /// Set the desired assembly level. The default is AssemblyLevel::FULL.
    /** This method must be called before assembly. */

fem/bilinearform_ext.cpp

@@ -160,7 +160,7 @@ void MFBilinearFormExtension::Mult(const Vector &x, Vector &y) const
          {
             intFaceIntegrators[i]->AddMultMF(faceIntX, faceIntY);
          }
-         int_face_restrict_lex->MultTranspose(faceIntY, y);
+         int_face_restrict_lex->AddMultTranspose(faceIntY, y);
       }
    }
 
@@ -176,7 +176,7 @@ void MFBilinearFormExtension::Mult(const Vector &x, Vector &y) const
          {
             bdrFaceIntegrators[i]->AddMultMF(faceBdrX, faceBdrY);
          }
-         bdr_face_restrict_lex->MultTranspose(faceBdrY, y);
+         bdr_face_restrict_lex->AddMultTranspose(faceBdrY, y);
       }
    }
 }
@@ -217,7 +217,7 @@ void MFBilinearFormExtension::MultTranspose(const Vector &x, Vector &y) const
          {
             intFaceIntegrators[i]->AddMultTransposeMF(faceIntX, faceIntY);
          }
-         int_face_restrict_lex->MultTranspose(faceIntY, y);
+         int_face_restrict_lex->AddMultTranspose(faceIntY, y);
       }
    }
 
@@ -233,7 +233,7 @@ void MFBilinearFormExtension::MultTranspose(const Vector &x, Vector &y) const
          {
             bdrFaceIntegrators[i]->AddMultTransposeMF(faceBdrX, faceBdrY);
          }
-         bdr_face_restrict_lex->MultTranspose(faceBdrY, y);
+         bdr_face_restrict_lex->AddMultTranspose(faceBdrY, y);
       }
    }
 }
@@ -417,7 +417,7 @@ void PABilinearFormExtension::Mult(const Vector &x, Vector &y) const
          {
             intFaceIntegrators[i]->AddMultPA(faceIntX, faceIntY);
          }
-         int_face_restrict_lex->MultTranspose(faceIntY, y);
+         int_face_restrict_lex->AddMultTranspose(faceIntY, y);
       }
    }
 
@@ -433,7 +433,7 @@ void PABilinearFormExtension::Mult(const Vector &x, Vector &y) const
          {
             bdrFaceIntegrators[i]->AddMultPA(faceBdrX, faceBdrY);
          }
-         bdr_face_restrict_lex->MultTranspose(faceBdrY, y);
+         bdr_face_restrict_lex->AddMultTranspose(faceBdrY, y);
       }
    }
 }
@@ -474,7 +474,7 @@ void PABilinearFormExtension::MultTranspose(const Vector &x, Vector &y) const
          {
             intFaceIntegrators[i]->AddMultTransposePA(faceIntX, faceIntY);
          }
-         int_face_restrict_lex->MultTranspose(faceIntY, y);
+         int_face_restrict_lex->AddMultTranspose(faceIntY, y);
       }
    }
 
@@ -490,7 +490,7 @@ void PABilinearFormExtension::MultTranspose(const Vector &x, Vector &y) const
          {
             bdrFaceIntegrators[i]->AddMultTransposePA(faceBdrX, faceBdrY);
          }
-         bdr_face_restrict_lex->MultTranspose(faceBdrY, y);
+         bdr_face_restrict_lex->AddMultTranspose(faceBdrY, y);
       }
    }
 }
@@ -657,7 +657,7 @@ void EABilinearFormExtension::Mult(const Vector &x, Vector &y) const
             Y(j, 0, f) += res;
          });
          // Apply the Interior Face Restriction transposed
-         int_face_restrict_lex->MultTranspose(faceIntY, y);
+         int_face_restrict_lex->AddMultTranspose(faceIntY, y);
       }
    }
 
@@ -688,7 +688,7 @@ void EABilinearFormExtension::Mult(const Vector &x, Vector &y) const
             Y(j, f) += res;
          });
          // Apply the Boundary Face Restriction transposed
-         bdr_face_restrict_lex->MultTranspose(faceBdrY, y);
+         bdr_face_restrict_lex->AddMultTranspose(faceBdrY, y);
       }
    }
 }
@@ -783,7 +783,7 @@ void EABilinearFormExtension::MultTranspose(const Vector &x, Vector &y) const
             Y(j, 0, f) += res;
          });
          // Apply the Interior Face Restriction transposed
-         int_face_restrict_lex->MultTranspose(faceIntY, y);
+         int_face_restrict_lex->AddMultTranspose(faceIntY, y);
       }
    }
 
@@ -814,7 +814,7 @@ void EABilinearFormExtension::MultTranspose(const Vector &x, Vector &y) const
             Y(j, f) += res;
          });
          // Apply the Boundary Face Restriction transposed
-         bdr_face_restrict_lex->MultTranspose(faceBdrY, y);
+         bdr_face_restrict_lex->AddMultTranspose(faceBdrY, y);
       }
    }
 }

fem/bilinearform_ext.hpp

@@ -72,8 +72,8 @@ protected:
    mutable Vector faceIntX, faceIntY;
    mutable Vector faceBdrX, faceBdrY;
    const Operator *elem_restrict; // Not owned
-   const Operator *int_face_restrict_lex; // Not owned
-   const Operator *bdr_face_restrict_lex; // Not owned
+   const FaceRestriction *int_face_restrict_lex; // Not owned
+   const FaceRestriction *bdr_face_restrict_lex; // Not owned
 
 public:
    PABilinearFormExtension(BilinearForm*);
@@ -143,8 +143,8 @@ protected:
    mutable Vector faceIntX, faceIntY;
    mutable Vector faceBdrX, faceBdrY;
    const Operator *elem_restrict; // Not owned
-   const Operator *int_face_restrict_lex; // Not owned
-   const Operator *bdr_face_restrict_lex; // Not owned
+   const FaceRestriction *int_face_restrict_lex; // Not owned
+   const FaceRestriction *bdr_face_restrict_lex; // Not owned
 
 public:
    MFBilinearFormExtension(BilinearForm *form);

fem/bilininteg.cpp

@@ -175,6 +175,11 @@ void BilinearFormIntegrator::AssembleFaceVector(
    elmat.Mult(elfun, elvect);
 }
 
+void TransposeIntegrator::SetIntRule(const IntegrationRule *ir)
+{
+   IntRule = ir;
+   bfi->SetIntRule(ir);
+}
 
 void TransposeIntegrator::AssembleElementMatrix (
    const FiniteElement &el, ElementTransformation &Trans, DenseMatrix &elmat)
@@ -202,6 +207,12 @@ void TransposeIntegrator::AssembleFaceMatrix (
    elmat.Transpose (bfi_elmat);
 }
 
+void LumpedIntegrator::SetIntRule(const IntegrationRule *ir)
+{
+   IntRule = ir;
+   bfi->SetIntRule(ir);
+}
+
 void LumpedIntegrator::AssembleElementMatrix (
    const FiniteElement &el, ElementTransformation &Trans, DenseMatrix &elmat)
 {
@@ -209,6 +220,12 @@ void LumpedIntegrator::AssembleElementMatrix (
    elmat.Lump();
 }
 
+void InverseIntegrator::SetIntRule(const IntegrationRule *ir)
+{
+   IntRule = ir;
+   integrator->SetIntRule(ir);
+}
+
 void InverseIntegrator::AssembleElementMatrix(
    const FiniteElement &el, ElementTransformation &Trans, DenseMatrix &elmat)
 {
@@ -216,6 +233,15 @@ void InverseIntegrator::AssembleElementMatrix(
    elmat.Invert();
 }
 
+void SumIntegrator::SetIntRule(const IntegrationRule *ir)
+{
+   IntRule = ir;
+   for (int i = 0; i < integrators.Size(); i++)
+   {
+      integrators[i]->SetIntRule(ir);
+   }
+}
+
 void SumIntegrator::AssembleElementMatrix(
    const FiniteElement &el, ElementTransformation &Trans, DenseMatrix &elmat)
 {
@@ -1751,15 +1777,16 @@ void DerivativeIntegrator::AssembleElementMatrix2 (
    int dim = trial_fe.GetDim();
    int trial_nd = trial_fe.GetDof();
    int test_nd = test_fe.GetDof();
+   int spaceDim = Trans.GetSpaceDim();
 
    int i, l;
    double det;
 
    elmat.SetSize (test_nd,trial_nd);
    dshape.SetSize (trial_nd,dim);
-   dshapedxt.SetSize(trial_nd,dim);
+   dshapedxt.SetSize(trial_nd, spaceDim);
    dshapedxi.SetSize(trial_nd);
-   invdfdx.SetSize(dim);
+   invdfdx.SetSize(dim, spaceDim);
    shape.SetSize (test_nd);
 
    const IntegrationRule *ir = IntRule;

fem/bilininteg.hpp

@@ -261,6 +261,8 @@ public:
    TransposeIntegrator (BilinearFormIntegrator *bfi_, int own_bfi_ = 1)
    { bfi = bfi_; own_bfi = own_bfi_; }
 
+   virtual void SetIntRule(const IntegrationRule *ir);
+
    virtual void AssembleElementMatrix(const FiniteElement &el,
                                       ElementTransformation &Trans,
                                       DenseMatrix &elmat);
@@ -328,6 +330,8 @@ public:
    LumpedIntegrator (BilinearFormIntegrator *bfi_, int own_bfi_ = 1)
    { bfi = bfi_; own_bfi = own_bfi_; }
 
+   virtual void SetIntRule(const IntegrationRule *ir);
+
    virtual void AssembleElementMatrix(const FiniteElement &el,
                                       ElementTransformation &Trans,
                                       DenseMatrix &elmat);
@@ -346,6 +350,8 @@ public:
    InverseIntegrator(BilinearFormIntegrator *integ, int own_integ = 1)
    { integrator = integ; own_integrator = own_integ; }
 
+   virtual void SetIntRule(const IntegrationRule *ir);
+
    virtual void AssembleElementMatrix(const FiniteElement &el,
                                       ElementTransformation &Trans,
                                       DenseMatrix &elmat);
@@ -364,6 +370,8 @@ private:
 public:
    SumIntegrator(int own_integs = 1) { own_integrators = own_integs; }
 
+   virtual void SetIntRule(const IntegrationRule *ir);
+
    void AddIntegrator(BilinearFormIntegrator *integ)
    { integrators.Append(integ); }
 

fem/ceed/algebraic.cpp

@@ -143,7 +143,7 @@ Solver *BuildSmootherFromCeed(ConstrainedOperator &op, bool chebyshev)
    if (chebyshev)
    {
       const int cheb_order = 3;
-      out = new OperatorChebyshevSmoother(&op, t_diag, ess_tdofs, cheb_order);
+      out = new OperatorChebyshevSmoother(op, t_diag, ess_tdofs, cheb_order);
    }
    else
    {

fem/coefficient.cpp

@@ -629,27 +629,6 @@ void MatrixVectorProductCoefficient::Eval(Vector &V, ElementTransformation &T,
    ma.Mult(vb, V);
 }
 
-
-MatrixMatrixProductCoefficient::MatrixMatrixProductCoefficient(MatrixCoefficient &A,
-                                           MatrixCoefficient &B)
-   : MatrixCoefficient(A.GetHeight(), A.GetWidth()),
-     a(&A), b(&B),
-     ma(A.GetHeight(), A.GetWidth()), 
-     mb(B.GetHeight(), B.GetWidth())
-{
-   MFEM_ASSERT(A.GetWidth() == B.GetHeight(),
-               "MatrixMatrixProductCoefficient:  "
-               "Arguments must have the same dimensions.");
-}
-
-void MatrixMatrixProductCoefficient::Eval(DenseMatrix &M, ElementTransformation &T,
-                                          const IntegrationPoint &ip)
-{
-   a->Eval(ma, T, ip);
-   b->Eval(mb, T, ip);
-   Mult(ma, mb, M);
-}
-
 void IdentityMatrixCoefficient::Eval(DenseMatrix &M, ElementTransformation &T,
                                      const IntegrationPoint &ip)
 {

fem/coefficient.hpp

@@ -1470,42 +1470,6 @@ public:
                      const IntegrationPoint &ip);
 };
 
-/** @brief Matrix coefficient defined as a product of two 
-    matrix coefficients */
-class MatrixMatrixProductCoefficient : public MatrixCoefficient
-{
-private:
-   MatrixCoefficient * a;
-   MatrixCoefficient * b;
-
-   mutable DenseMatrix ma;
-   mutable DenseMatrix mb;
-
-public:
-   /// Constructor with two coefficients.  Result is A*B.
-   MatrixMatrixProductCoefficient(MatrixCoefficient &A, MatrixCoefficient &B);
-
-   /// Reset the matrix coefficient
-   void SetACoef(MatrixCoefficient &A) { a = &A; }
-   /// Return the matrix coefficient
-   MatrixCoefficient * GetACoef() const { return a; }
-
-   /// Reset the vector coefficient
-   void SetBCoef(MatrixCoefficient &B) { b = &B; }
-   /// Return the vector coefficient
-   MatrixCoefficient * GetBCoef() const { return b; }
-
-   /// Evaluate the vector coefficient at @a ip.
-   virtual void Eval(DenseMatrix &M, ElementTransformation &T,
-                     const IntegrationPoint &ip);
-};
-
-/// Convenient alias for the MatrixVectorProductCoefficient
-typedef MatrixMatrixProductCoefficient MatMatCoefficient;
-
-
-
-
 /// Matrix coefficient defined as the linear combination of two matrices
 class MatrixSumCoefficient : public MatrixCoefficient
 {

fem/datacollection.cpp

@@ -17,6 +17,7 @@
 
 #include <cerrno>      // errno
 #include <sstream>
+#include <regex>
 
 #ifndef _WIN32
 #include <sys/stat.h>  // mkdir
@@ -764,7 +765,8 @@ ParaViewDataCollection::ParaViewDataCollection(const std::string&
    : DataCollection(collection_name, mesh_),
      levels_of_detail(1),
      pv_data_format(VTKFormat::BINARY),
-     high_order_output(false)
+     high_order_output(false),
+     restart_mode(false)
 {
 #ifdef MFEM_USE_ZLIB
    compression = -1; // default zlib compression level, equivalent to 6
@@ -842,17 +844,60 @@ void ParaViewDataCollection::Save()
    }
    // the directory is created
 
-   // create pvd file if needed
+   // create pvd file if needed. If we are not in restart mode, a new pvd file
+   // is always created. In restart mode, we keep any previously defined
+   // timestep values as long as they are less than the currently defined time.
+
    if (myid == 0 && !pvd_stream.is_open())
    {
       std::string dpath=GenerateCollectionPath();
       std::string pvdname=dpath+"/"+GeneratePVDFileName();
-      pvd_stream.open(pvdname.c_str(),std::ios::out);
-      // initialize the file
-      pvd_stream << "<?xml version=\"1.0\"?>\n";
-      pvd_stream << "<VTKFile type=\"Collection\" version=\"0.1\"";
-      pvd_stream << " byte_order=\"" << VTKByteOrder() << "\">\n";
-      pvd_stream << "<Collection>" << std::endl;
+
+      std::ifstream pvd_in;
+      if (restart_mode && (pvd_in.open(pvdname,std::ios::binary),pvd_in.good()))
+      {
+         // PVD file exists and restart mode enabled: preserve existing time
+         // steps less than the current time.
+         std::fstream::pos_type pos_begin = pvd_in.tellg();
+         std::fstream::pos_type pos_end = pos_begin;
+
+         std::regex regexp("timestep=\"([^[:space:]]+)\".*file=\"Cycle(\\d+)");
+         std::smatch match;
+
+         std::string line;
+         while (getline(pvd_in,line))
+         {
+            if (regex_search(line,match,regexp))
+            {
+               MFEM_ASSERT(match.size() == 3, "Unable to parse DataSet");
+               double tvalue = std::stod(match[1]);
+               if (tvalue >= GetTime()) { break; }
+               int cvalue = std::stoi(match[2]);
+               MFEM_VERIFY(cvalue < GetCycle(), "Cycle " << GetCycle() <<
+                           " is too small for restart mode: trying to overwrite"
+                           " existing data.");
+               pos_end = pvd_in.tellg();
+            }
+         }
+         size_t count = pos_end - pos_begin;
+         std::vector<char> buf(count);
+         pvd_in.clear();
+         pvd_in.seekg(pos_begin);
+         pvd_in.read(buf.data(), count);
+         pvd_in.close();
+         pvd_stream.open(pvdname.c_str(),std::ios::out);
+         pvd_stream.write(buf.data(), count);
+      }
+      else
+      {
+         // initialize new pvd file
+         pvd_stream.open(pvdname.c_str(),std::ios::out);
+         // initialize the file
+         pvd_stream << "<?xml version=\"1.0\"?>\n";
+         pvd_stream << "<VTKFile type=\"Collection\" version=\"0.1\"";
+         pvd_stream << " byte_order=\"" << VTKByteOrder() << "\">\n";
+         pvd_stream << "<Collection>" << std::endl;
+      }
    }
 
    // define the vtu file
@@ -1091,6 +1136,11 @@ void ParaViewDataCollection::SetCompression(bool compression_)
    }
 }
 
+void ParaViewDataCollection::UseRestartMode(bool restart_mode_)
+{
+   restart_mode = restart_mode_;
+}
+
 const char *ParaViewDataCollection::GetDataFormatString() const
 {
    if (pv_data_format == VTKFormat::ASCII)

fem/datacollection.hpp

@@ -488,6 +488,7 @@ private:
    std::fstream pvd_stream;
    VTKFormat pv_data_format;
    bool high_order_output;
+   bool restart_mode;
 
 protected:
    void SaveDataVTU(std::ostream &out, int ref);
@@ -545,6 +546,11 @@ public:
    /// by default). Reading high-order data requires ParaView 5.5 or later.
    void SetHighOrderOutput(bool high_order_output_);
 
+   /// Enable or disable restart mode. If restart is enabled, new writes will
+   /// preserve timestep metadata for any solutions prior to the currently
+   /// defined time.
+   void UseRestartMode(bool restart_mode_);
+
    /// Load the collection - not implemented in the ParaView writer
    virtual void Load(int cycle_ = 0) override;
 };

fem/fe.cpp

@@ -7948,7 +7948,27 @@ VectorTensorFiniteElement::VectorTensorFiniteElement(const int dims,
                          p, M, FunctionSpace::Qk),
      TensorBasisElement(dims, p, VerifyNodal(cbtype), dmtype),
      cbasis1d(poly1d.GetBasis(p, VerifyClosed(cbtype))),
-     obasis1d(poly1d.GetBasis(p - 1, VerifyOpen(obtype))) { }
+     obasis1d(poly1d.GetBasis(p - 1, VerifyOpen(obtype)))
+{
+   MFEM_VERIFY(dims > 1, "Constructor for VectorTensorFiniteElement with both "
+               "open and closed bases is not valid for 1D elements.");
+}
+
+VectorTensorFiniteElement::VectorTensorFiniteElement(const int dims,
+                                                     const int d,
+                                                     const int p,
+                                                     const int obtype,
+                                                     const int M,
+                                                     const DofMapType dmtype)
+   : VectorFiniteElement(dims, GetTensorProductGeometry(dims), d,
+                         p, M, FunctionSpace::Pk),
+     TensorBasisElement(dims, p, obtype, dmtype),
+     cbasis1d(poly1d.GetBasis(p, VerifyOpen(obtype))),
+     obasis1d(poly1d.GetBasis(p, VerifyOpen(obtype)))
+{
+   MFEM_VERIFY(dims == 1, "Constructor for VectorTensorFiniteElement without "
+               "closed basis is only valid for 1D elements.");
+}
 
 H1_SegmentElement::H1_SegmentElement(const int p, const int btype)
    : NodalTensorFiniteElement(1, p, VerifyClosed(btype), H1_DOF_MAP)
@@ -13055,9 +13075,8 @@ void ND_TriangleElement::CalcCurlShape(const IntegrationPoint &ip,
 const double ND_SegmentElement::tk[1] = { 1. };
 
 ND_SegmentElement::ND_SegmentElement(const int p, const int ob_type)
-   : VectorFiniteElement(1, Geometry::SEGMENT, p, p - 1,
-                         H_CURL, FunctionSpace::Pk),
-     obasis1d(poly1d.GetBasis(p - 1, VerifyOpen(ob_type))),
+   : VectorTensorFiniteElement(1, p, p - 1, ob_type, H_CURL,
+                               DofMapType::L2_DOF_MAP),
      dof2tk(dof)
 {
    if (obasis1d.IsIntegratedType()) { is_nodal = false; }

fem/fe.hpp

@@ -2239,6 +2239,11 @@ public:
                              const int cbtype, const int obtype,
                              const int M, const DofMapType dmtype);
 
+   // For 1D elements: there is only an "open basis", no "closed basis"
+   VectorTensorFiniteElement(const int dims, const int d, const int p,
+                             const int obtype, const int M,
+                             const DofMapType dmtype);
+
    const DofToQuad &GetDofToQuad(const IntegrationRule &ir,
                                  DofToQuad::Mode mode) const;
 
@@ -3311,11 +3316,9 @@ public:
 
 
 /// Arbitrary order Nedelec elements in 1D on a segment
-class ND_SegmentElement : public VectorFiniteElement
+class ND_SegmentElement : public VectorTensorFiniteElement
 {
    static const double tk[1];
-
-   Poly_1D::Basis &obasis1d;
    Array<int> dof2tk;
 
 public:

fem/fespace.cpp

@@ -1225,7 +1225,7 @@ const Operator *FiniteElementSpace::GetElementRestriction(
    return L2E_nat.Ptr();
 }
 
