vis script

.binder/environment.yml

@@ -1,12 +0,0 @@
-# extends https://github.com/jupyterhub/repo2docker/blob/main/repo2docker/buildpacks/conda/environment.yml
-# see https://mybinder.readthedocs.io/en/latest/using/config_files.html#environment-yml-install-a-conda-environment
-channels:
-- conda-forge
-dependencies:
-- xeus-cling=0.13.0
-- xwidgets=0.26.0
-# NOTE: it's possible these aren't needed for the lab frontend
-- widgetsnbextension=3.5.1
-- pip
-- pip:
-  - glvis==0.3.2

.binder/postBuild

@@ -1,26 +0,0 @@
-#!/bin/bash
-
-set -e
-
-# cling is installed here (in bin) and will look in {dir}/include and {dir}/lib
-# without extra intervention (jk it doesn't look in {dir}/lib unless something
-# has been #included from {dir}/include first...)
-install_dir=/srv/conda/envs/notebook
-mkdir -p $install_dir
-
-# build and install mfem, which is the directory we start in
-make serial SHARED=YES -j8
-make install PREFIX=$install_dir
-
-# install xeus-glvis
-git clone https://github.com/GLVis/xeus-glvis.git
-pushd xeus-glvis
-make install prefix=$install_dir
-popd
-
-# install jupyter-lab extension
-jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
-jupyter labextension install glvis-jupyter
-
-# fixup kernelspec, we could probably do this from sh but ¯\_(ツ)_/¯
-python .binder/update_kernel_env.py

.binder/update_kernel_env.py

@@ -1,14 +0,0 @@
-# Update the LD_LIBRARY_PATH of the C++14 kernel so it can find mfem without
-# extra pragma cling statements
-
-import json
-
-kernelspec = "/srv/conda/envs/notebook/share/jupyter/kernels/xcpp14/kernel.json"
-
-with open(kernelspec, "r") as f:
-    obj = json.load(f)
-
-obj["env"] = {"LD_LIBRARY_PATH": "/srv/conda/envs/notebook/lib"}
-
-with open(kernelspec, "w") as f:
-    json.dump(obj, f)

.github/workflows/mfem-analysis.yml

@@ -82,9 +82,9 @@ jobs:
       uses: mfem/github-actions/build-mfem@v2.0
       with:
         os: ${{ runner.os }}
-        target: opt
+        target: optim
         codecov: NO
-        mpi: par
+        mpi: parallel
         build-system: make
         hypre-dir: ${{ env.HYPRE_TOP_DIR }}
         metis-dir: ${{ env.METIS_TOP_DIR }}

.github/workflows/repo-check.yml

@@ -63,7 +63,7 @@ jobs:
         exit 1
 
   code-style:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-16.04 # needed for astyle 2.05.1
 
     steps:
     - name: checkout mfem
@@ -71,7 +71,7 @@ jobs:
 
     - name: get astyle
       run: |
-        sudo apt-get install astyle=3.1-1ubuntu2
+        sudo apt-get install astyle=2.05.1-0ubuntu1
 
     - name: style check
       run: |
@@ -105,9 +105,6 @@ jobs:
 
     - name: branch-history
       run: |
-        # We override origin to make sure we point to the main repo.
-        # This is to have consistent test results on PRs from forks.
-        git remote remove origin
-        git remote add origin https://github.com/mfem/mfem.git
+        git fetch origin master:master
         git checkout -b gh-actions-branch-history
         ./config/githooks/pre-push --history

.gitignore

@@ -51,8 +51,13 @@ examples/ex1[04-9]
 examples/ex1[0-9]p
 examples/ex2[0-9]
 examples/ex2[0-9]p
-examples/ex30
-examples/ex30p
+
+examples/soln-*
+examples/reference-*
+examples/*.dat
+examples/*.gif
+examples/*.mp4
+examples/*.gf
 
 examples/refined.mesh
 examples/displaced.mesh
@@ -225,14 +230,6 @@ miniapps/mtop/ParHeat*
 miniapps/mtop/seqheat
 miniapps/mtop/SeqHeat*
 
-miniapps/autodiff/paradiff
-miniapps/autodiff/seqadiff
-miniapps/autodiff/seqtest
-miniapps/autodiff/par_example
-miniapps/autodiff/seq_example
-miniapps/autodiff/seq_test
-miniapps/autodiff/Exampl*
-
 miniapps/navier/navier_mms
 miniapps/navier/navier_kovasznay
 miniapps/navier/navier_kovasznay_vs
@@ -298,15 +295,10 @@ miniapps/solvers/ParaView
 miniapps/solvers/mesh.*
 miniapps/solvers/sol.*
 
-miniapps/parelag/MultilevelHcurlHdivSolver
-miniapps/parelag/*.mesh
-
 # Unit test binary and outputs
 tests/unit/output_meshes
 tests/unit/unit_tests
 tests/unit/punit_tests
-tests/unit/cunit_tests
-tests/unit/pcunit_tests
 tests/unit/sedov_tests_*
 tests/unit/psedov_tests_*
 tests/unit/tmop_pa_tests_*
@@ -314,12 +306,6 @@ tests/unit/ptmop_pa_tests_*
 tests/unit/ceed_tests
 tests/unit/debug_device_tests
 
-# Benchmark binaries
-tests/benchmarks/bench_ceed
-tests/benchmarks/bench_tmop
-tests/benchmarks/bench_vector
-tests/benchmarks/bench_virtuals
-
 # Test script output
 tests/scripts/*.err
 tests/scripts/*.out
@@ -336,6 +322,3 @@ build-*/*
 # PETSc automated build
 petsc-build/*
 pkg.gitcommit
-
-# Jupyter Notebook Checkpoints
-.ipynb_checkpoints

.gitlab-ci.yml

@@ -13,84 +13,243 @@
 # at Lawrence Livermore National Laboratory (LLNL). This entire pipeline is
 # LLNL-specific!
 
+# We define the following GitLab pipeline variables:
+#
+# BUILD_ROOT:
+# The path to the shared resources 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
+#
+# 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.
+#
+# MFEM_ALLOC_NAME:
+# On LLNL's quartz, there is only one allocation shared among jobs in order to
+# save time and resources. This allocation has to be uniquely named so that we
+# are sure to retrieve it.
+#
+# TPLS_REPO & TESTS_REPO:
+# Git repositories used in the pipeline
+#
+# ARTIFACTS_DIR:
+# Directory used to place artifacts.
+
+variables:
+  BUILD_ROOT: ${CI_BUILDS_DIR}/MFEM/${CI_PROJECT_NAME}_${CI_COMMIT_REF_SLUG}_${CI_PIPELINE_ID}
+  AUTOTEST_ROOT: ${CI_BUILDS_DIR}/MFEM
+  REBASELINE: "NO"
+  AUTOTEST: "NO"
+  ALLOC_NAME: ${CI_PROJECT_NAME}_ci_${CI_PIPELINE_ID}
+  TPLS_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/tpls.git
+  TESTS_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/tests.git
+  AUTOTEST_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/autotest.git
+  MFEM_DATA_REPO: https://github.com/mfem/data.git
+  ARTIFACTS_DIR: artifacts
+  SLURM_OVERLAP: 1
 
 # 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 quartz resource are allocated/released once for all.
+# - Allocate/Release is where quartz resources are allocated/released once for all.
 # - Build and Test is where we build and MFEM for multiple toolchains.
 # - Baseline_checks gathers baseline-type test suites execution
 # - Baseline_publish, only available on master, allows to update baseline
 #   results
 stages:
-  - sub-pipelines
+  - setup
+  - q_allocate_resources
+  - q_build_and_test
+  - q_release_resources
+  - l_build_and_test
+  - c_build_and_test
+  - setup_baseline
+  - baseline_check
+  - baseline_to_autotest
+  - baseline_publish
 
-variables:
-  CUSTOM_CI_BUILDS_DIR: "/usr/workspace/mfem/gitlab-runner"
-  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"
-
-# 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: "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"
-
-# Trigger subpipelines:
-quartz-build-and-test:
-  stage: sub-pipelines
+# setup clones the mfem/data repo in ${BUILD_ROOT}. The build_and_test script
+# then symlinks the repo to the parent directory of the MFEM source directory.
+# Unit tests that depend on the mfem/data repo will then detect that this
+# directory is present and be enabled.
+setup:
+  tags:
+    - shell
+    - quartz
+  stage: setup
   variables:
-    # Explicitly pass down values that we want to be able to set when triggering
-    # pipelines manually or using scheduling
-    AUTOTEST: "${AUTOTEST}"
-    AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
-  trigger:
-    include: .gitlab/quartz-build-and-test.yml
-    strategy: depend
+    GIT_STRATEGY: none
+  script:
+    - mkdir -p ${BUILD_ROOT} && cd ${BUILD_ROOT}
+    - if [ ! -d data ]; then git clone ${MFEM_DATA_REPO}; fi
 
-quartz-baseline:
-  stage: sub-pipelines
+# The setup_baseline job in setup stage_baseline doesn't rely on MFEM git repo.
+# It prepares a pipeline-wide working directory downloading/updating external
+# repos. TODO: updating tests and tpls is not necessary anymore since pipelines
+# are now using unique directories so repo are never shared with another
+# pipeline. This is not memory efficient (we keep a lot of data), hence this
+# reminder.
+# Note: This job can start immediately.
+setup_baseline:
+  tags:
+    - shell
+    - quartz
+  stage: setup_baseline
   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/quartz-baseline.yml
-    strategy: depend
+    GIT_STRATEGY: none
+  script:
+    - mkdir -p ${BUILD_ROOT} && cd ${BUILD_ROOT}
+    - if [ ! -d "tpls" ]; then git clone ${TPLS_REPO}; fi
+    - if [ ! -d "tests" ]; then git clone ${TESTS_REPO}; fi
+    - cd tpls && git pull && cd ..
+    - cd tests && git pull && cd ..
+    - cd ${AUTOTEST_ROOT}
+    - if [ ! -d "autotest" ]; then git clone ${AUTOTEST_REPO}; fi
+    - cd autotest && git pull && cd ..
+  needs: []
 
-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
+.build_toss_3_x86_64_ib_script:
+  script:
+    - export THREADS=12
+    - echo ${ALLOC_NAME}
+    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
+    - echo ${JOBID}
+    - srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) -t 30 -N 1 tests/gitlab/build_and_test
 
-corona-build-and-test:
-  stage: sub-pipelines
+.build_toss_3_x86_64_ib_corona_script:
+  script:
+    - srun -p mi60 -t 15 -N 1 tests/gitlab/build_and_test
+
+# Lassen uses a different job scheduler (spectrum lsf) that does not allow
+# pre-allocation the same way slurm does.  We use pdebug queue on lassen to
+# speed-up the allocation.  However this would not be scalable to multiple
+# builds.
+.build_blueos_3_ppc64le_ib_script:
+  script:
+    - lalloc 1 -W 30 -q pdebug tests/gitlab/build_and_test
+
+# Shared script for baseline and sample-run-baseline, the value of BASELINE_TEST
+# differentiates between the two tests.
+.baseline_script: &baseline_script |
+  # locals
+  _glob_err=${BASELINE_TEST}.err
+  _base_diff=${BASELINE_TEST}-${SYS_TYPE}.diff
+  _base_patch=${BASELINE_TEST}-${SYS_TYPE}.patch
+  _base_out=${BASELINE_TEST}-${SYS_TYPE}.out
+  # prepare
+  cd ${BUILD_ROOT}
+  ln -snf ${CI_PROJECT_DIR} mfem
+  cd tests
+  mkdir _${BASELINE_TEST} && cd _${BASELINE_TEST}
+  # run
+  srun --nodes=1 -p pdebug ../runtest ../../mfem "${BASELINE_TEST} ${ADDITIONAL_DIR}"
+  # post
+  mkdir ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}
+  if [[ -s ${_glob_err} ]]
+  then
+    echo "ERROR during ${BASELINE_TEST} execution";
+    echo "Here is the ${_glob_err} file content";
+    cat ${_glob_err}
+    cp ${_glob_err} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_glob_err}
+    exit 1;
+  elif [[ ! -f ${_base_patch} && ! -f ${_base_out} ]]
+  then
+    echo "Something went WRONG in ${BASELINE_TEST}:";
+    echo "Either ${_base_patch} or ${_base_out} should exists";
+    exit 1;
+  elif [[ -f ${_base_patch} ]]
+  then
+    echo "${BASELINE_TEST}: Differences found, patch generated"
+    cp ${_base_patch} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_patch}
+  elif [[ -f ${_base_out} ]]
+  then
+    echo "${BASELINE_TEST}: Differences found, replacement file generated"
+    cp ${_base_out} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_out}
+  fi
+  # _base_diff won't even exist if there is no difference.
+  if [[ -f ${_base_diff} ]]
+  then
+    echo "${BASELINE_TEST}: Relevant differences (filtered diff) ..."
+    cat ${_base_diff}
+    cp ${_base_diff} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_diff}
+    # We create a .err file, because that's how we signal that there was a diff.
+    cp ${_base_diff} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/gitlab-${BASELINE_TEST}-${SYS_TYPE}.err
+  fi
+  if [[ ! -s ${_base_diff} ]]
+  then
+    echo "${BASELINE_TEST}: PASSED"
+    true
+  else
+    echo "${BASELINE_TEST}: FAILED"
+    false
+  fi
+
+# Actual templates for baseline checks
+.baselinecheck_mfem:
+  stage: baseline_check
   variables:
-    # Explicitly pass down values that we want to be able to set when triggering
-    # pipelines manually or using scheduling
-    AUTOTEST: "${AUTOTEST}"
-    AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
-  trigger:
-    include: .gitlab/corona-build-and-test.yml
-    strategy: depend
+    BASELINE_TEST: baseline
+    ADDITIONAL_DIR: ${BUILD_ROOT}/tpls
+  script:
+    - *baseline_script
+  artifacts:
+    when: always
+    paths:
+      - ${ARTIFACTS_DIR}
+  allow_failure: true
+
+.samplebaselinecheck_mfem:
+  stage: baseline_check
+  variables:
+    BASELINE_TEST: sample-runs-baseline
+    ADDITIONAL_DIR: ""
+  script:
+    - *baseline_script
+  timeout: 4h
+  artifacts:
+    when: always
+    paths:
+      - ${ARTIFACTS_DIR}
+  allow_failure: true
+
+# This job can only be manually triggered on a pipeline for master branch, or if
+# the pipeline was triggered with REBASELINE="YES"
+.rebaseline_mfem:
+  stage: baseline_publish
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master" || $REBASELINE == "YES"'
+      when: manual
+  script:
+    - export PATCH_FILE=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}.patch
+    - export FULL_FILE=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}.out
+    - export DIFF_FILE=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}.diff
+    - cd ${BUILD_ROOT}/tests
+    - |
+      if [[ ! -f "${DIFF_FILE}" ]]
+      then
+          echo "Nothing to be done: no relevant change in baseline"
+          exit 0
+      elif [[ -f "${PATCH_FILE}" ]]
+      then
+          patch "./baseline-${SYS_TYPE}.saved" < "${PATCH_FILE}"
+      elif [[ -f "${FULL_FILE}t" ]]
+      then
+          cp "${FULL_FILE}" "./baseline-${SYS_TYPE}.saved"
+      else
+          echo "File missing: expected ${PATCH_FILE} or ${FULL_FILE}"
+          exit 1
+      fi
+    - git add baseline-${SYS_TYPE}.saved
+    - git commit -m "${SYS_TYPE} rebaselined in GitLab pipeline ${CI_PIPELINE_ID}"
+    - git push origin master
+
+# The list on jobs is defined in machine-specific files.
+include:
+  - local: .gitlab/quartz.yml
+  - local: .gitlab/lassen.yml

.gitlab/README.md

@@ -1,94 +0,0 @@
-                    Finite Element Discretization Library
-                                   __
-                       _ __ ___   / _|  ___  _ __ ___
-                      | '_ ` _ \ | |_  / _ \| '_ ` _ \
-                      | | | | | ||  _||  __/| | | | | |
-                      |_| |_| |_||_|   \___||_| |_| |_|
-
-                               https://mfem.org
-
-
-This directory contains most of the GitLab CI configuration. MFEM runs both PR
-and nightly testing on GitLab.
-
-# Structure
-
-## Top level
-
-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:
-
-* Quartz: Intel bi-socket x86
-* Lassen: Power9 + Nvidia GPU
-* Corona: AMD GPU
-
-Test types include:
-
-* Build and test: Spack driven build of dependencies, mfem build, mfem
-  test
-* Baseline: Script driven build of dependencies, thorough testing
-
-⚠️ The sub-pipeline design allows to add a new machine or a new test type without
-altering the scheduling, execution and displaying of the others.
-
-## Sub-pipelines
-
-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
-though, the configuration is shared and is placed in `.gitlab/configs`.
-
-We try to keep scripts out of the CI config and share them among similar
-jobs. They are gathered in `.gitlab/scripts`.
-
-## Scripts
-
-Scripts specific to the CI only are in `.gitlab/scripts`. It is best practice
-to keep scripts outside the CI configuration (no bash scripts embedded in a
-yaml file) because it helps with readability, maintenance and also with
-transition to another CI system.
-
-⚠️ Most of the scripts there are driven by environment variables and do not have a
-usage function. This should be improved.
-
-
-# More testing
-
-## Adding a new target to a build_and_test pipeline
-
-`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 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`.
-
-In the end, the MFEM target for which to build the dependencies is expressed
-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 quartz for example resumes to:
-
-```yaml
-<job_name>:
-  variables:
-    SPEC: "<spack_spec>"
-  extends: .build_and_test_on_quartz
-```
-
-The remaining and non trivial work is to make sure this spec is working. To
-test a spec before adding it, or reproduce a CI configuration, please refer to
-`tests/gitlab/reproduce-ci-jobs-interactively.md`.
-
-⚠️ It is assumed that the spack spec applies to `mfem@develop`. That's why in the
-CI all the specs start with the compiler or the variants to apply to mfem. The
-mechanism still works with a full spec.

.gitlab/configs/common.yml

@@ -1,36 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# 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 quartz, 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

@@ -1,59 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# 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

@@ -1,49 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# 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 pdebug queue on lassen
-# to speed-up the allocation.  However this would not be scalable to
-# multiple builds.
-.build_and_test_on_lassen:
-  extends: [.on_lassen]
-  stage: build_and_test
-  script:
-    - echo ${MFEM_DATA_DIR}
-    - echo ${SPEC}
-    # Next script uses 'THREADS': leaving it empty --> it uses 'make all -j'
-    - lalloc 1 -W 30 -q pdebug tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
-  needs: [setup]

.gitlab/configs/quartz-config.yml

@@ -1,55 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# GitLab pipelines configurations for the Quartz machine at LLNL
-variables:
-  MACHINE_NAME: quartz
-
-.on_quartz:
-  tags:
-    - shell
-    - quartz
-  rules:
-    # Don't run quartz jobs if...
-    - if: '$CI_COMMIT_BRANCH =~ /_qnone/ || $ON_QUARTZ == "OFF"'
-      when: never
-    # Don't run autotest update if...
-    - if: '$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 quartz build job, extending build script
-.build_and_test_on_quartz:
-  extends: [.on_quartz]
-  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=${JOBID}" ) -t 30 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data

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

@@ -1,81 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# Jobs report
-.report_job_success:
-  script:
-    - echo ${MACHINE_NAME}
-    - echo ${AUTOTEST}
-    - echo ${AUTOTEST_COMMIT}
-    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
-    - cd ${AUTOTEST_ROOT}
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
-        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired lock on '$PWD/autotest.lock'"
-        date
-        # Report SUCCESS while holding the file lock on 'autotest.lock'.
-        # The next script uses the following environment variables:
-        # - 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 ${AUTOTEST_ROOT}
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
-        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired lock on '$PWD/autotest.lock'"
-        date
-        # Report FAILURE while holding the file lock on 'autotest.lock'.
-        # The next script uses the following environment variables:
-        # - 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/setup-baseline.yml

@@ -1,72 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# The setup_baseline job doesn't rely on MFEM git repo. It prepares a
-# pipeline-wide working directory downloading/updating external repos.
-# TODO:
-# updating tests and tpls is not necessary anymore since pipelines are now
-# using unique directories so repo are never shared with another pipeline. This
-# is not memory efficient (we keep a lot of data), hence this reminder.
-setup_baseline:
-  tags:
-    - shell
-    - quartz
-  stage: setup
-  variables:
-    GIT_STRATEGY: none
-  script:
-    #
-    # Setup ${BUILD_ROOT}/tpls and ${BUILD_ROOT}/tests:
-    #
-    - echo "MACHINE_NAME = ${MACHINE_NAME}"
-    - echo "REBASELINE = ${REBASELINE}"
-    - echo "AUTOTEST = ${AUTOTEST}"
-    - echo "AUTOTEST_COMMIT = ${AUTOTEST_COMMIT}"
-    - echo "BUILD_ROOT ${BUILD_ROOT}"
-    - mkdir -p ${BUILD_ROOT} && cd ${BUILD_ROOT}
-    - if [ ! -d "tpls" ]; then git clone ${TPLS_REPO}; fi
-    - if [ ! -d "tests" ]; then git clone ${TESTS_REPO}; fi
-    - cd tpls && git pull && cd ..
-    - cd tests && git pull origin && cd ..
-    #
-    # Setup ${AUTOTEST_ROOT}/autotest:
-    #
-    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
-    - mkdir -p ${AUTOTEST_ROOT} && cd ${AUTOTEST_ROOT}
-    - command -v flock || echo "Required command 'flock' not found"
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
-        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired 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/configs/setup-build-and-test.yml

@@ -1,94 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# Setup clones the mfem/data repo in ${SHARED_REPOS_DIR}. The build_and_test
-# script then symlinks the repo to the parent directory of the MFEM source
-# directory. Unit tests that depend on the mfem/data repo will then detect that
-# this directory is present and be enabled.
-setup:
-  tags:
-    - shell
-    - quartz
-  stage: setup
-  variables:
-    GIT_STRATEGY: none
-  script:
-    #
-    # Setup MFEM_DATA_DIR=${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 ${SHARED_REPOS_DIR}
-    - command -v flock || echo "Required command 'flock' not found"
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/mfem-data.lock' ..."
-        # try to get an excusive lock on fd 9 (mfem-data.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired 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 ${AUTOTEST_ROOT}
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
-        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired 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

@@ -1,67 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-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 ${ALLOC_NAME}
-    - salloc --exclusive --nodes=1 --partition=mi60 --time=30 --no-shell --job-name=${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/lassen.yml

@@ -9,31 +9,26 @@
 # terms of the BSD-3 license. We welcome feedback and contributions, see file
 # CONTRIBUTING.md for details.
 
-stages:
-  - setup
-  - build_and_test
-  - report
+# GitLab pipelines configurations for the Lassen machine at LLNL
+
+.on_lassen:
+  tags:
+    - shell
+    - lassen
+  rules:
+    - if: '$CI_COMMIT_BRANCH =~ /_lnone/ || $ON_LASSEN == "OFF"' #run except if ...
+      when: never
+    - when: on_success
+
+# Spack helped builds
+# Generic lassen build job, extending build script
+# Note: Lassen jobs can start as soon as the setup job is complete.
+.build_and_test_on_lassen:
+  extends: [.build_blueos_3_ppc64le_ib_script, .on_lassen]
+  stage: l_build_and_test
+  needs: [setup]
 
 opt_mpi_cuda_xl_16_1_1_8:
   variables:
     SPEC: "%xl@16.1.1.8 +mpi +cuda 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/quartz-baseline.yml

@@ -1,133 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-variables:
-  BASELINE_TEST: baseline
-
-stages:
-  - setup
-  - baseline_check
-  - baseline_report
-  - cleanup
-  - baseline_publish
-
-baselinecheck_mfem_intel_quartz:
-  extends: [.on_quartz]
-  stage: baseline_check
-  variables:
-    # TPLS_DIR is used in .gitlab/scripts/baseline to provide the tpls location
-    # when call the runtest script in MFEM test repo.
-    # Note: the value must be consistent with the setup performed in
-    #       .gitlab/configs/setup-baseline.yml.
-    TPLS_DIR: ${BUILD_ROOT}/tpls
-  script:
-    - echo ${BUILD_ROOT}
-    - echo ${TPLS_DIR}
-    # Used by the tests in MFEM/tests:
-    - export MFEM_TEST_NP=32
-    # The next script uses the following environment variables:
-    # * BASELINE_TEST, SYS_TYPE, CI_PROJECT_DIR, ARTIFACTS_DIR,
-    # * BUILD_ROOT, TPLS_DIR, MACHINE_NAME
-    - .gitlab/scripts/baseline
-  artifacts:
-    when: always
-    paths:
-      - ${ARTIFACTS_DIR}
-  allow_failure: true
-
-cleanup:
-  extends: .on_quartz
-  stage: cleanup
-  variables:
-    GIT_STRATEGY: none
-  script:
-    - echo "BUILD_ROOT=${BUILD_ROOT}"
-    - rm -rf "${BUILD_ROOT}" || true
-
-report_baseline:
-  extends: [.on_quartz]
-  stage: baseline_report
-  script:
-    - echo ${MACHINE_NAME}
-    - echo ${AUTOTEST}
-    - echo ${AUTOTEST_COMMIT}
-    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
-    - cd ${AUTOTEST_ROOT}
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
-        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired lock on '$PWD/autotest.lock'"
-        date
-        # ----------------------
-        cd ${AUTOTEST_ROOT}/autotest || \
-          { echo "Invalid 'autotest' dir: ${AUTOTEST_ROOT}/autotest"; exit 1; }
-        mkdir -p ${MACHINE_NAME}
-        rundir="${MACHINE_NAME}/$(date +%Y-%m-%d)-gitlab-${BASELINE_TEST}-${CI_COMMIT_REF_SLUG}"
-        rundir=$(${CI_PROJECT_DIR}/.gitlab/scripts/safe_create_rundir ${rundir})
-        cp ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/* ${rundir}
-        # We create an autotest-email.html file, because that's how we signal that there was a diff (temporary).
-        if [[ -f ${rundir}/${BASELINE_TEST}.err ]]; then
-          cp ${rundir}/${BASELINE_TEST}.err ${rundir}/autotest-email.html
-        fi
-        printf "%s\n" "" "Pipeline URL:" "$CI_PIPELINE_URL" \
-          >> ${rundir}/pipeline.txt
-        msg="GitLab CI log for ${BASELINE_TEST} on ${MACHINE_NAME} ($(date +%Y-%m-%d))"
-        if [[ "$AUTOTEST_COMMIT" != "NO" ]]; then
-          git pull && \
-          git add ${rundir} && \
-          git commit -m "${msg}" && \
-          git push origin master
-        else
-          for file in ${rundir}/*; do
-            echo "------------------------------"
-            echo "Content of '$file'"
-            echo "******************************"
-            cat $file
-            echo "******************************"
-          done
-          rm -rf ${rundir} || true
-        fi
-        err=$?
-        # ----------------------
-        # 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 $err
-      ) 9> autotest.lock
-
-baselinepublish_mfem_quartz:
-  extends: [.on_quartz]
-  stage: baseline_publish
-  rules:
-    # - if: '$CI_COMMIT_BRANCH == "master" || $REBASELINE == "YES"'
-    - if: '$REBASELINE == "YES"'
-      when: manual
-  script:
-    - echo ${BUILD_ROOT}
-    - echo ${PWD}
-    - echo ${ARTIFACTS_DIR}
-    - ls -lA ${ARTIFACTS_DIR}
-    - .gitlab/scripts/rebaseline
-
-include:
-  - local: .gitlab/configs/common.yml
-  - local: .gitlab/configs/quartz-config.yml
-  - local: .gitlab/configs/setup-baseline.yml

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

@@ -1,99 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-stages:
-  - setup
-  - allocate_resource
-  - build_and_test
-  - release_resource_and_report
-
-# Allocate
-allocate_resource:
-  variables:
-    GIT_STRATEGY: none
-  extends: .on_quartz
-  stage: allocate_resource
-  script:
-    - echo ${ALLOC_NAME}
-    - salloc --exclusive --nodes=1 --partition=pdebug --time=30 --no-shell --job-name=${ALLOC_NAME}
-  timeout: 6h
-
-# GitLab jobs for the Quartz machine at LLNL
-debug_ser_gcc_4_9_3:
-  variables:
-    SPEC: "%gcc@4.9.3 +debug~mpi"
-  extends: .build_and_test_on_quartz
-
-debug_ser_gcc_6_1_0:
-  variables:
-    SPEC: "%gcc@6.1.0 +debug~mpi"
-  extends: .build_and_test_on_quartz
-
-debug_par_gcc_6_1_0:
-  variables:
-    SPEC: "%gcc@6.1.0 +debug+mpi"
-  extends: .build_and_test_on_quartz
-
-opt_ser_gcc_6_1_0:
-  variables:
-    SPEC: "%gcc@6.1.0 ~mpi"
-  extends: .build_and_test_on_quartz
-
-opt_par_gcc_6_1_0:
-  variables:
-    SPEC: "%gcc@6.1.0"
-  extends: .build_and_test_on_quartz
-
-opt_par_gcc_6_1_0_sundials:
-  variables:
-    SPEC: "%gcc@6.1.0 +sundials"
-  extends: .build_and_test_on_quartz
-
-opt_par_gcc_6_1_0_petsc:
-  variables:
-    SPEC: "%gcc@6.1.0 +petsc ^petsc+mumps"
-  extends: .build_and_test_on_quartz
-
-opt_par_gcc_6_1_0_pumi:
-  variables:
-    SPEC: "%gcc@6.1.0 +pumi"
-  extends: .build_and_test_on_quartz
-
-# Release
-release_resource:
-  variables:
-    GIT_STRATEGY: none
-  extends: .on_quartz
-  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_quartz
-    - .report_job_success
-
-report_job_failure:
-  stage: release_resource_and_report
-  extends:
-    - .on_quartz
-    - .report_job_failure
-
-include:
-  - local: .gitlab/configs/common.yml
-  - local: .gitlab/configs/quartz-config.yml
-  - local: .gitlab/configs/setup-build-and-test.yml
-  - local: .gitlab/configs/report-build-and-test.yml

.gitlab/quartz.yml

@@ -0,0 +1,184 @@
+# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+# LICENSE and NOTICE for details. LLNL-CODE-806117.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability visit https://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the BSD-3 license. We welcome feedback and contributions, see file
+# CONTRIBUTING.md for details.
+
+# GitLab pipelines configurations for the Quartz machine at LLNL
+
+.on_quartz:
+  tags:
+    - shell
+    - quartz
+  rules:
+    # Don't run quartz jobs if...
+    - if: '$CI_COMMIT_BRANCH =~ /_qnone/ || $ON_QUARTZ == "OFF"'
+      when: never
+    # Don't run autotest update if...
+    - if: '$CI_JOB_NAME =~ /update_autotest/ && $AUTOTEST != "YES"'
+      when: never
+    # Don't run autotest update if...
+    - if: '$CI_JOB_NAME =~ /q_report/ && $AUTOTEST != "YES"'
+      when: never
+    # Report success on success status
+    - if: '$CI_JOB_NAME =~ /q_report_success/ && $AUTOTEST == "YES"'
+      when: on_success
+    # Report failure on failure status
+    - if: '$CI_JOB_NAME =~ /q_report_failure/ && $AUTOTEST == "YES"'
+      when: on_failure
+    # Always release resources
+    - if: '$CI_JOB_NAME =~ /release_resources/'
+      when: always
+    # Default is to run if previous stage succeeded
+    - when: on_success
+
+# This is a yaml anchor, it can be used to avoid duplication like here.
+# The code below will simply be pasted wherever the anchor is placed.
+.safe_create_rundir: &safe_create_rundir |
+  if ! mkdir ${rundir}; then
+    n=1
+    while ! mkdir ${rundir}_${n}
+    do
+      n=$((n+1))
+    done
+    rundir=${rundir}_${n}
+  fi
+
+# Allocate
+q_allocate_resources:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_quartz
+  stage: q_allocate_resources
+  script:
+    - salloc --exclusive --nodes=1 --partition=pdebug --time=30 --no-shell --job-name=${ALLOC_NAME}
+  timeout: 6h
+
+# Release
+q_release_resources:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_quartz
+  stage: q_release_resources
+  script:
+    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
+    - ([[ -n "${JOBID}" ]] && scancel ${JOBID})
+
+# Release
+q_report_success:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_quartz
+  stage: q_release_resources
+  script:
+    - echo "Can only run if all the quartz jobs passed"
+    - cd ${AUTOTEST_ROOT}/autotest && git pull
+    - rundir="gitlab/$(date +%Y-%m-%d)-github-${CI_COMMIT_REF_SLUG}"
+    - *safe_create_rundir
+    - echo "The Quartz jobs were successful" > ${rundir}/gitlab.out
+    - echo "See the pipeline here -> $CI_PIPELINE_URL" >> ${rundir}/gitlab.err
+    - git add ${rundir}
+    - git commit -am "Gitlab CI log for baseline on quartz with intel ($(date +%Y-%m-%d))"
+    - git push origin master
+
+q_report_failure:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_quartz
+  stage: q_release_resources
+  script:
+    - echo "Runs if there was at least one failure on quartz"
+    - cd ${AUTOTEST_ROOT}/autotest && git pull
+    - rundir="gitlab/$(date +%Y-%m-%d)-github-${CI_COMMIT_REF_SLUG}"
+    - *safe_create_rundir
+    - echo "There was an error while running CI on Quartz" > ${rundir}/gitlab.err
+    - echo "See the pipeline here -> $CI_PIPELINE_URL" >> ${rundir}/gitlab.err
+    - cp ${rundir}/gitlab.err ${rundir}/autotest-email.html
+    - git add ${rundir}
+    - git commit -am "Gitlab CI log for baseline on quartz with intel ($(date +%Y-%m-%d))"
+    - git push origin master
+
+# Spack helped builds
+# Generic quartz build job, extending build script
+.build_and_test_on_quartz:
+  extends: [.build_toss_3_x86_64_ib_script, .on_quartz]
+  stage: q_build_and_test
+
+# Build MFEM
+debug_ser_gcc_4_9_3:
+  variables:
+    SPEC: "%gcc@4.9.3 +debug~mpi"
+  extends: .build_and_test_on_quartz
+
+debug_ser_gcc_6_1_0:
+  variables:
+    SPEC: "%gcc@6.1.0 +debug~mpi"
+  extends: .build_and_test_on_quartz
+
+debug_par_gcc_6_1_0:
+  variables:
+    SPEC: "%gcc@6.1.0 +debug+mpi"
+  extends: .build_and_test_on_quartz
+
+opt_ser_gcc_6_1_0:
+  variables:
+    SPEC: "%gcc@6.1.0 ~mpi"
+  extends: .build_and_test_on_quartz
+
+opt_par_gcc_6_1_0:
+  variables:
+    SPEC: "%gcc@6.1.0"
+  extends: .build_and_test_on_quartz
+
+opt_par_gcc_6_1_0_sundials:
+  variables:
+    SPEC: "%gcc@6.1.0 +sundials"
+  extends: .build_and_test_on_quartz
+
+opt_par_gcc_6_1_0_petsc:
+  variables:
+    SPEC: "%gcc@6.1.0 +petsc ^petsc+mumps"
+  extends: .build_and_test_on_quartz
+
+opt_par_gcc_6_1_0_pumi:
+  variables:
+    SPEC: "%gcc@6.1.0 +pumi"
+  extends: .build_and_test_on_quartz
+
+# Baseline jobs form an independent set of jobs. We use `needs:[]` to specify
+# that "setup-baseline" can start immediately. Then, we have to use needs for
+# each one of the baseline jobs, otherwise they will wait for the rest of the
+# pipeline.
+
+baselinecheck_mfem_intel_quartz:
+  extends: [.baselinecheck_mfem, .on_quartz]
+  needs: [setup_baseline]
+
+update_autotest:
+  extends: [.on_quartz]
+  needs: [baselinecheck_mfem_intel_quartz]
+  stage: baseline_to_autotest
+  script:
+    - cd ${AUTOTEST_ROOT}/autotest && git pull
+    - rundir="quartz/$(date +%Y-%m-%d)-github-${CI_COMMIT_REF_SLUG}"
+    - *safe_create_rundir
+    - cp ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/* ${rundir}
+    # We create an autotest-email.html file, because that's how we signal that there was a diff (temporary).
+    - |
+      if [[ -f ${rundir}/*.err ]]
+      then
+        echo "See the pipeline here -> $CI_PIPELINE_URL" >> ${rundir}/*.err
+        cp ${rundir}/*.err ${rundir}/autotest-email.html
+      fi
+    - git add ${rundir}
+    - git commit -am "Gitlab CI log for baseline on quartz with intel ($(date +%Y-%m-%d))"
+    - git push origin master
+
+baselinepublish_mfem_quartz:
+  extends: [.on_quartz, .rebaseline_mfem]
+  needs: [baselinecheck_mfem_intel_quartz]

