Modify ex26 with anisotropic diffusion and ILU smoothing

.appveyor.yml

@@ -1,13 +1,10 @@
 version: '{build}'
 
 # https://www.appveyor.com/docs/build-environment/#build-worker-images
-image: Visual Studio 2019
+image: Visual Studio 2017
 
 install:
 
-# Start from outside clone directory
-- cd ..
-
 # Install MS-MPI
 - ps: Start-FileDownload 'https://download.microsoft.com/download/B/2/E/B2EB83FE-98C2-4156-834A-E1711E6884FB/MSMpiSetup.exe'
 - MSMpiSetup.exe -unattend
@@ -18,11 +15,6 @@ install:
 - msmpisdk.msi /passive
 - set PATH=C:\Program Files\Microsoft MPI\Bin;%PATH%
 
-# Set MSMPI environment variables needed for CMake detection
-- set MSMPI_LIB32=C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86
-- set MSMPI_LIB64=C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x64
-- set MSMPI_INC=C:\Program Files (x86)\Microsoft SDKs\MPI\Include
-
 # Install METIS, use a mirror because the original source server is not always
 # up. Original url:
 #    http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz
@@ -33,24 +25,20 @@ install:
 - cmake -H. -Bbuild
 # -DCMAKE_BUILD_TYPE=Release
 - cmake --build build
-- set METIS_PATH=%cd%
 - cd ..
 
 # Install hypre
 - ps: Start-FileDownload 'https://github.com/hypre-space/hypre/archive/v2.19.0.tar.gz'
 - 7z x v2.19.0.tar.gz -so | 7z x -si -ttar > nul
 - cd hypre-2.19.0/src
-- cmake -H. -Bbuild
+- cmake -H. -Bbuild -DMPI_C_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DMPI_C_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include"
 - cmake --build build
 - cmake --build build --target install
 - cd ../..
 
-# Return to clone directory
-- cd %APPVEYOR_BUILD_FOLDER%
-
 # MFEM
 before_build:
-- cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_parallel -DMFEM_USE_MPI=TRUE -DMFEM_USE_METIS_5=TRUE -DHYPRE_DIR=%cd%\..\hypre-2.19.0\src\hypre -DMETIS_LIBRARIES=%METIS_PATH%\build\libmetis\Debug\metis.lib -DMETIS_INCLUDE_DIRS=%METIS_PATH%\include
+- cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_parallel -DMFEM_USE_MPI=TRUE -DMFEM_USE_METIS_5=TRUE -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DHYPRE_DIR=%cd%\hypre-2.19.0\src\hypre -DMETIS_LIBRARIES=%cd%\metis-5.1.0\build\libmetis\Debug\metis.lib -DMETIS_INCLUDE_DIRS=%cd%\metis-5.1.0\include
 - cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_serial -DMFEM_USE_MPI=FALSE
 
 build_script:

.binder/environment.yml

@@ -5,7 +5,7 @@ channels:
 dependencies:
 - xeus-cling=0.13.0
 - xwidgets=0.26.0
-# NOTE: it is possible that these are not needed for the lab frontend
+# NOTE: it's possible these aren't needed for the lab frontend
 - widgetsnbextension=3.5.1
 - pip
 - pip:

.github/workflows/README.md

@@ -1,48 +0,0 @@
-                    Finite Element Discretization Library
-                                   __
-                       _ __ ___   / _|  ___  _ __ ___
-                      | '_ ` _ \ | |_  / _ \| '_ ` _ \
-                      | | | | | ||  _||  __/| | | | | |
-                      |_| |_| |_||_|   \___||_| |_| |_|
-
-                               https://mfem.org
-
-
-This directory contains the GitHub CI scripts for MFEM.
-
-Note that some of these scripts use the shared MFEM GitHub Actions from the external mfem/github-actions repository:
-
-  https://github.com/mfem/github-actions
-
-For a particular action, e.g. `mfem/github-actions/build-mfem@v2.1`, the `v2.1` suffix denotes the branch in the above from which the action is taken.
-
-The current CI workflows are:
-
-### `repo-check.yml`
-
-Runs a number of static repository-level sanity checks.
-
-- `file-headers-check` checks copyright date, license, etc. using the `--copyright`, `--license` and `--release` options of the `config/githooks/pre-push` script.
-
-- `code-style` checks the code style using the `--style` option of the `config/githooks/pre-push` script.
-
-- `documentation` checks the documentation build using the `tests/scripts/documentation` script.
-
-- `branch-history` guards against accidental commits of large files using the `--history` option of the `config/githooks/pre-push` script.
-
-### `mfem-analysis.yml` (`build-analysis`)
-
-Checks if the code builds and satisfies minimal requirements.
-
-- `gitignore` builds hypre, METIS, and MFEM using `mfem/github-actions/build-hypre`, `mfem/github-actions/build-metis`, and `mfem/github-actions/build-mfem` and checks for correct `.gitignore` settings by running the `tests/scripts/gitignore` script.
-
-### `builds-and-tests.yml`
-
-Runs a matrix of builds and tests runs with different compilers, OS, mfem/hypre settings, etc. Also processes and upload Codecov reports.
-
-Uses the following GitHub Actions from https://github.com/mfem/github-actions:
-
-- `mfem/github-actions/build-hypre`
-- `mfem/github-actions/build-metis`
-- `mfem/github-actions/build-mfem`
-- `mfem/github-actions/upload-coverage`

.github/workflows/build-container.yaml

@@ -1,82 +0,0 @@
-name: Build Deploy Container
-
-on:
-
-  # Always have a base image ready to go - this is a nightly build
-  schedule:
-    - cron: 0 3 * * *
-
-  # Allow manual trigger of a build
-  workflow_dispatch:
-
-  # On push to main we build and deploy images
-  push:
-    branches:
-      - master
-
-  # Publish packages on release
-  release:
-    types: [published]
-
-jobs:
-  build:
-    if: github.repository == 'mfem/mfem' # Don't run in forks
-    permissions:
-      packages: write
-    strategy:
-      fail-fast: false
-      matrix:
-
-        # Dockerfiles to build, a matrix supports future expanded builds
-        container: [["config/docker/Dockerfile.base", "ghcr.io/mfem/mfem-ubuntu-base"],
-                    ["config/docker/Dockerfile", "ghcr.io/mfem/mfem-ubuntu"]]
-
-    runs-on: ubuntu-latest
-    name: Build
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-
-      - name: Make Space For Build
-        run: |
-          sudo rm -rf /usr/share/dotnet
-          sudo rm -rf /opt/ghc
-
-       # It's easier to reference named variables than indexes of the matrix
-      - name: Set Environment
-        env:
-          dockerfile: ${{ matrix.container[0] }}
-          uri: ${{ matrix.container[1] }}
-        run: |
-          echo "dockerfile=$dockerfile" >> $GITHUB_ENV
-          echo "uri=$uri" >> $GITHUB_ENV
-
-      - name: Pull previous layers for cache
-        run: docker pull ${uri}:latest || echo "No container to pull"
-
-      - name: Build Container
-        run: |
-           container=$uri:latest
-           docker build -f ${dockerfile} -t ${container} .
-           echo "container=$container" >> $GITHUB_ENV
-
-      - name: GHCR Login
-        if: (github.event_name != 'pull_request')
-        uses: docker/login-action@v1
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Deploy
-        if: (github.event_name != 'pull_request')
-        run: |
-            docker push ${container}
-
-      - name: Tag and Push Release
-        if: (github.event_name == 'release')
-        run: |
-            tag=${GITHUB_REF#refs/tags/}
-            echo "Tagging and releasing ${uri}:${tag}"
-            docker tag ${uri}:latest ${uri}:${tag}
-            docker push ${uri}:${tag}

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

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -27,7 +27,6 @@ on:
       - master
       - next
   pull_request:
-  workflow_dispatch:
 
 env:
   HYPRE_ARCHIVE: v2.19.0.tar.gz
@@ -47,18 +46,11 @@ jobs:
   builds-and-tests:
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-10.15, windows-2022]
+        os: [ubuntu-18.04, macos-10.15]
         target: [dbg, opt]
         mpi: [seq, par]
-        build-system: [make, cmake]
+        build-system: [make]
         hypre-target: [int32]
-        exclude:
-          - os: ubuntu-20.04
-            build-system: cmake
-          - os: macos-10.15
-            build-system: cmake
-          - os: windows-2022
-            build-system: make
         # 'include' allows us to:
         # - Add a variable to all jobs without creating a new matrix dimension.
         #   Codecov is defined that way.
@@ -72,15 +64,13 @@ jobs:
             codecov: NO
           - target: opt
             codecov: YES
-          - os: windows-2022
-            codecov: NO
-          - os: ubuntu-20.04
+          - os: ubuntu-18.04
             target: opt
             codecov: NO
             mpi: par
             build-system: cmake
             hypre-target: int32
-          - os: ubuntu-20.04
+          - os: ubuntu-18.04
             target: opt
             codecov: NO
             mpi: par
@@ -112,13 +102,13 @@ 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 == 'par' && matrix.os == 'ubuntu-20.04'
+      if: matrix.mpi == 'par' && matrix.os == 'ubuntu-18.04'
       run: |
         sudo apt-get install mpich libmpich-dev
         export MAKE_CXX_FLAG="MPICXX=mpic++"
 
     - name: get lcov (Linux)
-      if: matrix.codecov == 'YES' && matrix.os == 'ubuntu-20.04'
+      if: matrix.codecov == 'YES' && matrix.os == 'ubuntu-18.04'
       run: |
         sudo apt-get install lcov
 
@@ -139,10 +129,6 @@ jobs:
         export HOMEBREW_NO_INSTALL_CLEANUP=1
         brew install lcov
 
-    - name: get MPI (Windows)
-      if: matrix.mpi == 'par' && matrix.os == 'windows-2022'
-      uses: mpi4py/setup-mpi@v1.0.3
-
     # Get Hypre through cache, or build it.
     # Install will only run on cache miss.
     - name: cache hypre
@@ -151,71 +137,36 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ${{ env.HYPRE_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-${{ matrix.hypre-target }}-v2.2
+        key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-${{ matrix.hypre-target }}-v2.0
 
     - name: get hypre
-      if: matrix.mpi == 'par' && steps.hypre-cache.outputs.cache-hit != 'true' && matrix.os != 'windows-2022'
-      uses: mfem/github-actions/build-hypre@v2.2
+      if: matrix.mpi == 'par' && steps.hypre-cache.outputs.cache-hit != 'true'
+      uses: mfem/github-actions/build-hypre@v2.0
       with:
         archive: ${{ env.HYPRE_ARCHIVE }}
         dir: ${{ env.HYPRE_TOP_DIR }}
         target: ${{ matrix.hypre-target }}
-        build-system: make
-
-    - name: get hypre (Windows)
-      if: matrix.mpi == 'par' && steps.hypre-cache.outputs.cache-hit != 'true' && matrix.os == 'windows-2022'
-      uses: mfem/github-actions/build-hypre@v2.2
-      with:
-        archive: ${{ env.HYPRE_ARCHIVE }}
-        dir: ${{ env.HYPRE_TOP_DIR }}
-        target: ${{ matrix.hypre-target }}
-        build-system: cmake
 
     # Get Metis through cache, or build it.
     # Install will only run on cache miss.
     - name: cache metis
       id: metis-cache
-      if: matrix.mpi == 'par' && matrix.os != 'windows-2022'
+      if: matrix.mpi == 'par'
       uses: actions/cache@v2
       with:
         path: ${{ env.METIS_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.2
+        key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.0
 
     - name: install metis
-      if: matrix.mpi == 'par' && matrix.os != 'windows-2022' && steps.metis-cache.outputs.cache-hit != 'true'
-      uses: mfem/github-actions/build-metis@v2.2
+      if: matrix.mpi == 'par' && steps.metis-cache.outputs.cache-hit != 'true'
+      uses: mfem/github-actions/build-metis@v2.0
       with:
         archive: ${{ env.METIS_ARCHIVE }}
         dir: ${{ env.METIS_TOP_DIR }}
 
-    - name: cache vcpkg (Windows)
-      id: vcpkg-cache
-      uses: actions/cache@v3
-      with:
-        path: vcpkg_cache
-        key: ${{ runner.os }}-${{ matrix.mpi }}-vcpkg-v1
-
-    - name: prepare binary cache location
-      if: matrix.os == 'windows-2022' && steps.vcpkg-cache.outputs.cache-hit != 'true'
-      run: |
-        mkdir -p vcpkg_cache
-
-    - name: install metis (Windows)
-      if: matrix.mpi == 'par' && matrix.os == 'windows-2022'
-      env:
-        VCPKG_DEFAULT_BINARY_CACHE: ${{ github.workspace }}/vcpkg_cache
-      run: |
-        $PortFile = 'C:\vcpkg\ports\metis\portfile.cmake'
-        $OriginalURL = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-${METIS_VERSION}.tar.gz'
-        $NewURL = 'https://github.com/mfem/tpls/raw/gh-pages/metis-5.1.0.tar.gz'
-        (Get-Content $PortFile).replace($OriginalURL, $NewURL) | Set-Content $PortFile
-        vcpkg install metis --triplet=x64-windows-static
-
     # MFEM build and test
     - name: build
-      uses: mfem/github-actions/build-mfem@v2.2
-      env:
-        VCPKG_DEFAULT_BINARY_CACHE: ${{ github.workspace }}/vcpkg_cache
+      uses: mfem/github-actions/build-mfem@v2.0
       with:
         os: ${{ matrix.os }}
         target: ${{ matrix.target }}
@@ -225,8 +176,6 @@ jobs:
         hypre-dir: ${{ env.HYPRE_TOP_DIR }}
         metis-dir: ${{ env.METIS_TOP_DIR }}
         mfem-dir: ${{ env.MFEM_TOP_DIR }}
-        config-options: ${{ env.MFEM_EXTRA_CONFIG }}
-        library-only: ${{ matrix.target == 'dbg' }}
 
     # Run checks (and only checks) on debug targets
     - name: checks
@@ -244,27 +193,10 @@ jobs:
       run: |
         cd ${{ env.MFEM_TOP_DIR }} && make test
 
-    - name: cmake checks
-      if: matrix.build-system == 'cmake' && matrix.target == 'dbg'
+    - name: cmake unit tests
+      if: matrix.build-system == 'cmake'
       run: |
-        CTEST_CONFIG="Debug"
-        cd ${{ env.MFEM_TOP_DIR }} && cmake --build build --target check --config ${CTEST_CONFIG}
-      shell: bash
-
-    - name: cmake unit tests (Ubuntu 20.04)
-      if: matrix.build-system == 'cmake' && matrix.target == 'opt' && matrix.os == 'ubuntu-20.04'
-      run: |
-        CTEST_CONFIG="Release"
-        [[ ${{ matrix.target }} == 'dbg' ]] && CTEST_CONFIG="Debug"
-        cd ${{ env.MFEM_TOP_DIR }}/build/tests/unit && ctest --output-on-failure -C ${CTEST_CONFIG}
-      shell: bash
-
-    - name: cmake tests
-      if: matrix.build-system == 'cmake' && matrix.target == 'opt' && matrix.os != 'ubuntu-20.04'
-      run: |
-        CTEST_CONFIG="Release"
-        cd ${{ env.MFEM_TOP_DIR }}/build && ctest --output-on-failure -C ${CTEST_CONFIG}
-      shell: bash
+        cd ${{ env.MFEM_TOP_DIR }}/build/tests/unit && ctest --output-on-failure
 