-const Operator *FiniteElementSpace::GetFaceRestriction(
+const FaceRestriction *FiniteElementSpace::GetFaceRestriction(
    ElementDofOrdering e_ordering, FaceType type, L2FaceValues mul) const
 {
    const bool is_dg_space = IsDGSpace();
@@ -1239,7 +1239,7 @@ const Operator *FiniteElementSpace::GetFaceRestriction(
    }
    else
    {
-      Operator* res;
+      FaceRestriction *res;
       if (is_dg_space)
       {
          res = new L2FaceRestriction(*this, e_ordering, type, m);

fem/fespace.hpp

@@ -164,7 +164,7 @@ protected:
                 + 8 * (int)std::get<3>(k);
       }
    };
-   using map_L2F = std::unordered_map<const key_face,Operator*,key_hash>;
+   using map_L2F = std::unordered_map<const key_face,FaceRestriction*,key_hash>;
    mutable map_L2F L2F;
 
    mutable Array<QuadratureInterpolator*> E2Q_array;
@@ -488,7 +488,7 @@ public:
    const Operator *GetElementRestriction(ElementDofOrdering e_ordering) const;
 
    /// Return an Operator that converts L-vectors to E-vectors on each face.
-   virtual const Operator *GetFaceRestriction(
+   virtual const FaceRestriction *GetFaceRestriction(
       ElementDofOrdering e_ordering, FaceType,
       L2FaceValues mul = L2FaceValues::DoubleValued) const;
 

fem/intrules.cpp

@@ -34,6 +34,7 @@ IntegrationRule::IntegrationRule(IntegrationRule &irx, IntegrationRule &iry)
    nx = irx.GetNPoints();
    ny = iry.GetNPoints();
    SetSize(nx * ny);
+   SetPointIndices();
 
    for (j = 0; j < ny; j++)
    {
@@ -48,8 +49,6 @@ IntegrationRule::IntegrationRule(IntegrationRule &irx, IntegrationRule &iry)
          ip.weight = ipx.weight * ipy.weight;
       }
    }
-
-   SetPointIndices();
 }
 
 IntegrationRule::IntegrationRule(IntegrationRule &irx, IntegrationRule &iry,
@@ -59,6 +58,7 @@ IntegrationRule::IntegrationRule(IntegrationRule &irx, IntegrationRule &iry,
    const int ny = iry.GetNPoints();
    const int nz = irz.GetNPoints();
    SetSize(nx*ny*nz);
+   SetPointIndices();
 
    for (int iz = 0; iz < nz; ++iz)
    {
@@ -78,8 +78,6 @@ IntegrationRule::IntegrationRule(IntegrationRule &irx, IntegrationRule &iry,
          }
       }
    }
-
-   SetPointIndices();
 }
 
 const Array<double> &IntegrationRule::GetWeights() const
@@ -125,6 +123,7 @@ void IntegrationRule::GrundmannMollerSimplexRule(int s, int n)
    }
    np /= f;
    SetSize(np);
+   SetPointIndices();
 
    int pt = 0;
    for (int i = 0; i <= s; i++)
@@ -375,6 +374,7 @@ public:
 void QuadratureFunctions1D::GaussLegendre(const int np, IntegrationRule* ir)
 {
    ir->SetSize(np);
+   ir->SetPointIndices();
 
    switch (np)
    {
@@ -477,6 +477,7 @@ void QuadratureFunctions1D::GaussLobatto(const int np, IntegrationRule* ir)
    */
 
    ir->SetSize(np);
+   ir->SetPointIndices();
    if ( np == 1 )
    {
       ir->IntPoint(0).Set1w(0.5, 1.0);
@@ -576,6 +577,7 @@ void QuadratureFunctions1D::GaussLobatto(const int np, IntegrationRule* ir)
 void QuadratureFunctions1D::OpenUniform(const int np, IntegrationRule* ir)
 {
    ir->SetSize(np);
+   ir->SetPointIndices();
 
    // The Newton-Cotes quadrature is based on weights that integrate exactly the
    // interpolatory polynomial through the equally spaced quadrature points.
@@ -591,6 +593,7 @@ void QuadratureFunctions1D::ClosedUniform(const int np,
                                           IntegrationRule* ir)
 {
    ir->SetSize(np);
+   ir->SetPointIndices();
    if ( np == 1 ) // allow this case as "closed"
    {
       ir->IntPoint(0).Set1w(0.5, 1.0);
@@ -608,6 +611,7 @@ void QuadratureFunctions1D::ClosedUniform(const int np,
 void QuadratureFunctions1D::OpenHalfUniform(const int np, IntegrationRule* ir)
 {
    ir->SetSize(np);
+   ir->SetPointIndices();
 
    // Open half points: the centers of np uniform intervals
    for (int i = 0; i < np ; ++i)
@@ -621,6 +625,7 @@ void QuadratureFunctions1D::OpenHalfUniform(const int np, IntegrationRule* ir)
 void QuadratureFunctions1D::ClosedGL(const int np, IntegrationRule* ir)
 {
    ir->SetSize(np);
+   ir->SetPointIndices();
    ir->IntPoint(0).x = 0.0;
    ir->IntPoint(np-1).x = 1.0;
 

fem/intrules.hpp

@@ -96,9 +96,6 @@ private:
        by request with the method GetWeights(). */
    mutable Array<double> weights;
 
-   /// Sets the indices of each quadrature point on initialization.
-   void SetPointIndices();
-
    /// Define n-simplex rule (triangle/tetrahedron for n=2/3) of order (2s+1)
    void GrundmannMollerSimplexRule(int s, int n = 3);
 
@@ -227,6 +224,11 @@ public:
       }
    }
 
+   /// Sets the indices of each quadrature point on initialization.
+   /** Note that most calls to IntegrationRule::SetSize should be paired with a
+       call to SetPointIndices in order for the indices to be set correctly. */
+   void SetPointIndices();
+
    /// Tensor product of two 1D integration rules
    IntegrationRule(IntegrationRule &irx, IntegrationRule &iry);
 

fem/linearform.cpp

@@ -26,14 +26,14 @@ LinearForm::LinearForm(FiniteElementSpace *f, LinearForm *lf)
    extern_lfs = 1;
 
    // Copy the pointers to the integrators
-   dlfi = lf->dlfi;
+   domain_integs = lf->domain_integs;
 
-   dlfi_delta = lf->dlfi_delta;
+   domain_delta_integs = lf->domain_delta_integs;
 
-   blfi = lf->blfi;
+   boundary_integs = lf->boundary_integs;
 
-   flfi = lf->flfi;
-   flfi_marker = lf->flfi_marker;
+   boundary_face_integs = lf->boundary_face_integs;
+   boundary_face_integs_marker = lf->boundary_face_integs_marker;
 }
 
 void LinearForm::AddDomainIntegrator(LinearFormIntegrator *lfi)
@@ -42,13 +42,13 @@ void LinearForm::AddDomainIntegrator(LinearFormIntegrator *lfi)
       dynamic_cast<DeltaLFIntegrator *>(lfi);
    if (!maybe_delta || !maybe_delta->IsDelta())
    {
-      dlfi.Append(lfi);
+      domain_integs.Append(lfi);
    }
    else
    {
-      dlfi_delta.Append(maybe_delta);
+      domain_delta_integs.Append(maybe_delta);
    }
-   dlfi_marker.Append(NULL);
+   domain_integs_marker.Append(NULL);
 }
 
 void LinearForm::AddDomainIntegrator(LinearFormIntegrator *lfi,
@@ -58,44 +58,45 @@ void LinearForm::AddDomainIntegrator(LinearFormIntegrator *lfi,
       dynamic_cast<DeltaLFIntegrator *>(lfi);
    if (!maybe_delta || !maybe_delta->IsDelta())
    {
-      dlfi.Append(lfi);
+      domain_integs.Append(lfi);
    }
    else
    {
-      dlfi_delta.Append(maybe_delta);
+      domain_delta_integs.Append(maybe_delta);
    }
-   dlfi_marker.Append(&elem_marker);
+   domain_integs_marker.Append(&elem_marker);
 }
 
 void LinearForm::AddBoundaryIntegrator (LinearFormIntegrator * lfi)
 {
-   blfi.Append (lfi);
-   blfi_marker.Append(NULL); // NULL -> all attributes are active
+   boundary_integs.Append (lfi);
+   boundary_integs_marker.Append(NULL); // NULL -> all attributes are active
 }
 
 void LinearForm::AddBoundaryIntegrator (LinearFormIntegrator * lfi,
                                         Array<int> &bdr_attr_marker)
 {
-   blfi.Append (lfi);
-   blfi_marker.Append(&bdr_attr_marker);
+   boundary_integs.Append (lfi);
+   boundary_integs_marker.Append(&bdr_attr_marker);
 }
 
 void LinearForm::AddBdrFaceIntegrator (LinearFormIntegrator * lfi)
 {
-   flfi.Append(lfi);
-   flfi_marker.Append(NULL); // NULL -> all attributes are active
+   boundary_face_integs.Append(lfi);
+   // NULL -> all attributes are active
+   boundary_face_integs_marker.Append(NULL);
 }
 
 void LinearForm::AddBdrFaceIntegrator(LinearFormIntegrator *lfi,
                                       Array<int> &bdr_attr_marker)
 {
-   flfi.Append(lfi);
-   flfi_marker.Append(&bdr_attr_marker);
+   boundary_face_integs.Append(lfi);
+   boundary_face_integs_marker.Append(&bdr_attr_marker);
 }
 
 void LinearForm::AddInteriorFaceIntegrator(LinearFormIntegrator *lfi)
 {
-   iflfi.Append(lfi);
+   interior_face_integs.Append(lfi);
 }
 
 void LinearForm::Assemble()
@@ -112,14 +113,14 @@ void LinearForm::Assemble()
    // The first use of AddElementVector() below will move it back to host
    // because both 'vdofs' and 'elemvect' are on host.
 
-   if (dlfi.Size())
+   if (domain_integs.Size())
    {
-      for (int k = 0; k < dlfi.Size(); k++)
+      for (int k = 0; k < domain_integs.Size(); k++)
       {
-         if (dlfi_marker[k] != NULL)
+         if (domain_integs_marker[k] != NULL)
          {
             MFEM_VERIFY(fes->GetMesh()->attributes.Size() ==
-                        dlfi_marker[k]->Size(),
+                        domain_integs_marker[k]->Size(),
                         "invalid element marker for domain linear form "
                         "integrator #" << k << ", counting from zero");
          }
@@ -128,14 +129,15 @@ void LinearForm::Assemble()
       for (i = 0; i < fes -> GetNE(); i++)
       {
          int elem_attr = fes->GetMesh()->GetAttribute(i);
-         for (int k = 0; k < dlfi.Size(); k++)
+         for (int k = 0; k < domain_integs.Size(); k++)
          {
-            if ( dlfi_marker[k] == NULL ||
-                 (*(dlfi_marker[k]))[elem_attr-1] == 1 )
+            if ( domain_integs_marker[k] == NULL ||
+                 (*(domain_integs_marker[k]))[elem_attr-1] == 1 )
             {
                fes -> GetElementVDofs (i, vdofs);
                eltrans = fes -> GetElementTransformation (i);
-               dlfi[k]->AssembleRHSElementVect(*fes->GetFE(i), *eltrans, elemvect);
+               domain_integs[k]->AssembleRHSElementVect(*fes->GetFE(i),
+                                                        *eltrans, elemvect);
                AddElementVector (vdofs, elemvect);
             }
          }
@@ -143,7 +145,7 @@ void LinearForm::Assemble()
    }
    AssembleDelta();
 
-   if (blfi.Size())
+   if (boundary_integs.Size())
    {
       Mesh *mesh = fes->GetMesh();
 
@@ -151,14 +153,14 @@ void LinearForm::Assemble()
       Array<int> bdr_attr_marker(mesh->bdr_attributes.Size() ?
                                  mesh->bdr_attributes.Max() : 0);
       bdr_attr_marker = 0;
-      for (int k = 0; k < blfi.Size(); k++)
+      for (int k = 0; k < boundary_integs.Size(); k++)
       {
-         if (blfi_marker[k] == NULL)
+         if (boundary_integs_marker[k] == NULL)
          {
             bdr_attr_marker = 1;
             break;
          }
-         Array<int> &bdr_marker = *blfi_marker[k];
+         Array<int> &bdr_marker = *boundary_integs_marker[k];
          MFEM_ASSERT(bdr_marker.Size() == bdr_attr_marker.Size(),
                      "invalid boundary marker for boundary integrator #"
                      << k << ", counting from zero");
@@ -174,18 +176,19 @@ void LinearForm::Assemble()
          if (bdr_attr_marker[bdr_attr-1] == 0) { continue; }
          fes -> GetBdrElementVDofs (i, vdofs);
          eltrans = fes -> GetBdrElementTransformation (i);
-         for (int k=0; k < blfi.Size(); k++)
+         for (int k=0; k < boundary_integs.Size(); k++)
          {
-            if (blfi_marker[k] &&
-                (*blfi_marker[k])[bdr_attr-1] == 0) { continue; }
+            if (boundary_integs_marker[k] &&
+                (*boundary_integs_marker[k])[bdr_attr-1] == 0) { continue; }
 
-            blfi[k]->AssembleRHSElementVect(*fes->GetBE(i), *eltrans, elemvect);
+            boundary_integs[k]->AssembleRHSElementVect(*fes->GetBE(i),
+                                                       *eltrans, elemvect);
 
             AddElementVector (vdofs, elemvect);
          }
       }
    }
-   if (flfi.Size())
+   if (boundary_face_integs.Size())
    {
       FaceElementTransformations *tr;
       Mesh *mesh = fes->GetMesh();
@@ -194,14 +197,14 @@ void LinearForm::Assemble()
       Array<int> bdr_attr_marker(mesh->bdr_attributes.Size() ?
                                  mesh->bdr_attributes.Max() : 0);
       bdr_attr_marker = 0;
-      for (int k = 0; k < flfi.Size(); k++)
+      for (int k = 0; k < boundary_face_integs.Size(); k++)
       {
-         if (flfi_marker[k] == NULL)
+         if (boundary_face_integs_marker[k] == NULL)
          {
             bdr_attr_marker = 1;
             break;
          }
-         Array<int> &bdr_marker = *flfi_marker[k];
+         Array<int> &bdr_marker = *boundary_face_integs_marker[k];
          MFEM_ASSERT(bdr_marker.Size() == bdr_attr_marker.Size(),
                      "invalid boundary marker for boundary face integrator #"
                      << k << ", counting from zero");
@@ -220,24 +223,26 @@ void LinearForm::Assemble()
          if (tr != NULL)
          {
             fes -> GetElementVDofs (tr -> Elem1No, vdofs);
-            for (int k = 0; k < flfi.Size(); k++)
+            for (int k = 0; k < boundary_face_integs.Size(); k++)
             {
-               if (flfi_marker[k] &&
-                   (*flfi_marker[k])[bdr_attr-1] == 0) { continue; }
+               if (boundary_face_integs_marker[k] &&
+                   (*boundary_face_integs_marker[k])[bdr_attr-1] == 0)
+               { continue; }
 
-               flfi[k] -> AssembleRHSElementVect (*fes->GetFE(tr -> Elem1No),
-                                                  *tr, elemvect);
+               boundary_face_integs[k]->
+               AssembleRHSElementVect(*fes->GetFE(tr->Elem1No),
+                                      *tr, elemvect);
                AddElementVector (vdofs, elemvect);
             }
          }
       }
    }
 
-   if (iflfi.Size())
+   if (interior_face_integs.Size())
    {
       Mesh *mesh = fes->GetMesh();
 
-      for (int k = 0; k < iflfi.Size(); k++)
+      for (int k = 0; k < interior_face_integs.Size(); k++)
       {
          for (i = 0; i < mesh->GetNumFaces(); i++)
          {
@@ -249,9 +254,10 @@ void LinearForm::Assemble()
                Array<int> vdofs2;
                fes -> GetElementVDofs (tr -> Elem2No, vdofs2);
                vdofs.Append(vdofs2);
-               iflfi[k] -> AssembleRHSElementVect (*fes->GetFE(tr -> Elem1No),
-                                                   *fes->GetFE(tr -> Elem2No),
-                                                   *tr, elemvect);
+               interior_face_integs[k]->
+               AssembleRHSElementVect(*fes->GetFE(tr->Elem1No),
+                                      *fes->GetFE(tr->Elem2No),
+                                      *tr, elemvect);
                AddElementVector (vdofs, elemvect);
             }
          }
@@ -277,40 +283,41 @@ void LinearForm::MakeRef(FiniteElementSpace *f, Vector &v, int v_offset)
 
 void LinearForm::AssembleDelta()
 {
-   if (dlfi_delta.Size() == 0) { return; }
+   if (domain_delta_integs.Size() == 0) { return; }
 
    if (!HaveDeltaLocations())
    {
       int sdim = fes->GetMesh()->SpaceDimension();
       Vector center;
-      DenseMatrix centers(sdim, dlfi_delta.Size());
+      DenseMatrix centers(sdim, domain_delta_integs.Size());
       for (int i = 0; i < centers.Width(); i++)
       {
          centers.GetColumnReference(i, center);
-         dlfi_delta[i]->GetDeltaCenter(center);
+         domain_delta_integs[i]->GetDeltaCenter(center);
          MFEM_VERIFY(center.Size() == sdim,
                      "Point dim " << center.Size() <<
                      " does not match space dim " << sdim);
       }
-      fes->GetMesh()->FindPoints(centers, dlfi_delta_elem_id, dlfi_delta_ip);
+      fes->GetMesh()->FindPoints(centers, domain_delta_integs_elem_id,
+                                 domain_delta_integs_ip);
    }
 
    Array<int> vdofs;
    Vector elemvect;
-   for (int i = 0; i < dlfi_delta.Size(); i++)
+   for (int i = 0; i < domain_delta_integs.Size(); i++)
    {
-      int elem_id = dlfi_delta_elem_id[i];
+      int elem_id = domain_delta_integs_elem_id[i];
       // The delta center may be outside of this sub-domain, or
       // (Par)Mesh::FindPoints() failed to find this point:
       if (elem_id < 0) { continue; }
 
-      const IntegrationPoint &ip = dlfi_delta_ip[i];
+      const IntegrationPoint &ip = domain_delta_integs_ip[i];
       ElementTransformation &Trans = *fes->GetElementTransformation(elem_id);
       Trans.SetIntPoint(&ip);
 
       fes->GetElementVDofs(elem_id, vdofs);
-      dlfi_delta[i]->AssembleDeltaElementVect(*fes->GetFE(elem_id), Trans,
-                                              elemvect);
+      domain_delta_integs[i]->AssembleDeltaElementVect(*fes->GetFE(elem_id),
+                                                       Trans, elemvect);
       AddElementVector(vdofs, elemvect);
    }
 }
@@ -333,11 +340,14 @@ LinearForm::~LinearForm()
    if (!extern_lfs)
    {
       int k;
-      for (k=0; k < dlfi_delta.Size(); k++) { delete dlfi_delta[k]; }
-      for (k=0; k < dlfi.Size(); k++) { delete dlfi[k]; }
-      for (k=0; k < blfi.Size(); k++) { delete blfi[k]; }
-      for (k=0; k < flfi.Size(); k++) { delete flfi[k]; }
-      for (k=0; k < iflfi.Size(); k++) { delete iflfi[k]; }
+      for (k=0; k < domain_delta_integs.Size(); k++)
+      { delete domain_delta_integs[k]; }
+      for (k=0; k < domain_integs.Size(); k++) { delete domain_integs[k]; }
+      for (k=0; k < boundary_integs.Size(); k++) { delete boundary_integs[k]; }
+      for (k=0; k < boundary_face_integs.Size(); k++)
+      { delete boundary_face_integs[k]; }
+      for (k=0; k < interior_face_integs.Size(); k++)
+      { delete interior_face_integs[k]; }
    }
 }
 

fem/linearform.hpp

@@ -26,43 +26,46 @@ protected:
    /// FE space on which the LinearForm lives. Not owned.
    FiniteElementSpace *fes;
 
-   /** @brief Indicates the LinearFormIntegrator%s stored in #dlfi, #dlfi_delta,
-       #blfi, and #flfi are owned by another LinearForm. */
+   /** @brief Indicates the LinearFormIntegrator%s stored in #domain_integs,
+       #domain_delta_integs, #boundary_integs, and #boundary_face_integs are
+       owned by another LinearForm. */
    int extern_lfs;
 
    /// Set of Domain Integrators to be applied.
-   Array<LinearFormIntegrator*> dlfi;
+   Array<LinearFormIntegrator*> domain_integs;
    /// Element attribute marker (should be of length mesh->attributes)
    /// Includes all by default.
    /// 0 - ignore attribute
    /// 1 - include attribute
-   Array<Array<int>*>           dlfi_marker;
+   Array<Array<int>*>           domain_integs_marker;
 
    /// Separate array for integrators with delta function coefficients.
-   Array<DeltaLFIntegrator*> dlfi_delta;
+   Array<DeltaLFIntegrator*>    domain_delta_integs;
 
    /// Set of Boundary Integrators to be applied.
-   Array<LinearFormIntegrator*> blfi;
-   Array<Array<int>*>           blfi_marker; ///< Entries are not owned.
+   Array<LinearFormIntegrator*> boundary_integs;
+   /// Entries are not owned.
+   Array<Array<int>*>           boundary_integs_marker;
 
    /// Set of Boundary Face Integrators to be applied.
-   Array<LinearFormIntegrator*> flfi;
-   Array<Array<int>*>           flfi_marker; ///< Entries are not owned.
+   Array<LinearFormIntegrator*> boundary_face_integs;
+   Array<Array<int>*> boundary_face_integs_marker; ///< Entries not owned.
 