.gitlab/scripts/baseline

@@ -1,88 +0,0 @@
-#!/bin/bash
-
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# locals
-glob_err=${BASELINE_TEST}.err
-base=${BASELINE_TEST}-${SYS_TYPE}
-base_diff=${base}.diff
-base_patch=${base}.patch
-base_out=${base}.out
-artifacts_path=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}
-
-# prepare
-cd ${BUILD_ROOT} || \
-  { echo "Invalid BUILD_ROOT=$BUILD_ROOT"; exit 1; }
-ln -snf ${CI_PROJECT_DIR} mfem
-cd tests
-[[ -d _${BASELINE_TEST} ]] && rm -rf _${BASELINE_TEST}
-mkdir _${BASELINE_TEST} && cd _${BASELINE_TEST}
-
-# run
-if [[ "${MACHINE_NAME}" == "quartz" || "${MACHINE_NAME}" == "ruby" ]]; then
-  srun --nodes=1 -p pdebug ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
-elif [[ ${MACHINE_NAME} == "corona" ]]; then
-  srun --nodes=1 -t 60 -p mi60 ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
-elif [[ ${MACHINE_NAME} == "lassen" ]]; then
-  lalloc 1 -q pdebug ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
-else
-  echo "Unknown machine: MACHINE_NAME=$MACHINE_NAME"
-  exit 1
-fi
-
-# post
-mkdir ${artifacts_path}
-
-if [[ -s ${glob_err} ]]
-then
-  echo "ERROR during ${BASELINE_TEST} execution";
-  echo "Here is the ${glob_err} file content";
-  cat ${glob_err}
-  cp ${glob_err} ${artifacts_path}/${glob_err}
-  exit 1;
-elif [[ ! -f ${base_patch} && ! -f ${base_out} ]]
-then
-  echo "Something went WRONG in ${BASELINE_TEST}:";
-  echo "Either ${base_patch} or ${base_out} should exists";
-  exit 1;
-elif [[ -f ${base_patch} ]]
-then
-  echo "${BASELINE_TEST}: Differences found, patch generated"
-  cp ${base_patch} ${artifacts_path}/${base_patch}
-elif [[ -f ${base_out} ]]
-then
-  echo "${BASELINE_TEST}: Differences found, replacement file generated"
-  cp ${base_out} ${artifacts_path}/${base_out}
-fi
-
-if [[ -f ${BASELINE_TEST}.out ]]; then
-  cp ${BASELINE_TEST}.out ${artifacts_path}
-fi
-
-# base_diff won't even exist if there is no difference.
-if [[ -f ${base_diff} ]]
-then
-  echo "${BASELINE_TEST}: Relevant differences (filtered diff) ..."
-  cat ${base_diff}
-  cp ${base_diff} ${artifacts_path}/${base_diff}
-  # We create a .err file, because that's how we signal that there was a diff.
-  cp ${base_diff} ${artifacts_path}/gitlab-${BASELINE_TEST}-${MACHINE_NAME}.err
-fi
-
-if [[ ! -s ${base_diff} ]]
-then
-  echo "${BASELINE_TEST}: PASSED"
-  true
-else
-  echo "${BASELINE_TEST}: FAILED"
-  false
-fi

.gitlab/scripts/rebaseline

@@ -1,49 +0,0 @@
-#!/bin/bash
-
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# There will be collision between corona and quartz baselines.
-# Once the corresponding files have been generated, we can switch to machine
-# specific ref.
-ARTIFACT_PATH=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}
-#ARTIFACT_PATH=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}-${MACHINE_NAME}
-
-PATCH_FILE=${ARTIFACT_PATH}.patch
-FULL_FILE=${ARTIFACT_PATH}.out
-DIFF_FILE=${ARTIFACT_PATH}.diff
-
-# There will be collision between corona and quartz baselines.
-# Once the corresponding files have been generated, we can switch to machine
-# specific ref.
-SAVED_NAME=baseline-${SYS_TYPE}.saved
-#SAVED_NAME=baseline-${SYS_TYPE}-${MACHINE_NAME}.saved
-
-cd ${BUILD_ROOT}/tests
-
-if [[ ! -f "${DIFF_FILE}" ]]
-then
-    echo "Nothing to be done: no relevant change in baseline"
-    exit 0
-elif [[ -f "${PATCH_FILE}" ]]
-then
-    patch "${SAVED_NAME}" < "${PATCH_FILE}"
-elif [[ -f "${FULL_FILE}" ]]
-then
-    cp "${FULL_FILE}" "${SAVED_NAME}"
-else
-    echo "File missing: expected ${PATCH_FILE} or ${FULL_FILE}"
-    exit 1
-fi
-
-git add "${SAVED_NAME}"
-git commit -m "${SYS_TYPE} (${MACHINE_NAME}) rebaselined in GitLab pipeline ${CI_PIPELINE_ID}"
-git push origin master

.gitlab/scripts/report_build_and_test_failure

@@ -1,45 +0,0 @@
-#!/bin/bash
-
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-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}" && \
-  git push origin master
-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

@@ -1,42 +0,0 @@
-#!/bin/bash
-
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-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}" && \
-  git push origin master
-else
-  for file in ${rundir}/*; do
-    echo "------------------------------"
-    echo "Content of '$file'"
-    echo "******************************"
-    cat $file
-    echo "******************************"
-  done
-  rm -rf ${rundir} || true
-fi

.gitlab/scripts/safe_create_rundir

@@ -1,42 +0,0 @@
-#!/bin/bash
-
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# This script takes a seed for a directory name and appends it with a counter
-# incremented until it can create a new directory with it.
-
-# Usage:
-#
-# Expects 1 argument: a string that is use as a seed for the directory name.
-#
-# > rundir="desired_name"
-# > rundir=$(./safe_create_rundir $rundir)
-
-set -o errexit
-set -o nounset
-
-rundir=${1:-""}
-if [[ -z ${rundir} ]]; then
-  >&2 echo "The script expects a string as argument for directory creation."
-  exit 1
-fi
-
-if ! mkdir ${rundir}; then
-  n=1
-  while ! mkdir ${rundir}_${n}
-  do
-    n=$((n+1))
-  done
-  rundir=${rundir}_${n}
-fi
-
-echo $rundir

CHANGELOG

@@ -10,43 +10,8 @@
 
 Version 4.3.1 (development)
 ===========================
-- Added support for automatic differentiation. Users can select between 
-  native implementation and external library implementation at the 
-  configuration phase. A parallel and two serial examples are implemented
-  in the autodiff miniapp directory.
-
-- Added support for mesh preprocessing to resolve fine scale problem data
-  before simulation. This feature uses adaptive mesh refinement to control the
-  associated data oscillation error. See the new Example 30/30p.
-
-- Switched from Artistic Style (astyle) version 2.05.1 to version 3.1 for code
-  formatting. See the "make style" target.
-
-- Split the fem/fe.?pp files into separate files in the new fem/fe/ directory
-  to simplify and clarify the organization of FiniteElement classes.
-
 - Added support for hr-adaptivity using TMOP-based error estimator.
 
-- Coefficient::SetTime now propagates the new time into internally stored
-  Coefficient objects.
-
-- Added initial support for google-benchmarks in the tests/benchmarks directory.
-  It can be enabled with MFEM_USE_BENCHMARK=YES.
-
-- Added Binder (mybinder.org) configuration files for C++ MFEM Jupyter Notebooks
-  with inline GLVis visualization as well as a new examples/jupyter/ directory
-  with a sample notebook based on Example 1. Implementation based on xeus-cling,
-  github.com/jupyter-xeus/xeus-cling + xeus-glvis, github.com/GLVis/xeus-glvis.
-
-- Added 'double' atomicAdd implementation for previous versions of CUDA.
-
-- Adding lowest order Nedelec and Raviart-Thomas basis functions on wedge
-  shaped elements.
-
-- Added initial support for meshes with pyramidal elements, including several
-  pyramidal meshes in the data/ directory and support for the lowest order H1,
-  Nedelec, Raviart-Thomas, and L2 basis functions on pyramids.
-
 - Updated the hypre interface according to changes in hypre-2.22.1. The ADS
   solver is now fully working on GPUs.
 
@@ -55,29 +20,6 @@ Version 4.3.1 (development)
   functions on wedges and pyramids which are not amenable to reordering. The
   ReorientTetMesh method of the Mesh and ParMesh classes has been deprecated.
 
-- Gmsh meshes where all elements have zero physical tag (the default Gmsh
-  output format if no physical groups are defined) are now successfully loaded,
-  and elements are reassigned attribute number 1.
-
-- Added new miniapps that use the ParELAG library, its hybrid smoothers, and the
-  hierarchy of spaces created by the element-based AMG (AMGe) methodology in
-  ParELAG to build multigrid solvers for H(curl) and H(div) forms. See the
-  miniapps/parelag directory for more details.
-
-- Fixed several MinGW build issues on Windows.
-
-- Remove the 'u' flag in the ar command, to update all files in the archive,
-  avoiding file name collisions from different subdirectories.
-
-- Added initial TMOP-based capabilities for surface fitting and tangential
-  relaxation in the mesh-optimizer and pmesh-optimizer miniapps.
- 
-- Added ParMesh Adjaceny Set (adjset) creation support to the Conduit Mesh
-  Blueprint MFEM wrapper functions in ConduitDataCollection.
-
-- `HypreParVector` and `Vector` now support move semantics, and the copy
-  constructor for `HypreParVector` now copies the local vector data.
-
 
 Version 4.3, released on July 29, 2021
 ======================================

CMakeLists.txt

@@ -90,11 +90,6 @@ include("${CMAKE_CURRENT_SOURCE_DIR}/config/XSDKDefaults.cmake")
 
 # Enable languages.
 enable_language(CXX)
-if (MINGW)
-   # MinGW GCC does not expose the functions jn/_jn, yn/_yn (used in Example
-   # 25/25p) unless we use '-std=gnu++11':
-   set(CMAKE_CXX_EXTENSIONS ON)
-endif()
 if (MFEM_USE_CUDA)
    if (MFEM_USE_HIP)
       message(FATAL_ERROR " *** MFEM_USE_HIP cannot be combined with MFEM_USE_CUDA.")
@@ -252,11 +247,6 @@ if (MFEM_USE_OPENMP OR MFEM_USE_LEGACY_OPENMP)
   endif()
   find_package(OpenMP REQUIRED)
   set(OPENMP_LIBRARIES ${OpenMP_CXX_LIBRARIES})
-  if(APPLE)
-    # On macOS, the compiler needs additional help to find the <omp.h> header.
-    # See issue #2642 for more information.
-    include_directories(${OpenMP_CXX_INCLUDE_DIRS})
-  endif(APPLE)
 endif()
 
 # SuiteSparse (before SUNDIALS which may depend on KLU)
@@ -338,11 +328,11 @@ if (MFEM_USE_AMGX)
 endif()
 
 if (MFEM_USE_CONDUIT)
-    find_package(Conduit REQUIRED conduit relay blueprint)
+    find_package(Conduit REQUIRED conduit relay blueprint )
 endif()
 
 if (MFEM_USE_FMS)
-    find_package(FMS REQUIRED fms)
+    find_package(FMS REQUIRED fms )
 endif()
 
 # Axom/Sidre
@@ -372,12 +362,6 @@ if (MFEM_USE_HIOP)
   # find_package updates HIOP_FOUND, HIOP_INCLUDE_DIRS, HIOP_LIBRARIES
 endif()
 
-# CoDiPack package
-if (MFEM_USE_CODIPACK)
-  find_package(CODIPACK REQUIRED)
-  # find_package updates CODIPACK_FOUND, CODIPACK_INCLUDE_DIRS, CODIPACK_LIBRARIES
-endif()
-
 # OCCA
 if (MFEM_USE_OCCA)
    find_package(OCCA REQUIRED)
@@ -393,11 +377,6 @@ if (MFEM_USE_UMPIRE)
    find_package(UMPIRE REQUIRED)
 endif()
 
-# GOOGLE-BENCHMARK
-if (MFEM_USE_BENCHMARK)
-   find_package(Benchmark REQUIRED)
-endif()
-
 # Caliper
 if (MFEM_USE_CALIPER)
   find_package(Caliper REQUIRED)
@@ -426,11 +405,6 @@ if (MFEM_USE_MKL_CPARDISO)
   endif()
 endif()
 
-# PARELAG
-if (MFEM_USE_PARELAG)
-   find_package(PARELAG REQUIRED)
-endif()
-
 # MFEM_TIMER_TYPE
 if (NOT DEFINED MFEM_TIMER_TYPE)
   if (APPLE)
@@ -454,10 +428,10 @@ endif()
 #    With newer versions of SuiteSparse which include METIS header using 64-bit
 #    integers, the METIS header (with 32-bit indices, as used by mfem) needs to
 #    be before SuiteSparse.
-set(MFEM_TPLS OPENMP HYPRE BLAS LAPACK SuperLUDist METIS SuiteSparse SUNDIALS PETSC
+set(MFEM_TPLS MPI_CXX OPENMP HYPRE BLAS LAPACK SuperLUDist METIS SuiteSparse SUNDIALS PETSC
     SLEPC MESQUITE MUMPS STRUMPACK AXOM FMS CONDUIT Ginkgo GNUTLS GSLIB NETCDF
     MPFR PUMI HIOP POSIXCLOCKS MFEMBacktrace ZLIB OCCA CEED RAJA UMPIRE ADIOS2
-    CUSPARSE MKL_CPARDISO AMGX CALIPER CODIPACK BENCHMARK PARELAG MPI_CXX)
+    CUSPARSE MKL_CPARDISO AMGX CALIPER)
 
 # Add all *_FOUND libraries in the variable TPL_LIBRARIES.
 set(TPL_LIBRARIES "")
@@ -522,9 +496,13 @@ set(MFEM_INSTALL_DIR ${CMAKE_INSTALL_PREFIX} CACHE PATH
 # Declaring the library
 mfem_add_library(mfem ${SOURCES} ${HEADERS} ${MASTER_HEADERS})
 # message(STATUS "TPL_LIBRARIES = ${TPL_LIBRARIES}")
-target_link_libraries(mfem PUBLIC ${TPL_LIBRARIES})
+if (CMAKE_VERSION VERSION_GREATER 2.8.11)
+  target_link_libraries(mfem PUBLIC ${TPL_LIBRARIES})
+else()
+  target_link_libraries(mfem ${TPL_LIBRARIES})
+endif()
 if (MINGW)
-  target_link_libraries(mfem PRIVATE ws2_32)
+  target_link_libraries(mfem ws2_32)
 endif()
 set_target_properties(mfem PROPERTIES VERSION "${mfem_VERSION}")
 set_target_properties(mfem PROPERTIES SOVERSION "${mfem_VERSION}")
@@ -563,21 +541,15 @@ endif()
 set(MFEM_CUSTOM_TARGET_PREFIX CACHE STRING "")
 
 #-------------------------------------------------------------------------------
-# Examples, miniapps, benchmarks and testing
+# Examples, miniapps, and testing
 #-------------------------------------------------------------------------------
 
-# Enable testing and benchmarks if required
+# Enable testing if required
 if (MFEM_ENABLE_TESTING)
   enable_testing()
   set(MFEM_ALL_TESTS_TARGET_NAME tests)
   add_mfem_target(${MFEM_ALL_TESTS_TARGET_NAME} OFF)
   add_subdirectory(tests EXCLUDE_FROM_ALL)
-
-  # Create a target for all benchmarks and, optionally, enable it.
-  set(MFEM_ALL_BENCHMARKS_TARGET_NAME benchmarks)
-  add_mfem_target(${MFEM_ALL_BENCHMARKS_TARGET_NAME}
-                  ${MFEM_ENABLE_GOOGLE_BENCHMARKS})
-  add_subdirectory(tests/benchmarks EXCLUDE_FROM_ALL)
 endif()
 
 # Define a target that all examples and miniapps will depend on.
@@ -587,11 +559,7 @@ add_custom_target(${MFEM_EXEC_PREREQUISITES_TARGET_NAME})
 # Create a target for all examples and, optionally, enable it.
 set(MFEM_ALL_EXAMPLES_TARGET_NAME examples)
 add_mfem_target(${MFEM_ALL_EXAMPLES_TARGET_NAME} ${MFEM_ENABLE_EXAMPLES})
-if (MFEM_ENABLE_EXAMPLES)
-  add_subdirectory(examples) #install examples if enabled
-else()
-  add_subdirectory(examples EXCLUDE_FROM_ALL)
-endif()
+add_subdirectory(examples EXCLUDE_FROM_ALL)
 
 # Create a target for all miniapps and, optionally, enable it.
 set(MFEM_ALL_MINIAPPS_TARGET_NAME miniapps)
@@ -601,7 +569,6 @@ add_subdirectory(miniapps EXCLUDE_FROM_ALL)
 # Target to build all executables, i.e. everything.
 add_custom_target(exec)
 add_dependencies(exec
-  ${MFEM_ALL_BENCHMARKS_TARGET_NAME}
   ${MFEM_ALL_EXAMPLES_TARGET_NAME}
   ${MFEM_ALL_MINIAPPS_TARGET_NAME}
   ${MFEM_ALL_TESTS_TARGET_NAME})

CONTRIBUTING.md

@@ -42,7 +42,6 @@ back to them before issuing pull requests:
   - [New Feature Development](#new-feature-development)
   - [Developer Guidelines](#developer-guidelines)
   - [Pull Requests](#pull-requests)
-  - [MFEM PR Rules](#mfem-pr-rules)
   - [Pull Request Checklist](#pull-request-checklist)
   - [Master/Next Workflow](#masternext-workflow)
   - [Releases](#releases)
@@ -68,9 +67,8 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
   with regards to documentation and code styling.
 - Please do not commit large/binary files to the central repository (use a fork
   instead).
-- Pull requests should be issued toward `mfem:master`. Make sure
-  to check the items off the [Pull Request Checklist](#pull-request-checklist) and
-  follow the [MFEM PR Rules](#mfem-pr-rules).
+- Pull requests  should be issued toward `mfem:master`. Make sure
+  to check the items off the [Pull Request Checklist](#pull-request-checklist).
 - When your contribution is fully working and ready to be reviewed, add
   the `ready-for-review` label.
 - PRs are treated similarly to journal submission with an "editor" assigning two
@@ -107,14 +105,12 @@ The MFEM source code has the following structure:
   │   ├── caliper
   │   ├── ginkgo
   │   ├── hiop
-  │   ├── jupyter
   │   ├── petsc
   │   ├── pumi
   │   ├── sundials
   |   └── superlu
   ├── fem
   │   ├── ceed
-  │   ├── fe
   │   ├── qinterp
   │   └── tmop
   ├── general
@@ -123,7 +119,6 @@ The MFEM source code has the following structure:
   ├── mesh
   ├── miniapps
   │   ├── adjoint
-  │   ├── autodiff
   │   ├── common
   │   ├── electromagnetics
   │   ├── gslib
@@ -131,7 +126,6 @@ The MFEM source code has the following structure:
   │   ├── mtop
   │   ├── navier
   │   ├── nurbs
-  │   ├── parelag
   │   ├── performance
   │   ├── shifted
   │   ├── solvers
@@ -329,22 +323,15 @@ Before you can start, you need a GitHub account, here are a few suggestions:
     change the code by default.
 
 - Code specifics
-  - All new public, protected, and private classes, methods, data members, and
-    functions have Doxygen-style documentation in source comments.
-  - In addition to arguments and functionality, documentation should include the
-    current limitations of the code, any background information that is
-    implicitly assumed in the implementation, and the ownership and lifetime
-    of data.
+  - All significant new classes, methods and functions have Doxygen-style
+    documentation in source comments.
   - Consistent code styling is enforced with `make style` in the top-level
     directory. This requires [Artistic Style](http://astyle.sourceforge.net) (we
-    specifically use version 3.1). See also the file `config/mfem.astylerc`.
+    specifically use version 2.05.1). See also the file `config/mfem.astylerc`.
   - Use `mfem::out` and `mfem::err` instead of `std::cout` and `std::cerr` in
     internal library code. (You can use `std` in examples and miniapps.)
   - When manually resolving conflicts during a merge, make sure to mention the
     conflicted files in the commit message.
-  - All significant new features and changes should be documented in CHANGELOG.
-  - New examples and miniapps should have documentation on the MFEM webpage.
-
 
 ### Pull Requests
 
@@ -410,83 +397,6 @@ Before you can start, you need a GitHub account, here are a few suggestions:
 - If triggered, track the status of the LLNL GitLab tests. If failing, ask
   one of the _LLNL developers_ for details.
 
-
-### MFEM PR Rules
-
-The Pull Request (PR) approval process in MFEM is similar to the approval of papers in a peer-reviewed journal. In particular:
-
-1. There is an MFEM board of "editors" that evaluates new PRs and assigns "reviewers" for each PR.
-
-2. The assigned reviewers are responsible to carefully review and test the proposed PR.
-
-3. A PR can be (manually) merged in the *next* branch only if 2 of the assigned reviewers have approved it and it has passed internal testing. This merge can be performed by any of the assigned reviewers or by any of the editors.
-
-4. A PR can be merged in the *master* branch only if it has been tested successfully for a week in *next* and an editor has (optionally) taken a final look. This merge can be performed only by one of the editors.
-
-#### Responsibilities of Editors
-
-The current list of MFEM editors is:
-
-- @v-dobrev (Veselin Dobrev)
-- @tzanio (Tzanio Kolev)
-- @pazner (Will Pazner)
-- @mlstowell (Mark Stowell)
-
-**The responsibilities of the editors are:**
-
-1. To assign appropriate milestone and labels for new PRs, e.g. *bugfix*, *minor*, *api-change*, *high-impact*, etc.
-
-2. To assign at least 2 reviewers for new PRs. An editor can also be a reviewer. The editor, reviewers, and author should be listed as "Assignees" on the GitHub PR page. After assignment, the `in-review` label should be added.
-
-3. To complete the initial PR evaluation and assignments in a timely manner: 1 week from submission.
-
-4. To assist reviewers when they need help with their reviews (but also to stay out of the way when they don't).
-
-5. To remind the reviewers about timely completion of their review.
-
-6. To take a final look and complete the PR merge in *master*. The final look step is optional and shouldn't take more than 3 days.
-
-7. The assignment of bugfixes should be expedited proportional to their importance, e.g. in some cases the editor can assign much shorter review window.
-
-#### Responsibilities of Reviewers
-
-Everyone on the MFEM team can be asked to serve as a reviewer on a PR in their area of expertise.
-
-**The responsibilities of the reviewers are:**
-
-1. To let the editors know if the proposed assignment is not a good match for them.
-
-2. To communicate with the PR author, provide feedback and work with them to resolve issues.
-
-3. To ensure the quality of the PR by making sure that the code adheres to the [Developer Guidelines](#developer-guidelines), e.g. all methods, data members, and functions have documentation, including data ownership and lifetime, new examples/miniapps have a corresponding PR in mfem/web, major features have `CHANGELOG` entries, etc.
-
-3. To seek help from the editors in case of difficulties.
-
-4. To complete the review in a timely manner: 3 weeks from assignment.
-
-5. To test the PR thoroughly before merging in *next*. The PR author is also encouraged to perform testing and inform the reviewers about the results.
-
-6. To monitor the PR impact on the testing in the *next* branch and alert the editors that the PR is ready for merging in *master*.
-
-7. The review of bugfixes should be expedited proportional to their importance. The review window can be much less than three weeks in such cases.
-
-#### Responsibilities of Authors
-
-Authors should clearly indicate when a PR is ready for review (before that the PR should be marked as `Draft` or `[WIP]`).
-
-**The responsibilities of the authors are:**
-
-1. To follow the instructions and PR checklist in the `CONTRIBUTING.md` document in the MFEM repository.
-
-2. To respond to reviewer feedback in a timely manner.
-
-3. Authors are encouraged to perform testing and inform the reviewers about the results.
-
-4. Authors can use the "Reviewers" section of the GitHub PR page to suggest reviewers, but the "Assignees" section will show who the editor has assigned to do the reviews.
-
-5. To indicate when the PR is ready for review by adding the `ready-for-review` label.
-
-
 ### Pull Request Checklist
 
 Before a PR can be merged, it should satisfy the following:
@@ -540,9 +450,7 @@ Before a PR can be merged, it should satisfy the following:
      - [ ] The miniapps go at the end of the page, and are usually listed only under a specific "Application (PDE)" category.
      - [ ] Add a short description of the miniapp in the "Extensive Examples" section of `features.md`.
 - [ ] New capability:
-   - [ ] All new public, protected, and private classes, methods, data members, and functions have full Doxygen-style documentation in source comments. Documentation should include descriptions of member data, function arguments and return values, template parameters, and prerequisites for calling new functions.
-   - [ ] Pointer arguments and return values must specify whether ownership is being transferred or lent with the call.
-   - [ ] Any new functions should include descriptions of their intended use e.g. for internal use only, user-facing, etc., along with references to example code whenever possible/appropriate.
+   - [ ] All significant new classes, methods and functions have Doxygen-style documentation in source comments.
    - [ ] Consider adding new sample runs in existing examples to highlight the new capability.
    - [ ] Consider saving cool simulation pictures with the new capability in the Confluence gallery (LLNL only) or submitting them, via pull request, to the gallery section of the `mfem/web` repo.
    - [ ] If this is a major new feature, consider mentioning it in the short summary inside `README` *(rare)*.
@@ -553,7 +461,6 @@ Before a PR can be merged, it should satisfy the following:
 - [ ] (LLNL only) After merging:
    - [ ] Update internal tests to include the new features.
 
-
 ### Master/Next Workflow
 
 MFEM uses a `master`/`next`-branch workflow as described below:
@@ -645,10 +552,8 @@ MFEM uses a `master`/`next`-branch workflow as described below:
     - Update version and shortlinks in `src/index.md` and `src/download.md`.
     -  Use [cloc-1.62.pl](http://cloc.sourceforge.net/) and `ls -lh` to estimate the SLOC and the tarball size in `src/download.md`.
 
-
 ## LLNL Workflow
 
-
 ### Mirroring on Bitbucket
 
 - The GitHub `master` and `next` branches are mirrored to the LLNL institutional
@@ -668,17 +573,16 @@ MFEM uses a `master`/`next`-branch workflow as described below:
   - `mfem:gh-next` -- Bleeding-edge development version, may be broken, use at
      your own risk.
 
-
 ### Mirroring on GitLab
 
 - MFEM repository is also mirrored on the LLNL GitLab instance, in a
   semi-automated manner.
 
 - This instance is meant to complete CI testing with tests on Livermore
-  Computing systems. GitLab pipeline status is reported in the corresponding
+  Computing systems. Gitlab pipeline status is reported in the corresponding
   GitHub pull request.
 
-- In GitLab pipelines, TPLs (dependencies) are built using Spack, driven by Uberenv.
+- In Gitlab pipelines, TPLs (dependencies) are built using Spack, driven by Uberenv.
 
 - No change to the MFEM repo can be made on this instance.
 
@@ -691,7 +595,6 @@ In addition, developers can set local git hooks to run some quick checks on
 commit or push, see the [README](config/githooks/README.md) in the `config/githooks`
 directory.
 
-
 ### Linux and Mac smoke tests
 We use GitHub Actions to drive the default tests on the `master` and `next`
 branches. See the `.github/workflows` files and the logs at
@@ -703,7 +606,6 @@ constraint on jobs. Two virtual machines are configured - Mac (OS X) and Linux.
 - Tests on the `master` branch are triggered whenever a PR is issued on this branch.
 - Tests on the `next` branch are currently scheduled to run each night.
 
-
 ### Windows smoke test
 We use Appveyor to test building with the MS Visual C++ compiler in a Windows
 environment, as well as to test the CMake build. See the `.appveyor` file and the
@@ -713,7 +615,6 @@ build logs at
 CMake is used to generate the MSVC Project files and drive the build.  A release
 and debug build is performed with a simple run of `ex1` to verify the executable.
 
-
 ### Tests at LLNL
 
 - We mirror the `master` and `next` branches internally (to `gh-master` and

INSTALL

@@ -459,22 +459,10 @@ MFEM_USE_UMPIRE = YES/NO
    discovery, provision, and management of memory on machines with multiple
    memory devices like NUMA and GPUs.
 
-MFEM_USE_BENCHMARK = YES/NO
-   Enables support for Google Benchmark, a library to support the benchmarking
-   of functions, in the tests/benchmarks directory.
-
 MFEM_USE_HIOP = YES/NO
    Enable the usage of HiOp (https://github.com/LLNL/hiop) in MFEM. HiOp is an
    HPC solver for nonlinear optimization problems.
 
-MFEM_USE_CODIPACK = YES/NO
-  Enable automatic differentiation using the CoDiPack library.
-  www.scicomp.uni-kl.de/codi/
-
-MFEM_USE_ADFORWARD = YES/NO
-  Enable forward mode for AD packages. This option is valid
-  only if the AD package supports two modes (backward/forward).
-
 MFEM_USE_CUDA = YES/NO
    Enables support for CUDA devices in MFEM. CUDA is a parallel computing
    platform and programming model for general computing on graphical processing
@@ -535,11 +523,6 @@ MFEM_USE_FMS = YES/NO
    convetion routines between FMS's FmsDataCollection structure and MFEM's
    DataCollection class, see the header file fem/fmsconvert.hpp.
 
-MFEM_USE_PARELAG = YES/NO
-   Enables the miniapps that use the ParELAG library. MFEM does not currently
-   use ParELAG. In fact, ParELAG is dependent on MFEM. Therefore, this option
-   currently only concerns the miniapps.
-
 MFEM_BUILD_TAG = (any value)
    An optional tag to characterize the build. Exported to config/config.mk.
    Can be used to identify the MFEM build from other makefiles.
@@ -709,12 +692,7 @@ The specific libraries and their options are:
 - HiOp (optional), used when MFEM_USE_HIOP = YES.
   URL: https://github.com/LLNL/hiop
   Options: HIOP_OPT, HIOP_LIB.
-  Versions: HIOP >= 0.4.6.
-
-- CoDiPack (optiobal), used with MFEM_USE_CODIPACK = YES
-  URL: https://www.scicomp.uni-kl.de/codi/
-  Options: CODIPACK_OPT
-  Versions: 1.9.3
+  Versions: HIOP >= 0.4.
 
 - GSLIB (optional), used when MFEM_USE_GSLIB = YES. The gslib library must be
   built prior to the MFEM build, as follows: download gslib-1.0.7, untar it at
@@ -752,10 +730,10 @@ The specific libraries and their options are:
   Versions: libCEED >= 0.8.
 
