Interior DoF for Cubic Quadrilateral Elements Fixed and currently implemented for Quadrant 1 Mesh

.appveyor.yml

@@ -26,24 +26,24 @@ install:
 - cd ..
 
 # Install hypre
-- ps: Start-FileDownload 'https://github.com/hypre-space/hypre/archive/V2-10-0b.tar.gz'
-- 7z x V2-10-0b.tar.gz -so | 7z x -si -ttar > nul
-- cd hypre-2-10-0b
-- cmake -H. -Bbuild -DHYPRE_USING_FEI=OFF -DMPI_C_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DMPI_C_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include"
+- ps: Start-FileDownload 'https://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz'
+- 7z x hypre-2.10.0b.tar.gz -so | 7z x -si -ttar > nul
+- cd hypre-2.10.0b
+- cmake -Hsrc -Bbuild -DMPI_C_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DMPI_C_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include"
+# - cmake -Hsrc -Bbuild -DCMAKE_BUILD_TYPE=Release -DMPI_C_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DMPI_C_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include"
 - cmake --build build
 - cmake --build build --target install
 - cd ..
 
 # MFEM
 before_build:
-- cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_parallel -DMFEM_USE_MPI=TRUE -DMFEM_USE_METIS_5=TRUE -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DHYPRE_LIBRARIES=%cd%\hypre-2-10-0b\hypre\lib\HYPRE.lib -DHYPRE_INCLUDE_DIRS=%cd%\hypre-2-10-0b\hypre\include -DHYPRE_VERSION=21000 -DMETIS_LIBRARIES=%cd%\metis-5.1.0\build\libmetis\Debug\metis.lib -DMETIS_INCLUDE_DIRS=%cd%\metis-5.1.0\include
-- cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_serial -DMFEM_USE_MPI=FALSE
+- cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_parallel -DMFEM_USE_MPI=TRUE -DMFEM_USE_METIS_5=TRUE -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DHYPRE_LIBRARIES=%cd%\hypre-2.10.0b\src\hypre\lib\HYPRE.lib -DHYPRE_INCLUDE_DIRS=%cd%\hypre-2.10.0b\src\hypre\include -DHYPRE_VERSION=21000 -DMETIS_LIBRARIES=%cd%\metis-5.1.0\build\libmetis\Debug\metis.lib -DMETIS_INCLUDE_DIRS=%cd%\metis-5.1.0\include
+- cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_serial -DMFEM_USE_MPI=FALSE -DMFEM_USE_METIS_5=TRUE -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DHYPRE_LIBRARIES=%cd%\hypre-2.10.0b\src\hypre\lib\HYPRE.lib -DHYPRE_INCLUDE_DIRS=%cd%\hypre-2.10.0b\src\hypre\include -DHYPRE_VERSION=21000 -DMETIS_LIBRARIES=%cd%\metis-5.1.0\build\libmetis\Debug\metis.lib -DMETIS_INCLUDE_DIRS=%cd%\metis-5.1.0\include
 
 build_script:
-- cmake --build build_parallel --config Release -j 4
-- cmake --build build_serial --config Release -j 4
-- cmake --build build_serial --target exec --config Release -j 4
+- cmake --build build_parallel
+- cmake --build build_serial
 
 after_build:
-- cd build_serial
-- ctest -C Release --output-on-failure
+# - cmake --build build_parallel --target check
+- cmake --build build_serial --target check

.gitignore

@@ -9,7 +9,6 @@
 # Object and library files
 *.o
 /libmfem.*
-/miniapps/common/libmfem-common.*
 
 # CMake generated files
 CMakeCache.txt
@@ -46,15 +45,12 @@ examples/ex[1-9]
 examples/ex[1-9]p
 examples/ex1[04-9]
 examples/ex1[0-9]p
-examples/ex2[0-9]
-examples/ex2[0-9]p
 
