Use external PA data

version 1: PA new
version 2: PA new (layout by vdim)
version 3: MF ∂fem
version 4: PA ∂fem
version 5: PA ∂fem new
version 6: Auto PA ∂fem
version 7: Auto PA ∂fem new

.github/actions/sanitize/mfem/action.yml

@@ -25,7 +25,7 @@ runs:
   steps:
     - uses: ./.github/actions/sanitize/config
 
-    - uses: actions/cache@v5
+    - uses: actions/cache@v4
       if: ${{env.DEBUG == 'true'}}
       id: debug
       with:

.github/actions/sanitize/restore/action.yml

@@ -36,7 +36,7 @@ runs:
   steps:
     - uses: ./.github/actions/sanitize/config
 
-    - uses: actions/cache@v5
+    - uses: actions/cache@v4
       if: ${{env.DEBUG == 'true' && inputs.cache-skip != 'true'}}
       id: debug
       with:

.github/actions/sanitize/setup/action.yml

@@ -23,7 +23,7 @@ inputs:
 runs:
   using: 'composite'
   steps:
-    - uses: actions/cache/restore@v5  # Cache for LLVM libcxx
+    - uses: actions/cache/restore@v4  # Cache for LLVM libcxx
       with:
         path: ${{env.LLVM_DIR}}
         fail-on-cache-miss: true
@@ -32,14 +32,14 @@ runs:
     - uses: ./.github/actions/sanitize/mpi
       if: ${{inputs.par == 'true'}}
 
-    - uses: actions/cache/restore@v5  # Cache for Hypre
+    - uses: actions/cache/restore@v4  # Cache for Hypre
       if: ${{inputs.par == 'true'}}
       with:
         path: ${{env.HYPRE_DIR}}
         fail-on-cache-miss: true
         key: ${{runner.os}}-ompi-build-${{env.HYPRE_DIR}}-int32-fp64-v2.5
 
-    - uses: actions/cache/restore@v5  # Cache for Metis
+    - uses: actions/cache/restore@v4  # Cache for Metis
       if: ${{inputs.par == 'true'}}
       with:
         path: ${{env.METIS_DIR}}
@@ -51,13 +51,13 @@ runs:
       run: ln -s -f ${{env.HYPRE_DIR}} hypre && ln -s -f ${{env.METIS_DIR}} metis-4.0
       shell: bash
 
-    - uses: actions/cache/restore@v5  # Cache for LSAN suppression file
+    - uses: actions/cache/restore@v4  # Cache for LSAN suppression file
       with:
         path: ${{env.LSAN_DIR}}
         fail-on-cache-miss: true
         key: build-lsan-suppression-file
 
-    - uses: actions/checkout@v6  # Checkout the repository
+    - uses: actions/checkout@v4  # Checkout the repository
       with:
         path: mfem
         # ref: ${{env.BRANCH}}

.github/workflows/build-container.yml

@@ -43,7 +43,7 @@ jobs:
           remove-docker-images: 'true'
 
       - name: Checkout
-        uses: actions/checkout@v6
+        uses: actions/checkout@v4
 
       # It's easier to reference named variables than indexes of the matrix
       - name: Set Environment

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

@@ -132,14 +132,12 @@ jobs:
             hypre-target: int32
             precision: fp64
             enzyme: true
-            config-opts: MFEM_USE_ENZYME=YES ENZYME_DIR=$(brew --prefix enzyme) LDFLAGS=-L$LLVM_PREFIX/lib/c++
+            config-opts: MFEM_USE_ENZYME=YES ENZYME_DIR=$(brew --prefix enzyme)
 
     name: ${{ matrix.os }}-${{ matrix.build-system }}-${{ matrix.target }}-${{ matrix.mpi }}-${{ matrix.hypre-target }}-${{ matrix.precision }}${{ matrix.enzyme && '-enzyme' || '' }}
 
     runs-on: ${{ matrix.os }}
 
-    continue-on-error: ${{ matrix.enzyme && true || false }}
-
     steps:
       # Fix 'No space left on device' errors for Ubuntu builds.
       - name: Run Actions Cleaner
@@ -153,7 +151,7 @@ jobs:
       # /home/runner/work/mfem/mfem/mfem
       # Note: Done now to access "install-hypre" and "install-metis" actions.
       - name: checkout mfem
-        uses: actions/checkout@v6
+        uses: actions/checkout@v4
         with:
           path: ${{ env.MFEM_TOP_DIR }}
           # Fetch the complete history for codecov to access commits ID
@@ -170,13 +168,10 @@ jobs:
           env
         shell: bash
 
-      # For info on Xcode see:
-      #  - https://github.com/actions/runner-images/issues/12541
-      #  - https://github.com/actions/runner-images/blob/releases/macos-15-arm64/20250811/images/macos/macos-15-arm64-Readme.md#xcode
       - name: Xcode version setup (MacOS)
         if: matrix.os == 'macos-latest'
         run: |
-          XCODE_PATH="/Applications/Xcode_16.4.app"
+          XCODE_PATH="/Applications/Xcode_15.3.app"
           echo "> sudo xcode-select -s ${XCODE_PATH}"
           sudo xcode-select -s ${XCODE_PATH}
           echo "> g++ -v"
@@ -225,7 +220,7 @@ jobs:
       - name: cache hypre
         id: hypre-cache
         if: matrix.mpi == 'par'
-        uses: actions/cache@v5
+        uses: actions/cache@v4
         with:
           path: ${{ env.HYPRE_TOP_DIR }}
           key: ${{ runner.os }}-ompi-build-${{ env.HYPRE_TOP_DIR }}-${{ matrix.hypre-target }}-${{ matrix.precision }}-v2.5
@@ -255,7 +250,7 @@ jobs:
       - name: cache metis
         id: metis-cache
         if: matrix.mpi == 'par' && matrix.os != 'windows-latest'
-        uses: actions/cache@v5
+        uses: actions/cache@v4
         with:
           path: ${{ env.METIS_TOP_DIR }}
           key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.5
@@ -270,7 +265,7 @@ jobs:
       - name: cache vcpkg (Windows)
         id: vcpkg-cache
         if: matrix.os == 'windows-latest'
-        uses: actions/cache@v5
+        uses: actions/cache@v4
         with:
           path: vcpkg_cache
           key: ${{ runner.os }}-${{ matrix.mpi }}-vcpkg-v1
@@ -294,13 +289,10 @@ jobs:
         run: |
           export HOMEBREW_NO_INSTALL_CLEANUP=1
           brew update
-          brew install enzyme
-          ENZYME_LLVM=$(brew info enzyme | sed -n 's/^Required.*:.*\(llvm[^ ]*\).*/\1/p')
-          echo "ENZYME_LLVM=$ENZYME_LLVM"
-          LLVM_PREFIX=$(brew --prefix $ENZYME_LLVM)
-          echo "LLVM_PREFIX=$LLVM_PREFIX" >> $GITHUB_ENV
-          echo "OMPI_CC=$LLVM_PREFIX/bin/clang" >> $GITHUB_ENV
-          echo "OMPI_CXX=$LLVM_PREFIX/bin/clang++" >> $GITHUB_ENV
+          brew install llvm@19 enzyme
+          echo "LLVM_PREFIX=$(brew --prefix llvm@19)" >> $GITHUB_ENV
+          echo "OMPI_CC=$(brew --prefix llvm@19)/bin/clang" >> $GITHUB_ENV
+          echo "OMPI_CXX=$(brew --prefix llvm@19)/bin/clang++" >> $GITHUB_ENV
 
       # MFEM build and test
       - name: build

.github/workflows/codeql-analysis.yml

@@ -40,11 +40,11 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v4
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v4
+        uses: github/codeql-action/init@v2
         with:
           languages: ${{ matrix.language }}
           # If you wish to specify custom queries, you can do so here or in a config file.
@@ -57,7 +57,7 @@ jobs:
       # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
       # If this step fails, then you should remove it and run the build manually (see below)
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v4
+        uses: github/codeql-action/autobuild@v2
 
       # ℹ️ Command-line programs to run using the OS shell.
       # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -70,4 +70,4 @@ jobs:
       #   ./location_of_script_within_repo/buildscript.sh
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v4
+        uses: github/codeql-action/analyze@v2

.github/workflows/mfem-analysis.yml

@@ -39,7 +39,7 @@ jobs:
 
     steps:
       - name: checkout MFEM
-        uses: actions/checkout@v6
+        uses: actions/checkout@v4
         with:
           path: mfem
 
@@ -50,7 +50,7 @@ jobs:
 
       - name: Cache Hypre Install
         id: hypre-cache
-        uses: actions/cache@v5
+        uses: actions/cache@v4
         with:
           path: ${{ env.HYPRE_TOP_DIR }}
           key: ${{ runner.os }}-ompi-build-${{ env.HYPRE_TOP_DIR }}-v2.5
@@ -65,7 +65,7 @@ jobs:
 
       - name: Cache Metis Install
         id: metis-cache
-        uses: actions/cache@v5
+        uses: actions/cache@v4
         with:
           path: ${{ env.METIS_TOP_DIR }}
           key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.5

.github/workflows/repo-check.yml

@@ -38,7 +38,7 @@ jobs:
        github.event.pull_request.head.repo.full_name != github.repository)
     steps:
       - name: checkout mfem
-        uses: actions/checkout@v6
+        uses: actions/checkout@v4
 
       - name: copyright check
         id: copyright
@@ -93,7 +93,7 @@ jobs:
        github.event.pull_request.head.repo.full_name != github.repository)
     steps:
       - name: checkout mfem
-        uses: actions/checkout@v6
+        uses: actions/checkout@v4
 
       - name: get astyle
         run: |
@@ -110,7 +110,7 @@ jobs:
        github.event.pull_request.head.repo.full_name != github.repository)
     steps:
       - name: checkout mfem
-        uses: actions/checkout@v6
+        uses: actions/checkout@v4
 
       - name: get doxygen and graphviz
         run: |
@@ -135,7 +135,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout mfem
-        uses: actions/checkout@v6
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/sanitize-build-hypre.yml

@@ -17,11 +17,11 @@ jobs:
     runs-on: ubuntu-latest
     name: 2.19.0
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/config
       - name: Cache
         id: cache
-        uses: actions/cache@v5
+        uses: actions/cache@v4
         with:
           path: ${{env.HYPRE_DIR}}
           key: ${{runner.os}}-ompi-build-${{env.HYPRE_DIR}}-int32-fp64-v2.5

.github/workflows/sanitize-build-libcxx.yml

@@ -27,13 +27,13 @@ jobs:
             llvm_use_sanitizer: "Undefined"
     name: ${{matrix.sanitizer}}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/config
         with:
           NO_FLAGS: true
       - name: Cache
         id: cache
-        uses: actions/cache@v5
+        uses: actions/cache@v4
         with:
           path: ${{env.LLVM_DIR}}
           key: build-libcxx-${{env.LLVM_VER}}-${{matrix.sanitizer}}

.github/workflows/sanitize-build-lsan.yml

@@ -17,11 +17,11 @@ jobs:
     runs-on: ubuntu-latest
     name: lsan.supp
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/config
       - name: Cache
         id: cache
-        uses: actions/cache@v5
+        uses: actions/cache@v4
         with:
           path: ${{env.LSAN_DIR}}
           key: build-lsan-suppression-file

.github/workflows/sanitize-build-metis.yml

@@ -17,11 +17,11 @@ jobs:
     runs-on: ubuntu-latest
     name: 4.0.3
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/config
       - name: Cache
         id: cache
-        uses: actions/cache@v5
+        uses: actions/cache@v4
         with:
           path: ${{env.METIS_DIR}}
           key: ${{runner.os}}-build-${{env.METIS_DIR}}-v2.5

.github/workflows/sanitize-tests.yml

@@ -28,7 +28,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/mfem
         with:
           par: ${{inputs.par}}
@@ -40,7 +40,7 @@ jobs:
     env:
       ex: ${{inputs.par && 'ex1p' || 'ex1'}}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/restore
         id: restore
         with:
@@ -58,7 +58,7 @@ jobs:
     env:
       exclude: ${{inputs.par && '-E "_ser"' || ''}}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/restore
         id: restore
         with:
@@ -82,7 +82,7 @@ jobs:
     env:
       exclude: ${{inputs.par && '-E "_ser"' || ''}}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/restore
         id: restore
         with:
@@ -107,7 +107,7 @@ jobs:
       run: ${{inputs.par && '-R "_cpu_np"' || ''}}
       exclude: ${{inputs.par && '"unit_tests|debug"' || '"^unit_tests$|debug"'}}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/restore
         id: restore
         with:
@@ -131,7 +131,7 @@ jobs:
     env:
       unit_tests: ${{inputs.par && 'punit_tests' || 'unit_tests'}}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/restore
         id: restore
         with:
@@ -165,7 +165,7 @@ jobs:
       unit_tests: ${{inputs.par && 'punit_tests' || 'unit_tests'}}
       np: ${{inputs.par && '_np=2' || ''}}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/sanitize/restore
         id: restore
         with:

.github/workflows/stale.yml

@@ -29,47 +29,3 @@ jobs:
         operations-per-run: 500
         exempt-issue-labels: "bug,WIP,ready-for-review,in-review,in-next"
         exempt-pr-labels: "bug,WIP,ready-for-review,in-review,in-next"
-
-  # Stale action for PRs with "in-review" label.
-  stale-in-review-pr:
-
-    runs-on: ubuntu-latest
-    permissions:
-      issues: write
-      pull-requests: write
-      actions: write
-
-    steps:
-    - uses: actions/stale@v9
-      with:
-        repo-token: ${{ secrets.GITHUB_TOKEN }}
-        stale-pr-message: ':warning: This PR has been automatically marked as stale because it has not had any activity in the last 150 days. *If no activity occurs in the next 30 days, it will be automatically closed.* Thank you for your contributions.'
-        only-pr-labels: "in-review"
-        days-before-pr-stale: 150
-        days-before-pr-close: 30
-        days-before-issue-stale: -1
-        days-before-issue-close: -1
-        stale-pr-label: 'stale'
-        operations-per-run: 500
-
-  # Stale action for PRs with "WIP" label.
-  stale-wip-pr:
-
-    runs-on: ubuntu-latest
-    permissions:
-      issues: write
-      pull-requests: write
-      actions: write
-
-    steps:
-    - uses: actions/stale@v9
-      with:
-        repo-token: ${{ secrets.GITHUB_TOKEN }}
-        stale-pr-message: ':warning: This PR has been automatically marked as stale because it has not had any activity in the last 300 days. *If no activity occurs in the next 30 days, it will be automatically closed.* Thank you for your contributions.'
-        only-pr-labels: "WIP"
-        days-before-pr-stale: 300
-        days-before-pr-close: 30
-        days-before-issue-stale: -1
-        days-before-issue-close: -1
-        stale-pr-label: 'stale'
-        operations-per-run: 500

.gitignore

@@ -19,15 +19,9 @@ CMakeFiles/
 # Clangd server cache
 *.cache*
 
-#vscode settings
-/.vscode/
-
 # Backup files
 *~
 
-# clangd index
-/.cache/
-
 # Default install location
 /mfem/
 
@@ -85,17 +79,12 @@ examples/sol_u.*
 examples/sol_p.*
 examples/sol_r.*
 examples/sol_i.*
-examples/sol_z.*
 examples/ex6p-checkpoint.*
 examples/order.*
 examples/ex9.mesh
 examples/ex9-mesh.*
 examples/ex9-init.*
 examples/ex9-final.*
-examples/ex41.mesh
-examples/ex41-mesh.*
-examples/ex41-init.*
-examples/ex41-final.*
 examples/deformed.*
 examples/velocity.*
 examples/elastic_energy.*
@@ -219,16 +208,10 @@ miniapps/electromagnetics/volta
 miniapps/electromagnetics/tesla
 miniapps/electromagnetics/maxwell
 miniapps/electromagnetics/joule
-miniapps/electromagnetics/lorentz
 miniapps/electromagnetics/Volta-AMR*
 miniapps/electromagnetics/Tesla-AMR*
 miniapps/electromagnetics/Maxwell-Parallel*
-miniapps/electromagnetics/Joule_[0-9]*
-miniapps/electromagnetics/Lorentz_[0-9]*
-miniapps/electromagnetics/Lorentz.dat
-
-miniapps/fluids/schrodinger-flow/schrodinger_flow
-miniapps/fluids/schrodinger-flow/pschrodinger_flow
+miniapps/electromagnetics/Joule_*
 
 miniapps/gslib/field-diff
 miniapps/gslib/field-interp
@@ -237,7 +220,6 @@ miniapps/gslib/pfindpts
 miniapps/gslib/schwarz_ex1
 miniapps/gslib/schwarz_ex1p
 miniapps/gslib/interpolated.gf
-miniapps/gslib/particles_redist
 
 miniapps/meshing/mobius-strip
 miniapps/meshing/klein-bottle
@@ -284,8 +266,10 @@ miniapps/meshing/refined.mesh
 miniapps/meshing/bounding-box*
 miniapps/meshing/jacobian-determinant*
 
-miniapps/mtop/ParaView/
-miniapps/mtop/mtop_test_iso_elasticity
+miniapps/mtop/parheat
+miniapps/mtop/ParHeat*
+miniapps/mtop/seqheat
+miniapps/mtop/SeqHeat*
 
 miniapps/autodiff/paradiff
 miniapps/autodiff/seqadiff
@@ -293,35 +277,29 @@ miniapps/autodiff/seqtest
 miniapps/autodiff/par_example
 miniapps/autodiff/seq_example
 miniapps/autodiff/seq_test
-miniapps/autodiff/Example/*
+miniapps/autodiff/Exampl*
 
-miniapps/fluids/navier/navier_mms
-miniapps/fluids/navier/navier_kovasznay
-miniapps/fluids/navier/navier_kovasznay_vs
-miniapps/fluids/navier/navier_tgv
-miniapps/fluids/navier/navier_shear
-miniapps/fluids/navier/navier_3dfoc
-miniapps/fluids/navier/navier_turbchan
-miniapps/fluids/navier/navier_cht
-miniapps/fluids/navier/navier_bifurcation
-miniapps/fluids/navier/Navier_Bifurcation_[0-9]*
-miniapps/fluids/navier/ParaView
-miniapps/fluids/navier/tgv_out*.txt
-miniapps/fluids/navier/*_output
+miniapps/navier/navier_mms
+miniapps/navier/navier_kovasznay
+miniapps/navier/navier_kovasznay_vs
+miniapps/navier/navier_tgv
+miniapps/navier/navier_shear
+miniapps/navier/navier_3dfoc
+miniapps/navier/navier_turbchan
+miniapps/navier/navier_cht
+miniapps/navier/tgv_out*.txt
+miniapps/navier/*_output
 
 miniapps/nurbs/nurbs_ex1
 miniapps/nurbs/nurbs_ex1p
 miniapps/nurbs/nurbs_ex3
 miniapps/nurbs/nurbs_ex5
-miniapps/nurbs/nurbs_ex10
-miniapps/nurbs/nurbs_ex10p
 miniapps/nurbs/nurbs_ex11p
 miniapps/nurbs/nurbs_ex24
 miniapps/nurbs/nurbs_solenoidal
 miniapps/nurbs/nurbs_printfunc
 miniapps/nurbs/nurbs_patch_ex1
 miniapps/nurbs/nurbs_curveint
-miniapps/nurbs/nurbs_surface
 miniapps/nurbs/refined.mesh
 miniapps/nurbs/mesh.*
 miniapps/nurbs/sol_?.gf
@@ -340,14 +318,6 @@ miniapps/nurbs/nurbs_naca_cmesh
 miniapps/nurbs/naca-cmesh.mesh
 miniapps/nurbs/glvis_naca-cmesh.mesh
 miniapps/nurbs/Naca_cmesh
-miniapps/nurbs/nurbs_mesh_info
-miniapps/nurbs/k*_*.dat
-miniapps/nurbs/*-Surface.mesh
-miniapps/nurbs/*.mesh
-miniapps/nurbs/*.sol
-miniapps/nurbs/deformed.*
-miniapps/nurbs/elastic_energy.*
-miniapps/nurbs/velocity.*
 
 miniapps/performance/ex1
 miniapps/performance/ex1p
@@ -369,7 +339,6 @@ miniapps/shifted/lsf_integral
 miniapps/tools/display-basis
 miniapps/tools/load-dc
 miniapps/tools/convert-dc
-miniapps/tools/compare-dc
 miniapps/tools/gridfunction-bounds
 miniapps/tools/lor-transfer
 miniapps/tools/plor-transfer
@@ -440,19 +409,12 @@ miniapps/tribol/contact-patch-test
 miniapps/diag-smoothers/abs-l1-jacobi
 miniapps/diag-smoothers/mg-abs-l1-jacobi
 
-miniapps/contact/contact
-miniapps/contact/ParaView
-
-miniapps/plasma/pic/electrostatic-*
-!miniapps/plasma/pic/electrostatic-*.cpp
-miniapps/plasma/pic/*.csv
-
 # Unit test binary and outputs
 tests/unit/output_meshes
 tests/unit/unit_tests
 tests/unit/punit_tests
-tests/unit/gpu_unit_tests
-tests/unit/pgpu_unit_tests
+tests/unit/cunit_tests
+tests/unit/pcunit_tests
 tests/unit/sedov_tests_*
 tests/unit/psedov_tests_*
 tests/unit/tmop_pa_tests_*

.gitlab-ci.yml

@@ -9,550 +9,91 @@
 # terms of the BSD-3 license. We welcome feedback and contributions, see file
 # CONTRIBUTING.md for details.
 
-# DESCRIPTION:
-###############################################################################
 # General GitLab pipelines configurations for supercomputers and Linux clusters
-# at Lawrence Livermore National Laboratory (LLNL).
-# This entire pipeline is LLNL-specific
-#
-# Important note: This file is a template provided by llnl/radiuss-shared-ci.
-# Remains to set variable values, change the reference to the radiuss-shared-ci
-# repo, opt-in and out optional features. The project can then extend it with
-# additional stages.
-#
-# In addition, each project should copy over and complete:
-# - .gitlab/custom-jobs-and-variables.yml
-# - .gitlab/subscribed-pipelines.yml
-#
-# The jobs should be specified in a file local to the project,
-# - .gitlab/jobs/${CI_MACHINE}.yml
-# or generated (see LLNL/Umpire for an example).
-###############################################################################
-#   MAP OF GITLAB CI
-#######################
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# File dependencies: direct, through jobs, through variables
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# .gitlab-ci.yml
-#  ├── .build-and-test  [job]
-#  │    ├── .gitlab/custom-jobs-and-variables.yml
-#  │    │    ├── .custom_job          [job]
-#  │    │    ├── .reproducer_vars     [job]
-#  │    │    ├── .report_job_success  [job]
-#  │    │    │    └── .gitlab/scripts/report_build_and_test    [script]
-#  │    │    │         ├── .gitlab/scripts/safe_create_rundir  [script]
-#  │    │    │         └── .gitlab/scripts/git_try_to_push     [script]
-#  │    │    ├── .report_job_failure  [job]
-#  │    │    │    └── .gitlab/scripts/report_build_and_test    [script]
-#  │    │    │         ├── .gitlab/scripts/safe_create_rundir  [script]
-#  │    │    │         └── .gitlab/scripts/git_try_to_push     [script]
-#  │    │    └── JOB_CMD              [var]
-#  │    │         └── tests/gitlab/build_and_test            [script]
-#  │    │              └── tests/gitlab/get_mfem_uberenv     [script]
-#  │    ├── <radiuss-shared-ci>/pipelines/matrix.yml  [conditional]
-#  │    │    ├── .on_matrix               [job]
-#  │    │    ├── .matrix_reproducer_init  [job]
-#  │    │    ├── .matrix_reproducer_vars  [job]
-#  │    │    ├── .matrix_reproducer_job   [job]
-#  │    │    ├── .matrix_job_command      [job]
-#  │    │    └── .job_on_matrix           [job]
-#  │    ├── <radiuss-shared-ci>/pipelines/dane.yml  [conditional]
-#  │    │    ├── .on_dane               [job]
-#  │    │    ├── .dane_reproducer_init  [job]
-#  │    │    ├── .dane_reproducer_vars  [job]
-#  │    │    ├── .dane_reproducer_job   [job]
-#  │    │    ├── .dane_job_command      [job]
-#  │    │    ├── .job_on_dane           [job]
-#  │    │    ├── allocate_resources     [job]
-#  │    │    └── release_resources      [job]
-#  │    ├── <radiuss-shared-ci>/pipelines/tioga.yml  [conditional]
-#  │    │    ├── .on_tioga               [job]
-#  │    │    ├── .tioga_reproducer_init  [job]
-#  │    │    ├── .tioga_reproducer_vars  [job]
-#  │    │    ├── .tioga_reproducer_job   [job]
-#  │    │    ├── .tioga_job_command      [job]
-#  │    │    ├── .job_on_tioga           [job]
-#  │    │    ├── allocate_resources      [job]
-#  │    │    └── release_resources       [job]
-#  │    ├── <artifact>/matrix-jobs.yml  [conditional, from 'generate-job-lists']
-#  │    │    ├── .gitlab/jobs/matrix.yml
-#  │    │    │    ├── .matrix_reproducer_vars      [job]
-#  │    │    │    ├── setup                        [job]
-#  │    │    │    │    └── ./tests/gitlab/build_and_test_setup  [script]
-#  │    │    │    ├── opt_mpi_cuda_gcc             [job]
-#  │    │    │    └── opt_mpi_cuda_hypre_cuda_gcc  [job]
-#  │    │    └── .gitlab/jobs/matrix-reports.yml  [used conditionally]
-#  │    │         ├── report_job_success
-#  │    │         └── report_job_failure
-#  │    ├── <artifact>/dane-jobs.yml    [conditional, from 'generate-job-lists']
-#  │    │    ├── .gitlab/jobs/dane.yml
-#  │    │    │    ├── .dane_reproducer_vars    [job]
-#  │    │    │    ├── setup                    [job]
-#  │    │    │    │    └── ./tests/gitlab/build_and_test_setup  [script]
-#  │    │    │    ├── debug_ser_gcc_10         [job]
-#  │    │    │    ├── debug_par_gcc_10         [job]
-#  │    │    │    ├── opt_ser_gcc_10           [job]
-#  │    │    │    ├── opt_par_gcc_10           [job]
-#  │    │    │    ├── opt_par_gcc_10_sundials  [job]
-#  │    │    │    ├── opt_par_gcc_10_petsc     [job]
-#  │    │    │    └── opt_par_gcc_10_pumi      [job]
-#  │    │    └── .gitlab/jobs/dane-reports.yml    [used conditionally]
-#  │    │         ├── report_job_success
-#  │    │         └── report_job_failure
-#  │    └── <artifact>/tioga-jobs.yml   [conditional, from 'generate-job-lists']
-#  │         ├── .gitlab/jobs/tioga.yml
-#  │         │    ├── .tioga_reproducer_vars  [job]
-#  │         │    ├── setup                   [job]
-#  │         │    │    └── ./tests/gitlab/build_and_test_setup  [script]
-#  │         │    └── cce_16_0_1              [job]
-#  │         └── .gitlab/jobs/tioga-reports.yml   [used conditionally]
-#  │              ├── report_job_success
-#  │              └── report_job_failure
-#  └── .gitlab/subscribed-pipelines.yml
-#       ├── .machine-check         [job]
-#       ├── generate-job-lists     [job]
-#       ├── dane-up-check          [job]
-#       ├── dane-build-and-test    [job]
-#       ├── dane-baseline          [job]
-#       │    └── .gitlab/dane-baseline.yml
-#       │         ├── .on_dane                       [job]
-#       │         ├── baselinecheck_mfem_intel_dane  [job]
-#       │         │    └── .gitlab/scripts/baseline            [script]
-#       │         ├── cleanup                        [job]
-#       │         ├── report_baseline                [job]
-#       │         │    ├── .gitlab/scripts/safe_create_rundir  [script]
-#       │         │    └── .gitlab/scripts/git_try_to_push     [script]
-#       │         ├── baselinepublish_mfem_dane      [job]
-#       │         │    └── .gitlab/scripts/rebaseline          [script]
-#       │         ├── .gitlab/custom-jobs-and-variables.yml
-#       │         │    └── <same as above: see .gitlab-ci.yml/.build-and-test>
-#       │         └── .gitlab/configs/setup-baseline.yml
-#       │              └── setup_baseline            [job]
-#       ├── tioga-up-check         [job]
-#       ├── tioga-build-and-test   [job]
-#       ├── matrix-up-check        [job]
-#       └── matrix-build-and-test  [job]
-#
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# File tree hierarchy with file contents highlights
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# In addition to the files in the MFEM repo, the Gitlab CI uses files from the
-# radiuss/radiuss-shared-ci project, see below, after the <mfem-root> tree.
-#
-# <mfem root>
-#  ├── .gitlab-ci.yml  [this file]
-#  │    ├── <jobs>
-#  │    │    └── .build-and-test
-#  │    ├── <included files>
-#  │    │    ├── .gitlab/subscribed-pipelines.yml
-#  │    │    ├── .gitlab/custom-jobs-and-variables.yml  [by ".build-and-test"]
-#  │    │    ├── <artifact>  [by ".build-and-test"]
-#  │    │    │    ├── artifact: '${CI_MACHINE}-jobs.yml'
-#  │    │    │    └── job:      'generate-job-lists'
-#  │    │    └── <external>  [by ".build-and-test"]
-#  │    │         ├── project: 'radiuss/radiuss-shared-ci'
-#  │    │         ├── ref:     'v2025.09.1'
-#  │    │         └── file:    'pipelines/${CI_MACHINE}.yml'
-#  │    └── <defined variables>
-#  │         ├── CUSTOM_CI_BUILDS_DIR
-#  │         ├── USER_CI_TOP_DIR
-#  │         ├── SHARED_REPOS_DIR
-#  │         ├── AUTOTEST_ROOT
-#  │         ├── MFEM_DATA_DIR
-#  │         ├── AUTOTEST
-#  │         ├── AUTOTEST_COMMIT
-#  │         ├── REBASELINE
-#  │         ├── GITHUB_PROJECT_NAME
-#  │         └── GITHUB_PROJECT_ORG
-#  ├── .gitlab
-#  │    ├── configs
-#  │    │    └── setup-baseline.yml
-#  │    │         ├── <jobs>
-#  │    │         │    └── setup_baseline
-#  │    │         └── <used variables>
-#  │    │              ├── MACHINE_NAME
-#  │    │              ├── REBASELINE
-#  │    │              ├── AUTOTEST
-#  │    │              ├── AUTOTEST_COMMIT
-#  │    │              ├── BUILD_ROOT
-#  │    │              ├── TPLS_REPO
-#  │    │              ├── TESTS_REPO
-#  │    │              ├── AUTOTEST_ROOT
-#  │    │              └── AUTOTEST_REPO
-#  │    ├── jobs
-#  │    │    ├── matrix-reports.yml
-#  │    │    │    ├── <jobs>
-#  │    │    │    │    ├── report_job_success
-#  │    │    │    │    └── report_job_failure
-#  │    │    │    └── <used jobs>
-#  │    │    │         ├── .on_matrix
-#  │    │    │         ├── .report_job_success
-#  │    │    │         └── .report_job_failure
-#  │    │    ├── matrix.yml
-#  │    │    │    ├── <jobs>
-#  │    │    │    │    ├── .matrix_reproducer_vars
-#  │    │    │    │    ├── setup
-#  │    │    │    │    ├── opt_mpi_cuda_gcc
-#  │    │    │    │    └── opt_mpi_cuda_hypre_cuda_gcc
-#  │    │    │    ├── <used jobs>
-#  │    │    │    │    ├── .reproducer_vars
-#  │    │    │    │    ├── .on_matrix
-#  │    │    │    │    └── .job_on_matrix
-#  │    │    │    ├── <included and used files>
-#  │    │    │    │    └── tests/gitlab/build_and_test_setup  [by "setup"]
-#  │    │    │    └── <defined variables>
-#  │    │    │         └── SPEC
-#  │    │    ├── dane-reports.yml
-#  │    │    │    ├── <jobs>
-#  │    │    │    │    ├── report_job_success
-#  │    │    │    │    └── report_job_failure
-#  │    │    │    └── <used jobs>
-#  │    │    │         ├── .on_dane
-#  │    │    │         ├── .report_job_success
-#  │    │    │         └── .report_job_failure
-#  │    │    ├── dane.yml
-#  │    │    │    ├── <jobs>
-#  │    │    │    │    ├── .dane_reproducer_vars
-#  │    │    │    │    ├── setup
-#  │    │    │    │    ├── debug_ser_gcc_10
-#  │    │    │    │    ├── debug_par_gcc_10
-#  │    │    │    │    ├── opt_ser_gcc_10
-#  │    │    │    │    ├── opt_par_gcc_10
-#  │    │    │    │    ├── opt_par_gcc_10_sundials
-#  │    │    │    │    ├── opt_par_gcc_10_petsc
-#  │    │    │    │    └── opt_par_gcc_10_pumi
-#  │    │    │    ├── <used jobs>
-#  │    │    │    │    ├── .reproducer_vars
-#  │    │    │    │    ├── .on_dane
-#  │    │    │    │    └── .job_on_dane
-#  │    │    │    ├── <included and used files>
-#  │    │    │    │    └── tests/gitlab/build_and_test_setup  [by "setup"]
-#  │    │    │    └── <defined variables>
-#  │    │    │         ├── SPEC
-#  │    │    │         └── THREADS
-#  │    │    ├── tioga-reports.yml
-#  │    │    │    ├── <jobs>
-#  │    │    │    │    ├── report_job_success
-#  │    │    │    │    └── report_job_failure
-#  │    │    │    └── <used jobs>
-#  │    │    │         ├── .on_tioga
-#  │    │    │         ├── .report_job_success
-#  │    │    │         └── .report_job_failure
-#  │    │    └── tioga.yml
-#  │    │         ├── <jobs>
-#  │    │         │    ├── .tioga_reproducer_vars
-#  │    │         │    ├── setup
-#  │    │         │    └── opt_mpi_rocm_hypre_rocm
-#  │    │         ├── <used jobs>
-#  │    │         │    ├── .reproducer_vars
-#  │    │         │    ├── .on_tioga
-#  │    │         │    └── .job_on_tioga
-#  │    │         ├── <included and used files>
-#  │    │         │    └── tests/gitlab/build_and_test_setup  [by "setup"]
-#  │    │         └── <defined variables>
-#  │    │              ├── SPEC
-#  │    │              └── THREADS
-#  │    ├── scripts
-#  │    │    ├── baseline
-#  │    │    │    └── <used variables>
-#  │    │    │         ├── BASELINE_TEST
-#  │    │    │         ├── SYS_TYPE
-#  │    │    │         ├── MACHINE_NAME
-#  │    │    │         ├── CI_PROJECT_DIR
-#  │    │    │         ├── ARTIFACTS_DIR
-#  │    │    │         ├── BUILD_ROOT
-#  │    │    │         └── TPLS_DIR
-#  │    │    ├── git_try_to_push
-#  │    │    ├── rebaseline
-#  │    │    │    └── <used variables>
-#  │    │    │         ├── CI_PROJECT_DIR
-#  │    │    │         ├── ARTIFACTS_DIR
-#  │    │    │         ├── SYS_TYPE
-#  │    │    │         ├── BUILD_ROOT
-#  │    │    │         ├── MACHINE_NAME
-#  │    │    │         └── CI_PIPELINE_ID
-#  │    │    ├── report_build_and_test
-#  │    │    │    ├── <used files>
-#  │    │    │    │    ├── .gitlab/scripts/safe_create_rundir
-#  │    │    │    │    └── .gitlab/scripts/git_try_to_push
-#  │    │    │    └── <used variables>
-#  │    │    │         ├── AUTOTEST_ROOT
-#  │    │    │         ├── CI_COMMIT_REF_SLUG
-#  │    │    │         ├── CI_PROJECT_DIR
-#  │    │    │         ├── CI_PIPELINE_URL
-#  │    │    │         ├── AUTOTEST_COMMIT
-#  │    │    │         └── CI_MACHINE
-#  │    │    └── safe_create_rundir
-#  │    ├── custom-jobs-and-variables.yml
-#  │    │    ├── <jobs>
-#  │    │    │    ├── .custom_job
-#  │    │    │    ├── .reproducer_vars
-#  │    │    │    ├── .report_job_success
-#  │    │    │    └── .report_job_failure
-#  │    │    ├── <used files>
-#  │    │    │    ├── tests/gitlab/build_and_test  [in JOB_CMD]
-#  │    │    │    └── .gitlab/scripts/report_build_and_test [by .report_job_*]
-#  │    │    ├── <defined variables>
-#  │    │    │    ├── JOB_CMD
-#  │    │    │    ├── BUILD_ROOT
-#  │    │    │    ├── ALLOC_NAME
-#  │    │    │    ├── TPLS_REPO
-#  │    │    │    ├── TESTS_REPO
-#  │    │    │    ├── AUTOTEST_REPO
-#  │    │    │    ├── MFEM_DATA_REPO
-#  │    │    │    ├── ARTIFACTS_DIR: artifacts
-#  │    │    │    ├── SLURM_OVERLAP: 1
-#  │    │    │    ├── DANE_SHARED_ALLOC
-#  │    │    │    ├── DANE_JOB_ALLOC
-#  │    │    │    ├── TIOGA_SHARED_ALLOC
-#  │    │    │    ├── TIOGA_JOB_ALLOC
-#  │    │    │    └── MATRIX_JOB_ALLOC
-#  │    │    └── <used variables>
-#  │    │         ├── SPEC
-#  │    │         ├── BUILD_ROOT
-#  │    │         └── ...
-#  │    ├── dane-baseline.yml
-#  │    │    ├── <jobs>
-#  │    │    │    ├── .on_dane
-#  │    │    │    ├── baselinecheck_mfem_intel_dane
-#  │    │    │    ├── cleanup
-#  │    │    │    ├── report_baseline
-#  │    │    │    └── baselinepublish_mfem_dane
-#  │    │    ├── <included and used files>
-#  │    │    │    ├── .gitlab/custom-jobs-and-variables.yml
-#  │    │    │    ├── .gitlab/configs/setup-baseline.yml
-#  │    │    │    ├── .gitlab/scripts/rebaseline
-#  │    │    │    ├── .gitlab/scripts/baseline
-#  │    │    │    └── .gitlab/scripts/git_try_to_push
-#  │    │    ├── <defined variables>
-#  │    │    │    ├── BASELINE_TEST: baseline
-#  │    │    │    ├── MACHINE_NAME: dane
-#  │    │    │    ├── TPLS_DIR
-#  │    │    │    └── export MFEM_TEST_NP
-#  │    │    └── <used variables>
-#  │    │         ├── ON_DANE
-#  │    │         ├── AUTOTEST       [defined by .gitlab-ci.yml]
-#  │    │         ├── BUILD_ROOT     [defined by custom-jobs-and-variables.yml]
-#  │    │         ├── TPLS_DIR       [defined by this file]
-#  │    │         ├── ARTIFACTS_DIR  [defined by custom-jobs-and-variables.yml]
-#  │    │         ├── MACHINE_NAME   [defined by this file]
-#  │    │         ├── AUTOTEST_COMMIT  [defined by .gitlab-ci.yml]
-#  │    │         ├── AUTOTEST_ROOT  [defined by .gitlab-ci.yml]
-#  │    │         ├── BASELINE_TEST  [defined by this file]
-#  │    │         └── REBASELINE     [defined by .gitlab-ci.yml]
-#  │    └── subscribed-pipelines.yml
-#  │         ├── <jobs>
-#  │         │    ├── .machine-check
-#  │         │    ├── generate-job-lists
-#  │         │    ├── dane-up-check
-#  │         │    ├── dane-build-and-test
-#  │         │    ├── dane-baseline
-#  │         │    ├── tioga-up-check
-#  │         │    ├── tioga-build-and-test
-#  │         │    ├── matrix-up-check
-#  │         │    └── matrix-build-and-test
-#  │         ├── <used jobs>
-#  │         │    └── .build-and-test  [from ".gitlab-ci.yml"]
-#  │         ├── <included files>
-#  │         │    └── .gitlab/dane-baseline.yml  [by "dane-baseline"]
-#  │         └── <used variables>
-#  │              ├── GITHUB_PROJECT_ORG
-#  │              ├── GITHUB_PROJECT_NAME
-#  │              ├── AUTOTEST
-#  │              ├── AUTOTEST_COMMIT
-#  │              └── REBASELINE
-#  └── tests
-#       ├── gitlab
-#       │    ├── build_and_test
-#       │    │    ├── <builds and tests a given MFEM spec with uberenv>
-#       │    │    ├── <used files>
-#       │    │    │    ├── tests/uberenv/uberenv.py        [deps mode, cloned]
-#       │    │    │    └── tests/gitlab/get_mfem_uberenv   [deps mode]
-#       │    │    └── <used variables>
-#       │    │         ├── SYS_TYPE
-#       │    │         ├── THREADS      [num. parallel jobs to build MFEM]
-#       │    │         ├── MODULE_LIST  [modules to load]
-#       │    │         ├── CI_JOB_ID
-#       │    │         ├── USE_DEV_SHM
-#       │    │         ├── SPACK_DEBUG
-#       │    │         ├── DEBUG_MODE
-#       │    │         ├── REGISTRY_TOKEN
-#       │    │         ├── CI_REGISTRY_USER  (defined by Gitlab)
-#       │    │         ├── USER
-#       │    │         ├── CI_REGISTRY_IMAGE (defined by Gitlab)
-#       │    │         └── CI_JOB_TOKEN      (defined by Gitlab)
-#       │    ├── build_and_test_setup
-#       │    │    ├── <updates MFEM_DATA_REPO and AUTOTEST_REPO using locks>
-#       │    │    └── <used variables>
-#       │    │         ├── MFEM_DATA_REPO
-#       │    │         ├── SHARED_REPOS_DIR
-#       │    │         ├── AUTOTEST_REPO
-#       │    │         └── AUTOTEST_ROOT
-#       │    └── get_mfem_uberenv
-#       │         ├── <github.com/mfem/mfem-uberenv.git -> tests/uberenv>
-#       │         └── <defines the uberenv hash to use>
-#       └── uberenv  [cloned by tests/gitlab/get_mfem_uberenv]
-#            └── uberenv.py
-#
-# <root of radiuss/radiuss-shared-ci, ref: 'v2025.09.1'>
-#  └── pipelines
-#       ├── matrix.yml
-#       │    ├── <jobs>
-#       │    │    ├── .on_matrix
-#       │    │    ├── .matrix_reproducer_init
-#       │    │    ├── .matrix_reproducer_vars
-#       │    │    ├── .matrix_reproducer_job
-#       │    │    ├── .matrix_job_command
-#       │    │    └── .job_on_matrix
-#       │    ├── <used jobs>
-#       │    │    └── .custom_job  [from .gitlab/custom-jobs-and-variables.yml]
-#       │    └── <used variables>
-#       │         ├── ON_MATRIX
-#       │         ├── ADVANCED_JOB
-#       │         ├── ALL_TARGETS
-#       │         ├── SYS_TYPE
-#       │         ├── LLNL_SERVICE_USER
-#       │         ├── USER
-#       │         ├── GITHUB_PROJECT_NAME
-#       │         ├── GITHUB_PROJECT_ORG
-#       │         ├── MATRIX_JOB_ALLOC
-#       │         └── JOB_CMD
-#       ├── dane.yml
-#       │    ├── <jobs>
-#       │    │    ├── .on_dane
-#       │    │    ├── .dane_reproducer_init
-#       │    │    ├── .dane_reproducer_vars
-#       │    │    ├── .dane_reproducer_job
-#       │    │    ├── .dane_job_command
-#       │    │    ├── .job_on_dane
-#       │    │    ├── allocate_resources
-#       │    │    └── release_resources
-#       │    ├── <used jobs>
-#       │    │    └── .custom_job  [from .gitlab/custom-jobs-and-variables.yml]
-#       │    ├── <defined variables>
-#       │    │    └── export JOBID
-#       │    └── <used variables>
-#       │         ├── ON_DANE
-#       │         ├── ADVANCED_JOB
-#       │         ├── ALL_TARGETS
-#       │         ├── SYS_TYPE
-#       │         ├── LLNL_SERVICE_USER
-#       │         ├── USER
-#       │         ├── GITHUB_PROJECT_NAME
-#       │         ├── GITHUB_PROJECT_ORG
-#       │         ├── DANE_JOB_ALLOC
-#       │         ├── JOB_CMD
-#       │         ├── JOBID
-#       │         ├── ALLOC_NAME
-#       │         └── DANE_SHARED_ALLOC
-#       └── tioga.yml
-#            ├── <jobs>
-#            │    ├── .on_tioga
-#            │    ├── .tioga_reproducer_init
-#            │    ├── .tioga_reproducer_vars
-#            │    ├── .tioga_reproducer_job
-#            │    ├── .tioga_job_command
-#            │    ├── .job_on_tioga
-#            │    ├── allocate_resources
-#            │    └── release_resources
-#            ├── <used jobs>
-#            │    └── .custom_job  [from .gitlab/custom-jobs-and-variables.yml]
-#            ├── <defined variables>
-#            │    └── PROXY
-#            └── <used variables>
-#                 ├── ON_TIOGA
-#                 ├── ADVANCED_JOB
-#                 ├── ALL_TARGETS
-#                 ├── SYS_TYPE
-#                 ├── LLNL_SERVICE_USER
-#                 ├── USER
-#                 ├── GITHUB_PROJECT_NAME
-#                 ├── GITHUB_PROJECT_ORG
-#                 ├── TIOGA_JOB_ALLOC
-#                 ├── JOB_CMD
-#                 ├── PROXY
-#                 ├── ALLOC_NAME
-#                 └── TIOGA_SHARED_ALLOC
+# at Lawrence Livermore National Laboratory (LLNL). This entire pipeline is
+# LLNL-specific!
+
+include:
+  - project: 'lc-templates/id_tokens'
+    file: 'id_tokens.yml'
+
+# The pipeline is divided into stages. Usually, jobs in a given stage wait for
+# the preceding stages to complete before to start. However, we sometimes use
+# the "needs" keyword and express the DAG of jobs for more efficiency.
+# - We use setup and setup_baseline phases to download content outside of mfem
+#   directory.
+# - Allocate/Release is where ruby resource are allocated/released once for all.
+# - Build and Test is where we build and MFEM for multiple toolchains.
+# - Baseline_checks gathers baseline-type test suites execution
+# - Baseline_publish, only available on master, allows to update baseline
+#   results
+stages:
+  - sub-pipelines
 
-###############################################################################
-# We define the following GitLab pipeline variables:
 variables:
-##### LC GITLAB CONFIGURATION
   CUSTOM_CI_BUILDS_DIR: "/usr/workspace/mfem/gitlab-runner"
-
-##### PROJECT VARIABLES
   USER_CI_TOP_DIR: "${CUSTOM_CI_BUILDS_DIR}/${GITLAB_USER_LOGIN}"
   SHARED_REPOS_DIR: "${USER_CI_TOP_DIR}/repos"
   AUTOTEST_ROOT: "${SHARED_REPOS_DIR}"
+  # MFEM_DATA_DIR is setup in '.gitlab/configs/setup-build-and-test.yml' and
+  # used in '.gitlab/configs/<machine>-config.yml':
   MFEM_DATA_DIR: "${SHARED_REPOS_DIR}/mfem-data"
-# AUTOTEST: enable (ON/YES) or disable (any other value) test reporting. See
-# also AUTOTEST_COMMIT.
-  AUTOTEST: "OFF"
-# AUTOTEST_COMMIT: used only when AUTOTEST is set to ON/YES.
-# * If AUTOTEST_COMMIT is set to ON/YES, reporting jobs will commit their
-#   files to the MFEM/autotest repo.
-# * If AUTOTEST_COMMIT is NOT set to ON/YES, reporting jobs will NOT commit
-#   their files to the MFEM/autotest repo. Instead they will just show the
-#   contents of the report files and remove them.
-  AUTOTEST_COMMIT: "ON"
-# REBASELINE:
+
 # Defines the default choice for updating the saved baseline results. By default
 # the baseline can only be updated from the master branch. This variable offers
 # the option to manually ask for rebaselining from another branch if necessary.
-  REBASELINE: "OFF"
+  REBASELINE: "NO"
+  AUTOTEST: "NO"
+  # AUTOTEST_COMMIT: used only when AUTOTEST is set to YES.
+  # * If AUTOTEST_COMMIT is NOT set to NO, reporting jobs will commit their
+  #   files to the MFEM/autotest repo.
+  # * If AUTOTEST_COMMIT is set to NO, reporting jobs will NOT commit their
+  #   files to the MFEM/autotest repo. Instead they will just show the contents
+  #   of the report files and remove them.
+  AUTOTEST_COMMIT: "YES"
 
-##### SHARED_CI CONFIGURATION
-# Required information about GitHub repository
-  GITHUB_PROJECT_NAME: "mfem"
-  GITHUB_PROJECT_ORG: "MFEM"
-# Override the pattern describing branches that will skip the "draft PR filter
-# test".  Add protected branches here. See default value in
-# preliminary-ignore-draft-pr.yml.
-#  ALWAYS_RUN_PATTERN: ""
-
-###############################################################################
-##### High level stages
-# We organize the test-pipelines stage with sub-pipelines. Each sub-pipeline
-# corresponds to a test batch on a given machine.
-stages:
-  - prerequisites
-  - test-pipelines
-
-###############################################################################
-# Template for jobs triggering a build-and-test sub-pipeline:
-.build-and-test:
-  stage: test-pipelines
+# Trigger subpipelines:
+ruby-build-and-test:
+  stage: sub-pipelines
   variables:
-    # Explicitly pass down values that are not always propagated to child
-    # pipelines, e.g. when a variable is set in the "Settings -> CI" web
-    # interface (project variables).
-    # Note: in some cases, this does not work as expected, e.g. when the
-    # variable is not re-defined in the web interface; in such cases, the child
-    # pipeline gets a definition like '${AUTOTEST}', i.e. it behaves as if
-    # AUTOTEST is undefined, even though there is a default value in
-    # .gitlab-ci.yml.
+    # Explicitly pass down values that we want to be able to set when triggering
+    # pipelines manually or using scheduling
     AUTOTEST: "${AUTOTEST}"
     AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
   trigger:
-    include:
-      - local: '.gitlab/custom-jobs-and-variables.yml'
-      - project: 'radiuss/radiuss-shared-ci'
-        ref: 'v2025.09.1'
-        file: 'pipelines/${CI_MACHINE}.yml'
-      - artifact: '${CI_MACHINE}-jobs.yml'
-        job: 'generate-job-lists'
+    include: .gitlab/ruby-build-and-test.yml
     strategy: depend
-    forward:
-      pipeline_variables: true
 
-###############################################################################
-include:
-  # Sets ID tokens for every job using `default:`
-  - project: 'lc-templates/id_tokens'
-    file: 'id_tokens.yml'
-  # [Optional] checks preliminary to running the actual CI test
-  #- project: 'radiuss/radiuss-shared-ci'
-  #  ref: 'v2025.09.1'
-  #  file: 'preliminary-ignore-draft-pr.yml'
-  # pipelines subscribed by the project
-  - local: '.gitlab/subscribed-pipelines.yml'
+ruby-baseline:
+  stage: sub-pipelines
+  variables:
+    # Explicitly pass down values that we want to be able to set when triggering
+    # pipelines manually or using scheduling
+    REBASELINE: "${REBASELINE}"
+    AUTOTEST: "${AUTOTEST}"
+    AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
+  trigger:
+    include: .gitlab/ruby-baseline.yml
+    strategy: depend
+
+lassen-build-and-test:
+  stage: sub-pipelines
+  variables:
+    # Explicitly pass down values that we want to be able to set when triggering
+    # pipelines manually or using scheduling
+    AUTOTEST: "${AUTOTEST}"
+    AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
+  trigger:
+    include: .gitlab/lassen-build-and-test.yml
+    strategy: depend
+
+corona-build-and-test:
+  stage: sub-pipelines
+  variables:
+    # Explicitly pass down values that we want to be able to set when triggering
+    # pipelines manually or using scheduling
+    AUTOTEST: "${AUTOTEST}"
+    AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
+  trigger:
+    include: .gitlab/corona-build-and-test.yml
+    strategy: depend

.gitlab/README.md

@@ -15,18 +15,18 @@ and nightly testing on GitLab.
 