 - RAJA (optional), used when MFEM_USE_RAJA = YES.
-  Beginning with MFEM v4.3, only RAJA v0.14.0+ is supported.
+  Beginning with MFEM v4.3, only RAJA v0.13.0+ is supported.
   URL: https://github.com/LLNL/RAJA
   Options: RAJA_DIR, RAJA_OPT, RAJA_LIB.
-  Versions: RAJA >= 0.14.0.
+  Versions: RAJA >= 0.13.0.
 
 - Caliper (optional), used when MFEM_USE_CALIPER = YES.
   URL: https://github.com/LLNL/Caliper
@@ -766,12 +744,7 @@ The specific libraries and their options are:
   Umpire requires camp when the Umpire version is >= 3.0.0.
   URL: https://github.com/LLNL/Umpire
   Options: UMPIRE_DIR, UMPIRE_OPT, UMPIRE_LIB.
-  Versions: Umpire >= 3.0.0.
-
-- Benchmark, used when MFEM_USE_BENCHMARK = YES.
-  URL: https://github.com/google/benchmark
-  Options: BENCHMARK_DIR, BENCHMARK_LIB.
-  Versions: Benchmark >= 1.5.6.
+  Versions: Umpire >= 2.0.0.
 
 - MPFR (optional), used when MFEM_USE_MPFR = YES.
   URL: http://mpfr.org, it depends on the GMP library: https://gmplib.org
@@ -793,10 +766,6 @@ The specific libraries and their options are:
   Options: FMS_OPT, FMS_LIB.
   Versions: FMS >= 0.2.
 
-- ParELAG, used when MFEM_USE_PARELAG = YES.
-  URL: https://github.com/LLNL/parelag
-  Options: PARELAG_DIR, PARELAG_OPT, PARELAG_LIB.
-
 Building with CMake
 ===================
 The MFEM build system consists of two steps: configuration and compilation.
@@ -921,8 +890,6 @@ MFEM_USE_MPFR
 MFEM_USE_ZLIB
 MFEM_USE_PUMI
 MFEM_USE_HIOP
-MFEM_USE_CODIPACK
-MFEM_USE_ADFORWARD
 MFEM_USE_CUDA
 MFEM_USE_OCCA
 MFEM_USE_CEED
@@ -931,8 +898,6 @@ MFEM_USE_UMPIRE
 MFEM_USE_SIDRE
 MFEM_USE_CALIPER
 MFEM_USE_FMS
-MFEM_USE_BENCHMARK
-MFEM_USE_PARELAG
 
 The following options are CMake specific:
 
@@ -982,15 +947,12 @@ The CMake build system adds auto-detection for the following packages/libraries:
  - POSIXCLOCKS
  - PUMI
  - HIOP
- - CoDiPack
  - OCCA
  - RAJA
  - UMPIRE
  - AXOM - Used when MFEM_USE_SIDRE is enabled
  - CALIPER
  - FMS
- - BENCHMARK
- - ParELAG
 
 The following built-in CMake packages are also used:
 

config/XSDKDefaults.cmake

@@ -283,11 +283,3 @@ ENDIF()
 IF (DEFINED TPL_ENABLE_UMPIRE)
   SET(MFEM_USE_UMPIRE ${TPL_ENABLE_UMPIRE} CACHE BOOL "Enable Umpire" FORCE)
 ENDIF()
-
-IF (DEFINED TPL_ENABLE_BENCHMARK)
-  SET(MFEM_USE_BENCHMARK ${TPL_ENABLE_BENCHMARK} CACHE BOOL "Enable Google-Benchmark" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_PARELAG)
-  SET(MFEM_USE_PARELAG ${TPL_ENABLE_PARELAG} CACHE BOOL "Enable ParELAG" FORCE)
-ENDIF()

config/cmake/MFEMConfig.cmake.in

@@ -54,11 +54,7 @@ set(MFEM_USE_CEED @MFEM_USE_CEED@)
 set(MFEM_USE_UMPIRE @MFEM_USE_UMPIRE@)
 set(MFEM_USE_SIMD @MFEM_USE_SIMD@)
 set(MFEM_USE_ADIOS2 @MFEM_USE_ADIOS2@)
-set(MFEM_USE_CODIPACK @MFEM_USE_CODIPACK@)
-set(MFEM_USE_ADFORWARD @MFEM_USE_ADFORWARD@)
 set(MFEM_USE_CALIPER @MFEM_USE_CALIPER@)
-set(MFEM_USE_BENCHMARK @MFEM_USE_BENCHMARK@)
-set(MFEM_USE_PARELAG @MFEM_USE_PARELAG@)
 
 set(MFEM_CXX_COMPILER "@CMAKE_CXX_COMPILER@")
 set(MFEM_CXX_FLAGS "@CMAKE_CXX_FLAGS@")

config/cmake/config.hpp.in

@@ -175,13 +175,4 @@
 // Enable interface to the MKL CPardiso library.
 #cmakedefine MFEM_USE_MKL_CPARDISO
 
-// Use forward mode for automatic differentiation
-#cmakedefine MFEM_USE_ADFORWARD
-
-// Enable the use of the CoDiPack library for AD
-#cmakedefine MFEM_USE_CODIPACK
-
-// Enable MFEM functionality based on the Google Benchmark library.
-#cmakedefine MFEM_USE_BENCHMARK
-
 #endif // MFEM_CONFIG_HEADER

config/cmake/modules/FindBenchmark.cmake

@@ -1,22 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# Defines the following variables:
-#   - BENCHMARK_FOUND
-#   - BENCHMARK_LIBRARIES
-#   - BENCHMARK_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(Benchmark BENCHMARK BENCHMARK_DIR
-        "include" "benchmark/benchmark.h"
-        "lib" "benchmark"
-        "Paths to headers required by Google Benchmark."
-        "Libraries required by Google Benchmark.")

config/cmake/modules/FindCODIPACK.cmake

@@ -1,24 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# Automatic differentiation using the CoDiPack library.
-#  www.scicomp.uni-kl.de/codi/
-# Sets the following variables:
-#   - CODIPACK_FOUND
-#   - CODIPACK_INCLUDE_DIRS
-#   - CODIPACK_LIBRARIES
-
-include(MfemCmakeUtilities)
-mfem_find_package(CODIPACK CODIPACK CODIPACK_DIR
-  "include" "codi.h"
-  "lib" ""
-  "Paths to headers required by CODIPACK."
-  "Libraries required by CODIPACK.")

config/cmake/modules/FindPARELAG.cmake

@@ -1,19 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# Defines the following variables:
-#   - PARELAG_FOUND
-#   - PARELAG_LIBRARIES
-#   - PARELAG_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(PARELAG PARELAG PARELAG_DIR "" "" "" ""
-  "Paths to headers required by ParELAG." "Libraries required by ParELAG.")

config/cmake/modules/MfemCmakeUtilities.cmake

@@ -100,8 +100,6 @@ macro(add_mfem_examples EXE_SRCS)
 
     string(REPLACE ".cpp" "" EXE_NAME "${EXE_PREFIX}${SRC_FILENAME}")
     mfem_add_executable(${EXE_NAME} ${SRC_FILE})
-    install(TARGETS ${EXE_NAME}
-            RUNTIME DESTINATION examples)
     add_dependencies(${MFEM_ALL_EXAMPLES_TARGET_NAME} ${EXE_NAME})
     if (EXE_NEEDED_BY)
       add_dependencies(${EXE_NEEDED_BY} ${EXE_NAME})
@@ -766,7 +764,7 @@ function(mfem_export_mk_files)
       MFEM_USE_GNUTLS MFEM_USE_GSLIB MFEM_USE_NETCDF MFEM_USE_PETSC
       MFEM_USE_SLEPC MFEM_USE_MPFR MFEM_USE_SIDRE MFEM_USE_CONDUIT MFEM_USE_PUMI
       MFEM_USE_CUDA MFEM_USE_OCCA MFEM_USE_RAJA MFEM_USE_UMPIRE MFEM_USE_SIMD
-      MFEM_USE_ADIOS2 MFEM_USE_BENCHMARK MFEM_USE_PARELAG)
+      MFEM_USE_ADIOS2)
   foreach(var ${CONFIG_MK_BOOL_VARS})
     if (${var})
       set(${var} YES)

config/config.hpp.in

@@ -180,13 +180,4 @@
 // Enable interface to the MKL CPardiso library.
 // #define MFEM_USE_MKL_CPARDISO
 
-// Use forward mode for automatic differentiation
-// #define MFEM_USE_ADFORWARD
-
-// Enable the use of the CoDiPack library for AD
-// #define MFEM_USE_CODIPACK
-
-// Enable functionality based on the Google Benchmark library.
-// #define MFEM_USE_BENCHMARK
-
 #endif // MFEM_CONFIG_HEADER

config/config.mk.in

@@ -58,10 +58,6 @@ MFEM_USE_UMPIRE        = @MFEM_USE_UMPIRE@
 MFEM_USE_SIMD          = @MFEM_USE_SIMD@
 MFEM_USE_ADIOS2        = @MFEM_USE_ADIOS2@
 MFEM_USE_MKL_CPARDISO  = @MFEM_USE_MKL_CPARDISO@
-MFEM_USE_ADFORWARD     = @MFEM_USE_ADFORWARD@
-MFEM_USE_CODIPACK      = @MFEM_USE_CODIPACK@
-MFEM_USE_BENCHMARK     = @MFEM_USE_BENCHMARK@
-MFEM_USE_PARELAG       = @MFEM_USE_PARELAG@
 
 # Compiler, compile options, and link options
 MFEM_CXX       = @MFEM_CXX@

config/defaults.cmake

@@ -58,10 +58,6 @@ option(MFEM_USE_SIMD "Enable use of SIMD intrinsics" OFF)
 option(MFEM_USE_ADIOS2 "Enable ADIOS2" OFF)
 option(MFEM_USE_CALIPER "Enable Caliper support" OFF)
 option(MFEM_USE_MKL_CPARDISO "Enable MKL CPardiso" OFF)
-option(MFEM_USE_ADFORWARD "Enable forward mode for AD" OFF)
-option(MFEM_USE_CODIPACK "Enable automatic differentiation (AD) using CoDiPack" OFF)
-option(MFEM_USE_BENCHMARK "Enable Google Benchmark" OFF)
-option(MFEM_USE_PARELAG "Enable ParELAG" OFF)
 
 # Optional overrides for autodetected MPIEXEC and MPIEXEC_NUMPROC_FLAG
 # set(MFEM_MPIEXEC "mpirun" CACHE STRING "Command for running MPI tests")
@@ -78,7 +74,6 @@ set(MFEM_MPI_NP 4 CACHE STRING "Number of processes used for MPI tests")
 option(MFEM_ENABLE_TESTING "Enable the ctest framework for testing" ON)
 option(MFEM_ENABLE_EXAMPLES "Build all of the examples" OFF)
 option(MFEM_ENABLE_MINIAPPS "Build all of the miniapps" OFF)
-option(MFEM_ENABLE_GOOGLE_BENCHMARKS "Build all of the Google benchmarks" OFF)
 
 # Setting CXX/MPICXX on the command line or in user.cmake will overwrite the
 # autodetected C++ compiler.
@@ -229,25 +224,12 @@ set(RAJA_DIR "${MFEM_DIR}/../raja" CACHE PATH "Path to RAJA")
 set(CEED_DIR "${MFEM_DIR}/../libCEED" CACHE PATH "Path to libCEED")
 set(UMPIRE_DIR "${MFEM_DIR}/../umpire" CACHE PATH "Path to Umpire")
 set(CALIPER_DIR "${MFEM_DIR}/../caliper" CACHE PATH "Path to Caliper")
-set(BENCHMARK_DIR "${MFEM_DIR}/../google-benchmark" CACHE PATH
-    "Path to Google Benchmark")
-
-# Provide paths, since ParELAG is dependent on MFEM and MFEM needs to be
-# compiled (or at least cmake needs to succeed) before compiling ParELAG.
-set(PARELAG_DIR "${MFEM_DIR}/../parelag" CACHE PATH "Path to ParELAG")
-set(PARELAG_INCLUDE_DIRS "${PARELAG_DIR}/src;${PARELAG_DIR}/build/src" CACHE
-    STRING "Path to ParELAG headers.")
-set(PARELAG_LIBRARIES "${PARELAG_DIR}/build/src/libParELAG.a" CACHE STRING
-    "The ParELAG library.")
 
 set(BLAS_INCLUDE_DIRS "" CACHE STRING "Path to BLAS headers.")
 set(BLAS_LIBRARIES "" CACHE STRING "The BLAS library.")
 set(LAPACK_INCLUDE_DIRS "" CACHE STRING "Path to LAPACK headers.")
 set(LAPACK_LIBRARIES "" CACHE STRING "The LAPACK library.")
 
-set(CODIPACK_INCLUDE_DIRS "${MFEM_DIR}/../CoDiPack/inlude" CACHE STRING "Path to CoDiPack headers.")
-set(CODIPACK_LIBRARIES "")
-
 # Some useful variables:
 set(CMAKE_SKIP_PREPROCESSED_SOURCE_RULES ON) # Skip *.i rules
 set(CMAKE_SKIP_ASSEMBLY_SOURCE_RULES  ON)    # Skip *.s rules

config/defaults.mk

@@ -59,12 +59,9 @@ HIP_FLAGS = --amdgpu-target=$(HIP_ARCH)
 HIP_XCOMPILER =
 HIP_XLINKER   = -Wl,
 
-# Flags for generating dependencies.
-DEP_FLAGS = -MM -MT
-
 ifneq ($(NOTMAC),)
    AR      = ar
-   ARFLAGS = crv
+   ARFLAGS = cruv
    RANLIB  = ranlib
    PICFLAG = $(XCOMPILER)-fPIC
    SO_EXT  = so
@@ -76,7 +73,7 @@ ifneq ($(NOTMAC),)
 else
    # Silence "has no symbols" warnings on Mac OS X
    AR      = ar
-   ARFLAGS = Scrv
+   ARFLAGS = Scruv
    RANLIB  = ranlib -no_warning_for_no_symbols
    PICFLAG = $(XCOMPILER)-fPIC
    SO_EXT  = dylib
@@ -89,9 +86,6 @@ else
    BUILD_RPATH = $(XLINKER)-undefined,dynamic_lookup
    INSTALL_SOFLAGS = $(subst $1 ,,$(call MAKE_SOFLAGS,$(MFEM_LIB_DIR)))
    INSTALL_RPATH = $(XLINKER)-undefined,dynamic_lookup
-   # Silence unused command line argument warnings when generating dependencies
-   # with mpicxx and clang
-   DEP_FLAGS := -Wno-unused-command-line-argument $(DEP_FLAGS)
 endif
 
 # Set CXXFLAGS to overwrite the default selection of DEBUG_FLAGS/OPTIM_FLAGS
@@ -157,10 +151,6 @@ MFEM_USE_UMPIRE        = NO
 MFEM_USE_SIMD          = NO
 MFEM_USE_ADIOS2        = NO
 MFEM_USE_MKL_CPARDISO  = NO
-MFEM_USE_ADFORWARD     = NO
-MFEM_USE_CODIPACK      = NO
-MFEM_USE_BENCHMARK     = NO
-MFEM_USE_PARELAG       = NO
 
 # MPI library compile and link flags
 # These settings are used only when building MFEM with MPI + HIP
@@ -416,11 +406,6 @@ HIOP_DIR = @MFEM_DIR@/../hiop/install
 HIOP_OPT = -I$(HIOP_DIR)/include
 HIOP_LIB = -L$(HIOP_DIR)/lib -lhiop $(LAPACK_LIB)
 
-# CoDiPack
-CODIPACK_DIR = @MFEM_DIR@/../CoDiPack
-CODIPACK_OPT = -I$(CODIPACK_DIR)
-CODIPACK_LIB =
-
 # GSLIB library
 GSLIB_DIR = @MFEM_DIR@/../gslib/build
 GSLIB_OPT = -I$(GSLIB_DIR)/include
@@ -444,11 +429,6 @@ CALIPER_DIR = @MFEM_DIR@/../caliper
 CALIPER_OPT = -I$(CALIPER_DIR)/include
 CALIPER_LIB = $(XLINKER)-rpath,$(CALIPER_DIR)/lib64 -L$(CALIPER_DIR)/lib64 -lcaliper
 
-# BENCHMARK library configuration
-BENCHMARK_DIR = @MFEM_DIR@/../google-benchmark
-BENCHMARK_OPT = -I$(BENCHMARK_DIR)/include
-BENCHMARK_LIB = -L$(BENCHMARK_DIR)/lib -lbenchmark -lpthread
-
 # libCEED library configuration
 CEED_DIR ?= @MFEM_DIR@/../libCEED
 CEED_OPT = -I$(CEED_DIR)/include
@@ -479,11 +459,6 @@ MKL_CPARDISO_LIB = $(XLINKER)-rpath,$(MKL_CPARDISO_DIR)/$(MKL_LIBRARY_SUBDIR)\
    -L$(MKL_CPARDISO_DIR)/$(MKL_LIBRARY_SUBDIR) -l$(MKL_MPI_WRAPPER)\
    -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
 
-# PARELAG library configuration
-PARELAG_DIR = @MFEM_DIR@/../parelag
-PARELAG_OPT = -I$(PARELAG_DIR)/src -I$(PARELAG_DIR)/build/src
-PARELAG_LIB = -L$(PARELAG_DIR)/build/src -lParELAG
-
 # If YES, enable some informational messages
 VERBOSE = NO
 

config/githooks/pre-push

@@ -87,12 +87,12 @@ fi
 ## style check
 #if [[ "${option}" == "--style" || "${option}" == "" ]]; then
 if [[ "${option}" == "--style" ]]; then
-  if which astyle && [[ "$(astyle --version)" == "Artistic Style Version 3.1" ]]; then
+  if which astyle && [[ "$(astyle --version)" == "Artistic Style Version 2.05.1" ]]; then
     cd tests/scripts
     if ! ./runtest code-style; then code=1; fi
     cd -
   else
-    echo "Warning: astyle not found or version is not 3.1"
+    echo "Warning: astyle not found or version is not 2.05.1"
   fi
 fi
 

data/inline-pyramid.mesh

@@ -1,9 +0,0 @@
-MFEM INLINE mesh v1.0
-
-type = pyramid
-nx = 4
-ny = 4
-nz = 4
-sx = 1.0
-sy = 1.0
-sz = 1.0

data/octahedron.mesh

@@ -1,43 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-# PYRAMID     = 7
-#
-
-dimension
-3
-
-elements
-2
-1 7 4 3 2 1 0
-1 7 1 2 3 4 5
-
-boundary
-8
-1 2 0 2 1
-2 2 0 3 2
-3 2 0 4 3
-4 2 0 1 4
-5 2 1 2 5
-6 2 2 3 5
-7 2 3 4 5
-8 2 4 1 5
-
-vertices
-6
-3
-0 0 -1
-1 0 0
-0 1 0
--1 0 0
-0 -1 0
-0 0 1

data/ref-pyramid.mesh

@@ -1,38 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-# PYRAMID     = 7
-#
-
-dimension
-3
-
-elements
-1
-1 7 0 1 2 3 4
-
-boundary
-5
-1 3 3 2 1 0
-2 2 0 1 4
-3 2 1 2 4
-4 2 2 3 4
-5 2 3 0 4
-
-vertices
-5
-3
-0 0 0
-1 0 0
-1 1 0
-0 1 0
-0 0 1

doc/CodeDocumentation.conf.in

@@ -765,7 +765,6 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/linalg \
                          @MFEM_SOURCE_DIR@/mesh \
                          @MFEM_SOURCE_DIR@/fem \
-                         @MFEM_SOURCE_DIR@/fem/fe \
                          @MFEM_SOURCE_DIR@/examples \
                          @MFEM_SOURCE_DIR@/examples/caliper \
                          @MFEM_SOURCE_DIR@/examples/amgx \
@@ -781,15 +780,13 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/miniapps/gslib \
                          @MFEM_SOURCE_DIR@/miniapps/meshing \
                          @MFEM_SOURCE_DIR@/miniapps/mtop \
-                         @MFEM_SOURCE_DIR@/miniapps/autodiff \
                          @MFEM_SOURCE_DIR@/miniapps/navier \
                          @MFEM_SOURCE_DIR@/miniapps/nurbs \
                          @MFEM_SOURCE_DIR@/miniapps/performance \
                          @MFEM_SOURCE_DIR@/miniapps/shifted \
                          @MFEM_SOURCE_DIR@/miniapps/solvers \
                          @MFEM_SOURCE_DIR@/miniapps/tools \
-                         @MFEM_SOURCE_DIR@/miniapps/toys \
-                         @MFEM_SOURCE_DIR@/miniapps/parelag
+                         @MFEM_SOURCE_DIR@/miniapps/toys
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

doc/CodeDocumentation.dox

@@ -194,8 +194,6 @@ namespace mfem {
  * - <a class="el" href="parheat_8cpp_source.html">Optimization gradients</a>: Gradients of PDE-constrained function
  * - <a class="el" href="miniapps_2performance_2ex1_8cpp_source.html">HPC Example 1</a>: high-performance nodal H1 FEM for the Laplace problem
  * - <a class="el" href="miniapps_2performance_2ex1p_8cpp_source.html">HPC Example 1p</a>: high-performance parallel nodal H1 FEM for the Laplace problem
- * - <a class="el" href="par__example_8cpp_source.html">Parallel pLaplacian example using AD</a>: Parallel pLaplacian example
- * - <a class="el" href="seq__example_8cpp_source.html">Serial pLaplacian example using AD</a>: Serial pLaplacian example
  *
  * See also the <a class="el" href="https://mfem.org/examples/">examples documentation</a> online.
  */

examples/CMakeLists.txt

@@ -37,7 +37,6 @@ list(APPEND ALL_EXE_SRCS
   ex27.cpp
   ex28.cpp
   ex29.cpp
-  ex30.cpp
   )
 
 if (MFEM_USE_MPI)
@@ -71,7 +70,6 @@ if (MFEM_USE_MPI)
     ex27p.cpp
     ex28p.cpp
     ex29p.cpp
-    ex30p.cpp
     )
 endif()
 
@@ -82,80 +80,78 @@ include_directories(BEFORE ${PROJECT_BINARY_DIR})
 add_mfem_examples(ALL_EXE_SRCS)
 
 # Add a test for each example
-if (MFEM_ENABLE_TESTING)
-  foreach(SRC_FILE ${ALL_EXE_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+foreach(SRC_FILE ${ALL_EXE_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
 
-    set(THIS_TEST_OPTIONS "-no-vis")
-    if (${TEST_NAME} MATCHES "ex0p?")
-      set(THIS_TEST_OPTIONS)
-    endif()
-    if (${TEST_NAME} MATCHES "ex10p*")
-      list(APPEND THIS_TEST_OPTIONS "-tf" "5")
-    elseif(${TEST_NAME} MATCHES "ex15p*")
-      list(APPEND THIS_TEST_OPTIONS "-e" "1")
-    elseif(${TEST_NAME} MATCHES "ex27p*")
-      list(APPEND THIS_TEST_OPTIONS "-dg")
-    endif()
+  set(THIS_TEST_OPTIONS "-no-vis")
+  if (${TEST_NAME} MATCHES "ex0p?")
+    set(THIS_TEST_OPTIONS)
+  endif()
+  if (${TEST_NAME} MATCHES "ex10p*")
+    list(APPEND THIS_TEST_OPTIONS "-tf" "5")
+  elseif(${TEST_NAME} MATCHES "ex15p*")
+    list(APPEND THIS_TEST_OPTIONS "-e" "1")
+  elseif(${TEST_NAME} MATCHES "ex27p*")
+    list(APPEND THIS_TEST_OPTIONS "-dg")
+  endif()
 
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    add_test(NAME ${TEST_NAME}_np=${MFEM_MPI_NP}
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()
+
+# Add CUDA/HIP tests.
+set(DEVICE_EXAMPLES
+    # serial examples with device support:
+    ex1 ex3 ex4 ex5 ex6 ex9 ex22 ex24 ex25 ex26
+    # parallel examples with device support:
+    ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex9p ex13p ex22p ex24p ex25p ex26p)
+set(MFEM_TEST_DEVICE)
+if (MFEM_USE_CUDA)
+  set(MFEM_TEST_DEVICE "cuda")
+elseif (MFEM_USE_HIP)
+  set(MFEM_TEST_DEVICE "hip")
+endif()
+if (MFEM_TEST_DEVICE)
+  foreach(TEST_NAME ${DEVICE_EXAMPLES})
+    set(THIS_TEST_OPTIONS "-no-vis" "-d" "${MFEM_TEST_DEVICE}")
     if (NOT (${TEST_NAME} MATCHES ".*p$"))
-      add_test(NAME ${TEST_NAME}_ser
+      add_test(NAME ${TEST_NAME}_${MFEM_TEST_DEVICE}_ser
         COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-    else()
-      add_test(NAME ${TEST_NAME}_np=${MFEM_MPI_NP}
+    elseif (MFEM_USE_MPI)
+      add_test(NAME ${TEST_NAME}_${MFEM_TEST_DEVICE}_np=${MFEM_MPI_NP}
         COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
         ${MPIEXEC_PREFLAGS}
         $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
         ${MPIEXEC_POSTFLAGS})
     endif()
   endforeach()
+endif()
 
-  # Add CUDA/HIP tests.
-  set(DEVICE_EXAMPLES
-      # serial examples with device support:
-      ex1 ex3 ex4 ex5 ex6 ex9 ex22 ex24 ex25 ex26
-      # parallel examples with device support:
-      ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex9p ex13p ex22p ex24p ex25p ex26p)
-  set(MFEM_TEST_DEVICE)
-  if (MFEM_USE_CUDA)
-    set(MFEM_TEST_DEVICE "cuda")
-  elseif (MFEM_USE_HIP)
-    set(MFEM_TEST_DEVICE "hip")
-  endif()
-  if (MFEM_TEST_DEVICE)
-    foreach(TEST_NAME ${DEVICE_EXAMPLES})
-      set(THIS_TEST_OPTIONS "-no-vis" "-d" "${MFEM_TEST_DEVICE}")
-      if (NOT (${TEST_NAME} MATCHES ".*p$"))
-        add_test(NAME ${TEST_NAME}_${MFEM_TEST_DEVICE}_ser
-          COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-      elseif (MFEM_USE_MPI)
-        add_test(NAME ${TEST_NAME}_${MFEM_TEST_DEVICE}_np=${MFEM_MPI_NP}
-          COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-          ${MPIEXEC_PREFLAGS}
-          $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-          ${MPIEXEC_POSTFLAGS})
-      endif()
-    endforeach()
-  endif()
+# If STRUMPACK is enabled, add a test run that uses it.
+if (MFEM_USE_STRUMPACK)
+  add_test(NAME ex11p_strumpack_np=${MFEM_MPI_NP}
+    COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+    ${MPIEXEC_PREFLAGS}
+    $<TARGET_FILE:ex11p> "-no-vis" "--strumpack"
+    ${MPIEXEC_POSTFLAGS})
+endif()
 
-  # If STRUMPACK is enabled, add a test run that uses it.
-  if (MFEM_USE_STRUMPACK)
-    add_test(NAME ex11p_strumpack_np=${MFEM_MPI_NP}
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-      ${MPIEXEC_PREFLAGS}
-      $<TARGET_FILE:ex11p> "-no-vis" "--strumpack"
-      ${MPIEXEC_POSTFLAGS})
-  endif()
-
-  # If SuperLU_DIST is enabled, add a test run that uses it.
-  if (MFEM_USE_SUPERLU)
-    add_test(NAME ex11p_superlu_np=${MFEM_MPI_NP}
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-      ${MPIEXEC_PREFLAGS}
-      $<TARGET_FILE:ex11p> "-no-vis" "--superlu"
-      ${MPIEXEC_POSTFLAGS})
-  endif()
+# If SuperLU_DIST is enabled, add a test run that uses it.
+if (MFEM_USE_SUPERLU)
+  add_test(NAME ex11p_superlu_np=${MFEM_MPI_NP}
+    COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+    ${MPIEXEC_PREFLAGS}
+    $<TARGET_FILE:ex11p> "-no-vis" "--superlu"
+    ${MPIEXEC_POSTFLAGS})
 endif()
 
 # Include the examples/amgx directory if AmgX is enabled

examples/amgx/CMakeLists.txt

@@ -50,32 +50,30 @@ add_mfem_examples(AMGX_EXAMPLES_SRCS ${PFX} copy_amgx_json_files test_amgx)
 # which builds the examples and runs:
 #   ctest -R amgx
 
-if (MFEM_ENABLE_TESTING)
-  # Command line options for the tests.
-  # Example 1/1p:
-  set(EX1_TEST_OPTS)
-  set(EX1P_TEST_OPTS)
+# Command line options for the tests.
+# Example 1/1p:
+set(EX1_TEST_OPTS)
+set(EX1P_TEST_OPTS)
 
-  # Add the tests: one test per source file.
-  foreach(SRC_FILE ${AMGX_EXAMPLES_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-    string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
-    set(TEST_NAME ${PFX}${TEST_NAME})
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${AMGX_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
+  set(TEST_NAME ${PFX}${TEST_NAME})
 
-    set(THIS_TEST_OPTIONS "-no-vis")
-    list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
-    # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
 
-    if (NOT (${TEST_NAME} MATCHES ".*p$"))
-      add_test(NAME ${TEST_NAME}_ser
-        COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-    else()
-      add_test(NAME ${TEST_NAME}_np=${MFEM_MPI_NP}
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    add_test(NAME ${TEST_NAME}_np=${MFEM_MPI_NP}
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

examples/caliper/CMakeLists.txt

@@ -30,22 +30,22 @@ set(PREFIX caliper_)
 add_mfem_examples(CALIPER_EXE_SRCS ${PREFIX})
 
 # Add a test for each example
-if (MFEM_ENABLE_TESTING)
-  foreach(SRC_FILE ${CALIPER_EXE_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+foreach(SRC_FILE ${CALIPER_EXE_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+
+  set(THIS_TEST_OPTIONS "-no-vis")
+
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    add_test(NAME ${TEST_NAME}_np=${MFEM_MPI_NP}
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()
 
-    set(THIS_TEST_OPTIONS "-no-vis")
 
-    if (NOT (${TEST_NAME} MATCHES ".*p$"))
-      add_test(NAME ${TEST_NAME}_ser
-        COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-    else()
-      add_test(NAME ${TEST_NAME}_np=${MFEM_MPI_NP}
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()

examples/combine-figures

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+# Use imagemagick to combine the figures into a composite view
+
+for i in {0..19}; do
+    ii=`printf %04d $i`
+
+    # label reference density
+    convert reference-$ii.png -gravity south -annotate -50+50 "Reference Fine" ,reference-$ii.png
+
+    # label optimal density
+    convert opt-soln-$ii.png -gravity south -annotate -50+50 "Optimal AMR" ,opt-soln-$ii.png
+
+    # label greedy density
+    convert greedy-soln-$ii.png -gravity south -annotate -50+50 "Max Current AMR" ,greedy-soln-$ii.png
+
+    # stack optimal on top of error plot
+    convert ,opt-soln-$ii.png opt-err-$i.png -append ,opt-soln-werr-$ii.png
+
+    # stack greedy on top of error plot
+    convert ,greedy-soln-$ii.png greedy-err-$i.png -append ,greedy-soln-werr-$ii.png
+    
+    # lay the 3 side by side
+    convert ,reference-$ii.png ,opt-soln-werr-$ii.png ,greedy-soln-werr-$ii.png +append ,ref-sbs-soln-$ii.1.png
+
+    # Label the composite image with timestep
+    convert ,ref-sbs-soln-$ii.1.png -gravity northwest -annotate +20+20 "Timestep $i" ref-sbs-soln-$ii.png
+done
+
+rm ,*

examples/ex1.cpp

@@ -9,7 +9,6 @@
 //               ex1 -m ../data/fichera.mesh
 //               ex1 -m ../data/fichera-mixed.mesh
 //               ex1 -m ../data/toroid-wedge.mesh
-//               ex1 -m ../data/octahedron.mesh -o 1
 //               ex1 -m ../data/periodic-annulus-sector.msh
 //               ex1 -m ../data/periodic-torus-sector.msh
 //               ex1 -m ../data/square-disc-p2.vtk -o 2

examples/ex14.cpp

@@ -135,8 +135,8 @@ int main(int argc, char *argv[])
    a->AddBdrFaceIntegrator(new DGDiffusionIntegrator(one, sigma, kappa));
    if (eta > 0)
    {
-      a->AddInteriorFaceIntegrator(new DGDiffusionBR2Integrator(*fespace, eta));
-      a->AddBdrFaceIntegrator(new DGDiffusionBR2Integrator(*fespace, eta));
+      a->AddInteriorFaceIntegrator(new DGDiffusionBR2Integrator(fespace, eta));
+      a->AddBdrFaceIntegrator(new DGDiffusionBR2Integrator(fespace, eta));
    }
    a->Assemble();
    a->Finalize();

examples/ex14p.cpp

@@ -199,8 +199,8 @@ int main(int argc, char *argv[])
    a->AddBdrFaceIntegrator(new DGDiffusionIntegrator(one, sigma, kappa));
    if (eta > 0)
    {
-      a->AddInteriorFaceIntegrator(new DGDiffusionBR2Integrator(*fespace, eta));
-      a->AddBdrFaceIntegrator(new DGDiffusionBR2Integrator(*fespace, eta));
+      a->AddInteriorFaceIntegrator(new DGDiffusionBR2Integrator(fespace, eta));
+      a->AddBdrFaceIntegrator(new DGDiffusionBR2Integrator(fespace, eta));
    }
    a->Assemble();
    a->Finalize();
@@ -221,7 +221,7 @@ int main(int argc, char *argv[])
    {
       HyprePCG pcg(*A);
       pcg.SetTol(1e-12);
-      pcg.SetMaxIter(500);
+      pcg.SetMaxIter(200);
       pcg.SetPrintLevel(2);
       pcg.SetPreconditioner(*amg);
       pcg.Mult(*B, *X);
@@ -232,7 +232,7 @@ int main(int argc, char *argv[])
       GMRESSolver gmres(MPI_COMM_WORLD);
       gmres.SetAbsTol(0.0);
       gmres.SetRelTol(1e-12);
-      gmres.SetMaxIter(500);
+      gmres.SetMaxIter(200);
       gmres.SetKDim(10);
       gmres.SetPrintLevel(1);
       gmres.SetOperator(*A);

examples/ex18.cpp

@@ -42,6 +42,7 @@
 #include <fstream>
 #include <sstream>
 #include <iostream>
+#include <set>
 