     # Code coverage (process and upload reports)
     - name: codecov

.github/workflows/mfem-analysis.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -20,7 +20,6 @@ on:
       - master
       - next
   pull_request:
-  workflow_dispatch:
 
 env:
   HYPRE_ARCHIVE: v2.19.0.tar.gz
@@ -54,11 +53,11 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ${{ env.HYPRE_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-v2.2
+        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@v2.2
+      uses: mfem/github-actions/build-hypre@v2.0
       with:
         archive: ${{ env.HYPRE_ARCHIVE }}
         dir: ${{ env.HYPRE_TOP_DIR }}
@@ -69,18 +68,18 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ${{ env.METIS_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.2
+        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@v2.2
+      uses: mfem/github-actions/build-metis@v2.0
       with:
         archive: ${{ env.METIS_ARCHIVE }}
         dir: ${{ env.METIS_TOP_DIR }}
 
     # MFEM build and test
     - name: build-mfem
-      uses: mfem/github-actions/build-mfem@v2.2
+      uses: mfem/github-actions/build-mfem@v2.0
       with:
         os: ${{ runner.os }}
         target: opt

.github/workflows/repo-check.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -16,28 +16,16 @@ permissions:
 
 on:
   push:
-  pull_request:
-  workflow_dispatch:
-
-# This workflow is run on pushes to any branch in the MFEM repo (with or without
-# PRs), as well as on updates to PRs from forks. In particular, we do not
-# duplicate work by running on both pushes and updates to local PRs. We do that
-# by checking if the workflow trigger is 'push' ("github.event_name == 'push'")
-# and if we are in a fork ("github.event.pull_request.head.repo.full_name !=
-# github.repository").
 
 jobs:
   file-headers-check:
     runs-on: ubuntu-18.04
-    if: |
-      (github.event_name == 'push' ||
-       github.event.pull_request.head.repo.full_name != github.repository)
+
     steps:
     - name: Cancel Previous Runs
       uses: styfle/cancel-workflow-action@0.9.0
       with:
         access_token: ${{ github.token }}
-
     - name: checkout mfem
       uses: actions/checkout@v2
 
@@ -61,10 +49,7 @@ jobs:
       continue-on-error: true
 
     - name: wrap-up
-      if: |
-        steps.copyright.outcome != 'success' ||
-        steps.license.outcome != 'success' ||
-        steps.release.outcome != 'success'
+      if: steps.copyright.outcome != 'success' || steps.license.outcome != 'success' || steps.release.outcome != 'success'
       run: |
         if [[ "${{ steps.copyright.outcome }}" != "success" ]]; then
           echo "copyright check failed, unroll log for details"
@@ -79,9 +64,7 @@ jobs:
 
   code-style:
     runs-on: ubuntu-18.04
-    if: |
-      (github.event_name == 'push' ||
-       github.event.pull_request.head.repo.full_name != github.repository)
+
     steps:
     - name: checkout mfem
       uses: actions/checkout@v2
@@ -96,9 +79,7 @@ jobs:
 
   documentation:
     runs-on: ubuntu-18.04
-    if: |
-      (github.event_name == 'push' ||
-       github.event.pull_request.head.repo.full_name != github.repository)
+
     steps:
     - name: checkout mfem
       uses: actions/checkout@v2
@@ -113,12 +94,9 @@ jobs:
         ./runtest documentation
 
   branch-history:
-    if: |
-      github.ref != 'refs/heads/next' &&
-      github.ref != 'refs/heads/master' &&
-      (github.event_name == 'push' ||
-       github.event.pull_request.head.repo.full_name != github.repository)
+    if: github.ref != 'refs/heads/next' && github.ref != 'refs/heads/master'
     runs-on: ubuntu-18.04
+
     steps:
     - name: checkout mfem
       uses: actions/checkout@v2

.gitignore

@@ -51,8 +51,8 @@ examples/ex1[04-9]
 examples/ex1[0-9]p
 examples/ex2[0-9]
 examples/ex2[0-9]p
-examples/ex3[0-9]
-examples/ex3[0-9]p
+examples/ex30
+examples/ex30p
 
 examples/refined.mesh
 examples/displaced.mesh
@@ -78,7 +78,6 @@ examples/deformed.*
 examples/velocity.*
 examples/elastic_energy.*
 examples/mode_*
-examples/mode_deriv_*
 examples/ex5-p-*.bp
 examples/ex9-p-*.bp
 examples/ex12-p-*.bp
@@ -240,7 +239,6 @@ miniapps/navier/navier_kovasznay_vs
 miniapps/navier/navier_tgv
 miniapps/navier/navier_shear
 miniapps/navier/navier_3dfoc
-miniapps/navier/navier_turbchan
 miniapps/navier/tgv_out*.txt
 miniapps/navier/*_output
 
@@ -261,14 +259,12 @@ miniapps/performance/sol.*
 
 miniapps/shifted/distance
 miniapps/shifted/ParaViewDistance
-miniapps/shifted/ParaViewLSF
 miniapps/shifted/extrapolate
 miniapps/shifted/ParaViewExtrapolate
 miniapps/shifted/diffusion
 miniapps/shifted/diffusion.mesh
 miniapps/shifted/diffusion.gf
 miniapps/shifted/ParaViewDiffusion
-miniapps/shifted/lsf_integral
 
 miniapps/tools/display-basis
 miniapps/tools/load-dc
@@ -307,8 +303,6 @@ miniapps/solvers/sol.*
 miniapps/parelag/MultilevelHcurlHdivSolver
 miniapps/parelag/*.mesh
 
-miniapps/hooke/hooke
-
 # Unit test binary and outputs
 tests/unit/output_meshes
 tests/unit/unit_tests

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

.gitlab/configs/common.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

.gitlab/configs/corona-config.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -18,14 +18,14 @@ variables:
     - shell
     - corona
   rules:
-    # Don't run corona jobs if...
+    # Don’t run corona jobs if...
     # Note: This makes corona an "opt-in" machine. To activate builds on corona
     # for a given GitLab clone of MFEM, go to Setting/CI-CD/variables, and set
     # "ON_CORONA" to "ON". An LC account on for corona is required to trigger a
     # pipeline there.
     - if: '$CI_COMMIT_BRANCH =~ /_cnone/ || $ON_CORONA != "ON"'
       when: never
-    # Don't run autotest update if...
+    # Don’t run autotest update if...
     - if: '$CI_JOB_NAME =~ /report/ && $AUTOTEST != "YES"'
       when: never
     # Report success on success status

.gitlab/configs/lassen-config.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -45,5 +45,5 @@ variables:
     - echo ${MFEM_DATA_DIR}
     - echo ${SPEC}
     # Next script uses 'THREADS': leaving it empty --> it uses 'make all -j'
-    - lalloc 1 -W 45 -q pdebug --atsdisable tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
+    - lalloc 1 -W 30 -q pdebug --atsdisable tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
   needs: [setup]

.gitlab/configs/quartz-config.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -52,4 +52,4 @@ variables:
     - echo ${JOBID}
     - echo ${MFEM_DATA_DIR}
     - echo ${SPEC}
-    - srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) -t 45 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
+    - srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) -t 30 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data

.gitlab/configs/report-build-and-test.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -20,8 +20,8 @@
     - |
       (
         date
-        echo "Waiting to acquire lock on '$PWD/autotest.lock' ..."
-        # try to get an exclusive lock on fd 9 (autotest.lock) repeating the try
+        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
+        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
         # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
         # command to hang indefinitely sometimes, so we use the timeout & retry
         # as a workaround; we may want to add a counter for the number of
@@ -29,7 +29,7 @@
         while ! flock -w 5 9; do
           true
         done
-        echo "Acquired lock on '$PWD/autotest.lock'"
+        echo "Aquired lock on '$PWD/autotest.lock'"
         date
         # Report SUCCESS while holding the file lock on 'autotest.lock'.
         # The next script uses the following environment variables:
@@ -55,8 +55,8 @@
     - |
       (
         date
-        echo "Waiting to acquire lock on '$PWD/autotest.lock' ..."
-        # try to get an exclusive lock on fd 9 (autotest.lock) repeating the try
+        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
+        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
         # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
         # command to hang indefinitely sometimes, so we use the timeout & retry
         # as a workaround; we may want to add a counter for the number of
@@ -64,7 +64,7 @@
         while ! flock -w 5 9; do
           true
         done
-        echo "Acquired lock on '$PWD/autotest.lock'"
+        echo "Aquired lock on '$PWD/autotest.lock'"
         date
         # Report FAILURE while holding the file lock on 'autotest.lock'.
         # The next script uses the following environment variables:

.gitlab/configs/setup-baseline.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -45,8 +45,8 @@ setup_baseline:
     - |
       (
         date
-        echo "Waiting to acquire lock on '$PWD/autotest.lock' ..."
-        # try to get an exclusive lock on fd 9 (autotest.lock) repeating the try
+        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
+        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
         # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
         # command to hang indefinitely sometimes, so we use the timeout & retry
         # as a workaround; we may want to add a counter for the number of
@@ -54,7 +54,7 @@ setup_baseline:
         while ! flock -w 5 9; do
           true
         done
-        echo "Acquired lock on '$PWD/autotest.lock'"
+        echo "Aquired lock on '$PWD/autotest.lock'"
         date
         # clone/update the autotest repo while holding the file lock on
         # 'autotest.lock'

.gitlab/configs/setup-build-and-test.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -34,8 +34,8 @@ setup:
     - |
       (
         date
-        echo "Waiting to acquire lock on '$PWD/mfem-data.lock' ..."
-        # try to get an exclusive lock on fd 9 (mfem-data.lock) repeating the try
+        echo "Waiting to aquire lock on '$PWD/mfem-data.lock' ..."
+        # try to get an excusive lock on fd 9 (mfem-data.lock) repeating the try
         # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
         # command to hang indefinitely sometimes, so we use the timeout & retry
         # as a workaround; we may want to add a counter for the number of
@@ -43,7 +43,7 @@ setup:
         while ! flock -w 5 9; do
           true
         done
-        echo "Acquired lock on '$PWD/mfem-data.lock'"
+        echo "Aquired lock on '$PWD/mfem-data.lock'"
         date
         # clone/update the mfem/data repo while holding the file lock on
         # 'mfem-data.lock'
@@ -67,8 +67,8 @@ setup:
     - |
       (
         date
-        echo "Waiting to acquire lock on '$PWD/autotest.lock' ..."
-        # try to get an exclusive lock on fd 9 (autotest.lock) repeating the try
+        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
+        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
         # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
         # command to hang indefinitely sometimes, so we use the timeout & retry
         # as a workaround; we may want to add a counter for the number of
@@ -76,7 +76,7 @@ setup:
         while ! flock -w 5 9; do
           true
         done
-        echo "Acquired lock on '$PWD/autotest.lock'"
+        echo "Aquired lock on '$PWD/autotest.lock'"
         date
         # clone/update the autotest repo while holding the file lock on
         # 'autotest.lock'

.gitlab/corona-build-and-test.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -23,7 +23,7 @@ allocate_resource:
   stage: allocate_resource
   script:
     - echo ${ALLOC_NAME}
-    - salloc --exclusive --nodes=1 --partition=mi60 --time=45 --no-shell --job-name=${ALLOC_NAME}
+    - salloc --exclusive --nodes=1 --partition=mi60 --time=30 --no-shell --job-name=${ALLOC_NAME}
   timeout: 6h
   needs: [setup]
 

.gitlab/lassen-build-and-test.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

.gitlab/quartz-baseline.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -64,8 +64,8 @@ report_baseline:
     - |
       (
         date
-        echo "Waiting to acquire lock on '$PWD/autotest.lock' ..."
-        # try to get an exclusive lock on fd 9 (autotest.lock) repeating the try
+        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
+        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
         # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
         # command to hang indefinitely sometimes, so we use the timeout & retry
         # as a workaround; we may want to add a counter for the number of
@@ -73,7 +73,7 @@ report_baseline:
         while ! flock -w 5 9; do
           true
         done
-        echo "Acquired lock on '$PWD/autotest.lock'"
+        echo "Aquired lock on '$PWD/autotest.lock'"
         date
         # ----------------------
         cd ${AUTOTEST_ROOT}/autotest || \

.gitlab/quartz-build-and-test.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -23,7 +23,7 @@ allocate_resource:
   stage: allocate_resource
   script:
     - echo ${ALLOC_NAME}
-    - salloc --exclusive --nodes=1 --partition=pdebug --time=45 --no-shell --job-name=${ALLOC_NAME}
+    - salloc --exclusive --nodes=1 --partition=pdebug --time=30 --no-shell --job-name=${ALLOC_NAME}
   timeout: 6h
 
 # GitLab jobs for the Quartz machine at LLNL

.gitlab/scripts/baseline

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

.gitlab/scripts/rebaseline

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

.gitlab/scripts/report_build_and_test_failure

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

.gitlab/scripts/report_build_and_test_success

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

.gitlab/scripts/safe_create_rundir

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

CHANGELOG

@@ -8,240 +8,98 @@
                                https://mfem.org
 
 
-Version 4.4.1 (development)
+Version 4.3.1 (development)
 ===========================
 
-Meshing improvements
---------------------
-- Added support for mixed meshes and pyramids in GSLIB-FindPoints.
+- Add hipSPARSE support for sparse mat-vec multiplications.
 
-Discretization improvements
----------------------------
-- Added support for assembling low-order-refined matrices using a GPU-enabled
-  "batched" algorithm. The lor_solvers and plor_solvers now fully support GPU
-  acceleration.
+- Added support for using the HYPRE library built with HIP support. Similar to
+  the HYPRE + CUDA support added earlier, most of the MFEM examples and miniapps
+  work transparently with HYPRE + HIP builds. This includes the BoomerAMG, AMS,
+  and ADS solvers.
 