 examples/refined.mesh
 examples/displaced.mesh
 examples/mesh.*
 examples/ex5.mesh
 examples/Example5*
-examples/ParaView
 examples/Example9*
 examples/Example15*
 examples/Example16*
@@ -62,8 +58,6 @@ examples/sphere_refined.*
 examples/sol.*
 examples/sol_u.*
 examples/sol_p.*
-examples/sol_r.*
-examples/sol_i.*
 examples/ex9.mesh
 examples/ex9-mesh.*
 examples/ex9-init.*
@@ -72,10 +66,6 @@ examples/deformed.*
 examples/velocity.*
 examples/elastic_energy.*
 examples/mode_*
-examples/ex5-p-*.bp
-examples/ex9-p-*.bp
-examples/ex12-p-*.bp
-examples/ex16-p-*.bp
 examples/ex16.mesh
 examples/ex16-mesh.*
 examples/ex16-init.*
@@ -86,19 +76,6 @@ examples/vortex-?-init.*
 examples/vortex-?-final.*
 examples/deformation.*
 examples/pressure.*
-examples/ex20.dat
-examples/ex20p_?????.dat
-examples/gnuplot_ex20.inp
-examples/gnuplot_ex20p.inp
-examples/ex21*.mesh
-examples/ex21*.sol
-examples/ex21p_*.*
-examples/ex23-*.gf
-examples/ex23*.mesh
-examples/Example23*
-examples/ex25.mesh
-examples/ex25-*.gf
-examples/ex25p-*.*
 
 examples/sundials/ex9
 examples/sundials/ex1[06]
@@ -127,7 +104,6 @@ examples/petsc/sol.*
 examples/petsc/sol_p.*
 examples/petsc/sol_u.*
 examples/petsc/Example5*
-examples/petsc/ex9.mesh
 examples/petsc/ex9-mesh.*
 examples/petsc/ex9-init.*
 examples/petsc/ex9-final.*
@@ -139,11 +115,6 @@ examples/petsc/elastic_energy.*
 examples/pumi/ex1
 examples/pumi/ex[126]p
 
-examples/hiop/ex9.mesh
-examples/hiop/ex9-mesh.*
-examples/hiop/ex9-init.*
-examples/hiop/ex9-final.*
-
 examples/pumi/refined.mesh
 examples/pumi/sol.gf
 examples/pumi/mesh.*
@@ -162,24 +133,16 @@ miniapps/electromagnetics/Joule_*
 
 miniapps/meshing/mobius-strip
 miniapps/meshing/klein-bottle
-miniapps/meshing/toroid
-miniapps/meshing/twist
 miniapps/meshing/mesh-explorer
 miniapps/meshing/shaper
-miniapps/meshing/extruder
 miniapps/meshing/mesh-optimizer
 miniapps/meshing/pmesh-optimizer
-miniapps/meshing/minimal-surface
-miniapps/meshing/pminimal-surface
 
 miniapps/meshing/mobius-strip.mesh
 miniapps/meshing/klein-bottle.mesh
-miniapps/meshing/toroid-*.mesh
-miniapps/meshing/twist-*.mesh
 miniapps/meshing/mesh-explorer.mesh
 miniapps/meshing/partitioning.txt
 miniapps/meshing/shaper.mesh
-miniapps/meshing/extruder.mesh
 miniapps/meshing/optimized*
 miniapps/meshing/perturbed*
 
@@ -193,63 +156,12 @@ miniapps/performance/sol.*
 miniapps/tools/display-basis
 miniapps/tools/load-dc
 miniapps/tools/convert-dc
-miniapps/tools/lor-transfer
-miniapps/tools/get-values
 
-miniapps/toys/automata
-miniapps/toys/life
-miniapps/toys/mandel
-miniapps/toys/rubik
-miniapps/toys/snake
-miniapps/toys/lissajous
-miniapps/toys/mondrian
-
-miniapps/toys/snake-init.mesh
-miniapps/toys/snake-user.mesh
-miniapps/toys/snake-joined.mesh
-miniapps/toys/snake-c*.mesh
-miniapps/toys/automata.gf
-miniapps/toys/automata.mesh
-miniapps/toys/rubik-init.mesh
-miniapps/toys/mandel.mesh
-miniapps/toys/life.gf
-miniapps/toys/life.mesh
-miniapps/toys/lissajous.mesh
-miniapps/toys/lissajous.gf
-miniapps/toys/mondrian.mesh
-
-miniapps/nurbs/nurbs_ex1
-miniapps/nurbs/nurbs_ex1p
-miniapps/nurbs/nurbs_ex11p
+miniapps/nurbs/ex1
+miniapps/nurbs/ex1p
+miniapps/nurbs/ex11p
 miniapps/nurbs/refined.mesh
 miniapps/nurbs/mesh.*
 miniapps/nurbs/sol.*
 miniapps/nurbs/mode_*
 miniapps/nurbs/Example1*
-
-miniapps/gslib/field-diff
-miniapps/gslib/findpts
-miniapps/gslib/pfindpts
-
-miniapps/navier/navier_mms
-miniapps/navier/navier_kovasznay
-miniapps/navier/navier_tgv
-miniapps/navier/navier_shear
-miniapps/navier/navier_3dfoc
-miniapps/navier/tgv_out*.txt
-miniapps/navier/*_output
-
-# Unit test binary and outputs
-tests/unit/output_meshes
-tests/unit/unit_tests
-tests/unit/punit_tests
-tests/unit/sedov_tests_*
-tests/unit/psedov_tests_*
-
-# Test script output
-tests/scripts/*.err
-tests/scripts/*.out
-tests/scripts/*.msg
-
-# VPATH builds
-build-*/*