 // Classes FE_Evolution, RiemannSolver, DomainIntegrator and FaceIntegrator
 // shared between the serial and parallel version of the example.
@@ -50,14 +51,177 @@
 // Choice for the problem setup. See InitialCondition in ex18.hpp.
 int problem;
 
+// The dim and hence number of equations is taken from the mesh.
+int dim;
+int num_equation;
+
 // Equation constant parameters.
-const int num_equation = 4;
 const double specific_heat_ratio = 1.4;
 const double gas_constant = 1.0;
 
 // Maximum characteristic speed (updated by integrators)
 double max_char_speed;
 
+void amr_update(FiniteElementSpace& fes,
+                FiniteElementSpace& dfes,
+                FiniteElementSpace& vfes,
+                BlockVector& u_block,
+                GridFunction& rho,
+                GridFunction& rho_u,
+                GridFunction& rho_e,
+                GridFunction& sol)
+{
+   fes.Update();
+   dfes.Update();
+   vfes.Update();
+
+   rho.Update();
+   rho_u.Update();
+   rho_e.Update();
+
+   Array<int> offsets(num_equation + 1);
+   for (int k = 0; k <= num_equation; k++) {
+      offsets[k] = k * vfes.GetNDofs();
+   }
+   u_block.Update(offsets);
+
+   Vector& sub0 = u_block.GetBlock(0);
+   Vector& sub1 = u_block.GetBlock(1);
+   Vector& sub2 = u_block.GetBlock(2);
+
+   sub0 = rho;
+   sub1 = rho_u;
+   sub2 = rho_e;
+
+   sol.MakeRef(&vfes, u_block.GetData());
+
+   rho.MakeRef(&fes, u_block.GetData() + offsets[0]);
+   rho_u.MakeRef(&dfes, u_block.GetData() + offsets[1]);
+   rho_e.MakeRef(&fes, u_block.GetData() + offsets[2]);
+}
+
+double estimate_dt(double cfl, Mesh& mesh,
+                   GridFunction& sol, NonlinearForm& A, int order)
+{
+   // Determine the minimum element size.
+   double hmin = 0.0;
+   hmin = mesh.GetElementSize(0, 1);
+   for (int i = 1; i < mesh.GetNE(); i++)
+   {
+      hmin = min(mesh.GetElementSize(i, 1), hmin);
+   }
+
+   double dt = -0.01;
+   // Find a safe dt, using a temporary vector. Calling Mult() computes the
+   // maximum char speed at all quadrature points on all faces.
+   Vector z(A.Width());
+   max_char_speed = 0.;
+   A.Mult(sol, z);
+   dt = cfl * hmin / max_char_speed / (2*order+1);
+
+   return dt;
+}
+
+void show_maps(Mesh& mesh, vector<int>& coarse_map, vector<int>& fine_map)
+{
+   for (int i = 0; i < mesh.GetNE(); i++) {
+      int depth = mesh.ncmesh->GetElementDepth(i);
+      if (depth == 0) {
+         printf("| %2d  ",i);
+      }
+      else {
+         printf("|%2d|%2d",i,i+1);
+         i++;
+      }
+   }
+   printf("| mesh i\n");
+
+   for (size_t i = 0; i < coarse_map.size(); i++) {
+      printf("| %2d  ",coarse_map[i]);
+   }
+   printf("| coarse map\n");
+
+   for (size_t i = 0; i < coarse_map.size(); i++) {
+      printf("| %2d  ",fine_map[i]);
+   }
+   printf("| fine map\n");
+
+   for (size_t i = 0; i < coarse_map.size(); i++) {
+      printf("| %2lu  ",i);
+   }
+   printf("| ref idx\n");
+
+   // some validation checks
+   for (size_t i = 0; i < coarse_map.size(); i++) {
+      //printf("checking reference index %d\n",i);
+      if (coarse_map[i] > -1) assert(  fine_map[i] == -1);
+      if (fine_map[i]   > -1) assert(coarse_map[i] == -1);
+      if (coarse_map[i] > -1) assert(mesh.ncmesh->GetElementDepth(coarse_map[i]) == 0);
+      if (fine_map[i]   > -1) assert(mesh.ncmesh->GetElementDepth(fine_map[i])   == 1);
+      if (fine_map[i]   > -1) assert(mesh.ncmesh->GetElementDepth(fine_map[i]+1) == 1);
+   }
+}
+
+void compute_reference_errors(int ti,
+                              FiniteElementCollection& fec,
+                              Mesh& mesh,
+                              GridFunction& den,
+                              const vector<int>& coarse_map,
+                              const vector<int>& fine_map,
+                              vector<double>& errors)
+{
+   // Create a temp copy of the mesh for refinement to reference resolution
+   Mesh tmp_mesh(mesh);
+   FiniteElementSpace tmp_fes(&tmp_mesh, &fec);
+   GridFunction tmp_den(&tmp_fes);
+   tmp_den = den; // copy data
+
+   // refine mesh and soln to reference resolution
+   Array<int> refs;
+   for (int i = 0; i < tmp_mesh.GetNE(); i++) {
+      if (tmp_mesh.ncmesh->GetElementDepth(i) == 0) {
+         refs.Append(i);
+      }
+   }
+   tmp_mesh.GeneralRefinement(refs);
+   tmp_den.FESpace()->Update();
+   tmp_den.Update();
+
+   // read in reference mesh
+   ostringstream fn;
+   fn << "reference-" << ti << ".mesh";
+   Mesh ref_mesh(fn.str().c_str());
+
+   // read in reference density
+   ostringstream sol_name;
+   sol_name << "reference-" << ti << "-" << 0 << ".gf";
+   ifstream gf_ifs(sol_name.str());
+   GridFunction ref_den(&ref_mesh, gf_ifs);
+
+   // integrate L2 errors
+   GridFunctionCoefficient ref_den_coeff(&ref_den);
+   Vector err(ref_mesh.GetNE());
+   tmp_den.ComputeElementL2Errors(ref_den_coeff, err);
+
+   {
+      ostringstream sol_name;
+      sol_name << "refined-current-rho-" << ti << ".gf";
+      ofstream sol_ofs(sol_name.str().c_str());
+      sol_ofs << tmp_den;
+   }
+
+
+   // sum L2 errors to reference mesh. The reference errors are always
+   // on a fully refined mesh.
+   int k = 0;
+   for (size_t i = 0; i < coarse_map.size(); i++) {
+      double e0 = err[k];
+      double e1 = err[k+1];
+      errors[i] = sqrt(e0*e0+e1*e1);
+      k += 2;
+   }
+}
+
 int main(int argc, char *argv[])
 {
    // 1. Parse command-line options.
@@ -69,8 +233,15 @@ int main(int argc, char *argv[])
    double t_final = 2.0;
    double dt = -0.01;
    double cfl = 0.3;
-   bool visualization = true;
+   bool visualization = false;
    int vis_steps = 50;
+   Array<int> rseq;
+   int nseq = 0;
+   int regrid_period = 1;
+   int greedy_refine = 0;
+   int lookahead_refine = 0;
+   int output_cycle_soln = 0;
+   int output_cycle_errors = 0;
 
    int precision = 8;
    cout.precision(precision);
@@ -98,6 +269,18 @@ int main(int argc, char *argv[])
                   "Enable or disable GLVis visualization.");
    args.AddOption(&vis_steps, "-vs", "--visualization-steps",
                   "Visualize every n-th timestep.");
+   args.AddOption(&rseq, "-rseq", "--refine-sequence",
+                  "Element sequence to refine.");
+   args.AddOption(&regrid_period, "-rp", "--regrid-period",
+                  "Timesteps per regrid.");
+   args.AddOption(&greedy_refine, "-gr", "--greedy-refine",
+                  "Use greedy refinement strategy.");
+   args.AddOption(&lookahead_refine, "-lr", "--lookahead-refine",
+                  "Use lookahead refinement strategy.");
+   args.AddOption(&output_cycle_soln, "-cs", "--output-cycle-solutions",
+                  "Output per-cycle solutions.");
+   args.AddOption(&output_cycle_errors, "-ce", "--output-cycle-errors",
+                  "Output per-cycle errors.");
 
    args.Parse();
    if (!args.Good())
@@ -107,12 +290,15 @@ int main(int argc, char *argv[])
    }
    args.PrintOptions(cout);
 
+   printf("dt = %f\n",dt);
+
    // 2. Read the mesh from the given mesh file. This example requires a 2D
    //    periodic mesh, such as ../data/periodic-square.mesh.
    Mesh mesh(mesh_file, 1, 1);
+   mesh.EnsureNCMesh();
    const int dim = mesh.Dimension();
 
-   MFEM_ASSERT(dim == 2, "Need a two-dimensional mesh for the problem definition");
+   num_equation = 2+dim;
 
    // 3. Define the ODE solver used for time integration. Several explicit
    //    Runge-Kutta methods are available.
@@ -162,7 +348,9 @@ int main(int argc, char *argv[])
    BlockVector u_block(offsets);
 
    // Momentum grid function on dfes for visualization.
-   GridFunction mom(&dfes, u_block.GetData() + offsets[1]);
+   GridFunction rho(&fes, u_block.GetData() + offsets[0]);
+   GridFunction rho_u(&dfes, u_block.GetData() + offsets[1]);
+   GridFunction rho_e(&fes, u_block.GetData() + offsets[2]);
 
    // Initialize the state.
    VectorFunctionCoefficient u0(num_equation, InitialCondition);
@@ -184,6 +372,7 @@ int main(int argc, char *argv[])
          sol_ofs.precision(precision);
          sol_ofs << uk;
       }
+
    }
 
    // 7. Set up the nonlinear form corresponding to the DG discretization of the
@@ -199,7 +388,7 @@ int main(int argc, char *argv[])
    // 8. 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).
-   FE_Evolution euler(vfes, A, Aflux.SpMat());
+   FE_Evolution euler(vfes, A, Aflux);
 
    // Visualize the density
    socketstream sout;
@@ -219,7 +408,7 @@ int main(int argc, char *argv[])
       else
       {
          sout.precision(precision);
-         sout << "solution\n" << mesh << mom;
+         sout << "solution\n" << mesh << rho;
          sout << "pause\n";
          sout << flush;
          cout << "GLVis visualization paused."
@@ -227,17 +416,6 @@ int main(int argc, char *argv[])
       }
    }
 
-   // Determine the minimum element size.
-   double hmin = 0.0;
-   if (cfl > 0)
-   {
-      hmin = mesh.GetElementSize(0, 1);
-      for (int i = 1; i < mesh.GetNE(); i++)
-      {
-         hmin = min(mesh.GetElementSize(i, 1), hmin);
-      }
-   }
-
    // Start the timer.
    tic_toc.Clear();
    tic_toc.Start();
@@ -246,27 +424,348 @@ int main(int argc, char *argv[])
    euler.SetTime(t);
    ode_solver->Init(euler);
 
-   if (cfl > 0)
-   {
-      // Find a safe dt, using a temporary vector. Calling Mult() computes the
-      // maximum char speed at all quadrature points on all faces.
-      Vector z(A.Width());
-      max_char_speed = 0.;
-      A.Mult(sol, z);
-      dt = cfl * hmin / max_char_speed / (2*order+1);
+   // map from base coarse numbering to current coarse numbering.
+   // -1 entries for elements that are currently refined.
+   vector<int> coarse_map(mesh.GetNE());
+   for (size_t i = 0; i < coarse_map.size(); ++i) {
+      coarse_map[i] = i;
    }
 
+   // map from base coarse numbering to current fine numbering. The
+   // second element is always this index+1.
+   // -1 entries for elements that are currently coarse.
+   vector<int> fine_map(mesh.GetNE());
+   for (size_t i = 0; i < fine_map.size(); ++i) {
+      fine_map[i] = -1;
+   }
+
+   //show_maps(mesh,coarse_map,fine_map);
+
+   // vector<int> coarse_map(mesh.GetNE());
+   // for (int i = 0; i < coarse_map.size(); ++i) {
+   //    coarse_map[i] = i;
+   // }
+
+   // the elements that are currently refined
+   set<int> cur_ref_set; // in base numbering
+
    // Integrate in time.
    bool done = false;
    for (int ti = 0; !done; )
    {
+
+      if (greedy_refine && !(ti % regrid_period )) {
+         vector<double> ref_errors(coarse_map.size());
+         compute_reference_errors(ti, fec, mesh, rho,
+                                  coarse_map, fine_map, ref_errors);
+         vector<double>::iterator it;
+         it = std::max_element(ref_errors.begin(), ref_errors.end());
+         int ref_max = std::distance(ref_errors.begin(), it);
+         std::cout << "max at: " << std::distance(ref_errors.begin(), it) << '\n';
+         rseq.SetSize(nseq+1);
+         rseq[nseq] = ref_max;
+      }
+
+      if (lookahead_refine && !(ti % regrid_period )) {
+
+         MFEM_ASSERT(cfl < 0, "need fixed time step for lookahead.");
+
+         double dt_real = min(dt, t_final - t);
+
+         // advance a copy of the solution
+         GridFunction tmp_sol(sol);
+
+         ode_solver->Step(tmp_sol, t, dt_real);
+
+         GridFunction tmp_rho(&fes, tmp_sol);
+
+         vector<double> ref_errors(coarse_map.size());
+         compute_reference_errors(ti+1, fec, mesh, tmp_rho,
+                                  coarse_map, fine_map, ref_errors);
+
+         vector<double>::iterator it;
+         it = std::max_element(ref_errors.begin(), ref_errors.end());
+         int ref_max = std::distance(ref_errors.begin(), it);
+         std::cout << "max at: " << std::distance(ref_errors.begin(), it) << '\n';
+         rseq.SetSize(nseq+1);
+         rseq[nseq] = ref_max;
+      }
+
+      // adapt mesh to new element(s)
+      if (rseq.Size() && !(ti % regrid_period )) {
+
+         //printf("*** begin refinement ***\n");
+         set<int> new_ref_set; // in base numbering
+
+         // use base numbering
+         int ne = coarse_map.size();
+         int el1 = rseq[nseq++];
+         int el2 = el1-1;
+         int el3 = el1+1;
+         el2 = (el2 + ne) % ne;
+         el3 = (el3 + ne) % ne;
+         new_ref_set.insert(el1);
+         new_ref_set.insert(el2);
+         new_ref_set.insert(el3);
+
+         // The coarsen set is elements from cur_ref_set not in new_ref_set
+         set<int> coarsen_set;
+         std::set_difference(cur_ref_set.begin(), cur_ref_set.end(),
+                             new_ref_set.begin(), new_ref_set.end(),
+                             std::inserter(coarsen_set, coarsen_set.begin()));
+
+         // The refine set is elements from new_ref_set not in cur_ref_set
+         set<int> refine_set;
+         std::set_difference(new_ref_set.begin(), new_ref_set.end(),
+                             cur_ref_set.begin(), cur_ref_set.end(),
+                             std::inserter(refine_set, refine_set.begin()));
+
+         set<int>::iterator it;
+
+         // printf("cur_ref set\n");
+         //
+         // for (it = cur_ref_set.begin(); it != cur_ref_set.end(); ++it) {
+         //    const int& i = *it;
+         //    printf("%d ",i);
+         // }
+         // printf("\n");
+
+         // printf("new_ref set\n");
+         // for (it = new_ref_set.begin(); it != new_ref_set.end(); ++it) {
+         //    const int& i = *it;
+         //    printf("%d ",i);
+         // }
+         // printf("\n");
+
+         // printf("refine set: ");
+         // for (it = refine_set.begin(); it != refine_set.end(); ++it) {
+         //    const int& i = *it;
+         //    printf("%d ",i);
+         // }
+         // printf("\n");
+
+         // printf("coarsen set: ");
+         // for (it = coarsen_set.begin(); it != coarsen_set.end(); ++it) {
+         //    const int& i = *it;
+         //    printf("%d ",i);
+         // }
+         // printf("\n");
+
+
+         // Perform any new refinements. Translate into current numbering.
+         Array<int> els;
+         for (it = refine_set.begin(); it != refine_set.end(); ++it) {
+            const int& i = *it;
+            assert(coarse_map[i] >= 0);
+            //printf("adding %d -> %d to be refined\n",i,coarse_map[i]);
+            els.Append(coarse_map[i]);
+         }
+
+         if (els.Size()) {
+            //printf("  ** start refinements **\n");
+            mesh.GeneralRefinement(els);
+
+            const CoarseFineTransformations &cft = mesh.GetRefinementTransforms();
+            //printf("updating coarse_map and fine_map after refinement\n");
+            Table c2f;
+            cft.GetCoarseToFineMap(mesh, c2f);
+            Array<int> row;
+            for (size_t i = 0; i < coarse_map.size(); ++i) {
+
+               int old = coarse_map[i];
+               if (old > -1) {
+                  // was coarse
+                  c2f.GetRow(old,row);
+                  if (row.Size() == 1) {
+                     // was coarse, still coarse
+                     coarse_map[i] = row[0];
+                  }
+                  else {
+                     // was coarse, now fine
+                     coarse_map[i] = -1;
+                     fine_map[i] = row[0];
+                  }
+               }
+               else {
+                  // was fine, still fine
+                  old = fine_map[i];
+                  assert(old != -1);
+                  c2f.GetRow(old,row);
+                  assert(row.Size() == 1);
+                  fine_map[i] = row[0];
+               }
+            }
+
+            // printf("new coarse_map is:\n");
+            // for (size_t i = 0; i < coarse_map.size(); i++) {
+            //    printf("%lu -> %d\n",i,coarse_map[i]);
+            // }
+            // printf("new fine_map is:\n");
+            // for (size_t i = 0; i < fine_map.size(); i++) {
+            //    printf("%lu -> %d\n",i,fine_map[i]);
+            // }
+
+            amr_update(fes, dfes, vfes, u_block, rho, rho_u, rho_e, sol);
+            A.Update();
+            Aflux.Update();
+            Aflux.Assemble();
+            euler.Update();
+            ode_solver->Init(euler);
+            //printf("  ** done refinements **\n");
+
+            //printf("maps after refinement\n");
+            //show_maps(mesh,coarse_map,fine_map);
+         }
+
+
+         cur_ref_set = new_ref_set;
+
+         // Perform any new derefinements
+         if (coarsen_set.size()) {
+
+            //printf("  ** start derefinements **\n");
+
+            Array<double> mock_error(mesh.GetNE());
+            mock_error = 1.0;
+
+            // We only mark one of the fine elements, but that's fine
+            // because we can set the threshold low enough to always
+            // derefine.
+            for (it = coarsen_set.begin(); it != coarsen_set.end(); ++it) {
+               const int& i = *it;
+               //printf("coarsening ref idx %d\n",i);
+               assert(coarse_map[i] == -1);
+               int i1 = fine_map[i];
+               //printf("which is fine element %d (and +1)\n",i1);
+               assert(i1 >= 0);
+               mock_error[i1] = 0.0;
+               //printf("setting mock error to 0.0 in %d\n",i1);
+            }
+            mesh.DerefineByError(mock_error, 2.0);
+            amr_update(fes, dfes, vfes, u_block, rho, rho_u, rho_e, sol);
+            A.Update();
+            Aflux.Update();
+            Aflux.Assemble();
+            euler.Update();
+            ode_solver->Init(euler);
+
+            //printf("updating coarse_map and fine_map after derefinement\n");
+
+            const CoarseFineTransformations& cft = mesh.ncmesh->GetDerefinementTransforms();
+
+            Table c2f;
+            cft.GetCoarseToFineMap(mesh, c2f);
+            //c2f.Print();
+
+            Array<int> row;
+            map<int,int> old2new;
+            for (int i = 0; i < c2f.Size(); ++i) {
+               c2f.GetRow(i,row);
+               for (int j = 0; j < row.Size(); j++) {
+                  old2new[row[j]] = i;
+               }
+            }
+
+            // map<int,int>::iterator it;
+            // printf("old2new\n");
+            // for (it = old2new.begin(); it != old2new.end(); ++it) {
+            //    printf("%d -> %d\n",it->first,it->second);
+            // }
+
+            for (size_t i = 0; i < coarse_map.size(); i++) {
+               //printf("ref i = %lu\n",i);
+               int jfine = fine_map[i];
+               int jcoarse = coarse_map[i];
+               //printf("mesh j old grid (fine) = %d\n",jfine);
+               if (jfine > -1) {
+                  int newj = old2new[jfine];
+                  //printf("mesh j new grid (coarse) = %d\n",newj);
+                  c2f.GetRow(newj,row);
+                  if (row.Size() > 1) {
+                     //printf("  was fine, now coarse\n");
+                     // was fine, now coarse
+                     coarse_map[i] = newj;
+                     fine_map[i] = -1;
+                  }
+                  else {
+                     //printf("  was fine, still fine\n");
+                     // was fine, still fine
+                     fine_map[i] = newj;
+                  }
+               }
+               //printf("mesh j old grid coarse = %d\n",jcoarse);
+               if (jcoarse > -1) {
+                  int newj = old2new[jcoarse];
+                  coarse_map[i] = newj;
+               }
+            }
+
+            // printf("new coarse_map is:\n");
+            // for (size_t i = 0; i < coarse_map.size(); i++) {
+            //    printf("%lu -> %d\n",i,coarse_map[i]);
+            // }
+            // printf("new fine_map is:\n");
+            // for (size_t i = 0; i < fine_map.size(); i++) {
+            //    printf("%lu -> %d\n",i,fine_map[i]);
+            // }
+
+            //printf("  ** done derefinements **\n");
+
+            //printf("maps after derefinement\n");
+            //show_maps(mesh,coarse_map,fine_map);
+
+         }
+
+      }
+
+      // Output the current solution.
+      if (output_cycle_soln) {
+
+         ostringstream fn;
+         fn << "soln-" << ti << ".mesh";
+         ofstream mesh_ofs(fn.str());
+         mesh_ofs.precision(precision);
+         mesh_ofs << mesh;
+
+         for (int k = 0; k < num_equation; k++)
+         {
+            GridFunction uk(&fes, u_block.GetBlock(k));
+            ostringstream sol_name;
+            sol_name << "soln-" << ti << "-" << k << ".gf";
+            ofstream sol_ofs(sol_name.str().c_str());
+            sol_ofs.precision(precision);
+            sol_ofs << uk;
+         }
+      }
+
+      // Output the current error on the reference mesh
+      if (output_cycle_errors) {
+         vector<double> ref_errors(coarse_map.size());
+         compute_reference_errors(ti, fec, mesh, rho,
+                                  coarse_map, fine_map, ref_errors);
+         ostringstream fn;
+         fn << "err-" << ti << ".dat";
+         ofstream err_ofs(fn.str());
+         vector<double>::iterator it;
+         for (it = ref_errors.begin(); it != ref_errors.end(); ++it) {
+            int i = std::distance(ref_errors.begin(), it);
+            double err = *it;
+            // "mark" refinements with negation. We'll use this to vis
+            // the refined regions on the error plots.
+            if (coarse_map[i] < 0) err *= -1;
+            err_ofs << i << " " << err << endl;
+         }
+      }
+
+
+      if (cfl > 0) {
+         dt = estimate_dt(cfl, mesh, sol, A, order);
+      }
+
       double dt_real = min(dt, t_final - t);
 
       ode_solver->Step(sol, t, dt_real);
-      if (cfl > 0)
-      {
-         dt = cfl * hmin / max_char_speed / (2*order+1);
-      }
+
       ti++;
 
       done = (t >= t_final - 1e-8*dt);
@@ -275,9 +774,10 @@ int main(int argc, char *argv[])
          cout << "time step: " << ti << ", time: " << t << endl;
          if (visualization)
          {
-            sout << "solution\n" << mesh << mom << flush;
+            sout << "solution\n" << mesh << rho_u << flush;
          }
       }
+
    }
 
    tic_toc.Stop();
@@ -285,21 +785,57 @@ int main(int argc, char *argv[])
 
    // 9. Save the final solution. This output can be viewed later using GLVis:
    //    "glvis -m vortex.mesh -g vortex-1-final.gf".
-   for (int k = 0; k < num_equation; k++)
    {
-      GridFunction uk(&fes, u_block.GetBlock(k));
-      ostringstream sol_name;
-      sol_name << "vortex-" << k << "-final.gf";
-      ofstream sol_ofs(sol_name.str().c_str());
-      sol_ofs.precision(precision);
-      sol_ofs << uk;
+      ofstream mesh_ofs("vortex-final.mesh");
+      mesh_ofs.precision(precision);
+      mesh_ofs << mesh;
+
+
+      for (int k = 0; k < num_equation; k++)
+      {
+         GridFunction uk(&fes, u_block.GetBlock(k));
+         ostringstream sol_name;
+         sol_name << "vortex-" << k << "-final.gf";
+         ofstream sol_ofs(sol_name.str().c_str());
+         sol_ofs.precision(precision);
+         sol_ofs << uk;
+      }
    }
 
    // 10. Compute the L2 solution error summed for all components.
-   if (t_final == 2.0)
+   if (rseq.Size())
    {
-      const double error = sol.ComputeLpError(2, u0);
-      cout << "Solution error: " << error << endl;
+      // const CoarseFineTransformations& cft = mesh.GetRefinementTransforms();
+      // Table c2f;
+      // cft.GetCoarseToFineMap(mesh, c2f);
+
+      // Refine to the reference mesh by refining every coarse el that
+      // wasn't refined.
+      Array<int> refs;
+      for (int i = 0; i < mesh.GetNE(); i++) {
+         if (mesh.ncmesh->GetElementDepth(i) == 0) {
+            refs.Append(i);
+         }
+      }
+      mesh.GeneralRefinement(refs);
+
+      amr_update(fes, dfes, vfes, u_block, rho, rho_u, rho_e, sol);
+
+      Mesh mesh_ref("reference.mesh");
+      ifstream rho_ifs("reference-rho.gf");
+      ifstream rho_u_ifs("reference-rho-u.gf");
+      ifstream rho_e_ifs("reference-rho-e.gf");
+      GridFunction rho_ref(&mesh_ref, rho_ifs);
+      GridFunction rho_u_ref(&mesh_ref, rho_u_ifs);
+      GridFunction rho_e_ref(&mesh_ref, rho_e_ifs);
+      rho_ref.Print();
+      rho.Print();
+
+      GridFunctionCoefficient rho_ref_coeff(&rho_ref);
+      const double err = rho.ComputeL2Error(rho_ref_coeff);
+      printf("final L2 error %e\n",err);
+      // const double error = sol.ComputeLpError(2, u0);
+      // cout << "Solution error: " << error << endl;
    }
 
    // Free the used memory.

examples/ex18.hpp

@@ -11,7 +11,8 @@ extern int problem;
 // Maximum characteristic speed (updated by integrators)
 extern double max_char_speed;
 
-extern const int num_equation;
+extern int num_equation;
+
 extern const double specific_heat_ratio;
 extern const double gas_constant;
 
@@ -24,7 +25,8 @@ private:
 
    FiniteElementSpace &vfes;
    Operator &A;
-   SparseMatrix &Aflux;
+   MixedBilinearForm& Aflux;
+   //SparseMatrix &Aflux;
    DenseTensor Me_inv;
 
    mutable Vector state;
@@ -36,10 +38,13 @@ private:
 
 public:
    FE_Evolution(FiniteElementSpace &vfes_,
-                Operator &A_, SparseMatrix &Aflux_);
+                Operator &A_,
+                MixedBilinearForm &Aflux_);
 
    virtual void Mult(const Vector &x, Vector &y) const;
 
+   void Update();
+
    virtual ~FE_Evolution() { }
 };
 
@@ -100,7 +105,7 @@ public:
 
 // Implementation of class FE_Evolution
 FE_Evolution::FE_Evolution(FiniteElementSpace &vfes_,
-                           Operator &A_, SparseMatrix &Aflux_)
+                           Operator &A_, MixedBilinearForm &Aflux_)
    : TimeDependentOperator(A_.Height()),
      dim(vfes_.GetFE(0)->GetDim()),
      vfes(vfes_),
@@ -123,6 +128,32 @@ FE_Evolution::FE_Evolution(FiniteElementSpace &vfes_,
       inv.Factor();
       inv.GetInverseMatrix(Me_inv(i));
    }
+   //Aflux.Assemble();
+}
+
+void FE_Evolution::Update()
+{
+   height = width = A.Height();
+
+   Me_inv.SetSize(vfes.GetFE(0)->GetDof(),
+                  vfes.GetFE(0)->GetDof(),
+                  vfes.GetNE());
+
+   Aflux.Assemble();
+
+   // Standard local assembly and inversion for energy mass matrices.
+   const int dof = vfes.GetFE(0)->GetDof();
+   DenseMatrix Me(dof);
+   DenseMatrixInverse inv(&Me);
+   MassIntegrator mi;
+   for (int i = 0; i < vfes.GetNE(); i++)
+   {
+      mi.AssembleElementMatrix(*vfes.GetFE(i), *vfes.GetElementTransformation(i), Me);
+      inv.Factor();
+      inv.GetInverseMatrix(Me_inv(i));
+   }
+
+   z.SetSize(A.Height());
 }
 
 void FE_Evolution::Mult(const Vector &x, Vector &y) const
@@ -385,6 +416,8 @@ void FaceIntegrator::AssembleFaceVector(const FiniteElement &el1,
                                         FaceElementTransformations &Tr,
                                         const Vector &elfun, Vector &elvect)
 {
+  int dim = el1.GetDim();
+
    // Compute the term <F.n(u),[w]> on the interior faces.
    const int dof1 = el1.GetDof();
    const int dof2 = el2.GetDof();
@@ -424,16 +457,25 @@ void FaceIntegrator::AssembleFaceVector(const FiniteElement &el1,
 
       Tr.SetAllIntPoints(&ip); // set face and element int. points
 
+      const IntegrationPoint &eip1 = Tr.GetElement1IntPoint();
+      const IntegrationPoint &eip2 = Tr.GetElement2IntPoint();
+
       // Calculate basis functions on both elements at the face
-      el1.CalcShape(Tr.GetElement1IntPoint(), shape1);
-      el2.CalcShape(Tr.GetElement2IntPoint(), shape2);
+      el1.CalcShape(eip1, shape1);
+      el2.CalcShape(eip2, shape2);
 
       // Interpolate elfun at the point
       elfun1_mat.MultTranspose(shape1, funval1);
       elfun2_mat.MultTranspose(shape2, funval2);
 
       // Get the normal vector and the flux on the face
-      CalcOrtho(Tr.Jacobian(), nor);
+      if (1 == dim) {
+	nor(0) = 2*eip1.x - 1.0;
+      }
+      else {
+	CalcOrtho(Tr.Jacobian(), nor);
+      }
+
       const double mcs = rsolver.Eval(funval1, funval2, nor, fluxN);
 
       // Update max char speed
@@ -504,62 +546,147 @@ bool StateIsPhysical(const Vector &state, const int dim)
 // Initial condition
 void InitialCondition(const Vector &x, Vector &y)
 {
-   MFEM_ASSERT(x.Size() == 2, "");
+  int dim = x.Size();
 
-   double radius = 0, Minf = 0, beta = 0;
-   if (problem == 1)
-   {
-      // "Fast vortex"
-      radius = 0.2;
-      Minf = 0.5;
-      beta = 1. / 5.;
-   }
-   else if (problem == 2)
-   {
-      // "Slow vortex"
-      radius = 0.2;
-      Minf = 0.05;
-      beta = 1. / 50.;
-   }
-   else
-   {
-      mfem_error("Cannot recognize problem."
-                 "Options are: 1 - fast vortex, 2 - slow vortex");
-   }
+  if (dim == 1) {
 
-   const double xc = 0.0, yc = 0.0;
+     double rho;
+     double u;
+     double e;
 
-   // Nice units
-   const double vel_inf = 1.;
-   const double den_inf = 1.;
+     if (problem == 1) {
 
-   // Derive remainder of background state from this and Minf
-   const double pres_inf = (den_inf / specific_heat_ratio) * (vel_inf / Minf) *
-                           (vel_inf / Minf);
-   const double temp_inf = pres_inf / (den_inf * gas_constant);
+        double xc = x[0]-0.5;
+        rho = 1.0;
+        u = 0.0;
+        e = 1.0+0.1*exp(-xc*xc);
 
-   double r2rad = 0.0;
-   r2rad += (x(0) - xc) * (x(0) - xc);
-   r2rad += (x(1) - yc) * (x(1) - yc);
-   r2rad /= (radius * radius);
+     }
+     else if (problem == 2) {
 
-   const double shrinv1 = 1.0 / (specific_heat_ratio - 1.);
+        u = 0.0;
+        double gamma = 1.4;
+        double gm1 = gamma -1.0;
 
-   const double velX = vel_inf * (1 - beta * (x(1) - yc) / radius * exp(
-                                     -0.5 * r2rad));
-   const double velY = vel_inf * beta * (x(0) - xc) / radius * exp(-0.5 * r2rad);
-   const double vel2 = velX * velX + velY * velY;
+        double rhoL = 1.0;
+        double pL = 1.0;
 
-   const double specific_heat = gas_constant * specific_heat_ratio * shrinv1;
-   const double temp = temp_inf - 0.5 * (vel_inf * beta) *
-                       (vel_inf * beta) / specific_heat * exp(-r2rad);
+        double rhoR = 0.125;
+        double pR = 0.1;
 