    /// Set of Internal Face Integrators to be applied.
-   Array<LinearFormIntegrator*> iflfi;
+   Array<LinearFormIntegrator*> interior_face_integs;
 
    /// The element ids where the centers of the delta functions lie
-   Array<int> dlfi_delta_elem_id;
+   Array<int> domain_delta_integs_elem_id;
 
    /// The reference coordinates where the centers of the delta functions lie
-   Array<IntegrationPoint> dlfi_delta_ip;
+   Array<IntegrationPoint> domain_delta_integs_ip;
 
    /// If true, the delta locations are not (re)computed during assembly.
-   bool HaveDeltaLocations() { return (dlfi_delta_elem_id.Size() != 0); }
+   bool HaveDeltaLocations()
+   { return (domain_delta_integs_elem_id.Size() != 0); }
 
    /// Force (re)computation of delta locations.
-   void ResetDeltaLocations() { dlfi_delta_elem_id.SetSize(0); }
+   void ResetDeltaLocations() { domain_delta_integs_elem_id.SetSize(0); }
 
 private:
    /// Copy construction is not supported; body is undefined.
@@ -150,22 +153,25 @@ public:
    /** @brief Access all integrators added with AddDomainIntegrator() which are
        not DeltaLFIntegrator%s or they are DeltaLFIntegrator%s with non-delta
        coefficients. */
-   Array<LinearFormIntegrator*> *GetDLFI() { return &dlfi; }
+   Array<LinearFormIntegrator*> *GetDLFI() { return &domain_integs; }
 
    /** @brief Access all integrators added with AddDomainIntegrator() which are
        DeltaLFIntegrator%s with delta coefficients. */
-   Array<DeltaLFIntegrator*> *GetDLFI_Delta() { return &dlfi_delta; }
+   Array<DeltaLFIntegrator*> *GetDLFI_Delta() { return &domain_delta_integs; }
 
    /// Access all integrators added with AddBoundaryIntegrator().
-   Array<LinearFormIntegrator*> *GetBLFI() { return &blfi; }
+   Array<LinearFormIntegrator*> *GetBLFI() { return &boundary_integs; }
 
    /// Access all integrators added with AddBdrFaceIntegrator().
-   Array<LinearFormIntegrator*> *GetFLFI() { return &flfi; }
+   Array<LinearFormIntegrator*> *GetFLFI() { return &boundary_face_integs; }
+
+   /// Access all integrators added with AddInteriorFaceIntegrator().
+   Array<LinearFormIntegrator*> *GetIFLFI() { return &interior_face_integs; }
 
    /** @brief Access all boundary markers added with AddBdrFaceIntegrator().
        If no marker was specified when the integrator was added, the
        corresponding pointer (to Array<int>) will be NULL. */
-   Array<Array<int>*> *GetFLFI_Marker() { return &flfi_marker; }
+   Array<Array<int>*> *GetFLFI_Marker() { return &boundary_face_integs_marker; }
 
    /// Assembles the linear form i.e. sums over all domain/bdr integrators.
    void Assemble();

fem/nonlinearform.cpp

@@ -979,6 +979,8 @@ void BlockNonlinearForm::ComputeGradientBlocked(const BlockVector &bx) const
 
             for (int k = 0; k < bfnfi.Size(); ++k)
             {
+               if (bfnfi_marker[k] &&
+                   (*bfnfi_marker[k])[bdr_attr-1] == 0) { continue; }
                bfnfi[k]->AssembleFaceGrad(fe, fe2, *tr, el_x_const, elmats);
                for (int l=0; l<fes.Size(); ++l)
                {

fem/nonlininteg.hpp

@@ -40,10 +40,10 @@ protected:
 public:
    /** @brief Prescribe a fixed IntegrationRule to use (when @a ir != NULL) or
        let the integrator choose (when @a ir == NULL). */
-   void SetIntRule(const IntegrationRule *ir) { IntRule = ir; }
+   virtual void SetIntRule(const IntegrationRule *ir) { IntRule = ir; }
 
    /// Prescribe a fixed IntegrationRule to use.
-   void SetIntegrationRule(const IntegrationRule &irule) { IntRule = &irule; }
+   void SetIntegrationRule(const IntegrationRule &ir) { SetIntRule(&ir); }
 
    /// Set the memory type used for GeometricFactors and other large allocations
    /// in PA extensions.

fem/pbilinearform.cpp

@@ -130,7 +130,7 @@ void ParBilinearForm::ParallelAssemble(OperatorHandle &A, SparseMatrix *A_local)
 
    OperatorHandle dA(A.Type()), Ph(A.Type()), hdA;
 
-   if (fbfi.Size() == 0)
+   if (interior_face_integs.Size() == 0)
    {
       // construct a parallel block-diagonal matrix 'A' based on 'a'
       dA.MakeSquareBlockDiag(pfes->GetComm(), pfes->GlobalVSize(),
@@ -214,11 +214,12 @@ void ParBilinearForm::AssembleSharedFaces(int skip_zeros)
          }
       }
       vdofs_all.Append(vdofs2);
-      for (int k = 0; k < fbfi.Size(); k++)
+      for (int k = 0; k < interior_face_integs.Size(); k++)
       {
-         fbfi[k]->AssembleFaceMatrix(*pfes->GetFE(T->Elem1No),
-                                     *pfes->GetFaceNbrFE(Elem2NbrNo),
-                                     *T, elemmat);
+         interior_face_integs[k]->
+         AssembleFaceMatrix(*pfes->GetFE(T->Elem1No),
+                            *pfes->GetFaceNbrFE(Elem2NbrNo),
+                            *T, elemmat);
          if (keep_nbr_block)
          {
             mat->AddSubMatrix(vdofs_all, vdofs_all, elemmat, skip_zeros);
@@ -233,7 +234,7 @@ void ParBilinearForm::AssembleSharedFaces(int skip_zeros)
 
 void ParBilinearForm::Assemble(int skip_zeros)
 {
-   if (fbfi.Size())
+   if (interior_face_integs.Size())
    {
       pfes->ExchangeFaceNbrData();
       if (!ext && mat == NULL)
@@ -244,7 +245,7 @@ void ParBilinearForm::Assemble(int skip_zeros)
 
    BilinearForm::Assemble(skip_zeros);
 
-   if (!ext && fbfi.Size() > 0)
+   if (!ext && interior_face_integs.Size() > 0)
    {
       AssembleSharedFaces(skip_zeros);
    }
@@ -316,7 +317,8 @@ ParallelEliminateEssentialBC(const Array<int> &bdr_attr_is_ess,
 void ParBilinearForm::TrueAddMult(const Vector &x, Vector &y, const double a)
 const
 {
-   MFEM_VERIFY(fbfi.Size() == 0, "the case of interior face integrators is not"
+   MFEM_VERIFY(interior_face_integs.Size() == 0,
+               "the case of interior face integrators is not"
                " implemented");
 
    if (X.ParFESpace() != pfes)

fem/pfespace.cpp

@@ -515,7 +515,7 @@ const FiniteElement *ParFiniteElementSpace::GetFE(int i) const
    else { return FiniteElementSpace::GetFE(i); }
 }
 
-const Operator *ParFiniteElementSpace::GetFaceRestriction(
+const FaceRestriction *ParFiniteElementSpace::GetFaceRestriction(
    ElementDofOrdering e_ordering, FaceType type, L2FaceValues mul) const
 {
    const bool is_dg_space = IsDGSpace();
@@ -529,7 +529,7 @@ const Operator *ParFiniteElementSpace::GetFaceRestriction(
    }
    else
    {
-      Operator* res;
+      FaceRestriction *res;
       if (is_dg_space)
       {
          res = new ParL2FaceRestriction(*this, e_ordering, type, m);

fem/pfespace.hpp

@@ -299,7 +299,7 @@ public:
        presence of shared faces. Shared faces are treated as interior faces,
        the returned operator handles the communication needed to get the
        shared face values from other MPI ranks */
-   virtual const Operator *GetFaceRestriction(
+   virtual const FaceRestriction *GetFaceRestriction(
       ElementDofOrdering e_ordering, FaceType type,
       L2FaceValues mul = L2FaceValues::DoubleValued) const;
 

fem/plinearform.cpp

@@ -47,7 +47,7 @@ void ParLinearForm::Assemble()
 {
    LinearForm::Assemble();
 
-   if (iflfi.Size())
+   if (interior_face_integs.Size())
    {
       pfes->ExchangeFaceNbrData();
       AssembleSharedFaces();
@@ -59,10 +59,10 @@ void ParLinearForm::AssembleSharedFaces()
    Array<int> vdofs;
    Vector elemvect;
 
-   if (iflfi.Size())
+   if (interior_face_integs.Size())
    {
       ParMesh *pmesh = pfes->GetParMesh();
-      for (int k = 0; k < iflfi.Size(); k++)
+      for (int k = 0; k < interior_face_integs.Size(); k++)
       {
          for (int i = 0; i < pmesh->GetNSharedFaces(); i++)
          {
@@ -73,9 +73,10 @@ void ParLinearForm::AssembleSharedFaces()
             {
                int Elem2Nbr = tr->Elem2No - pmesh->GetNE();
                fes -> GetElementVDofs (tr -> Elem1No, vdofs);
-               iflfi[0] -> AssembleRHSElementVect (*fes->GetFE(tr -> Elem1No),
-                                                   *pfes->GetFaceNbrFE(Elem2Nbr),
-                                                   *tr, elemvect);
+               interior_face_integs[k]->
+               AssembleRHSElementVect(*fes->GetFE(tr->Elem1No),
+                                      *pfes->GetFaceNbrFE(Elem2Nbr),
+                                      *tr, elemvect);
                AddElementVector (vdofs, elemvect);
             }
          }

fem/restriction.cpp

@@ -847,7 +847,7 @@ void H1FaceRestriction::Mult(const Vector& x, Vector& y) const
    });
 }
 
-void H1FaceRestriction::MultTranspose(const Vector& x, Vector& y) const
+void H1FaceRestriction::AddMultTranspose(const Vector& x, Vector& y) const
 {
    // Assumes all elements have the same number of dofs
    const int nd = dof;
@@ -856,7 +856,7 @@ void H1FaceRestriction::MultTranspose(const Vector& x, Vector& y) const
    auto d_offsets = offsets.Read();
    auto d_indices = gather_indices.Read();
    auto d_x = Reshape(x.Read(), nd, vd, nf);
-   auto d_y = Reshape(y.Write(), t?vd:ndofs, t?ndofs:vd);
+   auto d_y = Reshape(y.ReadWrite(), t?vd:ndofs, t?ndofs:vd);
    MFEM_FORALL(i, ndofs,
    {
       const int offset = d_offsets[i];
@@ -1267,7 +1267,7 @@ void L2FaceRestriction::Mult(const Vector& x, Vector& y) const
    }
 }
 
-void L2FaceRestriction::MultTranspose(const Vector& x, Vector& y) const
+void L2FaceRestriction::AddMultTranspose(const Vector& x, Vector& y) const
 {
    // Assumes all elements have the same number of dofs
    const int nd = dof;
@@ -1280,7 +1280,7 @@ void L2FaceRestriction::MultTranspose(const Vector& x, Vector& y) const
    if (m == L2FaceValues::DoubleValued)
    {
       auto d_x = Reshape(x.Read(), nd, vd, 2, nf);
-      auto d_y = Reshape(y.Write(), t?vd:ndofs, t?ndofs:vd);
+      auto d_y = Reshape(y.ReadWrite(), t?vd:ndofs, t?ndofs:vd);
       MFEM_FORALL(i, ndofs,
       {
          const int offset = d_offsets[i];
@@ -1304,7 +1304,7 @@ void L2FaceRestriction::MultTranspose(const Vector& x, Vector& y) const
    else
    {
       auto d_x = Reshape(x.Read(), nd, vd, nf);
-      auto d_y = Reshape(y.Write(), t?vd:ndofs, t?ndofs:vd);
+      auto d_y = Reshape(y.ReadWrite(), t?vd:ndofs, t?ndofs:vd);
       MFEM_FORALL(i, ndofs,
       {
          const int offset = d_offsets[i];

fem/restriction.hpp

@@ -21,10 +21,6 @@ namespace mfem
 class FiniteElementSpace;
 enum class ElementDofOrdering;
 
-/** An enum type to specify if only e1 value is requested (SingleValued) or both
-    e1 and e2 (DoubleValued). */
-enum class L2FaceValues : bool {SingleValued, DoubleValued};
-
 /// Operator that converts FiniteElementSpace L-vectors to E-vectors.
 /** Objects of this type are typically created and owned by FiniteElementSpace
     objects, see FiniteElementSpace::GetElementRestriction(). */
@@ -104,10 +100,75 @@ public:
    void FillJAndData(const Vector &ea_data, SparseMatrix &mat) const;
 };
 
-/// Operator that extracts Face degrees of freedom.
+/** An enum type to specify if only e1 value is requested (SingleValued) or both
+    e1 and e2 (DoubleValued). */
+enum class L2FaceValues : bool {SingleValued, DoubleValued};
+
+/** @brief Base class for operators that extracts Face degrees of freedom.
+
+    In order to compute quantities on the faces of a mesh, it is often useful to
+    extract the degrees of freedom on the faces of the elements. This class
+    provides an interface for such operations.
+
+    If the FiniteElementSpace is ordered by Ordering::byVDIM, then the expected
+    format for the L-vector is (vdim x ndofs), otherwise if Ordering::byNODES
+    the expected format is (ndofs x vdim), where ndofs is the total number of
+    degrees of freedom.
+    Since FiniteElementSpace can either be continuous or discontinuous, the
+    degrees of freedom on a face can either be single valued or double valued,
+    this is what we refer to as the multiplicity and is represented by the
+    L2FaceValues enum type.
+    The format of the output face E-vector of degrees of freedom is
+    (face_dofs x vdim x multiplicity x nfaces), where face_dofs is the number of
+    degrees of freedom on each face, and nfaces the number of faces of the
+    requested FaceType (see FiniteElementSpace::GetNFbyType).
+
+    @note Objects of this type are typically created and owned by
+    FiniteElementSpace objects, see FiniteElementSpace::GetFaceRestriction(). */
+class FaceRestriction : public Operator
+{
+public:
+   FaceRestriction(): Operator() { }
+
+   FaceRestriction(int h, int w): Operator(h, w) { }
+
+   virtual ~FaceRestriction() { }
+
+   /** @brief Extract the face degrees of freedom from @a x into @a y.
+
+       @param[in]  x The L-vector of degrees of freedom.
+       @param[out] y The degrees of freedom on the face, corresponding to a face
+                     E-vector.
+   */
+   void Mult(const Vector &x, Vector &y) const override = 0;
+
+   /** @brief Add the face degrees of freedom @a x to the element degrees of
+       freedom @a y.
+
+       @param[in]     x The face degrees of freedom on the face.
+       @param[in,out] y The L-vector of degrees of freedom to which we add the
+                        face degrees of freedom.
+   */
+   virtual void AddMultTranspose(const Vector &x, Vector &y) const = 0;
+
+   /** @brief Set the face degrees of freedom in the element degrees of freedom
+       @a y to the values given in @a x.
+
+       @param[in]     x The face degrees of freedom on the face.
+       @param[in,out] y The L-vector of degrees of freedom to which we add the
+                        face degrees of freedom.
+   */
+   void MultTranspose(const Vector &x, Vector &y) const override
+   {
+      y = 0.0;
+      AddMultTranspose(x, y);
+   }
+};
+
+/// Operator that extracts Face degrees of freedom for H1 FiniteElementSpaces.
 /** Objects of this type are typically created and owned by FiniteElementSpace
     objects, see FiniteElementSpace::GetFaceRestriction(). */
-class H1FaceRestriction : public Operator
+class H1FaceRestriction : public FaceRestriction
 {
 protected:
    const FiniteElementSpace &fes;
@@ -122,16 +183,42 @@ protected:
    Array<int> gather_indices;
 
 public:
-   H1FaceRestriction(const FiniteElementSpace&, const ElementDofOrdering,
-                     const FaceType);
-   void Mult(const Vector &x, Vector &y) const;
-   void MultTranspose(const Vector &x, Vector &y) const;
+   /** @brief Constructor for a H1FaceRestriction.
+
+       @param[in] fes The FiniteElementSpace on which this H1FaceRestriction
+                      operates.
+       @param[in] ordering The requested output ordering of the
+                           H1FaceRestriction, either Native or Lexicographic.
+       @param[in] type The requested type of faces on which this operator
+                       extracts the degrees of freedom, either Interior or
+                       Boundary.
+   */
+   H1FaceRestriction(const FiniteElementSpace& fes,
+                     const ElementDofOrdering ordering,
+                     const FaceType type);
+
+   /** @brief Extract the face degrees of freedom from @a x into @a y.
+
+       @param[in]  x The L-vector of degrees of freedom.
+       @param[out] y The degrees of freedom on the face, corresponding to a face
+                     E-vector.
+   */
+   void Mult(const Vector &x, Vector &y) const override;
+
+   /** @brief Add the face degrees of freedom @a x to the element degrees of
+       freedom @a y.
+
+       @param[in]     x The face degrees of freedom on the face.
+       @param[in,out] y The L-vector of degrees of freedom to which we add the
+                        face degrees of freedom.
+   */
+   void AddMultTranspose(const Vector &x, Vector &y) const override;
 };
 
-/// Operator that extracts Face degrees of freedom.
+/// Operator that extracts Face degrees of freedom on L2 FiniteElementSpaces.
 /** Objects of this type are typically created and owned by FiniteElementSpace
     objects, see FiniteElementSpace::GetFaceRestriction(). */
-class L2FaceRestriction : public Operator
+class L2FaceRestriction : public FaceRestriction
 {
 protected:
    const FiniteElementSpace &fes;
@@ -154,19 +241,38 @@ protected:
                      const L2FaceValues m = L2FaceValues::DoubleValued);
 
 public:
-   L2FaceRestriction(const FiniteElementSpace&, const ElementDofOrdering,
+   L2FaceRestriction(const FiniteElementSpace&,
+                     const ElementDofOrdering,
                      const FaceType,
                      const L2FaceValues m = L2FaceValues::DoubleValued);
-   virtual void Mult(const Vector &x, Vector &y) const;
-   void MultTranspose(const Vector &x, Vector &y) const;
+
+   /** @brief Extract the face degrees of freedom from @a x into @a y.
+
+       @param[in]  x The L-vector of degrees of freedom.
+       @param[out] y The degrees of freedom on the face, corresponding to a face
+                     E-vector.
+   */
+   void Mult(const Vector &x, Vector &y) const override;
+
+   /** @brief Add the face degrees of freedom @a x to the element degrees of
+       freedom @a y.
+
+       @param[in]     x The face degrees of freedom on the face.
+       @param[in,out] y The L-vector of degrees of freedom to which we add the
+                        face degrees of freedom.
+   */
+   void AddMultTranspose(const Vector &x, Vector &y) const override;
+
    /** Fill the I array of SparseMatrix corresponding to the sparsity pattern
        given by this L2FaceRestriction. */
    virtual void FillI(SparseMatrix &mat, const bool keep_nbr_block = false) const;
+
    /** Fill the J and Data arrays of SparseMatrix corresponding to the sparsity
        pattern given by this L2FaceRestriction, and the values of ea_data. */
    virtual void FillJAndData(const Vector &ea_data,
                              SparseMatrix &mat,
                              const bool keep_nbr_block = false) const;
+
    /// This methods adds the DG face matrices to the element matrices.
    void AddFaceMatricesToElementMatrices(Vector &fea_data,
                                          Vector &ea_data) const;

fem/tmop.cpp

@@ -34,6 +34,7 @@ void TMOP_Combo_QualityMetric::EvalP(const DenseMatrix &Jpt,
                                      DenseMatrix &P) const
 {
    DenseMatrix Pt(P.Size());
+   P = 0.0;
    for (int i = 0; i < tmop_q_arr.Size(); i++)
    {
       tmop_q_arr[i]->EvalP(Jpt, Pt);
@@ -50,6 +51,7 @@ void TMOP_Combo_QualityMetric::AssembleH(const DenseMatrix &Jpt,
    DenseMatrix At(A.Size());
    for (int i = 0; i < tmop_q_arr.Size(); i++)
    {
+      At = 0.0;
       tmop_q_arr[i]->AssembleH(Jpt, DS, weight, At);
       At *= wt_arr[i];
       A += At;

fem/tmop.hpp

@@ -371,6 +371,8 @@ public:
       AddQualityMetric(sh_metric, 1.-gamma_);
       AddQualityMetric(sz_metric, gamma_);
    }
+   virtual int Id() const { return 80; }
+   double GetGamma() const { return gamma; }
 
    virtual ~TMOP_Metric_080() { delete sh_metric; delete sz_metric; }
 };
@@ -590,6 +592,52 @@ public:
    virtual int Id() const { return 321; }
 };
 