.gitlab-ci.yml

@@ -1,292 +0,0 @@
-# Copyright (c) 2010-2020, 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.
-
-# General GitLab pipelines configurations for supercomputers and Linux clusters
-# 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
-#
-# BUILD_PATH:
-# In BUILD_ROOT, we want to separate builds depending on the machine used,
-# typically because we build on a set of dependencies per machine.
-#
-# 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: ${CI_BUILDS_DIR}/${CI_PROJECT_NAME}_${CI_COMMIT_REF_SLUG}_${CI_PIPELINE_ID}
-  BUILD_PATH: ${CI_BUILDS_DIR}/${CI_PROJECT_NAME}_${CI_COMMIT_REF_SLUG}_${CI_PIPELINE_ID}/${PLAT}/${TOOLCHAIN}
-  REBASELINE: "NO"
-  MFEM_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
-  ARTIFACTS_DIR: artifacts
-
-# The pipeline is divided into stages. Usually, these are also synchronization
-# points, however, we use "needs" keyword to express the DAG of jobs for more
-# efficiency.
-# - We use setup phase to download content outside of mfem directory.
-# - Allocate is where quartz resources are allocated once for all.
-# - Libs is where dependencies are built.
-# - Build is where we build MFEM for multiple toolchains.
-# - Test is where we perform a first set of tests on MFEM build.
-# - Baseline_checks gathers baseline-type test suites execution
-# - Baseline_publish, only available on master, allows to update baseline
-#   results
-# - Deallocate releases quartz resources
-stages:
-  - setup
-  - allocate
-  - libs
-  - build
-  - test
-  - deallocate
-  - baseline_check
-  - baseline_publish
-
-# The setup job in setup stage don’t rely on MFEM git repo. It prepares a
-# pipeline-wide working directory downloading/updating external repos.
-# TODO: updating tests and tpls is not necessary anymore since pipelines are
-# now using unique directories so repo are never shared with another pipeline.
-# This is not memory efficient (we keep a lot of data), hence this reminder.
-.setup:
-  stage: setup
-  variables:
-    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 ${TESTS_REPO}; fi
-    - cd tpls && git pull && cd ..
-    - cd tests && git pull && cd ..
-
-# Share configurations (templates) for toolchain configuration.
-# Note: Any job using this template shouldn't redefine "before_script" key.
-.with_gcc_6_1_0:
-  variables:
-    TOOLCHAIN: gcc_6_1_0
-    CXX: g++
-    CC: gcc
-  before_script:
-    - module load gcc/6.1.0
-
-.with_gcc_4_9_3:
-  variables:
-    TOOLCHAIN: gcc_4_9_3
-    CXX: g++
-    CC: gcc
-  before_script:
-    - module load gcc/4.9.3
-
-.if_srun_alloc_for_make: &if_srun_alloc_for_make |
-  if [[ "${MPIEXEC}" == "srun" ]]
-  then
-    export JOB_ID=$(squeue -h --name=${MFEM_ALLOC_NAME} --format=%A)
-    [[ -n "JOB_ID" ]] && export JOB_ID="--jobid=${JOB_ID}"
-    RESOURCES="--extra-node-info=1:${MAKE_PAR}:1 --cpus-per-task=${MAKE_PAR} --ntasks=1"
-    # Allocation prefix:
-    export EXEC_PREFIX="srun ${JOB_ID} ${RESOURCES}"
-  fi
-
-# Build of dependencies and mfem:
-# if on quartz, uses a part of preallocated resources
-# Note: Those jobs don't rely on MFEM repository, hence the use of
-# "GIT_STRATEGY: none" preventing its clone.
-.build_hypre:
-  variables:
-    EXEC_PREFIX: ""
-    GIT_STRATEGY: none
-  stage: libs
-  script:
-    - cd ${BUILD_ROOT}/tpls