-   const double den = den_inf * pow(temp/temp_inf, shrinv1);
-   const double pres = den * gas_constant * temp;
-   const double energy = shrinv1 * pres / den + 0.5 * vel2;
+        if (x[0] < 0.5) {
+           rho = rhoL;
+           e = 1./gm1*pL/rhoL;
+        }
+        else {
+           rho = rhoR;
+           e = 1./gm1*pR/rhoR;
+        }
+     }
+     else if (problem == 3) {
+
+        u = 0.0;
+        double gamma = 1.4;
+        double gm1 = gamma -1.0;
+
+        double rhoL = 1.0;
+        double pL = 1.0;
+
+        double rhoR = 0.125;
+        double pR = 0.1;
+
+        rho = rhoR;
+        e = 1./gm1*pR/rhoR;
+        if (x[0] > 0.3 && x[0] < 0.4) {
+           rho = rhoL;
+           e = 1./gm1*pL/rhoL;
+        }
+        if (x[0] > 0.5 && x[0] < 1.0) {
+           double xc = 0.75;
+           double x0 = x[0]-xc;
+           double a = 10.0;
+           double x1 = a*x0;
+           rho = rhoR +0.5*rhoL*exp(-x1*x1);
+           e = 1./gm1*pR/rhoL;
+        }
+     }
+     else {
+        printf("unknown problem!\n");
+        exit(1);
+     }
+
+    // if (x(0) < 0.5) {
+    //   rho = 1.0;
+    //   e = 1.05*(;
+    // }
+
+    int neq = 0;
+    y(neq++) = rho;
+    y(neq++) = rho * u;
+    y(neq++) = rho * e;
+  }
+  else {
+
+    MFEM_ASSERT(x.Size() == 2, "");
+
+    double radius = 0, Minf = 0, beta = 0;
+    if (problem == 1)
+      {
+	// "Fast vortex"
+	radius = 0.2;
+	Minf = 0.5;
+	beta = 1. / 5.;
+      }
+    else if (problem == 2)
+      {
+	// "Slow vortex"
+	radius = 0.2;
+	Minf = 0.05;
+	beta = 1. / 50.;
+      }
+    else
+      {
+	mfem_error("Cannot recognize problem."
+		   "Options are: 1 - fast vortex, 2 - slow vortex");
+      }
+
+    const double xc = 0.0, yc = 0.0;
+
+    // Nice units
+    const double vel_inf = 1.;
+    const double den_inf = 1.;
+
+    // Derive remainder of background state from this and Minf
+    const double pres_inf = (den_inf / specific_heat_ratio) * (vel_inf / Minf) *
+      (vel_inf / Minf);
+    const double temp_inf = pres_inf / (den_inf * gas_constant);
+
+    double r2rad = 0.0;
+    r2rad += (x(0) - xc) * (x(0) - xc);
+    r2rad += (x(1) - yc) * (x(1) - yc);
+    r2rad /= (radius * radius);
+
+    const double shrinv1 = 1.0 / (specific_heat_ratio - 1.);
+
+    const double velX = vel_inf * (1 - beta * (x(1) - yc) / radius * exp(
+									 -0.5 * r2rad));
+    const double velY = vel_inf * beta * (x(0) - xc) / radius * exp(-0.5 * r2rad);
+    const double vel2 = velX * velX + velY * velY;
+
+    const double specific_heat = gas_constant * specific_heat_ratio * shrinv1;
+    const double temp = temp_inf - 0.5 * (vel_inf * beta) *
+      (vel_inf * beta) / specific_heat * exp(-r2rad);
+
+    const double den = den_inf * pow(temp/temp_inf, shrinv1);
+    const double pres = den * gas_constant * temp;
+    const double energy = shrinv1 * pres / den + 0.5 * vel2;
+
+    int neq = 0;
+    y(neq++) = den;
+    y(neq++) = den * velX;
+    y(neq++) = den * velY;
+    y(neq++) = den * energy;
+
+  } // 2d
 
-   y(0) = den;
-   y(1) = den * velX;
-   y(2) = den * velY;
-   y(3) = den * energy;
 }

examples/ex1_es.cpp

@@ -1,266 +0,0 @@
-//                                MFEM Example 1
-//
-// Compile with: make ex1
-//
-// Sample runs:  ex1 -m ../data/square-disc.mesh
-//               ex1 -m ../data/star.mesh
-//               ex1 -m ../data/escher.mesh
-//               ex1 -m ../data/fichera.mesh
-//               ex1 -m ../data/square-disc-p2.vtk -o 2
-//               ex1 -m ../data/square-disc-p3.mesh -o 3
-//               ex1 -m ../data/square-disc-nurbs.mesh -o -1
-//               ex1 -m ../data/disc-nurbs.mesh -o -1
-//               ex1 -m ../data/pipe-nurbs.mesh -o -1
-//               ex1 -m ../data/star-surf.mesh
-//               ex1 -m ../data/square-disc-surf.mesh
-//               ex1 -m ../data/inline-segment.mesh
-//               ex1 -m ../data/amr-quad.mesh
-//               ex1 -m ../data/amr-hex.mesh
-//               ex1 -m ../data/fichera-amr.mesh
-//               ex1 -m ../data/mobius-strip.mesh
-//               ex1 -m ../data/mobius-strip.mesh -o -1 -sc
-//
-// 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>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   const char *mesh_file = "./star-set.mesh";
-   int order = 1;
-   int rs = -1;
-   int ra = 0;
-   int bt = EntitySets::INVALID;
-   const char *bs = "Origin";
-   bool static_cond = false;
-   bool visualization = 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(&rs, "-rs", "--refine-serial",
-                  "Number of serial refinement levels");
-   args.AddOption(&ra, "-ra", "--refine-adaptive",
-                  "Number of adaptive refinement levels");
-   args.AddOption(&bt, "-bt", "--bc-entity-type",
-                  "");
-   args.AddOption(&bs, "-bs", "--bc-entity-set-name",
-                  "");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   // 2. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral, hexahedral, surface and volume meshes with
-   //    the same code.
-   Mesh *mesh = new Mesh(mesh_file, 1, 1);
-   int dim = mesh->Dimension();
-
-   // 3. Refine the mesh 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 50,000
-   //    elements.
-   {
-      int ref_levels = ( rs >= 0 ) ? rs :
-                       (int)floor(log(50000./mesh->GetNE())/log(2.)/dim);
-      for (int l = 0; l < ref_levels; l++)
-      {
-         mesh->UniformRefinement();
-      }
-   }
-   if ( mesh->ent_sets )
-   {
-      cout << "mesh->ent_sets is non NULL" << endl;
-      mesh->ent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "mesh->ent_sets is NULL" << endl;
-   }
-
-   if ( ra > 0 )
-   {
-      cout << "calling EnsureNCMesh" << endl;
-      mesh->EnsureNCMesh();
-      cout << "back from EnsureNCMesh" << endl;
-   }
-   if ( mesh->ent_sets )
-   {
-      cout << "mesh->ent_sets is non NULL" << endl;
-   }
-   else
-   {
-      cout << "mesh->ent_sets is NULL" << endl;
-   }
-   cout << "Calling RandomRefinement " << ra << " times." << endl;
-   for (int l = 0; l < ra; l++)
-   {
-      mesh->RandomRefinement(0.2);
-   }
-   cout << "Done with refinement" << endl;
-   if ( mesh->ent_sets )
-   {
-      cout << "mesh->ent_sets is non NULL" << endl;
-      mesh->ent_sets->PrintSetInfo(cout);
-   }
-   if ( mesh->ncmesh )
-   {
-      mesh->ncmesh->PrintStats(cout);
-
-      ofstream ofsV("vp.out");
-      ofstream ofsE("ce.out");
-      mesh->ncmesh->PrintVertexParents(ofsV);
-      mesh->ncmesh->PrintCoarseElements(ofsE);
-   }
-
-   // 4. Define a finite element space on the mesh. Here we use continuous
-   //    Lagrange finite elements of the specified order. If order < 1, we
-   //    instead use an isoparametric/isogeometric space.
-   FiniteElementCollection *fec;
-   if (order > 0)
-   {
-      fec = new H1_FECollection(order, dim);
-   }
-   else if (mesh->GetNodes())
-   {
-      fec = mesh->GetNodes()->OwnFEC();
-      cout << "Using isoparametric FEs: " << fec->Name() << endl;
-   }
-   else
-   {
-      fec = new H1_FECollection(order = 1, dim);
-   }
-   FiniteElementSpace *fespace = new FiniteElementSpace(mesh, fec);
-   cout << "Number of finite element unknowns: "
-        << fespace->GetTrueVSize() << endl;
-
-   // 5. Determine the list of true (i.e. 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 ( bt == EntitySets::INVALID )
-   {
-      if (mesh->bdr_attributes.Size())
-      {
-         Array<int> ess_bdr(mesh->bdr_attributes.Max());
-         ess_bdr = 1;
-         fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-      }
-   }
-   else
-   {
-      fespace->GetEssentialTrueDofs((EntitySets::EntityType)bt, bs,
-                                    ess_tdof_list);
-   }
-
-   cout << "Number of Dirichlet dofs: " << ess_tdof_list.Size() << endl;
-
-   // 6. Set up the 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 the finite element fespace.
-   LinearForm *b = new LinearForm(fespace);
-   ConstantCoefficient one(1.0);
-   b->AddDomainIntegrator(new DomainLFIntegrator(one));
-   b->Assemble();
-
-   // 7. Define the solution vector x as a finite element grid function
-   //    corresponding to fespace. Initialize x with initial guess of zero,
-   //    which satisfies the boundary conditions.
-   GridFunction x(fespace);
-   x = 0.0;
-
-   // 8. Set up the bilinear form a(.,.) on the finite element space
-   //    corresponding to the Laplacian operator -Delta, by adding the Diffusion
-   //    domain integrator.
-   BilinearForm *a = new BilinearForm(fespace);
-   a->AddDomainIntegrator(new DiffusionIntegrator(one));
-
-   // 9. Assemble the bilinear form and the corresponding linear system,
-   //    applying any necessary transformations such as: eliminating boundary
-   //    conditions, applying conforming constraints for non-conforming AMR,
-   //    static condensation, etc.
-   if (static_cond) { a->EnableStaticCondensation(); }
-   a->Assemble();
-
-   SparseMatrix A;
-   Vector B, X;
-   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
-
-   cout << "Size of linear system: " << A.Height() << endl;
-
-#ifndef MFEM_USE_SUITESPARSE
-   // 10. Define a simple symmetric Gauss-Seidel preconditioner and use it to
-   //     solve the system A X = B with PCG.
-   GSSmoother M(A);
-   PCG(A, M, B, X, 1, 200, 1e-12, 0.0);
-#else
-   // 10. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
-   UMFPackSolver umf_solver;
-   umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-   umf_solver.SetOperator(A);
-   umf_solver.Mult(B, X);
-#endif
-
-   // 11. Recover the solution as a finite element grid function.
-   a->RecoverFEMSolution(X, *b, x);
-
-   // 12. Save the refined mesh and the solution. This output can be viewed later
-   //     using GLVis: "glvis -m refined.mesh -g sol.gf".
-   ofstream mesh_ofs("refined.mesh");
-   mesh_ofs.precision(8);
-   mesh->Print(mesh_ofs);
-   ofstream sol_ofs("sol.gf");
-   sol_ofs.precision(8);
-   x.Save(sol_ofs);
-
-   // 13. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << *mesh << x << flush;
-   }
-
-   // 14. Free the used memory.
-   delete a;
-   delete b;
-   delete fespace;
-   if (order > 0) { delete fec; }
-   delete mesh;
-
-   return 0;
-}

examples/ex1p.cpp

@@ -9,7 +9,6 @@
 //               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

examples/ex1p_es.cpp

@@ -1,388 +0,0 @@
-//                       MFEM Example 1 - Parallel Version
-//
-// 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/escher.mesh
-//               mpirun -np 4 ex1p -m ../data/fichera.mesh
-//               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/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/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
-//
-//               The following are examples of using EntitySets to define
-//               homogeneous Dirichlet boundary condition.  These examples
-//               require a modified mesh file and a specialized version of
-//               example 1 called "ex1p_es".
-//               mpirun -np 4 ex1p_es -m ./fichera-set.mesh -bt 0 -bs Origin
-//               mpirun -np 4 ex1p_es -m ./fichera-set.mesh -bt 1 -bs Axes
-//               mpirun -np 4 ex1p_es -m ./fichera-set.mesh
-//                                    -bt 1 -bs "Negative Axes"
-//               mpirun -np 4 ex1p_es -m ./fichera-set.mesh
-//                                    -bt 2 -bs "Interior Corner"
-//               mpirun -np 4 ex1p_es -m ./fichera-set.mesh
-//                                    -bt 2 -bs "Exterior Corner"
-//               mpirun -np 4 ex1p_es -m ./fichera-set.mesh
-//                                    -bt 3 -bs "Interior Corner"
-//               mpirun -np 4 ex1p_es -m ./fichera-set.mesh
-//                                    -bt 3 -bs "Exterior Corner"
-//               mpirun -np 4 ex1p_es -m ./fichera-set.mesh -bt 3 -bs "Steps"
-//
-// 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>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "./star-set.mesh";
-   int order = 1;
-   int rs = -1;
-   int rp = 2;
-   int ra = 0;
-   int bt = EntitySets::INVALID;
-   const char *bs = "Origin";
-   bool static_cond = false;
-   bool visualization = 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(&rs, "-rs", "--refine-serial",
-                  "Number of serial refinement levels");
-   args.AddOption(&rp, "-rp", "--refine-parallel",
-                  "Number of parallel refinement levels");
-   args.AddOption(&ra, "-ra", "--refine-adaptive",
-                  "Number of adaptive refinement levels");
-   args.AddOption(&bt, "-bt", "--bc-entity-type",
-                  "");
-   args.AddOption(&bs, "-bs", "--bc-entity-set-name",
-                  "");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 3. 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 = new Mesh(mesh_file, 1, 1);
-   int dim = mesh->Dimension();
-
-   // 4. 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 = ( rs >= 0 ) ? rs :
-                       (int)floor(log(10000./mesh->GetNE())/log(2.)/dim);
-      for (int l = 0; l < ref_levels; l++)
-      {
-         if ( myid == 0 ) { cout << "Uniform refinement in serial..."; }
-         mesh->UniformRefinement();
-      }
-      MPI_Barrier(MPI_COMM_WORLD);
-      if ( myid == 0 && rs > 0 ) { cout << "Done" << endl; }
-   }
-   if ( mesh->ent_sets )
-   {
-      cout << "mesh->ent_sets is non NULL" << endl;
-      mesh->ent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "mesh->ent_sets is NULL" << endl;
-   }
-   /*
-     At this point we have a serial mesh containing an EntitySets
-     object which stores the current node/edge/face/element indices
-     for each entity in each set.  This data is duplicated on each MPI
-     rank.
-    */
-   if ( ra > 0 )
-   {
-      cout << "calling EnsureNCMesh" << endl;
-      mesh->EnsureNCMesh();
-      cout << "back from EnsureNCMesh" << endl;
-   }
-   if ( mesh->ent_sets )
-   {
-      cout << "mesh->ent_sets is non NULL" << endl;
-      mesh->ent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "mesh->ent_sets is NULL" << endl;
-   }
-   /*
-     We now have an NCEntitySets object which stores the node indices
-     describing each enity in each node/edge/face set and the element
-     indices for the elements in each element set.  This data is
-     duplicated on each MPI rank.
-    */
-
-   // 5. 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.
-   cout << "creating ParMesh from serial mesh" << endl;
-   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
-   cout << "done creating ParMesh from serial mesh" << endl;
-   delete mesh;
-   if ( pmesh->pent_sets )
-   {
-      cout << "pmesh->pent_sets is non NULL" << endl;
-      pmesh->pent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "pmesh->pent_sets is NULL" << endl;
-   }
-   /*
-     We now have a ParEntitySets object which marshals the data stored
-     in EntitySets objects.  The data has now been pruned so that each
-     rank only contains indices of local entities.
-
-     The NCEntitySets object remains unchanged...
-
-     If we have an NC mesh a different path is taken and the
-     EntitySets are ignored.
-
-     1) ParNCMesh is created from NCMesh
-       a) Creates a ParNCEntitySets object from ncmesh (every rank contains
-          information to find every entity)
-     2) ParNCMesh is pruned which involves renumbering elements and vertices
-     3) ParMesh is initialized from ParNCMesh
-     4) ParNCMesh::OnMeshUpdated is called
-     5) Mesh::GenerateNCFaceInfo is called
-    */
-   {
-      int par_ref_levels = rp;
-      for (int l = 0; l < par_ref_levels; l++)
-      {
-         if ( myid == 0 ) { cout << "Uniform refinement in parallel..."; }
-         pmesh->UniformRefinement();
-      }
-      MPI_Barrier(MPI_COMM_WORLD);
-      if ( myid == 0 && rs > 0 ) { cout << "Done" << endl; }
-   }
-   /*
-     RandomRefinement will end up calling
-     ParMesh::NonconformingRefinement which will create a new ParMesh
-     object using the ParNCMesh object and then call
-     ParMesh::OnMeshUpdated on this new mesh.
-    */
-
-   for (int l = 0; l < ra; l++)
-   {
-      pmesh->RandomRefinement(0.2);
-   }
-   if ( ra > 0 )
-   {
-      if ( pmesh->pent_sets )
-      {
-         cout << "pmesh->pent_sets is non NULL post random refinement" << endl;
-         pmesh->pent_sets->PrintSetInfo(cout);
-      }
-      else
-      {
-         cout << "pmesh->pent_sets is NULL post random refinement" << endl;
-      }
-   }
-
-   // 6. 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;
-   if (order > 0)
-   {
-      fec = new H1_FECollection(order, dim);
-   }
-   else if (pmesh->GetNodes())
-   {
-      fec = pmesh->GetNodes()->OwnFEC();
-      if (myid == 0)
-      {
-         cout << "Using isoparametric FEs: " << fec->Name() << endl;
-      }
-   }
-   else
-   {
-      fec = new H1_FECollection(order = 1, dim);
-   }
-   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
-   HYPRE_Int size = fespace->GlobalTrueVSize();
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 7. Determine the list of true (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 ( bt == EntitySets::INVALID )
-   {
-      if (pmesh->bdr_attributes.Size())
-      {
-         Array<int> ess_bdr(pmesh->bdr_attributes.Max());
-         ess_bdr = 1;
-         fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-      }
-   }
-   else
-   {
-      fespace->GetEssentialTrueDofs((EntitySets::EntityType)bt, bs,
-                                    ess_tdof_list);
-   }
-   for (int i=0; i<num_procs; i++)
-   {
-      if (myid == i)
-      {
-         cout << "Number of Dirichlet dofs on proc " << i << ": "
-              << ess_tdof_list.Size() << endl;
-      }
-   }
-
-   // 8. 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 = new ParLinearForm(fespace);
-   ConstantCoefficient one(1.0);
-   b->AddDomainIntegrator(new DomainLFIntegrator(one));
-   b->Assemble();
-
-   // 9. 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;
-
-   // 10. 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 = new ParBilinearForm(fespace);
-   a->AddDomainIntegrator(new DiffusionIntegrator(one));
-
-   // 11. 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();
-
-   HypreParMatrix A;
-   Vector B, X;
-   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
-
-   if (myid == 0)
-   {
-      cout << "Size of linear system: " << A.GetGlobalNumRows() << endl;
-   }
-
-   // 12. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
-   //     preconditioner from hypre.
-   HypreSolver *amg = new HypreBoomerAMG(A);
-   HyprePCG *pcg = new HyprePCG(A);
-   pcg->SetTol(1e-12);
-   pcg->SetMaxIter(200);
-   pcg->SetPrintLevel(2);
-   pcg->SetPreconditioner(*amg);
-   pcg->Mult(B, X);
-
-   // 13. Recover the parallel grid function corresponding to X. This is the
-   //     local finite element solution on each processor.
-   a->RecoverFEMSolution(X, *b, x);
-
-   // 14. 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);
-   }
-
-   // 15. 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;
-   }
-
-   // 16. Free the used memory.
-   delete pcg;
-   delete amg;
-   delete a;
-   delete b;
-   delete fespace;
-   if (order > 0) { delete fec; }
-   delete pmesh;
-
-   MPI_Finalize();
-
-   return 0;
-}

examples/ex22.cpp

@@ -13,8 +13,6 @@
 //               ex22 -m ../data/inline-hex.mesh -o 2 -p 1
 //               ex22 -m ../data/inline-hex.mesh -o 2 -p 2
 //               ex22 -m ../data/inline-hex.mesh -o 2 -p 2 -pa
-//               ex22 -m ../data/inline-wedge.mesh -o 1
-//               ex22 -m ../data/inline-pyramid.mesh -o 1
 //               ex22 -m ../data/star.mesh -r 1 -o 2 -sigma 10.0
 //
 // Device sample runs:

examples/ex22p.cpp

@@ -13,8 +13,6 @@
 //               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 2 -p 1
 //               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 2 -p 2
 //               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 1 -p 2 -pa
-//               mpirun -np 4 ex22p -m ../data/inline-wedge.mesh -o 1
-//               mpirun -np 4 ex22p -m ../data/inline-pyramid.mesh -o 1
 //               mpirun -np 4 ex22p -m ../data/star.mesh -o 2 -sigma 10.0
 //
 // Device sample runs:

examples/ex25.cpp

@@ -92,7 +92,7 @@ class PMLDiagMatrixCoefficient : public VectorCoefficient
 {
 private:
    CartesianPML * pml = nullptr;
-   void (*Function)(const Vector &, CartesianPML *, Vector &);
+   void (*Function)(const Vector &, CartesianPML * , Vector &);
 public:
    PMLDiagMatrixCoefficient(int dim, void(*F)(const Vector &, CartesianPML *,
                                               Vector &),

examples/ex25p.cpp

@@ -92,7 +92,7 @@ class PMLDiagMatrixCoefficient : public VectorCoefficient
 {
 private:
    CartesianPML * pml = nullptr;
-   void (*Function)(const Vector &, CartesianPML *, Vector &);
+   void (*Function)(const Vector &, CartesianPML * , Vector &);
 public:
    PMLDiagMatrixCoefficient(int dim, void(*F)(const Vector &, CartesianPML *,
                                               Vector &),

examples/ex27.cpp

@@ -295,7 +295,17 @@ int main(int argc, char *argv[])
    //     element solution.
    a.RecoverFEMSolution(X, b, u);
 
-   // 13. Compute the various boundary integrals.
+   // 13. Build a mass matrix to help solve for n.Grad(u) where 'n' is a surface
+   //     normal.
+   BilinearForm m(&fespace);
+   m.AddDomainIntegrator(new MassIntegrator);
+   m.Assemble();
+
+   ess_tdof_list.SetSize(0);
+   OperatorPtr M;
+   m.FormSystemMatrix(ess_tdof_list, M);
+
+   // 14. Compute the various boundary integrals.
    mfem::out << endl
              << "Verifying boundary conditions" << endl
              << "=============================" << endl;
@@ -351,7 +361,7 @@ int main(int argc, char *argv[])
                 << " error " << err << endl;
    }
 
-   // 14. Save the refined mesh and the solution. This output can be viewed
+   // 15. Save the refined mesh and the solution. This output can be viewed
    //     later using GLVis: "glvis -m refined.mesh -g sol.gf".
    {
       ofstream mesh_ofs("refined.mesh");
@@ -362,7 +372,7 @@ int main(int argc, char *argv[])
       u.Save(sol_ofs);
    }
 
-   // 15. Send the solution by socket to a GLVis server.
+   // 16. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       string title_str = h1 ? "H1" : "DG";
@@ -375,7 +385,7 @@ int main(int argc, char *argv[])
                << " keys 'mmc'" << flush;
    }
 
-   // 16. Free the used memory.
+   // 17. Free the used memory.
    delete fec;
    delete mesh;
 

examples/ex27p.cpp

@@ -314,7 +314,17 @@ int main(int argc, char *argv[])
    //     local finite element solution on each processor.
    a.RecoverFEMSolution(X, b, u);
 
-   // 14. Compute the various boundary integrals.
+   // 14. Build a mass matrix to help solve for n.Grad(u) where 'n' is a surface
+   //     normal.
+   ParBilinearForm m(&fespace);
+   m.AddDomainIntegrator(new MassIntegrator);
+   m.Assemble();
+
+   ess_tdof_list.SetSize(0);
+   OperatorPtr M;
+   m.FormSystemMatrix(ess_tdof_list, M);
+
+   // 15. Compute the various boundary integrals.
    mfem::out << endl
              << "Verifying boundary conditions" << endl
              << "=============================" << endl;
@@ -370,7 +380,7 @@ int main(int argc, char *argv[])
                 << " error " << err << endl;
    }
 
-   // 15. Save the refined mesh and the solution in parallel. This output can be
+   // 16. 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;
@@ -386,7 +396,7 @@ int main(int argc, char *argv[])
       u.Save(sol_ofs);
    }
 
-   // 16. Send the solution by socket to a GLVis server.
+   // 17. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       string title_str = h1 ? "H1" : "DG";
@@ -401,7 +411,7 @@ int main(int argc, char *argv[])
                << " keys 'mmc'" << flush;
    }
 
-   // 17. Free the used memory.
+   // 18. Free the used memory.
    delete fec;
 
    return 0;

examples/ex3.cpp

@@ -16,8 +16,6 @@
 //               ex3 -m ../data/beam-hex-nurbs.mesh
 //               ex3 -m ../data/amr-hex.mesh
 //               ex3 -m ../data/fichera-amr.mesh
-//               ex3 -m ../data/ref-prism.mesh -o 1
-//               ex3 -m ../data/octahedron.mesh -o 1
 //               ex3 -m ../data/star-surf.mesh -o 1
 //               ex3 -m ../data/mobius-strip.mesh -f 0.1
 //               ex3 -m ../data/klein-bottle.mesh -f 0.1

examples/ex30.cpp

@@ -1,195 +0,0 @@
-//                            MFEM Example 30
-//
-// Compile with: make ex30
-//
-// Sample runs:  ex30 -m ../data/square-disc.mesh -o 1
-//               ex30 -m ../data/square-disc.mesh -o 2
-//               ex30 -m ../data/square-disc.mesh -o 2 -me 1e3
-//               ex30 -m ../data/square-disc-nurbs.mesh -o 2
-//               ex30 -m ../data/star.mesh -o 2 -eo 4
-//               ex30 -m ../data/fichera.mesh -o 2 -me 1e4
-//               ex30 -m ../data/disc-nurbs.mesh -o 2
-//               ex30 -m ../data/ball-nurbs.mesh -o 2 -eo 3 -e 1e-2 -me 1e4
-//               ex30 -m ../data/star-surf.mesh -o 2
-//               ex30 -m ../data/square-disc-surf.mesh -o 2
-//               ex30 -m ../data/amr-quad.mesh -l 2
-//
-// Description:  This is an example of adaptive mesh refinement preprocessing
-//               which lowers the data oscillation [1] to a user-defined
-//               relative threshold. There is no PDE being solved.
-//
-//               MFEM's capability to work with both conforming and
-//               nonconforming meshes is demonstrated in example 6. In some
-//               problems, the material data or loading data is not sufficiently
-//               resolved on the initial mesh. This missing fine scale data
-//               reduces the accuracy of the solution as well as the accuracy
-//               of some local error estimators. By preprocessing the mesh
-//               before solving the PDE, many issues can be avoided.
-//
-//               [1] Morin, P., Nochetto, R. H., & Siebert, K. G. (2000).
-//                   Data oscillation and convergence of adaptive FEM. SIAM
-//                   Journal on Numerical Analysis, 38(2), 466-488.
-//
-//               [2] Mitchell, W. F. (2013). A collection of 2D elliptic
-//                   problems for testing adaptive grid refinement algorithms.
-//                   Applied mathematics and computation, 220, 350-364.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-// Piecewise-affine function which is sometimes mesh-conforming
-double affine_function(const Vector &p)
-{
-   double x = p(0), y = p(1);
-   if (x < 0.0)
-   {
-      return 1.0 + x + y;
-   }
-   else
-   {
-      return 1.0;
-   }
-}
-
-// Piecewise-constant function which is never mesh-conforming
-double jump_function(const Vector &p)
-{
-   if (p.Normlp(2.0) > 0.4 && p.Normlp(2.0) < 0.6) { return 1.0; }
-   return 5.0;
-}
-
-// Singular function derived from the Laplacian of the "steep wavefront"
-// problem in [2].
-double singular_function(const Vector &p)
-{
-   double x = p(0), y = p(1);
-   double alpha = 1000.0;
-   double xc = 0.75, yc = 0.5;
-   double r0 = 0.7;
-   double r = sqrt(pow(x - xc,2.0) + pow(y - yc,2.0));
-   double num = - ( alpha - pow(alpha,3) * (pow(r,2) - pow(r0,2)) );
-   double denom = pow(r * ( pow(alpha,2) * pow(r0,2) + pow(alpha,2) * pow(r,2) \
-                            - 2 * pow(alpha,2) * r0 * r + 1.0 ),2);
-   denom = max(denom,1e-8);
-   return num / denom;
-}
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/star.mesh";
-   int order = 1;
-   int nc_limit = 1;
-   int max_elems = 1e5;
-   double double_max_elems = double(max_elems);
-   bool visualization = true;
-   double osc_threshold = 1e-3;
-   int enriched_order = 5;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&nc_limit, "-l", "--nc-limit",
-                  "Maximum level of hanging nodes.");
-   args.AddOption(&double_max_elems, "-me", "--max-elems",
-                  "Stop after reaching this many elements.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&osc_threshold, "-e", "--error",
-                  "relative data oscillation threshold.");
-   args.AddOption(&enriched_order, "-eo", "--enriched_order",
-                  "Enriched quadrature order.");
-
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   max_elems = int(double_max_elems);
-   Mesh mesh(mesh_file, 1, 1);
-
-   // 2. Since a NURBS mesh can currently only be refined uniformly, we need to
-   //    convert it to a piecewise-polynomial curved mesh. First we refine the
-   //    NURBS mesh a bit more and then project the curvature to quadratic Nodes.
-   if (mesh.NURBSext)
-   {
-      for (int i = 0; i < 2; i++)
-      {
-         mesh.UniformRefinement();
-      }
-      mesh.SetCurvature(2);
-   }
-
-   // 3. Define functions and refiner.
-   FunctionCoefficient affine_coeff(affine_function);
-   FunctionCoefficient jump_coeff(jump_function);
-   FunctionCoefficient singular_coeff(singular_function);
-   CoefficientRefiner coeffrefiner(affine_coeff, order);
-
-   // 4. Connect to GLVis.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock;
-   if (visualization)
-   {
-      sol_sock.open(vishost, visport);
-   }
-
-   // 5. Define custom integration rule (optional).
-   const IntegrationRule *irs[Geometry::NumGeom];
-   int order_quad = 2*order + enriched_order;
-   for (int i = 0; i < Geometry::NumGeom; ++i)
-   {
-      irs[i] = &(IntRules.Get(i, order_quad));
-   }
-
-   // 6. Apply custom refiner settings.
-   coeffrefiner.SetIntRule(irs);
-   coeffrefiner.SetMaxElements(max_elems);
-   coeffrefiner.SetThreshold(osc_threshold);
-   coeffrefiner.SetNCLimit(nc_limit);
-   coeffrefiner.PrintWarnings();
-
-   // 7. Preprocess mesh to control osc (piecewise-affine function).
-   //    This is mostly just a verification check. The oscillation should
-   //    be zero if the function is mesh-conforming and order > 0.
-   coeffrefiner.PreprocessMesh(mesh);
-
-   mfem::out  << "\n";
-   mfem::out << "Function 0 (affine) \n";
-   mfem::out << "Number of Elements " << mesh.GetNE() << "\n";
-   mfem::out << "Osc error " << coeffrefiner.GetOsc() << "\n";
-
-   // 8. Preprocess mesh to control osc (jump function).
-   coeffrefiner.ResetCoefficient(jump_coeff);
-   coeffrefiner.PreprocessMesh(mesh);
-
-   mfem::out  << "\n";
-   mfem::out << "Function 1 (discontinuous) \n";
-   mfem::out << "Number of Elements " << mesh.GetNE() << "\n";
-   mfem::out << "Osc error " << coeffrefiner.GetOsc() << "\n";
-
-   // 9. Preprocess mesh to control osc (singular function).
-   coeffrefiner.ResetCoefficient(singular_coeff);
-   coeffrefiner.PreprocessMesh(mesh);
-
-   mfem::out  << "\n";
-   mfem::out << "Function 2 (singular) \n";
-   mfem::out << "Number of Elements " << mesh.GetNE() << "\n";
-   mfem::out << "Osc error " << coeffrefiner.GetOsc() << "\n";
-
-   sol_sock.precision(8);
-   sol_sock << "mesh\n" << mesh << flush;
-
-   return 0;
-}