 ## Top level
 
-The root configuration file is `.gitlab-ci.yml` at the root of MFEM repo. This
-file only defines three stages, a prerequisites one, and two main stages in
-which we trigger several sub-pipelines.
+The root configuration file is `.gitlab-ci.yml` at the root of MFEM repo.
+This file only defines one stage, in which we trigger several
+sub-pipelines.
 
 We use sub-pipelines to isolate the test for one combination of `machine`
 and `test type`.
 
 Machines typically include:
 
-* Dane: Intel Sapphire Rapids
-* Matrix: Intel Sapphire Rapids + Nvidia H100 GPU
-* Tioga: AMD MI250X GPU
+* Ruby: 2nd Gen Intel Xeon (Cascade Lake)
+* Lassen: Power9 + Nvidia GPU
+* Corona: AMD GPU
 
 Test types include:
 
@@ -39,31 +39,9 @@ altering the scheduling, execution and displaying of the others.
 
 ## Sub-pipelines
 
-### build-and-test
-
-The build-and-test sub-pipelines leverage RADIUSS Shared CI to share most of
-the CI implementation. RADIUSS Shared CI provides a shared CI infrastructure
-vetted on most LC systems of interest and efficiently leveraging each machine
-scheduler to increase CI throughput. The maintenance of RADIUSS Shared CI is
-shared among several RADIUSS projects.
-
-Jobs for the build-and-test sub-pipelines are defined in the jobs directory.
-Because build-and-test jobs leverage Uberenv and Spack to build the
-dependencies automatically, the jobs essentially consists in a `spack spec`
-defined in the jobs files, and some scheduling parameters defined in the
-`.gitlab/custom-jobs-and-variables.yml` file.
-
-Build-and-test jobs all run the `tests/gitlab/build_and_test` script.
-
-The build-and-test pipelines are controlled by the
-`.gitlab/subscribed-pipelines.yml` which defines which machines to run on and
-implements additional features like machine availability check, and job list
-generation.
-
-### baseline
-
-Baseline sub-pipelines are described by files with names reflecting the
-machine it runs on, e.g. `dane-baseline`.
+Each file is this directory is the root configuration file for one
+sub-pipeline. The naming reflects the corresponding couple (`machine`,
+`test_type`).
 
 Those files define the *stages* and the *jobs* for the sub-pipeline. They
 also contain any configuration that cannot be shared. For the most part
@@ -85,11 +63,11 @@ usage function. This should be improved.
 
 # More testing
 
-## Adding a new target to a build-and-test pipeline
+## Adding a new target to a build_and_test pipeline
 
-`build-and-test` pipelines rely on Spack to install dependencies. Spack is
+`build_and_test` pipelines rely on Spack to install dependencies. Spack is
 driven by Uberenv which helps freezing Spack configuration: the goal being to
-point to a specific commit in Spack and isolate its configuration so that it is
+point to specific commit in Spack and isolate its configuration so that it is
 not influenced by the user environment. More documentation about this can be
 found in `tests/gitlab`.
 
@@ -98,13 +76,13 @@ with a spack spec of MFEM, within the limits permitted by the MFEM spack
 package.
 
 In any build-and-test sub-pipeline a job basically consists in defining the
-spack spec to use. Adding a job on Dane for example resumes to:
+spack spec to use. Adding a job on ruby for example resumes to:
 
 ```yaml
 <job_name>:
   variables:
     SPEC: "<spack_spec>"
-  extends: .job_on_dane
+  extends: .build_and_test_on_ruby
 ```
 
 The remaining and non trivial work is to make sure this spec is working. To

.gitlab/configs/common.yml

@@ -0,0 +1,40 @@
+# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
+# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+# LICENSE and NOTICE for details. LLNL-CODE-806117.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability visit https://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the BSD-3 license. We welcome feedback and contributions, see file
+# CONTRIBUTING.md for details.
+
+include:
+  - project: 'lc-templates/id_tokens'
+    file: 'id_tokens.yml'
+
+# We define the following GitLab pipeline variables:
+variables:
+
+# The path to the shared resource between all jobs. For example, external
+# repositories like 'tests' and 'tpls' are cloned here. Also, 'tpls' is built
+# once for all targets, so that build happen here. The BUILD_ROOT is unique to
+# the pipeline, preventing any form of concurrency with other pipelines. This
+# also means that the BUILD_ROOT directory will never be cleaned.
+# TODO: add a clean-up mechanism
+  BUILD_ROOT: ${USER_CI_TOP_DIR}/${CI_PROJECT_NAME}-${MACHINE_NAME}-pipeline-${CI_PIPELINE_ID}
+
+# On LLNL's ruby, there is only one allocation shared among jobs in order to
+# save time and resource. This allocation has to be uniquely named so that we
+# are sure to retrieve it.
+  ALLOC_NAME: ${CI_PROJECT_NAME}_ci_${CI_PIPELINE_ID}
+
+# Git repositories used in the pipeline
+  TPLS_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/tpls.git
+  TESTS_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/tests.git
+  AUTOTEST_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/autotest.git
+  MFEM_DATA_REPO: https://github.com/mfem/data.git
+
+# Directory used to place artifacts.
+  ARTIFACTS_DIR: artifacts
+  SLURM_OVERLAP: 1

.gitlab/configs/corona-config.yml

@@ -0,0 +1,59 @@
+# Copyright (c) 2010-2025, 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.
+
+# GitLab pipeline configuration for the Corona machine at LLNL
+variables:
+  MACHINE_NAME: corona
+
+.on_corona:
+  tags:
+    - shell
+    - corona
+  rules:
+    # 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/ || $ON_CORONA != "ON"'
+      when: never
+    # Don't run autotest update if...
+    - if: '$CI_JOB_NAME =~ /report/ && $AUTOTEST != "YES"'
+      when: never
+    # Report success on success status
+    - if: '$CI_JOB_NAME =~ /report_job_success/ && $AUTOTEST == "YES"'
+      when: on_success
+    # Report failure on failure status
+    - if: '$CI_JOB_NAME =~ /report_job_failure/ && $AUTOTEST == "YES"'
+      when: on_failure
+    # Always release resource
+    - if: '$CI_JOB_NAME =~ /release_resource/'
+      when: always
+    # Always cleanup
+    - if: '$CI_JOB_NAME =~ /cleanup/'
+      when: always
+    # Default is to run if previous stage succeeded
+    - when: on_success
+
+# Spack helped builds
+# Generic corona build job, extending build script
+.build_and_test_on_corona:
+  extends: [.on_corona]
+  stage: build_and_test
+  script:
+    # THREADS is used by 'tests/gitlab/build_and_test', run below
+    - export THREADS=12
+    - echo ${ALLOC_NAME}
+    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
+    - echo ${JOBID}
+    - echo ${MFEM_DATA_DIR}
+    - echo ${SPEC}
+    - srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) -t 15 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data

.gitlab/configs/lassen-config.yml

@@ -0,0 +1,48 @@
+# Copyright (c) 2010-2025, 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.
+
+# GitLab pipelines configurations for the Lassen machine at LLNL
+variables:
+  MACHINE_NAME: lassen
+
+.on_lassen:
+  tags:
+    - shell
+    - lassen
+  rules:
+    - if: '$CI_COMMIT_BRANCH =~ /_lnone/ || $ON_LASSEN == "OFF"' #run except if ...
+      when: never
+    # Don't run autotest update if...
+    - if: '$CI_JOB_NAME =~ /report/ && $AUTOTEST != "YES"'
+      when: never
+    # Report success on success status
+    - if: '$CI_JOB_NAME =~ /report_job_success/ && $AUTOTEST == "YES"'
+      when: on_success
+    # Report failure on failure status
+    - if: '$CI_JOB_NAME =~ /report_job_failure/ && $AUTOTEST == "YES"'
+      when: on_failure
+    # Always cleanup
+    - if: '$CI_JOB_NAME =~ /cleanup/'
+      when: always
+    - when: on_success
+
+# Lassen uses a different job scheduler (spectrum lsf) that does not allow
+# pre-allocation the same way slurm does.  We use the pci queue on lassen
+# to speed-up the allocation.
+.build_and_test_on_lassen:
+  extends: [.on_lassen]
+  stage: build_and_test
+  script:
+    - echo ${MFEM_DATA_DIR}
+    - echo ${SPEC}
+    # Next script uses 'THREADS': leaving it empty --> it uses 'make all -j'
+    - lalloc 1 -W 45 -q pci --atsdisable tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
+  needs: [setup]

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

@@ -0,0 +1,77 @@
+# Copyright (c) 2010-2025, 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.
+
+# Jobs report
+.report_job_success:
+  script:
+    - echo ${MACHINE_NAME}
+    - echo ${AUTOTEST}
+    - echo ${AUTOTEST_COMMIT}
+    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
+    - cd ${AUTOTEST_ROOT}
+    - |
+      (
+        date
+        echo "Waiting to acquire lock on '$PWD/autotest.lock' ..."
+        # try to get an exclusive lock on fd 9 (autotest.lock) repeating the try
+        # every 5 seconds; we may want to add a counter for the number of
+        # retries to interrupt a potential infinite loop
+        while ! flock -n 9; do
+          sleep 5
+        done
+        echo "Acquired lock on '$PWD/autotest.lock'"
+        date
+        # Report SUCCESS while holding the file lock on 'autotest.lock'.
+        # The next script uses the following environment variables:
+        # - MACHINE_NAME, AUTOTEST_ROOT, AUTOTEST_COMMIT
+        # - CI_COMMIT_REF_SLUG, CI_PROJECT_DIR, CI_PIPELINE_URL
+        # It also calls the script '.gitlab/scripts/safe_create_rundir'.
+        ${CI_PROJECT_DIR}/.gitlab/scripts/report_build_and_test_success
+        err=$?
+        # sleep for a period to allow NFS to propagate the above changes;
+        # clearly, there is no guarantee that other NFS clients will see the
+        # changes even after the timeout
+        sleep 10
+        exit $err
+      ) 9> autotest.lock
+
+.report_job_failure:
+  script:
+    - echo ${MACHINE_NAME}
+    - echo ${AUTOTEST}
+    - echo ${AUTOTEST_COMMIT}
+    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
+    - cd ${AUTOTEST_ROOT}
+    - |
+      (
+        date
+        echo "Waiting to acquire lock on '$PWD/autotest.lock' ..."
+        # try to get an exclusive lock on fd 9 (autotest.lock) repeating the try
+        # every 5 seconds; we may want to add a counter for the number of
+        # retries to interrupt a potential infinite loop
+        while ! flock -n 9; do
+          sleep 5
+        done
+        echo "Acquired lock on '$PWD/autotest.lock'"
+        date
+        # Report FAILURE while holding the file lock on 'autotest.lock'.
+        # The next script uses the following environment variables:
+        # - MACHINE_NAME, AUTOTEST_ROOT, AUTOTEST_COMMIT
+        # - CI_COMMIT_REF_SLUG, CI_PROJECT_DIR, CI_PIPELINE_URL
+        # It also calls the script '.gitlab/scripts/safe_create_rundir'.
+        ${CI_PROJECT_DIR}/.gitlab/scripts/report_build_and_test_failure
+        err=$?
+        # sleep for a period to allow NFS to propagate the above changes;
+        # clearly, there is no guarantee that other NFS clients will see the
+        # changes even after the timeout
+        sleep 10
+        exit $err
+      ) 9> autotest.lock

.gitlab/configs/ruby-config.yml

@@ -0,0 +1,55 @@
+# Copyright (c) 2010-2025, 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.
+
+# GitLab pipelines configurations for the Ruby machine at LLNL
+variables:
+  MACHINE_NAME: ruby
+
+.on_ruby:
+  tags:
+    - shell
+    - ruby
+  rules:
+    # Don't run ruby jobs if...
+    - if: '$CI_COMMIT_BRANCH =~ /_qnone/ || $ON_RUBY == "OFF"'
+      when: never
+    # Don't run autotest update if...
+    - if: '$CI_JOB_NAME =~ /report/ && $AUTOTEST != "YES"'
+      when: never
+    # Report success on success status
+    - if: '$CI_JOB_NAME =~ /report_job_success/ && $AUTOTEST == "YES"'
+      when: on_success
+    # Report failure on failure status
+    - if: '$CI_JOB_NAME =~ /report_job_failure/ && $AUTOTEST == "YES"'
+      when: on_failure
+    # Always release resource
+    - if: '$CI_JOB_NAME =~ /release_resource/'
+      when: always
+    # Always cleanup
+    - if: '$CI_JOB_NAME =~ /cleanup/'
+      when: always
+    # Default is to run if previous stage succeeded
+    - when: on_success
+
+# Spack helped builds
+# Generic ruby build job, extending build script
+.build_and_test_on_ruby:
+  extends: [.on_ruby]
+  stage: build_and_test
+  script:
+    # THREADS is used by 'tests/gitlab/build_and_test', run below
+    - export THREADS=16
+    - echo ${ALLOC_NAME}
+    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
+    - echo ${JOBID}
+    - echo ${MFEM_DATA_DIR}
+    - echo ${SPEC}
+    - srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) --reservation=ci -t 45 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data

.gitlab/configs/setup-baseline.yml

@@ -18,7 +18,7 @@
 setup_baseline:
   tags:
     - shell
-    - dane
+    - ruby
   stage: setup
   variables:
     GIT_STRATEGY: none

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

@@ -0,0 +1,90 @@
+# Copyright (c) 2010-2025, 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.
+
+# Setup clones the mfem/data repo in ${SHARED_REPOS_DIR}. The build_and_test
+# script then symlinks the repo to the parent directory of the MFEM source
+# directory. Unit tests that depend on the mfem/data repo will then detect that
+# this directory is present and be enabled.
+setup:
+  tags:
+    - shell
+    - ruby
+  stage: setup
+  variables:
+    GIT_STRATEGY: none
+  script:
+    #
+    # Setup MFEM_DATA_DIR=${SHARED_REPOS_DIR}/mfem-data, see '.gitlab-ci.yml'
+    # and '.gitlab/configs/<machine>-config.yml'
+    #
+    - echo "MACHINE_NAME = ${MACHINE_NAME}"
+    - echo "AUTOTEST = ${AUTOTEST}"
+    - echo "AUTOTEST_COMMIT = ${AUTOTEST_COMMIT}"
+    - echo "SHARED_REPOS_DIR ${SHARED_REPOS_DIR}"
+    - mkdir -p ${SHARED_REPOS_DIR} && cd ${SHARED_REPOS_DIR}
+    - command -v flock || echo "Required command 'flock' not found"
+    - |
+      (
+        date
+        echo "Waiting to acquire lock on '$PWD/mfem-data.lock' ..."
+        # try to get an exclusive lock on fd 9 (mfem-data.lock) repeating the
+        # try every 5 seconds; we may want to add a counter for the number of
+        # retries to interrupt a potential infinite loop
+        while ! flock -n 9; do
+          sleep 5
+        done
+        echo "Acquired lock on '$PWD/mfem-data.lock'"
+        date
+        # clone/update the mfem/data repo while holding the file lock on
+        # 'mfem-data.lock'
+        err=0
+        if [[ ! -d "mfem-data" ]]; then
+          git clone ${MFEM_DATA_REPO} "mfem-data"
+        else
+          cd "mfem-data" && git pull && cd ..
+        fi || err=1
+        # sleep for a period to allow NFS to propagate the above changes;
+        # clearly, there is no guarantee that other NFS clients will see the
+        # changes even after the timeout
+        sleep 10
+        exit $err
+      ) 9> mfem-data.lock
+    #
+    # Setup ${AUTOTEST_ROOT}/autotest:
+    #
+    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
+    - mkdir -p ${AUTOTEST_ROOT} && cd ${AUTOTEST_ROOT}
+    - |
+      (
+        date
+        echo "Waiting to acquire lock on '$PWD/autotest.lock' ..."
+        # try to get an exclusive lock on fd 9 (autotest.lock) repeating the try
+        # every 5 seconds; we may want to add a counter for the number of
+        # retries to interrupt a potential infinite loop
+        while ! flock -n 9; do
+          sleep 5
+        done
+        echo "Acquired lock on '$PWD/autotest.lock'"
+        date
+        # clone/update the autotest repo while holding the file lock on
+        # 'autotest.lock'
+        err=0
+        if [[ ! -d "autotest" ]]; then
+          git clone ${AUTOTEST_REPO}
+        else
+          cd autotest && git pull && cd ..
+        fi || err=1
+        # sleep for a period to allow NFS to propagate the above changes;
+        # clearly, there is no guarantee that other NFS clients will see the
+        # changes even after the timeout
+        sleep 10
+        exit $err
+      ) 9> autotest.lock

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

@@ -0,0 +1,67 @@
+# Copyright (c) 2010-2025, 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.
+
+stages:
+  - setup
+  - allocate_resource
+  - build_and_test
+  - release_resource_and_report
+
+# Slurm shared allocation
+allocate_resource:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_corona
+  stage: allocate_resource
+  script:
+    - echo ${ALLOC_NAME}
+    - salloc --exclusive --nodes=1 --partition=mi60 --time=45 --no-shell --job-name=${ALLOC_NAME}
+  timeout: 6h
+  needs: [setup]
+
+# Build and test jobs, simply provide a spec
+rocm_gcc_8.3.1:
+  variables:
+    SPEC: "@develop%gcc@8.3.1+rocm amdgpu_target=gfx906"
+  extends: .build_and_test_on_corona
+  needs: [allocate_resource]
+
+# Release slurm allocation
+release_resource:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_corona
+  stage: release_resource_and_report
+  script:
+    - echo ${ALLOC_NAME}
+    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
+    - echo ${JOBID}
+    - ([[ -n "${JOBID}" ]] && scancel ${JOBID})
+  needs: [rocm_gcc_8.3.1]
+
+# Jobs report
+report_job_success:
+  stage: release_resource_and_report
+  extends:
+    - .on_corona
+    - .report_job_success
+
+report_job_failure:
+  stage: release_resource_and_report
+  extends:
+    - .on_corona
+    - .report_job_failure
+
+include:
+  - local: .gitlab/configs/common.yml
+  - local: .gitlab/configs/corona-config.yml
+  - local: .gitlab/configs/setup-build-and-test.yml
+  - local: .gitlab/configs/report-build-and-test.yml

.gitlab/custom-jobs-and-variables.yml

@@ -1,132 +0,0 @@
-# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-include:
-  - project: 'lc-templates/id_tokens'
-    file: 'id_tokens.yml'
-
-# We define the following GitLab pipeline variables:
-variables:
-# Set the build-and-test command.
-# Nested variables are allowed and useful to customize the job command. We
-# protect variables with quotes so that their value may remain a string even if
-# they contain whitespaces.
-  JOB_CMD:
-    value: tests/gitlab/build_and_test --spec \"${SPEC}\" --data-dir ${MFEM_DATA_DIR} --data
-# The path to the shared resource between all jobs in the 'dane-baseline'
-# pipeline. For example, external repositories like 'tests' and 'tpls' are
-# cloned here. Also, 'tpls' is built once for all targets, so that build happens
-# here. The BUILD_ROOT is unique to the pipeline, preventing any form of
-# concurrency with other pipelines. This directory is removed by the 'cleanup'
-# stage in the 'dane-baseline' pipeline.
-  BUILD_ROOT: ${USER_CI_TOP_DIR}/${CI_PROJECT_NAME}-${CI_MACHINE}-pipeline-${CI_PIPELINE_ID}
-
-# On LLNL's dane and tioga, the 'build-and-test' pipelines creates only one
-# allocation shared among jobs in the pipeline in order to save time and
-# resources. This allocation has to be uniquely named so that we are sure to
-# retrieve it and avoid collisions.
-  ALLOC_NAME: ${CI_PROJECT_NAME}_ci_${CI_PIPELINE_ID}
-
-# Git repositories used in the pipelines:
-# - TPLS_REPO and TESTS_REPO are used only by the 'dane-baseline' pipeline
-# - AUTOTEST_REPO is used by all pipelines
-# - MFEM_DATA_REPO is used only by the 'build-and-test' pipelines
-  TPLS_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/tpls.git
-  TESTS_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/tests.git
-  AUTOTEST_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/autotest.git
-  MFEM_DATA_REPO: https://github.com/mfem/data.git
-
-# Directory used to place artifacts:
-# - ARTIFACTS_DIR is only used by the 'dane-baseline' pipeline
-  ARTIFACTS_DIR: artifacts
-  SLURM_OVERLAP: 1
-
-# Dane
-# Arguments for top level allocation
-  DANE_SHARED_ALLOC: "--exclusive --reservation=ci --time=60 --nodes=1"
-# Arguments for job level allocation
-# Note: We repeat the reservation, necessary when jobs are manually re-triggered.
-  DANE_JOB_ALLOC: "--reservation=ci --overlap --nodes=1"
-
-# Tioga
-# Arguments for top level allocation
-  TIOGA_SHARED_ALLOC: "--queue=pci --exclusive --time-limit=45m --nodes=1"
-# Arguments for job level allocation
-  TIOGA_JOB_ALLOC: "--nodes=1 --begin-time=+5s"
-
-# Matrix
-# Arguments for top level allocation
-  MATRIX_SHARED_ALLOC: "-p pdebug --exclusive --time=45 --nodes=1 -G 4"
-# Arguments for job level allocation
-# Note: We repeat the reservation, necessary when jobs are manually re-triggered.
-  MATRIX_JOB_ALLOC: "--overlap --nodes=1"
-
-# Configuration shared by build and test jobs specific to this project.
-# Not all configuration can be shared. Here projects can fine tune the
-# CI behavior.
-# See Umpire for an example (export junit test reports).
-.custom_job:
-  artifacts:
-    reports:
-
-# Note: this part is not used by the 'dane-baseline' pipeline.
-# FIXME: BUILD_ROOT, TPLS_REPO, TESTS_REPO are not needed here.
-#        Also, the definition of SHARED_REPOS_DIR is wrong.
-.reproducer_vars:
-  script:
-    - |
-      echo -e "
-      # Variables \n
-      export SPEC=\"${SPEC//\"/\\\"}\" \n
-      # Directories \n
-      export BUILD_ROOT=\"\${working_dir}\" \n
-      export SHARED_REPOS_DIR=\"\${BUILD_ROOT}/..\" \n
-      export MFEM_DATA_DIR=\"\${SHARED_REPOS_DIR}/mfem-data\" \n
-      # Repositories \n
-      export TPLS_REPO=\"${TPLS_REPO//\"/\\\"}\" \n
-      export TESTS_REPO=\"${TESTS_REPO//\"/\\\"}\" \n
-      export AUTOTEST_REPO=\"${AUTOTEST_REPO//\"/\\\"}\" \n
-      export MFEM_DATA_REPO=\"${MFEM_DATA_REPO//\"/\\\"}\" \n
-      # Setup directories \n
-      ./tests/gitlab/build_and_test_setup \n
-      # Using the CI build cache is optional and requires a token. Set it like so: \n
-      # export REGISTRY_TOKEN=\"<your token here>\" \n"
-      #
-
-# Jobs report
-.report_job_success:
-  script:
-    - ${CI_PROJECT_DIR}/.gitlab/scripts/report_build_and_test SUCCESS
-  rules:
-    - when: on_success
-
-.report_job_failure:
-  script:
-    - ${CI_PROJECT_DIR}/.gitlab/scripts/report_build_and_test FAILURE
-  rules:
-    - when: on_failure
-
-# Keep the following for debugging purposes: renaming this job from
-# '.show_variables' to 'show_variables' will insert this debug job at the
-# beginning of all child pipelines.
-.show_variables:
-  tags: [shell, oslic]
-  variables:
-    GIT_STRATEGY: none
-  stage: .pre
-  script:
-    - |
-      echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-      echo "AUTOTEST=${AUTOTEST}"
-      echo "AUTOTEST_COMMIT=${AUTOTEST_COMMIT}"
-      echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-      # Fail the job on purpose to prevent the rest of the pipeline from running
-      false

.gitlab/jobs/dane-reports.yml

@@ -1,19 +0,0 @@
-# Copyright (c) 2010-2025, 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.
-
-# Jobs report
-report_job_success:
-  extends: [.on_dane, .report_job_success]
-  stage: jobs-stage-3
-
-report_job_failure:
-  extends: [.on_dane, .report_job_failure]
-  stage: jobs-stage-3

.gitlab/jobs/dane.yml

@@ -1,92 +0,0 @@
-# Copyright (c) 2010-2025, 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.
-
-# Override reproducer section to define MFEM specific variables.
-.dane_reproducer_vars:
-  script:
-    - !reference [.reproducer_vars, script]
-
-# TODO: Setup script should be defined as a bash script (but then GIT_STRATEGY
-#       cannot be "none" anymore).
-
-# Setup clones the mfem/data repo in ${SHARED_REPOS_DIR}. The build_and_test
-# script then symlinks the repo to the parent directory of the MFEM source
-# directory. Unit tests that depend on the mfem/data repo will then detect that
-# this directory is present and be enabled.
-setup:
-  extends: .on_dane
-  stage: jobs-stage-1
-  script:
-    - ./tests/gitlab/build_and_test_setup
-
-
-########################
-# Overridden shared jobs
-########################
-# When using shared jobs, we can duplicate them here to override description and
-# add necessary changes.
-# We keep ${PROJECT_<MACHINE>_VARIANTS} and ${PROJECT_<MACHINE>_DEPS} So that
-# the comparison with the original job is easier.
-
-
-############
-# Extra jobs
-############
-# We do not recommend using ${PROJECT_<MACHINE>_VARIANTS} and
-# ${PROJECT_<MACHINE>_DEPS} in the extra jobs. There is not reason not to fully
-# describe the spec here.
-
-.mfem_job_on_dane:
-  extends: .job_on_dane
-  stage: jobs-stage-2
-  variables:
-    # Dane has 224 threads/node and we run 7 separate jobs: 224=7*32
-    THREADS: 28
-
-debug_ser_gcc_10:
-  extends: .mfem_job_on_dane
-  variables:
-    SPEC: "%gcc@10.3.1 +debug~mpi"
-
-debug_par_gcc_10:
-  extends: .mfem_job_on_dane
-  variables:
-    SPEC: "%gcc@10.3.1 +debug+mpi"
-
-opt_ser_gcc_10:
-  extends: .mfem_job_on_dane
-  variables:
-    SPEC: "%gcc@10.3.1 ~mpi"
-
-opt_par_gcc_10:
-  extends: .mfem_job_on_dane
-  variables:
-    SPEC: "%gcc@10.3.1"
-
-opt_par_gcc_10_sundials:
-  extends: .mfem_job_on_dane
-  variables:
-    SPEC: "%gcc@10.3.1 +sundials"
-
-opt_par_gcc_10_petsc:
-  extends: .mfem_job_on_dane
-  variables:
-    SPEC: "%gcc@10.3.1 +petsc ^petsc+mumps~superlu-dist"
-
-opt_par_gcc_10_pumi:
-  extends: .mfem_job_on_dane
-  variables:
-    SPEC: "%gcc@10.3.1 +pumi"
-
-opt_par_gcc_10_gslib:
-  extends: .mfem_job_on_dane
-  variables:
-    SPEC: "%gcc@10.3.1 +gslib"

.gitlab/jobs/matrix-reports.yml

@@ -1,19 +0,0 @@
-# Copyright (c) 2010-2025, 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.
-
-# Jobs report
-report_job_success:
-  extends: [.on_matrix, .report_job_success]
-  stage: jobs-stage-3
-
-report_job_failure:
-  extends: [.on_matrix, .report_job_failure]
-  stage: jobs-stage-3

.gitlab/jobs/matrix.yml

@@ -1,70 +0,0 @@
-# Copyright (c) 2010-2025, 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.
-
-# Override reproducer section to define UMPIRE specific variables.
-.matrix_reproducer_vars:
-  script:
-    - !reference [.reproducer_vars, script]
-
-#TODO: Setup script should be defined as a bash script (but then GIT_STRATEGY cannot be "none" anymore).
-
-# Setup clones the mfem/data repo in ${SHARED_REPOS_DIR}. The build_and_test
-# script then symlinks the repo to the parent directory of the MFEM source
-# directory. Unit tests that depend on the mfem/data repo will then detect that
-# this directory is present and be enabled.
-setup:
-  extends: .on_matrix
-  stage: jobs-stage-1
-  script:
-    - ./tests/gitlab/build_and_test_setup
-
-
-########################
-# Overridden shared jobs
-########################
-# When using shared jobs , we can duplicate them here to override description and add necessary changes.
-# We keep ${PROJECT_<MACHINE>_VARIANTS} and ${PROJECT_<MACHINE>_DEPS} So that
-# the comparison with the original job is easier.
-
-
-############
-# Extra jobs
-############
-# We do not recommend using ${PROJECT_<MACHINE>_VARIANTS} and
-# ${PROJECT_<MACHINE>_DEPS} in the extra jobs. There is not reason not to fully
-# describe the spec here.
-
-.mfem_job_on_matrix:
-  extends: .job_on_matrix
-  stage: jobs-stage-2
-  variables:
-    # We run 2 jobs on 1 node that has 112 threads
-    THREADS: 48
-    # These modules need to be consistent with the uberenv configurations:
-    MODULE_LIST: "gcc/10.3.1-magic cuda/12.9.1"
-
-allocate_resources:
-  timeout: 4h
-
-opt_mpi_cuda_gcc:
-  extends: .mfem_job_on_matrix
-  variables:
-    SPEC: "%gcc@10.3.1 +mpi +cuda cuda_arch=90"
-
-opt_mpi_cuda_hypre_cuda_gcc:
-  extends: .mfem_job_on_matrix
-  variables:
-    SPEC: "%gcc@10.3.1 +mpi +cuda cuda_arch=90 ^hypre+cuda"
-
-opt_mpi_cuda_gcc_gslib:
-  extends: .mfem_job_on_matrix
-  variables:
-    SPEC: "%gcc@10.3.1 +mpi +cuda +gslib cuda_arch=90 ^hypre+cuda"

.gitlab/jobs/tioga-reports.yml

@@ -1,20 +0,0 @@
-# Copyright (c) 2010-2025, 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.
-
-# Jobs report
-report_job_success:
-  extends: [.on_tioga, .report_job_success]
-  stage: jobs-stage-3
-
-report_job_failure:
-  extends: [.on_tioga, .report_job_failure]
-  stage: jobs-stage-3
-

.gitlab/jobs/tioga.yml

@@ -1,70 +0,0 @@
-# Copyright (c) 2010-2025, 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.
-
-# Override reproducer section to define UMPIRE specific variables.
-.tioga_reproducer_vars:
-  script:
-    - !reference [.reproducer_vars, script]
-
-#TODO: Setup script should be defined as a bash script (but then GIT_STRATEGY cannot be "none" anymore).
-
-# Setup clones the mfem/data repo in ${SHARED_REPOS_DIR}. The build_and_test
-# script then symlinks the repo to the parent directory of the MFEM source
-# directory. Unit tests that depend on the mfem/data repo will then detect that
-# this directory is present and be enabled.
-setup:
-  extends: .on_tioga
-  stage: jobs-stage-1
-  script:
-    - ./tests/gitlab/build_and_test_setup
-
-########################
-# Overridden shared jobs
-########################
-# When using shared jobs , we can duplicate them here to override description and add necessary changes.
-# We keep ${PROJECT_<MACHINE>_VARIANTS} and ${PROJECT_<MACHINE>_DEPS} So that
-# the comparison with the original job is easier.
-
-
-############
-# Extra jobs
-############
-# We do not recommend using ${PROJECT_<MACHINE>_VARIANTS} and
-# ${PROJECT_<MACHINE>_DEPS} in the extra jobs. There is not reason not to fully
-# describe the spec here.
-
-# Build and test jobs, simply provide a spec
-
-#.tioga_job_command:
-#  script:
-#    - echo PROXY="${PROXY}"
-#    - echo TIOGA_JOB_ALLOC="${TIOGA_JOB_ALLOC}"
-#    - "printf '#!/bin/bash\n%s\n' \"${JOB_CMD}\" > flux_script.sh"
-#    - cat flux_script.sh
-#    - ${PROXY} flux watch $( ${PROXY} flux batch -o output.stdout.type=kvs ${TIOGA_JOB_ALLOC} flux_script.sh )
-#    - rm -f flux_script.sh
-
-.mfem_job_on_tioga:
-  extends: .job_on_tioga
-  stage: jobs-stage-2
-  variables:
-    # We run 1 job on 1 node that has 64 threads
-    THREADS: 64
-
-opt_mpi_rocm_hypre_rocm:
-  extends: .mfem_job_on_tioga
-  variables:
-    SPEC: "%rocmcc@=6.3.1 +rocm amdgpu_target=gfx90a ^hypre+rocm"
-
-# cce_16_0_1:
-#   extends: .mfem_job_on_tioga
-#   variables:
-#     SPEC: "%cce@=16.0.1"

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

@@ -0,0 +1,44 @@
+# Copyright (c) 2010-2025, 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.
+
+stages:
+  - setup
+  - build_and_test
+  - report
+
+opt_mpi_cuda_gcc:
+  variables:
+    SPEC: "%gcc@8.3.1 +mpi +cuda cuda_arch=70"
+  extends: .build_and_test_on_lassen
+
+opt_mpi_cuda_hypre_cuda_gcc:
+  variables:
+    SPEC: "%gcc@8.3.1 +mpi +cuda cuda_arch=70 ^hypre+cuda~shared cuda_arch=70"
+  extends: .build_and_test_on_lassen
+
+# Jobs report
+report_job_success:
+  stage: report
+  extends:
+    - .on_lassen
+    - .report_job_success
+
+report_job_failure:
+  stage: report
+  extends:
+    - .on_lassen
+    - .report_job_failure
+
+include:
+  - local: .gitlab/configs/common.yml
+  - local: .gitlab/configs/lassen-config.yml
+  - local: .gitlab/configs/setup-build-and-test.yml
+  - local: .gitlab/configs/report-build-and-test.yml

.gitlab/ruby-baseline.yml

@@ -11,7 +11,6 @@
 
 variables:
   BASELINE_TEST: baseline
-  MACHINE_NAME: dane
 
 stages:
   - setup
@@ -20,27 +19,8 @@ stages:
   - cleanup
   - baseline_publish
 
-.on_dane:
-  tags:
-    - shell
-    - dane
-  rules:
-    # Don't run dane jobs if...
-    - if: '$ON_DANE == "OFF"'
-      when: never
-    # Don't run autotest update if...
-    # Note: in some cases, the content of AUTOTEST can be '${AUTOTEST}', so we
-    # need to treat that value as the default value of 'OFF'.
-    - if: '$CI_JOB_NAME =~ /report/ && $AUTOTEST != "ON" && $AUTOTEST != "YES"'
-      when: never
-    # Always cleanup
-    - if: '$CI_JOB_NAME =~ /cleanup/'
-      when: always
-    # Default is to run if previous stage succeeded
-    - when: on_success
-
-baselinecheck_mfem_intel_dane:
-  extends: [.on_dane]
+baselinecheck_mfem_intel_ruby:
+  extends: [.on_ruby]
   stage: baseline_check
   variables:
     # TPLS_DIR is used in .gitlab/scripts/baseline to provide the tpls location
@@ -49,13 +29,10 @@ baselinecheck_mfem_intel_dane:
     #       .gitlab/configs/setup-baseline.yml.
     TPLS_DIR: ${BUILD_ROOT}/tpls
   script:
-    - echo "AUTOTEST=$AUTOTEST"
-    - echo "AUTOTEST_COMMIT=$AUTOTEST_COMMIT"
-    - echo "AUTOTEST_ROOT=$AUTOTEST_ROOT"
     - echo ${BUILD_ROOT}
     - echo ${TPLS_DIR}
-    # Used by the tests in MFEM/tests, dane has 224 threads/node:
-    - export MFEM_TEST_NP=192
+    # Used by the tests in MFEM/tests:
+    - export MFEM_TEST_NP=48
     # The next script uses the following environment variables:
     # * BASELINE_TEST, SYS_TYPE, CI_PROJECT_DIR, ARTIFACTS_DIR,
     # * BUILD_ROOT, TPLS_DIR, MACHINE_NAME
@@ -67,7 +44,7 @@ baselinecheck_mfem_intel_dane:
   allow_failure: true
 
 cleanup:
-  extends: .on_dane
+  extends: .on_ruby
   stage: cleanup
   variables:
     GIT_STRATEGY: none
@@ -76,7 +53,7 @@ cleanup:
     - rm -rf "${BUILD_ROOT}" || true
 
 report_baseline:
-  extends: [.on_dane]
+  extends: [.on_ruby]
   stage: baseline_report
   script:
     - echo ${MACHINE_NAME}
@@ -112,13 +89,7 @@ report_baseline:
           cp ${rundir}/pipeline.txt ${rundir}/autotest-email.html
         fi
         msg="GitLab CI log for ${BASELINE_TEST} on ${MACHINE_NAME} ($(date +%Y-%m-%d))"
-        # Note: in some cases, the content of AUTOTEST_COMMIT can be
-        # '${AUTOTEST_COMMIT}', so we need to treat that value as the default
-        # value of 'ON'.
-        if [[ "$AUTOTEST_COMMIT" == '${AUTOTEST_COMMIT}' ]]; then
-          AUTOTEST_COMMIT="ON"
-        fi
-        if [[ "$AUTOTEST_COMMIT" == "ON" || "$AUTOTEST_COMMIT" == "YES" ]]; then
+        if [[ "$AUTOTEST_COMMIT" != "NO" ]]; then
           git pull && \
           git add ${rundir} && \
           git commit -m "${msg}" && \
@@ -142,12 +113,12 @@ report_baseline:
         exit $err
       ) 9> autotest.lock
 
-baselinepublish_mfem_dane:
-  extends: [.on_dane]
+baselinepublish_mfem_ruby:
+  extends: [.on_ruby]
   stage: baseline_publish
   rules:
-    # - if: '$CI_COMMIT_BRANCH == "master" || $REBASELINE == "ON"'
-    - if: '$REBASELINE == "ON"'
+    # - if: '$CI_COMMIT_BRANCH == "master" || $REBASELINE == "YES"'
+    - if: '$REBASELINE == "YES"'
       when: manual
   script:
     - echo ${BUILD_ROOT}
@@ -157,5 +128,6 @@ baselinepublish_mfem_dane:
     - .gitlab/scripts/rebaseline
 
 include:
-  - local: .gitlab/custom-jobs-and-variables.yml
+  - local: .gitlab/configs/common.yml
+  - local: .gitlab/configs/ruby-config.yml
   - local: .gitlab/configs/setup-baseline.yml

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

@@ -0,0 +1,94 @@
+# Copyright (c) 2010-2025, 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.
+
+stages:
+  - setup
+  - allocate_resource
+  - build_and_test
+  - release_resource_and_report
+
+# Allocate
+allocate_resource:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_ruby
+  stage: allocate_resource
+  script:
+    - echo ${ALLOC_NAME}
+    - salloc --exclusive --nodes=1 --reservation=ci --time=60 --no-shell --job-name=${ALLOC_NAME}
+  timeout: 6h
+
+# GitLab jobs for the Ruby machine at LLNL
+debug_ser_gcc_10:
+  variables:
+    SPEC: "%gcc@10.3.1 +debug~mpi"
+  extends: .build_and_test_on_ruby
+
+debug_par_gcc_10:
+  variables:
+    SPEC: "%gcc@10.3.1 +debug+mpi"
+  extends: .build_and_test_on_ruby
+
+opt_ser_gcc_10:
+  variables:
+    SPEC: "%gcc@10.3.1 ~mpi"
+  extends: .build_and_test_on_ruby
+
+opt_par_gcc_10:
+  variables:
+    SPEC: "%gcc@10.3.1"
+  extends: .build_and_test_on_ruby
+
+opt_par_gcc_10_sundials:
+  variables:
+    SPEC: "%gcc@10.3.1 +sundials"
+  extends: .build_and_test_on_ruby
+
+opt_par_gcc_10_petsc:
+  variables:
+    SPEC: "%gcc@10.3.1 +petsc ^petsc+mumps~superlu-dist"
+  extends: .build_and_test_on_ruby
+
+opt_par_gcc_10_pumi:
+  variables:
+    SPEC: "%gcc@10.3.1 +pumi"
+  extends: .build_and_test_on_ruby
+
+# Release
+release_resource:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_ruby
+  stage: release_resource_and_report
+  script:
+    - echo ${ALLOC_NAME}
+    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
+    - echo ${JOBID}
+    - ([[ -n "${JOBID}" ]] && scancel ${JOBID})
+
+# Jobs report
+report_job_success:
+  stage: release_resource_and_report
+  extends:
+    - .on_ruby
+    - .report_job_success
+
+report_job_failure:
+  stage: release_resource_and_report
+  extends:
+    - .on_ruby
+    - .report_job_failure
+
+include:
+  - local: .gitlab/configs/common.yml
+  - local: .gitlab/configs/ruby-config.yml
+  - local: .gitlab/configs/setup-build-and-test.yml
+  - local: .gitlab/configs/report-build-and-test.yml

.gitlab/scripts/baseline

@@ -14,7 +14,7 @@
 # locals
 glob_err=${BASELINE_TEST}.err
 base=${BASELINE_TEST}-${SYS_TYPE}
-if [[ "${MACHINE_NAME}" == "dane" ]]; then
+if [[ "${MACHINE_NAME}" == "ruby" ]]; then
   base="${BASELINE_TEST}-${MACHINE_NAME}"
 fi
 base_diff=${base}.diff
@@ -31,10 +31,12 @@ cd tests
 mkdir _${BASELINE_TEST} && cd _${BASELINE_TEST}
 
 # run
-if [[ "${MACHINE_NAME}" == "dane" ]]; then
-  srun --nodes=1 -t 60 --exclusive --reservation=ci ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
+if [[ "${MACHINE_NAME}" == "ruby" ]]; then
+  salloc --nodes=1 --exclusive --reservation=ci ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
 elif [[ ${MACHINE_NAME} == "corona" ]]; then
-  srun --nodes=1 -t 60 -p pbatch ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
+  salloc --nodes=1 -t 60 -p pbatch ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
+elif [[ ${MACHINE_NAME} == "lassen" ]]; then
+  lalloc 1 -q pci ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
 else
   echo "Unknown machine: MACHINE_NAME=$MACHINE_NAME"
   exit 1

.gitlab/scripts/rebaseline

@@ -11,7 +11,7 @@
 # terms of the BSD-3 license. We welcome feedback and contributions, see file
 # CONTRIBUTING.md for details.
 