+/// 3D barrier Shape+Size (VS) metric (polyconvex).
+class TMOP_Metric_332 : public TMOP_Combo_QualityMetric
+{
+protected:
+   double gamma;
+   TMOP_QualityMetric *sh_metric, *sz_metric;
+
+public:
+   TMOP_Metric_332(double gamma_) : gamma(gamma_),
+      sh_metric(new TMOP_Metric_302),
+      sz_metric(new TMOP_Metric_315)
+   {
+      // (1-gamma) mu_302 + gamma mu_315
+      AddQualityMetric(sh_metric, 1.-gamma_);
+      AddQualityMetric(sz_metric, gamma_);
+   }
+
+   virtual int Id() const { return 332; }
+   double GetGamma() const { return gamma; }
+
+   virtual ~TMOP_Metric_332() { delete sh_metric; delete sz_metric; }
+};
+
+/// 3D barrier Shape+Size (VS) metric (polyconvex).
+class TMOP_Metric_333 : public TMOP_Combo_QualityMetric
+{
+protected:
+   double gamma;
+   TMOP_QualityMetric *sh_metric, *sz_metric;
+
+public:
+   TMOP_Metric_333(double gamma_) : gamma(gamma_),
+      sh_metric(new TMOP_Metric_302),
+      sz_metric(new TMOP_Metric_316)
+   {
+      // (1-gamma) mu_302 + gamma mu_316
+      AddQualityMetric(sh_metric, 1.-gamma_);
+      AddQualityMetric(sz_metric, gamma_);
+   }
+
+   virtual int Id() const { return 333; }
+   double GetGamma() const { return gamma; }
+
+   virtual ~TMOP_Metric_333() { delete sh_metric; delete sz_metric; }
+};
+
 /// Shifted barrier form of 3D metric 16 (volume, ideal barrier metric), 3D
 class TMOP_Metric_352 : public TMOP_QualityMetric
 {

fem/tmop/tmop_pa_h2s.cpp

@@ -150,9 +150,49 @@ void EvalH_077(const int e, const int qx, const int qy,
    }
 }
 
+static MFEM_HOST_DEVICE inline
+void EvalH_080(const int e, const int qx, const int qy,
+               const double weight, const double gamma, const double *Jpt,
+               DeviceTensor<7,double> H)
+{
+   // h_80 = (1-gamma) h_2 + gamma h_77.
+
+   constexpr int DIM = 2;
+   double ddI1[4], ddI1b[4], dI2[4], dI2b[4], ddI2[4];
+   kernels::InvariantsEvaluator2D ie(Args()
+                                     .J(Jpt)
+                                     .dI2(dI2)
+                                     .ddI1(ddI1)
+                                     .ddI1b(ddI1b)
+                                     .dI2b(dI2b)
+                                     .ddI2(ddI2));
+
+   const double I2 = ie.Get_I2(), I2inv_sq = 1.0 / (I2 * I2);
+   ConstDeviceMatrix di2(ie.Get_dI2(),DIM,DIM);
+   for (int i = 0; i < DIM; i++)
+   {
+      for (int j = 0; j < DIM; j++)
+      {
+         ConstDeviceMatrix ddi1b(ie.Get_ddI1b(i,j),DIM,DIM);
+         ConstDeviceMatrix ddi2(ie.Get_ddI2(i,j),DIM,DIM);
+         for (int r = 0; r < DIM; r++)
+         {
+            for (int c = 0; c < DIM; c++)
+            {
+               H(r,c,i,j,qx,qy,e) =
+                  (1.0 - gamma) * 0.5 * weight * ddi1b(r,c) +
+                  gamma * ( weight * 0.5 * (1.0 - I2inv_sq) * ddi2(r,c) +
+                            weight * (I2inv_sq / I2) * di2(r,c) * di2(i,j) );
+            }
+         }
+      }
+   }
+}
+
 MFEM_REGISTER_TMOP_KERNELS(void, SetupGradPA_2D,
                            const Vector &x_,
                            const double metric_normal,
+                           const double metric_param,
                            const int mid,
                            const int NE,
                            const Array<double> &w_,
@@ -163,7 +203,7 @@ MFEM_REGISTER_TMOP_KERNELS(void, SetupGradPA_2D,
                            const int d1d,
                            const int q1d)
 {
-   MFEM_VERIFY(mid == 1 || mid == 2 || mid == 7 || mid == 77,
+   MFEM_VERIFY(mid == 1 || mid == 2 || mid == 7 || mid == 77 || mid == 80,
                "Metric not yet implemented!");
 
    constexpr int DIM = 2;
@@ -222,6 +262,7 @@ MFEM_REGISTER_TMOP_KERNELS(void, SetupGradPA_2D,
             if (mid ==  2) { EvalH_002(e,qx,qy,weight,Jpt,H); }
             if (mid ==  7) { EvalH_007(e,qx,qy,weight,Jpt,H); }
             if (mid == 77) { EvalH_077(e,qx,qy,weight,Jpt,H); }
+            if (mid == 80) { EvalH_080(e,qx,qy,weight,metric_param,Jpt,H); }
          } // qx
       } // qy
    });
@@ -241,7 +282,10 @@ void TMOP_Integrator::AssembleGradPA_2D(const Vector &X) const
    const Array<double> &G = PA.maps->G;
    Vector &H = PA.H;
 
-   MFEM_LAUNCH_TMOP_KERNEL(SetupGradPA_2D,id,X,mn,M,N,W,B,G,J,H);
+   double mp = 0.0;
+   if (auto m = dynamic_cast<TMOP_Metric_080 *>(metric)) { mp = m->GetGamma(); }
+
+   MFEM_LAUNCH_TMOP_KERNEL(SetupGradPA_2D,id,X,mn,mp,M,N,W,B,G,J,H);
 }
 
 } // namespace mfem

fem/tmop/tmop_pa_h3s.cpp

@@ -181,8 +181,58 @@ void EvalH_321(const int e, const int qx, const int qy, const int qz,
    }
 }
 
+// H_332 = (1-gamma) H_302 + gamma H_315
+static MFEM_HOST_DEVICE inline
+void EvalH_332(const int e, const int qx, const int qy, const int qz,
+               const double weight, const double gamma,
+               const double *J, DeviceTensor<8,double> dP)
+{
+   double B[9];
+   double         dI1b[9],          ddI1b[9];
+   double dI2[9], dI2b[9], ddI2[9], ddI2b[9];
+   double         dI3b[9],          ddI3b[9];
+   constexpr int DIM = 3;
+   kernels::InvariantsEvaluator3D ie(Args()
+                                     .J(J).B(B)
+                                     .dI1b(dI1b).ddI1b(ddI1b)
+                                     .dI2(dI2).dI2b(dI2b).ddI2(ddI2).ddI2b(ddI2b)
+                                     .dI3b(dI3b).ddI3b(ddI3b));
+   double sign_detJ;
+   const double c1 = weight/9.;
+   const double I1b = ie.Get_I1b();
+   const double I2b = ie.Get_I2b();
+   const double I3b = ie.Get_I3b(sign_detJ);
+   ConstDeviceMatrix di1b(ie.Get_dI1b(),DIM,DIM);
+   ConstDeviceMatrix di2b(ie.Get_dI2b(),DIM,DIM);
+   ConstDeviceMatrix di3b(ie.Get_dI3b(sign_detJ),DIM,DIM);
+   for (int i = 0; i < DIM; i++)
+   {
+      for (int j = 0; j < DIM; j++)
+      {
+         ConstDeviceMatrix ddi1b(ie.Get_ddI1b(i,j),DIM,DIM);
+         ConstDeviceMatrix ddi2b(ie.Get_ddI2b(i,j),DIM,DIM);
+         ConstDeviceMatrix ddi3b(ie.Get_ddI3b(i,j),DIM,DIM);
+         for (int r = 0; r < DIM; r++)
+         {
+            for (int c = 0; c < DIM; c++)
+            {
+               const double dp_302 =
+                  (di2b(r,c)*di1b(i,j) + di1b(r,c)*di2b(i,j))
+                  + ddi2b(r,c)*I1b
+                  + ddi1b(r,c)*I2b;
+               const double dp_315 = 2.0 * weight * (I3b - 1.0) * ddi3b(r,c) +
+                                     2.0 * weight * di3b(r,c) * di3b(i,j);
+               dP(r,c,i,j,qx,qy,qz,e) = (1.0 - gamma) * c1 * dp_302 +
+                                        gamma * dp_315;
+            }
+         }
+      }
+   }
+}
+
 MFEM_REGISTER_TMOP_KERNELS(void, SetupGradPA_3D,
                            const double metric_normal,
+                           const double metric_param,
                            const int mid,
                            const Vector &x_,
                            const int NE,
@@ -194,8 +244,8 @@ MFEM_REGISTER_TMOP_KERNELS(void, SetupGradPA_3D,
                            const int d1d,
                            const int q1d)
 {
-   MFEM_VERIFY(mid == 302 || mid == 303 || mid == 315 || mid == 321 ,
-               "3D metric not yet implemented!");
+   MFEM_VERIFY(mid == 302 || mid == 303 || mid == 315 ||
+               mid == 321 || mid == 332, "3D metric not yet implemented!");
 
    constexpr int DIM = 3;
    const int D1D = T_D1D ? T_D1D : d1d;
@@ -255,6 +305,7 @@ MFEM_REGISTER_TMOP_KERNELS(void, SetupGradPA_3D,
                if (mid == 303) { EvalH_303(e,qx,qy,qz,weight,Jpt,H); }
                if (mid == 315) { EvalH_315(e,qx,qy,qz,weight,Jpt,H); }
                if (mid == 321) { EvalH_321(e,qx,qy,qz,weight,Jpt,H); }
+               if (mid == 332) { EvalH_332(e,qx,qy,qz,weight,metric_param,Jpt,H); }
             } // qx
          } // qy
       } // qz
@@ -275,7 +326,10 @@ void TMOP_Integrator::AssembleGradPA_3D(const Vector &X) const
    const Array<double> &G = PA.maps->G;
    Vector &H = PA.H;
 
-   MFEM_LAUNCH_TMOP_KERNEL(SetupGradPA_3D,id,mn,M,X,N,W,B,G,J,H);
+   double mp = 0.0;
+   if (auto m = dynamic_cast<TMOP_Metric_332 *>(metric)) { mp = m->GetGamma(); }
+
+   MFEM_LAUNCH_TMOP_KERNEL(SetupGradPA_3D,id,mn,mp,M,X,N,W,B,G,J,H);
 }
 
 } // namespace mfem

fem/tmop/tmop_pa_p2.cpp

@@ -58,8 +58,24 @@ void EvalP_077(const double *Jpt, double *P)
    kernels::Set(2,2, 0.5 * (1.0 - 1.0 / (I2 * I2)), ie.Get_dI2(), P);
 }
 
+static MFEM_HOST_DEVICE inline
+void EvalP_080(const double *Jpt, double gamma, double *P)
+{
+   // p_80 = (1-gamma) p_2 + gamma p_77.
+
+   double dI1b[4], dI2[4], dI2b[4];
+   kernels::InvariantsEvaluator2D ie(Args().J(Jpt).
+                                     dI1b(dI1b).dI2(dI2).dI2b(dI2b));
+
+   kernels::Set(2,2, (1.0 - gamma) * 1./2., ie.Get_dI1b(), P);
+
+   const double I2 = ie.Get_I2();
+   kernels::Add(2,2, gamma * 0.5 * (1.0 - 1.0 / (I2 * I2)), ie.Get_dI2(), P);
+}
+
 MFEM_REGISTER_TMOP_KERNELS(void, AddMultPA_Kernel_2D,
                            const double metric_normal,
+                           const double metric_param,
                            const int mid,
                            const int NE,
                            const DenseTensor &j_,
@@ -71,7 +87,7 @@ MFEM_REGISTER_TMOP_KERNELS(void, AddMultPA_Kernel_2D,
                            const int d1d,
                            const int q1d)
 {
-   MFEM_VERIFY(mid == 1 || mid == 2 || mid == 7 || mid == 77,
+   MFEM_VERIFY(mid == 1 || mid == 2 || mid == 7 || mid == 77 || mid == 80,
                "Metric not yet implemented!");
 
    constexpr int DIM = 2;
@@ -132,6 +148,7 @@ MFEM_REGISTER_TMOP_KERNELS(void, AddMultPA_Kernel_2D,
             if (mid ==  2) { EvalP_002(Jpt, P); }
             if (mid ==  7) { EvalP_007(Jpt, P); }
             if (mid == 77) { EvalP_077(Jpt, P); }
+            if (mid == 80) { EvalP_080(Jpt, metric_param, P); }
             for (int i = 0; i < 4; i++) { P[i] *= weight; }
 
             // PMatO += DS . P^t += DSh . (Jrt . P^t)
@@ -160,7 +177,10 @@ void TMOP_Integrator::AddMultPA_2D(const Vector &X, Vector &Y) const
    const Array<double> &G = PA.maps->G;
    const double mn = metric_normal;
 
-   MFEM_LAUNCH_TMOP_KERNEL(AddMultPA_Kernel_2D,id,mn,M,N,J,W,B,G,X,Y);
+   double mp = 0.0;
+   if (auto m = dynamic_cast<TMOP_Metric_080 *>(metric)) { mp = m->GetGamma(); }
+
+   MFEM_LAUNCH_TMOP_KERNEL(AddMultPA_Kernel_2D,id,mn,mp,M,N,J,W,B,G,X,Y);
 }
 
 } // namespace mfem

fem/tmop/tmop_pa_p3.cpp

@@ -75,8 +75,29 @@ void EvalP_321(const double *J, double *P)
    kernels::Add(3,3, ie.Get_dI1(), P);
 }
 
+// P_332 = (1-gamma) P_302 + gamma P_315.
+static MFEM_HOST_DEVICE inline
+void EvalP_332(const double *J, double gamma, double *P)
+{
+   double B[9];
+   double dI1b[9], dI2[9], dI2b[9], dI3b[9];
+   kernels::InvariantsEvaluator3D ie(Args()
+                                     .J(J).B(B)
+                                     .dI1b(dI1b)
+                                     .dI2(dI2).dI2b(dI2b)
+                                     .dI3b(dI3b));
+   const double alpha = (1.0 - gamma) * ie.Get_I1b()/9.;
+   const double beta = (1.0 - gamma) * ie.Get_I2b()/9.;
+   kernels::Add(3,3, alpha, ie.Get_dI2b(), beta, ie.Get_dI1b(), P);
+
+   double sign_detJ;
+   const double I3b = ie.Get_I3b(sign_detJ);
+   kernels::Add(3,3, gamma * 2.0 * (I3b - 1.0), ie.Get_dI3b(sign_detJ), P);
+}
+
 MFEM_REGISTER_TMOP_KERNELS(void, AddMultPA_Kernel_3D,
                            const double metric_normal,
+                           double metric_param,
                            const int mid,
                            const int NE,
                            const DenseTensor &j_,
@@ -88,8 +109,8 @@ MFEM_REGISTER_TMOP_KERNELS(void, AddMultPA_Kernel_3D,
                            const int d1d,
                            const int q1d)
 {
-   MFEM_VERIFY(mid == 302 || mid == 303 || mid == 315 || mid == 321 ,
-               "3D metric not yet implemented!");
+   MFEM_VERIFY(mid == 302 || mid == 303 || mid == 315 ||
+               mid == 321 || mid == 332, "3D metric not yet implemented!");
 
    constexpr int DIM = 3;
    const int D1D = T_D1D ? T_D1D : d1d;
@@ -146,10 +167,11 @@ MFEM_REGISTER_TMOP_KERNELS(void, AddMultPA_Kernel_3D,
 
                // metric->EvalP(Jpt, P);
                double P[9];
-               if (mid == 302) { EvalP_302(Jpt,P); }
-               if (mid == 303) { EvalP_303(Jpt,P); }
-               if (mid == 315) { EvalP_315(Jpt,P); }
-               if (mid == 321) { EvalP_321(Jpt,P); }
+               if (mid == 302) { EvalP_302(Jpt, P); }
+               if (mid == 303) { EvalP_303(Jpt, P); }
+               if (mid == 315) { EvalP_315(Jpt, P); }
+               if (mid == 321) { EvalP_321(Jpt, P); }
+               if (mid == 332) { EvalP_332(Jpt, metric_param, P); }
                for (int i = 0; i < 9; i++) { P[i] *= weight; }
 
                // Y += DS . P^t += DSh . (Jrt . P^t)
@@ -180,7 +202,10 @@ void TMOP_Integrator::AddMultPA_3D(const Vector &X, Vector &Y) const
    const Array<double> &G = PA.maps->G;
    const double mn = metric_normal;
 
-   MFEM_LAUNCH_TMOP_KERNEL(AddMultPA_Kernel_3D,id,mn,M,N,J,W,B,G,X,Y);
+   double mp = 0.0;
+   if (auto m = dynamic_cast<TMOP_Metric_332 *>(metric)) { mp = m->GetGamma(); }
+
+   MFEM_LAUNCH_TMOP_KERNEL(AddMultPA_Kernel_3D,id,mn,mp,M,N,J,W,B,G,X,Y);
 }
 
 } // namespace mfem

fem/tmop/tmop_pa_w2.cpp

@@ -50,8 +50,15 @@ double EvalW_077(const double *Jpt)
    return 0.5*(I2b*I2b + 1./(I2b*I2b) - 2.);
 }
 
+static MFEM_HOST_DEVICE inline
+double EvalW_080(const double *Jpt, double gamma)
+{
+   return (1.0 - gamma) * EvalW_002(Jpt) + gamma * EvalW_077(Jpt);
+}
+
 MFEM_REGISTER_TMOP_KERNELS(double, EnergyPA_2D,
                            const double metric_normal,
+                           const double metric_param,
                            const int mid,
                            const int NE,
                            const DenseTensor &j_,
@@ -64,7 +71,7 @@ MFEM_REGISTER_TMOP_KERNELS(double, EnergyPA_2D,
                            const int d1d,
                            const int q1d)
 {
-   MFEM_VERIFY(mid == 1 || mid == 2 || mid == 7 || mid == 77,
+   MFEM_VERIFY(mid == 1 || mid == 2 || mid == 7 || mid == 77 || mid == 80,
                "2D metric not yet implemented!");
 
    constexpr int DIM = 2;
@@ -125,7 +132,8 @@ MFEM_REGISTER_TMOP_KERNELS(double, EnergyPA_2D,
             mid ==  1 ? EvalW_001(Jpt) :
             mid ==  2 ? EvalW_002(Jpt) :
             mid ==  7 ? EvalW_007(Jpt) :
-            mid == 77 ? EvalW_077(Jpt) : 0.0;
+            mid == 77 ? EvalW_077(Jpt) :
+            mid == 80 ? EvalW_080(Jpt, metric_param) : 0.0;
 
             E(qx,qy,e) = weight * EvalW;
          }
@@ -141,7 +149,7 @@ double TMOP_Integrator::GetLocalStateEnergyPA_2D(const Vector &X) const
    const int D1D = PA.maps->ndof;
    const int Q1D = PA.maps->nqpt;
    const int id = (D1D << 4 ) | Q1D;
-   const double m = metric_normal;
+   const double mn = metric_normal;
    const DenseTensor &J = PA.Jtr;
    const Array<double> &W = PA.ir->GetWeights();
    const Array<double> &B = PA.maps->B;
@@ -149,7 +157,10 @@ double TMOP_Integrator::GetLocalStateEnergyPA_2D(const Vector &X) const
    const Vector &O = PA.O;
    Vector &E = PA.E;
 
-   MFEM_LAUNCH_TMOP_KERNEL(EnergyPA_2D,id,m,M,N,J,W,B,G,X,O,E);
+   double mp = 0.0;
+   if (auto m = dynamic_cast<TMOP_Metric_080 *>(metric)) { mp = m->GetGamma(); }
+
+   MFEM_LAUNCH_TMOP_KERNEL(EnergyPA_2D,id,mn,mp,M,N,J,W,B,G,X,O,E);
 }
 
 } // namespace mfem

fem/tmop/tmop_pa_w3.cpp

@@ -58,8 +58,15 @@ double EvalW_321(const double *J)
    return ie.Get_I1() + ie.Get_I2()/ie.Get_I3() - 6.0;
 }
 
+static MFEM_HOST_DEVICE inline
+double EvalW_332(const double *J, double gamma)
+{
+   return (1.0 - gamma) * EvalW_302(J) + gamma * EvalW_315(J);
+}
+
 MFEM_REGISTER_TMOP_KERNELS(double, EnergyPA_3D,
                            const double metric_normal,
+                           const double metric_param,
                            const int mid,
                            const int NE,
                            const DenseTensor &j_,
@@ -72,8 +79,8 @@ MFEM_REGISTER_TMOP_KERNELS(double, EnergyPA_3D,
                            const int d1d,
                            const int q1d)
 {
-   MFEM_VERIFY(mid == 302 || mid == 303 || mid == 315 || mid == 321 ,
-               "3D metric not yet implemented!");
+   MFEM_VERIFY(mid == 302 || mid == 303 || mid == 315 ||
+               mid == 321 || mid == 332, "3D metric not yet implemented!");
 
    constexpr int DIM = 3;
    const int D1D = T_D1D ? T_D1D : d1d;
@@ -134,7 +141,8 @@ MFEM_REGISTER_TMOP_KERNELS(double, EnergyPA_3D,
                mid == 302 ? EvalW_302(Jpt) :
                mid == 303 ? EvalW_303(Jpt) :
                mid == 315 ? EvalW_315(Jpt) :
-               mid == 321 ? EvalW_321(Jpt) : 0.0;
+               mid == 321 ? EvalW_321(Jpt) :
+               mid == 332 ? EvalW_332(Jpt, metric_param) : 0.0;
 
                E(qx,qy,qz,e) = weight * EvalW;
             }
@@ -159,7 +167,10 @@ double TMOP_Integrator::GetLocalStateEnergyPA_3D(const Vector &X) const
    const Vector &O = PA.O;
    Vector &E = PA.E;
 
-   MFEM_LAUNCH_TMOP_KERNEL(EnergyPA_3D,id,mn,M,N,J,W,B,G,O,X,E);
+   double mp = 0.0;
+   if (auto m = dynamic_cast<TMOP_Metric_332 *>(metric)) { mp = m->GetGamma(); }
+
+   MFEM_LAUNCH_TMOP_KERNEL(EnergyPA_3D,id,mn,mp,M,N,J,W,B,G,O,X,E);
 }
 