examples/ex30p.cpp

@@ -1,241 +0,0 @@
-//                        MFEM Example 30 - Parallel Version
-//
-// Compile with: make ex30p
-//
-// Sample runs:  mpirun -np 4 ex30p -m ../data/square-disc.mesh -o 1
-//               mpirun -np 4 ex30p -m ../data/square-disc.mesh -o 2
-//               mpirun -np 4 ex30p -m ../data/square-disc.mesh -o 2 -me 1e3
-//               mpirun -np 4 ex30p -m ../data/square-disc-nurbs.mesh -o 2
-//               mpirun -np 4 ex30p -m ../data/star.mesh -o 2 -eo 4
-//               mpirun -np 4 oscp -m ../data/fichera.mesh -o 2 -me 1e4
-//               mpirun -np 4 ex30p -m ../data/disc-nurbs.mesh -o 2
-//               mpirun -np 4 ex30p -m ../data/ball-nurbs.mesh -o 2 -eo 3 -e 1e-2
-//               mpirun -np 4 ex30p -m ../data/star-surf.mesh -o 2
-//               mpirun -np 4 ex30p -m ../data/square-disc-surf.mesh -o 2
-//               mpirun -np 4 ex30p -m ../data/amr-quad.mesh -l 2
-//
-// Description:  This is an example of adaptive mesh refinement preprocessing
-//               which lowers the data oscillation [1] to a user-defined
-//               relative threshold. There is no PDE being solved.
-//
-//               MFEM's capability to work with both conforming and
-//               nonconforming meshes is demonstrated in example 6. In some
-//               problems, the material data or loading data is not sufficiently
-//               resolved on the initial mesh. This missing fine scale data
-//               reduces the accuracy of the solution as well as the accuracy
-//               of some local error estimators. By preprocessing the mesh
-//               before solving the PDE, many issues can be avoided.
-//
-//               [1] Morin, P., Nochetto, R. H., & Siebert, K. G. (2000).
-//                   Data oscillation and convergence of adaptive FEM. SIAM
-//                   Journal on Numerical Analysis, 38(2), 466-488.
-//
-//               [2] Mitchell, W. F. (2013). A collection of 2D elliptic
-//                   problems for testing adaptive grid refinement algorithms.
-//                   Applied mathematics and computation, 220, 350-364.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-// Piecewise-affine function which is sometimes mesh-conforming
-double affine_function(const Vector &p)
-{
-   double x = p(0), y = p(1);
-   if (x < 0.0)
-   {
-      return 1.0 + x + y;
-   }
-   else
-   {
-      return 1.0;
-   }
-}
-
-// Piecewise-constant function which is never mesh-conforming
-double jump_function(const Vector &p)
-{
-   if (p.Normlp(2.0) > 0.4 && p.Normlp(2.0) < 0.6) { return 1.0; }
-   return 5.0;
-}
-
-// Singular function derived from the Laplacian of the "steep wavefront"
-// problem in [2].
-double singular_function(const Vector &p)
-{
-   double x = p(0), y = p(1);
-   double alpha = 1000.0;
-   double xc = 0.75, yc = 0.5;
-   double r0 = 0.7;
-   double r = sqrt(pow(x - xc,2.0) + pow(y - yc,2.0));
-   double num = - ( alpha - pow(alpha,3) * (pow(r,2) - pow(r0,2)) );
-   double denom = pow(r * ( pow(alpha,2) * pow(r0,2) + pow(alpha,2) * pow(r,2) \
-                            - 2 * pow(alpha,2) * r0 * r + 1.0 ),2);
-   denom = max(denom,1e-8);
-   return num / denom;
-}
-
-int main(int argc, char *argv[])
-{
-   // 0. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/star.mesh";
-   int order = 1;
-   int nc_limit = 1;
-   int max_elems = 1e5;
-   double double_max_elems = double(max_elems);
-   bool visualization = true;
-   bool nc_simplices = true;
-   double osc_threshold = 1e-3;
-   int enriched_order = 5;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&nc_limit, "-l", "--nc-limit",
-                  "Maximum level of hanging nodes.");
-   args.AddOption(&double_max_elems, "-me", "--max-elems",
-                  "Stop after reaching this many elements.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&osc_threshold, "-e", "--error",
-                  "relative data oscillation threshold.");
-   args.AddOption(&enriched_order, "-eo", "--enriched_order",
-                  "Enriched quadrature order.");
-   args.AddOption(&nc_simplices, "-ns", "--nonconforming-simplices",
-                  "-cs", "--conforming-simplices",
-                  "For simplicial meshes, enable/disable nonconforming"
-                  " refinement");
-
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   max_elems = int(double_max_elems);
-   Mesh mesh(mesh_file, 1, 1);
-
-   // 2. Since a NURBS mesh can currently only be refined uniformly, we need to
-   //    convert it to a piecewise-polynomial curved mesh. First we refine the
-   //    NURBS mesh a bit more and then project the curvature to quadratic Nodes.
-   if (mesh.NURBSext)
-   {
-      for (int i = 0; i < 2; i++)
-      {
-         mesh.UniformRefinement();
-      }
-      mesh.SetCurvature(2);
-   }
-
-   // 3. Make sure the mesh is in the non-conforming mode to enable local
-   //    refinement of quadrilaterals/hexahedra. Simplices can be refined
-   //    either in conforming or in non-conforming mode. The conforming
-   //    mode however does not support dynamic partitioning.
-   mesh.EnsureNCMesh(nc_simplices);
-
-   // 4. Define a parallel mesh by partitioning the serial mesh.
-   //    Once the parallel mesh is defined, the serial mesh can be deleted.
-   ParMesh pmesh(MPI_COMM_WORLD, mesh);
-   mesh.Clear();
-
-   // 5. Define functions and refiner.
-   FunctionCoefficient affine_coeff(affine_function);
-   FunctionCoefficient jump_coeff(jump_function);
-   FunctionCoefficient singular_coeff(singular_function);
-   CoefficientRefiner coeffrefiner(affine_coeff,order);
-
-   // 6. Connect to GLVis.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock;
-   if (visualization)
-   {
-      sol_sock.open(vishost, visport);
-   }
-
-   // 7. Define custom integration rule (optional).
-   const IntegrationRule *irs[Geometry::NumGeom];
-   int order_quad = 2*order + enriched_order;
-   for (int i=0; i < Geometry::NumGeom; ++i)
-   {
-      irs[i] = &(IntRules.Get(i, order_quad));
-   }
-
-   // 8. Apply custom refiner settings.
-   coeffrefiner.SetIntRule(irs);
-   coeffrefiner.SetMaxElements(max_elems);
-   coeffrefiner.SetThreshold(osc_threshold);
-   coeffrefiner.SetNCLimit(nc_limit);
-   coeffrefiner.PrintWarnings();
-
-   // 9. Preprocess mesh to control osc (piecewise-affine function).
-   //    This is mostly just a verification check. The oscillation should
-   //    be zero if the function is mesh-conforming and order > 0.
-   coeffrefiner.PreprocessMesh(pmesh);
-
-   int globalNE = pmesh.GetGlobalNE();
-   double osc = coeffrefiner.GetOsc();
-   if (myid == 0)
-   {
-      mfem::out  << "\n";
-      mfem::out << "Function 0 (affine) \n";
-      mfem::out << "Number of Elements " << globalNE << "\n";
-      mfem::out << "Osc error " << osc << "\n";
-   }
-
-   // 10. Preprocess mesh to control osc (jump function).
-   coeffrefiner.ResetCoefficient(jump_coeff);
-   coeffrefiner.PreprocessMesh(pmesh);
-
-   globalNE = pmesh.GetGlobalNE();
-   osc = coeffrefiner.GetOsc();
-   if (myid == 0)
-   {
-      mfem::out  << "\n";
-      mfem::out << "Function 1 (discontinuous) \n";
-      mfem::out << "Number of Elements " << globalNE << "\n";
-      mfem::out << "Osc error " << osc << "\n";
-   }
-
-   // 11. Preprocess mesh to control osc (singular function).
-   coeffrefiner.ResetCoefficient(singular_coeff);
-   coeffrefiner.PreprocessMesh(pmesh);
-
-   globalNE = pmesh.GetGlobalNE();
-   osc = coeffrefiner.GetOsc();
-   if (myid == 0)
-   {
-      mfem::out  << "\n";
-      mfem::out << "Function 2 (singular) \n";
-      mfem::out << "Number of Elements " << globalNE << "\n";
-      mfem::out << "Osc error " << osc << "\n";
-   }
-
-   sol_sock.precision(8);
-   sol_sock << "parallel " << num_procs << " " << myid << "\n";
-   sol_sock << "mesh\n" << pmesh << flush;
-
-   MPI_Finalize();
-   return 0;
-}

examples/ex3p.cpp

@@ -16,8 +16,6 @@
 //               mpirun -np 4 ex3p -m ../data/beam-hex-nurbs.mesh
 //               mpirun -np 4 ex3p -m ../data/amr-quad.mesh -o 2
 //               mpirun -np 4 ex3p -m ../data/amr-hex.mesh
-//               mpirun -np 4 ex3p -m ../data/ref-prism.mesh -o 1
-//               mpirun -np 4 ex3p -m ../data/octahedron.mesh -o 1
 //               mpirun -np 4 ex3p -m ../data/star-surf.mesh -o 2
 //               mpirun -np 4 ex3p -m ../data/mobius-strip.mesh -o 2 -f 0.1
 //               mpirun -np 4 ex3p -m ../data/klein-bottle.mesh -o 2 -f 0.1

examples/ex3p_es.cpp

@@ -1,411 +0,0 @@
-//                       MFEM Example 3 - Parallel Version
-//
-// Compile with: make ex3p
-//
-// Sample runs:  mpirun -np 4 ex3p -m ../data/star.mesh
-//               mpirun -np 4 ex3p -m ../data/square-disc.mesh -o 2
-//               mpirun -np 4 ex3p -m ../data/beam-tet.mesh
-//               mpirun -np 4 ex3p -m ../data/beam-hex.mesh
-//               mpirun -np 4 ex3p -m ../data/escher.mesh
-//               mpirun -np 4 ex3p -m ../data/fichera.mesh
-//               mpirun -np 4 ex3p -m ../data/fichera-q2.vtk
-//               mpirun -np 4 ex3p -m ../data/fichera-q3.mesh
-//               mpirun -np 4 ex3p -m ../data/square-disc-nurbs.mesh
-//               mpirun -np 4 ex3p -m ../data/beam-hex-nurbs.mesh
-//               mpirun -np 4 ex3p -m ../data/amr-quad.mesh -o 2
-//               mpirun -np 4 ex3p -m ../data/amr-hex.mesh
-//               mpirun -np 4 ex3p -m ../data/star-surf.mesh -o 2
-//               mpirun -np 4 ex3p -m ../data/mobius-strip.mesh -o 2 -f 0.1
-//               mpirun -np 4 ex3p -m ../data/klein-bottle.mesh -o 2 -f 0.1
-//
-// Description:  This example code solves a simple electromagnetic diffusion
-//               problem corresponding to the second order definite Maxwell
-//               equation curl curl E + E = f with boundary condition
-//               E x n = <given tangential field>. Here, we use a given exact
-//               solution E and compute the corresponding r.h.s. f.
-//               We discretize with Nedelec finite elements in 2D or 3D.
-//
-//               The example demonstrates the use of H(curl) finite element
-//               spaces with the curl-curl and the (vector finite element) mass
-//               bilinear form, as well as the computation of discretization
-//               error when the exact solution is known. Static condensation is
-//               also illustrated.
-//
-//               We recommend viewing examples 1-2 before viewing this example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-// Exact solution, E, and r.h.s., f. See below for implementation.
-//void E_exact(const Vector &, Vector &);
-//void f_exact(const Vector &, Vector &);
-//double freq = 1.0, kappa;
-void f_const(const Vector &, Vector &);
-
-int dim;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "../data/beam-tet.mesh";
-   int order = 1;
-   int rs = -1;
-   int rp = 2;
-   int ra = 0;
-   int bt = EntitySets::INVALID;
-   const char *bs = "Origin";
-   bool static_cond = false;
-   bool visualization = 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).");
-   /*
-   args.AddOption(&freq, "-f", "--frequency", "Set the frequency for the exact"
-                  " solution.");
-   */
-   args.AddOption(&rs, "-rs", "--refine-serial",
-                  "Number of serial refinement levels");
-   args.AddOption(&rp, "-rp", "--refine-parallel",
-                  "Number of parallel refinement levels");
-   args.AddOption(&ra, "-ra", "--refine-adaptive",
-                  "Number of adaptive refinement levels");
-   args.AddOption(&bt, "-bt", "--bc-entity-type",
-                  "");
-   args.AddOption(&bs, "-bs", "--bc-entity-set-name",
-                  "");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-   // kappa = freq * M_PI;
-
-   // 3. 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 = new Mesh(mesh_file, 1, 1);
-   dim = mesh->Dimension();
-   int sdim = mesh->SpaceDimension();
-
-   // 4. 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 1,000 elements.
-   {
-      int ref_levels = ( rs >= 0 ) ? rs :
-                       (int)floor(log(1000./mesh->GetNE())/log(2.)/dim);
-      for (int l = 0; l < ref_levels; l++)
-      {
-         if ( myid == 0 ) { cout << "Uniform refinement in serial..."; }
-         mesh->UniformRefinement();
-      }
-      MPI_Barrier(MPI_COMM_WORLD);
-      if ( myid == 0 && rs > 0 ) { cout << "Done" << endl; }
-   }
-   if ( mesh->ent_sets )
-   {
-      cout << "mesh->ent_sets is non NULL" << endl;
-      mesh->ent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "mesh->ent_sets is NULL" << endl;
-   }
-   /*
-     At this point we have a serial mesh containing an EntitySets
-     object which stores the current node/edge/face/element indices
-     for each entity in each set.  This data is duplicated on each MPI
-     rank.
-    */
-   if ( ra > 0 )
-   {
-      cout << "calling EnsureNCMesh" << endl;
-      mesh->EnsureNCMesh();
-      cout << "back from EnsureNCMesh" << endl;
-   }
-   if ( mesh->ent_sets )
-   {
-      cout << "mesh->ent_sets is non NULL" << endl;
-      mesh->ent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "mesh->ent_sets is NULL" << endl;
-   }
-   /*
-     We now have an NCEntitySets object which stores the node indices
-     describing each enity in each node/edge/face set and the element
-     indices for the elements in each element set.  This data is
-     duplicated on each MPI rank.
-    */
-
-   // 5. 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. Tetrahedral
-   //    meshes need to be reoriented before we can define high-order Nedelec
-   //    spaces on them.
-   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
-   delete mesh;
-   if ( pmesh->pent_sets )
-   {
-      cout << "pmesh->pent_sets is non NULL" << endl;
-      pmesh->pent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "pmesh->pent_sets is NULL" << endl;
-   }
-   {
-      int par_ref_levels = rp;
-      for (int l = 0; l < par_ref_levels; l++)
-      {
-         if ( myid == 0 ) { cout << "Uniform refinement in parallel..."; }
-         pmesh->UniformRefinement();
-      }
-      MPI_Barrier(MPI_COMM_WORLD);
-      if ( myid == 0 && rs > 0 ) { cout << "Done" << endl; }
-   }
-   pmesh->ReorientTetMesh();
-   pmesh->ent_sets->PrintSetInfo(cout);
-
-   for (int l = 0; l < ra; l++)
-   {
-      pmesh->RandomRefinement(0.2);
-   }
-   if ( ra > 0 )
-   {
-      if ( pmesh->pent_sets )
-      {
-         cout << "pmesh->pent_sets is non NULL post random refinement" << endl;
-         pmesh->pent_sets->PrintSetInfo(cout);
-      }
-      else
-      {
-         cout << "pmesh->pent_sets is NULL post random refinement" << endl;
-      }
-   }
-
-   // 6. Define a parallel finite element space on the parallel mesh. Here we
-   //    use the Nedelec finite elements of the specified order.
-   FiniteElementCollection *fec = new ND_FECollection(order, dim);
-   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
-   HYPRE_Int size = fespace->GlobalTrueVSize();
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 7. Determine the list of true (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 ( bt == EntitySets::INVALID )
-   {
-      if (pmesh->bdr_attributes.Size())
-      {
-         Array<int> ess_bdr(pmesh->bdr_attributes.Max());
-         ess_bdr = 1;
-         fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-      }
-   }
-   else
-   {
-      fespace->GetEssentialTrueDofs((EntitySets::EntityType)bt, bs,
-                                    ess_tdof_list);
-   }
-   if (myid == 0)
-   {
-      cout << "Number of Dirichlet dofs: " << ess_tdof_list.Size() << endl;
-   }
-
-
-   // 8. Set up the parallel linear form b(.) which corresponds to the
-   //    right-hand side of the FEM linear system, which in this case is
-   //    (f,phi_i) where f is given by the function f_exact and phi_i are the
-   //    basis functions in the finite element fespace.
-   VectorFunctionCoefficient f(sdim, f_const);
-   ParLinearForm *b = new ParLinearForm(fespace);
-   b->AddDomainIntegrator(new VectorFEDomainLFIntegrator(f));
-   b->Assemble();
-
-   // 9. Define the solution vector x as a parallel finite element grid function
-   //    corresponding to fespace. Initialize x by projecting the exact
-   //    solution. Note that only values from the boundary edges will be used
-   //    when eliminating the non-homogeneous boundary condition to modify the
-   //    r.h.s. vector b.
-   ParGridFunction x(fespace);
-   // VectorFunctionCoefficient E(sdim, E_exact);
-   // x.ProjectCoefficient(E);
-   x = 0.0;
-
-   // 10. Set up the parallel bilinear form corresponding to the EM diffusion
-   //     operator curl muinv curl + sigma I, by adding the curl-curl and the
-   //     mass domain integrators.
-   Coefficient *muinv = new ConstantCoefficient(1.0);
-   Coefficient *sigma = new ConstantCoefficient(1.0);
-   ParBilinearForm *a = new ParBilinearForm(fespace);
-   a->AddDomainIntegrator(new CurlCurlIntegrator(*muinv));
-   a->AddDomainIntegrator(new VectorFEMassIntegrator(*sigma));
-
-   // 11. 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();
-
-   HypreParMatrix A;
-   Vector B, X;
-   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
-
-   if (myid == 0)
-   {
-      cout << "Size of linear system: " << A.GetGlobalNumRows() << endl;
-   }
-
-   // 12. Define and apply a parallel PCG solver for AX=B with the AMS
-   //     preconditioner from hypre.
-   ParFiniteElementSpace *prec_fespace =
-      (a->StaticCondensationIsEnabled() ? a->SCParFESpace() : fespace);
-   HypreSolver *ams = new HypreAMS(A, prec_fespace);
-   HyprePCG *pcg = new HyprePCG(A);
-   pcg->SetTol(1e-12);
-   pcg->SetMaxIter(500);
-   pcg->SetPrintLevel(2);
-   pcg->SetPreconditioner(*ams);
-   pcg->Mult(B, X);
-
-   // 13. Recover the parallel grid function corresponding to X. This is the
-   //     local finite element solution on each processor.
-   a->RecoverFEMSolution(X, *b, x);
-
-   /*
-   // 14. Compute and print the L^2 norm of the error.
-   {
-      double err = x.ComputeL2Error(E);
-      if (myid == 0)
-      {
-         cout << "\n|| E_h - E ||_{L^2} = " << err << '\n' << endl;
-      }
-   }
-   */
-   // 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.
-   delete pcg;
-   delete ams;
-   delete a;
-   delete sigma;
-   delete muinv;
-   delete b;
-   delete fespace;
-   delete fec;
-   delete pmesh;
-
-   MPI_Finalize();
-
-   return 0;
-}
-
-/*
-void E_exact(const Vector &x, Vector &E)
-{
-   if (dim == 3)
-   {
-      E(0) = sin(kappa * x(1));
-      E(1) = sin(kappa * x(2));
-      E(2) = sin(kappa * x(0));
-   }
-   else
-   {
-      E(0) = sin(kappa * x(1));
-      E(1) = sin(kappa * x(0));
-      if (x.Size() == 3) { E(2) = 0.0; }
-   }
-}
-
-void f_exact(const Vector &x, Vector &f)
-{
-   if (dim == 3)
-   {
-      f(0) = (1. + kappa * kappa) * sin(kappa * x(1));
-      f(1) = (1. + kappa * kappa) * sin(kappa * x(2));
-      f(2) = (1. + kappa * kappa) * sin(kappa * x(0));
-   }
-   else
-   {
-      f(0) = (1. + kappa * kappa) * sin(kappa * x(1));
-      f(1) = (1. + kappa * kappa) * sin(kappa * x(0));
-      if (x.Size() == 3) { f(2) = 0.0; }
-   }
-}
-*/
-void f_const(const Vector &x, Vector &f)
-{
-   if (dim == 3)
-   {
-      f(0) = 1.0;
-      f(1) = 1.0;
-      f(2) = 1.0;
-   }
-   else
-   {
-      f(0) = 1.0;
-      f(1) = 1.0;
-      if (x.Size() == 3) { f(2) = 0.0; }
-   }
-}

examples/ex4.cpp

@@ -19,8 +19,6 @@
 //               ex4 -m ../data/amr-hex.mesh
 //               ex4 -m ../data/amr-hex.mesh -o 2 -hb
 //               ex4 -m ../data/fichera-amr.mesh -o 2 -sc
-//               ex4 -m ../data/ref-prism.mesh -o 1
-//               ex4 -m ../data/octahedron.mesh -o 1
 //               ex4 -m ../data/star-surf.mesh -o 1
 //
 // Device sample runs:

examples/ex4p.cpp

@@ -19,8 +19,6 @@
 //               mpirun -np 3 ex4p -m ../data/amr-quad.mesh -o 2 -hb
 //               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/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:

examples/ex4p_es.cpp

@@ -1,438 +0,0 @@
-//                       MFEM Example 4 - Parallel Version
-//
-// Compile with: make ex4p
-//
-// Sample runs:  mpirun -np 4 ex4p -m ../data/square-disc.mesh
-//               mpirun -np 4 ex4p -m ../data/star.mesh
-//               mpirun -np 4 ex4p -m ../data/beam-tet.mesh
-//               mpirun -np 4 ex4p -m ../data/beam-hex.mesh
-//               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-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
-//               mpirun -np 4 ex4p -m ../data/beam-hex-nurbs.mesh -o 3
-//               mpirun -np 4 ex4p -m ../data/periodic-square.mesh -no-bc
-//               mpirun -np 4 ex4p -m ../data/periodic-cube.mesh -no-bc
-//               mpirun -np 4 ex4p -m ../data/amr-quad.mesh
-//               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/star-surf.mesh -o 3 -hb
-//
-// Description:  This example code solves a simple 2D/3D H(div) diffusion
-//               problem corresponding to the second order definite equation
-//               -grad(alpha div F) + beta F = f with boundary condition F dot n
-//               = <given normal field>. Here, we use a given exact solution F
-//               and compute the corresponding r.h.s. f.  We discretize with
-//               Raviart-Thomas finite elements.
-//
-//               The example demonstrates the use of H(div) finite element
-//               spaces with the grad-div and H(div) vector finite element mass
-//               bilinear form, as well as the computation of discretization
-//               error when the exact solution is known. Bilinear form
-//               hybridization and static condensation are also illustrated.
-//
-//               We recommend viewing examples 1-3 before viewing this example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-// Exact solution, F, and r.h.s., f. See below for implementation.
-//void F_exact(const Vector &, Vector &);
-//void f_exact(const Vector &, Vector &);
-//double freq = 1.0, kappa;
-void f_const(const Vector &, Vector &);
-
-int dim;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "../data/star.mesh";
-   int order = 1;
-   int rs = -1;
-   int rp = 2;
-   int ra = 0;
-   int bt = EntitySets::INVALID;
-   const char *bs = "Origin";
-   bool set_bc = true;
-   bool static_cond = false;
-   bool hybridization = false;
-   bool visualization = 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).");
-   args.AddOption(&set_bc, "-bc", "--impose-bc", "-no-bc", "--dont-impose-bc",
-                  "Impose or not essential boundary conditions.");
-   args.AddOption(&rs, "-rs", "--refine-serial",
-                  "Number of serial refinement levels");
-   args.AddOption(&rp, "-rp", "--refine-parallel",
-                  "Number of parallel refinement levels");
-   args.AddOption(&ra, "-ra", "--refine-adaptive",
-                  "Number of adaptive refinement levels");
-   args.AddOption(&bt, "-bt", "--bc-entity-type",
-                  "");
-   args.AddOption(&bs, "-bs", "--bc-entity-set-name",
-                  "");
-   // args.AddOption(&freq, "-f", "--frequency", "Set the frequency for the exact"
-   //                 " solution.");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&hybridization, "-hb", "--hybridization", "-no-hb",
-                  "--no-hybridization", "Enable hybridization.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-   // kappa = freq * M_PI;
-
-   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
-   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
-   //    and volume, as well as periodic meshes with the same code.
-   Mesh *mesh = new Mesh(mesh_file, 1, 1);
-   dim = mesh->Dimension();
-   int sdim = mesh->SpaceDimension();
-
-   // 4. 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 1,000 elements.
-   {
-      int ref_levels = ( rs >= 0 ) ? rs :
-                       (int)floor(log(1000./mesh->GetNE())/log(2.)/dim);
-      for (int l = 0; l < ref_levels; l++)
-      {
-         if ( myid == 0 ) { cout << "Uniform refinement in serial..."; }
-         mesh->UniformRefinement();
-      }
-      MPI_Barrier(MPI_COMM_WORLD);
-      if ( myid == 0 && rs > 0 ) { cout << "Done" << endl; }
-   }
-   if ( mesh->ent_sets )
-   {
-      cout << "mesh->ent_sets is non NULL" << endl;
-      mesh->ent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "mesh->ent_sets is NULL" << endl;
-   }
-   /*
-     At this point we have a serial mesh containing an EntitySets
-     object which stores the current node/edge/face/element indices
-     for each entity in each set.  This data is duplicated on each MPI
-     rank.
-    */
-   if ( ra > 0 )
-   {
-      cout << "calling EnsureNCMesh" << endl;
-      mesh->EnsureNCMesh();
-      cout << "back from EnsureNCMesh" << endl;
-   }
-   if ( mesh->ent_sets )
-   {
-      cout << "mesh->ent_sets is non NULL" << endl;
-      mesh->ent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "mesh->ent_sets is NULL" << endl;
-   }
-   /*
-     We now have an NCEntitySets object which stores the node indices
-     describing each enity in each node/edge/face set and the element
-     indices for the elements in each element set.  This data is
-     duplicated on each MPI rank.
-    */
-
-   // 5. 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. Tetrahedral
-   //    meshes need to be reoriented before we can define high-order Nedelec
-   //    spaces on them (this is needed in the ADS solver below).
-   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
-   delete mesh;
-   if ( pmesh->pent_sets )
-   {
-      cout << "pmesh->pent_sets is non NULL" << endl;
-      pmesh->pent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "pmesh->pent_sets is NULL" << endl;
-   }
-   {
-      int par_ref_levels = rp;
-      for (int l = 0; l < par_ref_levels; l++)
-      {
-         if ( myid == 0 ) { cout << "Uniform refinement in parallel..."; }
-         pmesh->UniformRefinement();
-      }
-   }
-   pmesh->ReorientTetMesh();
-
-   for (int l = 0; l < ra; l++)
-   {
-      pmesh->RandomRefinement(0.2);
-   }
-   if ( ra > 0 )
-   {
-      if ( pmesh->pent_sets )
-      {
-         cout << "pmesh->pent_sets is non NULL post random refinement" << endl;
-         pmesh->pent_sets->PrintSetInfo(cout);
-      }
-      else
-      {
-         cout << "pmesh->pent_sets is NULL post random refinement" << endl;
-      }
-   }
-
-   // 6. Define a parallel finite element space on the parallel mesh. Here we
-   //    use the Raviart-Thomas finite elements of the specified order.
-   FiniteElementCollection *fec = new RT_FECollection(order-1, dim);
-   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
-   HYPRE_Int size = fespace->GlobalTrueVSize();
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 7. Determine the list of true (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 ( bt == EntitySets::INVALID )
-   {
-      if (pmesh->bdr_attributes.Size())
-      {
-         Array<int> ess_bdr(pmesh->bdr_attributes.Max());
-         ess_bdr = set_bc ? 1 : 0;
-         fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-      }
-   }
-   else
-   {
-      fespace->GetEssentialTrueDofs((EntitySets::EntityType)bt, bs,
-                                    ess_tdof_list);
-   }
-   if (myid == 0)
-   {
-      cout << "Number of Dirichlet dofs: " << ess_tdof_list.Size() << endl;
-   }
-
-   // 8. Set up the parallel linear form b(.) which corresponds to the
-   //    right-hand side of the FEM linear system, which in this case is
-   //    (f,phi_i) where f is given by the function f_exact and phi_i are the
-   //    basis functions in the finite element fespace.
-   VectorFunctionCoefficient f(sdim, f_const);
-   ParLinearForm *b = new ParLinearForm(fespace);
-   b->AddDomainIntegrator(new VectorFEDomainLFIntegrator(f));
-   b->Assemble();
-
-   // 9. Define the solution vector x as a parallel finite element grid function
-   //    corresponding to fespace. Initialize x by projecting the exact
-   //    solution. Note that only values from the boundary faces will be used
-   //    when eliminating the non-homogeneous boundary condition to modify the
-   //    r.h.s. vector b.
-   ParGridFunction x(fespace);
-   // VectorFunctionCoefficient F(sdim, F_exact);
-   // x.ProjectCoefficient(F);
-   x = 0.0;
-
-   // 10. Set up the parallel bilinear form corresponding to the H(div)
-   //     diffusion operator grad alpha div + beta I, by adding the div-div and
-   //     the mass domain integrators.
-   Coefficient *alpha = new ConstantCoefficient(1.0);
-   Coefficient *beta  = new ConstantCoefficient(1.0);
-   ParBilinearForm *a = new ParBilinearForm(fespace);
-   a->AddDomainIntegrator(new DivDivIntegrator(*alpha));
-   a->AddDomainIntegrator(new VectorFEMassIntegrator(*beta));
-
-   // 11. 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,
-   //     hybridization, etc.
-   FiniteElementCollection *hfec = NULL;
-   ParFiniteElementSpace *hfes = NULL;
-   if (static_cond)
-   {
-      a->EnableStaticCondensation();
-   }
-   else if (hybridization)
-   {
-      hfec = new DG_Interface_FECollection(order-1, dim);
-      hfes = new ParFiniteElementSpace(pmesh, hfec);
-      a->EnableHybridization(hfes, new NormalTraceJumpIntegrator(),
-                             ess_tdof_list);
-   }
-   a->Assemble();
-
-   HypreParMatrix A;
-   Vector B, X;
-   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
-
-   HYPRE_Int glob_size = A.GetGlobalNumRows();
-   if (myid == 0)
-   {
-      cout << "Size of linear system: " << glob_size << endl;
-   }
-
-   // 12. Define and apply a parallel PCG solver for A X = B with the 2D AMS or
-   //     the 3D ADS preconditioners from hypre. If using hybridization, the
-   //     system is preconditioned with hypre's BoomerAMG.
-   HypreSolver *prec = NULL;
-   CGSolver *pcg = new CGSolver(A.GetComm());
-   pcg->SetOperator(A);
-   pcg->SetRelTol(1e-12);
-   pcg->SetMaxIter(500);
-   pcg->SetPrintLevel(1);
-   if (hybridization) { prec = new HypreBoomerAMG(A); }
-   else
-   {
-      ParFiniteElementSpace *prec_fespace =
-         (a->StaticCondensationIsEnabled() ? a->SCParFESpace() : fespace);
-      if (dim == 2)   { prec = new HypreAMS(A, prec_fespace); }
-      else            { prec = new HypreADS(A, prec_fespace); }
-   }
-   pcg->SetPreconditioner(*prec);
-   pcg->Mult(B, X);
-
-   // 13. Recover the parallel grid function corresponding to X. This is the
-   //     local finite element solution on each processor.
-   a->RecoverFEMSolution(X, *b, x);
-   /*
-   // 14. Compute and print the L^2 norm of the error.
-   {
-      double err = x.ComputeL2Error(F);
-      if (myid == 0)
-      {
-         cout << "\n|| F_h - F ||_{L^2} = " << err << '\n' << endl;
-      }
-   }
-   */
-   // 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.
-   delete pcg;
-   delete prec;
-   delete hfes;
-   delete hfec;
-   delete a;
-   delete alpha;
-   delete beta;
-   delete b;
-   delete fespace;
-   delete fec;
-   delete pmesh;
-
-   MPI_Finalize();
-
-   return 0;
-}
-
-/*
-// The exact solution (for non-surface meshes)
-void F_exact(const Vector &p, Vector &F)
-{
-   int dim = p.Size();
-
-   double x = p(0);
-   double y = p(1);
-   // double z = (dim == 3) ? p(2) : 0.0;
-
-   F(0) = cos(kappa*x)*sin(kappa*y);
-   F(1) = cos(kappa*y)*sin(kappa*x);
-   if (dim == 3)
-   {
-      F(2) = 0.0;
-   }
-}
-
-// The right hand side
-void f_exact(const Vector &p, Vector &f)
-{
-   int dim = p.Size();
-
-   double x = p(0);
-   double y = p(1);
-   // double z = (dim == 3) ? p(2) : 0.0;
-
-   double temp = 1 + 2*kappa*kappa;
-
-   f(0) = temp*cos(kappa*x)*sin(kappa*y);
-   f(1) = temp*cos(kappa*y)*sin(kappa*x);
-   if (dim == 3)
-   {
-      f(2) = 0;
-   }
-}
-*/
-void f_const(const Vector &x, Vector &f)
-{
-   if (dim == 3)
-   {
-      f(0) = 1.0;
-      f(1) = 1.0;
-      f(2) = 1.0;
-   }
-   else
-   {
-      f(0) = 1.0;
-      f(1) = 1.0;
-      if (x.Size() == 3) { f(2) = 0.0; }
-   }
-}