-- Added support for partial assembly and fully matrix-free operators on mixed
-  meshes (different element types and p-adaptivity) through libCEED, including
-  device acceleration, e.g. with NVIDIA and AMD GPUs. The p-adaptivity is
-  currently limited by MFEM capabilities, i.e. 2D serial meshes. All mixed
-  element topologies are supported in serial and parallel: segment, triangle,
-  square, tetrahedron, cube, prism, and pyramid.
-
-- Added full assembly and device support for several LinearForm integrators:
-  * DomainLF: (f, v)
-  * VectorDomainLF: ((f1,...,fn), (v1,...,vn))
-  * DomainLFGrad: (f, grad(v))
-  * VectorDomainLFGrad: ((f1x,f1y,f1z,...,fnx,fny,fnz), grad(v1,...,vn))
-
-- Added WhiteGaussianNoiseDomainLFIntegrator: a LinearFormIntegrator class for
-  spatial Gaussian white noise.
-
-- Added a new Zienkiewicz-Zhu patch recovery-based a posteriori error estimator.
-  See fem/estimators.hpp.
-
-Linear and nonlinear solvers
-----------------------------
-
-New and updated examples and miniapps
--------------------------------------
-- Added a new elasticity miniapp, Hooke, that showcases a low-level approach of
-  using MFEM to solve a nonlinear elasticity problem based on the fundamental
-  finite element operator decomposition. The miniapp also integrates with
-  automatic differentiation tools like a native dual number implementation or a
-  third party library such as Enzyme. See miniapps/elasticity for more details.
-
-- Add a new example code, Example 33/33p, to demonstrate the solution of
-  spectral fractional PDEs with MFEM.
-
-Integrations, testing and documentation
----------------------------------------
-- Added a Dockerfile for a simple MFEM container, see config/docker/README.md.
-
-- Added support for ParMoonolith, https://bitbucket.org/zulianp/par_moonolith,
-  which provides parallel non-conforming, non-matching, variational, volumetric
-  mesh information transfer. With ParMortarAssember, fields can be exchanged
-  between arbitrarily distributed and unrelated finite element meshes in a
-  variationally consistent way.
-
-- Added support for the LLVM-based automatic differentiation tool Enzyme, see
-  https://github.com/EnzymeAD/Enzyme. Build system flags and a convenience
-  header are provided. The functionality and interaction are demonstrated in a
-  new miniapp in miniapps/elasticity.
-
-- Added example for body-fitted volumetric and shape integration using the
-  Algoim library.
-
-- Added Windows 2022 CI testing with GitHub actions.
-
-Miscellaneous
--------------
-- Various other simplifications, extensions, and bugfixes in the code.
-
-
-- Added boundary elimination with device support for `SparseMatrix` and
-  `HypreParMatrix`.
-  
-- When using `AssemblyLevel::FULL`, `FABilinearFormExtension::FormSystemMatrix`
-  outputs an `OperatorHandle` containing a `SparseMatrix` in serial, and an
-  `HypreParMatrix` in parallel (instead of a `ConstrainedOperator`).
-
-- Added TMOP metrics for mesh untangling and worst-case quality improvement.
-
-Version 4.4, released on March 21, 2022
-=======================================
-
-Linear and nonlinear solvers
-----------------------------
-- Added support for using the hypre library built with HIP support. Similar to
-  the existing hypre + CUDA support, most of the MFEM examples and miniapps work
-  transparently with hypre + HIP builds. This includes the BoomerAMG, AMS, and
-  ADS solvers.
-
-- Added a simple singleton class, Hypre, to automatically set hypre's global
-  parameters, particularly GPU-relevant options. Updated parallel example codes
-  and miniapps to call Hypre::Init() where appropriate.
-
-- Added hipSPARSE support for sparse matrix-vector multiplications.
-
-- More explicit and consistent formatting of the output of iterative solvers
+- More explicit and consistent formating of the output of iterative solvers
   with the new IterativeSolver::PrintLevel options. See linalg/solvers.hpp.
 
-Meshing improvements
---------------------
-- New TMOP-based methods for hr-adaptivity, interface fitting, and tangential
-  relaxation of high-order meshes.
+- Added a miniapp for PDE-based extrapolation of finite element functions. See
+  miniapps/shifted/extrapolate.cpp.
+
+- Added support for automatic differentiation. Users can select between native
+  implementation and external library implementation during configuration. One
+  parallel and two serial examples are implemented in the miniapps/autodiff/
+  directory.
+
+- GridFunctionCoefficient (and the related vector, gradient, divergence, and
+  curl classes) now work properly with LORDiscretization and LORSolver.
+
+- Added support for mesh preprocessing to resolve fine scale problem data
+  before simulation. This feature uses adaptive mesh refinement to control the
+  associated data oscillation error. See the new Example 30/30p.
+
+- Switched from Artistic Style (astyle) version 2.05.1 to version 3.1 for code
+  formatting. See the "make style" target.
+
+- Split the fem/fe.?pp files into separate files in the new fem/fe/ directory
+  to simplify and clarify the organization of FiniteElement classes.
+
+- Added support for hr-adaptivity using TMOP-based error estimator.
+
+- Coefficient::SetTime now propagates the new time into internally stored
+  Coefficient objects.
+
+- Added initial support for google-benchmarks in the tests/benchmarks directory.
+  It can be enabled with MFEM_USE_BENCHMARK=YES.
+
+- Added Binder (mybinder.org) configuration files for C++ MFEM Jupyter Notebooks
+  with inline GLVis visualization as well as a new examples/jupyter/ directory
+  with a sample notebook based on Example 1. Implementation based on xeus-cling,
+  github.com/jupyter-xeus/xeus-cling + xeus-glvis, github.com/GLVis/xeus-glvis.
+
+- Added 'double' atomicAdd implementation for previous versions of CUDA.
+
+- Adding lowest order Nedelec and Raviart-Thomas basis functions on wedge
+  shaped elements.
 
 - Added initial support for meshes with pyramidal elements, including several
   pyramidal meshes in the data/ directory and support for the lowest order H1,
   Nedelec, Raviart-Thomas, and L2 basis functions on pyramids.
 
-- Added a simpler interface to access mesh face information, see FaceInformation
-  and GetFaceInformation in the Mesh class.
+- Updated the hypre interface according to changes in hypre-2.22.1. The ADS
+  solver is now fully working on GPUs.
 
-- Added the method ParMesh::GetSerialMesh() that reconstructs a partitioned
-  parallel mesh on a given single rank. Also, added the method
-  ParMesh::PrintAsSerial() that saves the reconstructed serial mesh to a C++
-  stream on rank 0.
+- Tetrahedral meshes no longer need to be reordered to support high order
+  Nedelec basis functions. This will allow future support for Nedelec basis
+  functions on wedges and pyramids which are not amenable to reordering. The
+  ReorientTetMesh method of the Mesh and ParMesh classes has been deprecated.
 
-- Gmsh meshes where all elements have zero physical tag (the default Gmsh output
-  format if no physical groups are defined) are now successfully loaded, and
-  elements are reassigned attribute number 1.
+- Gmsh meshes where all elements have zero physical tag (the default Gmsh
+  output format if no physical groups are defined) are now successfully loaded,
+  and elements are reassigned attribute number 1.
 
-- Added ParMesh adjacency set (adjset) creation support to the Conduit Mesh
-  Blueprint MFEM wrapper functions in ConduitDataCollection.
-
-Discretization improvements
----------------------------
-- Added general dof transformation to support high order Nedelec basis functions
-  on tetrahedral meshes without reordering. The ReorientTetMesh method of the
-  Mesh and ParMesh classes has been deprecated. See the new DofTransformation
-  class in fem/doftrans.hpp.
-
-- GPU-enabled partial (PA) and element (EA) assembly for discontinuous Galerkin
-  methods on nonconforming AMR meshes.
-
-- Support for arbitrary order Nedelec and Raviart-Thomas elements on wedges.
-
-- Added special Nedelec and Raviart-Thomas basis functions for modeling three
-  dimensional vector fields in 1D and 2D domains, see the new Example 31/31p.
-
-- GridFunctionCoefficient (and the related vector, gradient, divergence, and
-  curl classes) now work properly with LORDiscretization and LORSolver.
-
-- Added PA support for the action of MixedScalarCurlIntegrator in 2D and
-  MixedVectorGradientIntegrator in 2D and 3D, as well as their transposes.
-
-- Coefficient::SetTime now propagates the new time into internally stored
-  Coefficient objects.
-
-- Split the fem/fe.?pp files into separate files in the new fem/fe/ directory to
-  simplify and clarify the organization of FiniteElement classes.
-
-New and updated examples and miniapps
--------------------------------------
-- Added two new miniapps with initial support for automatic differentiation (AD)
-  in the miniapps/autodiff/ directory. Users can select between external library
-  and native implementation during configuration. The support for AD will be
-  extended in future releases of MFEM.
-
-- Added Binder (mybinder.org) configuration files for C++ MFEM Jupyter Notebooks
-  with inline GLVis visualization in the new examples/jupyter/ directory with a
-  sample notebook based on Example 1. The implementation is based on xeus-cling,
-  see github.com/jupyter-xeus/xeus-cling and github.com/GLVis/xeus-glvis.
-
-- Added a new miniapp (Extrapolation) for PDE-based extrapolation of finite
-  element functions from known values in a set of elements to the rest of the
-  computational domain. See miniapps/shifted/extrapolate.cpp.
-
-- Added new miniapp that uses the ParELAG library, its hybrid smoothers, and the
+- Added new miniapps that use the ParELAG library, its hybrid smoothers, and the
   hierarchy of spaces created by the element-based AMG (AMGe) methodology in
   ParELAG to build multigrid solvers for H(curl) and H(div) forms. See the
   miniapps/parelag directory for more details.
 
-- Added a new Example 30/30p demonstrating support for mesh preprocessing to
-  resolve fine scale problem data before simulation. This feature uses adaptive
-  mesh refinement to control the associated data oscillation error.
-
-- Added new Examples 31, 31p and 32p showing anisotropic definite Maxwell
-  serial/parallel solver and parallel eigensolver 1D, 2D, or 3D.
-
-- Updated the mesh-optimizer and pmesh-optimizer miniapps to demonstrate the
-  hr-adaptivity and interface fitting capability.
-
-- The HPC versions of ex1 and ex1p (in miniapps/performance) now support runtime
-  selection of either 2D or 3D meshes.
-
-Integrations, testing and documentation
----------------------------------------
-- Doxygen documentation for all releases is now available at docs.mfem.org.
-
-- The following integrations have updated minimum version requirements:
-  * HIOP >= 0.4.6
-  * HYPRE >= 2.23.0 for HIP support
-  * libCEED >= 0.10
-  * PUMI >= 2.2.6
-  * RAJA >= 0.14.0
-  * Umpire >= 3.0.0
-  see INSTALL for more details.
-
-- Added new optional integrations with ParELAG and CoDiPack (version >= 1.9.3+).
-
-- Added initial support for Google Benchmark (version >= 1.5.6) in the
-  tests/benchmarks directory. It can be enabled with MFEM_USE_BENCHMARK=YES.
-
-- Switched from Artistic Style (astyle) version 2.05.1 to version 3.1 for code
-  formatting. See the "make style" target.
-
-- New benchmark for the different assembly levels inspired by the CEED
-  Bake-Off Problems, see tests/benchmarks/bench_assembly_levels.cpp.
-
-Miscellaneous
--------------
-- Added a simple singleton class, Mpi, as a replacement for MPI_Session. New
-  code should use Mpi::Init() and other Mpi methods instead of MPI_Session.
-
-- Added ParaView visualization of QuadratureFunction fields, through both
-  QuadratureFunction::SaveVTU and ParaViewDataCollection::RegisterQField.
-
 - Fixed several MinGW build issues on Windows.
 
-- In various places in the library, replace the use of 'long' with 'long long'
-  to better support Win64 builds where 'long' is 32-bit and 'long long' is
-  64-bit. On Linux and MacOS, both types are typically 64-bit.
-
-- Update various "MemoryUsage" methods to return 'std::size_t' instead of 'long'
-  since the latter is 32-bit in Win64 builds.
-
-- Added 'double' atomicAdd implementation for previous versions of CUDA.
-
-- HypreParVector and Vector now support C++ move semantics, and the copy
-  constructor for HypreParVector now copies the local vector data.
-
-- Removed the 'u' flag in the ar command, to update all files in the archive,
+- Remove the 'u' flag in the ar command, to update all files in the archive,
   avoiding file name collisions from different subdirectories.
 
-- Various other simplifications, extensions, and bugfixes in the code.
+- Added initial TMOP-based capabilities for surface fitting and tangential
+  relaxation in the mesh-optimizer and pmesh-optimizer miniapps.
+
+- Added ParMesh Adjaceny Set (adjset) creation support to the Conduit Mesh
+  Blueprint MFEM wrapper functions in ConduitDataCollection.
+
+- `HypreParVector` and `Vector` now support move semantics, and the copy
+  constructor for `HypreParVector` now copies the local vector data.
+
+- The HPC versions of ex1 and ex1p (in miniapps/performance) now support
+  runtime selection of either 2D or 3D meshes.
+
+- Added ParaView visualization of `QuadratureFunction` fields, through both
+  `QuadratureFunction::SaveVTU` and `ParaViewDataCollection::RegisterQField`.
 
 
 Version 4.3, released on July 29, 2021

CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -51,7 +51,7 @@ project(mfem NONE)
 # Current version of MFEM, see also `makefile`.
 #   mfem_VERSION = (string)
 #   MFEM_VERSION = (int)   [automatically derived from mfem_VERSION]
-set(${PROJECT_NAME}_VERSION 4.4.1)
+set(${PROJECT_NAME}_VERSION 4.3.1)
 
 # Prohibit in-source build
 if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
@@ -136,8 +136,6 @@ if (MFEM_USE_CUDA)
        "CUDA flags set for MFEM" FORCE)
    set(CUSPARSE_FOUND TRUE)
    set(CUSPARSE_LIBRARIES "cusparse")
-   set(CUBLAS_FOUND TRUE)
-   set(CUSBLAS_LIBRARIES "cublas")
 endif()
 
 if (XSDK_ENABLE_C)
@@ -270,7 +268,7 @@ if (MFEM_USE_OPENMP OR MFEM_USE_LEGACY_OPENMP)
   if(APPLE)
     # On macOS, the compiler needs additional help to find the <omp.h> header.
     # See issue #2642 for more information.
-    set(OPENMP_INCLUDE_DIRS ${OpenMP_CXX_INCLUDE_DIRS})
+    include_directories(${OpenMP_CXX_INCLUDE_DIRS})
   endif(APPLE)
 endif()
 
@@ -381,21 +379,6 @@ if (MFEM_USE_PUMI)
   endif()
 endif()
 
-# Moonolith
-if(MFEM_USE_MOONOLITH)
-  find_package(ParMoonolith REQUIRED)
-  if(ParMoonolith_FOUND)
-    get_target_property(
-      MOONOLITH_INCLUDE_DIRS ParMoonolith::par_moonolith
-      INTERFACE_INCLUDE_DIRECTORIES)
-    set(MOONOLITH_FOUND TRUE)
-    set(MOONOLITH_LIBRARIES ParMoonolith::par_moonolith)
-    message(
-      STATUS
-      "MOONOLITH_LIBRARIES=${MOONOLITH_LIBRARIES}, MOONOLITH_INCLUDE_DIRS=${MOONOLITH_INCLUDE_DIRS}")
-  endif()
-endif()
-
 # HiOp optimizer
 if (MFEM_USE_HIOP)
   find_package(HIOP REQUIRED)
@@ -433,11 +416,6 @@ if (MFEM_USE_CALIPER)
   find_package(Caliper REQUIRED)
 endif()
 
-# Algoim
-if (MFEM_USE_ALGOIM)
-  find_package(Algoim REQUIRED)
-endif()
-
 # ADIOS2 for parallel I/O
 if (MFEM_USE_ADIOS2)
    find_package(ADIOS2 REQUIRED)
@@ -454,11 +432,6 @@ if (MFEM_USE_PARELAG)
    find_package(PARELAG REQUIRED)
 endif()
 