-    - mkdir -p ${BUILD_PATH}
-    - make clean
-    - *if_srun_alloc_for_make
-    - ${EXEC_PREFIX} make -j ${MAKE_PAR} hypre PREFIX=${BUILD_PATH}/hypre/src/ BUILD_DIR=${BUILD_PATH} LOG_DIR=${BUILD_PATH}
-
-.build_metis:
-  variables:
-    EXEC_PREFIX: ""
-    GIT_STRATEGY: none
-  stage: libs
-  script:
-    - cd ${BUILD_ROOT}/tpls
-    - mkdir -p ${BUILD_PATH}
-    - *if_srun_alloc_for_make
-    - ${EXEC_PREFIX} make -j ${MAKE_PAR} ${METIS} PREFIX=${BUILD_PATH}/ BUILD_DIR=${BUILD_PATH} LOG_DIR=${BUILD_PATH} CC=${CC} CXX=${CXX}
-
-# Building MFEM
-.build_mfem:
-  variables:
-    EXEC_PREFIX: ""
-  stage: build
-  script:
-    - mkdir -p ${BUILD_PATH}
-    - cp -r ${CI_PROJECT_DIR} ${BUILD_PATH}/${CI_PROJECT_NAME}_${MFEM_USE_MPI}_${MFEM_DEBUG}
-    - cd ${BUILD_PATH}/${CI_PROJECT_NAME}_${MFEM_USE_MPI}_${MFEM_DEBUG}
-    - *if_srun_alloc_for_make
-    - make config CXX=${CXX} MPICXX=mpicxx MFEM_USE_MPI=${MFEM_USE_MPI} MFEM_DEBUG=${MFEM_DEBUG} MFEM_MPIEXEC="${EXEC_PREFIX}" MFEM_MPIEXEC_NP=${MPIEXEC_NP}
-    - ${EXEC_PREFIX} make -j ${MAKE_PAR} all
-
-# TODO: Could this phase use a parallel run?
-.sanitycheck_mfem:
-  stage: test
-  variables:
-    GIT_STRATEGY: none
-  script:
-    - cd ${BUILD_PATH}/${CI_PROJECT_NAME}_${MFEM_USE_MPI}_${MFEM_DEBUG}
-    - make 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_out=${BASELINE_TEST}.out
-  _glob_err=${BASELINE_TEST}.err
-  _base_diff=${BASELINE_TEST}-${SYS_TYPE}.diff
-  _base_patch=${BASELINE_TEST}-${SYS_TYPE}.patch
-  _base_out=${BASELINE_TEST}-${SYS_TYPE}.out
-
-  _out=${BASELINE_TEST}-${SYS_TYPE}.out
-  _ref=../${BASELINE_TEST}-${SYS_TYPE}.saved
-  _out_txt=${BASELINE_TEST}.txt
-  _diff=${BASELINE_TEST}-diff.txt
-  # prepare
-  cd ${BUILD_ROOT}
-  ln -snf ${CI_PROJECT_DIR} mfem
-  cd tests
-  mkdir _${BASELINE_TEST} && cd _${BASELINE_TEST}
-  # run
-  salloc --nodes=1 -p pdebug ../runtest ../../mfem "${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}.txt
-    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}.txt
-  elif [[ -f ${_base_out} ]]
-  then
-    echo "${BASELINE_TEST}: Differences found, replacement file generated"
-    cp ${_base_out} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_out}.txt
-  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}.txt
-  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:
-    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:
-      - ${ARTIFACTS_DIR}
-  allow_failure: true
-
-# This job can only be manually triggers on a pipeline for master branch, or if
-# the pipeline was triggered with REBASELINE="YES"
-.rebaseline_mfem:
-  stage: baseline_publish
-  rules:
-    - if: '$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}.txt" ]]
-      then
-          echo "Nothing to be done: no relevant change in baseline"
-          exit 0
-      elif [[ -f "${PATCH_FILE}.txt" ]]
-      then
-          mv ${PATCH_FILE}.txt ${PATCH_FILE}
-          patch "./baseline-${SYS_TYPE}.saved" < "${PATCH_FILE}"
-      elif [[ -f "${FULL_FILE}.txt" ]]
-      then
-          cp "${FULL_FILE}.txt" "./baseline-${SYS_TYPE}.saved"
-      else
-          echo "File missing: expected ${PATCH_FILE}.txt or ${FULL_FILE}.txt"
-          exit 1
-      fi
-    - git add baseline-${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