 } // namespace mfem

general/binaryio.cpp

@@ -71,7 +71,7 @@ static const unsigned char b64table[] =
    255,255,255,255,255,255,255,255,255,255,255,255,255,255,255,255
 };
 
-void DecodeBase64(const char *src, size_t len, std::vector<unsigned char> &buf)
+void DecodeBase64(const char *src, size_t len, std::vector<char> &buf)
 {
    const unsigned char *in = (const unsigned char *)src;
    buf.clear();
@@ -79,7 +79,7 @@ void DecodeBase64(const char *src, size_t len, std::vector<unsigned char> &buf)
    for (size_t i=0; i<len; ++i) { if (b64table[in[i]] != 255) { ++count; } }
    if (count % 4 != 0) { return; }
    buf.resize(3*len/4);
-   unsigned char *out = buf.data();
+   unsigned char *out = (unsigned char *)buf.data();
    count = 0;
    int pad = 0;
    unsigned char c[4];
@@ -97,8 +97,10 @@ void DecodeBase64(const char *src, size_t len, std::vector<unsigned char> &buf)
          count = pad = 0;
       }
    }
-   buf.resize(out - buf.data());
+   buf.resize(out - (unsigned char *)buf.data());
 }
 
+size_t NumBase64Chars(size_t nbytes) { return ((4*nbytes/3) + 3) & ~3; }
+
 } // namespace mfem::bin_io
 } // namespace mfem

general/binaryio.hpp

@@ -50,6 +50,7 @@ inline T read(const char *buf)
    return value;
 }
 
+/// Append the binary representation of @a val to the byte buffer @a vec.
 template <typename T>
 void AppendBytes(std::vector<char> &vec, const T &val)
 {
@@ -57,9 +58,17 @@ void AppendBytes(std::vector<char> &vec, const T &val)
    vec.insert(vec.end(), ptr, ptr + sizeof(T));
 }
 
-void WriteBase64(std::ostream &out, const void *bytes, size_t length);
+/// Given a buffer @a buf of length @a nbytes, encode the data in base-64
+/// format, and write the encoded data to the output stream @a out.
+void WriteBase64(std::ostream &out, const void *bytes, size_t nbytes);
 
-void DecodeBase64(const char *src, size_t len, std::vector<unsigned char> &buf);
+/// Decode @a len base-64 encoded characters in the buffer @a src, and store the
+/// resulting decoded data in @a buf. @a buf will be resized as needed.
+void DecodeBase64(const char *src, size_t len, std::vector<char> &buf);
+
+/// Return the number of characters needed to encode @a nbytes in base-64. This
+/// is equal to 4*nbytes/3, rounded up to the nearest multiple of 4.
+size_t NumBase64Chars(size_t nbytes);
 
 } // namespace mfem::bin_io
 

linalg/CMakeLists.txt

@@ -17,6 +17,7 @@ list(APPEND SRCS
   complex_operator.cpp
   constraints.cpp
   densemat.cpp
+  fdsolver.cpp
   symmat.cpp
   handle.cpp
   matrix.cpp
@@ -39,6 +40,7 @@ list(APPEND HDRS
   dinvariants.hpp
   symmat.hpp
   dtensor.hpp
+  fdsolver.hpp
   handle.hpp
   invariants.hpp
   kernels.hpp

linalg/amgxsolver.cpp

@@ -208,11 +208,14 @@ void AmgXSolver::DefaultParameters(const AMGX_MODE amgxMode_,
                     " \"config_version\": 2, \n"
                     " \"solver\": { \n"
                     "   \"solver\": \"AMG\", \n"
+                    "   \"scope\": \"main\", \n"
+                    "   \"smoother\": \"JACOBI_L1\", \n"
                     "   \"presweeps\": 1, \n"
-                    "   \"postsweeps\": 1, \n"
                     "   \"interpolator\": \"D2\", \n"
-                    "   \"max_iters\": 2, \n"
-                    "   \"convergence\": \"ABSOLUTE\", \n"
+                    "   \"max_row_sum\" : 0.9, \n"
+                    "   \"strength_threshold\" : 0.25, \n"
+                    "   \"postsweeps\": 1, \n"
+                    "   \"max_iters\": 1, \n"
                     "   \"cycle\": \"V\"";
       if (verbose)
       {
@@ -239,22 +242,21 @@ void AmgXSolver::DefaultParameters(const AMGX_MODE amgxMode_,
                     "     \"solver\": \"AMG\", \n"
                     "     \"smoother\": { \n"
                     "     \"scope\": \"jacobi\", \n"
-                    "     \"solver\": \"BLOCK_JACOBI\", \n"
-                    "     \"relaxation_factor\": 0.7 \n"
+                    "     \"solver\": \"JACOBI_L1\" \n"
                     "       }, \n"
                     "     \"presweeps\": 1, \n"
                     "     \"interpolator\": \"D2\", \n"
                     "     \"max_row_sum\" : 0.9, \n"
                     "     \"strength_threshold\" : 0.25, \n"
-                    "     \"max_iters\": 2, \n"
+                    "     \"max_iters\": 1, \n"
                     "     \"scope\": \"amg\", \n"
                     "     \"max_levels\": 100, \n"
                     "     \"cycle\": \"V\", \n"
                     "     \"postsweeps\": 1 \n"
                     "    }, \n"
                     "  \"solver\": \"PCG\", \n"
-                    "  \"max_iters\": 100, \n"
-                    "  \"convergence\": \"RELATIVE_MAX\", \n"
+                    "  \"max_iters\": 150, \n"
+                    "  \"convergence\": \"RELATIVE_INI_CORE\", \n"
                     "  \"scope\": \"main\", \n"
                     "  \"tolerance\": 1e-12, \n"
                     "  \"monitor_residual\": 1, \n"

linalg/densemat.cpp

@@ -50,6 +50,10 @@ dsyevr_(char *JOBZ, char *RANGE, char *UPLO, int *N, double *A, int *LDA,
         double *W, double *Z, int *LDZ, int *ISUPPZ, double *WORK, int *LWORK,
         int *IWORK, int *LIWORK, int *INFO);
 extern "C" void
+dgeev_(const char * jobvl, const char * jobvr, int *n, double * A, int * lda,
+       double * wr, double * wl, double * vl, int * ldvl, double * vr, int * ldvr,
+       double * work, int * lwork, int * info);
+extern "C" void
 dsyev_(char *JOBZ, char *UPLO, int *N, double *A, int *LDA, double *W,
        double *WORK, int *LWORK, int *INFO);
 extern "C" void
@@ -174,7 +178,14 @@ const double &DenseMatrix::Elem(int i, int j) const
 
 void DenseMatrix::Mult(const double *x, double *y) const
 {
-   kernels::Mult(height, width, Data(), x, y);
+   const double *data = Read();
+   const int h = height;
+   const int w = width;
+
+   MFEM_FORALL(i, 1,
+   {
+      kernels::Mult(h, w, data, x, y);
+   });
 }
 
 void DenseMatrix::Mult(const Vector &x, Vector &y) const
@@ -182,7 +193,9 @@ void DenseMatrix::Mult(const Vector &x, Vector &y) const
    MFEM_ASSERT(height == y.Size() && width == x.Size(),
                "incompatible dimensions");
 
-   Mult((const double *)x, (double *)y);
+   const double *dx = x.Read();
+   double *dy = y.ReadWrite();
+   Mult(dx, dy);
 }
 
 double DenseMatrix::operator *(const DenseMatrix &m) const
@@ -2003,7 +2016,7 @@ void Mult(const DenseMatrix &b, const DenseMatrix &c, DenseMatrix &a)
    MFEM_ASSERT(a.Height() == b.Height() && a.Width() == c.Width() &&
                b.Width() == c.Height(), "incompatible dimensions");
 
-#ifdef MFEM_USE_LAPACK
+#if defined(MFEM_USE_LAPACK) && !defined(MFEM_USE_CUDA) && !defined(MFEM_USE_HIP)
    static char transa = 'N', transb = 'N';
    static double alpha = 1.0, beta = 0.0;
    int m = b.Height(), n = c.Width(), k = b.Width();
@@ -2014,10 +2027,13 @@ void Mult(const DenseMatrix &b, const DenseMatrix &c, DenseMatrix &a)
    const int ah = a.Height();
    const int aw = a.Width();
    const int bw = b.Width();
-   double *ad = a.Data();
-   const double *bd = b.Data();
-   const double *cd = c.Data();
-   kernels::Mult(ah,aw,bw,bd,cd,ad);
+   double *ad = a.ReadWrite();
+   const double *bd = b.Read();
+   const double *cd = c.Read();
+   MFEM_FORALL(i, 1,
+   {
+      kernels::Mult(ah, aw, bw, bd, cd, ad);
+   });
 #endif
 }
 
@@ -2859,6 +2875,155 @@ void AddMult_a_VVt(const double a, const Vector &v, DenseMatrix &VVt)
    }
 }
 
+void KronProd(const DenseMatrix & A, const DenseMatrix & B, DenseMatrix & C)
+{
+   const int ah = A.Height();
+   const int aw = A.Width();
+   const int bh = B.Height();
+   const int bw = B.Width();
+
+   C.SetSize(ah*bh,aw*bw);
+   const double * ad = A.Read();
+   const double * bd = B.Read();
+   double * cd = C.ReadWrite();
+
+   MFEM_FORALL(i, 1,
+   {
+      for (int ja = 0; ja<aw; ++ja)
+         for (int jb = 0; jb<bw; ++jb)
+            for (int ia = 0; ia<ah; ++ia)
+               for (int ib = 0; ib<bh; ++ib)
+                  cd[bh*ia + ib + ah*bh*(bw*ja + jb)]
+                     = ad[ia + ja * ah] * bd[ib + jb*bh];
+   });
+}
+
+#if 0 // this is a finer level parallel KronProd
+void KronProd2(const DenseMatrix & A, const DenseMatrix & B, DenseMatrix & C)
+{
+   const int ah = A.Height();
+   const int aw = A.Width();
+   const int bh = B.Height();
+   const int bw = B.Width();
+   const int ch = ah * bh;
+   const int cw = aw * bw;
+
+   C.SetSize(ch, cw);
+   const double *ad = A.Read();
+   const double *bd = B.Read();
+   double *cd = C.ReadWrite();
+
+   MFEM_FORALL(i, ch * cw,
+   {
+      const int jc = i / ch;
+      const int ic = i - jc * ch;
+      const int ja = jc / bw;
+      const int jb = jc - ja * bw;
+      const int ia = ic / bh;
+      const int ib = ic - ia * bh;
+      cd[jc * ch + ic] = ad[ja * ah + ia] * bd[jb * bh + ib];
+   });
+}
+#endif
+
+void KronMult(const DenseMatrix &A, const DenseMatrix &B, const Vector &r,
+              Vector &z)
+{
+   const int nA = A.Height();
+   const int mA = A.Width();
+   const int nB = B.Height();
+   const int mB = B.Width();
+   const int nr = r.Size();
+   MFEM_VERIFY(nr == mA*mB, "Wrong size of Vector r");
+   z.SetSize(nA*nB);
+#if !defined(MFEM_USE_CUDA)
+   DenseMatrix R(r.GetData(),mB,mA);
+   DenseMatrix X(nB,mA);
+   DenseMatrix Y(z.GetData(),nB,nA);
+   Mult(B,R,X);
+   MultABt(X,A,Y);
+#else
+   const double *ad = A.Read();
+   const double *bd = B.Read();
+   const double *rd = r.Read();
+   double *zd = z.Write();
+   MFEM_FORALL(i, 1,
+   {
+      kernels::KronMult(nA, mA, ad, nB, mB, bd, rd, zd);
+   });
+#endif
+}
+
+void KronMult(const DenseMatrix &A, const DenseMatrix &B, const DenseMatrix &R,
+              DenseMatrix & Z)
+{
+   const int nA = A.Height();
+   const int nB = B.Height();
+   const int nR = R.Height();
+   const int mR = R.Width();
+   Z.SetSize(nA*nB,mR);
+
+   Vector r,z;
+   double * dataR = R.Data();
+   for (int i = 0; i<mR; i++)
+   {
+      r.SetDataAndSize(&dataR[i*nR],nR);
+      KronMult(A,B,r,z);
+      Z.SetCol(i,z);
+   }
+}
+
+void KronMult(const DenseMatrix &A, const DenseMatrix &B, const DenseMatrix &C,
+              const Vector &r, Vector &z)
+{
+   const int nA = A.Height();
+   const int mA = A.Width();
+   const int nB = B.Height();
+   const int mB = B.Width();
+   const int nC = C.Height();
+   const int mC = C.Width();
+   const int nr = r.Size();
+   MFEM_VERIFY(nr == mA*mB*mC, "Wrong size of Vector r");
+   z.SetSize(nA*nB*nC);
+
+#if !defined(MFEM_USE_CUDA)
+   double * dataR = r.GetData();
+   DenseMatrix R(dataR,mC,mA*mB);
+   DenseMatrix X(nC,mA*mB);
+   Mult(C,R,X);
+   X.Transpose();
+   DenseMatrix Z(z.GetData(),mA*mB,nC);
+   KronMult(A,B,X,Z);
+   Z.Transpose();
+#else
+   const double *ad = A.Read();
+   const double *bd = B.Read();
+   const double *cd = C.Read();
+   const double *rd = r.Read();
+   double *zd = z.Write();
+   MFEM_FORALL(i, 1,
+   {
+      kernels::KronMult(nA, mA, ad, nB, mB, bd, nC, mC, cd, rd, zd);
+   });
+#endif
+}
+
+void KronMult(const Array<DenseMatrix *> & A, const Vector & r, Vector & z)
+{
+   int dim = A.Size();
+   if (dim == 2)
+   {
+      KronMult(*A[0],*A[1],r,z);
+   }
+   else if (dim == 3)
+   {
+      KronMult(*A[0],*A[1],*A[2], r,z);
+   }
+   else
+   {
+      MFEM_ABORT("KronMult::Wrong dimension");
+   }
+}
 
 bool LUFactors::Factor(int m, double TOL)
 {
@@ -3310,23 +3475,105 @@ DenseMatrixInverse::~DenseMatrixInverse()
    delete [] lu.ipiv;
 }
 
+void KronMult(const DenseMatrixInverse &A, const DenseMatrixInverse &B,
+              const Vector &r, Vector & z)
+{
+   // A and B are square matrices
+   z.SetSize(r.Size());
+   int nA = A.Height();
+   int nB = B.Height();
+   DenseMatrix R(r.GetData(),nB,nA);
+   DenseMatrix X(nB,nA);
+   B.Mult(R,X);
+   X.Transpose();
+   DenseMatrix Y(z.GetData(),nA,nB);
+   A.Mult(X,Y);
+   Y.Transpose();
+}
 
-DenseMatrixEigensystem::DenseMatrixEigensystem(DenseMatrix &m)
+void KronMult(const DenseMatrixInverse &A, const DenseMatrixInverse &B,
+              const DenseMatrix &R, DenseMatrix & Z)
+{
+   // A and B are square matrices
+   int nR = R.Height();
+   int mR = R.Width();
+   Z.SetSize(nR,mR);
+   Vector r(nR);
+   Vector z(nR);
+   double * dataR = R.GetData();
+   double * dataZ = Z.GetData();
+   for (int i = 0; i<mR; i++)
+   {
+      r.SetData(&dataR[i*nR]);
+      z.SetData(&dataZ[i*nR]);
+      KronMult(A,B,r,z);
+   }
+}
+
+void KronMult(const DenseMatrixInverse &A, const DenseMatrixInverse &B,
+              const DenseMatrixInverse &C, const Vector &r, Vector & z)
+{
+   // A, B and C are square matrices
+   int n = r.Size();
+   z.SetSize(n);
+   int nA = A.Height();
+   int nB = B.Height();
+   int nC = C.Height();
+   double * dataR = r.GetData();
+   DenseMatrix R(dataR,nC,nA*nB);
+   DenseMatrix X(nC,nA*nB);
+   C.Mult(R,X);
+   X.Transpose();
+   DenseMatrix Z(z.GetData(),nC,nA*nB);
+   KronMult(A,B,X,Z);
+   Z.Transpose();
+}
+
+void KronMult(const Array<DenseMatrixInverse *> & A, const Vector & r,
+              Vector & z)
+{
+   int dim = A.Size();
+   if (dim == 2)
+   {
+      KronMult(*A[0],*A[1],r,z);
+   }
+   else if (dim == 3)
+   {
+      KronMult(*A[0],*A[1],*A[2], r,z);
+   }
+   else
+   {
+      MFEM_ABORT("KronMult::Wrong dimension");
+   }
+}
+
+DenseMatrixEigensystem::DenseMatrixEigensystem(DenseMatrix &m, bool sym_)
    : mat(m)
 {
    n = mat.Width();
    EVal.SetSize(n);
+   EVali.SetSize(n);
    EVect.SetSize(n);
    ev.SetDataAndSize(NULL, n);
 
 #ifdef MFEM_USE_LAPACK
+   sym = sym_;
    jobz = 'V';
-   uplo = 'U';
    lwork = -1;
    double qwork;
-   dsyev_(&jobz, &uplo, &n, EVect.Data(), &n, EVal.GetData(),
-          &qwork, &lwork, &info);
-
+   if (sym)
+   {
+      uplo = 'U';
+      dsyev_(&jobz, &uplo, &n, EVect.Data(), &n, EVal.GetData(),
+             &qwork, &lwork, &info);
+   }
+   else
+   {
+      char jobvl = 'N';
+      int ldvl = 1;
+      dgeev_(&jobvl,&jobz,&n, mat.GetData(), &n, EVal.GetData(), EVali.GetData(),
+             nullptr, &ldvl, EVect.GetData(), &n, &qwork, &lwork, &info);
+   }
    lwork = (int) qwork;
    work = new double[lwork];
 #endif
@@ -3338,6 +3585,7 @@ DenseMatrixEigensystem::DenseMatrixEigensystem(
      n(other.n)
 {
 #ifdef MFEM_USE_LAPACK
+   sym = other.sym;
    jobz = other.jobz;
    uplo = other.uplo;
    lwork = other.lwork;
@@ -3356,13 +3604,24 @@ void DenseMatrixEigensystem::Eval()
 #endif
 
 #ifdef MFEM_USE_LAPACK
-   EVect = mat;
-   dsyev_(&jobz, &uplo, &n, EVect.Data(), &n, EVal.GetData(),
-          work, &lwork, &info);
-
+   if (sym)
+   {
+      EVect = mat;
+      dsyev_(&jobz, &uplo, &n, EVect.Data(), &n, EVal.GetData(),
+             work, &lwork, &info);
+   }
+   else
+   {
+      char jobvl = 'N';
+      int ldvl = 1;
+      DenseMatrix T = mat; // mat is overwritten by dgeev
+      dgeev_(&jobvl,&jobz,&n, T.GetData(), &n, EVal.GetData(), EVali.GetData(),
+             nullptr, &ldvl, EVect.GetData(), &n, work, &lwork, &info);
+   }
    if (info != 0)
    {
-      mfem::err << "DenseMatrixEigensystem::Eval(): DSYEV error code: "
+      string lpck = (sym) ? "DSYEV" : "DGEEV";
+      mfem::err << "DenseMatrixEigensystem::Eval(): " << lpck << "error code: "
                 << info << endl;
       mfem_error();
    }

linalg/densemat.hpp

@@ -523,6 +523,23 @@ void AddMult_a_VWt(const double a, const Vector &v, const Vector &w,
 /// VVt += a * v v^t
 void AddMult_a_VVt(const double a, const Vector &v, DenseMatrix &VVt);
 
+/// C = A ⊗ B
+void KronProd(const DenseMatrix & A, const DenseMatrix & B, DenseMatrix & C);
+void KronProd2(const DenseMatrix & A, const DenseMatrix & B, DenseMatrix & C);
+
+/// z = (A ⊗ B) r  = vec(B R A^T), where R := vec^-1 (r)
+void KronMult(const DenseMatrix &A, const DenseMatrix &B, const Vector &r,
+              Vector & z);
+
+/// z = (A ⊗ B) R
+void KronMult(const DenseMatrix &A, const DenseMatrix &B, const DenseMatrix &R,
+              DenseMatrix & Z);
+
+/// z = ( A ⊗ B ⊗ C ) r
+void KronMult(const DenseMatrix &A, const DenseMatrix &B, const DenseMatrix &C,
+              const Vector &r, Vector & z);
+
+void KronMult(const Array<DenseMatrix *> & A, const Vector & r, Vector & z);
 
 /** Class that can compute LU factorization of external data and perform various
     operations with the factored data. */
@@ -685,16 +702,33 @@ public:
    virtual ~DenseMatrixInverse();
 };
 
+/// z = (A^-1 ⊗ B^-1) r  = vec(B^-1 R A^-T), where R := vec^-1 (r)
+void KronMult(const DenseMatrixInverse &Ainv, const DenseMatrixInverse &Binv,
+              const Vector &r, Vector & z);
+
+/// z = (A^-1 ⊗ B^-1) R
+void KronMult(const DenseMatrixInverse &Ainv, const DenseMatrixInverse &Binv,
+              const DenseMatrix &R, DenseMatrix & Z);
+
+/// z = ( A^-1 ⊗ B^-1 ⊗ C^-1 ) r
+void KronMult(const DenseMatrixInverse &Ainv, const DenseMatrixInverse &Binv,
+              const DenseMatrixInverse &Cinv, const Vector &r, Vector & z);
+
+void KronMult(const Array<DenseMatrixInverse *> & A, const Vector & r,
+              Vector & z);
 
 class DenseMatrixEigensystem
 {
    DenseMatrix &mat;
    Vector      EVal;
+   // Possible non zero imaginary part of Eigenvalues
+   Vector      EVali;
    DenseMatrix EVect;
    Vector ev;
    int n;
 