-# Enzyme
-if (MFEM_USE_ENZYME)
-   find_package(ENZYME REQUIRED)
-endif()
-
 # MFEM_TIMER_TYPE
 if (NOT DEFINED MFEM_TIMER_TYPE)
   if (APPLE)
@@ -485,8 +458,8 @@ endif()
 set(MFEM_TPLS OPENMP HYPRE BLAS LAPACK SuperLUDist METIS SuiteSparse SUNDIALS
     PETSC SLEPC MESQUITE MUMPS STRUMPACK AXOM FMS CONDUIT Ginkgo GNUTLS GSLIB
     NETCDF MPFR PUMI HIOP POSIXCLOCKS MFEMBacktrace ZLIB OCCA CEED RAJA UMPIRE
-    ADIOS2 CUBLAS CUSPARSE MKL_CPARDISO AMGX CALIPER CODIPACK BENCHMARK PARELAG
-    MPI_CXX HIP HIPSPARSE MOONOLITH BLITZ ALGOIM ENZYME)
+    ADIOS2 CUSPARSE MKL_CPARDISO AMGX CALIPER CODIPACK BENCHMARK PARELAG
+    MPI_CXX HIP HIPSPARSE)
 
 # Add all *_FOUND libraries in the variable TPL_LIBRARIES.
 set(TPL_LIBRARIES "")
@@ -501,6 +474,7 @@ endforeach(TPL)
 list(REMOVE_DUPLICATES TPL_LIBRARIES)
 list(REMOVE_DUPLICATES TPL_INCLUDE_DIRS)
 # message(STATUS "TPL_INCLUDE_DIRS = ${TPL_INCLUDE_DIRS}")
+include_directories(${TPL_INCLUDE_DIRS})
 
 if (OPENMP_FOUND)
   message(STATUS "MFEM: using package OpenMP")
@@ -522,11 +496,6 @@ message(STATUS "MFEM git string: ${MFEM_GIT_STRING}")
 set(SOURCES "")
 set(HEADERS "")
 set(MFEM_SOURCE_DIRS general linalg mesh fem)
-
-if(MFEM_USE_MOONOLITH)
-  set(MFEM_SOURCE_DIRS ${MFEM_SOURCE_DIRS} fem/moonolith)
-endif()
-
 foreach(DIR IN LISTS MFEM_SOURCE_DIRS)
   add_subdirectory(${DIR})
 endforeach()
@@ -557,15 +526,6 @@ target_link_libraries(mfem PUBLIC ${TPL_LIBRARIES})
 if (MINGW)
   target_link_libraries(mfem PRIVATE ws2_32)
 endif()
-if (MSVC)
-  target_compile_options(mfem PUBLIC "/wd4819")
-endif()
-message(STATUS "TPL_INCLUDE_DIRS = ${TPL_INCLUDE_DIRS}")
-target_include_directories(mfem
-  PUBLIC
-    $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>
-    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
-    ${TPL_INCLUDE_DIRS})
 set_target_properties(mfem PROPERTIES VERSION "${mfem_VERSION}")
 set_target_properties(mfem PROPERTIES SOVERSION "${mfem_VERSION}")
 
@@ -694,10 +654,6 @@ set(INSTALL_LIB_DIR lib
 set(INSTALL_CMAKE_DIR lib/cmake/mfem
   CACHE PATH "Relative path for installing cmake config files.")
 
-target_include_directories(mfem
-  PUBLIC
-    $<INSTALL_INTERFACE:${INSTALL_INCLUDE_DIR}>)
-
 # The 'install' target will not depend on 'all'.
 # set(CMAKE_SKIP_INSTALL_ALL_DEPENDENCY TRUE)
 
@@ -731,7 +687,7 @@ endif()
 if (MFEM_USE_CEED)
   install(DIRECTORY ${MFEM_SOURCE_DIRS}
     DESTINATION ${INSTALL_INCLUDE_DIR}/mfem
-    FILES_MATCHING PATTERN "fem/ceed/integrators/*/*.h")
+    FILES_MATCHING PATTERN "fem/ceed/*.h")
 endif()
 
 # Install ${HEADERS}
@@ -762,8 +718,14 @@ export(TARGETS ${PROJECT_NAME}
 # TODO: How do we register the install-tree? Replacing the build-tree?
 export(PACKAGE ${PROJECT_NAME})
 
+# Extract the include directories required to use MFEM
+get_target_property(MFEM_TPL_INCLUDE_DIRS mfem INCLUDE_DIRECTORIES)
+if (NOT MFEM_TPL_INCLUDE_DIRS)
+  set(MFEM_TPL_INCLUDE_DIRS "")
+endif()
+
 # This is the build-tree version
-set(INCLUDE_INSTALL_DIRS ${PROJECT_BINARY_DIR} ${TPL_INCLUDE_DIRS})
+set(INCLUDE_INSTALL_DIRS ${PROJECT_BINARY_DIR} ${MFEM_TPL_INCLUDE_DIRS})
 set(LIB_INSTALL_DIR ${PROJECT_BINARY_DIR})
 configure_package_config_file(config/cmake/MFEMConfig.cmake.in
   ${CMAKE_CURRENT_BINARY_DIR}/MFEMConfig.cmake
@@ -771,7 +733,7 @@ configure_package_config_file(config/cmake/MFEMConfig.cmake.in
   PATH_VARS INCLUDE_INSTALL_DIRS LIB_INSTALL_DIR)
 
 # This is the version that will be installed
-set(INCLUDE_INSTALL_DIRS ${INSTALL_INCLUDE_DIR}  ${TPL_INCLUDE_DIRS})
+set(INCLUDE_INSTALL_DIRS ${INSTALL_INCLUDE_DIR}  ${MFEM_TPL_INCLUDE_DIRS})
 set(LIB_INSTALL_DIR ${INSTALL_LIB_DIR})
 configure_package_config_file(config/cmake/MFEMConfig.cmake.in
   ${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/MFEMConfig.cmake

CONTRIBUTING.md

@@ -8,7 +8,7 @@
 <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://docs.mfem.org/html/index.html"><img alt="Doxygen" src="https://img.shields.io/badge/code-documented-brightgreen.svg"></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>
 
 
@@ -119,7 +119,6 @@ The MFEM source code has the following structure:
   │   ├── ceed
   │   ├── fe
   │   ├── qinterp
-  │   ├── moonolith
   │   └── tmop
   ├── general
   ├── linalg
@@ -131,7 +130,6 @@ The MFEM source code has the following structure:
   │   ├── common
   │   ├── electromagnetics
   │   ├── gslib
-  │   ├── hooke
   │   ├── meshing
   │   ├── mtop
   │   ├── navier
@@ -143,7 +141,6 @@ The MFEM source code has the following structure:
   │   ├── tools
   │   └── toys
   └── tests
-      ├── benchmarks
       ├── convergence
       ├── gitlab
       ├── mem_manager
@@ -159,24 +156,24 @@ classes implementing the finite element, mesh and linear algebra concepts
 respectively.
 
 - The main mesh classes are:
-  + [`Mesh`](https://docs.mfem.org/html/classmfem_1_1Mesh.html)
-  + [`NCMesh`](https://docs.mfem.org/html/classmfem_1_1NCMesh.html)
-  + [`Element`](https://docs.mfem.org/html/classmfem_1_1Element.html)
-  + [`ElementTransformation`](https://docs.mfem.org/html/classmfem_1_1ElementTransformation.html)
+  + [`Mesh`](https://mfem.github.io/doxygen/html/classmfem_1_1Mesh.html)
+  + [`NCMesh`](https://mfem.github.io/doxygen/html/classmfem_1_1NCMesh.html)
+  + [`Element`](https://mfem.github.io/doxygen/html/classmfem_1_1Element.html)
+  + [`ElementTransformation`](https://mfem.github.io/doxygen/html/classmfem_1_1ElementTransformation.html)
 
 - The main finite element classes are:
-  + [`FiniteElement`](https://docs.mfem.org/html/classmfem_1_1FiniteElement.html)
-  + [`FiniteElementCollection`](https://docs.mfem.org/html/classmfem_1_1FiniteElement.html)
-  + [`FiniteElementSpace`](https://docs.mfem.org/html/classmfem_1_1FiniteElementSpace.html)
-  + [`GridFunction`](https://docs.mfem.org/html/classmfem_1_1GridFunction.html)
-  + [`BilinearFormIntegrator`](https://docs.mfem.org/html/classmfem_1_1BilinearFormIntegrator.html) and [`LinearFormIntegrator`](https://docs.mfem.org/html/classmfem_1_1LinearFormIntegrator.html)
-  + [`LinearForm`](https://docs.mfem.org/html/classmfem_1_1LinearFormIntegrator.html), [`BilinearForm`](https://docs.mfem.org/html/classmfem_1_1BilinearForm.html) and [`MixedBilinearForm`](https://docs.mfem.org/html/classmfem_1_1MixedBilinearForm.html)
+  + [`FiniteElement`](https://mfem.github.io/doxygen/html/classmfem_1_1FiniteElement.html)
+  + [`FiniteElementCollection`](https://mfem.github.io/doxygen/html/classmfem_1_1FiniteElement.html)
+  + [`FiniteElementSpace`](https://mfem.github.io/doxygen/html/classmfem_1_1FiniteElementSpace.html)
+  + [`GridFunction`](https://mfem.github.io/doxygen/html/classmfem_1_1GridFunction.html)
+  + [`BilinearFormIntegrator`](https://mfem.github.io/doxygen/html/classmfem_1_1BilinearFormIntegrator.html) and [`LinearFormIntegrator`](https://mfem.github.io/doxygen/html/classmfem_1_1LinearFormIntegrator.html)
+  + [`LinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1LinearFormIntegrator.html), [`BilinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html) and [`MixedBilinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1MixedBilinearForm.html)
 
 - The main linear algebra classes and sources are
-  + [`Operator`](https://docs.mfem.org/html/classmfem_1_1Operator.html) and [`BilinearForm`](https://docs.mfem.org/html/classmfem_1_1BilinearForm.html)
-  + [`Vector`](https://docs.mfem.org/html/classmfem_1_1BilinearForm.html) and [`LinearForm`](https://docs.mfem.org/html/classmfem_1_1LinearForm.html)
-  + [`DenseMatrix`](https://docs.mfem.org/html/classmfem_1_1DenseMatrix.html) and [`SparseMatrix`](https://docs.mfem.org/html/classmfem_1_1SparseMatrix.html)
-  + Sparse [smoothers](https://docs.mfem.org/html/sparsesmoothers_8hpp.html) and linear [solvers](https://docs.mfem.org/html/solvers_8hpp.html)
+  + [`Operator`](https://mfem.github.io/doxygen/html/classmfem_1_1Operator.html) and [`BilinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html)
+  + [`Vector`](https://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html) and [`LinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1LinearForm.html)
+  + [`DenseMatrix`](https://mfem.github.io/doxygen/html/classmfem_1_1DenseMatrix.html) and [`SparseMatrix`](https://mfem.github.io/doxygen/html/classmfem_1_1SparseMatrix.html)
+  + Sparse [smoothers](https://mfem.github.io/doxygen/html/sparsesmoothers_8hpp.html) and linear [solvers](https://mfem.github.io/doxygen/html/solvers_8hpp.html)
 
 #### Parallel implementation
 
@@ -186,13 +183,13 @@ shared geometric entities between different tasks. The parallel source files
 have a `p` prefix, e.g. `pmesh.cpp` vs. the serial `mesh.cpp`.
 
 - The main parallel classes are
-  + [`ParMesh`](https://docs.mfem.org/html/solvers_8hpp.html)
-  + [`ParNCMesh`](https://docs.mfem.org/html/classmfem_1_1ParMesh.html)
-  + [`ParFiniteElementSpace`](https://docs.mfem.org/html/classmfem_1_1ParFiniteElementSpace.html)
-  + [`ParGridFunction`](https://docs.mfem.org/html/classmfem_1_1ParGridFunction.html)
-  + [`ParBilinearForm`](https://docs.mfem.org/html/classmfem_1_1ParBilinearForm.html) and [`ParLinearForm`](https://docs.mfem.org/html/classmfem_1_1ParLinearForm.html)
-  + [`HypreParMatrix`](https://docs.mfem.org/html/classmfem_1_1HypreParMatrix.html) and [`HypreParVector`](https://docs.mfem.org/html/classmfem_1_1HypreParVector.html)
-  + [`HypreSolver`](https://docs.mfem.org/html/classmfem_1_1HypreSolver.html) and other [hypre classes](https://docs.mfem.org/html/hypre_8hpp.html)
+  + [`ParMesh`](https://mfem.github.io/doxygen/html/solvers_8hpp.html)
+  + [`ParNCMesh`](https://mfem.github.io/doxygen/html/classmfem_1_1ParMesh.html)
+  + [`ParFiniteElementSpace`](https://mfem.github.io/doxygen/html/classmfem_1_1ParFiniteElementSpace.html)
+  + [`ParGridFunction`](https://mfem.github.io/doxygen/html/classmfem_1_1ParGridFunction.html)
+  + [`ParBilinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1ParBilinearForm.html) and [`ParLinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1ParLinearForm.html)
+  + [`HypreParMatrix`](https://mfem.github.io/doxygen/html/classmfem_1_1HypreParMatrix.html) and [`HypreParVector`](https://mfem.github.io/doxygen/html/classmfem_1_1HypreParVector.html)
+  + [`HypreSolver`](https://mfem.github.io/doxygen/html/classmfem_1_1HypreSolver.html) and other [hypre classes](https://mfem.github.io/doxygen/html/hypre_8hpp.html)
 
 #### GPU and general device support
 
@@ -201,10 +198,10 @@ backends (CUDA, OCCA, RAJA, OpenMP, etc.) and an internal lightweight
 device/host memory manager.
 
 - The main device-relevant classes and sources are:
-  + [`Device`](https://docs.mfem.org/html/device_8hpp.html)
-  + [`MemoryManager`](https://docs.mfem.org/html/mem_manager_8hpp.html)
-  + the [`MFEM_FORALL`](https://docs.mfem.org/html/forall_8hpp.html) macro
-  + the [`cuda.hpp`](https://docs.mfem.org/html/cuda_8hpp.html) and [`occa.hpp`](https://docs.mfem.org/html/occa_8hpp.html) files
+  + [`Device`](https://mfem.github.io/doxygen/html/device_8hpp.html)
+  + [`MemoryManager`](https://mfem.github.io/doxygen/html/mem_manager_8hpp.html)
+  + the [`MFEM_FORALL`](https://mfem.github.io/doxygen/html/forall_8hpp.html) macro
+  + the [`cuda.hpp`](https://mfem.github.io/doxygen/html/cuda_8hpp.html) and [`occa.hpp`](https://mfem.github.io/doxygen/html/occa_8hpp.html) files
 
 #### Utilities, building and documentation
 - The `general/` directory contains C++ classes that serve as utilities for
@@ -212,7 +209,8 @@ device/host memory manager.
 - The `config/` directory contains build-related files, both for the plain
   Makefile and the CMake build options.
 - The `doc/` directory contains configuration for the Doxygen code documentation
-  that can either be built locally or browsed online at https://docs.mfem.org.
+  that can either be built locally or browsed online at
+  https://mfem.github.io/doxygen/html/index.html.
 