.gitlab/quartz.yml

@@ -1,149 +0,0 @@
-# Copyright (c) 2010-2020, 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
-  variables:
-    PLAT: quartz
-    MPIEXEC: srun
-    MPIEXEC_NP: "-n"
-    MAKE_PAR: 6
-    BASELINE_PAR: 18
-
-# Setup
-setup_quartz:
-  extends: [.setup, .on_quartz]
-
-# Allocate
-allocate_quartz:
-  variables:
-    GIT_STRATEGY: none
-  extends: .on_quartz
-  stage: allocate
-  script:
-    - |
-      if [[ "${MPIEXEC}" == "srun" ]]
-      then
-      salloc --nodes=1 --extra-node-info=2:18:1 --partition=pdebug --time=30 --no-shell --job-name=${MFEM_ALLOC_NAME}
-      fi
-  timeout: 6h
-
-# Release
-deallocate_quartz:
-  variables:
-    GIT_STRATEGY: none
-  extends: .on_quartz
-  stage: deallocate
-  script:
-    - |
-      if [[ "${MPIEXEC}" == "srun" ]]
-      then
-      export JOB_ID=$(squeue -h --name=${MFEM_ALLOC_NAME} --format=%A)
-      ([[ -n "${JOB_ID}" ]] && scancel ${JOB_ID})
-      fi
-  when: always
-
-# Build external libraries (tpls)
-build_hypre_gcc_6_1_0_quartz:
-  extends: [.build_hypre, .with_gcc_6_1_0, .on_quartz]
-
-build_parmetis_gcc_6_1_0_quartz:
-  extends: [.build_metis, .with_gcc_6_1_0, .on_quartz]
-  variables:
-    METIS: parmetis
-
-build_metis4_gcc_6_1_0_quartz:
-  extends: [.build_metis, .with_gcc_6_1_0, .on_quartz]
-  variables:
-    METIS: metis4
-
-build_metis5_gcc_6_1_0_quartz:
-  extends: [.build_metis, .with_gcc_6_1_0, .on_quartz]
-  variables:
-    METIS: metis5
-  allow_failure: true
-
-# Build MFEM
-build_mfem_debug_ser_gcc_4_9_3_quartz:
-  extends: [.build_mfem, .with_gcc_4_9_3, .on_quartz]
-  variables:
-    MFEM_DEBUG: "YES"
-    MFEM_USE_MPI: "NO"
-
-build_mfem_debug_ser_gcc_6_1_0_quartz:
-  extends: [.build_mfem, .with_gcc_6_1_0, .on_quartz]
-  variables:
-    MFEM_DEBUG: "YES"
-    MFEM_USE_MPI: "NO"
-
-build_mfem_debug_par_gcc_6_1_0_quartz:
-  extends: [.build_mfem, .with_gcc_6_1_0, .on_quartz]
-  variables:
-    MFEM_DEBUG: "YES"
-    MFEM_USE_MPI: "YES"
-  needs: [build_hypre_gcc_6_1_0_quartz, build_parmetis_gcc_6_1_0_quartz]
-
-build_mfem_opt_ser_gcc_6_1_0_quartz:
-  extends: [.build_mfem, .with_gcc_6_1_0, .on_quartz]
-  variables:
-    MFEM_DEBUG: "NO"
-    MFEM_USE_MPI: "NO"
-
-build_mfem_opt_par_gcc_6_1_0_quartz:
-  extends: [.build_mfem, .with_gcc_6_1_0, .on_quartz]
-  variables:
-    MFEM_DEBUG: "NO"
-    MFEM_USE_MPI: "YES"
-  needs: [build_hypre_gcc_6_1_0_quartz, build_parmetis_gcc_6_1_0_quartz]
-
-### Tests
-
-# Sanity check
-sanitycheck_mfem_debug_ser_gcc_4_9_3_quartz:
-  extends: [.sanitycheck_mfem, .with_gcc_4_9_3, .on_quartz]
-  variables:
-    MFEM_DEBUG: "YES"
-    MFEM_USE_MPI: "NO"
-  needs: [build_mfem_debug_ser_gcc_4_9_3_quartz, allocate_quartz]
-
-sanitycheck_mfem_debug_ser_gcc_6_1_0_quartz:
-  extends: [.sanitycheck_mfem, .with_gcc_6_1_0, .on_quartz]
-  variables:
-    MFEM_DEBUG: "YES"
-    MFEM_USE_MPI: "NO"
-  needs: [build_mfem_debug_ser_gcc_6_1_0_quartz, allocate_quartz]
-
-sanitycheck_opt_ser_mfem_gcc_6_1_0_quartz:
-  extends: [.sanitycheck_mfem, .with_gcc_6_1_0, .on_quartz]
-  variables:
-    MFEM_DEBUG: "NO"
-    MFEM_USE_MPI: "NO"
-  needs: [build_mfem_opt_ser_gcc_6_1_0_quartz, allocate_quartz]
-
-sanitycheck_opt_par_mfem_gcc_6_1_0_quartz:
-  extends: [.sanitycheck_mfem, .with_gcc_6_1_0, .on_quartz]
-  variables:
-    MFEM_DEBUG: "NO"
-    MFEM_USE_MPI: "YES"
-  needs: [build_mfem_opt_par_gcc_6_1_0_quartz, allocate_quartz]
-
-# Baseline
-baselinecheck_mfem_intel_quartz:
-  extends: [.baselinecheck_mfem, .on_quartz]
-  needs: [allocate_quartz]
-
-baselinepublish_mfem_quartz:
-  extends: [.rebaseline_mfem, .on_quartz]
-  needs: [baselinecheck_mfem_intel_quartz]