examples/ex6p_es.cpp

@@ -1,325 +0,0 @@
-//                       MFEM Example 6 - Parallel Version
-//
-// Compile with: make ex6p
-//
-// Sample runs:  mpirun -np 4 ex6p -m ../data/square-disc.mesh -o 1
-//               mpirun -np 4 ex6p -m ../data/square-disc.mesh -o 2
-//               mpirun -np 4 ex6p -m ../data/square-disc-nurbs.mesh -o 2
-//               mpirun -np 4 ex6p -m ../data/star.mesh -o 3
-//               mpirun -np 4 ex6p -m ../data/escher.mesh -o 2
-//               mpirun -np 4 ex6p -m ../data/fichera.mesh -o 2
-//               mpirun -np 4 ex6p -m ../data/disc-nurbs.mesh -o 2
-//               mpirun -np 4 ex6p -m ../data/ball-nurbs.mesh
-//               mpirun -np 4 ex6p -m ../data/pipe-nurbs.mesh
-//               mpirun -np 4 ex6p -m ../data/star-surf.mesh -o 2
-//               mpirun -np 4 ex6p -m ../data/square-disc-surf.mesh -o 2
-//               mpirun -np 4 ex6p -m ../data/amr-quad.mesh
-//
-// Description:  This is a version of Example 1 with a simple adaptive mesh
-//               refinement loop. The problem being solved is again the Laplace
-//               equation -Delta u = 1 with homogeneous Dirichlet boundary
-//               conditions. The problem is solved on a sequence of meshes which
-//               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
-//               to a simple ZZ error estimator.
-//
-//               The example demonstrates MFEM's capability to work with both
-//               conforming and nonconforming refinements, in 2D and 3D, on
-//               linear, curved and surface meshes. Interpolation of functions
-//               from coarse to fine meshes, as well as persistent GLVis
-//               visualization are also illustrated.
-//
-//               We recommend viewing Example 1 before viewing this example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-static int max_dofs = 100000;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "./star-set.mesh";
-   int order = 1;
-   int bt = EntitySets::INVALID;
-   const char *bs = "";
-   bool visualization = true;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&max_dofs, "-md", "--max-dofs",
-                  "Maximum number of degrees of freedom.");
-   args.AddOption(&bt, "-bt", "--bc-entity-type",
-                  "");
-   args.AddOption(&bs, "-bs", "--bc-entity-set-name",
-                  "");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 3. 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 = new Mesh(mesh_file, 1, 1);
-   int dim = mesh->Dimension();
-   int sdim = mesh->SpaceDimension();
-
-   // 4. Refine the serial mesh on all processors to increase the resolution.
-   //    Also project a NURBS mesh to a piecewise-quadratic curved mesh. Make
-   //    sure that the mesh is non-conforming.
-   if (mesh->NURBSext)
-   {
-      mesh->UniformRefinement();
-      mesh->SetCurvature(2);
-   }
-   mesh->EnsureNCMesh();
-   if ( mesh->ent_sets )
-   {
-      cout << "mesh->ent_sets is non NULL" << endl;
-      mesh->ent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "mesh->ent_sets is NULL" << endl;
-   }
-
-   // 5. Define a parallel mesh by partitioning the serial mesh.
-   //    Once the parallel mesh is defined, the serial mesh can be deleted.
-   ParMesh pmesh(MPI_COMM_WORLD, *mesh);
-   delete mesh;
-   if ( pmesh.pent_sets )
-   {
-      cout << "pmesh->pent_sets is non NULL" << endl;
-      pmesh.pent_sets->PrintSetInfo(cout);
-   }
-   else
-   {
-      cout << "pmesh->pent_sets is NULL" << endl;
-   }
-
-   // 6. Define a finite element space on the mesh. The polynomial order is
-   //    one (linear) by default, but this can be changed on the command line.
-   H1_FECollection fec(order, dim);
-   ParFiniteElementSpace fespace(&pmesh, &fec);
-
-   Array<int> ess_tdof_list;
-   if ( bt == EntitySets::INVALID )
-   {
-      if (pmesh.bdr_attributes.Size())
-      {
-         Array<int> ess_bdr(pmesh.bdr_attributes.Max());
-         ess_bdr = 1;
-         fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-      }
-   }
-   else
-   {
-      fespace.GetEssentialTrueDofs((EntitySets::EntityType)bt, bs,
-                                   ess_tdof_list);
-   }
-
-   // 7. As in Example 1p, we set up bilinear and linear forms corresponding to
-   //    the Laplace problem -\Delta u = 1. We don't assemble the discrete
-   //    problem yet, this will be done in the main loop.
-   ParBilinearForm a(&fespace);
-   ParLinearForm b(&fespace);
-
-   ConstantCoefficient one(1.0);
-
-   BilinearFormIntegrator *integ = new DiffusionIntegrator(one);
-   a.AddDomainIntegrator(integ);
-   b.AddDomainIntegrator(new DomainLFIntegrator(one));
-
-   // 8. The solution vector x and the associated finite element grid function
-   //    will be maintained over the AMR iterations. We initialize it to zero.
-   ParGridFunction x(&fespace);
-   x = 0;
-
-   // 9. Connect to GLVis.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-
-   socketstream sout;
-   if (visualization)
-   {
-      sout.open(vishost, visport);
-      if (!sout)
-      {
-         if (myid == 0)
-         {
-            cout << "Unable to connect to GLVis server at "
-                 << vishost << ':' << visport << endl;
-            cout << "GLVis visualization disabled.\n";
-         }
-         visualization = false;
-      }
-
-      sout.precision(8);
-   }
-
-   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
-   //     with L2 projection in the smoothing step to better handle hanging
-   //     nodes and parallel partitioning. We need to supply a space for the
-   //     discontinuous flux (L2) and a space for the smoothed flux (H(div) is
-   //     used here).
-   L2_FECollection flux_fec(order, dim);
-   ParFiniteElementSpace flux_fes(&pmesh, &flux_fec, sdim);
-   RT_FECollection smooth_flux_fec(order-1, dim);
-   ParFiniteElementSpace smooth_flux_fes(&pmesh, &smooth_flux_fec);
-   // Another possible option for the smoothed flux space:
-   // H1_FECollection smooth_flux_fec(order, dim);
-   // ParFiniteElementSpace smooth_flux_fes(&pmesh, &smooth_flux_fec, dim);
-   L2ZienkiewiczZhuEstimator estimator(*integ, x, flux_fes, smooth_flux_fes);
-
-   // 11. A refiner selects and refines elements based on a refinement strategy.
-   //     The strategy here is to refine elements with errors larger than a
-   //     fraction of the maximum element error. Other strategies are possible.
-   //     The refiner will call the given error estimator.
-   ThresholdRefiner refiner(estimator);
-   refiner.SetTotalErrorFraction(0.7);
-
-   // 12. The main AMR loop. In each iteration we solve the problem on the
-   //     current mesh, visualize the solution, and refine the mesh.
-   // const int max_dofs = 100000;
-   for (int it = 0; ; it++)
-   {
-      HYPRE_Int global_dofs = fespace.GlobalTrueVSize();
-      if (myid == 0)
-      {
-         cout << "\nAMR iteration " << it << endl;
-         cout << "Number of unknowns: " << global_dofs << endl;
-      }
-
-      // 13. Assemble the stiffness matrix and the right-hand side. Note that
-      //     MFEM doesn't care at this point that the mesh is nonconforming
-      //     and parallel. The FE space is considered 'cut' along hanging
-      //     edges/faces, and also across processor boundaries.
-      a.Assemble();
-      b.Assemble();
-
-      // 14. Create the parallel linear system: eliminate boundary conditions,
-      //     constrain hanging nodes and nodes across processor boundaries.
-      //     The system will be solved for true (unconstrained/unique) DOFs only.
-      // Array<int> ess_tdof_list;
-      if ( bt == EntitySets::INVALID )
-      {
-         if (pmesh.bdr_attributes.Size())
-         {
-            Array<int> ess_bdr(pmesh.bdr_attributes.Max());
-            ess_bdr = 1;
-            fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-         }
-      }
-      else
-      {
-         fespace.GetEssentialTrueDofs((EntitySets::EntityType)bt, bs,
-                                      ess_tdof_list);
-      }
-
-      HypreParMatrix A;
-      Vector B, X;
-      const int copy_interior = 1;
-      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
-
-      // 15. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
-      //     preconditioner from hypre.
-      HypreBoomerAMG amg;
-      amg.SetPrintLevel(0);
-      CGSolver pcg(A.GetComm());
-      pcg.SetPreconditioner(amg);
-      pcg.SetOperator(A);
-      pcg.SetRelTol(1e-6);
-      pcg.SetMaxIter(200);
-      pcg.SetPrintLevel(3); // print the first and the last iterations only
-      pcg.Mult(B, X);
-
-      // 16. Extract the parallel grid function corresponding to the finite element
-      //     approximation X. This is the local solution on each processor.
-      a.RecoverFEMSolution(X, b, x);
-
-      // 17. Send the solution by socket to a GLVis server.
-      if (visualization)
-      {
-         sout << "parallel " << num_procs << " " << myid << "\n";
-         sout << "solution\n" << pmesh << x << flush;
-      }
-
-      if (global_dofs > max_dofs)
-      {
-         if (myid == 0)
-         {
-            cout << "Reached the maximum number of dofs. Stop." << endl;
-         }
-         break;
-      }
-
-      // 18. Call the refiner to modify the mesh. The refiner calls the error
-      //     estimator to obtain element errors, then it selects elements to be
-      //     refined and finally it modifies the mesh. The Stop() method can be
-      //     used to determine if a stopping criterion was met.
-      refiner.Apply(pmesh);
-      if (refiner.Stop())
-      {
-         if (myid == 0)
-         {
-            cout << "Stopping criterion satisfied. Stop." << endl;
-         }
-         break;
-      }
-
-      // 19. Update the finite element space (recalculate the number of DOFs,
-      //     etc.) and create a grid function update matrix. Apply the matrix
-      //     to any GridFunctions over the space. In this case, the update
-      //     matrix is an interpolation matrix so the updated GridFunction will
-      //     still represent the same function as before refinement.
-      fespace.Update();
-      x.Update();
-
-      // 20. Load balance the mesh, and update the space and solution. Currently
-      //     available only for nonconforming meshes.
-      if (pmesh.Nonconforming())
-      {
-         pmesh.Rebalance();
-
-         // Update the space and the GridFunction. This time the update matrix
-         // redistributes the GridFunction among the processors.
-         fespace.Update();
-         x.Update();
-      }
-
-      // 21. Inform also the bilinear and linear forms that the space has
-      //     changed.
-      a.Update();
-      b.Update();
-   }
-
-   MPI_Finalize();
-   return 0;
-}

examples/fichera-mixed-set.mesh

@@ -1,162 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-#
-
-dimension
-3
-
-elements
-14
-1 4 13 15 21 25
-1 4 12 13 15 21
-1 4 13 21 22 25
-1 4 15 24 21 25
-1 4 13 15 25 16
-1 5  0  1  4  3  9 10 13 12
-1 5  8  9 12 11 17 18 21 20
-1 5  2  3  6  5 11 12 15 14
-1 6  3  4  6 12 13 15
-1 6  4  7  6 13 16 15
-1 6 12 13 21  9 10 18
-1 6 13 22 21 10 19 18
-1 6 11 14 20 12 15 21
-1 6 15 21 24 14 20 23
-
-boundary
-30
- 1 3  5  6  3  2
- 2 2  3  6  4
- 2 2  4  6  7
- 3 3  3  4  1  0
- 4 3 11 12  9  8
- 5 3  2  3 12 11
- 6 3  0  1 10  9
- 7 2  9 10 18
- 7 2 10 19 18
- 8 3  8  9 18 17
- 9 3  1  4 13 10
-10 3  4  7 16 13
-11 2 13 16 25
-11 2 13 25 22
-12 3 10 13 22 19
-13 3  7  6 15 16
-14 3  6  5 14 15
-15 3 15 14 23 24
-16 2 16 15 25
-16 2 15 24 25
-17 3  5  2 11 14
-18 3  3  0  9 12
-19 3 11  8 17 20
-20 2 11 20 14
-20 2 14 20 23
-21 3 17 18 21 20
-22 3 18 19 22 21
-23 2 21 22 25
-23 2 21 25 24
-24 3 20 21 24 23
-
-vertices
-26
-3
-0 -1 -1
-1 -1 -1
--1 0 -1
-0 0 -1
-1 0 -1
--1 1 -1
-0 1 -1
-1 1 -1
--1 -1 0
-0 -1 0
-1 -1 0
--1 0 0
-0 0 0
-1 0 0
--1 1 0
-0 1 0
-1 1 0
--1 -1 1
-0 -1 1
-1 -1 1
--1 0 1
-0 0 1
-1 0 1
--1 1 1
-0 1 1
-1 1 1
-
-MFEM sets v1.0
-
-vertex_sets
-1
-
-Origin
-1
-12
-
-edge_sets
-2
-
-Axes
-3
-12 13
-12 15
-12 21
-
-Negative Axes
-3
-12 9
-12 11
-12 3
-
-face_sets
-2
-
-Interior Corner
-3
-3 11 12  9 8
-3  2  3 12 11
-3  3  0  9 12
-
-Exterior Corner
-15
-2 13 16 25
-2 13 25 22
-2 16 15 25
-2 15 24 25
-2 21 22 25
-2 21 25 24
-3 10 13 22 19
-3 4 7 16 13
-3 1 4 13 10
-3 7 6 15 16
-3 6 5 14 15
-3 15 14 23 24
-3 20 21 24 23
-3 18 19 22 21
-3 17 18 21 20
-
-element_sets
-3
-
-Interior Corner
-3
-5 6 7
-
-Exterior Corner
-5
-0 1 2 3 4
-
-Steps
-3
-6 8 9

examples/fichera-set.mesh

@@ -1,145 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-#
-
-dimension
-3
-
-elements
-7
-1 5 0 1 4 3 9 10 13 12
-1 5 3 4 7 6 12 13 16 15
-1 5 2 3 6 5 11 12 15 14
-1 5 8 9 12 11 17 18 21 20
-1 5 9 10 13 12 18 19 22 21
-1 5 12 13 16 15 21 22 25 24
-1 5 11 12 15 14 20 21 24 23
-
-boundary
-24
-1 3 5 6 3 2
-2 3 6 7 4 3
-3 3 3 4 1 0
-4 3 11 12 9 8
-5 3 2 3 12 11
-6 3 0 1 10 9
-7 3 9 10 19 18
-8 3 8 9 18 17
-9 3 1 4 13 10
-10 3 4 7 16 13
-11 3 13 16 25 22
-12 3 10 13 22 19
-13 3 7 6 15 16
-14 3 6 5 14 15
-15 3 15 14 23 24
-16 3 16 15 24 25
-17 3 5 2 11 14
-18 3 3 0 9 12
-19 3 11 8 17 20
-20 3 14 11 20 23
-21 3 17 18 21 20
-22 3 18 19 22 21
-23 3 21 22 25 24
-24 3 20 21 24 23
-
-vertices
-26
-3
-0 -1 -1
-1 -1 -1
--1 0 -1
-0 0 -1
-1 0 -1
--1 1 -1
-0 1 -1
-1 1 -1
--1 -1 0
-0 -1 0
-1 -1 0
--1 0 0
-0 0 0
-1 0 0
--1 1 0
-0 1 0
-1 1 0
--1 -1 1
-0 -1 1
-1 -1 1
--1 0 1
-0 0 1
-1 0 1
--1 1 1
-0 1 1
-1 1 1
-
-MFEM sets v1.0
-
-vertex_sets
-1
-
-Origin
-1
-12
-
-edge_sets
-2
-
-Axes
-3
-12 13
-12 15
-12 21
-
-Negative Axes
-3
-12 9
-12 11
-12 3
-
-face_sets
-2
-
-Interior Corner
-3
-3 11 12  9 8
-3  2  3 12 11
-3  3  0  9 12
-
-Exterior Corner
-12
-3 13 16 25 22
-3 16 15 24 25
-3 21 22 25 24
-3 10 13 22 19
-3 4 7 16 13
-3 1 4 13 10
-3 7 6 15 16
-3 6 5 14 15
-3 15 14 23 24
-3 20 21 24 23
-3 18 19 22 21
-3 17 18 21 20
-
-element_sets
-3
-
-Interior Corner
-3
-0 2 3
-
-Exterior Corner
-1
-5
-
-Steps
-2
-1 3

examples/generate-glvis-script

@@ -0,0 +1,48 @@
+#!/bin/bash
+
+if [ $# -ne 2 ]; then
+    echo "Usage: generate-glvis-script <ncyc> <output-file-prefix>"
+fi
+
+ncyc=$1
+prefix=$2
+comp=0
+
+ncycm1=$(( $ncyc - 1 ))
+
+cat <<EOF > glvis-script
+window 0 0 400 400
+
+# Initial solution
+solution soln-$comp.mesh soln-0-$comp.gf
+
+# Setup the GLVis scene. Executed after pressing the space bar.
+{
+   perspective off
+   viewcenter 0.2 0
+   valuerange 0.0 1.0
+   keys ca
+   autoscale off
+}
+
+# Take multiple screenshots. Executed after pressing space bar.
+{
+EOF
+
+for i in `seq 0 $ncycm1`; do
+    if [ ! -f soln-$i.mesh ]; then
+	echo "The file soln-$i.mesh doesn't exist. Stopping."
+	exit 1
+    fi
+    if [ ! -f soln-$i-$comp.gf ]; then
+	echo "The file soln-$i-$comp.gf doesn't exist. Stopping."
+	exit 1
+    fi
+    ii=`printf %04d $i`
+    echo "solution soln-$i.mesh soln-$i-$comp.gf" >> glvis-script
+    #echo "valuerange 0.0 1.0" >> glvis-script
+    echo "screenshot $prefix-soln-$ii.png" >> glvis-script
+done
+echo "}" >> glvis-script
+
+echo "% glvis -run glvis-script"

examples/generate-screenshot-cmds

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+rm -f tmp
+for i in {0..19}; do
+    ii=`printf %04d $i`
+    echo "solution soln-$i.mesh soln-$i-0.gf" >> tmp
+    echo "valuerange 0.0 1.0" >> tmp
+    echo "screenshot greedy-soln-$ii.png" >> tmp
+done
+
+echo "output in ./tmp"

examples/ginkgo/CMakeLists.txt

@@ -31,31 +31,29 @@ add_mfem_examples(GINKGO_EXAMPLES_SRCS ${PFX} "" test_ginkgo)
 # which builds the examples and runs:
 #   ctest -R ginkgo
 
-if (MFEM_ENABLE_TESTING)
-  # Command line options for the tests.
-  set(EX1_COMMON_OPTS ex1 -m ../data/star.mesh --use_gko_solver)
-  set(EX1_TEST_OPTS ${EX9_COMMON_OPTS})
+# Command line options for the tests.
+set(EX1_COMMON_OPTS ex1 -m ../data/star.mesh --use_gko_solver)
+set(EX1_TEST_OPTS ${EX9_COMMON_OPTS})
 
-  # Add the tests: one test per source file.
-  foreach(SRC_FILE ${GINKGO_EXAMPLES_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-    string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
-    set(TEST_NAME ${PFX}${TEST_NAME})
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${GINKGO_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
+  set(TEST_NAME ${PFX}${TEST_NAME})
 
-    set(THIS_TEST_OPTIONS "-no-vis")
-    list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
-    # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
 
-    if (NOT (${TEST_NAME} MATCHES ".*p$"))
-      add_test(NAME ${TEST_NAME}_ser
-        COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-    else()
-      add_test(NAME ${TEST_NAME}_np=4
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    add_test(NAME ${TEST_NAME}_np=4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

examples/hiop/CMakeLists.txt

@@ -33,33 +33,31 @@ add_mfem_examples(HIOP_EXAMPLES_SRCS ${PFX} "" test_hiop)
 # which builds the examples and runs:
 #   ctest -R hiop
 
-if (MFEM_ENABLE_TESTING)
-  # Command line options for the tests.
-  # Example 9:
-  set(EX9_COMMON_OPTS -m ../../data/periodic-segment.mesh -p 0 -dt 0.005)
-  set(EX9_TEST_OPTS ${EX9_COMMON_OPTS}  -r  2 )
-  set(EX9P_TEST_OPTS ${EX9_COMMON_OPTS})
+# Command line options for the tests.
+# Example 9:
+set(EX9_COMMON_OPTS -m ../../data/periodic-segment.mesh -p 0 -dt 0.005)
+set(EX9_TEST_OPTS ${EX9_COMMON_OPTS}  -r  2 )
+set(EX9P_TEST_OPTS ${EX9_COMMON_OPTS})
 
-  # Add the tests: one test per source file.
-  foreach(SRC_FILE ${HIOP_EXAMPLES_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-    string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
-    set(TEST_NAME ${PFX}${TEST_NAME})
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${HIOP_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
+  set(TEST_NAME ${PFX}${TEST_NAME})
 
-    set(THIS_TEST_OPTIONS "-no-vis")
-    list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
-    # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
 
-    if (NOT (${TEST_NAME} MATCHES ".*p$"))
-      add_test(NAME ${TEST_NAME}_ser
-        COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-    else()
-      add_test(NAME ${TEST_NAME}_np=4
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    add_test(NAME ${TEST_NAME}_np=4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

examples/jupyter/README.md

@@ -1,31 +0,0 @@
-# Jupyter Notebooks using xeus-cling
-
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mfem/mfem/master?filepath=examples%2Fjupyter%2Fex.ipynb)
-
-[xeus-cling](https://github.com/jupyter-xeus/xeus-cling) is a C++ Jupyter Kernel based on [cling](https://github.com/root-project/cling),
-which can be used to create interactive C++ MFEM and GLVis notebooks.
-
-Click on the `binder` button above for an interactive example.
-
-## Installing Locally
-
-In order to run notebooks locally you will need `xeus-cling` along with `mfem` and `xglvis`. We recommend you use
-[miniconda](https://docs.conda.io/en/latest/miniconda.html) or, if you already have it installed,
-[conda](https://docs.conda.io/projects/conda/en/latest/).
-
-1. Follow the install steps on https://github.com/jupyter-xeus/xeus-cling to install the C++ kernels
-2. Build and install a _shared_ version of mfem
-    * for example: `make serial SHARED=YES`
-3. Install [pyglvis](https://github.com/glvis/pyglvis)
-    * for the widget frontend
-4. Get [xeus-glvis](https://github.com/glvis/xeus-glvis) and `cp` the header to `{PREFIX}/glvis/xglvis.hpp`
-    * (this could be improved)
-
-## Running Locally
-
-Once you've installed Jupyter, the C++ Kernel, mfem, and glvis start the notebook server (`jupyter-notebook`)
-and open an existing example or a new `C++ 1x` kernel.
-
-You will _always_ need to `#pragma cling load("mfem")` and you may need to point the `cling` runtime at your
-mfem and/or glvis installs, do this with the
-`#pragma cling` [statements](https://xeus-cling.readthedocs.io/en/latest/build_options.html#using-third-party-libraries).

examples/jupyter/ex.ipynb

@@ -1,155 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "owned-extraction",
-   "metadata": {},
-   "source": [
-    "## Load the MFEM library\n",
-    "\n",
-    "Any non-default libraries must be loaded before you can `#include` files that use them. For more info see the [xeus-cling help](https://xeus-cling.readthedocs.io/en/latest/build_options.html)."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "waiting-portrait",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#pragma cling load(\"mfem\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "foreign-recycling",
-   "metadata": {},
-   "source": [
-    "## MFEM Example 1"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "public-white",
-   "metadata": {},
-   "source": [
-    "This is the simplest MFEM example and a good starting point for new users. The example demonstrates the use of MFEM to define and solve an $H^1$ finite element discretization of the Laplace problem\n",
-    "\n",
-    "$$\n",
-    "-\\Delta u = 1\n",
-    "$$\n",
-    "\n",
-    "with homogeneous Dirichlet boundary conditions $u=0$.\n",
-    "\n",
-    "The example illustrates the use of the basic MFEM classes for defining the mesh, finite element space, as well as linear and bilinear forms corresponding to the left-hand side and right-hand side of the discrete linear system.\n",
-    "\n",
-    "Compare with MFEM's [ex1.cpp](https://github.com/mfem/mfem/blob/master/examples/ex1.cpp) and PyMFEM's [ex1.py](https://github.com/mfem/PyMFEM/blob/master/examples/ex1.py)."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "protective-darkness",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#include <fstream>\n",
-    "#include <iostream>\n",
-    "#include <sstream>\n",
-    "\n",
-    "#include <mfem.hpp>\n",
-    "#include <glvis/xglvis.hpp>"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "falling-monkey",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "using namespace std;\n",
-    "using namespace mfem;\n",
-    "\n",
-    "Mesh mesh = Mesh::MakeCartesian2D(5, 5, Element::TRIANGLE);\n",
-    "mesh.UniformRefinement();\n",
-    "\n",
-    "H1_FECollection fec(2, mesh.Dimension());\n",
-    "\n",
-    "FiniteElementSpace fespace(&mesh, &fec);\n",
-    "cout << \"Number of finite element unknowns: \" << fespace.GetTrueVSize() << endl;\n",
-    "\n",
-    "Array<int> ess_tdof_list;\n",
-    "if (mesh.bdr_attributes.Size())\n",
-    "{\n",
-    "  Array<int> ess_bdr(mesh.bdr_attributes.Max());\n",
-    "  ess_bdr = 1;\n",
-    "  fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);\n",
-    "}\n",
-    "\n",
-    "LinearForm b(&fespace);\n",
-    "ConstantCoefficient one(1.0);\n",
-    "b.AddDomainIntegrator(new DomainLFIntegrator(one));\n",
-    "b.Assemble();\n",
-    "\n",
-    "GridFunction x(&fespace);\n",
-    "x = 0.0;\n",
-    "\n",
-    "BilinearForm a(&fespace);\n",
-    "a.AddDomainIntegrator(new DiffusionIntegrator(one));\n",
-    "a.Assemble();\n",
-    "\n",
-    "OperatorPtr A;\n",
-    "Vector B, X;\n",
-    "a.FormLinearSystem(ess_tdof_list, x, b, A, X, B);\n",
-    "\n",
-    "cout << \"Size of linear system: \" << A->Height() << endl;\n",
-    "\n",
-    "GSSmoother M((SparseMatrix&)(*A));\n",
-    "PCG(*A, M, B, X, 1, 200, 1e-12, 0.0);\n",
-    "a.RecoverFEMSolution(X, b, x);"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "hawaiian-republican",
-   "metadata": {},
-   "source": [
-    "## GLVis Visualization\n",
-    "\n",
-    "For now we save the computational mesh and finite element solution in a string and pass that to the glvis widget, see https://github.com/glvis/xeus-glvis for the widget backend and https://github.com/GLVis/pyglvis/tree/master/js for the widget frontend."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ordinary-equation",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "std::stringstream ss;\n",
-    "ss << \"solution\\n\" << mesh << x << flush;\n",
-    "\n",
-    "auto glv = glvis::glvis();\n",
-    "glv.plot(ss.str() + \"keys Rjml\"); // the `+ \"keys ....\"' is optional\n",
-    "glv"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "C++14",
-   "language": "C++14",
-   "name": "xcpp14"
-  },
-  "language_info": {
-   "codemirror_mode": "text/x-c++src",
-   "file_extension": ".cpp",
-   "mimetype": "text/x-c++src",
-   "name": "c++",
-   "version": "14"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

examples/make-err-plots.py

@@ -0,0 +1,32 @@
+
+# Take err-N.dat files and create error plots for each cycle.
+# Negative values are interpreted as refined regions and plotted in
+# red.
+
+import math
+import matplotlib.pyplot as plt
+
+for i in range(20):
+    print(f"{i}")
+    with open(f"err-{i}.dat") as f:
+        lines = f.readlines()
+        x = [float(line.split()[0]) for line in lines]
+        y = [float(line.split()[1]) for line in lines]
+
+        # errors in refined zones are marked as negative by convention
+        # from ex18. in order to detect "negative zero", we use the
+        # copysign method, which distinguishes negative zero from
+        # zero.
+        r = [(x,-y) for x,y in zip(x,y) if math.copysign(1, y) == -1.0]
+        xr,yr = zip(*r)
+        print(xr)
+        print(yr)
+        plt.scatter(x,y)
+        plt.scatter(xr,yr,c='r')
+        plt.title(f"Timestep {i}")
+        plt.xlabel("reference el")
+        plt.ylabel("L2 error")
+        plt.ylim(0,0.05)
+        #plt.show()
+        plt.savefig(f"opt-err-{i}.png",dpi=60)
+        plt.clf()

examples/make-glvis-figs

@@ -0,0 +1,19 @@
+window 0 0 400 400
+
+# Initial solution
+solution soln-0.mesh soln-0-0.gf
+
+# Setup the GLVis scene. Executed after pressing the space bar.
+{
+   perspective off
+#   view 0 0
+   viewcenter 0.2 0
+   valuerange 0.0 1.0
+#   zoom 1.5
+   keys ca
+}
+
+# Take multiple screenshots. Executed after pressing the space bar.
+{
+#insert the screenshot commands here
+}

examples/make-periodic-mesh

@@ -0,0 +1,63 @@
+#!/bin/bash
+
+if [ $# -ne 1 ]; then
+    echo "Usage: ./make-periodic-mesh <NE>"
+fi
+
+NE=$1
+NEm1=$(( $NE - 1 ))
+NEm2=$(( $NE - 2 ))
+
+filename="periodic-segment-$NE.mesh"
+
+cat <<ENDHERE > $filename
+MFEM mesh v1.0
+
+#
+# MFEM Geometry Types (see mesh/geom.hpp):
+#
+# POINT       = 0
+# SEGMENT     = 1
+# TRIANGLE    = 2
+# SQUARE      = 3
+# TETRAHEDRON = 4
+# CUBE        = 5
+#
+
+dimension
+1
+
+# format: <attribute> <geometry type> <vertex 0> <vertex 1> ...
+elements
+ENDHERE
+
+echo "$NE" >> $filename
+for i in `seq 0 $NEm2`; do
+    echo "1 1 $i $((i+1))" >> $filename
+done
+echo "1 1 $((i+1)) 0" >> $filename
+
+cat <<EOF >> $filename
+
+boundary
+0
+
+vertices
+$NE
+
+nodes
+FiniteElementSpace
+FiniteElementCollection: L2_T1_1D_P1
+VDim: 1
+Ordering: 1
+ 
+EOF
+
+dx=`echo "1.0 / $NE" | bc -l`
+for i in `seq 0 $NEm1`; do
+    p1=`echo "$i * $dx" | bc -l`
+    p2=`echo "$((i+1)) * $dx" | bc -l`
+    echo "$p1 $p2" >> $filename
+done
+
+

examples/makefile

@@ -22,10 +22,10 @@ MFEM_LIB_FILE = mfem_is_not_built
 -include $(CONFIG_MK)
 
 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
+  ex17 ex18 ex19 ex20 ex21 ex22 ex23 ex24 ex25 ex26 ex27 ex28 ex29
 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
+  ex25p ex26p ex27p ex28p ex29p
 SEQ_DEVICE_EXAMPLES = ex1 ex3 ex4 ex5 ex6 ex9 ex22 ex24 ex25 ex26
 PAR_DEVICE_EXAMPLES = ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex9p ex13p ex22p \
   ex24p ex25p ex26p

examples/periodic-segment-16.mesh

@@ -0,0 +1,65 @@
+MFEM mesh v1.0
+
+#
+# MFEM Geometry Types (see mesh/geom.hpp):
+#
+# POINT       = 0
+# SEGMENT     = 1
+# TRIANGLE    = 2
+# SQUARE      = 3
+# TETRAHEDRON = 4
+# CUBE        = 5
+#
+
+dimension
+1
+
+# format: <attribute> <geometry type> <vertex 0> <vertex 1> ...
+elements
+16
+1 1 0 1
+1 1 1 2
+1 1 2 3
+1 1 3 4
+1 1 4 5
+1 1 5 6
+1 1 6 7
+1 1 7 8
+1 1 8 9
+1 1 9 10
+1 1 10 11
+1 1 11 12
+1 1 12 13
+1 1 13 14
+1 1 14 15
+1 1 15 0
+
+
+boundary
+0
+
+vertices
+16
+
+nodes
+FiniteElementSpace
+FiniteElementCollection: L2_T1_1D_P1
+VDim: 1
+Ordering: 1
+
+0.0000 0.0625
+0.0625 0.1250
+0.1250 0.1875
+0.1875 0.2500
+0.2500 0.3125
+0.3125 0.3750
+0.3750 0.4375
+0.4375 0.5000
+0.5000 0.5625
+0.5625 0.6250
+0.6250 0.6875
+0.6875 0.7500
+0.7500 0.8125
+0.8125 0.8750
+0.8750 0.9375
+0.9375 1.0000

examples/periodic-segment-8.mesh

@@ -0,0 +1,50 @@
+MFEM mesh v1.0
+
+#
+# MFEM Geometry Types (see mesh/geom.hpp):
+#
+# POINT       = 0
+# SEGMENT     = 1
+# TRIANGLE    = 2
+# SQUARE      = 3
+# TETRAHEDRON = 4
+# CUBE        = 5
+#
+
+dimension
+1
+
+# format: <attribute> <geometry type> <vertex 0> <vertex 1> ...
+elements
+8
+1 1 0 1
+1 1 1 2
+1 1 2 3
+1 1 3 4
+1 1 4 5
+1 1 5 6
+1 1 6 7
+1 1 7 0
+
+boundary
+0
+
+vertices
+8
+
+nodes
+FiniteElementSpace
+FiniteElementCollection: L2_T1_1D_P1
+VDim: 1
+Ordering: 1
+
+0.000 0.125
+0.125 0.250
+0.250 0.375
+0.375 0.500
+0.500 0.625
+0.625 0.750
+0.750 0.875
+0.875 1.000
+
+

examples/petsc/CMakeLists.txt

@@ -94,32 +94,30 @@ if (MFEM_USE_SLEPC)
 endif()
 
 # Add the tests: one test per command-line-variable.
-if (MFEM_ENABLE_TESTING)
-  set(TEST_OPTIONS_VARS
-      EX1_ARGS_W EX1_ARGS_P EX2_ARGS EX3_ARGS EX4_ARGS EX4_HYB_ARGS
-      EX5_BDDC_LB_ARGS EX5_BDDC_GB_ARGS EX5_FSPL_ARGS EX6_ARGS EX6_NONOVL_ARGS
-      EX9_E_ARGS EX9_ES_ARGS EX9_IS_ARGS EX10_ARGS)
-  if (MFEM_USE_SLEPC)
-      list(APPEND TEST_OPTIONS_VARS EX11_ARGS_SINV EX11_ARGS_LOBPCG EX11_ARGS_GD)
-  endif()
-
-  foreach(TEST_OPTIONS_VAR ${TEST_OPTIONS_VARS})
-    string(REGEX REPLACE "^(.+)_ARGS" "\\1" TEST_NAME_UC ${TEST_OPTIONS_VAR})
-    string(REGEX REPLACE "^([^_]+)" "\\1P" TEST_NAME_UC ${TEST_NAME_UC})
-    string(TOLOWER ${TEST_NAME_UC} TEST_NAME_FULL)
-    string(REGEX REPLACE "^([^_]+).*" "\\1" TEST_NAME ${TEST_NAME_FULL})
-    set(TEST_NAME_FULL ${PFX}${TEST_NAME_FULL})
-    set(TEST_NAME ${PFX}${TEST_NAME})
-    set(TEST_OPTIONS "-no-vis" ${${TEST_OPTIONS_VAR}})
-    # message(STATUS "${TEST_NAME_FULL} --> ${TEST_NAME} ${TEST_OPTIONS}")
-
-    # All PETSC tests are parallel.
-    if (MFEM_USE_MPI)
-      add_test(NAME ${TEST_NAME_FULL}_np=4
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
+set(TEST_OPTIONS_VARS
+    EX1_ARGS_W EX1_ARGS_P EX2_ARGS EX3_ARGS EX4_ARGS EX4_HYB_ARGS
+    EX5_BDDC_LB_ARGS EX5_BDDC_GB_ARGS EX5_FSPL_ARGS EX6_ARGS EX6_NONOVL_ARGS
+    EX9_E_ARGS EX9_ES_ARGS EX9_IS_ARGS EX10_ARGS)
+if (MFEM_USE_SLEPC)
+    list(APPEND TEST_OPTIONS_VARS EX11_ARGS_SINV EX11_ARGS_LOBPCG EX11_ARGS_GD)
 endif()
+
+foreach(TEST_OPTIONS_VAR ${TEST_OPTIONS_VARS})
+  string(REGEX REPLACE "^(.+)_ARGS" "\\1" TEST_NAME_UC ${TEST_OPTIONS_VAR})
+  string(REGEX REPLACE "^([^_]+)" "\\1P" TEST_NAME_UC ${TEST_NAME_UC})
+  string(TOLOWER ${TEST_NAME_UC} TEST_NAME_FULL)
+  string(REGEX REPLACE "^([^_]+).*" "\\1" TEST_NAME ${TEST_NAME_FULL})
+  set(TEST_NAME_FULL ${PFX}${TEST_NAME_FULL})
+  set(TEST_NAME ${PFX}${TEST_NAME})
+  set(TEST_OPTIONS "-no-vis" ${${TEST_OPTIONS_VAR}})
+  # message(STATUS "${TEST_NAME_FULL} --> ${TEST_NAME} ${TEST_OPTIONS}")
+
+  # All PETSC tests are parallel.
+  if (MFEM_USE_MPI)
+    add_test(NAME ${TEST_NAME_FULL}_np=4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

examples/pumi/CMakeLists.txt

@@ -37,39 +37,37 @@ add_mfem_examples(PUMI_EXAMPLES_SRCS ${PFX} "" test_pumi)
 # which builds the examples and runs:
 #   ctest -R pumi
 
-if (MFEM_ENABLE_TESTING)
-  # Command line options for the tests.
-  # TODO...
+# Command line options for the tests.
+# TODO...
 