 #### Examples and tests
 - `examples` and `miniapps` respectively gather simple and more fully-featured
@@ -432,10 +430,10 @@ The Pull Request (PR) approval process in MFEM is similar to the approval of pap
 
 The current list of MFEM editors is:
 
-- [@v-dobrev](https://github.com/v-dobrev) (Veselin Dobrev)
-- [@tzanio](https://github.com/tzanio) (Tzanio Kolev)
-- [@pazner](https://github.com/pazner) (Will Pazner)
-- [@mlstowell](https://github.com/mlstowell) (Mark Stowell)
+- @v-dobrev (Veselin Dobrev)
+- @tzanio (Tzanio Kolev)
+- @pazner (Will Pazner)
+- @mlstowell (Mark Stowell)
 
 **The responsibilities of the editors are:**
 
@@ -641,7 +639,7 @@ MFEM uses a `master`/`next`-branch workflow as described below:
   ```
 - [ ] Create the release tarball and push to `mfem/releases`.
 - [ ] Recreate the `next` branch as described in previous section.
-- [ ] Update and push documentation to `mfem/doxygen`. Update the `README.md` file and the `html` link in the `mfem/doxygen` repo.
+- [ ] Update and push documentation  to `mfem/doxygen`.
 - [ ] Update URL shortlinks:
     - [ ] Create a shortlink at [http://bit.ly/](http://bit.ly/) for the release tarball, e.g. https://mfem.github.io/releases/mfem-3.1.tgz.
     - [ ] (LLNL only) Add and commit the new shortlink in the `links` and `links-mfem` files of the internal `mfem/downloads` repo.

INSTALL

@@ -19,10 +19,10 @@ requires an MPI C++ compiler, as well as the following external libraries:
   http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
 
 The hypre dependency can be downloaded as a tarball from GitHub or from the
-project webpage https://www.llnl.gov/casc/hypre. For example, the 2.24.0 release
+project webpage https://www.llnl.gov/casc/hypre. For example, the 2.20.0 release
 of hypre is available at
 
-   https://github.com/hypre-space/hypre/archive/v2.24.0.tar.gz
+   https://github.com/hypre-space/hypre/archive/v2.20.0.tar.gz
 
 The METIS dependency can be disabled but that is not generally recommended, see
 the option MFEM_USE_METIS.
@@ -60,6 +60,7 @@ following package managers:
 - OpenHPC, http://openhpc.community
 - Conda-forge, https://conda-forge.org (pre-built binaries linked with
   OpenMPI/MPICH, hypre, and METIS)
+- Homebrew/Science, https://github.com/Homebrew/homebrew-science (deprecated)
 
 We also recommend downloading and building the MFEM-based GLVis visualization
 tool which can be used to visualize the meshes and solution in MFEM's examples
@@ -471,14 +472,6 @@ MFEM_USE_CODIPACK = YES/NO
   Enable automatic differentiation using the CoDiPack library.
   www.scicomp.uni-kl.de/codi/
 
-MFEM_USE_ALGOIM = YES/NO
-  Enable the usage of Algoim - a collection of high-order accurate numerical 
-  methods and C++ algorithms for working with implicitly-defined geometry and 
-  level set methods. The Algoim library requires the Blitz++ library. The MFEM 
-  provides interface to Algoim v1. Thus, to check out the specific state use: 
-  git checkout 9c9ca0ef094d8ab0390ed36367a1151b459bbe0a
-  https://algoim.github.io
-
 MFEM_USE_ADFORWARD = YES/NO
   Enable forward mode for AD packages. This option is valid
   only if the AD package supports two modes (backward/forward).
@@ -528,16 +521,6 @@ MFEM_USE_MKL_CPARDISO = YES/NO
    MFEM_USE_LAPACK=YES, verify that the MKL LAPACK libraries are used. The
    OpenMP capabilities are disabled at link time.
 
-MFEM_USE_MOONOLITH = YES/NO
-   Enables the ParMoonolith interface for parallel non-conforming, non-matching,
-   variational, volumetric mesh information transfer. It requires the variable
-   MOONOLITH_DIR=<path to installation> to be defined in the environment in
-   order to be used with the Makefile. Makefile users are also required to
-   install moonolith using the command `make install_all`, see
-   https://bitbucket.org/zulianp/par_moonolith for details.
-   Although Moonolith is an MPI-based library, both serial (MFEM_USE_MPI=NO) and
-   parallel (MFEM_USE_MPI=YES) versions of MFEM are supported.
-
 MFEM_USE_CALIPER = YES/NO
    Enables the interface to Caliper. Caliper is a library to integrate
    performance profiling capabilities into applications. To use Caliper,
@@ -558,14 +541,6 @@ MFEM_USE_PARELAG = YES/NO
    use ParELAG. In fact, ParELAG is dependent on MFEM. Therefore, this option
    currently only concerns the miniapps.
 
-MFEM_USE_ENZYME = YES/NO
-   Enables automatic differentiation support through the LLVM plugin Enzyme.
-   This requires the compiler to be set to clang (>=14.0.0). We also advise to
-   use the link time optimization (LTO) plugin, to enable functions that you
-   define over multiple files (compilation units) and want to be differentiated
-   automatically, to work. This requires to also use LLVM/LLD for linking.
-   Recommended options are in config/defaults.mk.
-
 MFEM_BUILD_TAG = (any value)
    An optional tag to characterize the build. Exported to config/config.mk.
    Can be used to identify the MFEM build from other makefiles.
@@ -592,8 +567,7 @@ The specific libraries and their options are:
   Options: HYPRE_OPT, HYPRE_LIB.
   Versions: HYPRE >= 2.10.0b  (HYPRE built without CUDA)
             HYPRE >= 2.20.0   (HYPRE built with '--enable-mixedint')
-            HYPRE >= 2.22.1   (HYPRE built with CUDA)
-            HYPRE >= 2.23.0   (HYPRE built with HIP)
+            HYPRE >= 2.22.1   (HYPRE built with CUDA or HIP)
 
 - METIS, used when MFEM_USE_METIS = YES. If using METIS 5, set
   MFEM_USE_METIS_5 = YES (default is to use METIS 4).
@@ -739,7 +713,7 @@ The specific libraries and their options are:
   Options: HIOP_OPT, HIOP_LIB.
   Versions: HIOP >= 0.4.6.
 
-- CoDiPack (optional), used with MFEM_USE_CODIPACK = YES
+- CoDiPack (optiobal), used with MFEM_USE_CODIPACK = YES
   URL: https://www.scicomp.uni-kl.de/codi/
   Options: CODIPACK_OPT
   Versions: 1.9.3
@@ -754,20 +728,6 @@ The specific libraries and their options are:
   Options: GSLIB_OPT, GSLIB_LIB.
   Versions: GSLIB >= 1.0.7.
 
-- ALGOIM (optional), used when MFE_USE_ALGOIM=YES. The library provides only
-  headers so it just needs to be downloaded at the same level as MFEM. Download
-  the specific version we use as:
-  "git clone https://github.com/algoim/algoim.git;
-   git checkout 9c9ca0ef094d8ab0390ed36367a1151b459bbe0a"
-  ALGOIM depends on BLITZ and rhe library must be built prior to the MFEM build.
-  Download v1.0.2, untar it at the same level as MFEM and create a symbolic link:
-  "ln -s blitz-1.0.2 blitz".
-  Build Blitz using CMake as:
-  "cmake . -DCMAKE_INSTALL_PREFIX=.; make lib; make install"
-  URL: https://github.com/blitzpp/blitz/archive/refs/tags/1.0.2.tar.gz
-  Options: BLITZ_OPT, BLITZ_LIB
-  Versions: BLITZ = 1.0.2
-
 - MKL CPardiso (optional), used when MFEM_USE_MKL_CPARDISO = YES.
   URL: https://software.intel.com/content/www/us/en/develop/tools/math-kernel-library.html
   Options: MKL_CPARDISO_OPT, MKL_CPARDISO_LIB.
@@ -791,7 +751,7 @@ The specific libraries and their options are:
   URL: https://github.com/CEED/libCEED
        https://ceed.exascaleproject.org/libceed
   Options: CEED_DIR, CEED_OPT, CEED_LIB.
-  Versions: libCEED >= 0.10.
+  Versions: libCEED >= 0.8.
 
 - RAJA (optional), used when MFEM_USE_RAJA = YES.
   Beginning with MFEM v4.3, only RAJA v0.14.0+ is supported.
@@ -799,11 +759,6 @@ The specific libraries and their options are:
   Options: RAJA_DIR, RAJA_OPT, RAJA_LIB.
   Versions: RAJA >= 0.14.0.
 
-- Moonolith (optional), use when MFEM_USE_MOONOLITH = YES.
-  URL: https://bitbucket.org/zulianp/par_moonolith
-  Options: MOONOLITH_DIR
-  Versions: MOONOLITH >= 1.1.0.
-
 - Caliper (optional), used when MFEM_USE_CALIPER = YES.
   URL: https://github.com/LLNL/Caliper
   Options: CALIPER_DIR
@@ -844,12 +799,6 @@ The specific libraries and their options are:
   URL: https://github.com/LLNL/parelag
   Options: PARELAG_DIR, PARELAG_OPT, PARELAG_LIB.
 
-- Enzyme, used when MFEM_USE_ENZYME = YES. Requires LLVM/Clang >= 14.0.0.
-  URL: https://github.com/EnzymeAD/Enzyme
-  Options: ENZYME_DIR, ENZYME_OPT, ENZYME_LIB.
-  Versions: Enzyme >= v0.0.33.
-
-
 Building with CMake
 ===================
 The MFEM build system consists of two steps: configuration and compilation.
@@ -983,12 +932,10 @@ MFEM_USE_CEED
 MFEM_USE_RAJA
 MFEM_USE_UMPIRE
 MFEM_USE_SIDRE
-MFEM_USE_MOONOLITH
 MFEM_USE_CALIPER
 MFEM_USE_FMS
 MFEM_USE_BENCHMARK
 MFEM_USE_PARELAG
-MFEM_USE_ENZYME
 
 The following options are CMake specific:
 
@@ -1043,12 +990,10 @@ The CMake build system adds auto-detection for the following packages/libraries:
  - RAJA
  - UMPIRE
  - AXOM - Used when MFEM_USE_SIDRE is enabled
- - MOONOLITH
  - CALIPER
  - FMS
  - BENCHMARK
  - ParELAG
- - Enzyme
 
 The following built-in CMake packages are also used:
 

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC
+Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README

@@ -7,24 +7,21 @@
 
                                https://mfem.org
 
-[MFEM](https://mfem.org) is a modular parallel C++ library for finite element
-methods. Its goal is to enable high-performance scalable finite element
-discretization research and application development on a wide variety of
-platforms, ranging from laptops to supercomputers.
+MFEM is a modular parallel C++ library for finite element methods. Its goal is
+to enable high-performance scalable finite element discretization research and
+application development on a wide variety of platforms, ranging from laptops to
+supercomputers.
 
 We welcome contributions and feedback from the community. Please see the file
-[CONTRIBUTING.md](CONTRIBUTING.md) for additional details about our development
-process.
+CONTRIBUTING.md for additional details about our development process.
 
-* For building instructions, see the file [INSTALL](INSTALL), or type "make help".
+* For building instructions, see the file INSTALL, or type "make help".
 
-* Copyright and licensing information can be found in files [LICENSE](LICENSE) and [NOTICE](NOTICE).
+* Copyright and licensing information can be found in files LICENSE and NOTICE.
 
 * The best starting point for new users interested in MFEM's features is to
   review the examples and miniapps at https://mfem.org/examples.
 
-* Instructions for learning with Docker are in [config/docker](config/docker).
-
 Conceptually, MFEM can be viewed as a finite element toolbox that provides the
 building blocks for developing finite element algorithms in a manner similar to
 that of MATLAB for linear algebra methods. In particular, MFEM provides support
@@ -61,16 +58,12 @@ solvers from the hypre library. Comprehensive support for other external
 packages, e.g. PETSc, SUNDIALS and libCEED is also included, giving access to
 additional linear and nonlinear solvers, preconditioners, time integrators, etc.
 
-For examples of using MFEM, see the [examples/](examples) and [miniapps/](miniapps)
-directories, as well as the OpenGL visualization tool GLVis which is available
-at https://glvis.org.
-
-## License
+For examples of using MFEM, see the examples/ and miniapps/ directories, as well
+as the OpenGL visualization tool GLVis which is available at https://glvis.org.
 
 MFEM is distributed under the terms of the BSD-3 license. All new contributions
-must be made under this license. See [LICENSE](LICENSE) and [NOTICE](NOTICE) for
-details.
+must be made under this license. See LICENSE and NOTICE for details.
 
-SPDX-License-Identifier: BSD-3-Clause <br>
-LLNL Release Number: LLNL-CODE-806117 <br>
+SPDX-License-Identifier: BSD-3-Clause
+LLNL Release Number: LLNL-CODE-806117
 DOI: 10.11578/dc.20171025.1248

config/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/MFEMConfig.cmake.in

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -54,14 +54,11 @@ set(MFEM_USE_CEED @MFEM_USE_CEED@)
 set(MFEM_USE_UMPIRE @MFEM_USE_UMPIRE@)
 set(MFEM_USE_SIMD @MFEM_USE_SIMD@)
 set(MFEM_USE_ADIOS2 @MFEM_USE_ADIOS2@)
-set(MFEM_USE_MOONOLITH @MFEM_USE_MOONOLITH@)
 set(MFEM_USE_CODIPACK @MFEM_USE_CODIPACK@)
 set(MFEM_USE_ADFORWARD @MFEM_USE_ADFORWARD@)
 set(MFEM_USE_CALIPER @MFEM_USE_CALIPER@)
-set(MFEM_USE_ALGOIM @MFEM_USE_ALGOIM@)
 set(MFEM_USE_BENCHMARK @MFEM_USE_BENCHMARK@)
 set(MFEM_USE_PARELAG @MFEM_USE_PARELAG@)
-set(MFEM_USE_ENZYME @MFEM_USE_ENZYME@)
 
 set(MFEM_CXX_COMPILER "@CMAKE_CXX_COMPILER@")
 set(MFEM_CXX_FLAGS "@CMAKE_CXX_FLAGS@")

config/cmake/config.hpp.in

@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+// 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.
 //
@@ -128,9 +128,6 @@
 // Enable MFEM functionality based on the PUMI library
 #cmakedefine MFEM_USE_PUMI
 
-// Enable MFEM functionality based on the Moonolith library
-#cmakedefine MFEM_USE_MOONOLITH
-
 // Enable MFEM functionality based on the HiOp library
 #cmakedefine MFEM_USE_HIOP
 