-# There will be collision between corona and dane baselines.
+# There will be collision between corona and ruby baselines.
 # Once the corresponding files have been generated, we can switch to machine
 # specific ref.
 ARTIFACT_PATH=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}
@@ -21,7 +21,7 @@ PATCH_FILE=${ARTIFACT_PATH}.patch
 FULL_FILE=${ARTIFACT_PATH}.out
 DIFF_FILE=${ARTIFACT_PATH}.diff
 
-# There will be collision between corona and dane baselines.
+# There will be collision between corona and ruby baselines.
 # Once the corresponding files have been generated, we can switch to machine
 # specific ref.
 SAVED_NAME=baseline-${SYS_TYPE}.saved

.gitlab/scripts/report_build_and_test

@@ -1,118 +0,0 @@
-#!/bin/bash
-
-# Copyright (c) 2010-2025, 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.
-
-function info_msg ()
-{
-  echo "[Information:] ${1}"
-}
-
-function error_msg ()
-{
-  echo "[Error:] ${1}"
-}
-
-# Perform a report while holding a lock file to prevent concurrency on
-# the destination.
-# Usage:
-# locked_clone <report_function> <lock_name>
-function locked_report ()
-{
-  if ! command -v flock
-  then
-    error_msg "Required command 'flock' not found"
-    exit 1
-  fi
-
-  info_msg "Will report ${1} while holding a lock in ${2}"
-
-  ( date; info_msg "Waiting to acquire lock on '${PWD}/${2}.lock' ..."
-    # try to get an exclusive lock on fd 9 (mfem-data.lock) repeating the
-    # try every 5 seconds; we may want to add a counter for the number of
-    # retries to interrupt a potential infinite loop
-    while ! flock -n 9; do sleep 5; done
-    date; info_msg "Acquired lock on '${PWD}/${2}.lock'"
-
-    report ${1}
-    err=$?
-
-    # sleep for a period to allow NFS to propagate the above changes;
-    # clearly, there is no guarantee that other NFS clients will see the
-    # changes even after the timeout
-    sleep 10
-    exit $err
-  ) 9> ${2}.lock
-}
-
-function report ()
-{
-  if [[ "${1}" == "SUCCESS" ]]
-  then
-    info_msg "All the ${MACHINE_NAME} jobs passed"
-    status_msg="The 'build-and-test' jobs on ${MACHINE_NAME} were SUCCESSFUL."
-  elif [[ "${1}" == "FAILURE" ]]
-  then
-    info_msg "At least one failure on ${MACHINE_NAME}"
-    status_msg="Some 'build-and-test' jobs on ${MACHINE_NAME} FAILED."
-  else
-    error_msg "Unknown status: ${1} ... aborting"
-    exit 1
-  fi
-
-  cd ${AUTOTEST_ROOT}/autotest || \
-    { error_msg "Invalid 'autotest' dir: ${AUTOTEST_ROOT}/autotest"; exit 1; }
-  mkdir -p ${MACHINE_NAME}
-
-  rundir="${MACHINE_NAME}/$(date +%Y-%m-%d)-gitlab-ci-${CI_COMMIT_REF_SLUG}"
-  rundir=$(${CI_PROJECT_DIR}/.gitlab/scripts/safe_create_rundir $rundir)
-
-  printf "%s\n" "${status_msg}" \
-    "Pipeline URL:" "$CI_PIPELINE_URL" > ${rundir}/gitlab.err
-
-  msg="GitLab CI log for build-and-test on ${MACHINE_NAME} ($(date +%Y-%m-%d))"
-
-  if [[ "${1}" == "FAILURE" ]]
-  then
-    # Create 'autotest-email.html' to indicate failure:
-    cp ${rundir}/gitlab.err ${rundir}/autotest-email.html
-  fi
-
-  # Note: in some cases, the content of AUTOTEST_COMMIT can be
-  # '${AUTOTEST_COMMIT}', so we need to treat that value as the default
-  # value of 'ON'.
-  if [[ "$AUTOTEST_COMMIT" == '${AUTOTEST_COMMIT}' ]]; then
-    AUTOTEST_COMMIT="ON"
-  fi
-  if [[ "$AUTOTEST_COMMIT" == "ON" || "$AUTOTEST_COMMIT" == "YES" ]]; then
-    git pull && \
-    git add ${rundir} && \
-    git commit -m "${msg}" && \
-    ${CI_PROJECT_DIR}/.gitlab/scripts/git_try_to_push
-  else
-    for file in ${rundir}/*; do
-      echo "------------------------------"
-      echo "Content of '$file'"
-      echo "******************************"
-      cat $file
-      echo "******************************"
-    done
-    rm -rf ${rundir} || true
-  fi
-}
-
-export MACHINE_NAME=${CI_MACHINE}
-info_msg "MACHINE_NAME is ${MACHINE_NAME}"
-info_msg "AUTOTEST_ROOT is ${AUTOTEST_ROOT}"
-info_msg "AUTOTEST=$AUTOTEST"
-info_msg "AUTOTEST_COMMIT=$AUTOTEST_COMMIT"
-
-cd ${AUTOTEST_ROOT} && locked_report ${1} autotest

.gitlab/scripts/report_build_and_test_failure

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+# Copyright (c) 2010-2025, 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.
+
+echo "Runs if there was at least one failure on ${MACHINE_NAME}"
+
+cd ${AUTOTEST_ROOT}/autotest || \
+  { echo "Invalid 'autotest' dir: ${AUTOTEST_ROOT}/autotest"; exit 1; }
+mkdir -p ${MACHINE_NAME}
+
+rundir="${MACHINE_NAME}/$(date +%Y-%m-%d)-gitlab-ci-${CI_COMMIT_REF_SLUG}"
+rundir=$(${CI_PROJECT_DIR}/.gitlab/scripts/safe_create_rundir $rundir)
+
+printf "%s\n" "Some 'build-and-test' jobs on ${MACHINE_NAME} FAILED." \
+  "Pipeline URL:" "$CI_PIPELINE_URL" > ${rundir}/gitlab.err
+
+msg="GitLab CI log for build-and-test on ${MACHINE_NAME} ($(date +%Y-%m-%d))"
+
+# Create 'autotest-email.html' to indicate failure:
+cp ${rundir}/gitlab.err ${rundir}/autotest-email.html
+
+if [[ "$AUTOTEST_COMMIT" != "NO" ]]; then
+  git pull && \
+  git add ${rundir} && \
+  git commit -m "${msg}" && \
+  ${CI_PROJECT_DIR}/.gitlab/scripts/git_try_to_push
+else
+  for file in ${rundir}/*; do
+    echo "------------------------------"
+    echo "Content of '$file'"
+    echo "******************************"
+    cat $file
+    echo "******************************"
+  done
+  rm -rf ${rundir} || true
+fi

.gitlab/scripts/report_build_and_test_success

@@ -0,0 +1,42 @@
+#!/bin/bash
+
+# Copyright (c) 2010-2025, 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.
+
+echo "Can only run if all the ${MACHINE_NAME} jobs passed"
+
+cd ${AUTOTEST_ROOT}/autotest || \
+  { echo "Invalid 'autotest' dir: ${AUTOTEST_ROOT}/autotest"; exit 1; }
+mkdir -p ${MACHINE_NAME}
+
+rundir="${MACHINE_NAME}/$(date +%Y-%m-%d)-gitlab-ci-${CI_COMMIT_REF_SLUG}"
+rundir=$(${CI_PROJECT_DIR}/.gitlab/scripts/safe_create_rundir $rundir)
+
+printf "%s\n" "The 'build-and-test' jobs on ${MACHINE_NAME} were SUCCESSFUL." \
+  "Pipeline URL:" "$CI_PIPELINE_URL" > ${rundir}/gitlab.out
+
+msg="GitLab CI log for build-and-test on ${MACHINE_NAME} ($(date +%Y-%m-%d))"
+
+if [[ "$AUTOTEST_COMMIT" != "NO" ]]; then
+  git pull && \
+  git add ${rundir} && \
+  git commit -m "${msg}" && \
+  ${CI_PROJECT_DIR}/.gitlab/scripts/git_try_to_push
+else
+  for file in ${rundir}/*; do
+    echo "------------------------------"
+    echo "Content of '$file'"
+    echo "******************************"
+    cat $file
+    echo "******************************"
+  done
+  rm -rf ${rundir} || true
+fi

.gitlab/subscribed-pipelines.yml

@@ -1,130 +0,0 @@
-# Copyright (c) 2010-2025, 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.
-
-# The template job to test whether a machine is up.
-# Expects CI_MACHINE defined to machine name.
-.machine-check:
-  stage: prerequisites
-  tags: [shell, oslic]
-  variables:
-    GIT_STRATEGY: none
-  script:
-    - |
-      if [[ $(jq '.[env.CI_MACHINE].total_nodes_up' /usr/global/tools/lorenz/data/loginnodeStatus) == 0 ]]
-      then
-        echo -e "\e[31mNo node available on ${CI_MACHINE}\e[0m"
-        false && \
-        curl --url "https://api.github.com/repos/${GITHUB_PROJECT_ORG}/${GITHUB_PROJECT_NAME}/statuses/${CI_COMMIT_SHA}" \
-             --header 'Content-Type: application/json' \
-             --header "authorization: Bearer ${GITHUB_TOKEN}" \
-             --data "{ \"state\": \"failure\", \"target_url\": \"${CI_PIPELINE_URL}\", \"description\": \"GitLab ${CI_MACHINE} down\", \"context\": \"ci/gitlab/${CI_MACHINE}\" }"
-        exit 1
-      fi
-
-###
-# Trigger a build-and-test pipeline for a machine.
-# Comment the jobs for machines you don’t need.
-###
-
-# One job to generate the job list for all the subpipelines
-generate-job-lists:
-  stage: prerequisites
-  tags: [shell, oslic]
-  variables:
-    LOCAL_JOBS_PATH: ".gitlab/jobs"
-  script:
-    - |
-      echo "AUTOTEST=$AUTOTEST"
-      echo "AUTOTEST_COMMIT=$AUTOTEST_COMMIT"
-      echo "AUTOTEST_ROOT=$AUTOTEST_ROOT"
-    - |
-      cat ${LOCAL_JOBS_PATH}/dane.yml > dane-jobs.yml
-      if [[ ${AUTOTEST} == "ON" || ${AUTOTEST} == "YES" ]]
-      then
-          cat ${LOCAL_JOBS_PATH}/dane-reports.yml >> dane-jobs.yml
-      fi
-    - |
-      cat ${LOCAL_JOBS_PATH}/matrix.yml > matrix-jobs.yml
-      if [[ ${AUTOTEST} == "ON" || ${AUTOTEST} == "YES" ]]
-      then
-          cat ${LOCAL_JOBS_PATH}/matrix-reports.yml >> matrix-jobs.yml
-      fi
-    - |
-      cat ${LOCAL_JOBS_PATH}/tioga.yml > tioga-jobs.yml
-      if [[ ${AUTOTEST} == "ON" || ${AUTOTEST} == "YES" ]]
-      then
-          cat ${LOCAL_JOBS_PATH}/tioga-reports.yml >> tioga-jobs.yml
-      fi
-  artifacts:
-    paths:
-      - dane-jobs.yml
-      - matrix-jobs.yml
-      - tioga-jobs.yml
-
-
-# DANE
-dane-up-check:
-  variables:
-    CI_MACHINE: "dane"
-  extends: [.machine-check]
-
-dane-build-and-test:
-  variables:
-    CI_MACHINE: "dane"
-  needs: [dane-up-check, generate-job-lists]
-  extends: [.build-and-test]
-
-# DANE, MFEM Specific
-dane-baseline:
-  stage: test-pipelines
-  variables:
-    # Explicitly pass down values that are not always propagated to child
-    # pipelines, e.g. when a variable is set in the "Settings -> CI" web
-    # interface (project variables).
-    # Note: in some cases, this does not work as expected, e.g. when the
-    # variable is not re-defined in the web interface; in such cases, the child
-    # pipeline gets a definition like '${AUTOTEST}', i.e. it behaves as if
-    # AUTOTEST is undefined, even though there is a default value in
-    # .gitlab-ci.yml.
-    AUTOTEST: "${AUTOTEST}"
-    AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
-  trigger:
-    include: .gitlab/dane-baseline.yml
-    strategy: depend
-    forward:
-      pipeline_variables: true
-  needs: [dane-up-check]
-
-
-# TIOGA
-tioga-up-check:
-  variables:
-    CI_MACHINE: "tioga"
-  extends: [.machine-check]
-
-tioga-build-and-test:
-  variables:
-    CI_MACHINE: "tioga"
-  needs: [tioga-up-check, generate-job-lists]
-  extends: [.build-and-test]
-
-
-# Matrix
-matrix-up-check:
-  variables:
-    CI_MACHINE: "matrix"
-  extends: [.machine-check]
-
-matrix-build-and-test:
-  variables:
-    CI_MACHINE: "matrix"
-  needs: [matrix-up-check, generate-job-lists]
-  extends: [.build-and-test]

CHANGELOG

@@ -8,44 +8,9 @@
                                https://mfem.org
 
 
-Version 4.9.1 (development)
+Version 4.8.1 (development)
 ===========================
 
-- Policy for AI-assisted contribution added to CONTRIBUTING.md
-
-Discretization improvements
----------------------------
-- Replaced legacy simplex quadrature rules with symmetric positive-weight
-  rules for triangles (orders 0-25) and tetrahedra (orders 0-20). These
-  rules guarantee all-positive weights and interior quadrature points,
-  improving numerical stability. Higher orders fall back to Grundmann-Moller.
-  Triangle rules: Witherden & Vincent, Comput. Math. Appl. 69(10):1232-1241,
-  2015.
-  Tet rules (d=1-13): Witherden & Vincent (ibid).
-  Tet rules (d=14-20): Chuluunbaatar et al., Comput. Math. Appl. 124:89-97,
-  2022.
-
-- Improved the gridfunction projection routines. Projections work for Scalar,
-  Vector and VectorFE, also NURBS versions. Optionally different types of
-  projections can be selected, default behaviour has not changed.
-
-- Added methods to estimate function extremum using piecewise linear bounds +
-  recursive subdivision.
-
-Meshing improvements
---------------------
-- Improved support for 1D NURBS meshes with variable order, including using
-  the patches construct for 1D NURBS meshes.
-
-New and updated examples and miniapps
--------------------------------------
-- Electromagnetics/lorentz miniapp has been updated to leverage the ParticleSet
-  capability.
-
-
-Version 4.9, released on Dec 11, 2025
-=====================================
-
 Starting with this version, MFEM requires a C++17 compiler.
 
 Discretization improvements
@@ -54,199 +19,57 @@ Discretization improvements
   nonlinear finite element operators, based on Enzyme or dual numbers AD at
   quadrature points. These features are part of the new mfem::future namespace
   and some of the API can change in the future. See the new dFEM minimal surface
-  miniapp in the miniapps/dfem/ directory for illustration of dFEM's use. Using
-  Enzyme for AD in MFEM is tested with clang v19 and requires clang/LLVM built
-  with plugin support. See INSTALL for more details.
+  miniapp in the miniapps/dfem/ directory for illustration of dFEM's use.
 
-- Introduced initial support for particle methods in MFEM with new classes
-  Particle, ParticleSet and ParticleVector.
-  * Particle is a convenient interface for individual particle data.
-  * ParticleSet manages and stores particle data in a struct-of-arrays form,
-    carrying particle coordinates and IDs along with an arbitrary number of
-    Vector and integer data for each particle.
-  * ParticleVector is a Vector-derived container that stores vector data for an
-    arbitrary number of particles contiguously based on specified vdim/ordering.
-  See the new particle miniapps in miniapps/gslib/ and miniapps/fluids/navier/.
-
-- Added a new miniapp and specialized AMG solver (AMGF) for optimization-based
-  contact mechanics. The miniapp solves large-scale frictionless contact using a
-  self-contained Interior Point (IP) solver, mortar-based contact constraints
-  provided by Tribol. The resulting linear systems are solved with the new AMGF
-  solver (see below). Benchmark examples include the two-block, ironing, and
-  beam-sphere problems. See the miniapps/contact/ directory.
-
-- Added support for boundary integration to the hyperbolic framework. Two new
-  classes BdrHyperbolicDirichletIntegrator and BoundaryHyperbolicFlowIntegrator
-  have been introduced for implementation of weak Dirichlet boundary conditions
-  with a general flux or for the linear case respectively.
-
-- Added a method to compute piecewise linear bounds on high-order functions on
-  tensor-product elements.
-
-- Added support for interior face integration enabling DG methods in
-  ParMixedBilinearForm, ParNonlinearForm and ParBlockNonlinearForm.
+- Using Enzyme for AD in MFEM is tested with clang v19 and requires clang/LLVM
+  built with plugin support. See INSTALL for more details.
 
 - In the ParMoonolith integration, added support for variational resampling of
   H1 vector fields.
 
-- Introduced IMEX ODE solvers based on a split-operator framework. Added
-  examples ex41 and ex41p demonstrating IMEX DG/CG discretizations of the
-  convection–diffusion equation, with ex41p using DG LOR preconditioning.
-
 Meshing improvements
 --------------------
-- The TMOP kernel hierarchy has been restructured to reduce compilation time.
-  Most large kernels have been split into smaller specific kernels for each
-  metric. The directory structure has been updated with assemble, metrics, mult
-  and tools subdirectories. New kernel dispatch and specialization system has
-  also been integrated. Unit tests have been revised to ensure --all tests pass.
-
-- Introduced NC-patch NURBS meshes, which are conforming element-wise but allow
-  for nonconforming patch topology. This new mesh format supports element
-  spacing formulas for refinement, as well as local refinement factors for a
-  subset of knot vectors.
-
-- Added a new miniapp for interpolating a surface grid of points in 3D using a
-  smooth NURBS surface, that can then be sampled at arbitrary resolution while
-  staying close to the original geometry. See miniapps/nurbs/nurbs_surface.
-
-- Parallel anisotropic refinement of hexahedral meshes is now supported,
-  provided that neighboring hexahedra are not refined in conflicting directions.
-  A new ParMesh method is added to check for such conflicts, before refinement.
-
-- Added support for higher order meshes in (Par)Mesh::MakeSimplicial.
-
-Linear and nonlinear solvers
-----------------------------
-- Added FilteredSolver: a base class for solvers with filtering. It handles
-  cases where a solver performs well except in small subspaces, by adding a
-  filtering step formulated as a subspace correction.
-
-- Added AMGFSolver: a derived class of FilteredSolver, specialized for AMG with
-  Filtering (AMGF), providing robust preconditioning for linear systems arising
-  in constrained optimization problems such as frictionless contact.
-
-  Added 'GetResiduals' and 'GetFinalAbsResidualNorm' to 'HyprePCG',
-  'HypreGMRES', and 'HypreFGMRES' to get 'r' and '|r|_p'. Note that the latter
-  computes '|r|_p' from 'r' instead of returning a cached value like the
-  relative 'GetFinalResidualNorm'. These require Hypre >= 2.15.0.
-
-  Changed the default solver parameters for 'HyprePCG' to 'tol=1e-6' and
-  'max_iter=1000'. This matches the default parameters in Hypre 3.0.
-
-  Added various helper functions for querying/modifying Hypre solvers:
-  'HypreSmoother::GetType', 'HypreSmoother::GetSOROptions',
-  'HypreSmoother::GetPolyOptions', 'HypreSmoother::GetWindowParameters',
-  'HypreSmoother::IsOperatorSymmetric', 'HyprePCG::GetTol',
-  'HyprePCG::GetAbsTol', 'HyprePCG::GetMaxIter', 'HyprePCG::SetUseTwoNorm',
-  'HypreGMRES::GetTol', 'HypreGMRES::GetAbsTol', 'HypreGMRES::GetMaxIter',
-  'HypreGMRES::GetKDim', 'HypreFGMRES::GetTol', 'HypreFGMRES::GetMaxIter',
-  'HypreFGMRES::GetKDim', and 'HypreBoomerAMG::GetMaxIter'.
+- Added support for higher order meshes in Mesh::MakeSimplicial and
+  ParMesh::MakeSimplicial.
 
 GPU computing
 -------------
-- Added the 'gpu', 'raja-gpu', and 'ceed-gpu' backend aliases/shortcuts which
-  automatically select between CUDA or HIP.
-
-- Added the option to enable GPU-aware MPI in MFEM using the environment
-  variable 'MFEM_GPU_AWARE_MPI' set to any value. Setting this environment
-  variable is an alternative to calling 'Device::SetGPUAwareMPI(true)'.
-
-- Implemented a GPU-accelerated matrix-free AMR derefinement GridFunction update
-  operator. This supports mixed geometry meshes and variable order spaces, and
-  is the default derefinement operator constructed by FiniteElementSpace::Update
-  and ParFiniteElementSpace::Update. The operator requires the finite element
-  space to be nonconforming.
-
+- The function Vector::SetSubVector(const Array<int> &, const real_t) now
+  executes on device if either the vector or the array have the device flag
+  set. This is most often used for setting constant essential boundary
+  conditions. A new function Vector::SetSubVectorHost has been added in cases
+  where host execution is always needed (e.g. when the DOFs array is small).
 - Introduced MFEM_FOREACH_THREAD_DIRECT, which directly maps loop tasks to GPU
   threads, assigning one task per thread.
 
-- The function Vector::SetSubVector(const Array<int> &, const real_t) now
-  executes on device if either the vector or the array have the device flag
-  set. This is most often used for setting constant essential BCs. A new method,
-  SetSubVectorHost, has been added for cases where host execution is always
-  needed (e.g. when the DOFs array is small).
-
-- Added GPU support in GradientGridFunction and InnerProduct Coefficient classes
-  by implementing their Project methods.
-
-- Added new method: GridFunction::GetGradients, with GPU support, for computing
-  the gradients of a GridFunction on all elements.
-
-- The CUDA-specific names used by some of the unit tests like 'cunit_tests' and
-  'pcunit_tests' were replaced by names using 'gpu' instead of 'c' (short for
-  CUDA) or 'cuda'. These tests automatically run the CUDA/HIP tests based on the
-  MFEM build configuration.
-
 New and updated examples and miniapps
 -------------------------------------
-- Added the miniapps/fluids directory and moved the previous Navier and the new
-  incompressible Schrödinger flow miniapps into it.
-
-- Introduced the new Incompressible Schrödinger Flow (ISF) miniapp, which models
-  inviscid fluid dynamics by solving the linear Schrödinger equation, leveraging
-  the hydrodynamical analogy to quantum mechanics.
-
-- New particle-related miniapps:
-  * New transient Navier-Stokes fluid-particles solver NavierParticles in
-    miniapps/fluids/navier/navier_particles, for modeling tracer particles in
-    fluid flow, demonstrating use of the new ParticleSet class.
-  * New Navier miniapp, miniapps/fluids/navier/navier_bifurcation, showing the
-    use of NavierParticles in a 2D bifurcating channel flow.
-  * New FindPointsGSLIB miniapp, miniapps/gslib/particles_redist, showing
-    parallel-redistribution of particle data between MPI ranks.
-  * Particle visualization features in common/particles_extras for viewing
-    particle locations and trajectories (ParticleTrajectories) using GLVis.
-
-- Added a new miniapp (meshing/mesh-bounding-boxes) that computes the bounding
-  boxes for each element of a given mesh, and the bounds on the determinant of
-  the Jacobian of the transformation.
-
-- Added a new miniapp (tools/gridfunction-bounds) to compute piecewise linear
-  bounds on a given high-order grid function.
-
-- Added a new miniapp (electromagnetics/lorentz) which computes the trajectory
-  of a charged particle, subject to Lorentz forces, in electrostatic and/or
-  magnetostatic fields as computed by the volta or tesla miniapps.
-
 - Added miniapps to demonstrate an implementation of the absolute-value
-  l1-Jacobi preconditioners in partially assembled operators. This includes
+  L(1)-Jacobi preconditioners in partially assembled operators. This includes
   Multigrid wrapper to demonstrate the effectiveness of these Jacobi-type
-  operators as smoothers. See the miniapps/diag-smoothers/ directory.
-
-- Updated the mtop miniapp with a GPU enabled forward and adjoint solver for
-  isotropic linear elasticity.
-
-Miscellaneous
--------------
-- Introduced MFEM_FETCH_TPLS CMake option to enable downloading, configuring,
-  and building of TPLs alongside MFEM (currently supported TPLs are hypre,
-  METIS, and GSLIB).
-
-- Added quadrature function support to the VisIt and Conduit data collections.
-
-- Added access to the internal parallel matrix in Par(Mixed)BilinearForm and
-  related utility methods for elimination of BCs.
-
-- FindPointsGSLIB has a new constructor that accepts the mesh object and
-  internally calls the Setup() method so users do not have to. The FreeData()
-  method has also been moved to the destructor so users do not need to manually
-  free-up the memory if the destructor is called before MPI_Finalize().
-
-- Added parallel Address Sanitizer, serial and parallel Undefined Behavior
-  Sanitizer and serial Memory Sanitizer GitHub actions tests on Ubuntu.
+  operators as smoothers.
+  These miniapps can be found in `miniapps/diag-smoothers`.
 
 API changes
 -----------
 - mfem::internal::tensor and mfem::internal::dual have been moved to
   mfem::future::tensor and mfem::future::dual.
+- API addition: in class `Operator`, added virtual functions: `AbsMult`, and
+  `AbsMultTranspose`; in class `Vector`, added `Abs` and `Pow`.
 
-- API addition: in class Operator, added virtual functions: AbsMult, and
-  AbsMultTranspose; in class Vector, added Abs and Pow.
-
-- ParBilinearForm::EliminateEssentialVDofsInRhs() has been deprecated in favor
-  of ParallelEliminateEssentialTDofsInRhs().
-
+Miscellaneous
+-------------
+- Added the "gpu", "raja-gpu", and "ceed-gpu" backend aliases/shortcuts which
+  automatically select between CUDA or HIP.
+- The CUDA-specific names used by some of the unit tests like 'cunit_tests' and
+  'pcunit_tests' were replaced by names using 'gpu' instead of 'c' (short for
+  CUDA) or 'cuda'. These tests automatically run the CUDA/HIP tests based on the
+  MFEM build configuration.
+- Added the option to enable GPU-aware MPI in MFEM using the environment
+  variable 'MFEM_GPU_AWARE_MPI' set to any value. Setting this environment
+  variable is an alternative to calling 'Device::SetGPUAwareMPI(true)'.
+- Added parallel Address Sanitizer, serial and parallel Undefined Behavior
+  Sanitizer and serial Memory Sanitizer GitHub actions tests on Ubuntu.
 
 Version 4.8, released on Apr 9, 2025
 ====================================

CMakeLists.txt

@@ -59,7 +59,7 @@ project(mfem NONE)
 # Current version of MFEM, see also `makefile`.
 #   mfem_VERSION = (string)
 #   MFEM_VERSION = (int)   [automatically derived from mfem_VERSION]
-set(${PROJECT_NAME}_VERSION 4.9.1)
+set(${PROJECT_NAME}_VERSION 4.8.1)
 
 # Prohibit in-source build
 if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
@@ -133,49 +133,33 @@ if (MFEM_USE_CUDA)
    if (NOT CMAKE_CUDA_HOST_COMPILER)
       set(CMAKE_CUDA_HOST_COMPILER ${CMAKE_CXX_COMPILER})
    endif()
-   if (NOT CMAKE_CUDA_ARCHITECTURES)
-      # make CUDA_ARCH resemble the same form as CMAKE_CUDA_ARCHITECTURES
-      string(REPLACE "sm_" "" CUDA_ARCH_TMP "${CUDA_ARCH}")
-      string(REPLACE "," ";" CUDA_ARCH "${CUDA_ARCH_TMP}")
-      set(CMAKE_CUDA_ARCHITECTURES "${CUDA_ARCH}")
+   if (CMAKE_VERSION VERSION_LESS 3.18.0)
+      set(CUDA_FLAGS "-arch=${CUDA_ARCH} ${CUDA_FLAGS}")
+   elseif (NOT CMAKE_CUDA_ARCHITECTURES)
+      string(REGEX REPLACE "^sm_" "" ARCH_NUMBER "${CUDA_ARCH}")
+      if ("${CUDA_ARCH}" STREQUAL "sm_${ARCH_NUMBER}")
+         set(CMAKE_CUDA_ARCHITECTURES "${ARCH_NUMBER}")
+      else()
+         message(FATAL_ERROR "Unknown CUDA_ARCH: ${CUDA_ARCH}")
+      endif()
    else()
       set(CUDA_ARCH "CMAKE_CUDA_ARCHITECTURES: ${CMAKE_CUDA_ARCHITECTURES}")
    endif()
    message(STATUS "Using CUDA architecture: ${CUDA_ARCH}")
    enable_language(CUDA)
    if (CMAKE_VERSION VERSION_LESS 3.18.0)
-      # backup try to detect if this is clang or nvcc
-      if(CMAKE_CUDA_COMPILER MATCHES "nvcc$")
-         # nvcc
-         set(MFEM_CUDA_COMPILER_IS_NVCC ON)
-         set(CUDA_FLAGS "${CUDA_FLAGS} --expt-extended-lambda --expt-relaxed-constexpr")
-         if ("all" STREQUAL "${CMAKE_CUDA_ARCHITECTURES}"
-             OR "native" STREQUAL "${CMAKE_CUDA_ARCHITECTURES}"
-             OR "all-major" STREQUAL "${CMAKE_CUDA_ARCHITECTURES}")
-            set(CUDA_FLAGS "-arch=${CMAKE_CUDA_ARCHITECTURES} ${CUDA_FLAGS}")
-         else()
-            # build -gencode sequence for multiple architectures
-            foreach(ENTRY IN LISTS CMAKE_CUDA_ARCHITECTURES)
-               set(CUDA_FLAGS
-                   "-gencode arch=compute_${ENTRY},code=sm_${ENTRY} ${CUDA_FLAGS}")
-            endforeach()
-         endif()
-      else()
-         # build cuda-gpu-arch sequence for multiple architectures
-         # does not support all/all-major/native
-         foreach(ENTRY IN LISTS CMAKE_CUDA_ARCHITECTURES)
-            set(CUDA_FLAGS "-cuda-gpu-arch=sm_${ENTRY} ${CUDA_FLAGS}")
-         endforeach()
-      endif()
+     # backup try to detect if this is clang or nvcc
+     if(CMAKE_CUDA_COMPILER MATCHES "nvcc$")
+       # nvcc
+       set(MFEM_CUDA_COMPILER_IS_NVCC ON)
+       set(CUDA_FLAGS "${CUDA_FLAGS} --expt-extended-lambda --expt-relaxed-constexpr")
+     endif()
    else()
-      # TODO: all, native, all-major require CMake 3.24+
-      # backport support for CMake 3.18 to 3.24
-      if (CMAKE_CUDA_COMPILER_ID STREQUAL "NVIDIA")
-         # nvcc
-         set(MFEM_CUDA_COMPILER_IS_NVCC ON)
-         set(CUDA_FLAGS
-             "${CUDA_FLAGS} --expt-extended-lambda --expt-relaxed-constexpr")
-      endif()
+     if (CMAKE_CUDA_COMPILER_ID STREQUAL "NVIDIA")
+       # nvcc
+       set(MFEM_CUDA_COMPILER_IS_NVCC ON)
+       set(CUDA_FLAGS "${CUDA_FLAGS} --expt-extended-lambda --expt-relaxed-constexpr")
+     endif()
    endif()
    set(CMAKE_CUDA_STANDARD ${CMAKE_CXX_STANDARD} CACHE STRING
       "CUDA standard to use.")
@@ -258,16 +242,10 @@ endif()
 
 # AMD HIP
 if (MFEM_USE_HIP)
-  if (NOT CMAKE_HIP_ARCHITECTURES)
-    if (HIP_ARCH)
-      set(CMAKE_HIP_ARCHITECTURES CACHE STRING "HIP targets to compile for" "${HIP_ARCH}")
-      set(GPU_TARGETS "${HIP_ARCH}" CACHE STRING "HIP targets to compile for" FORCE)
-    endif()
-  else()
-    set(HIP_ARCH CACHE STRING "HIP targets to compile for" "${CMAKE_HIP_ARCHITECTURES}")
-    set(GPU_TARGETS "${CMAKE_HIP_ARCHITECTURES}" CACHE STRING "HIP targets to compile for" FORCE)
+  if (HIP_ARCH)
+    message(STATUS "Using HIP architecture: ${HIP_ARCH}")
+    set(GPU_TARGETS "${HIP_ARCH}" CACHE STRING "HIP targets to compile for")
   endif()
-  message(STATUS "Using HIP architecture: ${CMAKE_HIP_ARCHITECTURES}")
   if (ROCM_PATH)
     list(INSERT CMAKE_PREFIX_PATH 0 ${ROCM_PATH})
   endif()
@@ -300,22 +278,6 @@ if (MFEM_USE_OPENMP OR MFEM_USE_LEGACY_OPENMP)
   endif()
 endif()
 
-# Warn user if deprecated FETCH_TPLS is provided
-if (DEFINED FETCH_TPLS)
-  message(STATUS "Setting MFEM_FETCH_TPLS to user-provided value of FETCH_TPLS (i.e., MFEM_FETCH_TPLS=${FETCH_TPLS})")
-  set (MFEM_FETCH_TPLS FETCH_TPLS)
-  message(DEPRECATION "The use of FETCH_TPLS is deprecated and will be removed in future verison. Please use MFEM_FETCH_TPLS instead.")
-endif()
-
-  # Umpire (must be included before hypre, so hypre can use it if needed)
-if (MFEM_USE_UMPIRE)
-   # umpire uses FindCUDA, which needs CMP0146=OLD in CMake >= 3.27
-   if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.27.0)
-      cmake_policy(SET CMP0146 OLD)
-   endif()
-   find_package(UMPIRE REQUIRED)
-endif()
-
 # MPI -> hypre; PETSc (optional)
 if (MFEM_USE_MPI)
   find_package(MPI REQUIRED)
@@ -533,13 +495,14 @@ endif()
 
 # RAJA
 if (MFEM_USE_RAJA)
-   # RAJA uses FindCUDA, which needs CMP0146=OLD in CMake >= 3.27
-   if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.27.0)
-      cmake_policy(SET CMP0146 OLD)
-   endif()
    find_package(RAJA REQUIRED)
 endif()
 
+# UMPIRE
+if (MFEM_USE_UMPIRE)
+   find_package(UMPIRE REQUIRED)
+endif()
+
 # GOOGLE-BENCHMARK
 if (MFEM_USE_BENCHMARK)
    find_package(Benchmark REQUIRED)
@@ -633,27 +596,18 @@ set(MFEM_TPLS OPENMP HYPRE LAPACK BLAS SuperLUDist STRUMPACK METIS SuiteSparse
     NETCDF MPFR PUMI HIOP POSIXCLOCKS MFEMBacktrace ZLIB OCCA CEED RAJA UMPIRE
     ADIOS2 MKL_CPARDISO MKL_PARDISO AMGX MAGMA CUSPARSE CUBLAS CALIPER CODIPACK
     BENCHMARK PARELAG TRIBOL MPI_CXX HIP HIPBLAS HIPSPARSE MOONOLITH BLITZ
-    ALGOIM ENZYME CUDA::cudart)
+    ALGOIM ENZYME)
 
-# Add all created targets and *_FOUND libraries in the variables TPL_TARGETS and
-# TPL_LIBRARIES, respectively.
-set(TPL_TARGETS)
+# Add all *_FOUND libraries in the variable TPL_LIBRARIES.
 set(TPL_LIBRARIES "")
 set(TPL_INCLUDE_DIRS "")
 foreach(TPL IN LISTS MFEM_TPLS)
-  if (${TPL}_FOUND OR TARGET ${TPL})
+  if (${TPL}_FOUND)
     message(STATUS "MFEM: using package ${TPL}")
-    if (TARGET ${TPL})
-      list(APPEND TPL_TARGETS ${TPL})
-    else()
-      list(APPEND TPL_LIBRARIES ${${TPL}_LIBRARIES})
-      list(APPEND TPL_INCLUDE_DIRS ${${TPL}_INCLUDE_DIRS})
-    endif()
+    list(APPEND TPL_LIBRARIES ${${TPL}_LIBRARIES})
+    list(APPEND TPL_INCLUDE_DIRS ${${TPL}_INCLUDE_DIRS})
   endif()
 endforeach(TPL)
-
-# reverse to remove the first instance of entries in TPL_LIBRARIES
-# so later duplicates are kept (for dependency ordering)
 list(REVERSE TPL_LIBRARIES)
 list(REMOVE_DUPLICATES TPL_LIBRARIES)
 list(REVERSE TPL_LIBRARIES)
@@ -725,12 +679,8 @@ set(MFEM_INSTALL_DIR ${CMAKE_INSTALL_PREFIX})
 
 # Declaring the library
 mfem_add_library(mfem ${SOURCES} ${HEADERS} ${MASTER_HEADERS})
-target_compile_features(mfem PUBLIC cxx_std_${CMAKE_CXX_STANDARD})
 # message(STATUS "TPL_LIBRARIES = ${TPL_LIBRARIES}")
-target_link_libraries(mfem PUBLIC ${TPL_LIBRARIES} ${TPL_TARGETS})
-if (TPL_TARGETS)
-  add_dependencies(mfem ${TPL_TARGETS})
-endif()
+target_link_libraries(mfem PUBLIC ${TPL_LIBRARIES})
 if (MINGW)
   target_link_libraries(mfem PRIVATE ws2_32)
 endif()
@@ -872,12 +822,11 @@ add_dependencies(exec
 #  - https://cmake.org/Bug/view.php?id=8438
 
 # Add a target to copy the mfem data directory to the build directory
-# Implementable as a single copy_directory_if_different command w/ CMake >= 3.26
-file(GLOB DATA_FILES CONFIGURE_DEPENDS ${PROJECT_SOURCE_DIR}/data/*)
-add_custom_target(copy_data
-  COMMAND ${CMAKE_COMMAND} -E make_directory data
-  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${DATA_FILES} data
-  COMMENT "Syncing the data directory ...")
+add_custom_command(OUTPUT data_is_copied
+  COMMAND ${CMAKE_COMMAND} -E copy_directory ${PROJECT_SOURCE_DIR}/data data
+  COMMAND ${CMAKE_COMMAND} -E touch data_is_copied
+  COMMENT "Copying the data directory ...")
+add_custom_target(copy_data DEPENDS data_is_copied)
 # Add 'copy_data' as a prerequisite for all executables, if the source and the
 # build directories are not the same.
 if (NOT ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}"))
@@ -1009,15 +958,9 @@ install(FILES
 install(EXPORT ${PROJECT_NAME_UC}Targets
     DESTINATION ${INSTALL_CMAKE_DIR})
 
-# Install the data directory if present, i.e. if the copy_data target is built
-install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/data
-  DESTINATION ${MFEM_INSTALL_DIR} OPTIONAL)
-
 #-------------------------------------------------------------------------------
 # Create 'config.mk' from 'config.mk.in' for the build and install locations and
 # define install rules for 'config.mk' and 'test.mk'
 #-------------------------------------------------------------------------------
-if (MFEM_USE_CUDA OR MFEM_USE_HIP)
-  option(MFEM_EXPORT_GPU_CONFIG "Export config.mk for GPU-enabled downstream packages" ON)
-endif()
+
 mfem_export_mk_files()

CONTRIBUTING.md

@@ -24,14 +24,6 @@ must be made under this license.
 Note also that MFEM has a [Code of Conduct](CODE_OF_CONDUCT.md). By participating
 in the MFEM community, you agree to abide by its rules.
 
-## AI Policy
-- Use of AI code generation in MFEM is allowed but must be disclosed, e.g. by
-  selecting the `AI-assisted` label on the PR.
-- By submitting a PR, the author acknowledges that they have reviewed and
-  understand the changes they are proposing.
-- PR authors are still responsible for correctness, licensing, and attribution
-  of all changes.
-
 If you plan on contributing to MFEM, consider reviewing the
 [issue tracker](https://github.com/mfem/mfem/issues) first to check if a thread
 already exists for your desired feature or the bug you ran into. Use a pull
@@ -137,10 +129,6 @@ The MFEM source code has the following structure:
   │   ├── moonolith
   │   ├── qinterp
   │   └── tmop
-  │   |   ├── assemble
-  │   |   ├── metrics
-  │   |   ├── mult
-  │   |   └── tools
   ├── general
   ├── linalg
   │   ├── batched
@@ -151,19 +139,16 @@ The MFEM source code has the following structure:
   │   ├── adjoint
   │   ├── autodiff
   │   ├── common
-  │   ├── contact
   │   ├── dfem
   │   ├── dpg
   │   ├── electromagnetics
-  │   ├── fluids
-  │   │   ├── navier
-  │   │   └── schrodinger-flow
   │   ├── gslib
   │   ├── hdiv-linear-solver
   │   ├── hooke
   │   ├── meshing
   │   ├── mtop
   │   ├── multidomain
+  │   ├── navier
   │   ├── nurbs
   │   ├── parelag
   │   ├── performance

INSTALL

@@ -121,11 +121,6 @@ Parallel build:
    make -j 4
 (For METIS 5, see https://mfem.org/building/#parallel-build-using-metis-5)
 
-Parallel build with fetching of hypre and METIS:
-   mkdir <mfem-buil-dir> ; cd <mfem-build-dir>
-   cmake <mfem-source-dir> -DMFEM_USE_MPI=YES -DMFEM_FETCH_TPLS=YES
-   make -j 4
-
 CUDA build:
    (this build requires CMake 3.17 or newer)
    mkdir <mfem-build-dir> ; cd <mfem-build-dir>
@@ -668,7 +663,6 @@ The specific libraries and their options are:
 - OpenMP (optional), usually part of compiler, used when either MFEM_USE_OPENMP
   or MFEM_USE_LEGACY_OPENMP is set to YES.
   Options: OPENMP_OPT, OPENMP_LIB.
-  Versions: OpenMP >= 3.1 when MFEM_USE_OPENMP=YES.
 
 - High-resolution POSIX clocks: when using MFEM_TIMER_TYPE = 2, it may be
   necessary to link with a system library (e.g. librt.so).
@@ -725,9 +719,7 @@ The specific libraries and their options are:
   URL: https://ginkgo-project.github.io
   Options: GINKGO_OPT, GINKGO_LIB, GINKGO_DIR, GINKGO_BUILD_TYPE (Release or
            Debug).
-  Versions: Ginkgo >= 1.9.0. When building Ginkgo with distributed support, a
-            recent version of the "develop" branch is required (1.11 as defined
-            in include/ginkgo/config.hpp).
+  Versions: Ginkgo >= 1.9.0.
 
 - AmgX (optional), used when MFEM_USE_AMGX = YES.
   URL: https://github.com/NVIDIA/AMGX
@@ -850,7 +842,6 @@ The specific libraries and their options are:
 - HIP (optional), used when MFEM_USE_HIP = YES.
   URL: https://rocmdocs.amd.com
   Options: HIP_CXX, HIP_ARCH, HIP_OPT, HIP_LIB.
-  Versions: ROCm >= 5.6.1.
 
 - OCCA (optional), used when MFEM_USE_OCCA = YES.
   URL: https://libocca.org
@@ -861,7 +852,7 @@ 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 >= 0.12.0.
+  Versions: libCEED >= 0.12.
 
 - RAJA (optional), used when MFEM_USE_RAJA = YES.
   Beginning with MFEM v4.5.1, only RAJA v2022.10.3+ is supported.
@@ -1083,10 +1074,6 @@ The following options are CMake specific:
 MFEM_ENABLE_TESTING  - Enable the ctest framework for testing.
 MFEM_ENABLE_EXAMPLES - Build all of the examples by default.
 MFEM_ENABLE_MINIAPPS - Build all of the miniapps by default.
-MFEM_FETCH_TPLS      - Enable fetching of all supported third-party libraries.
-MFEM_FETCH_GSLIB     - Enable fetching of gslib.
-MFEM_FETCH_HYPRE     - Enable fetching of hypre.
-MFEM_FETCH_METIS     - Enable fetching of metis.
 
 External libraries (CMake):
 ---------------------------
@@ -1148,13 +1135,6 @@ The following built-in CMake packages are also used:
       set the <LIBNAME>_LIBRARIES option directly; the configuration option
       <LIBNAME>_DIR is not supported.
 
-The MFEM CMake build system also provides fetching (automated building) for the
-packages/libraries listed below. Note that when fetching is enabled, any related
-auto-detection functionality is disabled.
-
- - GSLIB
- - HYPRE
- - METIS
 
 Building without GNU make or CMake
 ==================================

config/cmake/MFEMConfig.cmake.in

@@ -84,35 +84,6 @@ set_and_check(MFEM_LIBRARY_DIR "@PACKAGE_LIB_INSTALL_DIR@")
 
 check_required_components(MFEM)
 
-include(CMakeFindDependencyMacro)
-
-if (MFEM_USE_CUDA)
-  # required for projects linking to MFEM+CUDA, even if they don't use CUDA directly
-  find_dependency(CUDAToolkit)
-endif (MFEM_USE_CUDA)
-
-if (MFEM_USE_HIP)
-  # hip/rocm uses the modern MFEM way of linking to targets, need to find dependencies
-  find_dependency(HIP)
-  find_dependency(HIPBLAS)
-  find_dependency(HIPSPARSE)
-  if (MFEM_USE_MPI)
-    # assume HYPRE uses HIP
-    # alternatively could check HYPRE_USING_HIP
-    find_dependency(rocsparse)
-    find_dependency(rocrand)
-    find_dependency(rocsolver)
-  endif (MFEM_USE_MPI)
-endif (MFEM_USE_HIP)
-
-if (MFEM_USE_RAJA)
-   find_dependency(RAJA)
-endif()
-
-if (MFEM_USE_UMPIRE)
-   find_dependency(umpire)
-endif()
-
 if (NOT TARGET mfem)
   include(${CMAKE_CURRENT_LIST_DIR}/MFEMTargets.cmake)
 endif (NOT TARGET mfem)

config/cmake/modules/FindGSLIB.cmake

@@ -9,47 +9,10 @@
 # terms of the BSD-3 license. We welcome feedback and contributions, see file
 # CONTRIBUTING.md for details.
 