 #ifdef MFEM_USE_LAPACK
+   bool sym;
    double *work;
    char jobz, uplo;
    int lwork, info;
@@ -702,10 +736,10 @@ class DenseMatrixEigensystem
 
 public:
 
-   DenseMatrixEigensystem(DenseMatrix &m);
+   DenseMatrixEigensystem(DenseMatrix &m, bool sym_ = false);
    DenseMatrixEigensystem(const DenseMatrixEigensystem &other);
    void Eval();
-   Vector &Eigenvalues() { return EVal; }
+   Vector &Eigenvalues(bool imag = false) { return imag ? EVali : EVal; }
    DenseMatrix &Eigenvectors() { return EVect; }
    double Eigenvalue(int i) { return EVal(i); }
    const Vector &Eigenvector(int i)

linalg/fdsolver.cpp

@@ -0,0 +1,143 @@
+// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+// LICENSE and NOTICE for details. LLNL-CODE-806117.
+//
+// This file is part of the MFEM library. For more information and source code
+// availability visit https://mfem.org.
+//
+// MFEM is free software; you can redistribute it and/or modify it under the
+// terms of the BSD-3 license. We welcome feedback and contributions, see file
+// CONTRIBUTING.md for details.
+
+#include "linalg.hpp"
+
+namespace mfem
+{
+
+void KronProdInvDiag(const Vector & a, const Vector & b, Vector & dinv)
+{
+   int n = a.Size(), m = b.Size();
+   dinv.SetSize(n*m);
+
+   for (int j = 0; j<m; j++)
+      for (int i = 0; i<n; i++)
+      {
+         dinv(i*m+j) = 1./(a(i) + b(j));
+      }
+}
+
+void KronProdInvDiag(const Vector & a, const Vector & b,
+                     const Vector & c, Vector & dinv)
+{
+   int n = a.Size(), m = b.Size(), l = c.Size();
+   dinv.SetSize(n*m*l);
+
+   for (int k = 0; k<l; k++)
+      for (int j = 0; j<m; j++)
+         for (int i = 0; i<n; i++)
+         {
+            dinv(i*m*l+j*l+k) = 1./(a(i) + b(j) + c(k));
+         }
+}
+
+void KronProdInvDiag(const Array<Vector *> & X, Vector & dinv)
+{
+   int dim = X.Size();
+   if (dim == 1)
+   {
+      int n = X[0]->Size();
+      dinv.SetSize(n);
+      for (int i = 0; i<n; i++) { dinv(i) = 1./(*X[0])(i); }
+   }
+   else if (dim == 2)
+   {
+      KronProdInvDiag(*X[0], *X[1], dinv);
+   }
+   else if (dim == 3)
+   {
+      KronProdInvDiag(*X[0], *X[1], *X[2], dinv);
+   }
+   else
+   {
+      MFEM_ABORT("KronProdInvDiag::Wrong dimension");
+   }
+}
+
+#ifdef MFEM_USE_LAPACK
+
+FDSolver::FDSolver(const Array<DenseMatrix *> & A,
+                   const Array<DenseMatrix *> & B)
+{
+   MFEM_ASSERT(A.Size() == B.Size(), "DenseFDSolver: Incompatible Dimensions");
+   dim = A.Size();
+
+   int solver_size = 1;
+   for (int i = 0; i<dim; i++)
+   {
+      MFEM_ASSERT(A[i]->Height() == A[i]->Width(),
+                  "DenseFDSolver: Matrix is not square");
+      MFEM_ASSERT(B[i]->Height() == B[i]->Width(),
+                  "DenseFDSolver: Matrix is not square");
+      MFEM_ASSERT(A[i]->Height() == B[i]->Height(),
+                  "DenseFDSolver: Matrices A and B have incompatible size");
+      solver_size *= A[i]->Height();
+   }
+   this->height = solver_size;
+   this->width  = solver_size;
+   if (solver_size) { Setup(A,B); }
+}
+
+void FDSolver::Setup(const Array<DenseMatrix *> & A,
+                     const Array<DenseMatrix *> & B)
+{
+   EigSystem.SetSize(dim);
+   eigv.SetSize(dim);
+   Array<Vector *> evalues(dim);
+   SQ.SetSize(dim);
+   DenseMatrix D;
+   for (int i = 0; i<dim; i++)
+   {
+      DenseMatrixInverse Minv(*B[i]);
+      Minv.Mult(*A[i],D);
+      EigSystem[i] = new DenseMatrixEigensystem(D);
+      EigSystem[i]->Eval();
+      evalues[i] = &EigSystem[i]->Eigenvalues();
+      eigv[i] = &EigSystem[i]->Eigenvectors();
+      DenseMatrixInverse Qinv(*eigv[i]);
+      DenseMatrix Sdinv;
+      Minv.GetInverseMatrix(Sdinv);
+      SQ[i] = new DenseMatrix;
+      Qinv.Mult(Sdinv,*SQ[i]);
+   }
+   KronProdInvDiag(evalues,dinv);
+}
+
+
+void FDSolver::Mult(const Vector & r,Vector & z) const
+{
+   MFEM_ASSERT(height == r.Size(),
+               "DenseFDSolver::Mult: Inconsistent vector size");
+   if (r.Size() == 0) { return; }
+   Vector rtemp;
+   KronMult(SQ,r,rtemp);
+   // 2. Diagonal solve;
+   rtemp *= dinv;
+   // 3. Modify RHS; z <-- (Q1 x Q2) rtemp
+   KronMult(eigv,rtemp,z);
+}
+
+FDSolver::~FDSolver()
+{
+   if (height)
+   {
+      for (int i=0; i<dim; i++)
+      {
+         delete SQ[i];
+         delete EigSystem[i];
+      }
+   }
+}
+
+#endif // MFEM_USE_LAPACK
+
+} // namespace mfem

linalg/fdsolver.hpp

@@ -0,0 +1,60 @@
+// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+// LICENSE and NOTICE for details. LLNL-CODE-806117.
+//
+// This file is part of the MFEM library. For more information and source code
+// availability visit https://mfem.org.
+//
+// MFEM is free software; you can redistribute it and/or modify it under the
+// terms of the BSD-3 license. We welcome feedback and contributions, see file
+// CONTRIBUTING.md for details.
+
+#ifndef MFEM_FDSOLVER
+#define MFEM_FDSOLVER
+
+#include "../config/config.hpp"
+#include "densemat.hpp"
+
+namespace mfem
+{
+
+/// Computes the inverse diagonal dinv = (a⊗I + I⊗b)^-1
+/// where a, b are diagonal matrices and I is the identity of the
+/// appropriate size
+void KronProdInvDiag(const Vector & a, const Vector & b, Vector & dinv);
+
+/// Computes the inverse diagonal dinv = (a⊗I⊗I + I⊗b⊗I + I⊗I⊗c)^-1
+/// where a, b, c are diagonal matrices and I is the identity of the
+/// appropriate size
+void KronProdInvDiag(const Vector & a, const Vector & b,
+                     const Vector & c, Vector & dinv);
+
+void KronProdInvDiag(const Array<Vector *> & X, Vector & dinv);
+
+#ifdef MFEM_USE_LAPACK
+
+/// In 2D it solves the system (A_0 ⊗ B_1 + B_0 ⊗ A_1) z = r
+/// In 3D it solves the system
+///     (A_0 ⊗ B_1 ⊗ B_2 + B_0 ⊗ A_1 ⊗ B_2 + B_0 ⊗ B_1 ⊗ A_2) z = r
+class FDSolver: public Solver
+{
+private:
+   int dim = 2;
+   Array<DenseMatrixEigensystem *> EigSystem;
+   Array<DenseMatrix *> eigv; // eigenvectors
+   Array<DenseMatrix *> SQ;
+   mutable Vector dinv;
+   void Setup(const Array<DenseMatrix *> & A, const Array<DenseMatrix *> & B);
+public:
+   FDSolver(const Array<DenseMatrix *> & A, const Array<DenseMatrix *> & B);
+   virtual void SetOperator(const Operator &op) {}
+   virtual void Mult(const Vector &r, Vector &z) const;
+   virtual ~FDSolver();
+};
+
+#endif // MFEM_USE_LAPACK
+
+} // mfem name space
+
+
+#endif // MFEM_FDSOLVER

linalg/hypre.hpp

@@ -516,7 +516,14 @@ public:
 
    /// Initialize all entries with value.
    HypreParMatrix &operator=(double value)
-   { internal::hypre_ParCSRMatrixSetConstantValues(A, value); return *this; }
+   {
+#if MFEM_HYPRE_VERSION < 22200
+      internal::hypre_ParCSRMatrixSetConstantValues(A, value);
+#else
+      hypre_ParCSRMatrixSetConstantValues(A, value);
+#endif
+      return *this;
+   }
 
    /** Perform the operation `*this += B`, assuming that both matrices use the
        same row and column partitions and the same col_map_offd arrays, or B has

linalg/hypre_parcsr.cpp

@@ -1942,8 +1942,8 @@ HYPRE_Int
 hypre_ParCSRMatrixSetConstantValues(hypre_ParCSRMatrix *A,
                                     HYPRE_Complex       value)
 {
-   hypre_CSRMatrixSetConstantValues(hypre_ParCSRMatrixDiag(A), value);
-   hypre_CSRMatrixSetConstantValues(hypre_ParCSRMatrixOffd(A), value);
+   internal::hypre_CSRMatrixSetConstantValues(hypre_ParCSRMatrixDiag(A), value);
+   internal::hypre_CSRMatrixSetConstantValues(hypre_ParCSRMatrixOffd(A), value);
 
    return 0;
 }

linalg/hypre_parcsr.hpp

@@ -198,6 +198,16 @@ hypre_CSRMatrixSum(hypre_CSRMatrix *A,
                    HYPRE_Complex    beta,
                    hypre_CSRMatrix *B);
 
+#if MFEM_HYPRE_VERSION >= 22200
+/** Provide an overloaded function for code consistency between HYPRE API
+    versions. */
+inline hypre_CSRMatrix *hypre_CSRMatrixAdd(hypre_CSRMatrix *A,
+                                           hypre_CSRMatrix *B)
+{
+   return ::hypre_CSRMatrixAdd(1.0, A, 1.0, B);
+}
+#endif
+
 /** Return a new matrix containing the sum of A and B, assuming that both
     matrices use the same row and column partitions. The col_map_offd do not
     need to be the same, but a more efficient algorithm is used if that's the

linalg/kernels.hpp

@@ -160,7 +160,7 @@ double Norml2(const int size, const T *data)
     data of the input and output vectors. */
 template<typename TA, typename TX, typename TY>
 MFEM_HOST_DEVICE inline
-void Mult(const int height, const int width, TA *data, const TX *x, TY *y)
+void Mult(const int height, const int width, const TA *data, const TX *x, TY *y)
 {
    if (width == 0)
    {
@@ -170,7 +170,8 @@ void Mult(const int height, const int width, TA *data, const TX *x, TY *y)
       }
       return;
    }
-   TA *d_col = data;
+
+   TA *d_col = (TA *) data;
    TX x_col = x[0];
    for (int row = 0; row < height; row++)
    {
@@ -188,6 +189,52 @@ void Mult(const int height, const int width, TA *data, const TX *x, TY *y)
    }
 }
 
+template<typename TA, typename TB, typename TR, typename TZ>
+MFEM_HOST_DEVICE inline
+void KronMult(const int ah, const int aw, const TA *ad, const int bh, const int bw, const TB *bd, TR *r, TZ *z)
+{
+   for (int i = 0; i < bh; i++)
+   {
+      for (int l = 0; l < ah; l++)
+      {
+         TZ t1 = 0.0;
+         for (int j = 0; j < bw; j++)
+         {
+            const TB t2 = bd[i + j * bh];
+            for (int k = 0; k < aw; k++)
+            {
+               t1 += t2 * r[j + k * bw] * ad[l + k * ah];
+            }
+         }
+         z[i + l * bh] = t1;
+      }
+   }
+}
+
+template<typename TA, typename TB, typename TC, typename TR, typename TZ>
+MFEM_HOST_DEVICE inline
+void KronMult(const int ah, const int aw, const TA *ad, const int bh, const int bw, const TB *bd, const int ch, const int cw, const TC *cd, TR *r, TZ *z)
+{
+   for (int i = 0; i < ch; i++)
+   {
+      for (int l = 0; l < ah * bh; l++)
+      {
+         TZ t1 = 0.0;
+         for (int j = 0; j < cw; j++)
+         {
+            const TB t2 = cd[i + j * ch];
+            for (int k = 0; k < aw * bw; k++)
+            {
+               const TA ta = ad[(l / bh) + (k / bw) * ah];
+               const TB tb = bd[(l % bh) + (k % bw) * bh];
+               t1 += t2 * r[j + k * cw] * ta * tb;
+            }
+         }
+         z[i + l * ch] = t1;
+      }
+   }
+}
+
 /// Symmetrize a square matrix with given @a size and @a data: A -> (A+A^T)/2.
 template<typename T>
 MFEM_HOST_DEVICE inline
@@ -276,6 +323,20 @@ void Add(const int height, const int width, const TA *Adata, TB *Bdata)
    }
 }
 
+/** @brief Compute B +=alpha*A, where the matrices A and B are of size
+    @a height x @a width with data @a Adata and @a Bdata. */
+template<typename TA, typename TB>
+MFEM_HOST_DEVICE inline
+void Add(const int height, const int width,
+         const double alpha, const TA *Adata, TB *Bdata)
+{
+   const int m = height * width;
+   for (int i = 0; i < m; i++)
+   {
+      Bdata[i] += alpha * Adata[i];
+   }
+}
+
 /** @brief Compute B = alpha*A, where the matrices A and B are of size
     @a height x @a width with data @a Adata and @a Bdata. */
 template<typename TA, typename TB>
@@ -290,7 +351,6 @@ void Set(const int height, const int width,
    }
 }
 
-
 /** @brief Matrix-matrix multiplication: A = B * C, where the matrices A, B and
     C are of sizes @a Aheight x @a Awidth, @a Aheight x @a Bwidth and @a Bwidth
     x @a Awidth, respectively. */

linalg/linalg.hpp

@@ -31,6 +31,7 @@
 #include "invariants.hpp"
 #include "constraints.hpp"
 #include "auxiliary.hpp"
+#include "fdsolver.hpp"
 
 #ifdef MFEM_USE_AMGX
 #include "amgxsolver.hpp"

linalg/solvers.cpp

@@ -232,7 +232,7 @@ void OperatorJacobiSmoother::Mult(const Vector &x, Vector &y) const
    MFEM_FORALL(i, height, Y[i] += DI[i] * R[i]; );
 }
 
-OperatorChebyshevSmoother::OperatorChebyshevSmoother(Operator* oper_,
+OperatorChebyshevSmoother::OperatorChebyshevSmoother(const Operator &oper_,
                                                      const Vector &d,
                                                      const Array<int>& ess_tdofs,
                                                      int order_, double max_eig_estimate_)
@@ -246,15 +246,15 @@ OperatorChebyshevSmoother::OperatorChebyshevSmoother(Operator* oper_,
    coeffs(order),
    ess_tdof_list(ess_tdofs),
    residual(N),
-   oper(oper_) { Setup(); }
+   oper(&oper_) { Setup(); }
 
 #ifdef MFEM_USE_MPI
-OperatorChebyshevSmoother::OperatorChebyshevSmoother(Operator* oper_,
+OperatorChebyshevSmoother::OperatorChebyshevSmoother(const Operator &oper_,
                                                      const Vector &d,
                                                      const Array<int>& ess_tdofs,
                                                      int order_, MPI_Comm comm, int power_iterations, double power_tolerance)
 #else
-OperatorChebyshevSmoother::OperatorChebyshevSmoother(Operator* oper_,
+OperatorChebyshevSmoother::OperatorChebyshevSmoother(const Operator &oper_,
                                                      const Vector &d,
                                                      const Array<int>& ess_tdofs,
                                                      int order_, int power_iterations, double power_tolerance)
@@ -267,7 +267,7 @@ OperatorChebyshevSmoother::OperatorChebyshevSmoother(Operator* oper_,
      coeffs(order),
      ess_tdof_list(ess_tdofs),
      residual(N),
-     oper(oper_)
+     oper(&oper_)
 {
    OperatorJacobiSmoother invDiagOperator(diag, ess_tdofs, 1.0);
    ProductOperator diagPrecond(&invDiagOperator, oper, false, false);
@@ -284,6 +284,28 @@ OperatorChebyshevSmoother::OperatorChebyshevSmoother(Operator* oper_,
    Setup();
 }
 
+OperatorChebyshevSmoother::OperatorChebyshevSmoother(const Operator* oper_,
+                                                     const Vector &d,
+                                                     const Array<int>& ess_tdofs,
+                                                     int order_, double max_eig_estimate_)
+   : OperatorChebyshevSmoother(*oper_, d, ess_tdofs, order_, max_eig_estimate_) { }
+
+#ifdef MFEM_USE_MPI
+OperatorChebyshevSmoother::OperatorChebyshevSmoother(const Operator* oper_,
+                                                     const Vector &d,
+                                                     const Array<int>& ess_tdofs,
+                                                     int order_, MPI_Comm comm, int power_iterations, double power_tolerance)
+   : OperatorChebyshevSmoother(*oper_, d, ess_tdofs, order_, comm,
+                               power_iterations, power_tolerance) { }
+#else
+OperatorChebyshevSmoother::OperatorChebyshevSmoother(const Operator* oper_,
+                                                     const Vector &d,
+                                                     const Array<int>& ess_tdofs,
+                                                     int order_, int power_iterations, double power_tolerance)
+   : OperatorChebyshevSmoother(*oper_, d, ess_tdofs, order_, power_iterations,
+                               power_tolerance) { }
+#endif
+
 void OperatorChebyshevSmoother::Setup()
 {
    // Invert diagonal
@@ -2533,7 +2555,7 @@ BlockILU::BlockILU(int block_size_,
      reordering(reordering_)
 { }
 
-BlockILU::BlockILU(Operator &op,
+BlockILU::BlockILU(const Operator &op,
                    int block_size_,
                    Reordering reordering_,
                    int k_fill_)

linalg/solvers.hpp

@@ -208,7 +208,13 @@ public:
        the matrix-free setting. The estimated largest eigenvalue of the
        diagonally preconditoned operator must be provided via
        max_eig_estimate. */
-   OperatorChebyshevSmoother(Operator* oper_, const Vector &d,
+   OperatorChebyshevSmoother(const Operator &oper_, const Vector &d,
+                             const Array<int>& ess_tdof_list,
+                             int order, double max_eig_estimate);
+
+   /// Deprecated: see pass-by-reference version above
+   MFEM_DEPRECATED
+   OperatorChebyshevSmoother(const Operator* oper_, const Vector &d,
                              const Array<int>& ess_tdof_list,
                              int order, double max_eig_estimate);
 
@@ -220,13 +226,28 @@ public:
        accuracy of the estimated eigenvalue may be controlled via
        power_iterations and power_tolerance. */
 #ifdef MFEM_USE_MPI
-   OperatorChebyshevSmoother(Operator* oper_, const Vector &d,
+   OperatorChebyshevSmoother(const Operator &oper_, const Vector &d,
+                             const Array<int>& ess_tdof_list,
+                             int order, MPI_Comm comm = MPI_COMM_NULL,
+                             int power_iterations = 10,
+                             double power_tolerance = 1e-8);
+
+   /// Deprecated: see pass-by-reference version above
+   MFEM_DEPRECATED
+   OperatorChebyshevSmoother(const Operator* oper_, const Vector &d,
                              const Array<int>& ess_tdof_list,
                              int order, MPI_Comm comm = MPI_COMM_NULL,
                              int power_iterations = 10,
                              double power_tolerance = 1e-8);
 #else
-   OperatorChebyshevSmoother(Operator* oper_, const Vector &d,
+   OperatorChebyshevSmoother(const Operator &oper_, const Vector &d,
+                             const Array<int>& ess_tdof_list,
+                             int order, int power_iterations = 10,
+                             double power_tolerance = 1e-8);
+
+   /// Deprecated: see pass-by-reference version above
+   MFEM_DEPRECATED
+   OperatorChebyshevSmoother(const Operator* oper_, const Vector &d,
                              const Array<int>& ess_tdof_list,
                              int order, int power_iterations = 10,
                              double power_tolerance = 1e-8);
@@ -731,7 +752,7 @@ public:
     *  case that @a op is a HypreParMatrix, the ILU factorization is performed
     *  on the diagonal blocks of the parallel decomposition.
     */
-   BlockILU(Operator &op, int block_size_ = 1,
+   BlockILU(const Operator &op, int block_size_ = 1,
             Reordering reordering_ = Reordering::MINIMUM_DISCARDED_FILL,
             int k_fill_ = 0);
 

makefile

@@ -37,6 +37,7 @@ MFEM makefile targets:
    make distclean
    make style
    make tags
+   make hooks
 
 Examples:
 
@@ -96,6 +97,8 @@ make style
 make tags
    Generate a vi or Emacs compatible TAGS file in ${MFEM_DIR}/TAGS. Requires
    functional "etags" and "egrep" in the user ${PATH}.
+make hooks
+   Creates symlinks to the hooks in the `.git/hooks` directory.
 endef
 
 # Save the MAKEOVERRIDES for cases where we explicitly want to pass the command
@@ -759,6 +762,15 @@ endif
 	@cd $(MFEM_REAL_DIR) && $(ETAGS_BIN) --class-qualify \
 	--declarations -o $(MFEM_REAL_DIR)/TAGS $(MFEM_TRACKED_SOURCE)
 