@@ -160,9 +157,6 @@
 // Enable MFEM functionality based on the Caliper library
 #cmakedefine MFEM_USE_CALIPER
 
-// Enable MFEM functionality based on the Algoim library
-#cmakedefine MFEM_USE_ALGOIM
-
 // Which library functions to use in class StopWatch for measuring time.
 // For a list of the available options, see INSTALL.
 // If not defined, an option is selected automatically.
@@ -190,7 +184,4 @@
 // Enable MFEM functionality based on the Google Benchmark library.
 #cmakedefine MFEM_USE_BENCHMARK
 
-// Enable Enzyme for AD
-#cmakedefine MFEM_USE_ENZYME
-
 #endif // MFEM_CONFIG_HEADER

config/cmake/modules/FindAMGX.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindAlgoim.cmake

@@ -1,22 +0,0 @@
-# Copyright (c) 2010-2022, 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.
-
-# Defines the following variables:
-#   - ALGOIM_FOUND
-#   - ALGOIM_LIBRARIES
-#   - ALGOIM_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(Algoim ALGOIM ALGOIM_DIR
-       	"include" "algoim_quad.hpp"
-       	"" ""
-	"Paths to headers required by Algoim."
-	"Libraries required by Algoim.")

config/cmake/modules/FindAxom.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindBenchmark.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindBlitz.cmake

@@ -1,22 +0,0 @@
-# Copyright (c) 2010-2022, 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.
-
-# Defines the following variables:
-#   - BLITZ_FOUND
-#   - BLITZ_LIBRARIES
-#   - BLITZ_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(Blitz BLITZ BLITZ_DIR
-       	"include" "blitz/blitz.h"
-       	"lib" "blitz"
-  	"Paths to headers required by Blitz."
-       	"Libraries required by Blitz.")

config/cmake/modules/FindCODIPACK.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindCXXABIDemangle.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindCaliper.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindConduit.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindENZYME.cmake

@@ -1,27 +0,0 @@
-# Copyright (c) 2010-2022, 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.
-
-message(STATUS "Looking for ENZYME ...")
-message(STATUS "   in ENZYME_DIR = ${ENZYME_DIR}")
-
-# Make sure the directory and version combination works. Do nothing otherwise.
-if(EXISTS "${ENZYME_DIR}/ClangEnzyme-${ENZYME_VERSION}.so")
-  message(STATUS "Found ENZYME: ${ENZYME_DIR}/ClangEnzyme-${ENZYME_VERSION}.so")
-
-  # Set ENZYME_FOUND
-  set(ENZYME_FOUND TRUE CACHE BOOL "ENZYME was found." FORCE)
-
-  # Set CXX flags to accomodate the Enzyme Clang plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xclang -load -Xclang ${ENZYME_DIR}/ClangEnzyme-${ENZYME_VERSION}.so -mllvm -enzyme-loose-types=1")
-  set(MFEM_USE_ENZYME YES)
-else()
-
-endif()

config/cmake/modules/FindFMS.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindGSLIB.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -15,5 +15,5 @@
 #   - GSLIB_INCLUDE_DIRS
 
 include(MfemCmakeUtilities)
-mfem_find_package(GSLIB GSLIB GSLIB_DIR "include" gslib.h "lib" gs
+mfem_find_package(gslib GSLIB GSLIB_DIR "include" gslib.h "lib" gs
   "Paths to headers required by GSLIB." "Libraries required by GSLIB.")

config/cmake/modules/FindHIOP.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindHYPRE.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindLIBDL.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindLibunwind.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindMETIS.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindMFEMBacktrace.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindMKL_CPARDISO.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindMPFR.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindMUMPS.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindMesquite.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindNetCDF.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindOCCA.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindPARELAG.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindPOSIXClocks.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindParMETIS.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindRAJA.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindSLEPc.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindSTRUMPACK.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindSUNDIALS.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindScotch.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindSuiteSparse.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindSuperLUDist.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindUMPIRE.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/Find_GnuTLS.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/FindlibCEED.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/cmake/modules/MfemCmakeUtilities.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -893,8 +893,7 @@ function(mfem_export_mk_files)
       MFEM_USE_CONDUIT MFEM_USE_PUMI MFEM_USE_HIOP MFEM_USE_GSLIB MFEM_USE_CUDA
       MFEM_USE_HIP MFEM_USE_RAJA MFEM_USE_OCCA MFEM_USE_CEED MFEM_USE_CALIPER
       MFEM_USE_UMPIRE MFEM_USE_SIMD MFEM_USE_ADIOS2 MFEM_USE_MKL_CPARDISO
-      MFEM_USE_ADFORWARD MFEM_USE_CODIPACK MFEM_USE_BENCHMARK MFEM_USE_PARELAG
-      MFEM_USE_MOONOLITH MFEM_USE_ALGOIM MFEM_USE_ENZYME)
+      MFEM_USE_ADFORWARD MFEM_USE_CODIPACK MFEM_USE_BENCHMARK MFEM_USE_PARELAG)
   foreach(var ${CONFIG_MK_BOOL_VARS})
     if (${var})
       set(${var} YES)
@@ -978,11 +977,9 @@ function(mfem_export_mk_files)
       string(REGEX REPLACE "^SCOREC::" "" libname ${pumilib})
       string(FIND "${pumilib}" ".a" staticlib)
       string(FIND "${pumilib}" ".so" sharedlib)
-      string(FIND "${pumilib}" ".dylib" dynamiclib)
       find_library(lib ${libname} PATHS ${PUMI_DIR}/lib NO_DEFAULT_PATH)
       if (NOT "${sharedlib}" MATCHES "-1" OR
-          NOT "${staticlib}" MATCHES "-1" OR
-          NOT "${dynamiclib}" MATCHES "-1"  )
+          NOT "${staticlib}" MATCHES "-1"   )
         set(MFEM_EXT_LIBS "${pumilib} ${MFEM_EXT_LIBS}")
       elseif (NOT "${lib}" MATCHES "lib-NOTFOUND")
         set(MFEM_EXT_LIBS "${lib} ${MFEM_EXT_LIBS}")
@@ -997,7 +994,7 @@ function(mfem_export_mk_files)
   foreach(lib ${TPL_LIBRARIES})
     get_filename_component(suffix ${lib} EXT)
     # handle interfaces (e.g., SCOREC::apf)
-    if ("${lib}" MATCHES "SCOREC::.*" OR "${lib}" MATCHES "Ginkgo::.*" OR "${lib}" MATCHES "ParMoonolith::.*")
+    if ("${lib}" MATCHES "SCOREC::.*" OR "${lib}" MATCHES "Ginkgo::.*")
     elseif (TARGET "${lib}")
       mfem_get_target_options(${lib} CompileOpts LinkOpts)
       # Removing duplicates may lead to issues:

config/config.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+// 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.
 //

config/config.hpp.in

@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+// 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.
 //
@@ -138,9 +138,6 @@
 // Enable MFEM functionality based on the PUMI library
 // #define MFEM_USE_PUMI
 
-// Enable Moonolith-based general interpolation between finite element spaces.
-// #define MFEM_USE_MOONOLITH
-
 // Enable MFEM functionality based on the HIOP library.
 // #define MFEM_USE_HIOP
 
@@ -167,9 +164,6 @@
 // Enable functionality based on the Caliper library.
 // #define MFEM_USE_CALIPER
 
-// Enable functionality based on the Algoim library.
-// #define MFEM_USE_ALGOIM
-
 // Enable functionality based on the Umpire library.
 // #define MFEM_USE_UMPIRE
 
@@ -195,7 +189,4 @@
 // Enable functionality based on the Google Benchmark library.
 // #define MFEM_USE_BENCHMARK
 
-// Enable the Enzyme LLVM plugin
-// #define MFEM_USE_ENZYME
-
 #endif // MFEM_CONFIG_HEADER

config/config.mk.in

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -58,12 +58,10 @@ MFEM_USE_UMPIRE        = @MFEM_USE_UMPIRE@
 MFEM_USE_SIMD          = @MFEM_USE_SIMD@
 MFEM_USE_ADIOS2        = @MFEM_USE_ADIOS2@
 MFEM_USE_MKL_CPARDISO  = @MFEM_USE_MKL_CPARDISO@
-MFEM_USE_MOONOLITH     = @MFEM_USE_MOONOLITH@
 MFEM_USE_ADFORWARD     = @MFEM_USE_ADFORWARD@
 MFEM_USE_CODIPACK      = @MFEM_USE_CODIPACK@
 MFEM_USE_BENCHMARK     = @MFEM_USE_BENCHMARK@
 MFEM_USE_PARELAG       = @MFEM_USE_PARELAG@
-MFEM_USE_ENZYME        = @MFEM_USE_ENZYME@
 
 # Compiler, compile options, and link options
 MFEM_CXX       = @MFEM_CXX@

config/defaults.cmake

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -58,13 +58,11 @@ option(MFEM_USE_UMPIRE "Enable Umpire" OFF)
 option(MFEM_USE_SIMD "Enable use of SIMD intrinsics" OFF)
 option(MFEM_USE_ADIOS2 "Enable ADIOS2" OFF)
 option(MFEM_USE_CALIPER "Enable Caliper support" OFF)
-option(MFEM_USE_ALGOIM "Enable Algoim support" OFF)
 option(MFEM_USE_MKL_CPARDISO "Enable MKL CPardiso" OFF)
 option(MFEM_USE_ADFORWARD "Enable forward mode for AD" OFF)
 option(MFEM_USE_CODIPACK "Enable automatic differentiation (AD) using CoDiPack" OFF)
 option(MFEM_USE_BENCHMARK "Enable Google Benchmark" OFF)
 option(MFEM_USE_PARELAG "Enable ParELAG" OFF)
-option(MFEM_USE_ENZYME "Enable Enzyme" OFF)
 
 # Optional overrides for autodetected MPIEXEC and MPIEXEC_NUMPROC_FLAG
 # set(MFEM_MPIEXEC "mpirun" CACHE STRING "Command for running MPI tests")
@@ -238,11 +236,6 @@ set(RAJA_DIR "${MFEM_DIR}/../raja" CACHE PATH "Path to RAJA")
 set(CEED_DIR "${MFEM_DIR}/../libCEED" CACHE PATH "Path to libCEED")
 set(UMPIRE_DIR "${MFEM_DIR}/../umpire" CACHE PATH "Path to Umpire")
 set(CALIPER_DIR "${MFEM_DIR}/../caliper" CACHE PATH "Path to Caliper")
-set(BLITZ_DIR "${MFEM_DIR}/../blitz" CACHE PATH "Path to Blitz")
-set(ALGOIM_DIR "${MFEM_DIR}/../algoim" CACHE PATH "Path to Algoim")
-set(ALGOIM_REQUIRED_PACKAGES "BLITZ" CACHE STRING
-    "Packages that ALGOIM depends on.")
-
 set(BENCHMARK_DIR "${MFEM_DIR}/../google-benchmark" CACHE PATH
     "Path to Google Benchmark")
 

config/defaults.mk

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -42,9 +42,6 @@ STATIC = YES
 SHARED = NO
 
 # CUDA configuration options
-#
-# If you set MFEM_USE_ENZYME=YES, CUDA_CXX has to be configured to use cuda with
-# clang as its host compiler.
 CUDA_CXX = nvcc
 CUDA_ARCH = sm_60
 CUDA_FLAGS = -x=cu --expt-extended-lambda -arch=$(CUDA_ARCH)
@@ -156,17 +153,14 @@ MFEM_USE_RAJA          = NO
 MFEM_USE_OCCA          = NO
 MFEM_USE_CEED          = NO
 MFEM_USE_CALIPER       = NO
-MFEM_USE_ALGOIM        = NO
 MFEM_USE_UMPIRE        = NO
 MFEM_USE_SIMD          = NO
 MFEM_USE_ADIOS2        = NO
 MFEM_USE_MKL_CPARDISO  = NO
-MFEM_USE_MOONOLITH     = NO
 MFEM_USE_ADFORWARD     = NO
 MFEM_USE_CODIPACK      = NO
 MFEM_USE_BENCHMARK     = NO
 MFEM_USE_PARELAG       = NO
-MFEM_USE_ENZYME        = NO
 
 # MPI library compile and link flags
 # These settings are used only when building MFEM with MPI + HIP
@@ -207,7 +201,7 @@ HYPRE_OPT = -I$(HYPRE_DIR)/include
 HYPRE_LIB = -L$(HYPRE_DIR)/lib -lHYPRE
 ifeq (YES,$(MFEM_USE_CUDA))
    # This is only necessary when hypre is built with cuda:
-   HYPRE_LIB += -lcusparse -lcurand -lcublas
+   HYPRE_LIB += -lcusparse -lcurand
 endif
 ifeq (YES,$(MFEM_USE_HIP))
    # This is only necessary when hypre is built with hip:
@@ -393,11 +387,6 @@ ifeq ($(SLEPC_FOUND),YES)
       $(subst $(CXX_XLINKER),$(XLINKER),$(SLEPC_DEP))
 endif
 
-ifeq ($(MFEM_USE_MOONOLITH),YES)
-  include $(MOONOLITH_DIR)/config/moonolith-config.makefile
-  MOONOLITH_LIB=$(MOONOLITH_LIBRARIES)
-endif
-
 # MPFR library configuration
 MPFR_OPT =
 MPFR_LIB = -lmpfr
@@ -474,16 +463,6 @@ CALIPER_DIR = @MFEM_DIR@/../caliper
 CALIPER_OPT = -I$(CALIPER_DIR)/include
 CALIPER_LIB = $(XLINKER)-rpath,$(CALIPER_DIR)/lib64 -L$(CALIPER_DIR)/lib64 -lcaliper
 
-# BLITZ library configuration
-BLITZ_DIR = @MFEM_DIR@/../blitz
-BLITZ_OPT = -I$(BLITZ_DIR)/include
-BLITZ_LIB = $(XLINKER)-rpath,$(BLITZ_DIR)/lib -L$(BLITZ_DIR)/lib -lblitz
-
-# ALGOIM library configuration
-ALGOIM_DIR = @MFEM_DIR@/../algoim
-ALGOIM_OPT = -I$(ALGOIM_DIR)/src $(BLITZ_OPT)
-ALGOIM_LIB = $(BLITZ_LIB)
-
 # BENCHMARK library configuration
 BENCHMARK_DIR = @MFEM_DIR@/../google-benchmark
 BENCHMARK_OPT = -I$(BENCHMARK_DIR)/include
@@ -524,22 +503,6 @@ PARELAG_DIR = @MFEM_DIR@/../parelag
 PARELAG_OPT = -I$(PARELAG_DIR)/src -I$(PARELAG_DIR)/build/src
 PARELAG_LIB = -L$(PARELAG_DIR)/build/src -lParELAG
 
-# Enzyme configuration
-
-# If you want to enable automatic differentiation at compile time, use the
-# options below, adapted to your configuration. To be more flexible, we
-# recommend using the Enzyme plugin during link time optimization. One option is
-# to add your options to the global compiler/linker flags like
-#
-# BASE_FLAGS += -flto
-# CXX_XLINKER += -fuse-ld=lld -Wl,--lto-legacy-pass-manager\
-#                -Wl,-mllvm=-load=$(ENZYME_DIR)/LLDEnzyme-$(ENZYME_VERSION).so -Wl,
-#