-# Defines the following variables if fetching of TPLs is disabled (default):
+# Defines the following variables:
 #   - GSLIB_FOUND
 #   - GSLIB_LIBRARIES
 #   - GSLIB_INCLUDE_DIRS
-# otherwise, the following are defined:
-#   - GSLIB (imported library target)
-
-if (MFEM_FETCH_GSLIB OR MFEM_FETCH_TPLS)
-  enable_language(C)
-  string(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE)
-  set(GSLIB_FETCH_VERSION 1.0.9)
-  set(GSLIB_C_FLAGS ${CMAKE_C_FLAGS_${BUILD_TYPE}})
-  if (CMAKE_C_FLAGS)
-    set(GSLIB_C_FLAGS "${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BUILD_TYPE}}")
-  endif()
-  if (BUILD_SHARED_LIBS)
-    set(GSLIB_C_FLAGS "${GSLIB_C_FLAGS} -fPIC")
-  endif()
-  add_library(GSLIB STATIC IMPORTED)
-  # define external project and create future include directory so it is present
-  # to pass CMake checks at end of MFEM configuration step
-  message(STATUS "Will fetch GSLIB ${GSLIB_FETCH_VERSION} to be built with ${GSLIB_C_FLAGS}")
-  set(PREFIX ${CMAKE_BINARY_DIR}/fetch/gslib)
-  include(ExternalProject)
-  ExternalProject_Add(gslib
-    GIT_REPOSITORY https://github.com/Nek5000/gslib
-    GIT_TAG v${GSLIB_FETCH_VERSION}
-    GIT_SHALLOW TRUE
-    UPDATE_DISCONNECTED TRUE
-    PREFIX ${PREFIX}
-    CONFIGURE_COMMAND ""
-    BUILD_COMMAND cd ${PREFIX}/src/gslib && $(MAKE) clean && $(MAKE) DESTDIR=${PREFIX} MPI=$<BOOL:${MFEM_USE_MPI}> "CFLAGS= ${GSLIB_C_FLAGS}"
-    INSTALL_COMMAND "")
-  file(MAKE_DIRECTORY ${PREFIX}/include)
-  # set imported library target properties
-  add_dependencies(GSLIB gslib)
-  set_target_properties(GSLIB PROPERTIES
-    IMPORTED_LOCATION ${PREFIX}/lib/libgs.a
-    INTERFACE_INCLUDE_DIRECTORIES ${PREFIX}/include)
-  return()
-endif()
 
 include(MfemCmakeUtilities)
 mfem_find_package(GSLIB GSLIB GSLIB_DIR "include" gslib.h "lib" gs

config/cmake/modules/FindHYPRE.cmake

@@ -9,25 +9,21 @@
 # terms of the BSD-3 license. We welcome feedback and contributions, see file
 # CONTRIBUTING.md for details.
 
-# Defines the following variables if fetching of TPLs is disabled (default):
+# Defines the following variables:
 #   - HYPRE_FOUND
 #   - HYPRE_LIBRARIES
 #   - HYPRE_INCLUDE_DIRS
 #   - HYPRE_VERSION
 #   - HYPRE_USING_CUDA (internal)
 #   - HYPRE_USING_HIP (internal)
-# otherwise, the following are defined:
-#   - HYPRE (imported library target)
-#   - HYPRE_VERSION (cache variable)
 
-if (HYPRE_FOUND OR TARGET HYPRE)
+if (HYPRE_FOUND)
   if (HYPRE_USING_CUDA)
     find_package(CUDAToolkit REQUIRED)
   endif()
   if (HYPRE_USING_HIP)
     find_package(rocsparse REQUIRED)
     find_package(rocrand REQUIRED)
-    find_package(rocsolver REQUIRED)
   endif()
   if (HYPRE_LIBRARIES AND HYPRE_INCLUDE_DIRS AND HYPRE_VERSION)
     find_package_handle_standard_args(HYPRE
@@ -37,95 +33,6 @@ if (HYPRE_FOUND OR TARGET HYPRE)
   endif()
 endif()
 
-if (MFEM_FETCH_HYPRE OR MFEM_FETCH_TPLS)
-  set(HYPRE_FETCH_VERSION 2.33.0)
-  set(HYPRE_FETCH_TAG "v${HYPRE_FETCH_VERSION}" CACHE STRING "Tag, branch, or commit for HYPRE")
-  add_library(HYPRE STATIC IMPORTED)
-  # set options and associated dependencies
-  set(HYPRE_CMAKE_OPTIONS "")
-  list(APPEND HYPRE_CMAKE_OPTIONS -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE})
-  # collect all HYPRE_ENABLE variables and pass them to hypre, assuming they are BOOL.
-  get_cmake_property(all_vars VARIABLES)
-  foreach(var ${all_vars})
-    if(var MATCHES "^HYPRE_ENABLE")
-      list(APPEND HYPRE_CMAKE_OPTIONS "-D${var}:BOOL=${${var}}")
-    endif()
-  endforeach()
-  # process all MFEM_USE variables that impact hypre
-  if (MFEM_USE_CUDA)
-    list(APPEND HYPRE_CMAKE_OPTIONS -DHYPRE_ENABLE_CUDA:BOOL=ON -DCMAKE_CUDA_ARCHITECTURES:STRING=${CMAKE_CUDA_ARCHITECTURES})
-    find_package(CUDAToolkit REQUIRED)
-    target_link_libraries(HYPRE INTERFACE CUDA::cusparse CUDA::curand CUDA::cublas)
-  elseif (MFEM_USE_HIP)
-    list(APPEND HYPRE_CMAKE_OPTIONS -DHYPRE_ENABLE_HIP:BOOL=ON)
-    find_package(rocsparse REQUIRED)
-    find_package(rocrand REQUIRED)
-    target_link_libraries(HYPRE INTERFACE rocsparse rocrand)
-  endif()
-  if (MFEM_USE_CUDA OR MFEM_USE_HIP)
-    if (MFEM_USE_UMPIRE)
-      if (EXISTS ${umpire_DIR})
-        list(APPEND HYPRE_CMAKE_OPTIONS -DHYPRE_ENABLE_UMPIRE:BOOL=ON -Dumpire_DIR:PATH=${umpire_DIR})
-      else()
-        message(FATAL_ERROR "MFEM_USE_UMPIRE=ON, however umpire_DIR isn't visible to HYPRE")
-      endif()
-    else()
-      list(APPEND HYPRE_CMAKE_OPTIONS -DHYPRE_ENABLE_UMPIRE:BOOL=OFF)
-      message(WARNING
-"================================================================================
- Umpire is disabled while building HYPRE with GPU support.
- This is not recommended for performance reasons!
- Consider enabling Umpire with -DMFEM_USE_UMPIRE=ON and providing -DUMPIRE_DIR.
-================================================================================")
-    endif()
-  endif()
-  if (MFEM_USE_SINGLE)
-    list(APPEND HYPRE_CMAKE_OPTIONS -DHYPRE_ENABLE_SINGLE:BOOL=ON)
-  endif()
-  # define external project and create future include directory so it is present
-  # to pass CMake checks at end of MFEM configuration step
-  message(STATUS "Will fetch HYPRE ${HYPRE_FETCH_TAG} to be built with ${HYPRE_CMAKE_OPTIONS}")
-  set(HYPRE_INSTALL ${CMAKE_BINARY_DIR}/fetch/hypre)
-  include(ExternalProject)
-  ExternalProject_Add(hypre
-    GIT_REPOSITORY https://github.com/hypre-space/hypre.git
-    GIT_TAG ${HYPRE_FETCH_TAG}
-    GIT_SHALLOW TRUE
-    GIT_PROGRESS TRUE
-    UPDATE_DISCONNECTED TRUE
-    SOURCE_SUBDIR src
-    PREFIX ${HYPRE_INSTALL}
-    BUILD_COMMAND ${CMAKE_COMMAND} --build . -- -j${CMAKE_BUILD_PARALLEL_LEVEL}
-    CMAKE_CACHE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${HYPRE_INSTALL} -DCMAKE_INSTALL_LIBDIR:PATH=lib ${HYPRE_CMAKE_OPTIONS})
-  file(MAKE_DIRECTORY ${HYPRE_INSTALL}/include)
-  # set imported library target properties
-  add_dependencies(HYPRE hypre)
-  set_target_properties(HYPRE PROPERTIES
-    IMPORTED_LOCATION ${HYPRE_INSTALL}/lib/libHYPRE.a
-    INTERFACE_INCLUDE_DIRECTORIES ${HYPRE_INSTALL}/include)
-  # convert HYPRE version to integer
-  if (HYPRE_FETCH_TAG MATCHES "^v?([0-9]+)\\.([0-9]+)\\.([0-9]+)$")
-    # Exact release tag X.Y.Z
-    string(REGEX MATCHALL "[0-9]+" HYPRE_SPLIT_VERSION "${HYPRE_FETCH_TAG}")
-  elseif (HYPRE_FETCH_VERSION MATCHES "([0-9]+)\\.([0-9]+)(\\.([0-9]+))?")
-    string(REGEX MATCHALL "[0-9]+" HYPRE_SPLIT_VERSION "${HYPRE_FETCH_VERSION}")
-  else (NOT DEFINED HYPRE_VERSION)
-    message(FATAL_ERROR "Unable to find HYPRE release version. Please provide it via -DHYPRE_VERSION")
-  endif()
-  if (HYPRE_SPLIT_VERSION AND NOT DEFINED HYPRE_VERSION)
-    list(GET HYPRE_SPLIT_VERSION 0 HYPRE_MAJOR_VERSION)
-    list(GET HYPRE_SPLIT_VERSION 1 HYPRE_MINOR_VERSION)
-    if (HYPRE_SPLIT_VERSION GREATER 2)
-      list(GET HYPRE_SPLIT_VERSION 2 HYPRE_PATCH_VERSION)
-    else()
-      set(HYPRE_PATCH_VERSION 0)
-    endif()
-    math(EXPR HYPRE_VERSION "10000*${HYPRE_MAJOR_VERSION} + 100*${HYPRE_MINOR_VERSION} + ${HYPRE_PATCH_VERSION}")
-    set(HYPRE_VERSION ${HYPRE_VERSION} CACHE STRING "HYPRE version." FORCE)
-  endif()
-  return()
-endif()
-
 include(MfemCmakeUtilities)
 mfem_find_package(HYPRE HYPRE HYPRE_DIR "include" "HYPRE.h" "lib" "HYPRE"
   "Paths to headers required by HYPRE." "Libraries required by HYPRE."
@@ -190,8 +97,7 @@ endif()
 if (HYPRE_FOUND AND HYPRE_USING_HIP)
   find_package(rocsparse REQUIRED)
   find_package(rocrand REQUIRED)
-  find_package(rocsolver REQUIRED)
-  list(APPEND HYPRE_LIBRARIES ${rocsparse_LIBRARIES} ${rocrand_LIBRARIES} roc::rocsolver roc::rocblas)
+  list(APPEND HYPRE_LIBRARIES ${rocsparse_LIBRARIES} ${rocrand_LIBRARIES})
   set(HYPRE_LIBRARIES ${HYPRE_LIBRARIES} CACHE STRING
       "HYPRE libraries + dependencies." FORCE)
   message(STATUS "Updated HYPRE_LIBRARIES: ${HYPRE_LIBRARIES}")

config/cmake/modules/FindMETIS.cmake

@@ -9,39 +9,10 @@
 # terms of the BSD-3 license. We welcome feedback and contributions, see file
 # CONTRIBUTING.md for details.
 
-# Defines the following variables if fetching of TPLs is disabled (default):
+# Defines the following variables:
 #   - METIS_FOUND
 #   - METIS_LIBRARIES
 #   - METIS_INCLUDE_DIRS
-#   - METIS_VERSION_5
-# otherwise, the following are defined:
-#   - METIS (imported library target)
-#   - METIS_VERSION_5 (cache variable)
-
-if (MFEM_FETCH_METIS OR MFEM_FETCH_TPLS)
-  set(METIS_FETCH_VERSION 4.0.3)
-  add_library(METIS STATIC IMPORTED)
-  # define external project
-  message(STATUS "Will fetch METIS ${METIS_FETCH_VERSION} to be built with default options")
-  set(PREFIX ${CMAKE_BINARY_DIR}/fetch/metis)
-  include(ExternalProject)
-  ExternalProject_Add(metis
-    GIT_REPOSITORY https://github.com/mfem/tpls
-    GIT_TAG b60352fbe9675d374b00828055e55be4584c7995 # tag from 1/16/25
-    GIT_SHALLOW TRUE
-    UPDATE_DISCONNECTED TRUE
-    PREFIX ${PREFIX}
-    CONFIGURE_COMMAND tar -xzf ../metis/metis-${METIS_FETCH_VERSION}-mac.tgz --strip=1
-    BUILD_COMMAND $(MAKE) COPTIONS=-Wno-incompatible-pointer-types
-    INSTALL_COMMAND mkdir -p ${PREFIX}/lib && cp libmetis.a ${PREFIX}/lib/)
-  # set imported library target properties
-  add_dependencies(METIS metis)
-  set_target_properties(METIS PROPERTIES
-    IMPORTED_LOCATION ${PREFIX}/lib/libmetis.a)
-  # set cache variables that would otherwise be set after mfem_find_package call
-  set(METIS_VERSION_5 FALSE CACHE BOOL "Is METIS version 5?")
-  return()
-endif()
 
 include(MfemCmakeUtilities)
 mfem_find_package(METIS METIS METIS_DIR "include;Lib" "metis.h"

config/cmake/modules/FindUMPIRE.cmake

@@ -14,12 +14,12 @@
 #   - UMPIRE_LIBRARIES
 #   - UMPIRE_INCLUDE_DIRS
 
-if (NOT umpire_ROOT AND UMPIRE_DIR)
-  set(umpire_ROOT ${UMPIRE_DIR})
+if (NOT umpire_DIR AND UMPIRE_DIR)
+  set(umpire_DIR ${UMPIRE_DIR}/lib/cmake/umpire)
 endif()
 message(STATUS "Looking for UMPIRE ...")
 message(STATUS "   in UMPIRE_DIR = ${UMPIRE_DIR}")
-message(STATUS "      umpire_ROOT = ${umpire_ROOT}")
+message(STATUS "      umpire_DIR = ${umpire_DIR}")
 find_package(umpire CONFIG)
 set(UMPIRE_FOUND ${umpire_FOUND})
 set(UMPIRE_LIBRARIES "umpire")

config/cmake/modules/MfemCmakeUtilities.cmake

@@ -701,6 +701,7 @@ endfunction(mfem_find_library)
 # Extract compile and link options needed by the given target.
 #
 function(mfem_get_target_options Target CompileOptsVar LinkOptsVar)
+
   if (NOT TARGET ${Target})
     return()
   endif()
@@ -717,7 +718,7 @@ function(mfem_get_target_options Target CompileOptsVar LinkOptsVar)
   get_target_property(IsImported ${tgt} IMPORTED)
   # message(STATUS "${tgt}[IMPORTED]: ${IsImported}")
   # Generally, the possible target types are: STATIC_LIBRARY, MODULE_LIBRARY,
-  # SHARED_LIBRARY, INTERFACE_LIBRARY, UNKNOWN_LIBRARY, EXECUTABLE.
+  # SHARED_LIBRARY, INTERFACE_LIBRARY, EXECUTABLE.
   get_target_property(type ${tgt} TYPE)
   # message(STATUS "${tgt}[TYPE]: ${type}")
   unset(ImportConfig)
@@ -765,7 +766,7 @@ function(mfem_get_target_options Target CompileOptsVar LinkOptsVar)
     else()
       message(STATUS " *** Warning: [${tgt}] LOCATION not defined!")
     endif()
-  elseif ("${type}" STREQUAL "SHARED_LIBRARY" OR "${type}" STREQUAL "UNKNOWN_LIBRARY")
+  elseif ("${type}" STREQUAL "SHARED_LIBRARY")
     get_target_property(Location ${tgt} LOCATION)
     if (Location)
       get_filename_component(Dir ${Location} DIRECTORY)
@@ -798,12 +799,7 @@ function(mfem_get_target_options Target CompileOptsVar LinkOptsVar)
           # message(STATUS "Lib = ${Lib}")
           # Filter-out generator expressions
           if (NOT ("${Lib}" MATCHES "^\\$"))
-            if(NOT ("${Lib}" STREQUAL "dl"))
-              list(APPEND LinkOpts "${Lib}")
-            else()
-              # for some reason libdl doesn't include the "-l"
-              list(APPEND LinkOpts "-ldl")
-            endif()
+            list(APPEND LinkOpts "${Lib}")
           endif()
         else()
           mfem_get_target_options(${Lib} COpts LOpts)
@@ -892,18 +888,9 @@ function(mfem_export_mk_files)
       set(${var} NO)
     endif()
   endforeach()
-  if (MFEM_USE_CUDA AND MFEM_EXPORT_GPU_CONFIG)
-    set(MFEM_CXX ${CMAKE_CUDA_COMPILER})
-    if(MFEM_CUDA_COMPILER_IS_NVCC)
-      set(MFEM_HOST_CXX ${CMAKE_CUDA_HOST_COMPILER})
-    else()
-      set(MFEM_HOST_CXX ${CMAKE_CXX_COMPILER})
-    endif()
-  else()
-    # mfem doesn't use enable_language(HIP)
-    set(MFEM_CXX ${CMAKE_CXX_COMPILER})
-    set(MFEM_HOST_CXX ${CMAKE_CXX_COMPILER})
-  endif()
+  # TODO: Add support for MFEM_USE_CUDA=YES
+  set(MFEM_CXX ${CMAKE_CXX_COMPILER})
+  set(MFEM_HOST_CXX ${MFEM_CXX})
   set(MFEM_CPPFLAGS "")
   get_target_property(cxx_std mfem CXX_STANDARD)
   # For now, we ignore the setting of the CXX_EXTENSIONS property. If this
@@ -913,50 +900,6 @@ function(mfem_export_mk_files)
   string(STRIP
          "${cxx_std_flag} ${CMAKE_CXX_FLAGS_${BUILD_TYPE}} ${CMAKE_CXX_FLAGS}"
          MFEM_CXXFLAGS)
-  if(MFEM_EXPORT_GPU_CONFIG)
-    if (MFEM_USE_CUDA)
-      set(MFEM_CXXFLAGS "${MFEM_CXXFLAGS} ${CMAKE_CUDA_FLAGS}")
-      if (MFEM_CUDA_COMPILER_IS_NVCC)
-        set(MFEM_CXXFLAGS "-x=cu ${MFEM_CXXFLAGS} -ccbin ${CMAKE_CXX_COMPILER} --forward-unknown-to-host-compiler")
-        # The following intentionally hides CUDA deprecation warnings
-        foreach(ENTRY IN LISTS CUDAToolkit_INCLUDE_DIRS)
-          set(MFEM_CXXFLAGS "${MFEM_CXXFLAGS} -isystem ${ENTRY}")
-        endforeach()
-        if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.18.0)
-          # architecture flags not part of CMAKE_CUDA_FLAGS
-          if ("all" STREQUAL "${CMAKE_CUDA_ARCHITECTURES}"
-              OR "native" STREQUAL "${CMAKE_CUDA_ARCHITECTURES}"
-              OR "all-major" STREQUAL "${CMAKE_CUDA_ARCHITECTURES}")
-            set(MFEM_CXXFLAGS "${MFEM_CXXFLAGS} -arch=${CMAKE_CUDA_ARCHITECTURES}")
-          else()
-            foreach (ENTRY IN LISTS CMAKE_CUDA_ARCHITECTURES)
-              set(MFEM_CXXFLAGS
-                "${MFEM_CXXFLAGS} -gencode arch=compute_${ENTRY},code=sm_${ENTRY}")
-            endforeach()
-          endif()
-        endif()
-      else()
-        set(MFEM_CXXFLAGS "${MFEM_CXXFLAGS} -xcuda --cuda-path=${CUDAToolkit_LIBRARY_ROOT}")
-        if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.18.0)
-          # architecture flags not part of CMAKE_CUDA_FLAGS
-          if ("all" STREQUAL "${CMAKE_CUDA_ARCHITECTURES}"
-              OR "native" STREQUAL "${CMAKE_CUDA_ARCHITECTURES}"
-              OR "all-major" STREQUAL "${CMAKE_CUDA_ARCHITECTURES}")
-            # TODO: not supported
-          else()
-            foreach(ENTRY IN LISTS CMAKE_CUDA_ARCHITECTURES)
-              set(MFEM_CXXFLAGS "-cuda-gpu-arch=sm_${ENTRY} ${MFEM_CXXFLAGS}")
-            endforeach()
-          endif()
-        endif()
-      endif()
-    elseif (MFEM_USE_HIP)
-      set(MFEM_CXXFLAGS "${MFEM_CXXFLAGS} -xhip")
-      foreach(ENTRY IN LISTS CMAKE_HIP_ARCHITECTURES)
-        set(MFEM_CXXFLAGS "--offload-arch=${ENTRY} ${MFEM_CXXFLAGS}")
-      endforeach()
-    endif()
-  endif()
   set(MFEM_TPLFLAGS "")
   foreach(dir ${TPL_INCLUDE_DIRS})
     set(MFEM_TPLFLAGS "${MFEM_TPLFLAGS} -I${dir}")
@@ -987,26 +930,14 @@ function(mfem_export_mk_files)
     set(MFEM_SHARED NO)
     set(MFEM_STATIC YES)
   endif()
-  if (MFEM_USE_CUDA)
-    set(MFEM_EXT_LIBS "${MFEM_EXT_LIBS} -lcudart")
-  endif()
   set(MFEM_BUILD_TAG "${CMAKE_SYSTEM}")
   set(MFEM_PREFIX "${CMAKE_INSTALL_PREFIX}")
-  # For the next 4 variables, these are the values for the build-tree version of
+  # For the next 4 variable, these are the values for the build-tree version of
   # 'config.mk'
   set(MFEM_INC_DIR "${PROJECT_BINARY_DIR}")
   set(MFEM_LIB_DIR "${PROJECT_BINARY_DIR}")
   set(MFEM_TEST_MK "${PROJECT_SOURCE_DIR}/config/test.mk")
   set(MFEM_CONFIG_EXTRA "MFEM_BUILD_DIR ?= ${PROJECT_BINARY_DIR}")
-  if (MFEM_USE_CUDA AND MFEM_EXPORT_GPU_CONFIG)
-    if (MFEM_CUDA_COMPILER_IS_NVCC)
-      set(MFEM_XLINKER "-Xlinker=")
-    else()
-      set(MFEM_XLINKER "${CMAKE_CUDA_LINKER_WRAPPER_FLAG}")
-    endif()
-  else()
-    set(MFEM_XLINKER "${CMAKE_CXX_LINKER_WRAPPER_FLAG}")
-  endif()
   set(MFEM_MPIEXEC ${MPIEXEC})
   if (NOT MFEM_MPIEXEC)
     set(MFEM_MPIEXEC "mpirun")
@@ -1054,21 +985,16 @@ function(mfem_export_mk_files)
     # handle interfaces (e.g., SCOREC::apf)
     if ("${lib}" MATCHES "SCOREC::.*" OR "${lib}" MATCHES "Ginkgo::.*" OR "${lib}" MATCHES "ParMoonolith::.*")
     elseif (TARGET "${lib}")
-      mfem_get_target_options(${lib} CompileOpts2 LinkOpts2)
-      # remove generator expressions
-      string(GENEX_STRIP "${CompileOpts2}" CompileOpts)
-      string(GENEX_STRIP "${LinkOpts2}" LinkOpts)
+      mfem_get_target_options(${lib} CompileOpts LinkOpts)
       # Removing duplicates may lead to issues:
       # list(REMOVE_DUPLICATES CompileOpts)
       # list(REMOVE_DUPLICATES LinkOpts)
-      # message(WARNING "${lib}[LinkOpts]: ${LinkOpts}")      
-      # message(WARNING "${lib}[CompileOpts]: ${CompileOpts}")
-      foreach(LOpt IN LISTS LinkOpts)
-        set(MFEM_EXT_LIBS "${MFEM_EXT_LIBS} ${LOpt}")
-      endforeach()
-      foreach(COpt IN LISTS CompileOpts)
-        set(MFEM_TPLFLAGS "${MFEM_TPLFLAGS} ${COpt}")
-      endforeach()
+      string(REPLACE ";" " " COpts "${CompileOpts}")
+      string(REPLACE ";" " " LOpts "${LinkOpts}")
+      # message(STATUS "${lib}[COpts]: '${COpts}'")
+      # message(STATUS "${lib}[LOpts]: '${LOpts}'")
+      set(MFEM_TPLFLAGS "${MFEM_TPLFLAGS} ${COpts}")
+      set(MFEM_EXT_LIBS "${MFEM_EXT_LIBS} ${LOpts}")
       # message(FATAL_ERROR "***** interface lib found ... exiting *****")
       # handle static and shared libs
     elseif ("${suffix}" STREQUAL "${CMAKE_SHARED_LIBRARY_SUFFIX}")
@@ -1076,7 +1002,7 @@ function(mfem_export_mk_files)
       get_filename_component(fullLibName ${lib} NAME_WE)
       string(REGEX REPLACE "^lib" "" libname ${fullLibName})
       set(MFEM_EXT_LIBS
-        "${MFEM_EXT_LIBS} ${shared_link_flag}${dir} -L${dir} -l${libname}")
+          "${MFEM_EXT_LIBS} ${shared_link_flag}${dir} -L${dir} -l${libname}")
     else()
       set(MFEM_EXT_LIBS "${MFEM_EXT_LIBS} ${lib}")
     endif()
@@ -1085,7 +1011,7 @@ function(mfem_export_mk_files)
   # Create the build-tree version of 'config.mk'
   configure_file(
     "${PROJECT_SOURCE_DIR}/config/config.mk.in"
-    "${PROJECT_BINARY_DIR}/config/config.mk" @ONLY)
+    "${PROJECT_BINARY_DIR}/config/config.mk")
   # Copy 'test.mk' from the source-tree to the build-tree
   configure_file(
     "${PROJECT_SOURCE_DIR}/config/test.mk"
@@ -1103,7 +1029,7 @@ function(mfem_export_mk_files)
   # Create the install-tree version of 'config.mk'
   configure_file(
     "${PROJECT_SOURCE_DIR}/config/config.mk.in"
-    "${PROJECT_BINARY_DIR}/config/config-install.mk" @ONLY)
+    "${PROJECT_BINARY_DIR}/config/config-install.mk")
 
   # Install rules for 'config.mk' and 'test.mk'
   install(FILES ${PROJECT_SOURCE_DIR}/config/test.mk

config/config.hpp

@@ -23,14 +23,11 @@
 #include "_config.hpp"
 #endif
 
-#include <cstdint>
-#include <climits>
-
 namespace mfem
 {
 
 #if (defined(MFEM_USE_CUDA) && defined(__CUDACC__)) || \
-    (defined(MFEM_USE_HIP) && defined(__HIP__))
+    (defined(MFEM_USE_HIP) && defined(__HIPCC__))
 #define MFEM_HOST_DEVICE __host__ __device__
 #else
 #define MFEM_HOST_DEVICE
@@ -64,6 +61,15 @@ constexpr real_t operator""_r(unsigned long long v)
 
 } // namespace mfem
 
+// Defines 'MFEM_THROW' depending if we are compiled with -fno-exceptions
+#if defined(__EXCEPTIONS) || defined(__cpp_exceptions) || defined(_CPPUNWIND)
+#define MFEM_HAS_EXCEPTIONS
+#define MFEM_THROW(exception_type, msg) throw exception_type(msg)
+#else
+#undef MFEM_HAS_EXCEPTIONS
+#define MFEM_THROW(...)
+#endif
+
 // Return value for main function in examples that should be skipped by testing
 // in some case. This return value prevents failures in testing.
 #define MFEM_SKIP_RETURN_VALUE 242

config/config.mk.in

@@ -88,7 +88,6 @@ MFEM_BUILD_TAG = @MFEM_BUILD_TAG@
 MFEM_PREFIX    = @MFEM_PREFIX@
 MFEM_INC_DIR   = @MFEM_INC_DIR@
 MFEM_LIB_DIR   = @MFEM_LIB_DIR@
-MFEM_XLINKER   = @MFEM_XLINKER@
 
 # Location of test.mk
 MFEM_TEST_MK = @MFEM_TEST_MK@

config/defaults.cmake

@@ -89,13 +89,6 @@ option(MFEM_ENABLE_EXAMPLES "Build all of the examples" OFF)
 option(MFEM_ENABLE_MINIAPPS "Build all of the miniapps" OFF)
 option(MFEM_ENABLE_BENCHMARKS "Build all of the benchmarks" OFF)
 
-# Allow a user to specify fetching of certain third-party libraries instead of
-# searching for existing installations.
-option(MFEM_FETCH_TPLS "Enable fetching of all supported third-party libraries" OFF)
-option(MFEM_FETCH_GSLIB "Enable fetching of GSLIB" OFF)
-option(MFEM_FETCH_HYPRE "Enable fetching of hypre" OFF)
-option(MFEM_FETCH_METIS "Enable fetching of METIS" OFF)
-
 # Setting CXX/MPICXX on the command line or in user.cmake will overwrite the
 # autodetected C++ compiler.
 # set(CXX g++)

config/defaults.mk

@@ -18,7 +18,6 @@
 # Some choices below are based on the OS type:
 NOTMAC := $(subst Darwin,,$(shell uname -s))
 
-ASTYLE_BIN = astyle
 ETAGS_BIN = $(shell command -v etags 2> /dev/null)
 EGREP_BIN = $(shell command -v egrep 2> /dev/null)
 
@@ -58,7 +57,7 @@ CUDA_DIR = $(or $(CUDA_HOME),$(patsubst %/,%,$(dir \
 CLANG_CUDA_FLAGS = -xcuda --cuda-path=$(CUDA_DIR) --cuda-gpu-arch=$(CUDA_ARCH)
 # flags for nvcc
 NVCC_FLAGS = -x=cu --expt-extended-lambda --expt-relaxed-constexpr \
- -arch=$(CUDA_ARCH) -isystem "$(CUDA_DIR)/include"
+ -arch=$(CUDA_ARCH)
 # Prefixes for passing flags to the host compiler and linker when using
 # CUDA_CXX=nvcc
 CUDA_XCOMPILER = -Xcompiler=
@@ -408,7 +407,7 @@ AMGX_LIB = -L$(AMGX_DIR)/lib -lamgx -lcusparse -lcusolver -lcublas -lnvToolsExt
 # MAGMA library configuration
 MAGMA_DIR = @MFEM_DIR@/../magma
 MAGMA_OPT = -I$(MAGMA_DIR)/include
-MAGMA_LIB = -L$(MAGMA_DIR)/lib -l:libmagma.a $(LAPACK_LIB)
+MAGMA_LIB = -L$(MAGMA_DIR)/lib -l:libmagma.a -lcublas -lcusparse $(LAPACK_LIB)
 