+# Creates symlinks to the hooks in the `.git/hooks` directory. Individual
+# hooks can be enabled by manually creating symlinks. Hooks can be customized
+# using hard copies (trading off with automated updates).
+.PHONY: hooks
+hooks:
+	@cd $(MFEM_DIR)/.git/hooks && \
+	ln -s ../../config/githooks/pre-commit pre-commit; \
+	ln -s ../../config/githooks/pre-push pre-push;
+
 # Print the contents of a makefile variable, e.g.: 'make print-MFEM_LIBS'.
 print-%:
 	$(info [ variable name]: $*)

mesh/mesh.cpp

@@ -11478,10 +11478,10 @@ FaceGeometricFactors::FaceGeometricFactors(const Mesh *mesh,
    const int NF   = fespace->GetNFbyType(type);
    const int NQ   = ir.GetNPoints();
 
-   const Operator *face_restr = fespace->GetFaceRestriction(
-                                   ElementDofOrdering::LEXICOGRAPHIC,
-                                   type,
-                                   L2FaceValues::SingleValued );
+   const FaceRestriction *face_restr = fespace->GetFaceRestriction(
+                                          ElementDofOrdering::LEXICOGRAPHIC,
+                                          type,
+                                          L2FaceValues::SingleValued );
    Vector Fnodes(face_restr->Height());
    face_restr->Mult(*nodes, Fnodes);
 

mesh/mesh_readers.cpp

@@ -691,16 +691,31 @@ struct BufferReader : BufferReaderBase
    BufferReader(bool compressed_, HeaderType header_type_)
       : compressed(compressed_), header_type(header_type_) { }
 
-   /// Return the number of bytes in the header. The header consists of one
-   /// integer if the data is uncompressed, and four integers if the data is
-   /// compressed. The integers are either 32 or 64 bytes depending on the value
-   /// of @a header_type.
-   int NumHeaderBytes() const
+   /// Return the number of bytes of each header entry.
+   size_t HeaderEntrySize() const
    {
-      int num_entries = compressed ? 4 : 1;
-      int entry_size = (header_type == UINT64_HEADER)
-                       ? sizeof(uint64_t) : sizeof(uint32_t);
-      return num_entries*entry_size;
+      return header_type == UINT64_HEADER ? sizeof(uint64_t) : sizeof(uint32_t);
+   }
+
+   /// Return the value of the header entry pointer to by @a header_buf. The
+   /// value is stored as either uint32_t or uint64_t, according to the @a
+   /// header_type, and is returned as uint64_t.
+   uint64_t ReadHeaderEntry(const char *header_buf) const
+   {
+      return (header_type == UINT64_HEADER) ? bin_io::read<uint64_t>(header_buf)
+             : bin_io::read<uint32_t>(header_buf);
+   }
+
+   /// Return the number of bytes in the header. The header consists of one
+   /// integer if the data is uncompressed, and @a N + 3 integers if the data is
+   /// compressed, where @a N is the number of blocks. The integers are either
+   /// 32 or 64 bytes depending on the value of @a header_type. The number of
+   /// blocks is determined by reading the first integer (of type @a
+   /// header_type) pointed to by @a header_buf.
+   int NumHeaderBytes(const char *header_buf) const
+   {
+      if (!compressed) { return HeaderEntrySize(); }
+      return (3 + ReadHeaderEntry(header_buf))*HeaderEntrySize();
    }
 
    /// Read @a n elements of type @a F from the source buffer @a buf into the
@@ -711,32 +726,42 @@ struct BufferReader : BufferReaderBase
    void ReadBinaryWithHeader(const char *header_buf, const char *buf,
                              void *dest_void, int n) const
    {
-      std::vector<unsigned char> uncompressed_data;
+      std::vector<char> uncompressed_data;
       T *dest = static_cast<T*>(dest_void);
 
       if (compressed)
       {
 #ifdef MFEM_USE_ZLIB
-         uint64_t header[4];
-         if (header_type == UINT32_HEADER)
+         // The header has format (where header_t is uint32_t or uint64_t):
+         //    header_t number_of_blocks;
+         //    header_t uncompressed_block_size;
+         //    header_t uncompressed_last_block_size;
+         //    header_t compressed_size[number_of_blocks];
+         int header_entry_size = HeaderEntrySize();
+         int nblocks = ReadHeaderEntry(header_buf);
+         header_buf += header_entry_size;
+         std::vector<int> header(nblocks + 2);
+         for (int i=0; i<nblocks+2; ++i)
          {
-            uint32_t *header_32 = (uint32_t *)header_buf;
-            for (int i=0; i<4; ++i) { header[i] = header_32[i]; }
+            header[i] = ReadHeaderEntry(header_buf);
+            header_buf += header_entry_size;
          }
-         else
+         uncompressed_data.resize((nblocks-1)*header[0] + header[1]);
+         Bytef *dest_ptr = (Bytef *)uncompressed_data.data();
+         Bytef *dest_start = dest_ptr;
+         const Bytef *source_ptr = (const Bytef *)buf;
+         for (int i=0; i<nblocks; ++i)
          {
-            uint64_t *header_64 = (uint64_t *)header_buf;
-            for (int i=0; i<4; ++i) { header[i] = header_64[i]; }
+            uLongf source_len = header[i+2];
+            uLong dest_len = (i == nblocks-1) ? header[1] : header[0];
+            int res = uncompress(dest_ptr, &dest_len, source_ptr, source_len);
+            MFEM_VERIFY(res == Z_OK, "Error uncompressing");
+            dest_ptr += dest_len;
+            source_ptr += source_len;
          }
-
-         MFEM_VERIFY(header[0] == 1, "Multiple compressed blocks not supported");
-         uLongf dest_len = header[1];
-         uncompressed_data.resize(dest_len);
-         int res = uncompress(uncompressed_data.data(), &dest_len,
-                              (const Bytef *)buf, header[3]);
-         MFEM_VERIFY(res == Z_OK, "Error uncompressing");
-         MFEM_VERIFY(sizeof(F)*n == dest_len, "AppendedData: wrong data size");
-         buf = (const char *)uncompressed_data.data();
+         MFEM_VERIFY(int(sizeof(F)*n) == (dest_ptr - dest_start),
+                     "AppendedData: wrong data size");
+         buf = uncompressed_data.data();
 #else
          MFEM_ABORT("MFEM must be compiled with zlib enabled to uncompress.")
 #endif
@@ -779,7 +804,7 @@ struct BufferReader : BufferReaderBase
    /// buffer @a dest. The input buffer contains both the header and the data.
    void ReadBinary(const char *buf, void *dest, int n) const override
    {
-      ReadBinaryWithHeader(buf, buf + NumHeaderBytes(), dest, n);
+      ReadBinaryWithHeader(buf, buf + NumHeaderBytes(buf), dest, n);
    }
 
    /// Read @a n elements of type @a F from base-64 encoded source buffer into
@@ -796,21 +821,25 @@ struct BufferReader : BufferReaderBase
       }
       if (compressed)
       {
-         std::vector<unsigned char> data, header;
+         // Decode the first entry of the header, which we need to determine
+         // how long the rest of the header is.
+         std::vector<char> nblocks_buf;
+         int nblocks_b64 = bin_io::NumBase64Chars(HeaderEntrySize());
+         bin_io::DecodeBase64(txt, nblocks_b64, nblocks_buf);
+         std::vector<char> data, header;
          // Compute number of characters needed to encode header in base 64,
          // then round to nearest multiple of 4 to take padding into account.
-         int b64_header = ((4*NumHeaderBytes()/3) + 3) & ~3;
+         int header_b64 = bin_io::NumBase64Chars(NumHeaderBytes(nblocks_buf.data()));
          // If data is compressed, header is encoded separately
-         bin_io::DecodeBase64(txt, b64_header, header);
-         bin_io::DecodeBase64(txt + b64_header, strlen(txt)-b64_header, data);
-         ReadBinaryWithHeader((const char *)header.data(),
-                              (const char *)data.data(), dest, n);
+         bin_io::DecodeBase64(txt, header_b64, header);
+         bin_io::DecodeBase64(txt + header_b64, strlen(txt)-header_b64, data);
+         ReadBinaryWithHeader(header.data(), data.data(), dest, n);
       }
       else
       {
-         std::vector<unsigned char> data;
+         std::vector<char> data;
          bin_io::DecodeBase64(txt, strlen(txt), data);
-         ReadBinary((const char *)data.data(), dest, n);
+         ReadBinary(data.data(), dest, n);
       }
    }
 };

mesh/ncmesh.cpp

@@ -4321,7 +4321,7 @@ const CoarseFineTransformations& NCMesh::GetRefinementTransforms()
    if (!transforms.embeddings.Size())
    {
       transforms.Clear();
-      transforms.embeddings.SetSize(leaf_elements.Size());
+      transforms.embeddings.SetSize(NElements);
 
       std::string ref_path;
       ref_path.reserve(100);
@@ -4455,7 +4455,8 @@ struct RefType
 void CoarseFineTransformations::GetCoarseToFineMap(
    const mfem::Mesh &fine_mesh, Table &coarse_to_fine,
    Array<int> &coarse_to_ref_type, Table &ref_type_to_matrix,
-   Array<mfem::Geometry::Type> &ref_type_to_geom) const
+   Array<mfem::Geometry::Type> &ref_type_to_geom,
+   bool get_coarse_to_fine_only) const
 {
    const int fine_ne = embeddings.Size();
    int coarse_ne = -1;
@@ -4495,6 +4496,11 @@ void CoarseFineTransformations::GetCoarseToFineMap(
       coarse_to_fine.GetJ()[i] = cf_j[i].two;
    }
 
+   if (get_coarse_to_fine_only) { return; }
+   MFEM_VERIFY(fine_mesh.GetLastOperation() != Mesh::Operation::DEREFINE,
+               "GetCoarseToFineMap is not fully supported for derefined meshes."
+               " Set 'get_coarse_to_fine_only=true'.")
+
    using internal::RefType;
    using std::map;
    using std::pair;
@@ -4536,6 +4542,18 @@ void CoarseFineTransformations::GetCoarseToFineMap(
    ref_type_to_matrix.ShiftUpI();
 }
 
+void CoarseFineTransformations::GetCoarseToFineMap(const Mesh &fine_mesh,
+                                                   Table &coarse_to_fine) const
+{
+   Array<int> coarse_to_ref_type;
+   Table ref_type_to_matrix;
+   Array<mfem::Geometry::Type> ref_type_to_geom;
+   bool get_coarse_to_fine_only = true;
+   GetCoarseToFineMap(fine_mesh, coarse_to_fine, coarse_to_ref_type,
+                      ref_type_to_matrix, ref_type_to_geom,
+                      get_coarse_to_fine_only);
+}
+
 void NCMesh::ClearTransforms()
 {
    coarse_elements.DeleteAll();

mesh/ncmesh.hpp

@@ -68,7 +68,11 @@ struct CoarseFineTransformations
                            Table &coarse_to_fine,
                            Array<int> &coarse_to_ref_type,
                            Table &ref_type_to_matrix,
-                           Array<Geometry::Type> &ref_type_to_geom) const;
+                           Array<Geometry::Type> &ref_type_to_geom,
+                           bool get_coarse_to_fine_only = false) const;
+
+   void GetCoarseToFineMap(const Mesh &fine_mesh,
+                           Table &coarse_to_fine) const;
 
    void Clear();
    bool IsInitialized() const;

mesh/pncmesh.hpp

@@ -297,9 +297,6 @@ protected: // implementation
 
    virtual void Update();
 
-   virtual int GetNumGhostElements() const { return NGhostElements; }
-   virtual int GetNumGhostVertices() const { return NGhostVertices; }
-
    /// Return the processor number for a global element number.
    int Partition(long index, long total_elements) const
    { return index * NRanks / total_elements; }

miniapps/shifted/diffusion.cpp

@@ -109,15 +109,19 @@ int main(int argc, char *argv[])
    args.Parse();
    if (!args.Good())
    {
-      args.PrintUsage(cout);
+      if (myid == 0)
+      {
+         args.PrintUsage(cout);
+      }
+      MPI_Finalize();
       return 1;
    }
-   args.PrintOptions(cout);
+   if (myid == 0) { args.PrintOptions(cout); }
 
    // Enable hardware devices such as GPUs, and programming models such as CUDA,
    // OCCA, RAJA and OpenMP based on command line options.
    Device device("cpu");
-   device.Print();
+   if (myid == 0) { device.Print(); }
 
    // Refine the mesh.
    Mesh mesh(mesh_file, 1, 1);

miniapps/solvers/div_free_solver.cpp

@@ -96,7 +96,7 @@ SparseMatrix* AggToInteriorDof(const Array<int>& bdr_truedofs,
                                const SparseMatrix& agg_elem,
                                const SparseMatrix& elem_dof,
                                const HypreParMatrix& dof_truedof,
-                               Array<int>& agg_starts)
+                               Array<HYPRE_Int>& agg_starts)
 {
    OperatorPtr agg_dof(Mult(agg_elem, elem_dof));
    SparseMatrix& agg_dof_ref = *agg_dof.As<SparseMatrix>();
@@ -131,7 +131,7 @@ SparseMatrix* AggToInteriorDof(const Array<int>& bdr_truedofs,
 
 void DFSSpaces::MakeDofRelationTables(int level)
 {
-   Array<int> agg_starts(Array<int>(l2_0_fes_->GetDofOffsets(), 2));
+   Array<HYPRE_Int> agg_starts(Array<HYPRE_Int>(l2_0_fes_->GetDofOffsets(), 2));
    auto& elem_agg = (const SparseMatrix&)*l2_0_fes_->GetUpdateOperator();
    OperatorPtr agg_elem(Transpose(elem_agg));
    SparseMatrix& agg_el = *agg_elem.As<SparseMatrix>();

tests/gitlab/build_and_test

@@ -110,6 +110,7 @@ then
     echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 
     cp ${hostconfig_path} ${project_dir}/config/
+    ln -sf ${build_root}/data ${project_dir}/../
 
     make all -j ${threads}
 fi

tests/unit/CMakeLists.txt

@@ -28,6 +28,7 @@ set(UNIT_TESTS_SRCS
   linalg/test_complex_operator.cpp
   linalg/test_constrainedsolver.cpp
   linalg/test_direct_solvers.cpp
+  linalg/test_fdsolver.cpp
   linalg/test_hypre_ilu.cpp
   linalg/test_ilu.cpp
   linalg/test_matrix_block.cpp

tests/unit/cunit_test_main.cpp

@@ -11,48 +11,14 @@
 
 #define CATCH_CONFIG_RUNNER
 #include "mfem.hpp"
-#include "unit_tests.hpp"
+#include "run_unit_tests.hpp"
 
 bool launch_all_non_regression_tests = false;
+std::string mfem_data_dir;
 
 int main(int argc, char *argv[])
 {
    mfem::Device device("cuda");
-
-   // There must be exactly one instance.
-   Catch::Session session;
-
-   // Build a new command line parser on top of Catch's
-   using namespace Catch::clara;
-   auto cli = session.cli() |
-              Opt(launch_all_non_regression_tests) ["--all"] ("all tests");
-   session.cli(cli);
-
-   // For floating point comparisons, print 8 digits for single precision
-   // values, and 16 digits for double precision values.
-   Catch::StringMaker<float>::precision = 8;
-   Catch::StringMaker<double>::precision = 16;
-
-   // Apply provided command line arguments.
-   int r = session.applyCommandLine(argc, argv);
-   if (r != 0) { return r; }
-
-   auto cfg = session.configData();
-
-   cfg.testsOrTags.push_back("[CUDA]");
-
-#ifdef MFEM_USE_MPI
-   // Exclude tests marked as Parallel in a serial run, even when compiled with
-   // MPI. This is done because there is no MPI session initialized.
-   cfg.testsOrTags.push_back("~[Parallel]");
-#endif
-
-   std::cout << "INFO: Test filter: [CUDA] ~[Parallel]" << std::endl;
-   device.Print();
-
-   session.useConfigData(cfg);
-
-   int result = session.run();
-
-   return result;
+   // Include only tests labeled with CUDA. Exclude parallel tests.
+   return RunCatchSession(argc, argv, {"[CUDA]", "~[Parallel]"});
 }

tests/unit/fem/test_datacollection.cpp

@@ -11,6 +11,7 @@
 
 #include "mfem.hpp"
 #include "unit_tests.hpp"
+#include "general/tinyxml2.h"
 #include <stdio.h>
 
 #ifndef _WIN32
@@ -235,3 +236,86 @@ TEST_CASE("Save and load from collections", "[DataCollection]")
    }
 
 }
+
+void SaveDataCollection(DataCollection &dc, int cycle, double t)
+{
+   dc.SetCycle(cycle);
+   dc.SetTime(t);
+   dc.Save();
+}
+
+TEST_CASE("ParaView restart mode", "[ParaView]")
+{
+   Mesh mesh = Mesh::MakeCartesian2D(2, 3, Element::QUADRILATERAL);
+   H1_FECollection fec(1, mesh.Dimension());
+   FiniteElementSpace fes(&mesh, &fec);
+   GridFunction u(&fes);
+   u = 0.0;
+
+   // Write initial dataset with three timesteps: 0, 1, 2.
+   {
+      ParaViewDataCollection dc("ParaView", &mesh);
+      dc.RegisterField("u", &u);
+      SaveDataCollection(dc, 0, 0);
+      SaveDataCollection(dc, 1, 1);
+      SaveDataCollection(dc, 2, 2);
+   }
+
+   // Using restart mode, append to the existing dataset, overwriting timesteps
+   // 1 and 2 with 1 and 1.5.
+   {
+      ParaViewDataCollection dc("ParaView", &mesh);
+      dc.UseRestartMode(true);
+      dc.RegisterField("u", &u);
+      SaveDataCollection(dc, 1, 1.0);
+      SaveDataCollection(dc, 2, 1.5);
+   }
+
+   // Parse the resulting PVD file, and verify that the structure is correct,
+   // and that it contains three timesteps: 0, 1, and 1.5.
+   using namespace tinyxml2;
+   auto StringCompare = [](const char *s1, const char *s2)
+   {
+      if (s1 == NULL || s2 == NULL) { return false; }
+      return strcmp(s1, s2) == 0;
+   };
+   auto VerifyDataset = [StringCompare](const XMLElement *ds, double t_ref)
+   {
+      REQUIRE(ds);
+      REQUIRE(StringCompare(ds->Name(), "DataSet"));
+      const char *timestep = ds->Attribute("timestep");
+      REQUIRE(timestep);
+      double t = std::stod(timestep);
+      REQUIRE(t == MFEM_Approx(t_ref));
+   };
+
+   XMLDocument xml;
+   xml.LoadFile("ParaView/ParaView.pvd");
+   REQUIRE(xml.ErrorID() == XML_SUCCESS);
+
+   const XMLElement *vtkfile = xml.FirstChildElement();
+   REQUIRE(vtkfile);
+   REQUIRE(StringCompare(vtkfile->Name(), "VTKFile"));
+   const XMLElement *collection = vtkfile->FirstChildElement();
+   REQUIRE(collection);
+   REQUIRE(StringCompare(collection->Name(), "Collection"));
+
+   const XMLElement *dataset = collection->FirstChildElement();
+   VerifyDataset(dataset, 0.0);
+   dataset = dataset->NextSiblingElement();
+   VerifyDataset(dataset, 1.0);
+   dataset = dataset->NextSiblingElement();
+   VerifyDataset(dataset, 1.5);
+   REQUIRE(dataset->NextSiblingElement() == NULL);
+
+   // Clean up
+   for (int c=0; c<=2; ++c)
+   {
+      std::string prefix = "ParaView/Cycle00000" + std::to_string(c);
+      REQUIRE(remove((prefix + "/data.pvtu").c_str()) == 0);
+      REQUIRE(remove((prefix + "/proc000000.vtu").c_str()) == 0);
+      REQUIRE(rmdir(prefix.c_str()) == 0);
+   }
+   REQUIRE(remove("ParaView/ParaView.pvd") == 0);
+   REQUIRE(rmdir("ParaView") == 0);
+}

tests/unit/fem/test_sum_bilin.cpp

@@ -167,9 +167,9 @@ TEST_CASE("DG SumIntegrator", "[SumIntegrator][PartialAssembly]")
    integ2.AssemblePAInteriorFaces(fes);
    integ_sum.AssemblePAInteriorFaces(fes);
 
-   const Operator *R_int = fes.GetFaceRestriction(
-                              ElementDofOrdering::LEXICOGRAPHIC,
-                              FaceType::Interior);
+   const FaceRestriction *R_int = fes.GetFaceRestriction(
+                                     ElementDofOrdering::LEXICOGRAPHIC,
+                                     FaceType::Interior);
 
    int n_int = R_int->Height();
    Vector x(n_int), y1(n_int), y2(n_int);
@@ -198,10 +198,10 @@ TEST_CASE("DG SumIntegrator", "[SumIntegrator][PartialAssembly]")
    integ2.AssemblePABoundaryFaces(fes);
    integ_sum.AssemblePABoundaryFaces(fes);
 
-   const Operator *R_bdr = fes.GetFaceRestriction(
-                              ElementDofOrdering::LEXICOGRAPHIC,
-                              FaceType::Boundary,
-                              L2FaceValues::DoubleValued);
+   const FaceRestriction *R_bdr = fes.GetFaceRestriction(
+                                     ElementDofOrdering::LEXICOGRAPHIC,
+                                     FaceType::Boundary,
+                                     L2FaceValues::DoubleValued);
 
    int n_bdr = R_bdr->Height();
    x.SetSize(n_bdr);

tests/unit/linalg/test_chebyshev.cpp

@@ -38,7 +38,7 @@ TEST_CASE("OperatorChebyshevSmoother", "[Chebyshev symmetry]")
       Vector diag(fespace.GetTrueVSize());
       aform.AssembleDiagonal(diag);
 