-ENZYME_DIR ?= @MFEM_DIR@/../enzyme
-ENZYME_VERSION ?= 14
-ENZYME_OPT = -fno-experimental-new-pass-manager -Xclang -load -Xclang $(ENZYME_DIR)/ClangEnzyme-$(ENZYME_VERSION).so
-ENZYME_LIB = ""
-
 # If YES, enable some informational messages
 VERBOSE = NO
 

config/docker/Dockerfile

@@ -1,27 +0,0 @@
-FROM ghcr.io/mfem/mfem-ubuntu-base:latest as builder
-
-# docker build -t ghcr.io/mfem/mfem-ubuntu .
-
-COPY ./config/docker/spack.yaml /opt/mfem-env/spack.yaml
-RUN apt-get install -y python3 && \
-    cd /opt/mfem-env && \
-    . /opt/spack/share/spack/setup-env.sh && \
-    spack env activate . && \
-    spack env view regenerate
-
-FROM ubuntu:22.04
-
-COPY --from=builder /opt/view /opt/view
-COPY --from=builder /opt/mfem-view /opt/mfem-view
-
-RUN apt-get update && \
-    apt-get install -y unzip gfortran && \
-    apt-get install -y libcurl4-openssl-dev libssl-dev
-
-ENV PATH=$PATH:/opt/mfem-view/bin
-ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mfem-view/lib:/opt/mfem-view/lib64
-ENV DEBIAN_FRONTEND=noninteractive
-
-# The user will see the view on shell into the container
-WORKDIR /opt/mfem-view
-ENTRYPOINT ["/bin/bash"]

config/docker/Dockerfile.base

@@ -1,47 +0,0 @@
-FROM ghcr.io/rse-ops/cuda-ubuntu-20.04:cuda-11.0.3
-
-# docker build -f Dockerfile.base -t ghcr.io/mfem/mfem-ubuntu-base .
-
-RUN apt-get update && \
-    apt-get install -y unzip gfortran && \
-    spack compiler find && \
-    apt-get install -y libcurl4-openssl-dev libssl-dev
-
-# /code is the working directory for code
-WORKDIR /code
-COPY . /code
-
-# This is for a spack environment/view to install from there
-RUN mkdir -p /opt/mfem-env \
-&&  (echo "spack:" \
-&&   echo "  view:" \
-&&   echo "    mfem:" \
-&&   echo "      root: /opt/mfem-view" \
-&&   echo "      link_type: copy" \
-&&   echo "  packages:" \
-&&   echo "    all:" \
-&&   echo "      target:" \
-&&   echo "      - x86_64_v3" \
-&&   echo "  config:" \
-&&   echo "    concretizer: clingo" \
-&&   echo "    compiler:" \
-&&   echo "      target:" \
-&&   echo "      - x86_64_v3" \
-&&   echo "    install_missing_compilers: true" \
-&&   echo "  concretization: together") > /opt/mfem-env/spack.yaml
-
-RUN cd /opt/mfem-env && \
-    . /opt/spack/share/spack/setup-env.sh && \
-    spack env activate . && \
-    spack develop --path /code mfem@master+examples+miniapps && \
-    spack add mfem@master+examples+miniapps # && \
-#    spack install
-
-# ensure mfem always on various paths
-#RUN cd /opt/mfem-env && \
-#    spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
-
-# Present the software install when we shell in
-# The view is at /opt/mfem-env/.spack-env/view
-#WORKDIR /opt/software
-#ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l", "-c"]

config/docker/README.md

@@ -1,147 +0,0 @@
-# mfem Docker
-
-We provide a [Dockerfile.base](Dockerfile.base) to build an ubuntu base image,
-and a [Dockerfile](Dockerfile) to build a smaller one with a multi-stage build.
-You can use this image for a demo of using mfem! 🎉️
-
-Updated containers are built and deployed on merges to the main branch and releases.
-If you want to request a build on demand, you can [manually run the workflow](https://docs.github.com/en/actions/managing-workflow-runs/manually-running-a-workflow) thanks to the workflow dispatch event.
-
-### Usage
-
-Here is how to build the container. Note that we build so it belongs to the same
-namespace as the repository here. "ghcr.io" means "GitHub Container Registry" and
-is the [GitHub packages](https://github.com/features/packages) registry that supports
- Docker images and other OCI artifacts. From the root of the repository:
-
-```bash
-$ docker build -f config/docker/Dockerfile -t ghcr.io/mfem/mfem-ubuntu .
-$ docker build -f config/docker/Dockerfile.base -t ghcr.io/mfem/mfem-ubuntu-base .
-```
-
-### Shell Ubuntu
-
-To shell into the container:
-
-```bash
-$ docker run -it ghcr.io/mfem/mfem-ubuntu
-```
-
-This smaller image has a view where everything is installed.
-
-```bash
-$ ls
-bin  etc  include  lib  libexec  sbin  share  var
-```
-
- - Examples are in share/mfem/examples
- - Examples are in share/mfem/miniapps
-
-You can read more about interaction with these examples and miniapps below.
-
-### Shell Ubuntu Base
-
-To shell into the container:
-
-```bash
-$ docker run -it ghcr.io/mfem/mfem-ubuntu-base bash
-```
-
-Off the bat, you can see mfem libraries are in your path so you can jump into development:
-
-```bash
-env | grep mfem
-```
-```bash
-PKG_CONFIG_PATH=/opt/mfem-env/.spack-env/view/lib/pkgconfig:/opt/mfem-env/.spack-env/view/share/pkgconfig:/opt/mfem-env/.spack-env/view/lib64/pkgconfig
-PWD=/opt/mfem-env
-MANPATH=/opt/mfem-env/.spack-env/view/share/man:/opt/mfem-env/.spack-env/view/man:
-CMAKE_PREFIX_PATH=/opt/mfem-env/.spack-env/view
-SPACK_ENV=/opt/mfem-env
-ACLOCAL_PATH=/opt/mfem-env/.spack-env/view/share/aclocal
-LD_LIBRARY_PATH=/opt/mfem-env/.spack-env/view/lib:/opt/mfem-env/.spack-env/view/lib64
-PATH=/opt/mfem-env/.spack-env/view/bin:/opt/view/bin:/opt/spack/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-```
-
-#### Examples and MiniApps
-
-If you want to develop a tool that _uses_ mfem, you can find the built libraries in:
-
-```
-$ ls /opt/mfem-env/.spack-env/view/
-bin  etc  include  lib  libexec  sbin  share  var
-```
-
-And yes, this is the working directory when you shell into the container!
-You can find the examples here:
-
-
-```bash
-cd share/mfem/examples
-```
-```bash
-$ ./ex0
-Options used:
-   --mesh ../data/star.mesh
-   --order 1
-Number of unknowns: 101
-   Iteration :   0  (B r, r) = 0.184259
-   Iteration :   1  (B r, r) = 0.102754
-   Iteration :   2  (B r, r) = 0.00558141
-   Iteration :   3  (B r, r) = 1.5247e-05
-   Iteration :   4  (B r, r) = 1.13807e-07
-   Iteration :   5  (B r, r) = 6.27231e-09
-   Iteration :   6  (B r, r) = 3.76268e-11
-   Iteration :   7  (B r, r) = 6.07423e-13
-   Iteration :   8  (B r, r) = 4.10615e-15
-Average reduction factor = 0.140201
-```
-
-Try running a few, and look at the associated .cpp file for the source code!
-You can also explore the "mini apps," also in share/mfem, but under miniapps.
-
-```bash
-# This is run from the examples directory
-$ cd ../miniapps
-```
-```bash
-$ ls
-CMakeLists.txt  common            meshing  nurbs        shifted  toys
-adjoint         electromagnetics  mtop     parelag      solvers
-autodiff        gslib             navier   performance  tools
-```
-
-And an example in "toys"
-
-```bash
-cd toys
-```
-```bash
-$ ./automata -no-vis
-Options used:
-   --num-steps 16
-   --rule 90
-   --no-visualization
-
-Rule:
- 111 110 101 100 011 010 001 000
-  0   1   0   1   1   0   1   0
-
-Applying rule...done.
-```
-
-Have fun!
-
-
-#### Your own App
-If you want to develop with your own code base
-(and mfem as is in the container) you can bind to somewhere else in the container (e.g., src)
-
-```bash
-$ docker run -it ghcr.io/mfem/mfem-ubuntu-base -v $PWD:/src bash
-```
-
-In the above, we can pretend your project is in the present working directory (PWD) and we are
-binding to source. You can then use the mfem in the container for development, and if you
-want to distribute your library or app in a container, you can use the mfem container as the base.
-

config/docker/spack.yaml

@@ -1,11 +0,0 @@
-spack:
-  specs: [mfem@master+examples+miniapps]
-  view: 
-    mfem:
-      root: /opt/mfem-view 
-      link_type: copy
-  concretization: together
-  develop:
-    mfem:
-      path: /code
-      spec: mfem@master+examples+miniapps

config/get_hypre_version.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+// 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.
 //

config/get_mumps_version.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+// 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.
 //

config/githooks/pre-push

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -35,8 +35,8 @@ cd $(git rev-parse --show-toplevel)
 # copyright check
 copyright=true
 if [[ "${option}" == "--copyright" || "${option}" == "" ]]; then
-  if git grep -l "^\(#\|//\).*\(\-2021\|\ 2010,\)" > matches.txt; then
-    echo "Please update the following files to Copyright (c) 2010-2022:"
+  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

config/makefile

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

config/sample-runs.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -32,7 +32,7 @@ groups_serial=(
 '"examples"
    "Examples:"
    "examples"
-   "ex{,1,2,3}[0-9].cpp"'
+   "ex{,1,2}[0-9].cpp"'
 #   "ex1.cpp"'
 '"sundials"
    "SUNDIALS examples:"
@@ -83,13 +83,11 @@ groups_serial=(
 '"tools"
    "Tools miniapps:"
    "miniapps/tools"
-   "convert-dc.cpp display-basis.cpp get-values.cpp load-dc.cpp
-    lor-transfer.cpp"'
+   "convert-dc.cpp display-basis.cpp get-values.cpp load-dc.cpp lor-transfer.cpp"'
 '"toys"
    "Toys miniapps:"
    "miniapps/toys"
-   "automata.cpp life.cpp lissajous.cpp mandel.cpp mondrian.cpp rubik.cpp
-    snake.cpp"'
+   "automata.cpp life.cpp lissajous.cpp mandel.cpp mondrian.cpp rubik.cpp snake.cpp"'
 '"convergence"
    "Convergence tests:"
    "tests/convergence"
@@ -100,7 +98,7 @@ groups_parallel=(
 '"examples"
    "Examples:"
    "examples"
-   "ex{,1,2,3}[0-9]p.cpp"'
+   "ex{,1,2}[0-9]p.cpp"'
 #   "ex1p.cpp"'
 '"sundials"
    "SUNDIALS examples:"
@@ -186,7 +184,7 @@ groups_all=(
 '"examples"
    "Examples:"
    "examples"
-   "ex\"{,1,2,3}[0-9]\"{,p}.cpp"'
+   "ex\"{,1,2}[0-9]\"{,p}.cpp"'
 '"sundials"
    "SUNDIALS examples:"
    "examples/sundials"
@@ -240,8 +238,7 @@ groups_all=(
 '"gslib"
    "GSLIB miniapps:"
    "miniapps/gslib"
-   "field-diff.cpp field-interp.cpp findpts.cpp schwarz_ex1.cpp pfindpts.cpp
-    schwarz_ex1p.cpp"'
+   "field-diff.cpp field-interp.cpp findpts.cpp schwarz_ex1.cpp pfindpts.cpp schwarz_ex1p.cpp"'
 '"navier"
    "Navier miniapps:"
    "miniapps/navier"
@@ -261,13 +258,11 @@ groups_all=(
 '"tools"
    "Tools miniapps:"
    "miniapps/tools"
-   "convert-dc.cpp display-basis.cpp get-values.cpp load-dc.cpp
-    lor-transfer.cpp"'
+   "convert-dc.cpp display-basis.cpp get-values.cpp load-dc.cpp lor-transfer.cpp"'
 '"toys"
    "Toys miniapps:"
    "miniapps/toys"
-   "automata.cpp life.cpp lissajous.cpp mandel.cpp mondrian.cpp rubik.cpp
-    snake.cpp"'
+   "automata.cpp life.cpp lissajous.cpp mandel.cpp mondrian.cpp rubik.cpp snake.cpp"'
 '"convergence"
    "Convergence tests:"
    "tests/convergence"

config/tconfig.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+// 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.
 //

config/test.mk

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

data/hexagon.mesh

@@ -1,43 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-#
-
-dimension
-2
-
-# format: <attribute> <geometry type> <vertex 0> <vertex 1> ...
-elements
-3
-
-1 3 0 1 2 3
-2 3 0 3 4 5
-3 3 0 5 6 1
-
-boundary
-6
-1 1 1 2
-2 1 2 3
-3 1 3 4
-4 1 4 5
-5 1 5 6
-6 1 6 1
-
-vertices
-7
-2
-0.0 0.0
--0.50 -0.8660254037844386
-0.50 -0.8660254037844386
-1.0 0.0
-0.50 0.8660254037844386
--0.50 0.8660254037844386
--1.0 0.0

data/star-q3.fms

@@ -15,146 +15,146 @@ DataCollection/Fields/0/NumberOfVectorComponents: 2
 DataCollection/Fields/0/FieldDescriptorName: CoordsDescriptor
 DataCollection/Fields/0/Data/Size: 422
 DataCollection/Fields/0/Data/Type: FMS_DOUBLE
-DataCollection/Fields/0/Data/Values: [-0.016886, 1.000000, 0.309017,
-1.309020, -0.809017, -0.500000,
--0.809017, -1.618030, 0.309017,
--0.500000, 1.309020, 0.519420,
-1.154510, 0.809019, 0.147680,
--0.095492, -0.654508, -0.415586,
--1.213520, -1.213520, -0.392210,
--0.654508, -0.095492, 0.139949,
-0.809019, 1.154510, 0.660184,
--0.264063, -0.800064, -0.231060,
-0.663691, 0.183114, 0.317639,
-0.543082, 0.598483, 0.345112,
-0.478298, 0.027703, 0.095229,
-0.012368, -0.092534, -0.334412,
--0.313767, -0.140526, -0.293881,
--0.534056, -0.660290, -0.537646,
--0.655590, -0.121396, -0.274504,
--0.346497, -0.296570, 0.004737,
--0.098835, 0.069287, 0.082675,
-0.318799, 0.467183, 0.564505,
-0.595190, 0.846237, 0.671735,
-1.051500, 1.103010, 0.964008,
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-0.717257, 0.475684, 0.642352,
-0.268930, 0.211049, 0.174181,
-0.039345, -0.147746, -0.177481,
--0.365164, -0.230328, -0.551503,
--0.603005, -0.497587, -0.389864,
--0.757514, -0.706011, -0.675487,
--0.528946, -0.943851, -1.078690,
--1.087600, -0.955467, -1.483190,
--1.348360, -1.483190, -1.348360,
--1.085930, -0.938010, -0.943851,
--1.078690, -0.681476, -0.540944,
--0.757514, -0.706011, -0.540614,
--0.367058, -0.551503, -0.603005,
--0.365164, -0.230328, -0.138552,
--0.206896, 0.174181, 0.039345,
-0.268468, 0.222269, 0.475684,
-0.642352, 0.759791, 0.719381,
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-1.051500, 1.103010, 0.214572,