 # GnuTLS library configuration
 GNUTLS_OPT =

config/docker/README.md

@@ -101,7 +101,7 @@ $ cd ../miniapps
 $ ls
 CMakeLists.txt  common            meshing  nurbs        shifted  toys
 adjoint         electromagnetics  mtop     parelag      solvers
-autodiff        gslib             fluids   performance  tools
+autodiff        gslib             navier   performance  tools
 ```
 
 And an example in "toys"

config/sample-runs.sh

@@ -85,10 +85,6 @@ groups_serial=(
    "DPG miniapps:"
    "miniapps/dpg"
    "{acoustics,convection-diffusion,diffusion,maxwell}.cpp"'
-'"isf"
-   "Schrodinger flow miniapps:"
-   "miniapps/fluids/schrodinger-flow"
-   "schrodinger_flow.cpp"'
 '"gslib"
    "GSLIB miniapps:"
    "miniapps/gslib"
@@ -170,10 +166,6 @@ groups_parallel=(
    "miniapps/electromagnetics"
    "joule.cpp"'
 #   "{joule,maxwell,tesla,volta}.cpp"' # todo: multiline sample runs
-'"isf"
-   "Schrodinger flow miniapps:"
-   "miniapps/fluids/schrodinger-flow"
-   "pschrodinger_flow.cpp"'
 '"adjoint"
    "Adjoint miniapps:"
    "miniapps/adjoint"
@@ -199,7 +191,7 @@ groups_parallel=(
 # todo: miniapps/multidomain
 '"navier"
    "Navier miniapps:"
-   "miniapps/fluids/navier"
+   "miniapps/navier"
    "navier_cht.cpp"'
 # todo: add other navier miniapps
 '"nurbs"
@@ -289,10 +281,6 @@ groups_all=(
    "miniapps/electromagnetics"
    "joule.cpp"'
 #   "{joule,maxwell,tesla,volta}.cpp"' # todo: multiline sample runs
-'"isf"
-   "Schrodinger flow miniapps:"
-   "miniapps/fluids/schrodinger-flow"
-   "{,p}schrodinger_flow.cpp"'
 '"adjoint"
    "Adjoint miniapps:"
    "miniapps/adjoint"
@@ -320,7 +308,7 @@ groups_all=(
 # todo: miniapps/multidomain
 '"navier"
    "Navier miniapps:"
-   "miniapps/fluids/navier"
+   "miniapps/navier"
    "navier_cht.cpp"'
 # todo: add other navier miniapps
 '"nurbs"

data/channel-bifurcation-2d.mesh

@@ -1,156 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see fem/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-# PYRAMID     = 7
-#
-
-dimension
-2
-
-elements
-25
-3 3 0 1 2 3
-3 3 1 4 5 2
-3 3 4 6 7 5
-3 3 6 8 9 7
-3 3 8 10 11 9
-3 3 10 12 13 11
-3 3 12 14 15 13
-3 3 14 16 17 15
-3 3 16 18 19 17
-3 3 18 20 21 19
-3 3 20 22 23 21
-3 3 22 24 25 23
-3 3 24 26 27 25
-3 3 26 28 29 27
-3 3 28 30 31 29
-3 3 30 32 33 31
-3 3 32 34 35 33
-3 3 17 19 36 37
-3 3 37 36 38 39
-3 3 39 38 40 41
-3 3 41 40 42 43
-3 3 43 42 44 45
-3 3 45 44 46 47
-3 3 47 46 48 49
-3 3 49 48 50 51
-
-boundary
-52
-2 1 0 1
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-3 1 34 35
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-
-vertices
-52
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-9 8
-8 8
-9 9
-8 9

data/mfem.mesh

@@ -1,593 +0,0 @@
-MFEM mesh v1.0
-
-# Created by: Pointwise
-
-# MFEM Geometry Types:
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-
-dimension
-2
-
-elements
-160
-1 3 1 164 163 0
-1 3 164 165 162 163
-1 3 2 166 164 1
-1 3 166 132 165 164
-1 3 3 167 166 2
-1 3 167 131 132 166
-1 3 4 168 167 3
-1 3 168 130 131 167
-1 3 5 169 168 4
-1 3 169 129 130 168
-1 3 6 170 169 5
-1 3 170 128 129 169
-1 3 171 172 170 6
-1 3 172 127 128 170
-1 3 124 125 172 171
-1 3 125 126 127 172
-1 3 162 165 173 161
-1 3 165 132 133 173
-1 3 161 173 174 160
-1 3 173 133 134 174
-1 3 160 174 175 159
-1 3 174 134 135 175
-1 3 6 7 176 171
-1 3 7 8 177 176
-1 3 171 176 123 124
-1 3 176 177 122 123
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-1 3 175 135 136 178
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-15.500 1
-15.500 0.5

data/nc-nurbs3d.mesh

@@ -1,342 +0,0 @@
-MFEM NURBS NC-patch mesh v1.0
-dimension
-3
-
-elements
-13
-0 1 5 0 8 10 11 9 4 6 7 5
-0 1 5 0 18 8 24 32 30 23 36 38
-0 1 5 0 0 18 32 14 12 30 38 29
-0 1 5 0 32 24 10 20 38 36 26 35
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-0 1 5 0 30 23 36 38 31 22 37 39
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-0 1 5 0 38 36 26 35 39 37 27 34
-0 1 5 0 29 38 35 16 28 39 34 17
-0 1 5 0 31 22 37 39 19 9 25 33
-0 1 5 0 13 31 39 28 1 19 33 15
-0 1 5 0 39 37 27 34 33 25 11 21
-0 1 5 0 28 39 34 17 15 33 21 3
-
-boundary
-31
-9999 3 8 10 6 4
-9999 3 10 11 7 6
-9999 3 11 9 5 7
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-9999 3 4 6 7 5
-9999 3 32 24 8 18
-9999 3 18 8 23 30
-9999 3 14 32 18 0
-9999 3 0 18 30 12
-9999 3 14 0 12 29
-9999 3 20 10 24 32
-9999 3 10 20 35 26
-9999 3 2 20 32 14
-9999 3 20 2 16 35
-9999 3 2 14 29 16
-9999 3 30 23 22 31
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-9999 3 29 12 13 28
-9999 3 26 35 34 27
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-9999 3 13 31 19 1
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-9999 3 1 19 33 15
-9999 3 27 34 21 11
-9999 3 33 25 11 21
-9999 3 34 17 3 21
-9999 3 17 28 15 3
-9999 3 15 33 21 3
-
-vertex_to_knotspan
-8
-23 0 1 8 10 11 9
-22 0 2 8 10 11 9
-24 1 0 8 10 11 9
-36 1 1 8 10 11 9
-37 1 2 8 10 11 9
-25 1 3 8 10 11 9
-26 2 1 8 10 11 9
-27 2 2 8 10 11 9
-
-coordinates
-40
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-0 0 0
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-0 0.666666666666667 0
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-4 0.666666666666667 0
-0 0 1
-0 1 1
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-4 1 1
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-4 0.666666666666667 2
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-0 0.333333333333333 1
-0 0.666666666666667 1
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-2 0.666666666666667 2
-1.81325211007895 0.333333333333333 1
-1.81325211007895 0.666666666666667 1
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-edges
-87
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-
-knotvectors
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-1 3 0 0 0.5 1 1
-1 2 0 0 1 1
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-1 2 0 0 1 1
-
-spacing
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-
-weights
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-FiniteElementSpace
-FiniteElementCollection: NURBS1
-VDim: 3
-Ordering: 1
-
-0 0 0
-0 1 0
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-4 0.333333333333333 1
-2 0.333333333333333 2
-2 0.666666666666667 2
-1.81325211007895 0.333333333333333 1
-1.81325211007895 0.666666666666667 1
-2 0 4
-4 0.333333333333333 4
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-2 1 4
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-0 0 3
-4 0 3
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-0 1 3
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-2 0.666666666666667 4
-2 0.333333333333333 3
-2 0.666666666666667 3

data/nc3-nurbs.mesh

@@ -1,96 +0,0 @@
-MFEM NURBS NC-patch mesh v1.0
-dimension
-2
-
-# rank attr geom ref_type nodes/children
-elements
-3
-0 1 3 0 0 4 5 1
-0 1 3 0 6 7 4 2
-0 1 3 0 6 3 5 7
-
-# attr geom nodes
-boundary
-7
-1 1 0 4
-1 1 5 1
-1 1 1 0
-1 1 2 6
-1 1 6 3
-1 1 4 2
-1 1 5 3
-
-vertex_to_knotspan
-1
-7 1 4 5
-
-# top-level node coordinates
-coordinates
-8
-2
-0 0
-0 1
-2 0
-2 1
-1 0
-1 1
-2 0.5
-1 0.5
-
-edges
-11
-0 0 4
-1 4 5
-0 1 5
-1 0 1
-2 6 7
-4 7 4
-2 2 4
-4 6 2
-3 6 3
-2 3 5
-3 7 5
-
-knotvectors
-5
-1 3 0 0 0.5 1 1
-1 3 0 0 0.5 1 1
-1 2 0 0 1 1
-1 2 0 0 1 1
-1 2 0 0 1 1
-
-spacing
-0
-
-weights
-1.0
-1.0
-1.0
-1.0
-1.0
-1.0
-1.0
-1.0
-1.0
-1.0
-1.0
-1.0
-
-FiniteElementSpace
-FiniteElementCollection: NURBS1
-VDim: 2
-Ordering: 1
-
-0 0
-0 1
-2 0
-2 1
-1 0
-1 1
-2 0.5
-1 0.5
-0.5 0
-0.5 1
-0 0.5
-0.5 0.5
-mfem_mesh_end

data/nurbs-segments2d-patches-multispan.mesh

@@ -1,86 +0,0 @@
-MFEM NURBS mesh v1.0
-
-dimension
-1
-
-# Four segments with different NURBS orders, described via patches.
-elements
-4
-1 1 0 1
-2 1 2 3
-3 1 4 5
-4 1 6 7
-
-boundary
-0
-
-edges
-4
-0 0 1
-1 2 3
-2 4 5
-3 6 7
-
-vertices
-8
-
-patches
-
-# Patch 0: linear (order 1, 3 spans)
-knotvectors
-1
-1 4  0 0  .4 .6 1 1
-
-dimension
-2
-
-controlpoints
-0.0  0.0  1.0
-0.6  0.4  1.0
-0.4  0.6  1.0
-1.0  1.0  1.0
-
-# Patch 1: quadratic (order 2, 2 spans)
-knotvectors
-1
-2 4  0 0 0  .5 1 1 1
-
-dimension
-2
-
-controlpoints
-1.0  0.0  1.0
-1.9  0.0  1.21
-2.0  0.9  1.22
-2.0  1.0  1.0
-
-# Patch 2: cubic (order 3, 3 spans)
-knotvectors
-1
-3 6  0 0 0 0 .33 .66 1 1 1 1
-
-dimension
-2
-
-controlpoints
-2.0   0.0  1.0
-2.1   0.2  1.31
-3.5   0.4  1.32
-2.5   0.6  1.33
-2.9   1.0  1.34
-3.0   1.0  1.0
-
-# Patch 3: quartic (order 4, 1 span)
-knotvectors
-1
-4 5  0 0 0 0 0 1 1 1 1 1
-
-dimension
-2
-
-controlpoints
-3.0    0.0  1.0
-3.45   0.5  1.41
-3.50   1.0  1.42
-3.75   0.8  1.43
-4.0    0.0  1.0

data/nurbs-segments2d-patches.mesh

@@ -1,79 +0,0 @@
-MFEM NURBS mesh v1.0
-
-#
-# MFEM Geometry Types (see fem/geom.hpp):
-#
-# SEGMENT     = 1
-# SQUARE      = 3
-# CUBE        = 5
-#
-
-dimension
-1
-
-# Three segments with different NURBS orders, described via patches.
-elements
-3
-1 1 0 1
-2 1 2 3
-3 1 4 5
-
-boundary
-6
-1 0 0
-1 0 1
-1 0 2
-1 0 3
-1 0 4
-1 0 5
-
-edges
-3
-0 0 1
-1 2 3
-2 4 5
-
-vertices
-6
-
-patches
-
-# Patch 0: linear (order 1, 2 control points)
-knotvectors
-1
-1 2  0 0  1 1
-
-dimension
-2
-
-controlpoints
-0.0  0.0  1.0
-1.0  1.0  1.0
-
-# Patch 1: quadratic (order 2, 3 control points)
-knotvectors
-1
-2 3  0 0 0  1 1 1
-
-dimension
-2
-
-controlpoints
-1.0  0.0   1.0
-1.02 1.02  1.2
-2.0  1.0   1.0
-
-# Patch 2: cubic (order 3, 4 control points)
-knotvectors
-1
-3 4  0 0 0 0  1 1 1 1
-
-dimension
-2
-
-controlpoints
-2.0   0.0   1.0
-2.03  0.83  1.31
-2.33  1.03  1.32
-3.0   1.0   1.0
-

data/nurbs-segments2d.mesh

@@ -1,72 +0,0 @@
-MFEM NURBS mesh v1.0
-
-#
-# MFEM Geometry Types (see fem/geom.hpp):
-#
-# SEGMENT     = 1
-# SQUARE      = 3
-# CUBE        = 5
-#
-
-dimension
-1
-
-elements
-3
-1 1 0 1
-2 1 2 3
-3 1 4 5
-
-boundary
-6
-1 0 0
-1 0 1
-1 0 2
-1 0 3
-1 0 4
-1 0 5
-
-edges
-3
-0 0 1
-1 2 3
-2 4 5
-
-vertices
-6
-
-# Edge 0: linear (order 1, 2 control points)
-# Edge 1: quadratic (order 2, 3 control points)
-# Edge 2: cubic (order 3, 4 control points)
-knotvectors
-3
-1 2  0 0  1 1
-2 3  0 0 0  1 1 1
-3 4  0 0 0 0  1 1 1 1
-
-# One weight per control point, in the same order as the control points; (2 + 3 + 4) = 9 weights total
-weights
-1
-1
-1
-1
-1
-1
-1.2
-1.31
-1.32
-
-FiniteElementSpace
-FiniteElementCollection: NURBS
-VDim: 2
-Ordering: 1
-
-0.0  0.0
-1.0  1.0
-1.0  0.0
-2.0  1.0
-2.0  0.0
-3.0  1.0
-1.02 1.02
-2.03 0.83
-2.33 1.03

data/nurbs-segments3d-patches.mesh

@@ -1,79 +0,0 @@
-MFEM NURBS mesh v1.0
-
-#
-# MFEM Geometry Types (see fem/geom.hpp):
-#
-# SEGMENT     = 1
-# SQUARE      = 3
-# CUBE        = 5
-#
-
-dimension
-1
-
-# Three segments with different NURBS orders, described via patches.
-elements
-3
-1 1 0 1
-2 1 2 3
-3 1 4 5
-
-boundary
-6
-1 0 0
-1 0 1
-1 0 2
-1 0 3
-1 0 4
-1 0 5
-
-edges
-3
-0 0 1
-1 2 3
-2 4 5
-
-vertices
-6
-
-patches
-
-# Patch 0: linear (order 1, 2 control points)
-knotvectors
-1
-1 2  0 0  1 1
-
-dimension
-3
-
-controlpoints
-0.0  0.0  0.01 1.0
-1.0  1.0  1.01 1.0
-
-# Patch 1: quadratic (order 2, 3 control points)
-knotvectors
-1
-2 3  0 0 0  1 1 1
-
-dimension
-3
-
-controlpoints
-1.0  0.0   0.02 1.0
-1.02 1.02  0.52 1.2
-2.0  1.0   1.02 1.0
-
-# Patch 2: cubic (order 3, 4 control points)
-knotvectors
-1
-3 4  0 0 0 0  1 1 1 1
-
-dimension
-3
-
-controlpoints
-2.0   0.0   0.03 1.0
-2.03  0.83  0.33 1.31
-2.33  1.03  0.63 1.32
-3.0   1.0   1.03 1.0
-

data/nurbs-segments3d.mesh

@@ -1,72 +0,0 @@
-MFEM NURBS mesh v1.0
-
-#
-# MFEM Geometry Types (see fem/geom.hpp):
-#
-# SEGMENT     = 1
-# SQUARE      = 3
-# CUBE        = 5
-#
-
-dimension
-1
-
-elements
-3
-1 1 0 1
-2 1 2 3
-3 1 4 5
-
-boundary
-6
-1 0 0
-1 0 1
-1 0 2
-1 0 3
-1 0 4
-1 0 5
-
-edges
-3
-0 0 1
-1 2 3
-2 4 5
-
-vertices
-6
-
-# Edge 0: linear (order 1, 2 control points)
-# Edge 1: quadratic (order 2, 3 control points)
-# Edge 2: cubic (order 3, 4 control points)
-knotvectors
-3
-1 2  0 0  1 1
-2 3  0 0 0  1 1 1
-3 4  0 0 0 0  1 1 1 1
-
-# One weight per control point, in the same order as the control points; (2 + 3 + 4) = 9 weights total
-weights
-1
-1
-1
-1
-1
-1
-1.2
-1.31
-1.32
-
-FiniteElementSpace
-FiniteElementCollection: NURBS
-VDim: 3
-Ordering: 1
-
-0.0  0.0   0.01
-1.0  1.0   1.01
-1.0  0.0   0.02
-2.0  1.0   1.02
-2.0  0.0   0.03
-3.0  1.0   1.03
-1.02 1.02  0.52
-2.03 0.83  0.33
-2.33 1.03  0.63

doc/CodeDocumentation.conf.in

@@ -48,7 +48,7 @@ PROJECT_NAME           = MFEM
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v4.9.1
+PROJECT_NUMBER         = v4.8.1
 
 # 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
@@ -973,13 +973,10 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/miniapps/adjoint \
                          @MFEM_SOURCE_DIR@/miniapps/autodiff \
                          @MFEM_SOURCE_DIR@/miniapps/common \
-                         @MFEM_SOURCE_DIR@/miniapps/contact \
                          @MFEM_SOURCE_DIR@/miniapps/dfem \
                          @MFEM_SOURCE_DIR@/miniapps/dpg \
                          @MFEM_SOURCE_DIR@/miniapps/dpg/util \
                          @MFEM_SOURCE_DIR@/miniapps/electromagnetics \
-                         @MFEM_SOURCE_DIR@/miniapps/fluids/navier \
-                         @MFEM_SOURCE_DIR@/miniapps/fluids/schrodinger-flow \
                          @MFEM_SOURCE_DIR@/miniapps/gslib \
                          @MFEM_SOURCE_DIR@/miniapps/hdiv-linear-solver \
                          @MFEM_SOURCE_DIR@/miniapps/hooke \
@@ -990,6 +987,7 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/miniapps/meshing \
                          @MFEM_SOURCE_DIR@/miniapps/mtop \
                          @MFEM_SOURCE_DIR@/miniapps/multidomain \
+                         @MFEM_SOURCE_DIR@/miniapps/navier \
                          @MFEM_SOURCE_DIR@/miniapps/nurbs \
                          @MFEM_SOURCE_DIR@/miniapps/parelag \
                          @MFEM_SOURCE_DIR@/miniapps/performance \

doc/CodeDocumentation.dox

@@ -117,8 +117,6 @@ namespace mfem {
  * - <a class="el" href="ex39p_8cpp_source.html">Example 39p</a>: parallel named mesh attributes
  * - <a class="el" href="ex40_8cpp_source.html">Example 40</a>: eikonal equation
  * - <a class="el" href="ex40p_8cpp_source.html">Example 40p</a>: parallel eikonal equation
- * - <a class="el" href="ex41_8cpp_source.html">Example 41</a>: DG/CG IMEX time-dependent advection-diffusion
- * - <a class="el" href="ex41p_8cpp_source.html">Example 41p</a>: parallel DG/CG IMEX time-dependent advection-diffusion
  *
  * <H4>AmgX Examples</H4>
  * - Variants of Examples
@@ -190,8 +188,6 @@ namespace mfem {
  *  <a class="el" href="nurbs__ex1p_8cpp_source.html">1p</a>,
  *  <a class="el" href="nurbs__ex3_8cpp_source.html">3</a>,
  *  <a class="el" href="nurbs__ex5_8cpp_source.html">5</a>,
- *  <a class="el" href="nurbs__ex10_8cpp_source.html">10</a>,
- *  <a class="el" href="nurbs__ex10p_8cpp_source.html">10p</a>,
  *  <a class="el" href="nurbs__ex11p_8cpp_source.html">11p</a>, and
  *  <a class="el" href="nurbs__ex24_8cpp_source.html">24</a>,
  *   demonstrating howto perform NURBS-based Isogeometric Analysis.
@@ -200,14 +196,12 @@ namespace mfem {
  * - <a class="el" href="nurbs__curveint_8cpp_source.html">NURBS Interpolation</a>: NURBS interpolation of given geometry
  * - <a class="el" href="nurbs__naca__cmesh_8cpp_source.html">NURBS NACA Mesher</a>: generate NURBS based mesh around a NACA foil
  * - <a class="el" href="nurbs__printfunc_8cpp_source.html">NURBS Printer</a>: print the NURBS-basis
- * - <a class="el" href="nurbs__mesh_info_8cpp_source.html">NURBS Mesh info</a>: print the info of a NURBS mesh
  *
  * <H3>Miniapps</H3>
  * - <a class="el" href="volta_8cpp_source.html">Volta</a>: simple electrostatics simulation code
  * - <a class="el" href="tesla_8cpp_source.html">Tesla</a>: simple magnetostatics simulation code
  * - <a class="el" href="maxwell_8cpp_source.html">Maxwell</a>: simple transient full-wave electromagnetics simulation code
  * - <a class="el" href="joule_8cpp_source.html">Joule</a>: transient magnetics and Joule heating miniapp
- * - <a class="el" href="lorentz_8cpp_source.html">Lorentz</a>: simple particle tracking code based on the Lorentz force
  * - <a class="el" href="classmfem_1_1navier_1_1NavierSolver.html">Navier</a>: solve the transient incompressible Navier-Stokes equations
  * - <a class="el" href="mobius-strip_8cpp_source.html">Mobius Strip</a>: generate various Mobius strip-like meshes
  * - <a class="el" href="klein-bottle_8cpp_source.html">Klein Bottle</a>: generate three types of Klein bottle surfaces
@@ -239,8 +233,7 @@ namespace mfem {
  * - <a class="el" href="miniapps_2performance_2ex1_8cpp_source.html">HPC Example 1</a>: high-performance nodal H1 FEM for the Poisson problem
  * - <a class="el" href="miniapps_2performance_2ex1p_8cpp_source.html">HPC Example 1p</a>: high-performance parallel nodal H1 FEM for the Poisson problem
  * - <a class="el" href="generate__random__field_8cpp_source.html">SPDE Solvers</a>: SPDE solver random field generation
- * - <a class="el" href="contact-patch-test_8cpp_source.html">Tribol</a>: mortar contact patch test for elasticity
- * - <a class="el" href="contact_8cpp_source.html">Contact</a>: Frictionless contact examples using <a class="el" href="classmfem_1_1IPSolver.html#details">IP optimization</a> and the <a class="el" href="classmfem_1_1AMGFSolver.html#details">AMGF solver</a>
+ * - <a class="el" href="contact-patch-test_8cpp_source.html">Contact</a>: mortar contact patch test for elasticity
  * - <a class="el" href="multidomain_8cpp_source.html">Multidomain miniapp</a>: Multidomain and Submesh demonstration miniapp
  * - <a class="el" href="pdiffusion_8cpp_source.html">DPG Diffusion example</a>: DPG formulation for the diffusion problem
  * - <a class="el" href="pmaxwell_8cpp_source.html">DPG Maxwell example</a>: DPG formulation for the indefinite Maxwell problem

examples/CMakeLists.txt

@@ -46,7 +46,6 @@ list(APPEND ALL_EXE_SRCS
   ex38.cpp
   ex39.cpp
   ex40.cpp
-  ex41.cpp
   )
 
 if (MFEM_USE_MPI)
@@ -90,7 +89,6 @@ if (MFEM_USE_MPI)
     ex37p.cpp
     ex39p.cpp
     ex40p.cpp
-    ex41p.cpp
   )
 endif()
 
@@ -133,8 +131,6 @@ if (MFEM_ENABLE_TESTING)
       list(APPEND THIS_TEST_OPTIONS "-dg")
     elseif(${TEST_NAME} MATCHES "ex37p*")
       list(APPEND THIS_TEST_OPTIONS "-mi" "3")
-    elseif(${TEST_NAME} MATCHES "ex41p*")
-      list(APPEND THIS_TEST_OPTIONS "-tf" "1.0")
     endif()
 
     if (NOT (${TEST_NAME} MATCHES ".*p$"))
@@ -209,15 +205,6 @@ if (MFEM_ENABLE_TESTING)
       $<TARGET_FILE:ex25p> "-no-vis" "--mumps-solver"
       ${MPIEXEC_POSTFLAGS})
   endif()
-
-  # Parallel libCEED example
-  if (MFEM_USE_CEED AND MFEM_USE_MPI)
-    add_test(NAME ex1p_ceed_np=${MFEM_MPI_NP}
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-      ${MPIEXEC_PREFLAGS}
-      $<TARGET_FILE:ex1p> "-no-vis" "-d" "ceed-cpu" "-pa" "-a"
-      ${MPIEXEC_POSTFLAGS})
-  endif()
 endif()
 
 # Include the examples/amgx directory if AmgX is enabled

examples/amgx/makefile

@@ -64,7 +64,7 @@ PARALLEL_NAME := Parallel AMGX example
 $(MFEM_LIB_FILE):
 	$(error The MFEM library is not build)
 
-clean: clean-build clean-exec
+clean: clean-build
 
 clean-build:
 	rm -f *.o *~ $(SEQ_EXAMPLES) $(PAR_EXAMPLES)

examples/caliper/makefile

@@ -64,12 +64,12 @@ ex1p-test-par: ex1p
 $(MFEM_LIB_FILE):
 	$(error The MFEM library is not built)
 
-clean: clean-build clean-exec
+clean: clean-build clean-exec $(SUBDIRS_CLEAN)
 
 clean-build:
 	rm -f *.o *~ $(SEQ_EXAMPLES) $(PAR_EXAMPLES)
 	rm -rf *.dSYM *.TVD.*breakpoints
 
 clean-exec:
-	@rm -f refined.mesh mesh.*
-	@rm -f sol.*
+	@rm -f refined.mesh displaced.mesh mesh.* ex5.mesh
+	@rm -f sphere_refined.* sol.* sol_u.* sol_p.* sol_r.* sol_i.*

examples/ex1.cpp

@@ -27,7 +27,6 @@
 //               ex1 -m ../data/fichera-amr.mesh
 //               ex1 -m ../data/mobius-strip.mesh
 //               ex1 -m ../data/mobius-strip.mesh -o -1 -sc
-//               ex1 -m ../data/nc3-nurbs.mesh -o -1
 //
 // Device sample runs:
 //               ex1 -pa -d cuda

examples/ex12p.cpp

@@ -5,9 +5,9 @@
 // Sample runs:
 //    mpirun -np 4 ex12p -m ../data/beam-tri.mesh
 //    mpirun -np 4 ex12p -m ../data/beam-quad.mesh
-//    mpirun -np 4 ex12p -m ../data/beam-tet.mesh -s 464 -n 10 -o 2 -elast
+//    mpirun -np 4 ex12p -m ../data/beam-tet.mesh -s 462 -n 10 -o 2 -elast
 //    mpirun -np 4 ex12p -m ../data/beam-hex.mesh -s 3878
-//    mpirun -np 4 ex12p -m ../data/beam-wedge.mesh -s 82
+//    mpirun -np 4 ex12p -m ../data/beam-wedge.mesh -s 81
 //    mpirun -np 4 ex12p -m ../data/beam-tri.mesh -s 3877 -o 2 -sys
 //    mpirun -np 4 ex12p -m ../data/beam-quad.mesh -s 4544 -n 6 -o 3 -elast
 //    mpirun -np 4 ex12p -m ../data/beam-quad-nurbs.mesh

examples/ex16.cpp

@@ -105,7 +105,6 @@ int main(int argc, char *argv[])
    bool visualization = true;
    bool visit = false;
    int vis_steps = 5;
-   bool solve_implicit_state = false;
 
    int precision = 8;
    cout.precision(precision);
@@ -127,9 +126,6 @@ int main(int argc, char *argv[])
                   "Alpha coefficient.");
    args.AddOption(&kappa, "-k", "--kappa",
                   "Kappa coefficient offset.");
-   args.AddOption(&solve_implicit_state, "-imp-state", "--implicit-state",
-                  "-imp-slope", "--implicit-slope",
-                  "Implicitly solve for stage state or slope.");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -183,11 +179,6 @@ int main(int argc, char *argv[])
 
    // 7. Initialize the conduction operator and the visualization.
    ConductionOperator oper(fespace, alpha, kappa, u);
-   using ImplicitVariableType = ConductionOperator::ImplicitVariableType;
-   ImplicitVariableType imp_var = solve_implicit_state ?
-                                  ImplicitVariableType::STATE
-                                  : ImplicitVariableType::SLOPE;
-   oper.SetImplicitVariableType(imp_var);
 
    u_gf.SetFromTrueDofs(u);
    {
@@ -325,14 +316,11 @@ void ConductionOperator::Mult(const Vector &u, Vector &du_dt) const
 }
 
 void ConductionOperator::ImplicitSolve(const real_t dt,
-                                       const Vector &u, Vector &k)
+                                       const Vector &u, Vector &du_dt)
 {
    // Solve the equation:
-   //    M*k = -K(u + dt*k) for k = du/dt, if solving for stage-slope
-   // or
-   //    M*k = -dt*K(k) + M*u for k = u_s, if solving for stage-state
-   // where K is linearized by using u from the previous timestep, and
-   // the stage-state and slope relation: du/dt = (u_s - u)/dt.
+   //    du_dt = M^{-1}*[-K(u + dt*du_dt)]
+   // for du_dt, where K is linearized by using u from the previous timestep
    if (!T)
    {
       T = Add(1.0, Mmat, dt, Kmat);
@@ -340,20 +328,9 @@ void ConductionOperator::ImplicitSolve(const real_t dt,
       T_solver.SetOperator(*T);
    }
    MFEM_VERIFY(dt == current_dt, ""); // SDIRK methods use the same dt
-
-   // Construct current right-hand side for stage state vs. slope solve
-   if (ImplicitVarTypeIsState())
-   {
-      // k, on return, is the stage value u_s
-      Mmat.Mult(u, z);
-   }
-   else
-   {
-      // k, on return, is the stage slope du/dt
-      Kmat.Mult(u, z);
-      z.Neg();
-   }
-   T_solver.Mult(z, k);
+   Kmat.Mult(u, z);
+   z.Neg();
+   T_solver.Mult(z, du_dt);
 }
 
 void ConductionOperator::SetParameters(const Vector &u)

examples/ex16p.cpp

@@ -115,7 +115,6 @@ int main(int argc, char *argv[])
    bool visit = false;
    int vis_steps = 5;
    bool adios2 = false;
-   bool solve_implicit_state = false;
 
    int precision = 8;
    cout.precision(precision);
@@ -139,9 +138,6 @@ int main(int argc, char *argv[])
                   "Alpha coefficient.");
    args.AddOption(&kappa, "-k", "--kappa",
                   "Kappa coefficient offset.");
-   args.AddOption(&solve_implicit_state, "-imp-state", "--implicit-state",
-                  "-imp-slope", "--implicit-slope",
-                  "Implicitly solve for stage state or slope.");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -216,11 +212,6 @@ int main(int argc, char *argv[])
 
    // 9. Initialize the conduction operator and the VisIt visualization.
    ConductionOperator oper(fespace, alpha, kappa, u);
-   using ImplicitVariableType = ConductionOperator::ImplicitVariableType;
-   ImplicitVariableType imp_var = solve_implicit_state ?
-                                  ImplicitVariableType::STATE
-                                  : ImplicitVariableType::SLOPE;
-   oper.SetImplicitVariableType(imp_var);
 
    u_gf.SetFromTrueDofs(u);
    {
@@ -416,14 +407,11 @@ void ConductionOperator::Mult(const Vector &u, Vector &du_dt) const
 }
 
 void ConductionOperator::ImplicitSolve(const real_t dt,
-                                       const Vector &u, Vector &k)
+                                       const Vector &u, Vector &du_dt)
 {
    // Solve the equation:
-   //    M*k = -K(u + dt*k) for k = du/dt, if solving for stage-slope
-   // or
-   //    M*k = -dt*K(k) + M*u for k = u_s, if solving for stage-state
-   // where K is linearized by using u from the previous timestep, and
-   // the stage-state and slope relation: du/dt = (u_s - u)/dt.
+   //    du_dt = M^{-1}*[-K(u + dt*du_dt)]
+   // for du_dt, where K is linearized by using u from the previous timestep
    if (!T)
    {
       T = Add(1.0, Mmat, dt, Kmat);
@@ -431,20 +419,9 @@ void ConductionOperator::ImplicitSolve(const real_t dt,
       T_solver.SetOperator(*T);
    }
    MFEM_VERIFY(dt == current_dt, ""); // SDIRK methods use the same dt
-
-   // Construct current right-hand side for stage state vs. slope solve
-   if (ImplicitVarTypeIsState())
-   {
-      // k, on return, is the stage value u
-      Mmat.Mult(u, z);
-   }
-   else
-   {
-      // k, on return, is the stage slope du/dt
-      Kmat.Mult(u, z);
-      z.Neg();
-   }
-   T_solver.Mult(z, k);
+   Kmat.Mult(u, z);
+   z.Neg();
+   T_solver.Mult(z, du_dt);
 }
 
 void ConductionOperator::SetParameters(const Vector &u)

examples/ex21.cpp

@@ -119,7 +119,7 @@ int main(int argc, char *argv[])
    }
 
    LinearForm b(&fespace);
-   b.AddBoundaryIntegrator(new VectorBoundaryLFIntegrator(f));
+   b.AddDomainIntegrator(new VectorBoundaryLFIntegrator(f));
 
    // 6. Set up the bilinear form a(.,.) on the finite element space
    //    corresponding to the linear elasticity integrator with piece-wise

examples/ex21p.cpp

@@ -140,7 +140,7 @@ int main(int argc, char *argv[])
    }
 
    ParLinearForm b(&fespace);
-   b.AddBoundaryIntegrator(new VectorBoundaryLFIntegrator(f));
+   b.AddDomainIntegrator(new VectorBoundaryLFIntegrator(f));
 
    // 6. Set up the bilinear form a(.,.) on the finite element space
    //    corresponding to the linear elasticity integrator with piece-wise

examples/ex22.cpp

@@ -471,13 +471,10 @@ int main(int argc, char *argv[])
 
       ofstream sol_r_ofs("sol_r.gf");
       ofstream sol_i_ofs("sol_i.gf");
-      ofstream sol_z_ofs("sol_z.gf");
       sol_r_ofs.precision(8);
       sol_i_ofs.precision(8);
-      sol_z_ofs.precision(8);
       u.real().Save(sol_r_ofs);
       u.imag().Save(sol_i_ofs);
-      u.Save(sol_z_ofs);
    }
 
    // 14. Send the solution by socket to a GLVis server.

examples/ex22p.cpp

@@ -302,21 +302,15 @@ int main(int argc, char *argv[])
       char vishost[] = "localhost";
       int  visport   = 19916;
       socketstream sol_sock_r(vishost, visport);
+      socketstream sol_sock_i(vishost, visport);
       sol_sock_r << "parallel " << num_procs << " " << myid << "\n";
+      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
       sol_sock_r.precision(8);
+      sol_sock_i.precision(8);
       sol_sock_r << "solution\n" << *pmesh << u_exact->real()
                  << "window_title 'Exact: Real Part'" << flush;
-      // Make sure all ranks have sent their real solution before initiating
-      // another set of GLVis connections (one from each rank):
-      MPI_Barrier(pmesh->GetComm());
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_i.precision(8);
       sol_sock_i << "solution\n" << *pmesh << u_exact->imag()
                  << "window_title 'Exact: Imaginary Part'" << flush;
-      // Make sure all ranks have sent their imaginary solution before initiating
-      // another set of GLVis connections (one from each rank):
-      MPI_Barrier(pmesh->GetComm());
    }
 
    // 11. Set up the parallel sesquilinear form a(.,.) on the finite element
@@ -513,11 +507,10 @@ int main(int argc, char *argv[])
    // 15. Save the refined mesh and the solution in parallel. This output can be
    //     viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
    {
-      ostringstream mesh_name, sol_r_name, sol_i_name, sol_z_name;
+      ostringstream mesh_name, sol_r_name, sol_i_name;
       mesh_name << "mesh." << setfill('0') << setw(6) << myid;
       sol_r_name << "sol_r." << setfill('0') << setw(6) << myid;
       sol_i_name << "sol_i." << setfill('0') << setw(6) << myid;
-      sol_z_name << "sol_z." << setfill('0') << setw(6) << myid;
 
       ofstream mesh_ofs(mesh_name.str().c_str());
       mesh_ofs.precision(8);
@@ -525,13 +518,10 @@ int main(int argc, char *argv[])
 
       ofstream sol_r_ofs(sol_r_name.str().c_str());
       ofstream sol_i_ofs(sol_i_name.str().c_str());
-      ofstream sol_z_ofs(sol_z_name.str().c_str());
       sol_r_ofs.precision(8);
       sol_i_ofs.precision(8);
-      sol_z_ofs.precision(8);
       u.real().Save(sol_r_ofs);
       u.imag().Save(sol_i_ofs);
-      u.Save(sol_z_ofs);
    }
 
    // 16. Send the solution by socket to a GLVis server.
@@ -540,21 +530,15 @@ int main(int argc, char *argv[])
       char vishost[] = "localhost";
       int  visport   = 19916;
       socketstream sol_sock_r(vishost, visport);
+      socketstream sol_sock_i(vishost, visport);
       sol_sock_r << "parallel " << num_procs << " " << myid << "\n";
+      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
       sol_sock_r.precision(8);
+      sol_sock_i.precision(8);
       sol_sock_r << "solution\n" << *pmesh << u.real()
                  << "window_title 'Solution: Real Part'" << flush;
-      // Make sure all ranks have sent their real solution before initiating
-      // another set of GLVis connections (one from each rank):
-      MPI_Barrier(pmesh->GetComm());
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_i.precision(8);
       sol_sock_i << "solution\n" << *pmesh << u.imag()
                  << "window_title 'Solution: Imaginary Part'" << flush;
-      // Make sure all ranks have sent their imaginary solution before initiating
-      // another set of GLVis connections (one from each rank):
-      MPI_Barrier(pmesh->GetComm());
    }
    if (visualization && exact_sol)
    {
@@ -563,21 +547,15 @@ int main(int argc, char *argv[])
       char vishost[] = "localhost";
       int  visport   = 19916;
       socketstream sol_sock_r(vishost, visport);
+      socketstream sol_sock_i(vishost, visport);
       sol_sock_r << "parallel " << num_procs << " " << myid << "\n";
+      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
       sol_sock_r.precision(8);
+      sol_sock_i.precision(8);
       sol_sock_r << "solution\n" << *pmesh << u_exact->real()
                  << "window_title 'Error: Real Part'" << flush;
-      // Make sure all ranks have sent their real solution before initiating
-      // another set of GLVis connections (one from each rank):
-      MPI_Barrier(pmesh->GetComm());
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_i.precision(8);
       sol_sock_i << "solution\n" << *pmesh << u_exact->imag()
                  << "window_title 'Error: Imaginary Part'" << flush;
-      // Make sure all ranks have sent their imaginary solution before initiating
-      // another set of GLVis connections (one from each rank):
-      MPI_Barrier(pmesh->GetComm());
    }
    if (visualization)
    {

examples/ex37.cpp

@@ -5,8 +5,8 @@
 // Sample runs:
 //     ex37 -alpha 10
 //     ex37 -alpha 10 -pv
-//     ex37 -lambda 0.1 -mu 0.1 -growth 1
-//     ex37 -o 2 -alpha 10.0 -mi 50 -vf 0.4 -ntol 1e-5 -growth 1.5
+//     ex37 -lambda 0.1 -mu 0.1
+//     ex37 -o 2 -alpha 5.0 -mi 50 -vf 0.4 -ntol 1e-5
 //     ex37 -r 6 -o 1 -alpha 25.0 -epsilon 0.02 -mi 50 -ntol 1e-5
 //
 // Description: This example code demonstrates the use of MFEM to solve a
@@ -55,6 +55,53 @@
 using namespace std;
 using namespace mfem;
 
+/**
+ * @brief Bregman projection of ρ = sigmoid(ψ) onto the subspace
+ *        ∫_Ω ρ dx = θ vol(Ω) as follows:
+ *
+ *        1. Compute the root of the R → R function
+ *            f(c) = ∫_Ω sigmoid(ψ + c) dx - θ vol(Ω)
+ *        2. Set ψ ← ψ + c.
+ *
+ * @param psi a GridFunction to be updated
+ * @param target_volume θ vol(Ω)
+ * @param tol Newton iteration tolerance
+ * @param max_its Newton maximum iteration number
+ * @return real_t Final volume, ∫_Ω sigmoid(ψ)
+ */
+real_t proj(GridFunction &psi, real_t target_volume, real_t tol=1e-12,
+            int max_its=10)
+{
+   MappedGridFunctionCoefficient sigmoid_psi(&psi, sigmoid);
+   MappedGridFunctionCoefficient der_sigmoid_psi(&psi, der_sigmoid);
+
+   LinearForm int_sigmoid_psi(psi.FESpace());
+   int_sigmoid_psi.AddDomainIntegrator(new DomainLFIntegrator(sigmoid_psi));
+   LinearForm int_der_sigmoid_psi(psi.FESpace());
+   int_der_sigmoid_psi.AddDomainIntegrator(new DomainLFIntegrator(
+                                              der_sigmoid_psi));
+   bool done = false;
+   for (int k=0; k<max_its; k++) // Newton iteration
+   {
+      int_sigmoid_psi.Assemble(); // Recompute f(c) with updated ψ
+      const real_t f = int_sigmoid_psi.Sum() - target_volume;
+
+      int_der_sigmoid_psi.Assemble(); // Recompute df(c) with updated ψ
+      const real_t df = int_der_sigmoid_psi.Sum();
+
+      const real_t dc = -f/df;
+      psi += dc;
+      if (abs(dc) < tol) { done = true; break; }
+   }
+   if (!done)
+   {
+      mfem_warning("Projection reached maximum iteration without converging. "
+                   "Result may not be accurate.");
+   }
+   int_sigmoid_psi.Assemble();
+   return int_sigmoid_psi.Sum();
+}
+
 /*
  * ---------------------------------------------------------------
  *                      ALGORITHM PREAMBLE
@@ -133,11 +180,10 @@ int main(int argc, char *argv[])
    int ref_levels = 5;
    int order = 2;
    real_t alpha = 1.0;
-   real_t growth = 2;
    real_t epsilon = 0.01;
    real_t vol_fraction = 0.5;
    int max_it = 1e3;
-   real_t itol = 1e-2;
+   real_t itol = 1e-1;
    real_t ntol = 1e-4;
    real_t rho_min = 1e-6;
    real_t lambda = 1.0;
@@ -152,8 +198,6 @@ int main(int argc, char *argv[])
                   "Order (degree) of the finite elements.");
    args.AddOption(&alpha, "-alpha", "--alpha-step-length",
                   "Step length for gradient descent.");
-   args.AddOption(&growth, "-growth", "--alpha-growth-rate",
-                  "Growth rate of step length for gradient descent.");
    args.AddOption(&epsilon, "-epsilon", "--epsilon-thickness",
                   "Length scale for ρ.");
    args.AddOption(&max_it, "-mi", "--max-it",
@@ -288,7 +332,6 @@ int main(int argc, char *argv[])
    }
    FilterSolver->SetEssentialBoundary(ess_bdr_filter);
    FilterSolver->SetupFEM();
-   FilterSolver->AssembleDiffusionBilinear();
 
    BilinearForm mass(&control_fes);
    mass.AddDomainIntegrator(new InverseIntegrator(new MassIntegrator(one)));
@@ -342,7 +385,7 @@ int main(int argc, char *argv[])
    // 11. Iterate:
    for (int k = 1; k <= max_it; k++)
    {
-      if (k > 1) { alpha = std::pow((real_t) k,growth); }
+      if (k > 1) { alpha *= ((real_t) k) / ((real_t) k-1); }
 
       mfem::out << "\nStep = " << k << std::endl;
 
@@ -379,9 +422,7 @@ int main(int argc, char *argv[])
 
       // Step 5 - Update design variable ψ ← proj(ψ - αG)
       psi.Add(-alpha, grad);
-      GridFunction alpha_grad(grad);
-      alpha_grad *= alpha;
-      const real_t material_volume = proj(psi, alpha_grad, target_volume);
+      const real_t material_volume = proj(psi, target_volume);
 
       // Compute ||ρ - ρ_old|| in control fes.
       real_t norm_increment = zerogf.ComputeL1Error(succ_diff_rho);

examples/ex37.hpp

@@ -137,7 +137,7 @@ public:
         exponent(exponent_), rho_min(rho_min_)
    {
       MFEM_ASSERT(rho_min_ >= 0.0, "rho_min must be >= 0");
-      MFEM_ASSERT(rho_min_ < 1.0,  "rho_min must be < 1");
+      MFEM_ASSERT(rho_min_ < 1.0,  "rho_min must be > 1");
       MFEM_ASSERT(u, "displacement field is not set");
       MFEM_ASSERT(rho_filter, "density field is not set");
    }
@@ -231,12 +231,9 @@ private:
    FiniteElementCollection * fec = nullptr;
    FiniteElementSpace * fes = nullptr;
    Array<int> ess_bdr;
-   Array<int> ess_tdof_list;
    Array<int> neumann_bdr;
    GridFunction * u = nullptr;
    LinearForm * b = nullptr;
-   BilinearForm * a = nullptr;
-   OperatorPtr A;
    bool parallel;
 #ifdef MFEM_USE_MPI
    ParMesh * pmesh = nullptr;
@@ -270,8 +267,6 @@ public:
    void ResetFEM();
    void SetupFEM();
 
-   void UpdateEssentialTDofs();
-   void AssembleDiffusionBilinear(bool update_ess_tdofs=true);
    void Solve();
    GridFunction * GetFEMSolution();
    LinearForm * GetLinearForm() {return b;}
@@ -376,130 +371,6 @@ public:
 
 };
 
-/**
- * @brief Bregman projection of ρ = sigmoid(ψ) onto the subspace
- *        ∫_Ω ρ dx = θ vol(Ω) as follows:
- *
- *        1. Compute the root of the R → R function
- *            f(c) = ∫_Ω sigmoid(ψ + c) dx - θ vol(Ω)
- *           using the Illinois method
- *        2. Set ψ ← ψ + c.
- *
- * @param psi a GridFunction to be updated
- * @param alpha_grad alpha multiplied by gradient
- * @param target_volume θ vol(Ω)
- * @param tol Illinois iteration tolerance
- * @param max_its Illinois maximum iteration number
- * @return real_t Final volume (∫_Ω sigmoid(ψ) dx)
- */
-real_t proj(GridFunction &psi, GridFunction &alpha_grad, real_t target_volume,
-            real_t tol = 1e-12, int max_its = 100)
-{
-#ifdef MFEM_USE_MPI
-   FiniteElementSpace *fes = psi.FESpace();
-   ParFiniteElementSpace *pfes = dynamic_cast<ParFiniteElementSpace*>(fes);
-#endif
-   ConstantCoefficient zero_cf(0.0);
-   real_t a = -alpha_grad.ComputeMaxError(zero_cf);
-   real_t b = -a;
-   real_t y = 0.0;
-
-   MappedGridFunctionCoefficient sigmoid_psi(
-   &psi, [&y](const real_t x) { return sigmoid(x + y); });
-   std::unique_ptr<LinearForm> int_sigmoid_psi;
-#ifdef MFEM_USE_MPI
-   ParGridFunction *par_psi = dynamic_cast<ParGridFunction *>(&psi);
-   if (par_psi)
-   {
-      int_sigmoid_psi.reset(new ParLinearForm(par_psi->ParFESpace()));
-   }
-   else
-   {
-      int_sigmoid_psi.reset(new LinearForm(psi.FESpace()));
-   }
-#else
-   int_sigmoid_psi.reset(new LinearForm(psi.FESpace()));
-#endif
-   int_sigmoid_psi->AddDomainIntegrator(new DomainLFIntegrator(sigmoid_psi));
-
-   y = a;
-   int_sigmoid_psi->Assemble();
-   real_t f_a = int_sigmoid_psi->Sum();  // f_a := f(a) + θ vol(Ω)
-
-   y = b;
-   int_sigmoid_psi->Assemble();
-   real_t f_b = int_sigmoid_psi->Sum();  // f_b := f(b) + θ vol(Ω)
-#ifdef MFEM_USE_MPI
-   if (pfes)
-   {
-      MPI_Allreduce(MPI_IN_PLACE, &f_a, 1, MPITypeMap<real_t>::mpi_type,
-                    MPI_SUM, MPI_COMM_WORLD);
-      MPI_Allreduce(MPI_IN_PLACE, &f_b, 1, MPITypeMap<real_t>::mpi_type,
-                    MPI_SUM, MPI_COMM_WORLD);
-   }
-#endif
-   f_a -= target_volume; // f_a := f(a)
-   f_b -= target_volume; // f_b := f(b)
-   real_t c = 0.0;
-   real_t f_c = 0.0;
-   int side = 0;
-
-   bool done = false;
-   for (int k=0; k < max_its; k++)
-   {
-      c = (f_a * b - f_b * a) / (f_a - f_b);
-
-      if (abs(b - a) < tol * abs(b + a)) { done = true; break; }
-
-      y = c;
-      int_sigmoid_psi->Assemble();
-      f_c = int_sigmoid_psi->Sum(); // f_c := f(c) + θ vol(Ω)
-#ifdef MFEM_USE_MPI
-      if (pfes)
-      {
-         MPI_Allreduce(MPI_IN_PLACE, &f_c, 1, MPITypeMap<real_t>::mpi_type,
-                       MPI_SUM, MPI_COMM_WORLD);
-      }
-#endif
-      f_c -= target_volume; // f_c := f(c)
-
-      if (f_c * f_b > 0)
-      {
-         b = c;
-         f_b = f_c;
-         if (side == -1) { f_a /= 2.0; }
-         side = -1;
-      }
-      else if (f_c * f_a > 0)
-      {
-         a = c;
-         f_a = f_c;
-         if (side == 1) { f_b /= 2.0; }
-         side = 1;
-      }
-      else
-      {
-         done = true; break;
-      }
-   }
-   if (!done)
-   {
-      mfem_warning("Projection reached maximum iteration without converging. "
-                   "Result may not be accurate.");
-   }
-   y = 0.0;
-   psi += c;
-   int_sigmoid_psi->Assemble();
-   real_t material_volume = int_sigmoid_psi->Sum();
-#ifdef MFEM_USE_MPI
-   if (pfes)
-   {
-      MPI_Allreduce(MPI_IN_PLACE, &material_volume, 1,
-                    MPITypeMap<real_t>::mpi_type, MPI_SUM, MPI_COMM_WORLD);
-   }
-#endif
-   return material_volume;
-}
 
 // Poisson solver
 
@@ -551,8 +422,12 @@ void DiffusionSolver::SetupFEM()
    }
 }
 
-void DiffusionSolver::UpdateEssentialTDofs()
+void DiffusionSolver::Solve()
 {
+   OperatorPtr A;
+   Vector B, X;
+   Array<int> ess_tdof_list;
+
 #ifdef MFEM_USE_MPI
    if (parallel)
    {
@@ -565,39 +440,7 @@ void DiffusionSolver::UpdateEssentialTDofs()
 #else
    fes->GetEssentialTrueDofs(ess_bdr,ess_tdof_list);
 #endif
-}
-
-void DiffusionSolver::AssembleDiffusionBilinear(bool update_ess_tdofs)
-{
-   if (update_ess_tdofs)
-   {
-      UpdateEssentialTDofs();
-   }
-#ifdef MFEM_USE_MPI
-   if (parallel)
-   {
-      a = new ParBilinearForm(pfes);
-   }
-   else
-   {
-      a = new BilinearForm(fes);
-   }
-#else
-   a = new BilinearForm(fes);
-#endif
-   a->AddDomainIntegrator(new DiffusionIntegrator(*diffcf));
-   if (masscf)
-   {
-      a->AddDomainIntegrator(new MassIntegrator(*masscf));
-   }
-   a->Assemble();
-   a->FormSystemMatrix(ess_tdof_list, A);
-}
-
-void DiffusionSolver::Solve()
-{
-   Vector B, X;
-
+   *u=0.0;
    if (b)
    {
       delete b;
@@ -632,33 +475,31 @@ void DiffusionSolver::Solve()
 
    b->Assemble();
 
-   *u=0.0;
-   if (essbdr_cf)
-   {
-      u->ProjectBdrCoefficient(*essbdr_cf,ess_bdr);
-   }
+   BilinearForm * a = nullptr;
 
 #ifdef MFEM_USE_MPI
    if (parallel)
    {
-      X.SetSize(pfes->TrueVSize());
-      B.SetSize(pfes->TrueVSize());
-      dynamic_cast<ParGridFunction*>(u)->ParallelAssemble(X);
-      dynamic_cast<ParLinearForm*>(b)->ParallelAssemble(B);
-      dynamic_cast<ParBilinearForm*>(a)->ParallelEliminateTDofsInRHS(