-  # Set the number of processors for the parallel examples. The value of
-  # MFEM_MPI_NP is ignored.
-  set(EX1_TEST_NP 1)
-  set(EX1P_TEST_NP 8)
-  set(EX2_TEST_NP 1)
-  set(EX6P_TEST_NP 8)
+# Set the number of processors for the parallel examples. The value of
+# MFEM_MPI_NP is ignored.
+set(EX1_TEST_NP 1)
+set(EX1P_TEST_NP 8)
+set(EX2_TEST_NP 1)
+set(EX6P_TEST_NP 8)
 
-  # Add the tests: one test per source file.
-  foreach(SRC_FILE ${PUMI_EXAMPLES_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-    string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
-    set(TEST_NAME ${PFX}${TEST_NAME})
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${PUMI_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
+  set(TEST_NAME ${PFX}${TEST_NAME})
 
-    set(THIS_TEST_OPTIONS "-no-vis")
-    list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
-    # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
 
-    # All PUMI examples require MPI
-    if (FALSE)
-      add_test(NAME ${TEST_NAME}_ser
-        COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-    else()
-      set(TEST_NP ${${UP_TEST_NAME}_TEST_NP})
-      add_test(NAME ${TEST_NAME}_np=${TEST_NP}
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${TEST_NP}
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()
+  # All PUMI examples require MPI
+  if (FALSE)
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    set(TEST_NP ${${UP_TEST_NAME}_TEST_NP})
+    add_test(NAME ${TEST_NAME}_np=${TEST_NP}
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${TEST_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

examples/run-search

@@ -0,0 +1,43 @@
+#!/bin/bash
+
+# sod 5 regrids
+options="-dt 0.01 --cfl-number -1 " # fixed timestep
+options+="--regrid-period 4 "       # regrid period
+options+="--problem 2 "             # Sod problem
+options+="--order 0 "               # 0th order DG
+options+="--refine 0 "              # no initial uniform refinement
+options+="--t-final 0.20 "
+
+# create reference solution on 16 element mesh
+./ex18 $options -m periodic-segment-20.mesh
+./save-reference
+
+ne=10
+nem1=$((ne-1))
+
+echo "" > err-results.dat
+for i1 in $(seq 0 $nem1); do
+    for i2 in $(seq 0 $nem1); do
+	for i3 in $(seq 0 $nem1); do
+	    for i4 in $(seq 0 $nem1); do
+		for i5 in $(seq 0 $nem1); do
+		    dir="seq-$i1$i2$i3$i4$i5"
+		    mkdir $dir
+		    cd $dir
+		    ln -s ../reference.mesh .
+		    ln -s ../reference-rho.gf .
+		    ln -s ../reference-rho-u.gf .
+		    ln -s ../reference-rho-e.gf .
+		    echo "running $i1$i2$i3$i4$i5"
+		    seq="$i1 $i2 $i3 $i4 $i5"
+		    cmd="../ex18 -rseq \"$seq\" $options -m ../periodic-segment-10.mesh | grep err | awk \"{print \$2}\""
+		    echo "$cmd" > runcode
+		    err=$( source runcode )
+		    cd ..
+		    echo "$i1 $i2 $i3 $i4 $i5 $err" >> err-results.dat
+		done
+	    done
+	done
+    done
+done
+

examples/save-reference

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# The final time is the reference solution
+mv vortex.mesh reference.mesh
+mv vortex-0-final.gf reference-rho.gf
+mv vortex-1-final.gf reference-rho-u.gf
+mv vortex-2-final.gf reference-rho-e.gf
+
+# Save the timesteps as well for errors
+for i in {0..19}
+do
+    mv soln-$i.mesh reference-$i.mesh
+    mv soln-$i-0.gf reference-$i-0.gf
+    mv soln-$i-1.gf reference-$i-1.gf
+    mv soln-$i-2.gf reference-$i-2.gf
+done

examples/star-mixed-set.mesh

@@ -1,158 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-#
-
-dimension
-2
-
-elements
-30
-1 3 0 11 26 14
-1 3 0 14 27 17
-1 3 0 17 28 20
-1 3 0 20 29 23
-1 3 0 23 30 11
-1 2 11 1 26
-1 2 1 12 26
-1 3 26 12 3 13
-1 2 26 13 2
-1 2 14 26 2
-1 2 14 2 27
-1 2 2 15 27
-1 3 27 15 5 16
-1 2 27 16 4
-1 2 17 27 4
-1 2 17 4 28
-1 2 4 18 28
-1 3 28 18 7 19
-1 2 28 19 6
-1 2 20 28 6
-1 2 20 6 29
-1 2 6 21 29
-1 3 29 21 9 22
-1 2 29 22 8
-1 2 23 29 8
-1 2 23 8 30
-1 2 8 24 30
-1 3 30 24 10 25
-1 2 30 25 1
-1 2 11 30 1
-
-boundary
-20
-1 1 13 2
-1 1 12 3
-1 1 16 4
-1 1 15 5
-1 1 19 6
-1 1 18 7
-1 1 22 8
-1 1 21 9
-1 1 25 1
-1 1 24 10
-1 1 3 13
-1 1 1 12
-1 1 5 16
-1 1 2 15
-1 1 7 19
-1 1 4 18
-1 1 9 22
-1 1 6 21
-1 1 10 25
-1 1 8 24
-
-vertices
-31
-2
-0 0
-1 0
-0.309017 0.951057
-1.30902 0.951057
--0.809017 0.587785
--0.5 1.53884
--0.809017 -0.587785
--1.61803 0
-0.309017 -0.951057
--0.5 -1.53884
-1.30902 -0.951057
-0.5 0
-1.15451 0.475529
-0.809019 0.951057
-0.154508 0.475529
--0.0954915 1.24495
--0.654508 1.06331
--0.404508 0.293893
--1.21352 0.293893
--1.21352 -0.293892
--0.404508 -0.293893
--0.654508 -1.06331
--0.0954915 -1.24495
-0.154508 -0.475529
-0.809019 -0.951057
-1.15451 -0.475529
-0.654509 0.475529
--0.25 0.769421
--0.809016 0
--0.25 -0.76942
-0.654509 -0.475529
-
-MFEM sets v1.0
-
-vertex_sets
-3
-
-Origin
-1
-0
-
-Tent
-5
-1 2 4 6 8
-
-Gazebo
-5
-3 5 7 9 10
-
-edge_sets
-2
-
-Columbine
-5
-1 11
-2 14
-4 17
-6 20
-8 23
-
-Lily
-5
-0 11
-0 14
-0 17
-0 20
-0 23
-
-element_sets
-3
-
-Flying Squirrel
-3
-7 17 27
-
-Sea Lion
-4
-12 17 22 27
-
-Pinwheel
-5
-8 13 18 23 28

examples/star-set.mesh

@@ -1,143 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-#
-
-dimension
-2
-
-elements
-20
-1 3 0 11 26 14
-1 3 0 14 27 17
-1 3 0 17 28 20
-1 3 0 20 29 23
-1 3 0 23 30 11
-1 3 11 1 12 26
-1 3 26 12 3 13
-1 3 14 26 13 2
-1 3 14 2 15 27
-1 3 27 15 5 16
-1 3 17 27 16 4
-1 3 17 4 18 28
-1 3 28 18 7 19
-1 3 20 28 19 6
-1 3 20 6 21 29
-1 3 29 21 9 22
-1 3 23 29 22 8
-1 3 23 8 24 30
-1 3 30 24 10 25
-1 3 11 30 25 1
-
-boundary
-20
-1 1 13 2
-1 1 12 3
-1 1 16 4
-1 1 15 5
-1 1 19 6
-1 1 18 7
-1 1 22 8
-1 1 21 9
-1 1 25 1
-1 1 24 10
-1 1 3 13
-1 1 1 12
-1 1 5 16
-1 1 2 15
-1 1 7 19
-1 1 4 18
-1 1 9 22
-1 1 6 21
-1 1 10 25
-1 1 8 24
-
-vertices
-31
-2
-0 0
-1 0
-0.309017 0.951057
-1.30902 0.951057
--0.809017 0.587785
--0.5 1.53884
--0.809017 -0.587785
--1.61803 0
-0.309017 -0.951057
--0.5 -1.53884
-1.30902 -0.951057
-0.5 0
-1.15451 0.475529
-0.809019 0.951057
-0.154508 0.475529
--0.0954915 1.24495
--0.654508 1.06331
--0.404508 0.293893
--1.21352 0.293893
--1.21352 -0.293892
--0.404508 -0.293893
--0.654508 -1.06331
--0.0954915 -1.24495
-0.154508 -0.475529
-0.809019 -0.951057
-1.15451 -0.475529
-0.654509 0.475529
--0.25 0.769421
--0.809016 0
--0.25 -0.76942
-0.654509 -0.475529
-
-MFEM sets v1.0
-
-vertex_sets
-3
-
-Origin
-1
-0
-
-Tent
-5
-1 2 4 6 8
-
-Gazebo
-5
-3 5 7 9 10
-
-edge_sets
-2
-
-Columbine
-5
-1 11
-2 14
-4 17
-6 20
-8 23
-
-Lily
-5
-0 11
-0 14
-0 17
-0 20
-0 23
-
-element_sets
-2
-
-Flying Squirrel
-3
-6 12 18
-
-Sea Lion
-4
-9 12 15 18

examples/sundials/CMakeLists.txt

@@ -41,38 +41,36 @@ add_mfem_examples(SUNDIALS_EXAMPLES_SRCS ${PFX} "" test_sundials)
 # which builds the examples and runs:
 #   ctest -R sundials
 
-if (MFEM_ENABLE_TESTING)
-  # Command line options for the tests.
-  # Example 9: test CVODE with CV_ADAMS (non-stiff implicit) time stepping
-  set(EX9_COMMON_OPTS -m ../../data/periodic-hexagon.mesh -p 0 -s 7)
-  set(EX9_TEST_OPTS ${EX9_COMMON_OPTS}  -r  2 -dt 0.0018 -vs 25)
-  set(EX9P_TEST_OPTS ${EX9_COMMON_OPTS} -rp 1 -dt 0.0009 -vs 50)
-  # Example 10: test CVODE with CV_BDF (stiff implicit) time stepping
-  set(EX10_COMMON_OPTS -m ../../data/beam-quad.mesh -o 2 -s 5 -dt 0.15 -tf 6 -vs 10)
-  set(EX10_TEST_OPTS ${EX10_COMMON_OPTS}  -r  2)
-  set(EX10P_TEST_OPTS ${EX10_COMMON_OPTS} -rp 1)
-  # Example 16: use the default options
+# Command line options for the tests.
+# Example 9: test CVODE with CV_ADAMS (non-stiff implicit) time stepping
+set(EX9_COMMON_OPTS -m ../../data/periodic-hexagon.mesh -p 0 -s 7)
+set(EX9_TEST_OPTS ${EX9_COMMON_OPTS}  -r  2 -dt 0.0018 -vs 25)
+set(EX9P_TEST_OPTS ${EX9_COMMON_OPTS} -rp 1 -dt 0.0009 -vs 50)
+# Example 10: test CVODE with CV_BDF (stiff implicit) time stepping
+set(EX10_COMMON_OPTS -m ../../data/beam-quad.mesh -o 2 -s 5 -dt 0.15 -tf 6 -vs 10)
+set(EX10_TEST_OPTS ${EX10_COMMON_OPTS}  -r  2)
+set(EX10P_TEST_OPTS ${EX10_COMMON_OPTS} -rp 1)
+# Example 16: use the default options
 
-  # Add the tests: one test per source file.
-  foreach(SRC_FILE ${SUNDIALS_EXAMPLES_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-    string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
-    set(TEST_NAME ${PFX}${TEST_NAME})
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${SUNDIALS_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
+  set(TEST_NAME ${PFX}${TEST_NAME})
 
-    set(THIS_TEST_OPTIONS "-no-vis")
-    list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
-    # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
 
-    if (NOT (${TEST_NAME} MATCHES ".*p$"))
-      add_test(NAME ${TEST_NAME}_ser
-        COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-    else()
-      add_test(NAME ${TEST_NAME}_np=4
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    add_test(NAME ${TEST_NAME}_np=4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

examples/superlu/CMakeLists.txt

@@ -32,32 +32,31 @@ add_mfem_examples(SUPERLU_EXAMPLES_SRCS ${PFX} "" test_superlu)
 # The SuperLU tests can be run separately using the target "test_superlu"
 # which builds the examples and runs:
 #   ctest -R superlu
-if (MFEM_ENABLE_TESTING)
-  # Command line options for the tests.
-  # Example 1: Test SuperLU on the simple Poisson problem
-  set(EX1_COMMON_OPTS -m ../../data/star.mesh -p 2)
-  set(EX1P_TEST_OPTS ${EX1_COMMON_OPTS})
 
-  # Add the tests: one test per source file.
-  foreach(SRC_FILE ${SUPERLU_EXAMPLES_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-    string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
-    set(TEST_NAME ${PFX}${TEST_NAME})
+# Command line options for the tests.
+# Example 1: Test SuperLU on the simple Poisson problem
+set(EX1_COMMON_OPTS -m ../../data/star.mesh -p 2)
+set(EX1P_TEST_OPTS ${EX1_COMMON_OPTS})
 
-    set(THIS_TEST_OPTIONS "-no-vis")
-    list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
-    # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${SUPERLU_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
+  set(TEST_NAME ${PFX}${TEST_NAME})
 
-    if (NOT (${TEST_NAME} MATCHES ".*p$"))
-      add_test(NAME ${TEST_NAME}_ser
-        COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-    else()
-      add_test(NAME ${TEST_NAME}_np=4
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    add_test(NAME ${TEST_NAME}_np=4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

fem/CMakeLists.txt

@@ -43,15 +43,6 @@ set(SRCS
   eltrans.cpp
   estimators.cpp
   fe.cpp
-  fe/fe_base.cpp
-  fe/fe_fixed_order.cpp
-  fe/fe_h1.cpp
-  fe/fe_l2.cpp
-  fe/fe_nd.cpp
-  fe/fe_nurbs.cpp
-  fe/fe_pos.cpp
-  fe/fe_rt.cpp
-  fe/fe_ser.cpp
   fe_coll.cpp
   fespace.cpp
   geom.cpp
@@ -133,15 +124,6 @@ set(HDRS
   eltrans.hpp
   estimators.hpp
   fe.hpp
-  fe/fe_base.hpp
-  fe/fe_fixed_order.hpp
-  fe/fe_h1.hpp
-  fe/fe_l2.hpp
-  fe/fe_nd.hpp
-  fe/fe_nurbs.hpp
-  fe/fe_pos.hpp
-  fe/fe_rt.hpp
-  fe/fe_ser.hpp
   fe_coll.hpp
   fem.hpp
   fespace.hpp

fem/bilinearform.cpp

@@ -969,7 +969,6 @@ void BilinearForm::EliminateVDofs(const Array<int> &vdofs,
                                   const Vector &sol, Vector &rhs,
                                   DiagonalPolicy dpolicy)
 {
-   vdofs.HostRead();
    for (int i = 0; i < vdofs.Size(); i++)
    {
       int vdof = vdofs[i];

fem/bilininteg.cpp

@@ -747,7 +747,6 @@ void DiffusionIntegrator::AssembleElementMatrix
 #ifdef MFEM_THREAD_SAFE
    DenseMatrix dshape(nd, dim), dshapedxt(nd, spaceDim);
    DenseMatrix dshapedxt_m(nd, MQ ? spaceDim : 0);
-   DenseMatrix M(MQ ? spaceDim : 0);
    Vector D(VQ ? VQ->GetVDim() : 0);
 #else
    dshape.SetSize(nd, dim);
@@ -985,8 +984,6 @@ void DiffusionIntegrator::ComputeElementFlux
                   "Unexpected height for MatrixCoefficient");
    }
 
-   MFEM_VERIFY(!SMQ, "SymmetricMatrixCoefficient not supported here");
-
 #ifdef MFEM_THREAD_SAFE
    DenseMatrix dshape(nd,dim), invdfdx(dim, spaceDim);
    DenseMatrix M(MQ ? spaceDim : 0);
@@ -999,7 +996,7 @@ void DiffusionIntegrator::ComputeElementFlux
 #endif
    vec.SetSize(dim);
    vecdxt.SetSize(spaceDim);
-   pointflux.SetSize(MQ || VQ ? spaceDim : 0);
+   pointflux.SetSize(MQ ? spaceDim : 0);
 
    const IntegrationRule &ir = fluxelem.GetNodes();
    fnd = ir.GetNPoints();
@@ -1015,45 +1012,36 @@ void DiffusionIntegrator::ComputeElementFlux
       CalcInverse(Trans.Jacobian(), invdfdx);
       invdfdx.MultTranspose(vec, vecdxt);
 
-      if (with_coef)
+      if (!MQ && !VQ)
       {
-         if (!MQ && !VQ)
+         if (Q && with_coef)
          {
-            if (Q)
-            {
-               vecdxt *= Q->Eval(Trans,ip);
-            }
-            for (j = 0; j < spaceDim; j++)
-            {
-               flux(fnd*j+i) = vecdxt(j);
-            }
+            vecdxt *= Q->Eval(Trans,ip);
          }
-         else
+         for (j = 0; j < spaceDim; j++)
          {
-            if (MQ)
-            {
-               MQ->Eval(M, Trans, ip);
-               M.Mult(vecdxt, pointflux);
-            }
-            else
-            {
-               VQ->Eval(D, Trans, ip);
-               for (int j=0; j<spaceDim; ++j)
-               {
-                  pointflux[j] = D[j] * vecdxt[j];
-               }
-            }
-            for (j = 0; j < spaceDim; j++)
-            {
-               flux(fnd*j+i) = pointflux(j);
-            }
+            flux(fnd*j+i) = vecdxt(j);
          }
       }
       else
       {
+         if (MQ)
+         {
+            MQ->Eval(M, Trans, ip);
+            M.Mult(vecdxt, pointflux);
+         }
+         else
+         {
+            VQ->Eval(D, Trans, ip);
+            for (int j=0; j<spaceDim; ++j)
+            {
+               pointflux[j] = D[j] * vecdxt[j];
+            }
+
+         }
          for (j = 0; j < spaceDim; j++)
          {
-            flux(fnd*j+i) = vecdxt(j);
+            flux(fnd*j+i) = pointflux(j);
          }
       }
    }
@@ -1069,13 +1057,8 @@ double DiffusionIntegrator::ComputeFluxEnergy
 
 #ifdef MFEM_THREAD_SAFE
    DenseMatrix M;
-   Vector D(VQ ? VQ->GetVDim() : 0);
-#else
-   D.SetSize(VQ ? VQ->GetVDim() : 0);
 #endif
 
-   MFEM_VERIFY(!SMQ, "SymmetricMatrixCoefficient not supported here");
-
    shape.SetSize(nd);
    pointflux.SetSize(spaceDim);
    if (d_energy) { vec.SetSize(spaceDim); }
@@ -1104,23 +1087,17 @@ double DiffusionIntegrator::ComputeFluxEnergy
       Trans.SetIntPoint(&ip);
       double w = Trans.Weight() * ip.weight;
 
-      if (MQ)
-      {
-         MQ->Eval(M, Trans, ip);
-         energy += w * M.InnerProduct(pointflux, pointflux);
-      }
-      else if (VQ)
-      {
-         VQ->Eval(D, Trans, ip);
-         D *= pointflux;
-         energy += w * (D * pointflux);
-      }
-      else
+      if (!MQ)
       {
          double e = (pointflux * pointflux);
          if (Q) { e *= Q->Eval(Trans, ip); }
          energy += w * e;
       }
+      else
+      {
+         MQ->Eval(M, Trans, ip);
+         energy += w * M.InnerProduct(pointflux, pointflux);
+      }
 
       if (d_energy)
       {
@@ -1130,7 +1107,7 @@ double DiffusionIntegrator::ComputeFluxEnergy
          {
             (*d_energy)[k] += w * vec[k] * vec[k];
          }
-         // TODO: Q, VQ, MQ
+         // TODO: Q, MQ
       }
    }
 

fem/bilininteg.hpp

@@ -1982,32 +1982,24 @@ private:
 
 public:
    /// Construct a diffusion integrator with coefficient Q = 1
-   DiffusionIntegrator(const IntegrationRule *ir = nullptr)
-      : BilinearFormIntegrator(ir),
-        Q(NULL), VQ(NULL), MQ(NULL), SMQ(NULL), maps(NULL), geom(NULL) { }
+   DiffusionIntegrator()
+      : Q(NULL), VQ(NULL), MQ(NULL), SMQ(NULL), maps(NULL), geom(NULL) { }
 
    /// Construct a diffusion integrator with a scalar coefficient q
-   DiffusionIntegrator(Coefficient &q, const IntegrationRule *ir = nullptr)
-      : BilinearFormIntegrator(ir),
-        Q(&q), VQ(NULL), MQ(NULL), SMQ(NULL), maps(NULL), geom(NULL) { }
+   DiffusionIntegrator(Coefficient &q)
+      : Q(&q), VQ(NULL), MQ(NULL), SMQ(NULL), maps(NULL), geom(NULL) { }
 
    /// Construct a diffusion integrator with a vector coefficient q
-   DiffusionIntegrator(VectorCoefficient &q,
-                       const IntegrationRule *ir = nullptr)
-      : BilinearFormIntegrator(ir),
-        Q(NULL), VQ(&q), MQ(NULL), SMQ(NULL), maps(NULL), geom(NULL) { }
+   DiffusionIntegrator(VectorCoefficient &q)
+      : Q(NULL), VQ(&q), MQ(NULL), SMQ(NULL), maps(NULL), geom(NULL) { }
 
    /// Construct a diffusion integrator with a matrix coefficient q
-   DiffusionIntegrator(MatrixCoefficient &q,
-                       const IntegrationRule *ir = nullptr)
-      : BilinearFormIntegrator(ir),
-        Q(NULL), VQ(NULL), MQ(&q), SMQ(NULL), maps(NULL), geom(NULL) { }
+   DiffusionIntegrator(MatrixCoefficient &q)
+      : Q(NULL), VQ(NULL), MQ(&q), SMQ(NULL), maps(NULL), geom(NULL) { }
 
    /// Construct a diffusion integrator with a symmetric matrix coefficient q
-   DiffusionIntegrator(SymmetricMatrixCoefficient &q,
-                       const IntegrationRule *ir = nullptr)
-      : BilinearFormIntegrator(ir),
-        Q(NULL), VQ(NULL), MQ(NULL), SMQ(&q), maps(NULL), geom(NULL) { }
+   DiffusionIntegrator(SymmetricMatrixCoefficient &q)
+      : Q(NULL), VQ(NULL), MQ(NULL), SMQ(&q), maps(NULL), geom(NULL) { }
 
    /** Given a particular Finite Element computes the element stiffness matrix
        elmat. */
@@ -2676,9 +2668,6 @@ public:
    VectorDiffusionIntegrator(Coefficient &q)
       : Q(&q) { }
 
-   VectorDiffusionIntegrator(Coefficient &q, const IntegrationRule *ir)
-      : BilinearFormIntegrator(ir), Q(&q) { }
-
    /** \brief Integrator with scalar coefficient for caller-specified vector
        dimension.
 
@@ -2938,11 +2927,10 @@ public:
 
     sum_e eta (r_e([u]), r_e([v]))
 
-    where r_e is the lifting operator defined on each edge e (potentially
-    weighted by a coefficient Q). The parameter eta can be chosen to be one to
-    obtain a stable discretization. The constructor for this integrator requires
-    the finite element space because the lifting operator depends on the
-    element-wise inverse mass matrix.
+    where r_e is the lifting operator defined on each edge e. The parameter eta
+    can be chosen to be one to obtain a stable discretization. The constructor
+    for this integrator requires the finite element space because the lifting
+    operator depends on the element-wise inverse mass matrix.
 
     BR2 stands for the second method of Bassi and Rebay:
 
@@ -2965,28 +2953,14 @@ protected:
    Array<int> ipiv;
    Array<int> ipiv_offsets, Minv_offsets;
 
-   Coefficient *Q;
-
    Vector shape1, shape2;
 
    DenseMatrix R11, R12, R21, R22;
    DenseMatrix MinvR11, MinvR12, MinvR21, MinvR22;
    DenseMatrix Re, MinvRe;
 
-   /// Precomputes the inverses (LU factorizations) of the local mass matrices.
-   /** @a fes must be a DG space, so the mass matrix is block diagonal, and its
-       inverse can be computed locally. This is required for the computation of
-       the lifting operators @a r_e.
-   */
-   void PrecomputeMassInverse(class FiniteElementSpace &fes);
-
 public:
-   DGDiffusionBR2Integrator(class FiniteElementSpace &fes, double e = 1.0);
-   DGDiffusionBR2Integrator(class FiniteElementSpace &fes, Coefficient &Q_,
-                            double e = 1.0);
-   MFEM_DEPRECATED DGDiffusionBR2Integrator(class FiniteElementSpace *fes,
-                                            double e = 1.0);
-
+   DGDiffusionBR2Integrator(class FiniteElementSpace *fes, double e = 1.0);
    using BilinearFormIntegrator::AssembleFaceMatrix;
    virtual void AssembleFaceMatrix(const FiniteElement &el1,
                                    const FiniteElement &el2,

fem/bilininteg_br2.cpp

@@ -16,39 +16,20 @@
 namespace mfem
 {
 
-DGDiffusionBR2Integrator::DGDiffusionBR2Integrator(
-   FiniteElementSpace &fes, double e) : eta(e), Q(NULL)
+DGDiffusionBR2Integrator::DGDiffusionBR2Integrator(FiniteElementSpace *fes,
+                                                   double e) : eta(e)
 {
-   PrecomputeMassInverse(fes);
-}
-
-DGDiffusionBR2Integrator::DGDiffusionBR2Integrator(
-   FiniteElementSpace &fes, Coefficient &Q_, double e) : eta(e), Q(&Q_)
-{
-   PrecomputeMassInverse(fes);
-}
-
-DGDiffusionBR2Integrator::DGDiffusionBR2Integrator(
-   FiniteElementSpace *fes, double e) : eta(e), Q(NULL)
-{
-   PrecomputeMassInverse(*fes);
-}
-
-void DGDiffusionBR2Integrator::PrecomputeMassInverse(FiniteElementSpace &fes)
-{
-   MFEM_VERIFY(fes.IsDGSpace(),
-               "The BR2 integrator is only defined for DG spaces.");
    // Precompute local mass matrix inverses needed for the lifting operators
    // First compute offsets and total size needed (e.g. for mixed meshes or
    // p-refinement)
-   int nel = fes.GetNE();
+   int nel = fes->GetNE();
    Minv_offsets.SetSize(nel+1);
    ipiv_offsets.SetSize(nel+1);
    ipiv_offsets[0] = 0;
    Minv_offsets[0] = 0;
    for (int i=0; i<nel; ++i)
    {
-      int dof = fes.GetFE(i)->GetDof();
+      int dof = fes->GetFE(i)->GetDof();
       ipiv_offsets[i+1] = ipiv_offsets[i] + dof;
       Minv_offsets[i+1] = Minv_offsets[i] + dof*dof;
    }
@@ -56,7 +37,7 @@ void DGDiffusionBR2Integrator::PrecomputeMassInverse(FiniteElementSpace &fes)
 #ifdef MFEM_USE_MPI
    // When running in parallel, we also need to compute the local mass matrices
    // of face neighbor elements
-   ParFiniteElementSpace *pfes = dynamic_cast<ParFiniteElementSpace *>(&fes);
+   ParFiniteElementSpace *pfes = dynamic_cast<ParFiniteElementSpace *>(fes);
    if (pfes != NULL)
    {
       ParMesh *pmesh = pfes->GetParMesh();
@@ -83,15 +64,15 @@ void DGDiffusionBR2Integrator::PrecomputeMassInverse(FiniteElementSpace &fes)
    {
       const FiniteElement *fe = NULL;
       ElementTransformation *tr = NULL;
-      if (i < fes.GetNE())
+      if (i < fes->GetNE())
       {
-         fe = fes.GetFE(i);
-         tr = fes.GetElementTransformation(i);
+         fe = fes->GetFE(i);
+         tr = fes->GetElementTransformation(i);
       }
       else
       {
 #ifdef MFEM_USE_MPI
-         int inbr = i - fes.GetNE();
+         int inbr = i - fes->GetNE();
          fe = pfes->GetFaceNbrFE(inbr);
          tr = pfes->GetParMesh()->GetFaceNbrElementTransformation(inbr);
 #endif
@@ -170,24 +151,21 @@ void DGDiffusionBR2Integrator::AssembleFaceMatrix(
    for (int p = 0; p < ir->GetNPoints(); p++)
    {
       const IntegrationPoint &ip = ir->IntPoint(p);
-      Trans.SetAllIntPoints(&ip);
+      IntegrationPoint eip1, eip2;
 
-      const IntegrationPoint &eip1 = Trans.Elem1->GetIntPoint();
+      Trans.Loc1.Transform(ip, eip1);
       el1.CalcShape(eip1, shape1);
-      double q = Q ? Q->Eval(*Trans.Elem1, eip1) : 1.0;
       if (ndof2)
       {
-         const IntegrationPoint &eip2 = Trans.Elem2->GetIntPoint();
+         Trans.Loc2.Transform(ip, eip2);
          el2.CalcShape(eip2, shape2);
-         // Set coefficient value q to the average of the values on either side
-         if (Q) { q = 0.5*(q + Q->Eval(*Trans.Elem2, eip2)); }
       }
-      // Take sqrt here because
-      //    eta (r_e([u]), r_e([v])) = (sqrt(eta) r_e([u]), sqrt(eta) r_e([v]))
-      double w = sqrt((factor + 1)*eta*q)*ip.weight*Trans.Face->Weight();
-      // r_e is defined by, (r_e([u]), tau) = <[u], {tau}>, so we pick up a
-      // factor of 0.5 on interior faces from the average term.
-      if (ndof2) { w *= 0.5; }
+
+      double w = factor*sqrt(eta)*ip.weight*Trans.Face->Weight();
+      if (ndof2)
+      {
+         w /= 2;
+      }
 
       for (int i = 0; i < ndof1; i++)
       {