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--0.086700, -0.027358, -0.200560,
--0.166595, -0.271802, -0.418426,
--0.426131, -0.551441, -0.096117,
--0.206969, -0.027946, -0.184969,
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--0.078026, -0.007795, -0.329488,
--0.302967, -0.488115, -0.439332,
--0.498515, -0.453527, -0.633059,
--0.570251, -0.655787, -0.791132,
--0.802013, -0.956872, -1.094720,
--1.208560, -1.207720, -1.339910,
--0.693371, -0.795404, -0.803594,
--0.945068, -0.464668, -0.631721,
--0.458968, -0.547876, -0.332878,
--0.485696, -0.286385, -0.408481,
-0.053021, -0.058200, 0.110846,
--0.002086, 0.381384, 0.416784,
-0.551133, 0.613261, 0.872474,
-0.901208, 1.038300, 1.084660,
-0.737459, 0.751250, 0.890002,
-0.915210, 0.010915, 0.000000,
-0.951057, 0.951057, 0.587785,
-1.538840, -0.587785, 0.000000,
--0.951057, -1.538840, -0.951057,
--0.015847, 0.475529, 0.951057,
-0.492248, 1.244950, 1.063310,
-0.274399, 0.293893, -0.293892,
--0.296404, -1.063310, -1.244950,
--0.453865, -0.951057, -0.475529,
-0.466620, 0.792932, -0.013913,
--0.748783, -0.497528, 0.021382,
--0.017158, 0.172591, 0.330125,
-0.458568, 0.457971, 0.137740,
-0.299049, 0.588394, 0.667324,
-0.432341, 0.634346, 0.117322,
-0.193603, 0.211702, 0.098278,
--0.199438, -0.077304, -0.082243,
--0.216296, -0.458634, -0.592374,
--0.563926, -0.680404, -0.135751,
--0.302942, -0.469005, -0.453640,
--0.182727, -0.314240, 0.024270,
-0.021546, 0.158510, 0.317019,
-0.485799, 0.492951, 0.792548,
-0.634038, 0.951057, 0.951057,
-0.777915, 0.613430, 0.951057,
-0.951057, 0.793994, 0.635800,
-1.049020, 1.146990, 1.084480,
-0.924310, 1.440880, 1.342910,
-1.380330, 1.221820, 0.948209,
-0.856297, 0.746293, 0.904802,
-0.476242, 0.393234, 0.489821,
-0.391857, 0.194471, 0.075751,
-0.097964, 0.195929, -0.097964,
--0.195928, -0.173234, -0.078922,
--0.489821, -0.391856, -0.467007,
--0.397859, -0.746293, -0.904802,
--0.945206, -0.849559, -1.380330,
--1.221820, -1.440880, -1.342910,
--1.100830, -0.923191, -1.049020,
--1.146990, -0.774515, -0.621542,
--0.951057, -0.951057, -0.803055,
--0.635255, -0.951057, -0.951057,
--0.792548, -0.634038, -0.454301,
--0.479369, -0.158510, -0.317019,
-0.149331, 0.178643, 0.295860,
-0.306275, 0.246225, 0.406610,
-0.367954, 0.498458, -0.014929,
-0.084917, -0.094272, -0.000726,
--0.245374, -0.340755, -0.435351,
--0.490564, -0.176355, -0.294974,
--0.148010, -0.328246, 0.136248,
-0.182883, 0.328957, 0.309903,
-0.646446, 0.622546, 0.800859,
-0.801803, 0.643087, 0.654473,
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-1.049540, 1.162660, 1.115310,
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-0.656318, 0.783152, 0.302716,
-0.403858, 0.219006, 0.309252,
-0.009667, 0.107161, -0.118211,
-0.011786, -0.284704, -0.179858,
--0.411567, -0.296676, -0.570168,
--0.635348, -0.726784, -0.793211,
--1.016860, -1.112970, -1.170910,
--1.281530, -0.737860, -0.851723,
--0.883732, -0.995070, -0.653153,
--0.769939, -0.631918, -0.797688,
--0.616289, -0.806819, -0.638485,
--0.790356, -0.136399, -0.322769,
+DataCollection/Fields/0/Data/Values: [-0.016886, 1.000000, 0.309017, 
+1.309020, -0.809017, -0.500000, 
+-0.809017, -1.618030, 0.309017, 
+-0.500000, 1.309020, 0.519420, 
+1.154510, 0.809019, 0.147680, 
+-0.095492, -0.654508, -0.415586, 
+-1.213520, -1.213520, -0.392210, 
+-0.654508, -0.095492, 0.139949, 
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+0.011786, -0.284704, -0.179858, 
+-0.411567, -0.296676, -0.570168, 
+-0.635348, -0.726784, -0.793211, 
+-1.016860, -1.112970, -1.170910, 
+-1.281530, -0.737860, -0.851723, 
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+-0.790356, -0.136399, -0.322769, 
 -0.165339, -0.309622]
 DataCollection/Mesh/PartitionInfo/Size: 2
 DataCollection/Mesh/PartitionInfo/Type: FMS_UINT64
@@ -170,69 +170,69 @@ DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/EntityType: FMS_EDGE
 DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/NumEntities: 50
 DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/Size: 100
 DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/Type: FMS_INT32
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/Values: [11, 0, 26,
-11, 26, 14,
-14, 0, 27,
-14, 27, 17,
-17, 0, 28,
-17, 28, 20,
-20, 0, 29,
-20, 29, 23,
-23, 0, 30,
-23, 30, 11,
-11, 1, 12,
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-12, 3, 13,
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-13, 2, 14,
-2, 15, 2,
-27, 15, 15,
-5, 16, 5,
-27, 16, 16,
-4, 17, 4,
-18, 4, 28,
-18, 18, 7,
-19, 7, 28,
-19, 19, 6,
-20, 6, 21,
-6, 29, 21,
-21, 9, 22,
-9, 29, 22,
-22, 8, 23,
-8, 24, 8,
-30, 24, 24,
-10, 25, 10,
+DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/Values: [11, 0, 26, 
+11, 26, 14, 
+14, 0, 27, 
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+8, 24, 8, 
+30, 24, 24, 
+10, 25, 10, 
 30, 25, 25, 1]
 DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/EntityType: FMS_QUADRILATERAL
 DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/NumEntities: 20
 DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/Size: 80
 DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/Type: FMS_INT32
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/Values: [0, 1, 2,
-3, 3, 4,
-5, 6, 6,
-7, 8, 9,
-9, 10, 11,
-12, 12, 13,
-14, 0, 15,
-16, 17, 1,
-17, 18, 19,
-20, 2, 20,
-21, 22, 22,
-23, 24, 4,
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-34, 8, 34,
-35, 36, 36,
-37, 38, 10,
-38, 39, 40,
-41, 11, 41,
-42, 43, 43,
-44, 45, 13,
-45, 46, 47,
-48, 14, 48,
+DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/Values: [0, 1, 2, 
+3, 3, 4, 
+5, 6, 6, 
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+41, 11, 41, 
+42, 43, 43, 
+44, 45, 13, 
+45, 46, 47, 
+48, 14, 48, 
 49, 15]
 DataCollection/Mesh/Components/0/Name: volume
 DataCollection/Mesh/Components/0/Dimension: 2

data/tinyzoo-3d.mesh

@@ -1,56 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geomety Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-# PYRAMID     = 7
-
-dimension
-3
-
-elements
-4
-1 5 0 1 4 3 6 7 10 9
-1 6 4 1 5 10 7 11
-1 7 11 7 1 5 8
-1 4 2 5 1 8
-
-boundary
-14
-1 3 0 3 4 1
-1 3 6 7 10 9
-1 3 0 6 9 3
-1 3 0 1 7 6
-1 3 3 9 10 4
-1 2 1 5 2
-1 2 1 4 5
-1 2 1 8 7
-1 2 1 2 8
-1 2 2 5 8
-1 2 5 11 8
-1 2 7 8 11
-1 2 7 11 10
-1 3 4 10 11 5
-
-vertices
-12
-3
-0 0 0
-1 0 0
-2 0 0
-0 1 0
-1 1 0
-2 1 0
-0 0 1
-1 0 1
-2 0 1
-0 1 1
-1 1 1
-2 1 1

doc/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

doc/CodeDocumentation.conf.in

@@ -38,7 +38,7 @@ PROJECT_NAME           = "MFEM"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v4.4.1
+PROJECT_NUMBER         = v4.3.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -765,14 +765,11 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/linalg \
                          @MFEM_SOURCE_DIR@/mesh \
                          @MFEM_SOURCE_DIR@/fem \
-                         @MFEM_SOURCE_DIR@/fem/moonolith \
                          @MFEM_SOURCE_DIR@/fem/fe \
-                         @MFEM_SOURCE_DIR@/fem/lor \
                          @MFEM_SOURCE_DIR@/examples \
                          @MFEM_SOURCE_DIR@/examples/caliper \
                          @MFEM_SOURCE_DIR@/examples/amgx \
                          @MFEM_SOURCE_DIR@/examples/ginkgo \
-                         @MFEM_SOURCE_DIR@/examples/moonolith \
                          @MFEM_SOURCE_DIR@/examples/hiop \
                          @MFEM_SOURCE_DIR@/examples/petsc \
                          @MFEM_SOURCE_DIR@/examples/pumi \

doc/CodeDocumentation.dox

@@ -98,13 +98,6 @@ namespace mfem {
  * - <a class="el" href="ex28p_8cpp_source.html">Example 28p</a>: parallel sliding contact in elasticity
  * - <a class="el" href="ex29_8cpp_source.html">Example 29</a>: Laplace solve on a 3D-embedded surface
  * - <a class="el" href="ex29p_8cpp_source.html">Example 29p</a>: parallel Laplace solve on a 3D-embedded surface
- * - <a class="el" href="ex30_8cpp_source.html">Example 30</a>: mesh preprocessing to resolve problem data
- * - <a class="el" href="ex30p_8cpp_source.html">Example 30p</a>: parallel mesh preprocessing to resolve problem data
- * - <a class="el" href="ex31_8cpp_source.html">Example 31</a>: Nedelec H(curl) FEM for the definite anisotropic Maxwell problem
- * - <a class="el" href="ex31p_8cpp_source.html">Example 31p</a>: parallel Nedelec H(curl) FEM for the definite anisotropic Maxwell problem
- * - <a class="el" href="ex32p_8cpp_source.html">Example 32p</a>: parallel anisotropic Maxwell eigensolver
- * - <a class="el" href="ex33_8cpp_source.html">Example 33</a>: nodal H1 FEM for the fractional Laplacian problem
- * - <a class="el" href="ex33p_8cpp_source.html">Example 33p</a>: parallel nodal H1 FEM for the fractional Laplacian problem
  *
  * <H4>AmgX Examples</H4>
  * - Variants of Examples
@@ -197,13 +190,12 @@ namespace mfem {
  * - <a class="el" href="field-interp_8cpp_source.html">Field Interp</a>: transfer a grid functions between meshes
  * - <a class="el" href="distance_8cpp_source.html">Distance</a>: finite element distance function solver
  * - <a class="el" href="diffusion_8cpp_source.html">Shifted Diffusion</a>: shifted boundary diffusion solver
- * - <a class="el" href="extrapolate_8cpp_source.html">Extrapolation</a>: PDE-based extrapolation of finite element functions
  * - <a class="el" href="distance_8cpp_source.html">Block Solvers</a>: comparison of saddle point system solvers
  * - <a class="el" href="parheat_8cpp_source.html">Optimization gradients</a>: Gradients of PDE-constrained function
- * - <a class="el" href="par__example_8cpp_source.html">Parallel AD</a>: Parallel p-Laplacian example
- * - <a class="el" href="seq__example_8cpp_source.html">Serial AD</a>: Serial p-Laplacian example
  * - <a class="el" href="miniapps_2performance_2ex1_8cpp_source.html">HPC Example 1</a>: high-performance nodal H1 FEM for the Laplace problem
  * - <a class="el" href="miniapps_2performance_2ex1p_8cpp_source.html">HPC Example 1p</a>: high-performance parallel nodal H1 FEM for the Laplace problem
+ * - <a class="el" href="par__example_8cpp_source.html">Parallel pLaplacian example using AD</a>: Parallel pLaplacian example
+ * - <a class="el" href="seq__example_8cpp_source.html">Serial pLaplacian example using AD</a>: Serial pLaplacian example
  *
  * See also the <a class="el" href="https://mfem.org/examples/">examples documentation</a> online.
  */

doc/README

@@ -21,7 +21,8 @@ create the file CodeDocumentation.html, which can be viewed in any web browser.
 
 Alternatively, the (pre-build) documentation can be browsed directly online at
 
-   https://docs.mfem.org
+   https://mfem.github.io/doxygen/html/index.html
+
 
 Some building considerations:
 

doc/makefile

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -16,7 +16,7 @@ DOXYGEN_CONF = CodeDocumentation.conf
 # doxygen uses: graphviz, latex
 html: $(DOXYGEN_CONF)
 	@# Generate the html documentation
-	@( cat $(DOXYGEN_CONF) ; echo "$(MFEM_DOXYGEN_FLAGS)" ) | doxygen -
+	@doxygen $(DOXYGEN_CONF)
 	@echo "<meta http-equiv=\"REFRESH\" content=\"0;URL=CodeDocumentation/html/index.html\">" > CodeDocumentation.html
 	@cat warnings.log 1>&2
 	@# Generate the log of undocumented methods
@@ -29,3 +29,4 @@ clean:
 $(DOXYGEN_CONF): $(MFEM_DIR)/doc/$(DOXYGEN_CONF).in
 	@sed -e 's%@MFEM_SOURCE_DIR@%$(MFEM_DIR)%g' $(<) \
 	  > $(DOXYGEN_CONF)
+

examples/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #
@@ -38,8 +38,6 @@ list(APPEND ALL_EXE_SRCS
   ex28.cpp
   ex29.cpp
   ex30.cpp
-  ex31.cpp
-  ex33.cpp
   )
 
 if (MFEM_USE_MPI)
@@ -74,9 +72,6 @@ if (MFEM_USE_MPI)
     ex28p.cpp
     ex29p.cpp
     ex30p.cpp
-    ex31p.cpp
-    ex32p.cpp
-    ex33p.cpp
     )
 endif()
 
@@ -201,7 +196,3 @@ endif()
 if (MFEM_USE_SUPERLU)
   add_subdirectory(superlu)
 endif()
-
-if(MFEM_USE_MOONOLITH)
-  add_subdirectory(moonolith)
-endif()

examples/amgx/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #

examples/amgx/ex1p.cpp

@@ -37,11 +37,11 @@ using namespace mfem;
 
 int main(int argc, char *argv[])
 {
-   // 1. Initialize MPI and HYPRE.
-   Mpi::Init(argc, argv);
-   int num_procs = Mpi::WorldSize();
-   int myid = Mpi::WorldRank();
-   Hypre::Init();
+   // 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.
    const char *mesh_file = "../../data/star.mesh";
@@ -87,6 +87,7 @@ int main(int argc, char *argv[])
       {
          args.PrintUsage(cout);
       }
+      MPI_Finalize();
       return 1;
    }
    if (myid == 0)
@@ -319,6 +320,7 @@ int main(int argc, char *argv[])
    {
       delete fec;
    }
+   MPI_Finalize();
 
    return 0;
 }

examples/amgx/makefile

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# 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.
 #