-         ess_tdof_list, X, B);
+      a = new ParBilinearForm(pfes);
    }
    else
    {
-      X.NewDataAndSize(u->GetData(), u->Size());
-      B.NewDataAndSize(b->GetData(), b->Size());
-      a->EliminateVDofsInRHS(ess_tdof_list, X, B);
+      a = new BilinearForm(fes);
    }
 #else
-   X.NewDataAndSize(u->GetData(), u->Size());
-   B.NewDataAndSize(b->GetData(), b->Size());
-   a->EliminateVDofsInRHS(ess_tdof_list, X, B);
+   a = new BilinearForm(fes);
 #endif
+   a->AddDomainIntegrator(new DiffusionIntegrator(*diffcf));
+   if (masscf)
+   {
+      a->AddDomainIntegrator(new MassIntegrator(*masscf));
+   }
+   a->Assemble();
+   if (essbdr_cf)
+   {
+      u->ProjectBdrCoefficient(*essbdr_cf,ess_bdr);
+   }
+   a->FormLinearSystem(ess_tdof_list, *u, *b, A, X, B);
 
    CGSolver * cg = nullptr;
    Solver * M = nullptr;
@@ -687,6 +528,7 @@ void DiffusionSolver::Solve()
    delete M;
    delete cg;
    a->RecoverFEMSolution(X, *b, *u);
+   delete a;
 }
 
 GridFunction * DiffusionSolver::GetFEMSolution()
@@ -718,8 +560,6 @@ DiffusionSolver::~DiffusionSolver()
 #endif
    delete fec; fec = nullptr;
    delete b;
-   A.Clear();
-   delete a;
 }
 
 

examples/ex37p.cpp

@@ -4,8 +4,8 @@
 //
 // Sample runs:
 //    mpirun -np 4 ex37p -alpha 10 -pv
-//    mpirun -np 4 ex37p -lambda 0.1 -mu 0.1 -growth 1
-//    mpirun -np 4 ex37p -o 2 -alpha 10.0 -mi 50 -vf 0.4 -ntol 1e-5 -growth 1.5
+//    mpirun -np 4 ex37p -lambda 0.1 -mu 0.1
+//    mpirun -np 4 ex37p -o 2 -alpha 5.0 -mi 50 -vf 0.4 -ntol 1e-5
 //    mpirun -np 4 ex37p -r 6 -o 2 -alpha 10.0 -epsilon 0.02 -mi 50 -ntol 1e-5
 //
 // Description: This example code demonstrates the use of MFEM to solve a
@@ -54,6 +54,61 @@
 using namespace std;
 using namespace mfem;
 
+/**
+ * @brief Bregman projection of ρ = sigmoid(ψ) onto the subspace
+ *        ∫_Ω ρ dx = θ vol(Ω) as follows:
+ *
+ *        1. Compute the root of the R → R function
+ *            f(c) = ∫_Ω sigmoid(ψ + c) dx - θ vol(Ω)
+ *        2. Set ψ ← ψ + c.
+ *
+ * @param psi a GridFunction to be updated
+ * @param target_volume θ vol(Ω)
+ * @param tol Newton iteration tolerance
+ * @param max_its Newton maximum iteration number
+ * @return real_t Final volume, ∫_Ω sigmoid(ψ)
+ */
+real_t proj(ParGridFunction &psi, real_t target_volume, real_t tol=1e-12,
+            int max_its=10)
+{
+   MappedGridFunctionCoefficient sigmoid_psi(&psi, sigmoid);
+   MappedGridFunctionCoefficient der_sigmoid_psi(&psi, der_sigmoid);
+
+   ParLinearForm int_sigmoid_psi(psi.ParFESpace());
+   int_sigmoid_psi.AddDomainIntegrator(new DomainLFIntegrator(sigmoid_psi));
+   ParLinearForm int_der_sigmoid_psi(psi.ParFESpace());
+   int_der_sigmoid_psi.AddDomainIntegrator(new DomainLFIntegrator(
+                                              der_sigmoid_psi));
+   bool done = false;
+   for (int k=0; k<max_its; k++) // Newton iteration
+   {
+      int_sigmoid_psi.Assemble(); // Recompute f(c) with updated ψ
+      real_t f = int_sigmoid_psi.Sum();
+      MPI_Allreduce(MPI_IN_PLACE, &f, 1, MPITypeMap<real_t>::mpi_type,
+                    MPI_SUM, MPI_COMM_WORLD);
+      f -= target_volume;
+
+      int_der_sigmoid_psi.Assemble(); // Recompute df(c) with updated ψ
+      real_t df = int_der_sigmoid_psi.Sum();
+      MPI_Allreduce(MPI_IN_PLACE, &df, 1, MPITypeMap<real_t>::mpi_type,
+                    MPI_SUM, MPI_COMM_WORLD);
+
+      const real_t dc = -f/df;
+      psi += dc;
+      if (abs(dc) < tol) { done = true; break; }
+   }
+   if (!done)
+   {
+      mfem_warning("Projection reached maximum iteration without converging. "
+                   "Result may not be accurate.");
+   }
+   int_sigmoid_psi.Assemble();
+   real_t material_volume = int_sigmoid_psi.Sum();
+   MPI_Allreduce(MPI_IN_PLACE, &material_volume, 1,
+                 MPITypeMap<real_t>::mpi_type, MPI_SUM, MPI_COMM_WORLD);
+   return material_volume;
+}
+
 /*
  * ---------------------------------------------------------------
  *                      ALGORITHM PREAMBLE
@@ -138,11 +193,10 @@ int main(int argc, char *argv[])
    int ref_levels = 5;
    int order = 2;
    real_t alpha = 1.0;
-   real_t growth = 2;
    real_t epsilon = 0.01;
    real_t vol_fraction = 0.5;
    int max_it = 1e3;
-   real_t itol = 1e-2;
+   real_t itol = 1e-1;
    real_t ntol = 1e-4;
    real_t rho_min = 1e-6;
    real_t lambda = 1.0;
@@ -157,8 +211,6 @@ int main(int argc, char *argv[])
                   "Order (degree) of the finite elements.");
    args.AddOption(&alpha, "-alpha", "--alpha-step-length",
                   "Step length for gradient descent.");
-   args.AddOption(&growth, "-growth", "--alpha-growth-rate",
-                  "Growth rate of step length for gradient descent.");
    args.AddOption(&epsilon, "-epsilon", "--epsilon-thickness",
                   "Length scale for ρ.");
    args.AddOption(&max_it, "-mi", "--max-it",
@@ -307,7 +359,6 @@ int main(int argc, char *argv[])
    }
    FilterSolver->SetEssentialBoundary(ess_bdr_filter);
    FilterSolver->SetupFEM();
-   FilterSolver->AssembleDiffusionBilinear();
 
    ParBilinearForm mass(&control_fes);
    mass.AddDomainIntegrator(new InverseIntegrator(new MassIntegrator(one)));
@@ -361,7 +412,7 @@ int main(int argc, char *argv[])
    // 11. Iterate:
    for (int k = 1; k <= max_it; k++)
    {
-      if (k > 1) { alpha = std::pow((real_t) k,growth); }
+      if (k > 1) { alpha *= ((real_t) k) / ((real_t) k-1); }
 
       if (myid == 0)
       {
@@ -401,9 +452,7 @@ int main(int argc, char *argv[])
 
       // Step 5 - Update design variable ψ ← proj(ψ - αG)
       psi.Add(-alpha, grad);
-      ParGridFunction alpha_grad(grad);
-      alpha_grad *= alpha;
-      const real_t material_volume = proj(psi, alpha_grad, target_volume);
+      const real_t material_volume = proj(psi, target_volume);
 
       // Compute ||ρ - ρ_old|| in control fes.
       real_t norm_increment = zerogf.ComputeL1Error(succ_diff_rho);

examples/ex4.cpp

@@ -9,7 +9,6 @@
 //               ex4 -m ../data/beam-hex.mesh -o 2 -pa
 //               ex4 -m ../data/escher.mesh
 //               ex4 -m ../data/fichera.mesh -o 2 -hb
-//               ex4 -m ../data/fichera.mesh -o 2 -hb -ea
 //               ex4 -m ../data/fichera-q2.vtk
 //               ex4 -m ../data/fichera-q3.mesh -o 2 -sc
 //               ex4 -m ../data/square-disc-nurbs.mesh
@@ -19,7 +18,6 @@
 //               ex4 -m ../data/amr-quad.mesh
 //               ex4 -m ../data/amr-hex.mesh
 //               ex4 -m ../data/amr-hex.mesh -o 2 -hb
-//               ex4 -m ../data/amr-hex.mesh -o 2 -hb -ea
 //               ex4 -m ../data/fichera-amr.mesh -o 2 -sc
 //               ex4 -m ../data/ref-prism.mesh -o 1
 //               ex4 -m ../data/octahedron.mesh -o 1
@@ -27,8 +25,6 @@
 //
 // Device sample runs:
 //               ex4 -m ../data/star.mesh -pa -d cuda
-//               ex4 -m ../data/star.mesh -hb -ea -d cuda
-//               ex4 -m ../data/amr-quad.mesh -hb -ea -d cuda
 //               ex4 -m ../data/star.mesh -pa -d raja-cuda
 //               ex4 -m ../data/star.mesh -pa -d raja-omp
 //               ex4 -m ../data/beam-hex.mesh -pa -d cuda
@@ -197,7 +193,7 @@ int main(int argc, char *argv[])
    cout << "Size of linear system: " << A->Height() << endl;
 
    // 11. Solve the linear system A X = B.
-   if (!pa && (!ea || hybridization))
+   if (!pa)
    {
 #ifndef MFEM_USE_SUITESPARSE
       // Use a simple symmetric Gauss-Seidel preconditioner with PCG.

examples/ex41.cpp

@@ -1,589 +0,0 @@
-//                                MFEM Example 41
-//
-// Compile with: make ex41
-//
-// Sample runs:
-//  ex41
-//  ex41 -cg
-//  ex41 -m ../data/periodic-hexagon.mesh -p 0 -r 2 -dt 0.005 -tf 10
-//  ex41 -m ../data/periodic-square.mesh -p 1 -r 2 -dt 0.005 -tf 9
-//  ex41 -m ../data/periodic-hexagon.mesh -p 1 -r 2 -dt 0.005 -tf 9
-//  ex41 -m ../data/amr-quad.mesh -p 1 -r 2 -dt 0.002 -tf 9
-//  ex41 -m ../data/star-q3.mesh -p 1 -r 2 -dt 0.001 -tf 9
-//  ex41 -m ../data/star-mixed.mesh -p 1 -r 2 -dt 0.005 -tf 9
-//  ex41 -m ../data/disc-nurbs.mesh -p 1 -r 3 -dt 0.005 -tf 9
-//  ex41 -m ../data/disc-nurbs.mesh -p 2 -r 3 -dt 0.005 -tf 9
-//  ex41 -m ../data/periodic-square.mesh -p 3 -r 4 -dt 0.0025 -tf 9 -vs 20
-//  ex41 -m ../data/periodic-cube.mesh -p 0 -r 2 -o 2 -dt 0.01 -tf 8
-//
-// Device sample runs:
-//
-// Description:  This example code solves the time-dependent advection-diffusion
-//               equation du/dt + v.grad(u) - a div(grad(u)) = 0, where v is a
-//               given fluid velocity, a is the diffusion coefficient, and
-//               u0(x)=u(0,x) is a given initial condition.
-//
-//               The example demonstrates the use of Discontinuous Galerkin (DG)
-//               bilinear forms in MFEM (face integrators), and the use of IMEX
-//               ODE time integrators.
-//
-//               The option to use continuous finite elements is available too.
-
-#include "mfem.hpp"
-
-using namespace std;
-using namespace mfem;
-
-// Mesh bounding box
-Vector bb_min, bb_max;
-
-// Velocity coefficient
-template<int problem=0>
-void velocity_function(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-
-   // map to the reference [-1,1] domain
-   Vector X(dim);
-   for (int i = 0; i < dim; i++)
-   {
-      real_t center = (bb_min[i] + bb_max[i]) * 0.5;
-      X(i) = 2 * (x(i) - center) / (bb_max[i] - bb_min[i]);
-   }
-   switch (problem)
-   {
-      case 0:
-      {
-         // Translations in 1D, 2D, and 3D
-         switch (dim)
-         {
-            case 1: v(0) = 1.0; break;
-            case 2: v(0) = sqrt(2./3.); v(1) = sqrt(1./3.); break;
-            case 3: v(0) = sqrt(3./6.); v(1) = sqrt(2./6.); v(2) = sqrt(1./6.);
-               break;
-         }
-         break;
-      }
-      case 1:
-      case 2:
-      {
-         // Clockwise rotation in 2D around the origin
-         const real_t w = M_PI/2;
-         switch (dim)
-         {
-            case 1: v(0) = 1.0; break;
-            case 2: v(0) = w*X(1); v(1) = -w*X(0); break;
-            case 3: v(0) = w*X(1); v(1) = -w*X(0); v(2) = 0.0; break;
-         }
-         break;
-      }
-      case 3:
-      {
-         // Clockwise twisting rotation in 2D around the origin
-         const real_t w = M_PI/2;
-         real_t d = max((X(0)+1.)*(1.-X(0)),0.) * max((X(1)+1.)*(1.-X(1)),0.);
-         d = d*d;
-         switch (dim)
-         {
-            case 1: v(0) = 1.0; break;
-            case 2: v(0) = d*w*X(1); v(1) = -d*w*X(0); break;
-            case 3: v(0) = d*w*X(1); v(1) = -d*w*X(0); v(2) = 0.0; break;
-         }
-         break;
-      }
-   }
-}
-
-// Initial condition
-template<int problem=0>
-real_t u0_function(const Vector &x)
-{
-   int dim = x.Size();
-
-   // map to the reference [-1,1] domain
-   Vector X(dim);
-   for (int i = 0; i < dim; i++)
-   {
-      real_t center = (bb_min[i] + bb_max[i]) * 0.5;
-      X(i) = 2 * (x(i) - center) / (bb_max[i] - bb_min[i]);
-   }
-
-   switch (problem)
-   {
-      case 0:
-      case 1:
-      {
-         switch (dim)
-         {
-            case 1:
-               return exp(-40.*pow(X(0)-0.5,2));
-            case 2:
-            case 3:
-            {
-               real_t rx = 0.45, ry = 0.25, cx = 0., cy = -0.2, w = 10.;
-               if (dim == 3)
-               {
-                  const real_t s = (1. + 0.25*cos(2*M_PI*X(2)));
-                  rx *= s;
-                  ry *= s;
-               }
-               return ( std::erfc(w*(X(0)-cx-rx))*std::erfc(-w*(X(0)-cx+rx)) *
-                        std::erfc(w*(X(1)-cy-ry))*std::erfc(-w*(X(1)-cy+ry)) )/16;
-            }
-         }
-      }
-      case 2:
-      {
-         real_t x_ = X(0), y_ = X(1), rho, phi;
-         rho = std::hypot(x_, y_);
-         phi = atan2(y_, x_);
-         return pow(sin(M_PI*rho),2)*sin(3*phi);
-      }
-      case 3:
-      {
-         const real_t f = M_PI;
-         return sin(f*X(0))*sin(f*X(1));
-      }
-   }
-   return 0.0;
-}
-
-/// Solver for the implicit part of the ODE (the diffusion term).
-/// Solves systems of the form: (M + dt*S) k = rhs.
-class Implicit_Solver : public Solver
-{
-private:
-   SparseMatrix &M, &S, A;
-   CGSolver linear_solver;
-   BlockILU prec;
-   real_t dt;
-public:
-   Implicit_Solver(SparseMatrix &M_, SparseMatrix &S_,
-                   const FiniteElementSpace &fes)
-      : M(M_),
-        S(S_),
-        prec(fes.GetTypicalFE()->GetDof(),
-             BlockILU::Reordering::MINIMUM_DISCARDED_FILL),
-        dt(1.0)
-   {
-      linear_solver.iterative_mode = false;
-      linear_solver.SetRelTol(1e-9);
-      linear_solver.SetAbsTol(0.0);
-      linear_solver.SetMaxIter(100);
-      linear_solver.SetPrintLevel(0);
-      linear_solver.SetPreconditioner(prec);
-   }
-
-   void SetTimeStep(real_t dt_)
-   {
-      real_t ddt = dt-dt_;
-
-      real_t epsilon;
-      epsilon = std::numeric_limits<real_t>::epsilon();
-      epsilon*=10;
-
-      if (std::abs(ddt) > epsilon)
-      {
-         dt = dt_;
-         // Form operator A = M + dt*S
-         A = S;
-         A *= dt;
-         A += M;
-
-         // this will also call SetOperator on the preconditioner
-         linear_solver.SetOperator(A);
-      }
-   }
-
-   void SetOperator(const Operator &op) override
-   {
-      linear_solver.SetOperator(op);
-   }
-
-   void Mult(const Vector &x, Vector &y) const override
-   {
-      linear_solver.Mult(x, y);
-   }
-};
-
-/** A time-dependent operator for the right-hand side of the ODE. The weak
-    form of the advection-diffusion equation is M du/dt = K u - S u + b,
-    where M is the mass matrix, K and S are the advection and diffusion
-    matrices, and b describes the flow on the boundary. In the case of IMEX
-    evolution, the diffusion term is treated implicitly, and the advection
-    term is treated explicitly.  */
-class IMEX_Evolution : public TimeDependentOperator
-{
-private:
-   BilinearForm &M, &K, &S;
-   const Vector &b;
-   unique_ptr<Solver> M_prec;
-   CGSolver M_solver;
-   unique_ptr<Implicit_Solver> implicit_solver;
-
-   mutable Vector z;
-
-public:
-   IMEX_Evolution(BilinearForm &M_, BilinearForm &K_, BilinearForm &S_,
-                  const Vector &b_);
-
-   /// Evaluate k1=M^{-1}*G1(u,t); -> k1 = M^{-1}*(K*u + b)
-   void Mult1(const Vector &x, Vector &y) const;
-
-   /// Evaluate k2: M*k2 = G2(u+k2*dt,t); -> (M+S*dt)*k2=-S*u
-   void ImplicitSolve2(const real_t dt, const Vector &x, Vector &k);
-
-   void Mult(const Vector &x, Vector &y) const override
-   {
-      if (TimeDependentOperator::EvalMode::ADDITIVE_TERM_1 == GetEvalMode())
-      {
-         Mult1(x,y);
-      }
-      else
-      {
-         mfem_error("TimeDependentOperator::Mult() is not overridden!");
-      }
-   }
-
-   void ImplicitSolve(const real_t dt, const Vector &x, Vector &k) override
-   {
-      if (TimeDependentOperator::EvalMode::ADDITIVE_TERM_2 == GetEvalMode())
-      {
-         ImplicitSolve2(dt,x,k);
-      }
-      else
-      {
-         mfem_error("TimeDependentOperator::ImplicitSolve() is not overridden!");
-      }
-   }
-
-};
-
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   int problem = 0;
-   const char *mesh_file = "../data/periodic-square.mesh";
-   int ref_levels = 2;
-   int order = 3;
-   int ode_solver_type = 64; //IMEXRK3(3,4,3)
-   real_t t_final = 10.0;
-   real_t dt = 0.01;
-   bool paraview = false;
-   bool cg = false;
-   int vis_steps = 50;
-   real_t diffusion_term = 0.01;
-   real_t kappa = -1.0;
-   real_t sigma = -1.0;
-   bool visualization = true;
-   bool visit = false;
-   bool binary = false;
-   int precision = 8;
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh", "Mesh file to use.");
-   args.AddOption(&problem, "-p", "--problem",
-                  "Problem setup to use. See options in velocity_function().");
-   args.AddOption(&ref_levels, "-r", "--refine",
-                  "Number of times to refine the mesh uniformly.");
-   args.AddOption(&order, "-o", "--order", "Order of the finite elements.");
-   args.AddOption(&ode_solver_type, "-s", "--ode-solver",
-                  ODESolver::IMEXTypes.c_str());
-   args.AddOption(&t_final, "-tf", "--t-final", "Final time; start time is 0.");
-   args.AddOption(&dt, "-dt", "--time-step", "Time step.");
-   args.AddOption(&diffusion_term, "-dc", "--diffusion-coeff",
-                  "Diffusion coefficient in the PDE.");
-   args.AddOption(&paraview, "-paraview", "--paraview-datafiles", "-no-paraview",
-                  "--no-paraview-datafiles",
-                  "Save data files for ParaView (paraview.org) visualization.");
-   args.AddOption(&vis_steps, "-vs", "--visualization-steps",
-                  "Visualize every n-th timestep.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&binary, "-binary", "--binary-datafiles", "-ascii",
-                  "--ascii-datafiles",
-                  "Use binary (Sidre) or ascii format for VisIt data files.");
-   args.AddOption(&visit, "-visit", "--visit-datafiles", "-no-visit",
-                  "--no-visit-datafiles",
-                  "Save data files for VisIt (visit.llnl.gov) visualization.");
-   args.AddOption(&cg, "-cg", "--continuous-galerkin", "-dg",
-                  "--discontinuous-galerkin",
-                  "Use Continuous-Galerkin Finite elements (Default is DG)");
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   if (kappa < 0)
-   {
-      kappa = (order+1)*(order+1);
-   }
-   args.PrintOptions(cout);
-
-   // 2. Read the mesh from the given mesh file. We can handle geometrically
-   //    periodic meshes in this code.
-   Mesh mesh(mesh_file);
-   const int dim = mesh.Dimension();
-
-   // 3. Define the IMEX (Split) ODE solver used for time integration. The IMEX
-   // solvers currently available are: 61 - Forward Backward Euler,
-   // 62 - IMEXRK2(2,2,2), 63 - IMEXRK2(2,3,2), and  64 - IMEX_DIRK_RK3.
-   unique_ptr<ODESolver> ode_solver = ODESolver::SelectIMEX(ode_solver_type);
-
-   // 4. Refine the mesh to increase the resolution. In this example we do
-   //    'ref_levels' of uniform refinement, where 'ref_levels' is a
-   //    command-line parameter.
-   for (int lev = 0; lev < ref_levels; lev++) {mesh.UniformRefinement();}
-   if (mesh.NURBSext) {mesh.SetCurvature(max(order, 1));}
-   mesh.GetBoundingBox(bb_min, bb_max, max(order, 1));
-
-   // 5. Define the discontinuous DG finite element space of the given
-   //    polynomial order on the refined mesh.
-   FiniteElementCollection *fec = NULL;
-   if (cg)
-   {
-      fec = new H1_FECollection(order, dim);
-   }
-   else
-   {
-      fec = new DG_FECollection(order, dim, BasisType::GaussLobatto);
-   }
-   FiniteElementSpace fes(&mesh, fec);
-
-   cout << "Number of unknowns: " << fes.GetVSize() << endl;
-
-   // 6. Set up and assemble the bilinear and linear forms corresponding to the
-   //    DG discretization. The DGTraceIntegrator involves integrals over mesh
-   //    interior faces.
-   std::unique_ptr<VectorFunctionCoefficient> velocity;
-   if (0==problem)
-   {
-      velocity.reset(new VectorFunctionCoefficient(dim, velocity_function<0>));
-   }
-   else if (1==problem)
-   {
-      velocity.reset(new VectorFunctionCoefficient(dim, velocity_function<1>));
-   }
-   else if (2==problem)
-   {
-      velocity.reset(new VectorFunctionCoefficient(dim, velocity_function<2>));
-   }
-   else if (3==problem)
-   {
-      velocity.reset(new VectorFunctionCoefficient(dim, velocity_function<3>));
-   }
-
-   ConstantCoefficient diff_coeff(diffusion_term);
-
-   BilinearForm m(&fes);
-   BilinearForm k(&fes);
-   BilinearForm s(&fes);
-
-   Vector b(fes.GetTrueVSize());
-   b = 0.0; //The inflow on the boundaries is set to zero.
-
-   m.AddDomainIntegrator(new MassIntegrator);
-
-   constexpr real_t alpha = -1.0;
-   k.AddDomainIntegrator(new ConvectionIntegrator(*velocity, alpha));
-
-   s.AddDomainIntegrator(new DiffusionIntegrator(diff_coeff));
-   if (!cg)
-   {
-      k.AddInteriorFaceIntegrator(new NonconservativeDGTraceIntegrator(*velocity,
-                                                                       alpha));
-      k.AddBdrFaceIntegrator(new NonconservativeDGTraceIntegrator(*velocity, alpha));
-      s.AddInteriorFaceIntegrator(new DGDiffusionIntegrator(diff_coeff, sigma,
-                                                            kappa));
-      s.AddBdrFaceIntegrator(new DGDiffusionIntegrator(diff_coeff, sigma, kappa));
-   }
-
-
-   int skip_zeros = 0;
-   m.Assemble(skip_zeros);
-   k.Assemble(skip_zeros);
-   s.Assemble(skip_zeros);
-
-   m.Finalize(skip_zeros);
-   k.Finalize(skip_zeros);
-   s.Finalize(skip_zeros);
-
-   // 7. Define the initial conditions.
-   std::unique_ptr<FunctionCoefficient> u0;
-   if (0==problem)
-   {
-      u0.reset(new FunctionCoefficient(u0_function<0>));
-   }
-   else if (1==problem)
-   {
-      u0.reset(new FunctionCoefficient(u0_function<1>));
-   }
-   else if (2==problem)
-   {
-      u0.reset(new FunctionCoefficient(u0_function<2>));
-   }
-   else if (3==problem)
-   {
-      u0.reset(new FunctionCoefficient(u0_function<3>));
-   }
-
-   GridFunction u(&fes);
-   u.ProjectCoefficient(*u0);
-
-   // Create data collection for solution output: either VisItDataCollection for
-   // ascii data files, or SidreDataCollection for binary data files.
-   DataCollection *dc = NULL;
-   if (visit)
-   {
-      if (binary)
-      {
-#ifdef MFEM_USE_SIDRE
-         dc = new SidreDataCollection("Example41", &mesh);
-#else
-         MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
-#endif
-      }
-      else
-      {
-         dc = new VisItDataCollection("Example41", &mesh);
-         dc->SetPrecision(precision);
-      }
-      dc->RegisterField("solution", &u);
-      dc->SetCycle(0);
-      dc->SetTime(0.0);
-      dc->Save();
-   }
-
-   // 8. Set up paraview visualization, if desired.
-   unique_ptr<ParaViewDataCollection> pv;
-   if (paraview)
-   {
-      pv = make_unique<ParaViewDataCollection>("Example41", &mesh);
-      pv->SetPrefixPath("ParaView");
-      pv->RegisterField("solution", &u);
-      pv->SetLevelsOfDetail(order);
-      pv->SetDataFormat(VTKFormat::BINARY);
-      pv->SetHighOrderOutput(true);
-      pv->SetCycle(0);
-      pv->SetTime(0.0);
-      pv->Save();
-   }
-
-   socketstream sout;
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      sout.open(vishost, visport);
-      if (!sout)
-      {
-         cout << "Unable to connect to GLVis server at "
-              << vishost << ':' << visport << endl;
-         visualization = false;
-         cout << "GLVis visualization disabled.\n";
-      }
-      else
-      {
-         sout.precision(precision);
-         sout << "solution\n" << mesh << u;
-         sout << "pause\n";
-         sout << flush;
-         cout << "GLVis visualization paused."
-              << " Press space (in the GLVis window) to resume it.\n";
-      }
-   }
-
-   // 9. Define the time-dependent evolution operator describing the ODE
-   //    right-hand side, and perform time-integration (looping over the time
-   //    iterations, ti, with a time-step dt).
-   IMEX_Evolution adv(m, k, s, b);
-
-   real_t t = 0.0;
-   adv.SetTime(t);
-   ode_solver->Init(adv);
-
-   bool done = false;
-   for (int ti = 0; !done; )
-   {
-      real_t dt_real = min(dt, t_final - t);
-      ode_solver->Step(u, t, dt_real);
-      ti++;
-
-      done = (t >= t_final - 1e-8*dt);
-
-      if (done || ti % vis_steps == 0)
-      {
-         cout << "time step: " << ti << ", time: " << t << endl;
-         if (paraview)
-         {
-            pv->SetCycle(ti);
-            pv->SetTime(t);
-            pv->Save();
-         }
-         if (visualization)
-         {
-            sout << "solution\n" << mesh << u << flush;
-         }
-         if (visit)
-         {
-            dc->SetCycle(ti);
-            dc->SetTime(t);
-            dc->Save();
-         }
-
-      }
-   }
-
-   delete fec;
-   return 0;
-}
-
-
-// Implementation of class IMEX_Evolution
-IMEX_Evolution::IMEX_Evolution(BilinearForm &M_, BilinearForm &K_,
-                               BilinearForm &S_, const Vector &b_)
-   : TimeDependentOperator(M_.FESpace()->GetTrueVSize()),
-     M(M_), K(K_), S(S_), b(b_), z(height)
-{
-   Array<int> ess_tdof_list;
-   if (M.GetAssemblyLevel() == AssemblyLevel::LEGACY)
-   {
-      M_prec = make_unique<DSmoother>(M.SpMat());
-      M_solver.SetOperator(M.SpMat());
-      implicit_solver = make_unique<Implicit_Solver>(M.SpMat(), S.SpMat(),
-                                                     *M.FESpace());
-   }
-   else
-   {
-      MFEM_ABORT("Implicit time integration is not supported with partial assembly");
-   }
-   M_solver.SetPreconditioner(*M_prec);
-   M_solver.iterative_mode = false;
-   M_solver.SetRelTol(1e-9);
-   M_solver.SetAbsTol(0.0);
-   M_solver.SetMaxIter(100);
-   M_solver.SetPrintLevel(0);
-}
-
-void IMEX_Evolution::Mult1(const Vector &x, Vector &y) const
-{
-   // Perform the explicit step
-   // y = M^{-1} (K x + b)
-   K.Mult(x, z);
-   z += b;
-   M_solver.Mult(z, y);
-}
-
-void IMEX_Evolution::ImplicitSolve2(const real_t dt, const Vector &x, Vector &k)
-{
-   // Perform the implicit step
-   // solve for k, k = -(M+dt S)^{-1} S x
-   MFEM_VERIFY(implicit_solver != NULL,
-               "Implicit time integration is not supported with partial assembly");
-   S.Mult(x, z);
-   z.Neg();
-   implicit_solver->SetTimeStep(dt);
-   implicit_solver->Mult(z, k);
-}

examples/ex41p.cpp

@@ -1,737 +0,0 @@
-//                                MFEM Example 41 - Parallel Version
-//
-// Compile with: make ex41p
-//
-// Sample runs:
-//  mpirun -np 4 ex41p
-//  mpirun -np 4 ex41p -cg
-//  mpirun -np 4 ex41p -m ../data/periodic-hexagon.mesh -p 0 -dt 0.005 -tf 10
-//  mpirun -np 4 ex41p -m ../data/periodic-square.mesh -p 1 -dt 0.005 -tf 9
-//  mpirun -np 4 ex41p -m ../data/periodic-hexagon.mesh -p 1  -dt 0.005 -tf 9
-//  mpirun -np 4 ex41p -m ../data/star-q3.mesh -p 1 -rp 1 -dt 0.001 -tf 9
-//  mpirun -np 4 ex41p -m ../data/disc-nurbs.mesh -p 1 -rp 1 -dt 0.005 -tf 9
-//  mpirun -np 4 ex41p -m ../data/disc-nurbs.mesh -p 2 -rp 1 -dt 0.005 -tf 9
-//  mpirun -np 4 ex41p -m ../data/periodic-square.mesh -rp 2 -dt 0.0025 -tf 9 -vs 20
-//  mpirun -np 4 ex41p -m ../data/periodic-cube.mesh -p 0 -rs 2 -o 2 -dt 0.01 -tf 8
-//
-// Device sample runs:
-//
-// Description:  This example code solves the time-dependent advection-diffusion
-//               equation du/dt + v.grad(u) - a div(grad(u)) = 0, where v is a
-//               given fluid velocity, a is the diffusion coefficient, and
-//               u0(x)=u(0,x) is a given initial condition.
-//
-//               The example demonstrates the use of Discontinuous Galerkin (DG)
-//               bilinear forms in MFEM (face integrators), DG-LOR Preconditioning
-//               and the use of IMEX ODE time integrators.
-//
-//               The Option to use Continuous Finite Elements is available too.
-
-#include "mfem.hpp"
-
-using namespace std;
-using namespace mfem;
-
-// Mesh bounding box
-Vector bb_min, bb_max;
-
-// Velocity coefficient
-template<int problem=0>
-void velocity_function(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-
-   // map to the reference [-1,1] domain
-   Vector X(dim);
-   for (int i = 0; i < dim; i++)
-   {
-      real_t center = (bb_min[i] + bb_max[i]) * 0.5;
-      X(i) = 2 * (x(i) - center) / (bb_max[i] - bb_min[i]);
-   }
-   switch (problem)
-   {
-      case 0:
-      {
-         // Translations in 1D, 2D, and 3D
-         switch (dim)
-         {
-            case 1: v(0) = 1.0; break;
-            case 2: v(0) = sqrt(2./3.); v(1) = sqrt(1./3.); break;
-            case 3: v(0) = sqrt(3./6.); v(1) = sqrt(2./6.); v(2) = sqrt(1./6.);
-               break;
-         }
-         break;
-      }
-      case 1:
-      case 2:
-      {
-         // Clockwise rotation in 2D around the origin
-         const real_t w = M_PI/2;
-         switch (dim)
-         {
-            case 1: v(0) = 1.0; break;
-            case 2: v(0) = w*X(1); v(1) = -w*X(0); break;
-            case 3: v(0) = w*X(1); v(1) = -w*X(0); v(2) = 0.0; break;
-         }
-         break;
-      }
-      case 3:
-      {
-         // Clockwise twisting rotation in 2D around the origin
-         const real_t w = M_PI/2;
-         real_t d = max((X(0)+1.)*(1.-X(0)),0.) * max((X(1)+1.)*(1.-X(1)),0.);
-         d = d*d;
-         switch (dim)
-         {
-            case 1: v(0) = 1.0; break;
-            case 2: v(0) = d*w*X(1); v(1) = -d*w*X(0); break;
-            case 3: v(0) = d*w*X(1); v(1) = -d*w*X(0); v(2) = 0.0; break;
-         }
-         break;
-      }
-   }
-}
-
-
-// Initial condition
-template<int problem=0>
-real_t u0_function(const Vector &x)
-{
-   int dim = x.Size();
-
-   // map to the reference [-1,1] domain
-   Vector X(dim);
-   for (int i = 0; i < dim; i++)
-   {
-      real_t center = (bb_min[i] + bb_max[i]) * 0.5;
-      X(i) = 2 * (x(i) - center) / (bb_max[i] - bb_min[i]);
-   }
-
-   switch (problem)
-   {
-      case 0:
-      case 1:
-      {
-         switch (dim)
-         {
-            case 1:
-               return exp(-40.*pow(X(0)-0.5,2));
-            case 2:
-            case 3:
-            {
-               real_t rx = 0.45, ry = 0.25, cx = 0., cy = -0.2, w = 10.;
-               if (dim == 3)
-               {
-                  const real_t s = (1. + 0.25*cos(2*M_PI*X(2)));
-                  rx *= s;
-                  ry *= s;
-               }
-               return ( std::erfc(w*(X(0)-cx-rx))*std::erfc(-w*(X(0)-cx+rx)) *
-                        std::erfc(w*(X(1)-cy-ry))*std::erfc(-w*(X(1)-cy+ry)) )/16;
-            }
-         }
-      }
-      case 2:
-      {
-         real_t x_ = X(0), y_ = X(1), rho, phi;
-         rho = std::hypot(x_, y_);
-         phi = atan2(y_, x_);
-         return pow(sin(M_PI*rho),2)*sin(3*phi);
-      }
-      case 3:
-      {
-         const real_t f = M_PI;
-         return sin(f*X(0))*sin(f*X(1));
-      }
-   }
-   return 0.0;
-}
-
-
-class Implicit_Solver : public Solver
-{
-private:
-   HypreParMatrix &M, &S;
-   HypreParMatrix *A;
-   CGSolver linear_solver;
-   real_t dt;
-   SparseMatrix M_diag;
-public:
-   Implicit_Solver(HypreParMatrix &M_, HypreParMatrix &S_,
-                   const FiniteElementSpace &fes)
-      : M(M_),
-        S(S_),
-        A(nullptr),
-        linear_solver(M.GetComm()),
-        dt(1.0)
-   {
-      linear_solver.iterative_mode = false;
-      linear_solver.SetRelTol(1e-9);
-      linear_solver.SetAbsTol(0.0);
-      linear_solver.SetMaxIter(100);
-      linear_solver.SetPrintLevel(0);
-
-      M.GetDiag(M_diag);
-   }
-
-   void SetTimeStep(real_t dt_)
-   {
-      real_t ddt = dt-dt_;
-
-      // syncronize ddt across all processes
-      MPI_Comm comm = M.GetComm();
-      int myrank;
-      MPI_Comm_rank(comm, &myrank);
-      MPI_Bcast(&ddt, 1, MPI_DOUBLE, 0, comm);
-
-      real_t epsilon;
-      epsilon = std::numeric_limits<real_t>::epsilon();
-      // allow for some tolerance in the time stepping process
-      epsilon*=10;
-
-      if (fabs(ddt) > epsilon)
-      {
-         if (0==myrank)
-         {
-            cout << "Updating Implicit_Solver time step from " << dt
-                 << " to " << dt_ << endl;
-         }
-
-         delete A;
-         dt = dt_;
-         // Form operator A = M + dt*S
-         A = Add(dt, S, 1.0, M);
-         linear_solver.SetOperator(*A);
-      }
-   }
-
-   void SetOperator(const Operator &op) override
-   {
-      linear_solver.SetOperator(op);
-   }
-
-   void Mult(const Vector &x, Vector &y) const override
-   {
-      linear_solver.Mult(x, y);
-   }
-
-   void SetPreconditioner(Solver &precond)
-   {
-      linear_solver.SetPreconditioner(precond);
-   }
-
-   ~Implicit_Solver() override
-   {
-      delete A;
-   }
-};
-
-/** A time-dependent operator for the right-hand side of the ODE. The DG weak
-    form of the advection-diffusion equation is (M + dt S) du/dt = Su - K u + b
-    , where M and K are the mass and advection matrices, and b describes the
-    flow on the boundary. In the case of IMEX evolution, the diffusion term is
-    treated implicitly, and the advection term is treated explicitly.  */
-class IMEX_Evolution : public TimeDependentOperator
-{
-private:
-   OperatorHandle M, K, S, A;
-   const Vector &b;
-   Solver *M_prec;
-   CGSolver M_solver;
-   Implicit_Solver *implicit_solver;
-   LORSolver<HypreBoomerAMG>* lor_solver;
-
-   mutable Vector z;
-   mutable Vector w;
-
-public:
-   IMEX_Evolution(ParBilinearForm &M_, ParBilinearForm &K_, ParBilinearForm &S_,
-                  const Vector &b_, ParBilinearForm &A_);
-
-   virtual
-   ~IMEX_Evolution()
-   {
-      delete implicit_solver;
-      delete lor_solver;
-      delete M_prec;
-   }
-
-   void Mult1(const Vector &x, Vector &y) const;
-
-   void ImplicitSolve2(const real_t dt, const Vector &x, Vector &k);
-
-   void Mult(const Vector &x, Vector &y) const override
-   {
-      if (TimeDependentOperator::EvalMode::ADDITIVE_TERM_1 == GetEvalMode())
-      {
-         Mult1(x,y);
-      }
-      else
-      {
-         mfem_error("TimeDependentOperator::Mult() is not overridden!");
-      }
-   }
-
-   void ImplicitSolve(const real_t dt, const Vector &x, Vector &k) override
-   {
-      if (TimeDependentOperator::EvalMode::ADDITIVE_TERM_2 == GetEvalMode())
-      {
-         ImplicitSolve2(dt,x,k);
-      }
-      else
-      {
-         mfem_error("TimeDependentOperator::ImplicitSolve() is not overridden!");
-      }
-   }
-};
-
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI and HYPRE.
-   Mpi::Init();
-   int num_procs = Mpi::WorldSize();
-   int myid = Mpi::WorldRank();
-   Hypre::Init();
-
-   // 2. Parse command-line options.
-   int problem = 0;
-   const char *mesh_file = "../data/periodic-square.mesh";
-   int ser_ref_levels = 2;
-   int par_ref_levels = 0;
-   int order = 3;
-   int ode_solver_type = 64; // 61 - Forward Backward Euler
-   // 62 - IMEXRK2(2,2,2)
-   // 63 - IMEXRK2(2,3,2)
-   // 64 - IMEXRK3(3,4,3)
-   real_t t_final = 10.0;
-   real_t dt = 0.01;
-   bool paraview = false;
-   bool cg = false;
-   int vis_steps = 50;
-   bool adios2 = false;
-   bool binary = false;
-   real_t diffusion_term = 0.01;
-   real_t kappa = -1.0;
-   real_t sigma = -1.0;
-   bool visualization = true;
-   bool visit = false;
-   int precision = 16;
-   cout.precision(precision);
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&problem, "-p", "--problem",
-                  "Problem setup to use. See options in velocity_function().");
-   args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
-                  "Number of times to refine the mesh uniformly in serial.");
-   args.AddOption(&par_ref_levels, "-rp", "--refine-parallel",
-                  "Number of times to refine the mesh uniformly in parallel.");
-   args.AddOption(&order, "-o", "--order",
-                  "Order (degree) of the finite elements.");
-   args.AddOption(&ode_solver_type, "-s", "--ode-solver",
-                  ODESolver::IMEXTypes.c_str());
-   args.AddOption(&t_final, "-tf", "--t-final",
-                  "Final time; start time is 0.");
-   args.AddOption(&dt, "-dt", "--time-step",
-                  "Time step.");
-   args.AddOption(&diffusion_term, "-dc", "--diffusion-coeff",
-                  "Diffusion coefficient in the PDE.");
-   args.AddOption(&paraview, "-paraview", "--paraview-datafiles", "-no-paraview",
-                  "--no-paraview-datafiles",
-                  "Save data files for ParaView (paraview.org) visualization.");
-   args.AddOption(&visit, "-visit", "--visit-datafiles", "-no-visit",
-                  "--no-visit-datafiles",
-                  "Save data files for VisIt (visit.llnl.gov) visualization.");
-   args.AddOption(&adios2, "-adios2", "--adios2-streams", "-no-adios2",
-                  "--no-adios2-streams",
-                  "Save data using adios2 streams.");
-   args.AddOption(&binary, "-binary", "--binary-datafiles", "-ascii",
-                  "--ascii-datafiles",
-                  "Use binary (Sidre) or ascii format for VisIt data files.");
-   args.AddOption(&vis_steps, "-vs", "--visualization-steps",
-                  "Visualize every n-th timestep.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&cg, "-cg", "--continuous-galerkin", "-dg",
-                  "--discontinuous-galerkin",
-                  "Use Continuous-Galerkin Finite elements (Default is DG)");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (Mpi::Root())
-      {
-         args.PrintUsage(cout);
-      }
-      return 1;
-   }
-   if (Mpi::Root())
-   {
-      args.PrintOptions(cout);
-   }
-   if (kappa < 0)
-   {
-      kappa = (order+1)*(order+1);
-   }
-
-   // 3. Read the mesh from the given mesh file. We can handle geometrically
-   //    periodic meshes in this code.
-   Mesh *mesh = new Mesh(mesh_file);
-   const int dim = mesh->Dimension();
-
-   // 4. Define the IMEX (Split) ODE solver used for time integration. The IMEX
-   // solvers currently available are: 55 - Forward Backward Euler,
-   // 56 - IMEXRK2(2,2,2), 57 - IMEXRK2(2,3,2), and
-   unique_ptr<ODESolver> ode_solver = ODESolver::SelectIMEX(ode_solver_type);
-
-   // 5. Refine the mesh to increase the resolution. In this example we do
-   //    'ref_levels' of uniform refinement, where 'ref_levels' is a
-   //    command-line parameter.
-   for (int lev = 0; lev < ser_ref_levels; lev++) { mesh->UniformRefinement(); }
-   if (mesh->NURBSext)
-   {
-      mesh->SetCurvature(max(order, 1));
-   }
-   mesh->GetBoundingBox(bb_min, bb_max, max(order, 1));
-
-
-   // 6. Define the parallel mesh by a partitioning of the serial mesh. Refine
-   //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
-   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
-   delete mesh;
-   for (int lev = 0; lev < par_ref_levels; lev++)
-   {
-      pmesh->UniformRefinement();
-   }
-
-   // 7. Define the discontinuous DG finite element space of the given
-   //    polynomial order on the refined mesh.
-   FiniteElementCollection *fec = NULL;
-   if (cg)
-   {
-      fec = new H1_FECollection(order, dim);
-   }
-   else
-   {
-      fec = new DG_FECollection(order, dim, BasisType::GaussLobatto);
-   }
-   ParFiniteElementSpace *fes = new ParFiniteElementSpace(pmesh, fec);
-
-   HYPRE_BigInt global_vSize = fes->GlobalTrueVSize();
-   if (Mpi::Root())
-   {
-      cout << "Number of unknowns: " << global_vSize << endl;
-   }
-
-   // 8. Set up and assemble the bilinear and linear forms corresponding to the
-   //    DG discretization. The DGTraceIntegrator involves integrals over mesh
-   //    interior faces.
-   std::unique_ptr<VectorFunctionCoefficient> velocity;
-   if (0==problem)
-   {
-      velocity.reset(new VectorFunctionCoefficient(dim, velocity_function<0>));
-   }
-   else if (1==problem)
-   {
-      velocity.reset(new VectorFunctionCoefficient(dim, velocity_function<1>));
-   }
-   else if (2==problem)
-   {
-      velocity.reset(new VectorFunctionCoefficient(dim, velocity_function<2>));
-   }
-   else if (3==problem)
-   {
-      velocity.reset(new VectorFunctionCoefficient(dim, velocity_function<3>));
-   }
-   ConstantCoefficient diff_coeff(diffusion_term);
-   ConstantCoefficient dt_diff_coeff(dt*diffusion_term);
-
-   ParBilinearForm *m = new ParBilinearForm(fes);
-   ParBilinearForm *k = new ParBilinearForm(fes);
-   ParBilinearForm *s = new ParBilinearForm(fes);
-
-   m->AddDomainIntegrator(new MassIntegrator());
-
-   constexpr real_t alpha = -1.0;
-   k->AddDomainIntegrator(new ConvectionIntegrator(*velocity, alpha));
-
-   s->AddDomainIntegrator(new DiffusionIntegrator(diff_coeff));
-
-   // For the preconditioner - create billinear form corresponding to
-   // operator (M + dt S)
-   ParBilinearForm *a = new ParBilinearForm(fes);
-   a->AddDomainIntegrator(new MassIntegrator);
-   a->AddDomainIntegrator(new DiffusionIntegrator(dt_diff_coeff));
-   if (!cg)
-   {
-      k->AddInteriorFaceIntegrator(new NonconservativeDGTraceIntegrator(*velocity,
-                                                                        alpha));
-      k->AddBdrFaceIntegrator(new NonconservativeDGTraceIntegrator(*velocity, alpha));
-      s->AddInteriorFaceIntegrator(new DGDiffusionIntegrator(diff_coeff, sigma,
-                                                             kappa));
-      s->AddBdrFaceIntegrator(new DGDiffusionIntegrator(diff_coeff, sigma, kappa));
-      a->AddInteriorFaceIntegrator(new DGDiffusionIntegrator(dt_diff_coeff, sigma,
-                                                             kappa));
-      a->AddBdrFaceIntegrator(new DGDiffusionIntegrator(dt_diff_coeff, sigma, kappa));
-   }
-
-   int skip_zeros = 0;
-   m->Assemble(skip_zeros);
-   k->Assemble(skip_zeros);
-   s->Assemble(skip_zeros);
-   a->Assemble();
-
-   m->Finalize(skip_zeros);
-   k->Finalize(skip_zeros);
-   s->Finalize(skip_zeros);
-   a->Finalize(skip_zeros);
-   HypreParVector b(fes);
-   b = 0.0;
-
-   // 9. Define the initial conditions. Set up visualization (if desired).
-   std::unique_ptr<FunctionCoefficient> u0;
-   if (0==problem)
-   {
-      u0.reset(new FunctionCoefficient(u0_function<0>));
-   }
-   else if (1==problem)
-   {
-      u0.reset(new FunctionCoefficient(u0_function<1>));
-   }
-   else if (2==problem)
-   {
-      u0.reset(new FunctionCoefficient(u0_function<2>));
-   }
-   else if (3==problem)
-   {
-      u0.reset(new FunctionCoefficient(u0_function<3>));
-   }
-   ParGridFunction *u = new ParGridFunction(fes);
-   u->ProjectCoefficient(*u0);
-   HypreParVector *U = u->GetTrueDofs();
-
-   DataCollection *dc = NULL;
-   if (visit)
-   {
-      if (binary)
-      {
-#ifdef MFEM_USE_SIDRE
-         dc = new SidreDataCollection("Example41-Parallel", pmesh);
-#else
-         MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
-#endif
-      }
-      else
-      {
-         dc = new VisItDataCollection("Example41-Parallel", pmesh);
-         dc->SetPrecision(precision);
-         // To save the mesh using MFEM's parallel mesh format:
-         // dc->SetFormat(DataCollection::PARALLEL_FORMAT);
-      }
-      dc->RegisterField("solution", u);
-      dc->SetCycle(0);
-      dc->SetTime(0.0);
-      dc->Save();
-   }
-   ParaViewDataCollection *pd = NULL;