-      Solver* smoother = new OperatorChebyshevSmoother(opr.Ptr(), diag, ess_tdof_list,
+      Solver* smoother = new OperatorChebyshevSmoother(*opr, diag, ess_tdof_list,
                                                        cheb_order);
 
       int n = smoother->Width();

tests/unit/linalg/test_fdsolver.cpp

@@ -0,0 +1,126 @@
+// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+// LICENSE and NOTICE for details. LLNL-CODE-806117.
+//
+// This file is part of the MFEM library. For more information and source code
+// availability visit https://mfem.org.
+//
+// MFEM is free software; you can redistribute it and/or modify it under the
+// terms of the BSD-3 license. We welcome feedback and contributions, see file
+// CONTRIBUTING.md for details.
+
+#include "mfem.hpp"
+#include "unit_tests.hpp"
+
+using namespace mfem;
+
+#ifdef MFEM_USE_LAPACK
+
+TEST_CASE("FDSolver",
+          "[FDSolver]")
+{
+   double tol = 1e-10;
+
+   // SPD matrices
+   DenseMatrix A0(
+   {
+      {
+         1.29919, 0.61256, 0.82545
+      },
+      {0.61256, 0.57891, 0.39662},
+      {0.82545, 0.39662, 0.57541}
+   });
+
+   DenseMatrix A1(
+   {
+      {0.748236, 0.701663, 0.607517, 0.236740},
+      {0.701663, 0.809316, 0.713186, 0.256070},
+      {0.607517, 0.713186, 0.794221, 0.233943},
+      {0.236740, 0.256070, 0.233943, 0.083129}
+   });
+
+   DenseMatrix B0(
+   {
+      {0.13483, 0.51389, 0.43052},
+      {0.51389, 2.26750, 1.86331},
+      {0.43052, 1.86331, 1.59869}
+   });
+
+   DenseMatrix B1(
+   {
+      {0.94177, 1.02400, 1.14743, 0.35723},
+      {1.02400, 1.79087, 1.78708, 0.78304},
+      {1.14743, 1.78708, 2.06259, 0.80837},
+      {0.35723, 0.78304, 0.80837, 1.01798}
+   });
+
+
+   SECTION("2D")
+   {
+      Array<DenseMatrix *> A(2), B(2);
+      A[0] = &A0;  A[1] = &A1;
+      B[0] = &B0;  B[1] = &B1;
+
+      Vector y(12); y.Randomize(1);
+      Vector x(12), diff(12);
+
+      FDSolver S(A,B);
+      S.Mult(y,x);
+
+      DenseMatrix C1, C;
+      KronProd(A0, B1, C1);
+      KronProd(B0, A1, C);
+
+      C.Add(1., C1);
+
+      DenseMatrixInverse Cinv(C);
+      Cinv.Mult(y,diff);
+
+      diff-=x;
+      REQUIRE(diff.Norml2() < tol);
+   }
+
+
+   SECTION("3D")
+   {
+      DenseMatrix A2(
+      {
+         {1.14593, 0.76119},
+         {0.76119, 0.78993}
+      });
+      DenseMatrix B2(
+      {
+         {0.88088, 0.37899},
+         {0.37899, 0.45096}
+      });
+      Array<DenseMatrix *> A(3), B(3);
+      A[0] = &A0;  A[1] = &A1; A[2] = &A2;
+      B[0] = &B0;  B[1] = &B1; B[2] = &B2;
+
+      Vector y(24); y.Randomize(1);
+      Vector x(24), diff(24);
+
+      FDSolver S(A,B);
+      S.Mult(y,x);
+
+      DenseMatrix Temp, C0, C1, C;
+
+      KronProd(A0, B1, Temp);
+      KronProd(Temp, B2, C0);
+      KronProd(B0, A1, Temp);
+      KronProd(Temp, B2, C1);
+      KronProd(B0, B1, Temp);
+      KronProd(Temp, A2, C);
+
+      C.Add(1.,C0);
+      C.Add(1.,C1);
+
+      DenseMatrixInverse Cinv(C);
+      Cinv.Mult(y,diff);
+
+      diff-=x;
+      REQUIRE(diff.Norml2() < tol);
+   }
+}
+
+#endif // if MFEM_USE_LAPACK

tests/unit/linalg/test_matrix_dense.cpp

@@ -12,6 +12,8 @@
 #include "mfem.hpp"
 #include "unit_tests.hpp"
 #include "linalg/dtensor.hpp"
+#include "nvToolsExt.h"
+#include "nvToolsExtCudaRt.h"
 
 using namespace mfem;
 
@@ -239,6 +241,212 @@ TEST_CASE("DenseMatrix A*B^T methods",
    }
 }
 
+TEST_CASE("KronMult methods",
+          "[DenseMatrix], [CUDA]")
+{
+   double tol = 1e-12;
+   int nA = 3, mA = 4;
+   int nB = 5, mB = 6;
+   DenseMatrix A(nA,mA);
+   DenseMatrix B(nB,mB);
+
+   for (int i = 0; i<nA; i++)
+      for (int j = 0; j<mA; j++)
+      {
+         A(i,j) = ((double)rand()/(double)RAND_MAX);
+      }
+
+   for (int i = 0; i<nB; i++)
+      for (int j = 0; j<mB; j++)
+      {
+         B(i,j) = ((double)rand()/(double)RAND_MAX);
+      }
+
+   DenseMatrix AB;
+   KronProd(A,B,AB);
+   AB.HostRead();
+
+   // (A ⊗ B) r
+   SECTION("KronMultABr")
+   {
+      nvtxRangePush("KronMultABr");
+      Vector r(mA*mB);
+      MFEM_VERIFY(r.Size() == AB.Width(), "Check r size");
+
+      r.HostReadWrite();
+      r.Randomize();
+
+      Vector z0(AB.Height());
+      AB.Mult(r,z0);
+      //z0.HostRead();
+      Vector z1;
+      KronMult(A,B,r,z1);
+      MFEM_VERIFY(z0.Size() == z1.Size(), "Check z1 size");
+      z0-=z1;
+      REQUIRE(z0.Norml2() < tol);
+      nvtxRangePop();
+   }
+
+
+   // (A ⊗ B) R
+   SECTION("KronMultABR")
+   {
+      nvtxRangePush("KronMultABR");
+      int nR = mA*mB;
+      int mR = 7;
+      DenseMatrix R(nR, mR);
+      R.HostReadWrite();
+
+      for (int i = 0; i<nR; i++)
+         for (int j = 0; j<mR; j++)
+         {
+            R(i,j) = ((double)rand()/(double)RAND_MAX);
+         }
+
+      DenseMatrix Z0(nA*nB,mR);
+      Mult(AB,R,Z0);
+
+      DenseMatrix Z1;
+      KronMult(A,B,R,Z1);
+      MFEM_VERIFY(Z0.Height() == Z1.Height() &&
+                  Z0.Width() == Z1.Width(), "Check z1 size");
+      Z0-=Z1;
+
+      REQUIRE(Z0.MaxMaxNorm() < tol);
+
+      nvtxRangePop();
+   }
+
+   // (A ⊗ B ⊗ C) r
+   SECTION("KronMultABCr")
+   {
+      nvtxRangePush("KronMultABCr");
+
+      int nC = 7, mC = 2;
+      DenseMatrix C(nC, mC);
+
+      C.HostReadWrite();
+
+      for (int i = 0; i<nC; i++)
+         for (int j = 0; j<mC; j++)
+         {
+            C(i,j) = ((double)rand()/(double)RAND_MAX);
+         }
+
+      DenseMatrix ABC;
+      KronProd(AB,C,ABC);
+
+      Vector r(mA*mB*mC);
+      r.HostReadWrite();
+      r.Randomize();
+
+      MFEM_VERIFY(r.Size() == ABC.Width(), "Check r size");
+      Vector z0(nA*nB*nC);
+      ABC.Mult(r,z0);
+
+      Vector z1;
+      KronMult(A,B,C,r,z1);
+      MFEM_VERIFY(z0.Size() == z1.Size(), "Check z1 size");
+      z0-=z1;
+      REQUIRE(z0.Norml2() < tol);
+
+      nvtxRangePop();
+   }
+}
+
+TEST_CASE("KronMultInv methods",
+          "[DenseMatrixInverse]")
+{
+   double tol = 1e-12;
+   int nA = 3;
+   int nB = 2;
+   DenseMatrix A(
+   {
+      { 1.0,  0.2, 3.4},
+      {-2.0, -1.0, 3.1},
+      { 0.7,  1.4,-0.9}
+   });
+   DenseMatrix B(
+   {
+      {-10.1, 5.7},
+      {-3.0,  4.2}
+   });
+
+   DenseMatrixInverse Ainv(A);
+   DenseMatrixInverse Binv(B);
+
+   DenseMatrix AB;
+   KronProd(A,B,AB);
+
+   // (A^-1 ⊗ B^-1) r
+   SECTION("KronMultInvABr")
+   {
+
+      Vector r(nA*nB); r.Randomize();
+      MFEM_VERIFY(r.Size() == AB.Width(), "Check r size");
+      Vector z0(AB.Height());
+      DenseMatrixInverse ABinv(AB);
+      ABinv.Mult(r,z0);
+
+      Vector z1;
+      KronMult(Ainv,Binv,r,z1);
+      MFEM_VERIFY(z0.Size() == z1.Size(), "Check z1 size");
+      z0-=z1;
+      REQUIRE(z0.Norml2() < tol);
+   }
+
+   // (A^-1 ⊗ B^-1) R
+   SECTION("KronMultInvABR")
+   {
+      int nR = nA*nB;
+      int mR = 7;
+      DenseMatrix R(nR, mR);
+      for (int i = 0; i<nR; i++)
+         for (int j = 0; j<mR; j++)
+         {
+            R(i,j) = ((double)rand()/(double)RAND_MAX);
+         }
+
+      DenseMatrixInverse ABinv(AB);
+      DenseMatrix Z0(nA*nB,mR);
+      ABinv.Mult(R,Z0);
+
+      DenseMatrix Z1;
+      KronMult(Ainv,Binv,R,Z1);
+      MFEM_VERIFY(Z0.Height() == Z1.Height() &&
+                  Z0.Width() == Z1.Width(), "Check z1 size");
+      Z0-=Z1;
+
+      REQUIRE(Z0.MaxMaxNorm() < tol);
+   }
+
+   // (A^-1 ⊗ B^-1 ⊗ C^-1) r
+   SECTION("KronMultInvABCr")
+   {
+      int nC = 4;
+      DenseMatrix C(
+      {
+         {-2.1, 1.6, -3.4,  17.5},
+         {-7.1, 1.3, -7.5, -12.5},
+         { 0.5, 5.7, -6.0, -0.5},
+         { 9.2, 0.3, -1.4, -14.9}
+      });
+      DenseMatrix ABC;
+      KronProd(AB,C,ABC);
+      DenseMatrixInverse ABCInv(ABC);
+      Vector r(nA*nB*nC); r.Randomize();
+      MFEM_VERIFY(r.Size() == ABC.Width(), "Check r size");
+      Vector z0(nA*nB*nC);
+      ABCInv.Mult(r,z0);
+
+      DenseMatrixInverse Cinv(C);
+      Vector z1;
+      KronMult(Ainv,Binv,Cinv,r,z1);
+      MFEM_VERIFY(z0.Size() == z1.Size(), "Check z1 size");
+      z0-=z1;
+      REQUIRE(z0.Norml2() < tol);
+   }
+}
 
 TEST_CASE("LUFactors RightSolve", "[DenseMatrix]")
 {
@@ -314,6 +522,88 @@ TEST_CASE("DenseTensor LinearSolve methods",
    }
 }
 
+#ifdef MFEM_USE_LAPACK
+
+TEST_CASE("EigenSystem methods",
+          "[DenseMatrix]")
+{
+   double tol = 1e-12;
+   SECTION("SPD Matrix")
+   {
+      DenseMatrix A({{0.56806, 0.29211, 0.48315, 0.70024},
+         {0.29211, 0.85147, 0.68123, 0.70689},
+         {0.48315, 0.68123, 1.07229, 1.02681},
+         {0.70024, 0.70689, 1.02681, 1.15468}
+      });
+      DenseMatrix V, AV(4);
+      Vector Lambda;
+      for (bool sym: { false, true })
+      {
+         DenseMatrixEigensystem  EigA(A,sym);
+         EigA.Eval();
+         V = EigA.Eigenvectors();
+         Lambda = EigA.Eigenvalues();
+         Mult(A,V,AV);
+         V.RightScaling(Lambda);
+         AV -= V;
+         REQUIRE(AV.MaxMaxNorm() < tol);
+      }
+   }
+
+   SECTION("Indefinite Matrix")
+   {
+      DenseMatrix A({{0.486278, 0.041135, 0.480727, 0.616026},
+         {0.523599, 0.119827, 0.087808, 0.415241},
+         {0.214454, 0.661631, 0.909626, 0.744259},
+         {0.107007, 0.630604, 0.077862, 0.221006}
+      });
+      DenseMatrixEigensystem  EigA(A);
+      EigA.Eval();
+
+      Vector Lambda_r, Lambda_i;
+      // Real part of eigenvalues
+      Lambda_r = EigA.Eigenvalues();
+      // Imag part of eigenvalues
+      Lambda_i = EigA.Eigenvalues(true);
+
+      DenseMatrix V;
+      V = EigA.Eigenvectors();
+      // Real part of eigenvectors
+      DenseMatrix Vr(4), Vi(4);
+      Vr.SetCol(0,V.GetColumn(0));
+      Vr.SetCol(1,V.GetColumn(1));
+      Vr.SetCol(2,V.GetColumn(1));
+      Vr.SetCol(3,V.GetColumn(3));
+
+      // Imag part of eigenvectors
+      Vector vi(4); V.GetColumn(2,vi);
+      Vi.SetCol(0,0.);
+      Vi.SetCol(1,vi); vi *= -1.;
+      Vi.SetCol(2,vi);
+      Vi.SetCol(3,0.);
+
+      // Check that A*V = V * Lambda
+      // or A * (V_r + i V_i ) = (V_r + i V_i)*(Lamda_r + i Lambda_i)
+      // or  A * V_r = V_r * Lambda_r -  V_i * Lambda_i
+      // and A * V_i = V_r ( Lambda_i +  V_i * Lambda_r
+      DenseMatrix AVr(4), AVi(4);
+      Mult(A,Vr, AVr);
+      Mult(A,Vi, AVi);
+
+      DenseMatrix Vrlr = Vr; Vrlr.RightScaling(Lambda_r);
+      DenseMatrix Vrli = Vr; Vrli.RightScaling(Lambda_i);
+      DenseMatrix Vilr = Vi; Vilr.RightScaling(Lambda_r);
+      DenseMatrix Vili = Vi; Vili.RightScaling(Lambda_i);
+
+      AVr -= Vrlr; AVr+= Vili;
+      AVi -= Vrli; AVi-= Vilr;
+
+      REQUIRE(AVr.MaxMaxNorm() < tol);
+      REQUIRE(AVi.MaxMaxNorm() < tol);
+   }
+}
+
+#endif // if MFEM_USE_LAPACK
 TEST_CASE("DenseTensor copy", "[DenseMatrix][DenseTensor]")
 {
    DenseTensor t1(2,3,4);

tests/unit/makefile

@@ -214,21 +214,27 @@ $(DATA_DIR):
 MFEM_TESTS = UNIT_TESTS
 include $(MFEM_TEST_MK)
 
+ifeq (,$(wildcard $(MFEM_DIR)/../data))
+   MFEM_DATA_FLAG =
+else
+   MFEM_DATA_FLAG = --data $(MFEM_DIR)/../data
+endif
+
 %-test-seq: %
-	@$(call mfem-test,$<,, Unit tests,,SKIP-NO-VIS)
+	@$(call mfem-test,$<,, Unit tests,$(MFEM_DATA_FLAG),SKIP-NO-VIS)
 
 ceed_tests-test-seq: ceed_tests
-	@$(call mfem-test,$<,, CEED Unit tests (cpu),--device ceed-cpu,SKIP-NO-VIS)
+	@$(call mfem-test,$<,, CEED Unit tests (cpu),--device ceed-cpu $(MFEM_DATA_FLAG),SKIP-NO-VIS)
 ifeq ($(MFEM_USE_CUDA),YES)
-	@$(call mfem-test,$<,, CEED Unit tests (cuda-ref),--device ceed-cuda:/gpu/cuda/ref,SKIP-NO-VIS)
-	@$(call mfem-test,$<,, CEED Unit tests (cuda-shared),--device ceed-cuda:/gpu/cuda/shared,SKIP-NO-VIS)
-	@$(call mfem-test,$<,, CEED Unit tests (cuda-gen),--device ceed-cuda:/gpu/cuda/gen,SKIP-NO-VIS)
+	@$(call mfem-test,$<,, CEED Unit tests (cuda-ref),--device ceed-cuda:/gpu/cuda/ref $(MFEM_DATA_FLAG),SKIP-NO-VIS)
+	@$(call mfem-test,$<,, CEED Unit tests (cuda-shared),--device ceed-cuda:/gpu/cuda/shared $(MFEM_DATA_FLAG),SKIP-NO-VIS)
+	@$(call mfem-test,$<,, CEED Unit tests (cuda-gen),--device ceed-cuda:/gpu/cuda/gen $(MFEM_DATA_FLAG),SKIP-NO-VIS)
 endif
 
 RUN_MPI = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP)
 %-test-par: %
-	@$(call mfem-test,$<, $(RUN_MPI) 1, Parallel unit tests,,SKIP-NO-VIS)
-	@$(call mfem-test,$<, $(RUN_MPI) $(MFEM_MPI_NP), Parallel unit tests,,SKIP-NO-VIS)
+	@$(call mfem-test,$<, $(RUN_MPI) 1, Parallel unit tests,$(MFEM_DATA_FLAG),SKIP-NO-VIS)
+	@$(call mfem-test,$<, $(RUN_MPI) $(MFEM_MPI_NP), Parallel unit tests,$(MFEM_DATA_FLAG),SKIP-NO-VIS)
 
 # Generate an error message if the MFEM library is not built and exit
 $(MFEM_LIB_FILE):
@@ -237,4 +243,3 @@ $(MFEM_LIB_FILE):
 clean:
 	rm -f $(SEQ_UNIT_TESTS) $(PAR_UNIT_TESTS) *.o */*.o */*~ *~
 	rm -rf *.dSYM output_meshes
-

tests/unit/mesh/test_vtu.cpp

@@ -41,3 +41,21 @@ TEST_CASE("VTU XML Reader", "[Mesh][VTU][XML]")
       REQUIRE(mesh.GetNumGeometries(2) == 1);
    }
 }
+
+TEST_CASE("VTU XML Compressed Blocks", "[VTU][XML][MFEMData]")
+{
+   auto filename = GENERATE(
+                      "bracket_appended_compressed.vtu",
+                      "bracket_appended_encoded_compressed.vtu",
+                      "bracket_inline_compressed.vtu"
+                   );
+
+   std::string mesh_path = mfem_data_dir + "/vtk/" + filename;
+   Mesh mesh = Mesh::LoadFromFile(mesh_path.c_str());
+
+   REQUIRE(mesh.Dimension() == 3);
+   REQUIRE(mesh.GetNE() == 206208);
+   REQUIRE(mesh.GetNV() == 50000);
+   REQUIRE(mesh.HasGeometry(Geometry::TETRAHEDRON));
+   REQUIRE(mesh.GetNumGeometries(3) == 1);
+}

tests/unit/miniapps/test_tmop_pa.cpp

@@ -186,10 +186,12 @@ int tmop(int id, Req &res, int argc, char *argv[])
       case   2: metric = new TMOP_Metric_002; break;
       case   7: metric = new TMOP_Metric_007; break;
       case  77: metric = new TMOP_Metric_077; break;
+      case  80: metric = new TMOP_Metric_080(0.5); break;
       case 302: metric = new TMOP_Metric_302; break;
       case 303: metric = new TMOP_Metric_303; break;
       case 315: metric = new TMOP_Metric_315; break;
       case 321: metric = new TMOP_Metric_321; break;
+      case 332: metric = new TMOP_Metric_332(0.5); break;
       default:
       {
          if (id == 0) { cout << "Unknown metric_id: " << metric_id << endl; }
@@ -740,6 +742,13 @@ static void tmop_tests(int id = 0, bool all = false)
           POR({1,2}).QOR({2,4}).
           TID({4}).MID({1,2})).Run(id,all);
 
+   Launch(Launch::Args("Square01 + Adapted discrete size").
+          MESH("../../miniapps/meshing/square01.mesh").REFINE(1).
+          NORMALIZATION(true).
+          POR({1,2}).QOR({4,6}).
+          LINEAR_ITERATIONS(150).
+          TID({5}).MID({80}).LS({3})).Run(id,all);
+
    Launch(Launch::Args("Blade").
           MESH("../../miniapps/meshing/blade.mesh").
           POR({1,2}).QOR({2,4}).
@@ -768,6 +777,12 @@ static void tmop_tests(int id = 0, bool all = false)
           POR({1,2}).QOR({4,2}).
           TID({7}).MID({302,321})).Run(id,all);
 
+   Launch(Launch::Args("Cube + Discrete size + normalization").
+          MESH("../../miniapps/meshing/cube.mesh").
+          NORMALIZATION(true).
+          POR({1,2}).QOR({4,2}).
+          TID({5}).MID({332})).Run(id,all);
+
    // Note: order 1 has no interior nodes, so all residuals are zero and the
    // Newton iteration exits immediately.
    Launch(Launch::Args("Toroid-Hex").