-   if (paraview)
-   {
-      pd = new ParaViewDataCollection("Example41P", pmesh);
-      pd->SetPrefixPath("ParaView");
-      pd->RegisterField("solution", u);
-      pd->SetLevelsOfDetail(order);
-      pd->SetDataFormat(VTKFormat::BINARY);
-      pd->SetHighOrderOutput(true);
-      pd->SetCycle(0);
-      pd->SetTime(0.0);
-      pd->Save();
-   }
-   socketstream sout;
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      sout.open(vishost, visport);
-      if (!sout)
-      {
-         if (Mpi::Root())
-         {
-            cout << "Unable to connect to GLVis server at "
-                 << vishost << ':' << visport << endl;
-         }
-         visualization = false;
-         if (Mpi::Root())
-         {
-            cout << "GLVis visualization disabled.\n";
-         }
-      }
-      else
-      {
-         sout << "parallel " << num_procs << " " << myid << "\n";
-         sout.precision(precision);
-         sout << "solution\n" << *pmesh << *u;
-         sout << "pause\n";
-         sout << flush;
-         if (Mpi::Root())
-         {
-            cout << "GLVis visualization paused."
-                 << " Press space (in the GLVis window) to resume it.\n";
-         }
-      }
-   }
-#ifdef MFEM_USE_ADIOS2
-   ADIOS2DataCollection *adios2_dc = NULL;
-   if (adios2)
-   {
-      std::string postfix(mesh_file);
-      postfix.erase(0, std::string("../data/").size() );
-      postfix += "_o" + std::to_string(order);
-      const std::string collection_name = "ex41-p-" + postfix + ".bp";
-
-      adios2_dc = new ADIOS2DataCollection(MPI_COMM_WORLD, collection_name, pmesh);
-      // output data substreams are half the number of mpi processes
-      adios2_dc->SetParameter("SubStreams", std::to_string(num_procs/2) );
-      // adios2_dc->SetLevelsOfDetail(2);
-      adios2_dc->RegisterField("solution", u);
-      adios2_dc->SetCycle(0);
-      adios2_dc->SetTime(0.0);
-      adios2_dc->Save();
-   }
-#endif
-
-
-   // 10. Define the time-dependent evolution operator describing the
-   //     ODE right-hand side, and perform time-integration (looping
-   //     over the time iterations, ti, with a time-step dt).
-   IMEX_Evolution adv(*m, *k, *s, b, *a);
-
-   real_t t = 0.0;
-   adv.SetTime(t);
-   ode_solver->Init(adv);
-
-
-   bool done = false;
-   for (int ti = 0; !done; )
-   {
-      real_t dt_real = min(dt, t_final - t);
-      ode_solver->Step(*U, t, dt_real);
-      ti++;
-
-      done = (t >= t_final - 1e-8*dt);
-
-      if (done || ti % vis_steps == 0)
-      {
-         if (Mpi::Root())
-         {
-            cout << "time step: " << ti << ", time: " << t << endl;
-         }
-         *u = *U;
-         if (visualization)
-         {
-            sout << "parallel " << num_procs << " " << myid << "\n";
-            sout << "solution\n" << *pmesh << *u << flush;
-         }
-         if (paraview)
-         {
-            pd->SetCycle(ti);
-            pd->SetTime(t);
-            pd->Save();
-         }
-#ifdef MFEM_USE_ADIOS2
-         // transient solutions can be visualized with ParaView
-         if (adios2)
-         {
-            adios2_dc->SetCycle(ti);
-            adios2_dc->SetTime(t);
-            adios2_dc->Save();
-         }
-#endif
-      }
-   }
-
-   // 11. Free the used memory.
-   delete pd;
-   delete U;
-   delete u;
-   delete a;
-   delete s;
-   delete k;
-   delete m;
-   delete fes;
-   delete pmesh;
-   delete dc;
-   delete fec;
-
-   return 0;
-}
-
-// Implementation of class IMEX_Evolution
-IMEX_Evolution::IMEX_Evolution(ParBilinearForm &M_, ParBilinearForm &K_,
-                               ParBilinearForm &S_, const Vector &b_, ParBilinearForm &A_)
-   : TimeDependentOperator(M_.ParFESpace()->GetTrueVSize()), b(b_),
-     M_solver(M_.ParFESpace()->GetComm()), z(height), w(height)
-{
-   if (M_.GetAssemblyLevel()==AssemblyLevel::LEGACY)
-   {
-      M.Reset(M_.ParallelAssemble(), true);
-      K.Reset(K_.ParallelAssemble(), true);
-      S.Reset(S_.ParallelAssemble(), true);
-   }
-   else
-   {
-      M.Reset(&M_, false);
-      K.Reset(&K_, false);
-      S.Reset(&S_, false);
-   }
-
-   M_solver.SetOperator(*M);
-
-   Array<int> ess_tdof_list;
-   if (M_.GetAssemblyLevel() == AssemblyLevel::LEGACY)
-   {
-      A.Reset(A_.ParallelAssemble(), true);
-      HypreParMatrix &M_mat = *M.As<HypreParMatrix>();
-      HypreParMatrix &S_mat = *S.As<HypreParMatrix>();
-      HypreSmoother *hypre_prec = new HypreSmoother(M_mat, HypreSmoother::Jacobi);
-      M_prec = hypre_prec;
-
-      implicit_solver = new Implicit_Solver(M_mat, S_mat, *M_.FESpace());
-      lor_solver = new LORSolver<HypreBoomerAMG>(A_, ess_tdof_list);
-      lor_solver->GetSolver().SetSystemsOptions(A_.ParFESpace()->GetVDim(), true);
-      implicit_solver -> SetPreconditioner(*lor_solver);
-   }
-   else
-   {
-      MFEM_ABORT("Implicit time integration is not supported with partial assembly");
-   }
-   M_solver.SetPreconditioner(*M_prec);
-   M_solver.iterative_mode = false;
-   M_solver.SetRelTol(1e-9);
-   M_solver.SetAbsTol(0.0);
-   M_solver.SetMaxIter(100);
-   M_solver.SetPrintLevel(0);
-}
-
-void IMEX_Evolution::Mult1(const Vector &x, Vector &y) const
-{
-   // Perform the explicit step
-   // y = M^{-1} (K x + b)
-   K->Mult(x, z);
-   z += b;
-   M_solver.Mult(z, y);
-}
-
-void IMEX_Evolution::ImplicitSolve2(const real_t dt, const Vector &x, Vector &k)
-{
-   // Perform the implicit step
-   // solve for k, k = -(M+dt S)^{-1} S x
-   MFEM_VERIFY(implicit_solver != NULL,
-               "Implicit time integration is not supported with partial assembly");
-   S->Mult(x, z);
-   z*= -1.0;
-   implicit_solver->SetTimeStep(dt);
-   implicit_solver->Mult(z, k);
-}

examples/ex4p.cpp

@@ -9,7 +9,6 @@
 //               mpirun -np 4 ex4p -m ../data/beam-hex.mesh -o 2 -pa
 //               mpirun -np 4 ex4p -m ../data/escher.mesh -o 2 -sc
 //               mpirun -np 4 ex4p -m ../data/fichera.mesh -o 2 -hb
-//               mpirun -np 4 ex4p -m ../data/fichera.mesh -o 2 -hb -ea
 //               mpirun -np 4 ex4p -m ../data/fichera-q2.vtk
 //               mpirun -np 4 ex4p -m ../data/fichera-q3.mesh -o 2 -sc
 //               mpirun -np 4 ex4p -m ../data/square-disc-nurbs.mesh -o 3
@@ -18,18 +17,14 @@
 //               mpirun -np 4 ex4p -m ../data/periodic-cube.mesh -no-bc
 //               mpirun -np 4 ex4p -m ../data/amr-quad.mesh
 //               mpirun -np 3 ex4p -m ../data/amr-quad.mesh -o 2 -hb
-//               mpirun -np 3 ex4p -m ../data/amr-quad.mesh -o 2 -hb -ea
 //               mpirun -np 4 ex4p -m ../data/amr-hex.mesh -o 2 -sc
 //               mpirun -np 4 ex4p -m ../data/amr-hex.mesh -o 2 -hb
-//               mpirun -np 4 ex4p -m ../data/amr-hex.mesh -o 2 -hb -ea
 //               mpirun -np 4 ex4p -m ../data/ref-prism.mesh -o 1
 //               mpirun -np 4 ex4p -m ../data/octahedron.mesh -o 1
 //               mpirun -np 4 ex4p -m ../data/star-surf.mesh -o 3 -hb
 //
 // Device sample runs:
 //               mpirun -np 4 ex4p -m ../data/star.mesh -pa -d cuda
-//               mpirun -np 4 ex4p -m ../data/star.mesh -ea -hb -d cuda
-//               mpirun -np 4 ex4p -m ../data/amr-hex.mesh -ea -hb -d cuda
 //               mpirun -np 4 ex4p -m ../data/star.mesh -pa -d raja-cuda
 //               mpirun -np 4 ex4p -m ../data/star.mesh -pa -d raja-omp
 //               mpirun -np 4 ex4p -m ../data/beam-hex.mesh -pa -d cuda
@@ -235,7 +230,7 @@ int main(int argc, char *argv[])
    pcg->SetMaxIter(2000);
    pcg->SetPrintLevel(1);
    if (hybridization) { prec = new HypreBoomerAMG(*A.As<HypreParMatrix>()); }
-   else if (pa || ea) { prec = new OperatorJacobiSmoother(*a, ess_tdof_list); }
+   else if (pa) { prec = new OperatorJacobiSmoother(*a, ess_tdof_list); }
    else
    {
       ParFiniteElementSpace *prec_fespace =

examples/ex9.cpp

@@ -160,7 +160,6 @@ int main(int argc, char *argv[])
    bool paraview = false;
    bool binary = false;
    int vis_steps = 5;
-   bool solve_implicit_state = false;
 
    int precision = 8;
    cout.precision(precision);
@@ -188,9 +187,6 @@ int main(int argc, char *argv[])
                   "Final time; start time is 0.");
    args.AddOption(&dt, "-dt", "--time-step",
                   "Time step.");
-   args.AddOption(&solve_implicit_state, "-imp-state", "--implicit-state",
-                  "-imp-slope", "--implicit-slope",
-                  "Implicitly solve for stage state or slope.");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -370,11 +366,6 @@ int main(int argc, char *argv[])
    //    right-hand side, and perform time-integration (looping over the time
    //    iterations, ti, with a time-step dt).
    FE_Evolution adv(m, k, b);
-   using ImplicitVariableType = FE_Evolution::ImplicitVariableType;
-   ImplicitVariableType imp_var = solve_implicit_state ?
-                                  ImplicitVariableType::STATE
-                                  : ImplicitVariableType::SLOPE;
-   adv.SetImplicitVariableType(imp_var);
 
    real_t t = 0.0;
    adv.SetTime(t);
@@ -468,17 +459,7 @@ void FE_Evolution::ImplicitSolve(const real_t dt, const Vector &x, Vector &k)
 {
    MFEM_VERIFY(dg_solver != NULL,
                "Implicit time integration is not supported with partial assembly");
-   // Construct current right-hand side for stage state vs. slope solve
-   if (ImplicitVarTypeIsState())
-   {
-      // k, on return, is the stage value u
-      M.Mult(x, z);
-   }
-   else
-   {
-      // k, on return, is the stage slope du/dt
-      K.Mult(x, z);
-   }
+   K.Mult(x, z);
    z += b;
    dg_solver->SetTimeStep(dt);
    dg_solver->Mult(z, k);

examples/ex9p.cpp

@@ -257,7 +257,6 @@ int main(int argc, char *argv[])
    bool adios2 = false;
    bool binary = false;
    int vis_steps = 5;
-   bool solve_implicit_state = false;
 #if MFEM_HYPRE_VERSION >= 21800
    PrecType prec_type = PrecType::AIR;
 #else
@@ -291,9 +290,6 @@ int main(int argc, char *argv[])
                   "Final time; start time is 0.");
    args.AddOption(&dt, "-dt", "--time-step",
                   "Time step.");
-   args.AddOption(&solve_implicit_state, "-imp-state", "--implicit-state",
-                  "-imp-slope", "--implicit-slope",
-                  "Implicitly solve for stage state or slope.");
    args.AddOption((int *)&prec_type, "-pt", "--prec-type", "Preconditioner for "
                   "implicit solves. 0 for ILU, 1 for pAIR-AMG.");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
@@ -540,11 +536,6 @@ int main(int argc, char *argv[])
    //     right-hand side, and perform time-integration (looping over the time
    //     iterations, ti, with a time-step dt).
    FE_Evolution adv(*m, *k, *B, prec_type);
-   using ImplicitVariableType = FE_Evolution::ImplicitVariableType;
-   ImplicitVariableType imp_var = solve_implicit_state ?
-                                  ImplicitVariableType::STATE
-                                  : ImplicitVariableType::SLOPE;
-   adv.SetImplicitVariableType(imp_var);
 
    real_t t = 0.0;
    adv.SetTime(t);
@@ -685,17 +676,7 @@ FE_Evolution::FE_Evolution(ParBilinearForm &M_, ParBilinearForm &K_,
 //    (M - dt*K) d = K*u + b
 void FE_Evolution::ImplicitSolve(const real_t dt, const Vector &x, Vector &k)
 {
-   // Construct current right-hand side for stage state vs. slope solve
-   if (ImplicitVarTypeIsState())
-   {
-      // k, on return, is the stage value u
-      M->Mult(x, z);
-   }
-   else
-   {
-      // k, on return, is the stage slope du/dt
-      K->Mult(x, z);
-   }
+   K->Mult(x, z);
    z += b;
    dg_solver->SetTimeStep(dt);
    dg_solver->Mult(z, k);

examples/ginkgo/CMakeLists.txt

@@ -14,12 +14,6 @@ list(APPEND GINKGO_EXAMPLES_SRCS
   ex1.cpp
 )
 
-if (MFEM_USE_MPI AND GINKGO_BUILD_MPI)
-    list(APPEND GINKGO_EXAMPLES_SRCS
-    ex1p.cpp
-)
-endif()
-
 # Include the source directory where mfem.hpp and mfem-performance.hpp are.
 include_directories(BEFORE ${PROJECT_BINARY_DIR})
 

examples/ginkgo/ex1.cpp

@@ -207,7 +207,7 @@ int main(int argc, char *argv[])
             Ginkgo::IcPreconditioner ginkgo_precond(exec, "paric", 30);
             Ginkgo::CGSolver ginkgo_solver(exec, ginkgo_precond);
             ginkgo_solver.SetPrintLevel(print_lvl);
-            ginkgo_solver.SetRelTol(sqrt(1e-12));
+            ginkgo_solver.SetRelTol(1e-12);
             ginkgo_solver.SetAbsTol(0.0);
             ginkgo_solver.SetMaxIter(400);
             ginkgo_solver.SetOperator(*(A.Ptr()));
@@ -225,7 +225,7 @@ int main(int argc, char *argv[])
             Ginkgo::MFEMPreconditioner gko_M(exec, M);
             Ginkgo::CGSolver ginkgo_solver(exec, gko_M);
             ginkgo_solver.SetPrintLevel(print_lvl);
-            ginkgo_solver.SetRelTol(sqrt(1e-12));
+            ginkgo_solver.SetRelTol(1e-12);
             ginkgo_solver.SetAbsTol(0.0);
             ginkgo_solver.SetMaxIter(400);
             ginkgo_solver.SetOperator(*(A.Ptr()));
@@ -283,7 +283,7 @@ int main(int argc, char *argv[])
                Ginkgo::MFEMPreconditioner gko_M(exec, M);
                Ginkgo::CGSolver ginkgo_solver(exec, gko_M);
                ginkgo_solver.SetPrintLevel(print_lvl);
-               ginkgo_solver.SetRelTol(sqrt(1e-12));
+               ginkgo_solver.SetRelTol(1e-12);
                ginkgo_solver.SetAbsTol(0.0);
                ginkgo_solver.SetMaxIter(400);
                ginkgo_solver.SetOperator(*(A.Ptr()));

examples/ginkgo/ex1p.cpp

@@ -1,436 +0,0 @@
-//                       MFEM Example 1 - Parallel Version
-//                             GINKGO Modification
-//
-// Compile with: make ex1p
-//
-// Sample runs:  mpirun -np 4 ex1p -m ../data/square-disc.mesh
-//               mpirun -np 4 ex1p -m ../data/star.mesh
-//               mpirun -np 4 ex1p -m ../data/star-mixed.mesh
-//               mpirun -np 4 ex1p -m ../data/escher.mesh
-//               mpirun -np 4 ex1p -m ../data/fichera.mesh
-//               mpirun -np 4 ex1p -m ../data/fichera-mixed.mesh
-//               mpirun -np 4 ex1p -m ../data/toroid-wedge.mesh
-//               mpirun -np 4 ex1p -m ../data/octahedron.mesh -o 1
-//               mpirun -np 4 ex1p -m ../data/periodic-annulus-sector.msh
-//               mpirun -np 4 ex1p -m ../data/periodic-torus-sector.msh
-//               mpirun -np 4 ex1p -m ../data/square-disc-p2.vtk -o 2
-//               mpirun -np 4 ex1p -m ../data/square-disc-p3.mesh -o 3
-//               mpirun -np 4 ex1p -m ../data/square-disc-nurbs.mesh -o -1
-//               mpirun -np 4 ex1p -m ../data/star-mixed-p2.mesh -o 2
-//               mpirun -np 4 ex1p -m ../data/disc-nurbs.mesh -o -1
-//               mpirun -np 4 ex1p -m ../data/pipe-nurbs.mesh -o -1
-//               mpirun -np 4 ex1p -m ../data/ball-nurbs.mesh -o 2
-//               mpirun -np 4 ex1p -m ../data/fichera-mixed-p2.mesh -o 2
-//               mpirun -np 4 ex1p -m ../data/star-surf.mesh
-//               mpirun -np 4 ex1p -m ../data/square-disc-surf.mesh
-//               mpirun -np 4 ex1p -m ../data/inline-segment.mesh
-//               mpirun -np 4 ex1p -m ../data/amr-quad.mesh
-//               mpirun -np 4 ex1p -m ../data/amr-hex.mesh
-//               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh
-//               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh -o -1 -sc
-//
-// Device sample runs:
-//               mpirun -np 4 ex1p -pa -d cuda
-//               mpirun -np 4 ex1p -fa -d cuda
-//               mpirun -np 4 ex1p -pa -d occa-cuda
-//               mpirun -np 4 ex1p -pa -d raja-omp
-//               mpirun -np 4 ex1p -pa -d ceed-cpu
-//               mpirun -np 4 ex1p -pa -d ceed-cpu -o 4 -a
-//               mpirun -np 4 ex1p -pa -d ceed-cpu -m ../data/square-mixed.mesh
-//               mpirun -np 4 ex1p -pa -d ceed-cpu -m ../data/fichera-mixed.mesh
-//             * mpirun -np 4 ex1p -pa -d ceed-cuda
-//             * mpirun -np 4 ex1p -pa -d ceed-hip
-//               mpirun -np 4 ex1p -pa -d ceed-cuda:/gpu/cuda/shared
-//               mpirun -np 4 ex1p -pa -d ceed-cuda:/gpu/cuda/shared -m ../data/square-mixed.mesh
-//               mpirun -np 4 ex1p -pa -d ceed-cuda:/gpu/cuda/shared -m ../data/fichera-mixed.mesh
-//               mpirun -np 4 ex1p -m ../data/beam-tet.mesh -pa -d ceed-cpu
-//
-// Description:  This example code demonstrates the use of MFEM to define a
-//               simple finite element discretization of the Laplace problem
-//               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
-//               Specifically, we discretize using a FE space of the specified
-//               order, or if order < 1 using an isoparametric/isogeometric
-//               space (i.e. quadratic for quadratic curvilinear mesh, NURBS for
-//               NURBS mesh, etc.)
-//
-//               The example highlights the use of mesh refinement, finite
-//               element grid functions, as well as linear and bilinear forms
-//               corresponding to the left-hand side and right-hand side of the
-//               discrete linear system. We also cover the explicit elimination
-//               of essential boundary conditions, static condensation, and the
-//               optional connection to the GLVis tool for visualization.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-#ifndef MFEM_USE_GINKGO
-#error This example requires that MFEM is built with MFEM_USE_GINKGO=YES
-#endif
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI and HYPRE.
-   Mpi::Init();
-   int num_procs = Mpi::WorldSize();
-   int myid = Mpi::WorldRank();
-   Hypre::Init();
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "../../data/star.mesh";
-   int order = 1;
-   bool static_cond = false;
-   bool pa = false;
-   bool fa = false;
-   const char *device_config = "cpu";
-   bool visualization = true;
-   int solver_config = 0;
-   int print_lvl = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree) or -1 for"
-                  " isoparametric space.");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&fa, "-fa", "--full-assembly", "-no-fa",
-                  "--no-full-assembly", "Enable Full Assembly.");
-   args.AddOption(&device_config, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&solver_config, "-s", "--solver-config",
-                  "Solver and preconditioner combination: \n\t"
-                  "   0 - Ginkgo solver and Ginkgo preconditioner, \n\t"
-                  "   1 - Ginkgo solver and MFEM preconditioner, \n\t"
-                  "   2 - MFEM solver and Ginkgo preconditioner, \n\t"
-                  "   3 - MFEM solver and MFEM preconditioner.");
-   args.AddOption(&print_lvl, "-pl", "--print-level",
-                  "Print level for iterative solver (1 prints every iteration).");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 3. Enable hardware devices such as GPUs, and programming models such as
-   //    CUDA, OCCA, RAJA and OpenMP based on command line options.
-   Device device(device_config);
-   device.SetGPUAwareMPI(true);
-   if (myid == 0) { device.Print(); }
-
-   // 4. Read the (serial) mesh from the given mesh file on all processors.  We
-   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
-   //    and volume meshes with the same code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
-
-   // 5. Refine the serial mesh on all processors to increase the resolution. In
-   //    this example we do 'ref_levels' of uniform refinement. We choose
-   //    'ref_levels' to be the largest number that gives a final mesh with no
-   //    more than 10,000 elements.
-   {
-      int ref_levels =
-         (int)floor(log(10000./mesh.GetNE())/log(2.)/dim);
-      for (int l = 0; l < ref_levels; l++)
-      {
-         mesh.UniformRefinement();
-      }
-   }
-
-   // 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
-   //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
-   ParMesh pmesh(MPI_COMM_WORLD, mesh);
-   mesh.Clear();
-   {
-      int par_ref_levels = 2;
-      for (int l = 0; l < par_ref_levels; l++)
-      {
-         pmesh.UniformRefinement();
-      }
-   }
-
-   // 7. Define a parallel finite element space on the parallel mesh. Here we
-   //    use continuous Lagrange finite elements of the specified order. If
-   //    order < 1, we instead use an isoparametric/isogeometric space.
-   FiniteElementCollection *fec;
-   bool delete_fec;
-   if (order > 0)
-   {
-      fec = new H1_FECollection(order, dim);
-      delete_fec = true;
-   }
-   else if (pmesh.GetNodes())
-   {
-      fec = pmesh.GetNodes()->OwnFEC();
-      delete_fec = false;
-      if (myid == 0)
-      {
-         cout << "Using isoparametric FEs: " << fec->Name() << endl;
-      }
-   }
-   else
-   {
-      fec = new H1_FECollection(order = 1, dim);
-      delete_fec = true;
-   }
-   ParFiniteElementSpace fespace(&pmesh, fec);
-   HYPRE_BigInt size = fespace.GlobalTrueVSize();
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 8. Determine the list of true (i.e. parallel conforming) essential
-   //    boundary dofs. In this example, the boundary conditions are defined
-   //    by marking all the boundary attributes from the mesh as essential
-   //    (Dirichlet) and converting them to a list of true dofs.
-   Array<int> ess_tdof_list;
-   if (pmesh.bdr_attributes.Size())
-   {
-      Array<int> ess_bdr(pmesh.bdr_attributes.Max());
-      ess_bdr = 1;
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   // 9. Set up the parallel linear form b(.) which corresponds to the
-   //    right-hand side of the FEM linear system, which in this case is
-   //    (1,phi_i) where phi_i are the basis functions in fespace.
-   ParLinearForm b(&fespace);
-   ConstantCoefficient one(1.0);
-   b.AddDomainIntegrator(new DomainLFIntegrator(one));
-   b.Assemble();
-
-   // 10. Define the solution vector x as a parallel finite element grid
-   //     function corresponding to fespace. Initialize x with initial guess of
-   //     zero, which satisfies the boundary conditions.
-   ParGridFunction x(&fespace);
-   x = 0.0;
-
-   // 11. Set up the parallel bilinear form a(.,.) on the finite element space
-   //     corresponding to the Laplacian operator -Delta, by adding the
-   //     Diffusion domain integrator.
-   ParBilinearForm a(&fespace);
-   if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
-   if (fa)
-   {
-      a.SetAssemblyLevel(AssemblyLevel::FULL);
-      // Sort the matrix column indices when running on GPU or with OpenMP (i.e.
-      // when Device::IsEnabled() returns true). This makes the results
-      // bit-for-bit deterministic at the cost of somewhat longer run time.
-      a.EnableSparseMatrixSorting(Device::IsEnabled());
-   }
-   a.AddDomainIntegrator(new DiffusionIntegrator(one));
-
-   // 12. Assemble the parallel bilinear form and the corresponding linear
-   //     system, applying any necessary transformations such as: parallel
-   //     assembly, eliminating boundary conditions, applying conforming
-   //     constraints for non-conforming AMR, static condensation, etc.
-   if (static_cond) { a.EnableStaticCondensation(); }
-   a.Assemble();
-
-   OperatorPtr A;
-   Vector B, X;
-   a.FormLinearSystem(ess_tdof_list, x, b, A, X, B);
-
-   // 13. Solve the linear system A X = B.
-   if (!pa)
-   {
-      switch (solver_config)
-      {
-         // Solve the linear system with CG + Schwarz (with IC) from Ginkgo
-         case 0:
-         {
-            if (myid == 0) { cout << "Using Ginkgo solver + preconditioner...\n"; }
-            Ginkgo::GinkgoExecutor exec(device);
-            Ginkgo::IcPreconditioner local_solver(exec, "exact");
-            Ginkgo::SchwarzPreconditioner gko_M(exec, MPI_COMM_WORLD, local_solver);
-            Ginkgo::CGSolver ginkgo_solver(exec, MPI_COMM_WORLD, gko_M);
-            ginkgo_solver.SetPrintLevel(print_lvl);
-            ginkgo_solver.SetRelTol(sqrt(1e-12));
-            ginkgo_solver.SetAbsTol(0.0);
-            ginkgo_solver.SetMaxIter(400);
-            ginkgo_solver.SetOperator(*(A.Ptr()));
-            ginkgo_solver.Mult(B, X);
-            break;
-         }
-
-         // Solve the linear system with CG from Ginkgo + MFEM preconditioner
-         case 1:
-         {
-            if (myid == 0) { cout << "Using Ginkgo solver + MFEM preconditioner...\n"; }
-            Ginkgo::GinkgoExecutor exec(device);
-            //Create MFEM preconditioner and wrap it for Ginkgo's use.
-            HypreBoomerAMG M((HypreParMatrix&)(*A));
-            Ginkgo::MFEMPreconditioner gko_M(exec, M, MPI_COMM_WORLD);
-            Ginkgo::CGSolver ginkgo_solver(exec, MPI_COMM_WORLD, gko_M);
-            ginkgo_solver.SetPrintLevel(print_lvl);
-            ginkgo_solver.SetRelTol(sqrt(1e-12));
-            ginkgo_solver.SetAbsTol(0.0);
-            ginkgo_solver.SetMaxIter(400);
-            ginkgo_solver.SetOperator(*(A.Ptr()));
-            ginkgo_solver.Mult(B, X);
-            break;
-         }
-
-         // Ginkgo Schwarz preconditioner (local ParIC) +  MFEM CG solver
-         case 2:
-         {
-            if (myid == 0) { cout << "Using MFEM solver + Ginkgo preconditioner...\n"; }
-            Ginkgo::GinkgoExecutor exec(device);
-            Ginkgo::IcPreconditioner local_M(exec, "exact");
-            Ginkgo::SchwarzPreconditioner M(exec, MPI_COMM_WORLD, local_M);
-            M.SetOperator(*(A.Ptr()));  // Generate the preconditioner for the matrix A.
-            CGSolver cg(MPI_COMM_WORLD);
-            cg.SetRelTol(sqrt(1e-12));
-            cg.SetMaxIter(400);
-            cg.SetPrintLevel(1);
-            cg.SetPreconditioner(M);
-            cg.SetOperator(*A);
-            cg.Mult(B, X);
-            break;
-         }
-
-         // MFEM solver + MFEM preconditioner
-         case 3:
-         {
-            if (myid == 0) { cout << "Using MFEM solver + MFEM preconditioner...\n"; }
-            HypreBoomerAMG M((HypreParMatrix&)(*A));
-            CGSolver cg(MPI_COMM_WORLD);
-            cg.SetRelTol(sqrt(1e-12));
-            cg.SetMaxIter(400);
-            cg.SetPrintLevel(1);
-            cg.SetPreconditioner(M);
-            cg.SetOperator(*A);
-            cg.Mult(B, X);
-            break;
-         }
-      } // End switch on solver_config
-   }
-   // Partial assembly mode.  Cannot use Ginkgo preconditioners, but can use Ginkgo
-   // solvers.
-   else
-   {
-      if (UsesTensorBasis(fespace))
-      {
-         // Use Jacobi preconditioning in partial assembly mode.
-         OperatorJacobiSmoother M(a, ess_tdof_list);
-         switch (solver_config)
-         {
-            case 0:
-            {
-               if (myid == 0) { cout << "Using Ginkgo solver + preconditioner...\n"; }
-               MFEM_ABORT("Cannot use Ginkgo preconditioner in partial assembly mode.\n"
-                          "            Try -s 1 to test Ginkgo solver with an MFEM preconditioner.");
-               break;
-            }
-
-            // Use Ginkgo solver with MFEM preconditioner
-            case 1:
-            {
-               if (myid == 0) { cout << "Using Ginkgo solver + MFEM preconditioner...\n"; }
-               Ginkgo::GinkgoExecutor exec(device);
-               // Wrap MFEM preconditioner for Ginkgo's use.
-               Ginkgo::MFEMPreconditioner gko_M(exec, M, MPI_COMM_WORLD);
-               Ginkgo::CGSolver ginkgo_solver(exec, MPI_COMM_WORLD, gko_M);
-               ginkgo_solver.SetPrintLevel(print_lvl);
-               ginkgo_solver.SetRelTol(sqrt(1e-12));
-               ginkgo_solver.SetAbsTol(0.0);
-               ginkgo_solver.SetMaxIter(400);
-               ginkgo_solver.SetOperator(*(A.Ptr()));
-               ginkgo_solver.Mult(B, X);
-               break;
-            }
-
-            // No Ginkgo preconditioners work with matrix-free; error
-            case 2:
-            {
-               if (myid == 0) { cout << "Using Ginkgo solver + preconditioner...\n"; }
-               MFEM_ABORT("Cannot use Ginkgo preconditioner in partial assembly mode.\n"
-                          "            Try -s 1 to test Ginkgo solver with an MFEM preconditioner.");
-               break;
-            }
-
-            // Use MFEM solver and preconditioner
-            case 3:
-            {
-               if (myid == 0) { cout << "Using MFEM solver + MFEM preconditioner...\n"; }
-               CGSolver cg(MPI_COMM_WORLD);
-               cg.SetRelTol(sqrt(1e-12));
-               cg.SetMaxIter(400);
-               cg.SetPrintLevel(1);
-               cg.SetPreconditioner(M);
-               cg.SetOperator(*A);
-               cg.Mult(B, X);
-               break;
-            }
-         } // End switch on solver_config
-      }
-      else // CG with no preconditioning
-      {
-         if (myid == 0) { cout << "Using MFEM solver + no preconditioner...\n"; }
-         CGSolver cg(MPI_COMM_WORLD);
-         cg.SetRelTol(sqrt(1e-12));
-         cg.SetMaxIter(400);
-         cg.SetPrintLevel(1);
-         cg.SetOperator(*A);
-         cg.Mult(B, X);
-      }
-   }
-
-   // 14. Recover the parallel grid function corresponding to X. This is the
-   //     local finite element solution on each processor.
-   a.RecoverFEMSolution(X, b, x);
-
-   // 15. Save the refined mesh and the solution in parallel. This output can
-   //     be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
-   {
-      ostringstream mesh_name, sol_name;
-      mesh_name << "mesh." << setfill('0') << setw(6) << myid;
-      sol_name << "sol." << setfill('0') << setw(6) << myid;
-
-      ofstream mesh_ofs(mesh_name.str().c_str());
-      mesh_ofs.precision(8);
-      pmesh.Print(mesh_ofs);
-
-      ofstream sol_ofs(sol_name.str().c_str());
-      sol_ofs.precision(8);
-      x.Save(sol_ofs);
-   }
-
-   // 16. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << pmesh << x << flush;
-   }
-
-   // 17. Free the used memory.
-   if (delete_fec)
-   {
-      delete fec;
-   }
-
-   return 0;
-}

examples/ginkgo/makefile

@@ -20,8 +20,9 @@ CONFIG_MK = $(or $(wildcard $(MFEM_BUILD_DIR)/config/config.mk),\
 MFEM_LIB_FILE = mfem_is_not_built
 -include $(CONFIG_MK)
 
+# Currently there are only serial Ginkgo examples
 SEQ_EXAMPLES = ex1
-PAR_EXAMPLES = ex1p
+PAR_EXAMPLES =
 ifeq ($(MFEM_USE_MPI),NO)
    EXAMPLES = $(SEQ_EXAMPLES)
 else
@@ -76,4 +77,4 @@ clean-build:
 	rm -rf *.dSYM *.TVD.*breakpoints
 
 clean-exec:
-	@rm -f refined.mesh sol.gf mesh.* sol.*
+	@rm -f refined.mesh sol.gf

examples/makefile

@@ -22,11 +22,11 @@ MFEM_LIB_FILE = mfem_is_not_built
 
 SEQ_EXAMPLES = ex0 ex1 ex2 ex3 ex4 ex5 ex6 ex7 ex8 ex9 ex10 ex14 ex15 ex16 \
    ex17 ex18 ex19 ex20 ex21 ex22 ex23 ex24 ex25 ex26 ex27 ex28 ex29 ex30 \
-   ex31 ex33 ex34 ex36 ex37 ex38 ex39 ex40 ex41
+   ex31 ex33 ex34 ex36 ex37 ex38 ex39 ex40
 PAR_EXAMPLES = ex0p ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex8p ex9p ex10p ex11p \
    ex12p ex13p ex14p ex15p ex16p ex17p ex18p ex19p ex20p ex21p ex22p ex24p \
    ex25p ex26p ex27p ex28p ex29p ex30p ex31p ex32p ex33p ex34p ex35p ex36p \
-   ex37p ex39p ex40p ex41p
+   ex37p ex39p ex40p
 SEQ_DEVICE_EXAMPLES = ex1 ex3 ex4 ex5 ex6 ex9 ex14 ex22 ex24 ex25 ex26 ex34
 PAR_DEVICE_EXAMPLES = ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex9p ex13p ex14p \
    ex22p ex24p ex25p ex26p ex34p ex35p
@@ -71,7 +71,6 @@ endif
 
 SUBDIRS_ALL = $(addsuffix /all,$(SUBDIRS))
 SUBDIRS_TEST = $(addsuffix /test,$(SUBDIRS))
-SUBDIRS_TEST_NOCLEAN = $(addsuffix /test-noclean,$(SUBDIRS))
 SUBDIRS_CLEAN = $(addsuffix /clean,$(SUBDIRS))
 SUBDIRS_TPRINT = $(addsuffix /test-print,$(SUBDIRS))
 
@@ -88,9 +87,8 @@ SUBDIRS_TPRINT = $(addsuffix /test-print,$(SUBDIRS))
 
 all: $(EXAMPLES) $(SUBDIRS_ALL)
 
-.PHONY: $(SUBDIRS_ALL) $(SUBDIRS_TEST) $(SUBDIRS_TEST_NOCLEAN) \
-   $(SUBDIRS_CLEAN) $(SUBDIRS_TPRINT)
-$(SUBDIRS_ALL) $(SUBDIRS_TEST) $(SUBDIRS_TEST_NOCLEAN) $(SUBDIRS_CLEAN):
+.PHONY: $(SUBDIRS_ALL) $(SUBDIRS_TEST) $(SUBDIRS_CLEAN) $(SUBDIRS_TPRINT)
+$(SUBDIRS_ALL) $(SUBDIRS_TEST) $(SUBDIRS_CLEAN):
 	$(MAKE) -C $(@D) $(@F)
 $(SUBDIRS_TPRINT):
 	@$(MAKE) -C $(@D) $(@F)
@@ -109,7 +107,6 @@ endif
 MFEM_TESTS = EXAMPLES
 include $(MFEM_TEST_MK)
 test: $(SUBDIRS_TEST)
-test-noclean: $(SUBDIRS_TEST_NOCLEAN)
 test-print: $(SUBDIRS_TPRINT)
 
 # Testing: Parallel vs. serial runs
@@ -160,12 +157,6 @@ ex37-test-seq: ex37
 	@$(call mfem-test,$<,, Serial example,-mi 3)
 ex37p-test-par: ex37p
 	@$(call mfem-test,$<, $(RUN_MPI), Parallel example,-mi 3)
-ex39-test-seq: ex39
-	@$(call mfem-test,$<,, Serial example,-m ../data/compass.mesh)
-ex41-test-seq: ex41
-	@$(call mfem-test,$<,, Serial example,-tf 1.0)
-ex41p-test-par: ex41p
-	@$(call mfem-test,$<, $(RUN_MPI), Parallel example,-tf 1.0)
 # Testing: optional tests
 ifeq ($(MFEM_USE_STRUMPACK),YES)
 ex11p-test-strumpack: ex11p
@@ -182,12 +173,6 @@ ex11p-test-cpardiso: ex11p
 	@$(call mfem-test,$<, $(RUN_MPI), MKL_CPARDISO example,--cpardiso)
 test-par-YES: ex11p-test-cpardiso
 endif
-ifeq ($(MFEM_USE_CEED),YES)
-ex1p-test-ceed: ex1p
-	@$(call mfem-test,$<, $(RUN_MPI),\
-	   Parallel libCEED example,-d ceed-cpu -pa -a)
-test-par-YES: ex1p-test-ceed
-endif
 
 # Testing: "test" target and mfem-test* variables are defined in config/test.mk
 
@@ -204,8 +189,8 @@ clean-build:
 clean-exec:
 	@rm -f refined.mesh displaced.mesh mesh.* ex5.mesh ex6p-checkpoint.*
 	@rm -rf Example5* Example9* Example15* Example16* Example23* ParaView
-	@rm -f sphere_refined.* sol.* sol_u.* sol_p.* sol_r.* sol_i.* sol_z.*
-	@rm -f order.* ex9.mesh ex9-mesh.* ex9-init.* ex9-final.*
+	@rm -f sphere_refined.* sol.* sol_u.* sol_p.* sol_r.* sol_i.* order.*
+	@rm -f ex9.mesh ex9-mesh.* ex9-init.* ex9-final.*
 	@rm -f deformed.* velocity.* elastic_energy.* mode_* mode_deriv_* flux.*
 	@rm -f ex5-p-*.bp ex9-p-*.bp ex12-p-*.bp ex16-p-*.bp
 	@rm -f ex16.mesh ex16-mesh.* ex16-init.* ex16-final.*

fem/CMakeLists.txt

@@ -82,8 +82,6 @@ set(SRCS
   fe/fe_ser.cpp
   fe_coll.cpp
   fespace.cpp
-  derefmat_op.cpp
-  pderefmat_op.cpp
   geom.cpp
   gridfunc.cpp
   hybridization.cpp
@@ -128,46 +126,32 @@ set(SRCS
   normal_deriv_restriction.cpp
   staticcond.cpp
   tmop.cpp
-  tmop/pa.cpp
-  tmop/assemble/diag2_limit.cpp
-  tmop/assemble/diag2.cpp
-  tmop/assemble/grad2_limit.cpp
-  tmop/assemble/grad2.cpp
-  tmop/assemble/diag3_limit.cpp  
-  tmop/assemble/diag3.cpp
-  tmop/assemble/grad3_limit.cpp
-  tmop/assemble/grad3.cpp
-  tmop/metrics/001.cpp
-  tmop/metrics/002.cpp
-  tmop/metrics/007.cpp
-  tmop/metrics/056.cpp
-  tmop/metrics/077.cpp
-  tmop/metrics/080.cpp
-  tmop/metrics/094.cpp
-  tmop/metrics/302.cpp
-  tmop/metrics/303.cpp
-  tmop/metrics/315.cpp
-  tmop/metrics/318.cpp
-  tmop/metrics/321.cpp
-  tmop/metrics/332.cpp
-  tmop/metrics/338.cpp
-  tmop/mult/grad2_limit.cpp
-  tmop/mult/grad2.cpp
-  tmop/mult/mult2_limit.cpp
-  tmop/mult/mult2.cpp
-  tmop/mult/grad3_limit.cpp
-  tmop/mult/grad3.cpp
-  tmop/mult/mult3_limit.cpp
-  tmop/mult/mult3.cpp
-  tmop/tools/det2_jpr.cpp
-  tmop/tools/det3_jpr.cpp
-  tmop/tools/discrete.cpp
-  tmop/tools/energy2_limit.cpp
-  tmop/tools/energy2.cpp
-  tmop/tools/energy3_limit.cpp
-  tmop/tools/energy3.cpp
-  tmop/tools/target2.cpp
-  tmop/tools/target3.cpp
+  tmop/tmop_pa.cpp
+  tmop/tmop_pa_da3.cpp
+  tmop/tmop_pa_h2d.cpp
+  tmop/tmop_pa_h2d_c0.cpp
+  tmop/tmop_pa_h2m.cpp
+  tmop/tmop_pa_h2m_c0.cpp
+  tmop/tmop_pa_h2s.cpp
+  tmop/tmop_pa_h2s_c0.cpp
+  tmop/tmop_pa_h3d.cpp
+  tmop/tmop_pa_h3d_c0.cpp
+  tmop/tmop_pa_h3m.cpp
+  tmop/tmop_pa_h3m_c0.cpp
+  tmop/tmop_pa_h3s.cpp
+  tmop/tmop_pa_h3s_c0.cpp
+  tmop/tmop_pa_jp2.cpp
+  tmop/tmop_pa_jp3.cpp
+  tmop/tmop_pa_p2.cpp
+  tmop/tmop_pa_p2_c0.cpp
+  tmop/tmop_pa_p3.cpp
+  tmop/tmop_pa_p3_c0.cpp
+  tmop/tmop_pa_tc2.cpp
+  tmop/tmop_pa_tc3.cpp
+  tmop/tmop_pa_w2.cpp
+  tmop/tmop_pa_w2_c0.cpp
+  tmop/tmop_pa_w3.cpp
+  tmop/tmop_pa_w3_c0.cpp
   tmop_tools.cpp
   tmop_amr.cpp
   gslib.cpp
@@ -179,26 +163,18 @@ set(SRCS
   hyperbolic.cpp
   integrator.cpp
   bounds.cpp
-  particleset.cpp
   )
 
 set(HDRS
   bilinearform.hpp
   bilinearform_ext.hpp
   bilininteg.hpp
-  integ/lininteg_domain_kernels.hpp
-  integ/bilininteg_dgdiffusion_kernels.hpp
-  integ/bilininteg_dgtrace_kernels.hpp
-  integ/bilininteg_vecdiffusion_kernels.hpp
-  integ/bilininteg_convection_kernels.hpp
   integ/bilininteg_diffusion_kernels.hpp
   integ/bilininteg_elasticity_kernels.hpp
   integ/bilininteg_hcurl_kernels.hpp
   integ/bilininteg_hdiv_kernels.hpp
   integ/bilininteg_hcurlhdiv_kernels.hpp
   integ/bilininteg_mass_kernels.hpp
-  integ/bilininteg_vecdiffusion_pa.hpp
-  integ/bilininteg_vecmass_pa.hpp
   coefficient.hpp
   complex_fem.hpp
   convergence.hpp
@@ -263,13 +239,8 @@ set(HDRS
   lor/lor_ams.hpp
   lor/lor_batched.hpp
   lor/lor_h1.hpp
-  lor/lor_dg.hpp
   lor/lor_nd.hpp
   lor/lor_rt.hpp
-  lor/lor_h1_impl.hpp
-  lor/lor_dg_impl.hpp
-  lor/lor_nd_impl.hpp
-  lor/lor_rt_impl.hpp
   lor/lor_util.hpp
   multigrid.hpp
   nonlinearform.hpp
@@ -296,12 +267,7 @@ set(HDRS
   tfespace.hpp
   tintrules.hpp
   tmop.hpp
-  tmop/pa.hpp
-  tmop/assemble/grad2.hpp
-  tmop/assemble/grad2.hpp
-  tmop/mult/mult2.hpp
-  tmop/mult/mult3.hpp
-  tmop/tools/energy2.hpp
+  tmop/tmop_pa.hpp
   tmop_tools.hpp
   tmop_amr.hpp
   gslib.hpp
@@ -309,7 +275,6 @@ set(HDRS
   hyperbolic.hpp
   integrator.hpp
   bounds.hpp
-  particleset.hpp
   )
 
 if (MFEM_USE_SIDRE)

fem/bilinearform.cpp

@@ -729,8 +729,7 @@ void BilinearForm::Assemble(int skip_zeros)
          tr = mesh -> GetBdrFaceTransformations (i);
          if (tr != NULL)
          {
-            mfem::DofTransformation doftrans;
-            fes -> GetElementVDofs (tr -> Elem1No, vdofs, doftrans);
+            fes -> GetElementVDofs (tr -> Elem1No, vdofs);
             fe1 = fes -> GetFE (tr -> Elem1No);
             // The fe2 object is really a dummy and not used on the boundaries,
             // but we can't dereference a NULL pointer, and we don't want to
@@ -744,7 +743,6 @@ void BilinearForm::Assemble(int skip_zeros)
 
                boundary_face_integs[k] -> AssembleFaceMatrix (*fe1, *fe2, *tr,
                                                               elemmat);
-               doftrans.TransformDual(elemmat);
                mat -> AddSubMatrix (vdofs, vdofs, elemmat, skip_zeros);
             }
          }
@@ -827,46 +825,14 @@ void BilinearForm::FormLinearSystem(const Array<int> &ess_tdof_list, Vector &x,
                                     Vector &b, OperatorHandle &A, Vector &X,
                                     Vector &B, int copy_interior)
 {
-   const SparseMatrix *P = fes->GetConformingProlongation();
-   const SparseMatrix *R = fes->GetConformingRestriction();
    if (ext)
    {
       if (hybridization)
       {
          FormSystemMatrix(ess_tdof_list, A);
-
-         std::unique_ptr<ConstrainedOperator> A_constrained([&]()
-         {
-            Operator *op;
-            Operator::FormSystemOperator(ess_tdof_list, op);
-            return dynamic_cast<ConstrainedOperator*>(op);
-         }());
-         MFEM_ASSERT(A_constrained != nullptr, "");
-
-         Vector conf_b, conf_x;
-         if (P)
-         {
-            // Nonconforming
-            conf_b.SetSize(P->Width());
-            conf_x.SetSize(P->Width());
-            P->MultTranspose(b, conf_b);
-            R->Mult(x, conf_x);
-         }
-         else
-         {
-            // Conforming
-            conf_b.MakeRef(b, 0, b.Size());
-            conf_x.MakeRef(x, 0, x.Size());
-         }
-
-         A_constrained->EliminateRHS(conf_x, conf_b);
-
-         if (P)
-         {
-            R->MultTranspose(conf_b, b); // store eliminated rhs in b
-         }
-
-         hybridization->ReduceRHS(conf_b, B);
+         ConstrainedOperator A_constrained(this, ess_tdof_list);
+         A_constrained.EliminateRHS(x, b);
+         hybridization->ReduceRHS(b, B);
          X.SetSize(B.Size());
          X = 0.0;
       }
@@ -876,6 +842,7 @@ void BilinearForm::FormLinearSystem(const Array<int> &ess_tdof_list, Vector &x,
       }
       return;
    }
+   const SparseMatrix *P = fes->GetConformingProlongation();
    FormSystemMatrix(ess_tdof_list, A);
 
    // Transform the system and perform the elimination in B, based on the
@@ -911,6 +878,7 @@ void BilinearForm::FormLinearSystem(const Array<int> &ess_tdof_list, Vector &x,
       if (hybridization)
       {
          // Reduction to the Lagrange multipliers system
+         const SparseMatrix *R = fes->GetConformingRestriction();
          Vector conf_b(P->Width()), conf_x(P->Width());
          P->MultTranspose(b, conf_b);
          R->Mult(x, conf_x);
@@ -923,6 +891,7 @@ void BilinearForm::FormLinearSystem(const Array<int> &ess_tdof_list, Vector &x,
       else
       {
          // Variational restriction with P
+         const SparseMatrix *R = fes->GetConformingRestriction();
          B.SetSize(P->Width());
          P->MultTranspose(b, B);
          X.SetSize(R->Height());
@@ -1725,7 +1694,6 @@ void MixedBilinearForm::Assemble(int skip_zeros)
          }
       }
 
-      DofTransformation dom_dof_trans, ran_dof_trans;
       for (int i = 0; i < trial_fes -> GetNBE(); i++)
       {
          const int bdr_attr = mesh->GetBdrAttribute(i);
@@ -1734,8 +1702,8 @@ void MixedBilinearForm::Assemble(int skip_zeros)
          ftr = mesh -> GetBdrFaceTransformations (i);
          if (ftr != NULL)
          {
-            trial_fes->GetElementVDofs(ftr->Elem1No, trial_vdofs, dom_dof_trans);
-            test_fes->GetElementVDofs(ftr->Elem1No, test_vdofs, ran_dof_trans);
+            trial_fes->GetElementVDofs(ftr->Elem1No, trial_vdofs);
+            test_fes->GetElementVDofs(ftr->Elem1No, test_vdofs);
             trial_fe1 = trial_fes->GetFE(ftr->Elem1No);
             test_fe1 = test_fes->GetFE(ftr->Elem1No);
             // The test_fe2 object is really a dummy and not used on the
@@ -1751,7 +1719,6 @@ void MixedBilinearForm::Assemble(int skip_zeros)
                boundary_face_integs[k]->AssembleFaceMatrix(*trial_fe1, *test_fe1, *trial_fe2,
                                                            *test_fe2,
                                                            *ftr, elemmat);
-               TransformDual(ran_dof_trans, dom_dof_trans, elemmat);
                mat->AddSubMatrix(test_vdofs, trial_vdofs, elemmat, skip_zeros);
             }
          }

fem/bilinearform_ext.cpp

@@ -266,7 +266,11 @@ void PABilinearFormExtension::SetupRestrictionOperators(const L2FaceValues m)
 
       // Gather the attributes on the host from all the elements
       const Mesh &mesh = *trial_fes->GetMesh();
-      elem_attributes = &mesh.GetElementAttributes();
+      elem_attributes.SetSize(mesh.GetNE());
+      for (int i = 0; i < mesh.GetNE(); ++i)
+      {
+         elem_attributes[i] = mesh.GetAttribute(i);
+      }
    }
 
    // Construct face restriction operators only if the bilinear form has
@@ -325,7 +329,45 @@ void PABilinearFormExtension::SetupRestrictionOperators(const L2FaceValues m)
          bdr_face_dYdn.SetSize(bdr_face_restrict_lex->Height());
       }
 
-      bdr_face_attributes = &trial_fes->GetMesh()->GetBdrFaceAttributes();
+      const Mesh &mesh = *trial_fes->GetMesh();
+      // See LinearFormExtension::Update for explanation of f_to_be logic.
+      std::unordered_map<int,int> f_to_be;
+      for (int i = 0; i < mesh.GetNBE(); ++i)
+      {
+         const int f = mesh.GetBdrElementFaceIndex(i);
+         f_to_be[f] = i;
+      }
+      const int nf_bdr = trial_fes->GetNFbyType(FaceType::Boundary);
+      bdr_attributes.SetSize(nf_bdr);
+      int f_ind = 0;
+      int missing_bdr_elems = 0;
+      for (int f = 0; f < mesh.GetNumFaces(); ++f)
+      {
+         if (!mesh.GetFaceInformation(f).IsOfFaceType(FaceType::Boundary))
+         {
+            continue;
+         }
+         int attribute = 1; // default value
+         if (f_to_be.find(f) != f_to_be.end())
+         {
+            const int be = f_to_be[f];
+            attribute = mesh.GetBdrAttribute(be);
+         }
+         else
+         {
+            // If a boundary face does not correspond to the a boundary element,
+            // we assign it the default attribute of 1. We also generate a
+            // warning at runtime with the number of such missing elements.
+            ++missing_bdr_elems;
+         }
+         bdr_attributes[f_ind] = attribute;
+         ++f_ind;
+      }
+      if (missing_bdr_elems)
+      {
+         MFEM_WARNING("Missing " << missing_bdr_elems << " boundary elements "
+                      "for boundary faces.");
+      }
    }
 }
 
@@ -387,7 +429,7 @@ void PABilinearFormExtension::AssembleDiagonal(Vector &y) const
          mfem::forall(ne, [=] MFEM_HOST_DEVICE (int e)
          {
             const int attr = d_attr[e];
-            if (attr <= 0 || d_m[attr - 1] == 0)
+            if (d_m[attr - 1] == 0)
             {
                for (int i = 0; i < nd; ++i)
                {
@@ -408,7 +450,7 @@ void PABilinearFormExtension::AssembleDiagonal(Vector &y) const
          for (int i = 0; i < iSz; ++i)
          {
             assemble_diagonal_with_markers(*integrators[i], elem_markers[i],
-                                           *elem_attributes, localY);
+                                           elem_attributes, localY);
          }
          const ElementRestriction* H1elem_restrict =
             dynamic_cast<const ElementRestriction*>(elem_restrict);
@@ -434,7 +476,7 @@ void PABilinearFormExtension::AssembleDiagonal(Vector &y) const
       for (int i = 0; i < iSz; ++i)
       {
          assemble_diagonal_with_markers(*integrators[i], elem_markers[i],
-                                        *elem_attributes, y);
+                                        elem_attributes, y);
       }
    }
 
@@ -447,7 +489,7 @@ void PABilinearFormExtension::AssembleDiagonal(Vector &y) const
       for (int i = 0; i < n_bdr_integs; ++i)
       {
          assemble_diagonal_with_markers(*bdr_integs[i], bdr_markers[i],
-                                        *bdr_face_attributes, bdr_face_Y);
+                                        bdr_attributes, bdr_face_Y);
       }
       bdr_face_restrict_lex->AddAbsMultTranspose(bdr_face_Y, y);
    }
@@ -546,7 +588,7 @@ void PABilinearFormExtension::MultInternal(const Vector &x, Vector &y,
          for (int i = 0; i < iSz; ++i)
          {
             AddMultWithMarkers(*integrators[i], localX, elem_markers[i],
-                               *elem_attributes, false, localY, useAbs);
+                               elem_attributes, false, localY, useAbs);
          }
          if (H1elem_restrict && useAbs)
          {
@@ -648,8 +690,8 @@ void PABilinearFormExtension::MultInternal(const Vector &x, Vector &y,
          }
          for (int i = 0; i < n_bdr_integs; ++i)
          {
-            AddMultWithMarkers(*bdr_integs[i], bdr_face_X, bdr_markers[i],
-                               *bdr_face_attributes, false, bdr_face_Y);
+            AddMultWithMarkers(*bdr_integs[i], bdr_face_X, bdr_markers[i], bdr_attributes,
+                               false, bdr_face_Y);
          }
          for (int i = 0; i < n_bdr_face_integs; ++i)
          {
@@ -657,14 +699,12 @@ void PABilinearFormExtension::MultInternal(const Vector &x, Vector &y,
             {
                AddMultNormalDerivativesWithMarkers(
                   *bdr_face_integs[i], bdr_face_X, bdr_face_dXdn,
-                  bdr_face_markers[i], *bdr_face_attributes, bdr_face_Y,
-                  bdr_face_dYdn);
+                  bdr_face_markers[i], bdr_attributes, bdr_face_Y, bdr_face_dYdn);
             }
             else
             {
-               AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X,
-                                  bdr_face_markers[i], *bdr_face_attributes, false,
-                                  bdr_face_Y);
+               AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X, bdr_face_markers[i],
+                                  bdr_attributes, false, bdr_face_Y);
             }
          }
          bdr_face_restrict_lex->AddMultTransposeInPlace(bdr_face_Y, y);
@@ -687,7 +727,7 @@ void PABilinearFormExtension::MultTranspose(const Vector &x, Vector &y) const
       localY = 0.0;
       for (int i = 0; i < iSz; ++i)
       {
-         AddMultWithMarkers(*integrators[i], localX, elem_markers[i], *elem_attributes,
+         AddMultWithMarkers(*integrators[i], localX, elem_markers[i], elem_attributes,
                             true, localY);
       }
       elem_restrict->MultTranspose(localY, y);
@@ -734,14 +774,13 @@ void PABilinearFormExtension::MultTranspose(const Vector &x, Vector &y) const
          bdr_face_Y = 0.0;
          for (int i = 0; i < n_bdr_integs; ++i)
          {
-            AddMultWithMarkers(*bdr_integs[i], bdr_face_X, bdr_markers[i],
-                               *bdr_face_attributes, true, bdr_face_Y);
+            AddMultWithMarkers(*bdr_integs[i], bdr_face_X, bdr_markers[i], bdr_attributes,
+                               true, bdr_face_Y);
          }
          for (int i = 0; i < n_bdr_face_integs; ++i)
          {
-            AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X,
-                               bdr_face_markers[i], *bdr_face_attributes, true,
-                               bdr_face_Y);
+            AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X, bdr_face_markers[i],
+                               bdr_attributes, true, bdr_face_Y);
          }
          bdr_face_restrict_lex->AddMultTransposeInPlace(bdr_face_Y, y);
       }
@@ -765,7 +804,7 @@ static void AddWithMarkers_(
    mfem::forall(ne, [=] MFEM_HOST_DEVICE (int e)
    {
       const int attr = d_attr[e];
-      if (attr <= 0 || d_m[attr - 1] == 0) { return; }
+      if (d_m[attr - 1] == 0) { return; }
       for (int i = 0; i < nd; ++i)
       {
          d_y(i, e) += d_x(i, e);
@@ -881,8 +920,7 @@ void EABilinearFormExtension::Assemble()
       {
          const int i = idx % sz;
          const int e = idx / sz;
-         const real_t val =
-            d_a[e] > 0 ? (d_m[d_a[e] - 1] ? d_ea_1(i, e) : 0) : 0;
+         const real_t val = d_m[d_a[e] - 1] ? d_ea_1(i, e) : 0.0;
          if (add)
          {
             d_ea_2(i, e) += val;
@@ -915,7 +953,7 @@ void EABilinearFormExtension::Assemble()
             ea_data_tmp.SetSize(ea_data.Size());
             integrators[i]->AssembleEA(*a->FESpace(), ea_data_tmp, false);
             add_with_markers(ea_data_tmp, ea_data, ne, *markers,
-                             *elem_attributes, add);
+                             elem_attributes, add);
          }
       }
    }
@@ -944,7 +982,7 @@ void EABilinearFormExtension::Assemble()
             ea_data_tmp.SetSize(ea_data_bdr.Size());
             bdr_integs[i]->AssembleEABoundary(*a->FESpace(), ea_data_tmp, add);
             add_with_markers(ea_data_tmp, ea_data_bdr, nf_bdr, *markers,
-                             *bdr_face_attributes, add);
+                             bdr_attributes, add);
          }
       }
    }
@@ -993,7 +1031,7 @@ void EABilinearFormExtension::Assemble()
                                                         ea_data_tmp,
                                                         add);
             add_with_markers(ea_data_tmp, ea_data_bdr, nf_bdr, *markers,
-                             *bdr_face_attributes, add);
+                             bdr_attributes, add);
          }
       }
    }

fem/bilinearform_ext.hpp

@@ -69,8 +69,7 @@ class PABilinearFormExtension : public BilinearFormExtension
 protected:
    const FiniteElementSpace *trial_fes, *test_fes; // Not owned
    /// Attributes of all mesh elements.
-   const Array<int> *elem_attributes; // Not owned
-   const Array<int> *bdr_face_attributes; // Not owned
+   Array<int> elem_attributes, bdr_attributes;
    mutable Vector tmp_evec; // Work array
    mutable Vector localX, localY;
    mutable Vector int_face_X, int_face_Y;

fem/bilininteg.cpp

@@ -3066,6 +3066,7 @@ void VectorDiffusionIntegrator::AssembleElementMatrix(
 
    for (int i = 0; i < ir -> GetNPoints(); i++)
    {
+
       const IntegrationPoint &ip = ir->IntPoint(i);
       el.CalcDShape(ip, dshape);
 

fem/bilininteg.hpp

@@ -23,8 +23,6 @@
 
 namespace mfem
 {
-class QuadratureSpace;
-class FaceQuadratureSpace;
 
 /// Abstract base class BilinearFormIntegrator
 class BilinearFormIntegrator : public NonlinearFormIntegrator
@@ -814,7 +812,7 @@ protected:
       const FiniteElement & test_fe) const
    {
       return (trial_fe.GetDim() == 1 && test_fe.GetDim() == 1 &&
-              trial_fe.GetDerivType() == mfem::FiniteElement::GRAD &&
+              trial_fe.GetDerivType() == mfem::FiniteElement::GRAD  &&
               test_fe.GetRangeType()  == mfem::FiniteElement::SCALAR );
    }
 
@@ -886,7 +884,7 @@ protected:
       const FiniteElement & trial_fe,
       const FiniteElement & test_fe) const
    {
-      return (trial_fe.GetDerivType() == mfem::FiniteElement::DIV &&
+      return (trial_fe.GetDerivType() == mfem::FiniteElement::DIV  &&
               test_fe.GetRangeType()  == mfem::FiniteElement::SCALAR );
    }
 
@@ -921,7 +919,7 @@ protected:
       const FiniteElement & trial_fe,
       const FiniteElement & test_fe) const
    {
-      return (trial_fe.GetDerivType() == mfem::FiniteElement::DIV &&
+      return (trial_fe.GetDerivType() == mfem::FiniteElement::DIV  &&
               test_fe.GetRangeType()  == mfem::FiniteElement::VECTOR );
    }
 
@@ -1602,7 +1600,7 @@ public:
    {
       return (trial_fe.GetCurlDim() == 3 && test_fe.GetRangeDim() == 3 &&
               trial_fe.GetRangeType() == mfem::FiniteElement::VECTOR &&
-              trial_fe.GetDerivType() == mfem::FiniteElement::CURL  &&
+              trial_fe.GetDerivType() == mfem::FiniteElement::CURL   &&
               test_fe.GetRangeType()  == mfem::FiniteElement::VECTOR );
    }
 
@@ -1637,7 +1635,7 @@ public:
    {
       return (trial_fe.GetDim() == 2 && test_fe.GetDim() == 2 &&
               trial_fe.GetRangeType() == mfem::FiniteElement::VECTOR &&
-              trial_fe.GetDerivType() == mfem::FiniteElement::CURL  &&
+              trial_fe.GetDerivType() == mfem::FiniteElement::CURL   &&
               test_fe.GetRangeType()  == mfem::FiniteElement::VECTOR );
    }
 
@@ -1671,7 +1669,7 @@ public:
    {
       return (trial_fe.GetDim() == 2 && test_fe.GetDim() == 2 &&
               trial_fe.GetRangeType() == mfem::FiniteElement::SCALAR &&
-              trial_fe.GetDerivType() == mfem::FiniteElement::GRAD  &&
+              trial_fe.GetDerivType() == mfem::FiniteElement::GRAD   &&
               test_fe.GetRangeType()  == mfem::FiniteElement::SCALAR );
    }
 
@@ -1762,7 +1760,7 @@ public:
       const FiniteElement & test_fe) const
    {
       return (trial_fe.GetRangeType() == mfem::FiniteElement::SCALAR &&
-              trial_fe.GetDerivType() == mfem::FiniteElement::GRAD  &&
+              trial_fe.GetDerivType() == mfem::FiniteElement::GRAD   &&
               test_fe.GetRangeType()  == mfem::FiniteElement::SCALAR );
    }
 
@@ -1795,7 +1793,7 @@ public:
       const FiniteElement & test_fe) const
    {
       return (trial_fe.GetRangeType() == mfem::FiniteElement::SCALAR &&
-              trial_fe.GetDerivType() == mfem::FiniteElement::GRAD  &&
+              trial_fe.GetDerivType() == mfem::FiniteElement::GRAD   &&
               test_fe.GetRangeType()  == mfem::FiniteElement::VECTOR &&
               test_fe.GetDerivType()  == mfem::FiniteElement::DIV   );
    }
@@ -1834,7 +1832,7 @@ public:
       const FiniteElement & test_fe) const
    {
       return (trial_fe.GetRangeType() == mfem::FiniteElement::VECTOR &&
-              trial_fe.GetDerivType() == mfem::FiniteElement::DIV   &&
+              trial_fe.GetDerivType() == mfem::FiniteElement::DIV    &&
               test_fe.GetRangeType()  == mfem::FiniteElement::SCALAR &&
               test_fe.GetDerivType()  == mfem::FiniteElement::GRAD
              );
@@ -1975,7 +1973,7 @@ protected:
       const FiniteElement & test_fe) const override
    {
       return (trial_fe.GetCurlDim() == 3 && test_fe.GetRangeDim() == 3 &&
-              trial_fe.GetDerivType() == mfem::FiniteElement::CURL &&
+              trial_fe.GetDerivType() == mfem::FiniteElement::CURL  &&
               test_fe.GetRangeType()  == mfem::FiniteElement::VECTOR );
    }
 
@@ -2178,18 +2176,22 @@ class DiffusionIntegrator: public BilinearFormIntegrator
 {
 public:
 
-   using ApplyKernelType = void(*)(const int, const bool, const Array<real_t>&,
-                                   const Array<real_t>&, const Array<real_t>&,
-                                   const Array<real_t>&,
-                                   const Vector&, const Vector&,
-                                   Vector&, const int, const int);
+   using DiffusionApplyKernelType = void(*)(const int, const bool,
+                                            const Array<real_t>&,
+                                            const Array<real_t>&, const Array<real_t>&,
+                                            const Array<real_t>&,
+                                            const Vector&, const Vector&,
+                                            Vector&, const int, const int);
 
-   using DiagonalKernelType = void(*)(const int, const bool, const Array<real_t>&,
-                                      const Array<real_t>&, const Vector&, Vector&,
-                                      const int, const int);
+   using DiffusionDiagonalKernelType = void(*)(const int, const bool,
+                                               const Array<real_t>&,
+                                               const Array<real_t>&, const Vector&, Vector&,
+                                               const int, const int);
 
-   MFEM_REGISTER_KERNELS(ApplyPAKernels, ApplyKernelType, (int, int, int));
-   MFEM_REGISTER_KERNELS(DiagonalPAKernels, DiagonalKernelType, (int, int, int));
+   MFEM_REGISTER_KERNELS(DiffusionApplyPAKernel, DiffusionApplyKernelType,
+                         (int, int, int));
+   MFEM_REGISTER_KERNELS(DiffusionDiagonalPAKernel, DiffusionDiagonalKernelType,
+                         (int, int, int));
    struct Kernels { Kernels(); };
 
 protected:
@@ -2209,6 +2211,7 @@ private:
    const FiniteElementSpace *fespace;
    const DofToQuad *maps;         ///< Not owned
    const GeometricFactors *geom;  ///< Not owned
+public:
    int dim, ne, dofs1D, quad1D;
    Vector pa_data;
    bool symmetric = true; ///< False if using a nonsymmetric matrix coefficient
@@ -2350,8 +2353,8 @@ public:
    template <int DIM, int D1D, int Q1D>
    static void AddSpecialization()
    {
-      ApplyPAKernels::Specialization<DIM,D1D,Q1D>::Add();
-      DiagonalPAKernels::Specialization<DIM,D1D,Q1D>::Add();
+      DiffusionApplyPAKernel::Specialization<DIM,D1D,Q1D>::Add();
+      DiffusionDiagonalPAKernel::Specialization<DIM,D1D,Q1D>::Add();
    }
 protected:
    const IntegrationRule* GetDefaultIntegrationRule(
@@ -2496,7 +2499,8 @@ private:
 #endif
 
 public:
-   ConvectionIntegrator(VectorCoefficient &q, real_t a = 1.0);
+   ConvectionIntegrator(VectorCoefficient &q, real_t a = 1.0)
+      : Q(&q) { alpha = a; }
 
    void AssembleElementMatrix(const FiniteElement &,
                               ElementTransformation &,
@@ -2529,28 +2533,6 @@ public:
 
    bool SupportsCeed() const override { return DeviceCanUseCeed(); }
 
-   /// arguments: NE, B, G, Bt, Gt, pa_data, x, y, D1D, Q1D
-   using ApplyKernelType = void (*)(const int, const Array<real_t> &,
-                                    const Array<real_t> &,
-                                    const Array<real_t> &,
-                                    const Array<real_t> &, const Vector &,
-                                    const Vector &, Vector &, const int,
-                                    const int);
-
-   /// arguments: DIMS, D1D, Q1D
-   MFEM_REGISTER_KERNELS(ApplyPAKernels, ApplyKernelType, (int, int, int));
-   /// arguments: DIMS, D1D, Q1D
-   MFEM_REGISTER_KERNELS(ApplyPATKernels, ApplyKernelType, (int, int, int));
-
-   template <int DIM, int D1D, int Q1D>
-   static void AddSpecialization()
-   {
-      ApplyPAKernels::Specialization<DIM, D1D, Q1D>::Add();
-      ApplyPATKernels::Specialization<DIM, D1D, Q1D>::Add();
-   }
-
-   struct Kernels { Kernels(); };
-
 protected:
    const IntegrationRule* GetDefaultIntegrationRule(
       const FiniteElement& trial_fe,
@@ -2596,40 +2578,41 @@ public:
     by scalar FE through standard transformation. */
 class VectorMassIntegrator: public BilinearFormIntegrator
 {
-   int vdim = -1, Q_order = 0;
+private:
+   int vdim;
    Vector shape, te_shape, vec;
    DenseMatrix partelmat;
    DenseMatrix mcoeff;
+   int Q_order;
 
 protected:
-   Coefficient *Q = nullptr;
-   VectorCoefficient *VQ = nullptr;
-   MatrixCoefficient *MQ = nullptr;
+   Coefficient *Q;
+   VectorCoefficient *VQ;
+   MatrixCoefficient *MQ;
    // PA extension
+   Vector pa_data;
    const DofToQuad *maps;         ///< Not owned
    const GeometricFactors *geom;  ///< Not owned
-   int ne, dim, dofs1D, quad1D, coeff_vdim;
-   Vector pa_data;
+   int dim, ne, nq, dofs1D, quad1D;
 
 public:
    /// Construct an integrator with coefficient 1.0
-   VectorMassIntegrator() = default;
-
+   VectorMassIntegrator()
+      : vdim(-1), Q_order(0), Q(NULL), VQ(NULL), MQ(NULL) { }
    /** Construct an integrator with scalar coefficient q.  If possible, save
        memory by using a scalar integrator since the resulting matrix is block
        diagonal with the same diagonal block repeated. */
-   VectorMassIntegrator(Coefficient &q, int qo = 0): Q_order(qo), Q(&q) { }
-
-   VectorMassIntegrator(Coefficient &q, const IntegrationRule *ir):
-      BilinearFormIntegrator(ir), Q(&q) { }
-
+   VectorMassIntegrator(Coefficient &q, int qo = 0)
+      : vdim(-1), Q_order(qo), Q(&q), VQ(NULL), MQ(NULL) { }
+   VectorMassIntegrator(Coefficient &q, const IntegrationRule *ir)
+      : BilinearFormIntegrator(ir), vdim(-1), Q_order(0), Q(&q), VQ(NULL),
+        MQ(NULL) { }
    /// Construct an integrator with diagonal coefficient q
-   VectorMassIntegrator(VectorCoefficient &q, int qo = 0):
-      vdim(q.GetVDim()), Q_order(qo), VQ(&q) { }
-
+   VectorMassIntegrator(VectorCoefficient &q, int qo = 0)
+      : vdim(q.GetVDim()), Q_order(qo), Q(NULL), VQ(&q), MQ(NULL) { }
    /// Construct an integrator with matrix coefficient q
-   VectorMassIntegrator(MatrixCoefficient &q, int qo = 0):
-      vdim(q.GetVDim()), Q_order(qo), MQ(&q) { }
+   VectorMassIntegrator(MatrixCoefficient &q, int qo = 0)
+      : vdim(q.GetVDim()), Q_order(qo), Q(NULL), VQ(NULL), MQ(&q) { }
 
    int GetVDim() const { return vdim; }
    void SetVDim(int vdim_) { vdim = vdim_; }
@@ -2641,7 +2624,6 @@ public:
                                const FiniteElement &test_fe,
                                ElementTransformation &Trans,
                                DenseMatrix &elmat) override;
-
    using BilinearFormIntegrator::AssemblePA;
    void AssemblePA(const FiniteElementSpace &fes) override;
    void AssembleMF(const FiniteElementSpace &fes) override;
@@ -2650,15 +2632,6 @@ public:
    void AddMultPA(const Vector &x, Vector &y) const override;
    void AddMultMF(const Vector &x, Vector &y) const override;
    bool SupportsCeed() const override { return DeviceCanUseCeed(); }
-
-   using VectorMassAddMultPAType =
-      void(*)(const int,  const int,
-              const Array<real_t>&, const Vector&,
-              const Vector&, Vector&, const int, const int);
-
-   MFEM_REGISTER_KERNELS(VectorMassAddMultPA,
-                         VectorMassAddMultPAType,
-                         (int, int, int));
 };
 
 
@@ -2710,7 +2683,7 @@ public:
 
 
 /** Integrator for $(-Q u, \nabla v)$ for Nedelec ($u$) and $H^1$ ($v$) elements.
-    This is equivalent to a weak divergence of the $H(curl)$ basis functions. */
+    This is equivalent to a weak divergence of the $H(curl$ basis functions. */
 class VectorFEWeakDivergenceIntegrator: public BilinearFormIntegrator
 {
 protected:
@@ -2830,13 +2803,15 @@ protected:
    bool symmetric = true; ///< False if using a nonsymmetric matrix coefficient
 
 public:
-   CurlCurlIntegrator();
+   CurlCurlIntegrator() { Q = NULL; DQ = NULL; MQ = NULL; }
    /// Construct a bilinear form integrator for Nedelec elements
-   CurlCurlIntegrator(Coefficient &q, const IntegrationRule *ir = nullptr);
+   CurlCurlIntegrator(Coefficient &q, const IntegrationRule *ir = NULL) :
+      BilinearFormIntegrator(ir), Q(&q), DQ(NULL), MQ(NULL) { }
    CurlCurlIntegrator(DiagonalMatrixCoefficient &dq,
-                      const IntegrationRule *ir = nullptr);
-   CurlCurlIntegrator(MatrixCoefficient &mq,
-                      const IntegrationRule *ir = nullptr);
+                      const IntegrationRule *ir = NULL) :
+      BilinearFormIntegrator(ir), Q(NULL), DQ(&dq), MQ(NULL) { }
+   CurlCurlIntegrator(MatrixCoefficient &mq, const IntegrationRule *ir = NULL) :
+      BilinearFormIntegrator(ir), Q(NULL), DQ(NULL), MQ(&mq) { }
 
    /* Given a particular Finite Element, compute the
       element curl-curl matrix elmat */
@@ -2866,34 +2841,6 @@ public:
    void AssembleDiagonalPA(Vector& diag) override;
 
    const Coefficient *GetCoefficient() const { return Q; }
-
-   /// arguments: d1d, q1d, symmetric, NE, bo, bc, bot, bct, gc, gct, pa_data,
-   /// x, y, useAbs
-   using ApplyKernelType = void (*)(
-                              const int, const int, const bool, const int, const Array<real_t> &,
-                              const Array<real_t> &, const Array<real_t> &, const Array<real_t> &,
-                              const Array<real_t> &, const Array<real_t> &, const Vector &,
-                              const Vector &, Vector &, const bool);
-
-   /// arguments: d1d, q1d, symmetric, ne, Bo, Bc, Go, Gc, pa_data, diag
-   using DiagonalKernelType = void (*)(const int, const int, const bool,
-                                       const int, const Array<real_t> &,
-                                       const Array<real_t> &,
-                                       const Array<real_t> &,
-                                       const Array<real_t> &, const Vector &,
-                                       Vector &);
-
-   /// parameters: dim, d1d, q1d
-   MFEM_REGISTER_KERNELS(ApplyPAKernels, ApplyKernelType, (int, int, int));
-   /// parameters: dim, d1d, q1d
-   MFEM_REGISTER_KERNELS(DiagonalPAKernels, DiagonalKernelType, (int, int, int));
-   struct Kernels { Kernels(); };
-
-   template <int DIM, int D1D, int Q1D> static void AddSpecialization()
-   {
-      ApplyPAKernels::Specialization<DIM, D1D, Q1D>::Add();
-      DiagonalPAKernels::Specialization<DIM, D1D, Q1D>::Add();
-   }
 };
 
 /** Integrator for $(\mathrm{curl}(u), \mathrm{curl}(v))$ for FE spaces defined by 'dim' copies of a
@@ -3129,34 +3076,39 @@ public:
     to be the spatial dimension (i.e. 2-dimension or 3-dimension). */
 class VectorDiffusionIntegrator : public BilinearFormIntegrator
 {
-   int vdim = -1;
-   DenseMatrix dshape, dshapedxt, pelmat;
-   DenseMatrix mcoeff;
-   Vector vcoeff;
-
 protected:
-   Coefficient *Q = nullptr;
-   VectorCoefficient *VQ = nullptr;
-   MatrixCoefficient *MQ = nullptr;
+   Coefficient *Q = NULL;
+   VectorCoefficient *VQ = NULL;
+   MatrixCoefficient *MQ = NULL;
+
    // PA extension
    const DofToQuad *maps;         ///< Not owned
    const GeometricFactors *geom;  ///< Not owned
-   int ne, dim, sdim, dofs1D, quad1D, coeff_vdim;
+   int dim, sdim, ne, dofs1D, quad1D;
    Vector pa_data;
 
+private:
+   DenseMatrix dshape, dshapedxt, pelmat;
+   int vdim = -1;
+   DenseMatrix mcoeff;
+   Vector vcoeff;
+
 public:
-   VectorDiffusionIntegrator(const IntegrationRule *ir = nullptr);
+   VectorDiffusionIntegrator() { }
 
    /** \brief Integrator with unit coefficient for caller-specified vector
        dimension.
 
        If the vector dimension does not match the true dimension of the space,
        the resulting element matrix will be mathematically invalid. */
-   VectorDiffusionIntegrator(int vector_dimension);
+   VectorDiffusionIntegrator(int vector_dimension)
+      : vdim(vector_dimension) { }
 
-   VectorDiffusionIntegrator(Coefficient &q);
+   VectorDiffusionIntegrator(Coefficient &q)
+      : Q(&q) { }
 
-   VectorDiffusionIntegrator(Coefficient &q, const IntegrationRule *ir);
+   VectorDiffusionIntegrator(Coefficient &q, const IntegrationRule *ir)
+      : BilinearFormIntegrator(ir), Q(&q) { }
 
    /** \brief Integrator with scalar coefficient for caller-specified vector
        dimension.
@@ -3166,7 +3118,8 @@ public:
 
        If the vector dimension does not match the true dimension of the space,
        the resulting element matrix will be mathematically invalid. */
-   VectorDiffusionIntegrator(Coefficient &q, int vector_dimension);
+   VectorDiffusionIntegrator(Coefficient &q, int vector_dimension)
+      : Q(&q), vdim(vector_dimension) { }
 
    /** \brief Integrator with \c VectorCoefficient. The vector dimension of the
        \c FiniteElementSpace is assumed to be the same as the dimension of the
@@ -3177,7 +3130,8 @@ public:
 
        If the vector dimension does not match the true dimension of the space,
        the resulting element matrix will be mathematically invalid. */
-   VectorDiffusionIntegrator(VectorCoefficient &vq);
+   VectorDiffusionIntegrator(VectorCoefficient &vq)
+      : VQ(&vq), vdim(vq.GetVDim()) { }
 
    /** \brief Integrator with \c MatrixCoefficient. The vector dimension of the
        \c FiniteElementSpace is assumed to be the same as the dimension of the
@@ -3188,7 +3142,8 @@ public:
 
        If the vector dimension does not match the true dimension of the space,
        the resulting element matrix will be mathematically invalid. */
-   VectorDiffusionIntegrator(MatrixCoefficient& mq);
+   VectorDiffusionIntegrator(MatrixCoefficient& mq)
+      : MQ(&mq), vdim(mq.GetVDim()) { }
 
    void AssembleElementMatrix(const FiniteElement &el,
                               ElementTransformation &Trans,
@@ -3196,7 +3151,6 @@ public:
    void AssembleElementVector(const FiniteElement &el,
                               ElementTransformation &Tr,
                               const Vector &elfun, Vector &elvect) override;
-
    using BilinearFormIntegrator::AssemblePA;
    void AssemblePA(const FiniteElementSpace &fes) override;
    void AssembleMF(const FiniteElementSpace &fes) override;
@@ -3205,23 +3159,6 @@ public:
    void AddMultPA(const Vector &x, Vector &y) const override;
    void AddMultMF(const Vector &x, Vector &y) const override;
    bool SupportsCeed() const override { return DeviceCanUseCeed(); }
-
-   /// arguments: ne, coeff_vdim, B, G, pa_data, x, y, d1d, q1d, vdim
-   using ApplyKernelType = void (*)(const int, const int,
-                                    const Array<real_t> &, const Array<real_t> &,
-                                    const Vector &, const Vector &, Vector &,
-                                    const int, const int, const int);
-
-   /// arguments: dim, vdim, d1d, q1d
-   MFEM_REGISTER_KERNELS(ApplyPAKernels, ApplyKernelType, (int, int, int, int));
-
-   template <int DIM, int VDIM, int D1D, int Q1D>
-   static void AddSpecialization()
-   {
-      ApplyPAKernels::Specialization<DIM, VDIM, D1D, Q1D>::Add();
-   }
-
-   // struct Kernels { Kernels(); };
 };
 
 /** Integrator for the linear elasticity form:
@@ -3375,8 +3312,8 @@ public:
 class DGTraceIntegrator : public BilinearFormIntegrator
 {
 protected:
-   Coefficient *rho = nullptr;
-   VectorCoefficient *u = nullptr;
+   Coefficient *rho;
+   VectorCoefficient *u;
    real_t alpha, beta;
    // PA extension
    Vector pa_data;
@@ -3389,16 +3326,17 @@ private:
    Vector tr_shape1, te_shape1, tr_shape2, te_shape2;
 
 public:
-   DGTraceIntegrator(real_t a, real_t b);
-
    /// Construct integrator with $\rho = 1$, $\beta = \alpha/2$.
-   DGTraceIntegrator(VectorCoefficient &u_, real_t a);
+   DGTraceIntegrator(VectorCoefficient &u_, real_t a)
+   { rho = NULL; u = &u_; alpha = a; beta = 0.5*a; }
 
    /// Construct integrator with $\rho = 1$.
-   DGTraceIntegrator(VectorCoefficient &u_, real_t a, real_t b);
+   DGTraceIntegrator(VectorCoefficient &u_, real_t a, real_t b)
+   { rho = NULL; u = &u_; alpha = a; beta = b; }
 
    DGTraceIntegrator(Coefficient &rho_, VectorCoefficient &u_,
-                     real_t a, real_t b);
+                     real_t a, real_t b)
+   { rho = &rho_; u = &u_; alpha = a; beta = b; }
 
    using BilinearFormIntegrator::AssembleFaceMatrix;
    void AssembleFaceMatrix(const FiniteElement &el1,
@@ -3437,26 +3375,6 @@ public:
    static const IntegrationRule &GetRule(Geometry::Type geom, int order,
                                          const ElementTransformation &T);
 
-   /// arguments: nf, B, Bt, pa_data, x, y, dofs1D, quad1D
-   using ApplyKernelType = void (*)(const int, const Array<real_t> &,
-                                    const Array<real_t> &, const Vector &,
-                                    const Vector &, Vector &, const int,
-                                    const int);
-
-   /// arguments: DIM, d1d, q1d
-   MFEM_REGISTER_KERNELS(ApplyPAKernels, ApplyKernelType, (int, int, int));
-   /// arguments: DIM, d1d, q1d
-   MFEM_REGISTER_KERNELS(ApplyPATKernels, ApplyKernelType, (int, int, int));
-
-   template <int DIM, int D1D, int Q1D> static void AddSpecialization()
-   {
-      ApplyPAKernels::Specialization<DIM, D1D, Q1D>::Add();
-      ApplyPATKernels::Specialization<DIM, D1D, Q1D>::Add();
-   }
-
-   struct Kernels { Kernels(); };
-
-
 private:
    void SetupPA(const FiniteElementSpace &fes, FaceType type);
 };
@@ -3503,8 +3421,8 @@ public:
 class DGDiffusionIntegrator : public BilinearFormIntegrator
 {
 protected:
-   Coefficient *Q = nullptr;
-   MatrixCoefficient *MQ = nullptr;
+   Coefficient *Q;
+   MatrixCoefficient *MQ;
    real_t sigma, kappa;
 
    // these are not thread-safe!
@@ -3519,11 +3437,15 @@ protected:
    IntegrationRules irs{0, Quadrature1D::GaussLobatto};
 
 public:
-   DGDiffusionIntegrator(const real_t s, const real_t k);
-   DGDiffusionIntegrator(Coefficient &q, const real_t s, const real_t k);
-   DGDiffusionIntegrator(MatrixCoefficient &q, const real_t s, const real_t k);
+   DGDiffusionIntegrator(const real_t s, const real_t k)
+      : Q(NULL), MQ(NULL), sigma(s), kappa(k) { }
+   DGDiffusionIntegrator(Coefficient &q, const real_t s, const real_t k)
+      : Q(&q), MQ(NULL), sigma(s), kappa(k) { }
+   DGDiffusionIntegrator(MatrixCoefficient &q, const real_t s, const real_t k)
+      : Q(NULL), MQ(&q), sigma(s), kappa(k) { }
    using BilinearFormIntegrator::AssembleFaceMatrix;
-   void AssembleFaceMatrix(const FiniteElement &el1, const FiniteElement &el2,
+   void AssembleFaceMatrix(const FiniteElement &el1,
+                           const FiniteElement &el2,
                            FaceElementTransformations &Trans,
                            DenseMatrix &elmat) override;
 
@@ -3542,28 +3464,6 @@ public:
 
    const IntegrationRule &GetRule(int order, Geometry::Type geom);
 
-   real_t GetPenaltyParameter() const { return kappa; }
-
-   /// arguments: nf, B, Bt, G, Gt, sigma, pa_data, x, dxdn, y, dydn, dofs1D,
-   /// quad1D
-   using ApplyKernelType = void (*)(const int, const Array<real_t> &,
-                                    const Array<real_t> &,
-                                    const Array<real_t> &,
-                                    const Array<real_t> &, const real_t,
-                                    const Vector &, const Vector &_,
-                                    const Vector &, Vector &, Vector &,
-                                    const int, const int);
-
-   /// arguments: DIM, d1d, q1d
-   MFEM_REGISTER_KERNELS(ApplyPAKernels, ApplyKernelType, (int, int, int));
-
-   template <int DIM, int D1D, int Q1D> static void AddSpecialization()
-   {
-      ApplyPAKernels::Specialization<DIM, D1D, Q1D>::Add();
-   }
-
-   struct Kernels { Kernels(); };
-
 private:
    void SetupPA(const FiniteElementSpace &fes, FaceType type);
 };

fem/bounds.cpp

@@ -39,16 +39,11 @@ void PLBound::Setup(const int nb_i, const int ncp_i,
    b_type = b_type_i;
    cp_type = cp_type_i;
    tol = tol_i;
-   lbound.SetSize(ncp, nb);
-   ubound.SetSize(ncp, nb);
-   lbound_t.SetSize(nb, ncp);
-   ubound_t.SetSize(nb, ncp);
+   lbound.SetSize(nb, ncp);
+   ubound.SetSize(nb, ncp);
    nodes.SetSize(nb);
    weights.SetSize(nb);
    control_points.SetSize(ncp);
-   xhat.SetSize(nb);
-   what.SetSize(nb);
-   cphat.SetSize(ncp);
 
    auto scalenodes = [](const Vector &in, const real_t a, const real_t b) -> Vector
    {
@@ -95,10 +90,6 @@ void PLBound::Setup(const int nb_i, const int ncp_i,
       MFEM_ABORT("Unsupported interval points. Use [0,1].\n");
    }
    control_points = scalenodes(control_points, 0.0, 1.0); // rescale to [0,1]
-   for (int i = 0; i < ncp; i++)
-   {
-      cphat(i) = 2.0*control_points(i) - 1.0;
-   }
 
    Poly_1D::Basis &basis1d(poly1d.GetBasis(nb-1, b_type));
 
@@ -134,28 +125,22 @@ void PLBound::Setup(const int nb_i, const int ncp_i,
       {
          if (j == 0)
          {
-            lbound(j,i) = bv(i);
-            ubound(j,i) = bv(i);
+            lbound(i, j) = bv(i);
+            ubound(i, j) = bv(i);
          }
          else if (j == ncp-1)
          {
-            lbound(j,i) = bv(i);
-            ubound(j,i) = bv(i);
+            lbound(i, j) = bv(i);
+            ubound(i, j) = bv(i);
          }
          else
          {
             vals(0)  = bv(i);
             vals(1) =  bmv(i) +  dm*bdmv(i);
             vals(2) =  bpv(i) +  dp*bdpv(i);
-            lbound(j,i) = vals.Min()-tol; // tolerance for good measure
-            ubound(j,i) = vals.Max()+tol; // tolerance for good measure
-            if (b_type == 2)
-            {
-               lbound(j,i) = std::max(lbound(j,i),0_r);
-            }
+            lbound(i, j) = vals.Min()-tol; // tolerance for good measure
+            ubound(i, j) = vals.Max()+tol; // tolerance for good measure
          }
-         lbound_t(i,j) = lbound(j,i);
-         ubound_t(i,j) = ubound(j,i);
       }
    }
 
@@ -187,11 +172,6 @@ void PLBound::Setup(const int nb_i, const int ncp_i,
          nodes(i) = irule.IntPoint(i).x;
       }
    }
-   for (int i = 0; i < nb; i++)
-   {
-      xhat(i) = 2.0*nodes(i) - 1.0;
-      what(i) = 2.0*weights(i);
-   }
 
    if (b_type == 2)
    {
@@ -227,8 +207,7 @@ void PLBound::Setup(const int nb_i, const int ncp_i,
    }
 }
 
-PLBound::PLBound(const FiniteElementSpace *fes, const int ncp_i,
-                 const int cp_type_i)
+PLBound::PLBound(FiniteElementSpace *fes, int ncp_i, int cp_type_i)
 {
    MFEM_VERIFY(!fes->IsVariableOrder(),
                "Variable order meshes not yet supported.");
@@ -285,15 +264,15 @@ PLBound::PLBound(const FiniteElementSpace *fes, const int ncp_i,
    Setup(nb, ncp, b_type, cp_type, tol);
 }
 
-void PLBound::Get1DBounds(const Vector &coeff, Vector &intmin,
-                          Vector &intmax) const
+void PLBound::Get1DBounds(Vector &coeff, Vector &intmin, Vector &intmax) const
 {
    real_t x,w;
    intmin.SetSize(ncp);
    intmax.SetSize(ncp);
    intmin = 0.0;
    intmax = 0.0;
-   Vector coeffm;
+   Vector coeffm(nb);
+   coeffm = 0.0;
 
    real_t a0 = 0.0;
    real_t a1 = 0.0;
@@ -321,8 +300,6 @@ void PLBound::Get1DBounds(const Vector &coeff, Vector &intmin,
    // compute L2 projection for linear bases: a0 + a1*x
    if (proj)
    {
-      coeffm.SetSize(nb);
-      coeffm = 0.0;
       for (int i = 0; i < nb; i++)
       {
          x = 2.0*nodes_int(i)-1;
@@ -363,14 +340,13 @@ void PLBound::Get1DBounds(const Vector &coeff, Vector &intmin,
       real_t c = coeffm(i);
       for (int j = 0; j < ncp; j++)
       {
-         intmin(j) += min(lbound(j,i)*c, ubound(j,i)*c);
-         intmax(j) += max(lbound(j,i)*c, ubound(j,i)*c);
+         intmin(j) += min(lbound(i,j)*c, ubound(i,j)*c);
+         intmax(j) += max(lbound(i,j)*c, ubound(i,j)*c);
       }
    }
 }
 
-void PLBound::Get2DBounds(const Vector &coeff, Vector &intmin,
-                          Vector &intmax) const
+void PLBound::Get2DBounds(Vector &coeff, Vector &intmin, Vector &intmax) const
 {
    intmin.SetSize(ncp*ncp);
    intmax.SetSize(ncp*ncp);
@@ -495,10 +471,10 @@ void PLBound::Get2DBounds(const Vector &coeff, Vector &intmin,
          real_t w1 = intmaxT(id2++);
          for (int k = 0; k < ncp; k++) // kth row
          {
-            vals(0) = w0*lbound(k,j);
-            vals(1) = w0*ubound(k,j);
-            vals(2) = w1*lbound(k,j);
-            vals(3) = w1*ubound(k,j);
+            vals(0) = w0*lbound(j,k);
+            vals(1) = w0*ubound(j,k);
+            vals(2) = w1*lbound(j,k);
+            vals(3) = w1*ubound(j,k);
             intmin(k*ncp+i) += vals.Min();
             intmax(k*ncp+i) += vals.Max();
          }
@@ -506,8 +482,7 @@ void PLBound::Get2DBounds(const Vector &coeff, Vector &intmin,
    }
 }
 
-void PLBound::Get3DBounds(const Vector &coeff, Vector &intmin,
-                          Vector &intmax) const
+void PLBound::Get3DBounds(Vector &coeff, Vector &intmin, Vector &intmax) const
 {
    int nb2 = nb*nb,
        ncp2 = ncp*ncp,
@@ -574,17 +549,17 @@ void PLBound::Get3DBounds(const Vector &coeff, Vector &intmin,
             for (int i = 0; i < nb; i++)
             {
                x = 2.0*nodes(i)-1; // x-coordinate
-               minNodalVals(i) -= a0V(j) + a1V(j)*x;
-               maxNodalVals(i) -= a0V(j) + a1V(j)*x;
+               minBounds(i) -= a0V(j) + a1V(j)*x;
+               maxBounds(i) -= a0V(j) + a1V(j)*x;
             }
             // Compute Bernstein coefficients
             LUFactors lu(basisMatLU.GetData(), lu_ip.GetData());
-            lu.Solve(nb, 1, minNodalVals.GetData());
-            lu.Solve(nb, 1, maxNodalVals.GetData());
+            lu.Solve(nb, 1, minBounds.GetData());
+            lu.Solve(nb, 1, maxBounds.GetData());
             for (int i = 0; i < nb; i++)
             {
-               intminT(i*ncp2+j) = minNodalVals(i);
-               intmaxT(i*ncp2+j) = maxNodalVals(i);
+               intminT(i*ncp2+j) = minBounds(i);
+               intmaxT(i*ncp2+j) = maxBounds(i);
             }
          }
       }
@@ -638,10 +613,10 @@ void PLBound::Get3DBounds(const Vector &coeff, Vector &intmin,
          real_t w1 = intmaxT(id2++);
          for (int k = 0; k < ncp; k++) // kth slice
          {
-            vals(0) = w0*lbound(k,j);
-            vals(1) = w0*ubound(k,j);
-            vals(2) = w1*lbound(k,j);
-            vals(3) = w1*ubound(k,j);
+            vals(0) = w0*lbound(j,k);
+            vals(1) = w0*ubound(j,k);
+            vals(2) = w1*lbound(j,k);
+            vals(3) = w1*ubound(j,k);
             intmin(k*ncp2+i) += vals.Min();
             intmax(k*ncp2+i) += vals.Max();
          }
@@ -649,7 +624,7 @@ void PLBound::Get3DBounds(const Vector &coeff, Vector &intmin,
    }
 }
 
-void PLBound::GetNDBounds(const int rdim, const Vector &coeff,
+void PLBound::GetNDBounds(int rdim, Vector &coeff,
                           Vector &intmin, Vector &intmax) const
 {
    if (rdim == 1)
@@ -674,8 +649,7 @@ void PLBound::SetupBernsteinBasisMat(DenseMatrix &basisMat,
                                      Vector &nodesBern) const
 {
    const int nbern = nodesBern.Size();
-   L2_SegmentElement el(nbern-1, 2);
-   // we use L2 to leverage lexicographic order
+   L2_SegmentElement el(nbern-1, 2); // we use L2 to leverage lexicographic order
    Array<int> ordering = el.GetLexicographicOrdering();
    basisMat.SetSize(nbern, nbern);
    Vector shape(nbern);
@@ -688,39 +662,6 @@ void PLBound::SetupBernsteinBasisMat(DenseMatrix &basisMat,
    }
 }
 
-DenseMatrix PLBound::GetBoundingMatrix(int dim, bool is_lower) const
-{
-   if (dim > 1)
-   {
-      const int ncpd = static_cast<int>(std::pow(ncp, dim));
-      const int nbd = static_cast<int>(std::pow(nb, dim));
-      DenseMatrix boundND(ncpd, nbd);
-      Vector phimin, phimax, col;
-      Vector coeffs(nbd);
-      coeffs = 0.0;
-      for (int j = 0; j < nbd; j++)
-      {
-         coeffs(j) = 1.0;
-         boundND.GetColumnReference(j, col);
-         GetNDBounds(dim, coeffs, phimin, phimax);
-         col = is_lower ? phimin : phimax;
-         coeffs(j) = 0.0;
-      }
-      return boundND;
-   }
-   return is_lower ? lbound : ubound;
-}
-
-DenseMatrix PLBound::GetLowerBoundMatrix(int dim) const
-{
-   return GetBoundingMatrix(dim, true);
-}
-
-DenseMatrix PLBound::GetUpperBoundMatrix(int dim) const
-{
-   return GetBoundingMatrix(dim, false);
-}
-
 constexpr int PLBound::min_ncp_gl_x[2][11];
 constexpr int PLBound::min_ncp_gll_x[2][11];
 constexpr int PLBound::min_ncp_pos_x[2][11];