.travis.yml

@@ -1,125 +1,28 @@
-# Copyright (c) 2010-2020, 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.
+sudo: false
 
 language: cpp
 
-sudo: false
-
-stages:
-  - checks
-  - tests
-  - optional
-
-jobs:
+matrix:
   include:
-
-    # ========================
-    #         Checks
-    # ========================
-    # - code-style
-    # - documentation
-    # - gitignore
-
-    - stage: checks
-      os: linux
-      name: "code-style"
-      addons:
-        apt:
-          packages:
-            - astyle=2.05.1-0ubuntu1
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - cd tests/scripts
-        - ./runtest code-style
-
-    - stage: checks
-      os: linux
-      name: "documentation"
-      addons:
-        apt:
-          packages:
-            - doxygen
-            - graphviz
-            - mpich
-            - libmpich-dev
-      env: MPI=YES
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - cd tests/scripts
-        - ./runtest documentation
-
-    - stage: checks
-      os: linux
-      name: "gitignore"
-      addons:
-        apt:
-          packages:
-            - mpich
-            - libmpich-dev
-      env: MPI=YES
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - make config MFEM_USE_MPI=YES MFEM_MPI_NP=2
-        - make all -j3
-        - make test-noclean
-        - cd tests/scripts
-        - ./runtest gitignore
-
-    # ========================
-    #  Optional Checks/Tests
-    # ========================
-    # - branch-history
-
-    - stage: optional
-      name: "branch-history"
-      # need full git history for the binary/big files check
-      git:
-        depth: false
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        # update master
-        - git fetch origin master:master
-        # checkout a branch (otherwise Travis works in detached head)
-        - git checkout -b travis_tests
-        - cd tests/scripts
-        - ./runtest branch-history
-
-    # ========================
-    #       Linux tests
-    # ========================
-    # - serial + debug
-    # - serial
-    # - parallel + debug
-    # - parallel
-
-    - stage: tests
-      os: linux
+    #
+    # Linux
+    #
+    - os: linux
       compiler: gcc
-      name: "Linux: Serial + Debug"
       env: DEBUG=YES
            MPI=NO
            CODECOV=NO
            MFEM_TEST_TARGET=check
-
+    #
     - os: linux
       compiler: gcc
-      name: "Linux: Serial"
       env: DEBUG=NO
            MPI=NO
            CODECOV=NO
            MFEM_TEST_TARGET=test
-
+    #
     - os: linux
       compiler: gcc
-      name: "Linux: Parallel + Debug"
       addons:
         apt:
           # sources:
@@ -145,12 +48,10 @@ jobs:
           - $TRAVIS_BUILD_DIR/../metis-4.0
       before_cache:
         - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
-
+          mv libmetis.a ..; rm -rf *; mv ../libmetis.a .
+    #
     - os: linux
       compiler: gcc
-      name: "Linux: Parallel"
       addons:
         apt:
           # sources:
@@ -176,71 +77,29 @@ jobs:
           - $TRAVIS_BUILD_DIR/../metis-4.0
       before_cache:
         - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
-
-    - os: linux
-      compiler: gcc
-      name: "Linux: Parallel (cmake)"
-      addons:
-        apt:
-          packages:
-            - mpich
-            - libmpich-dev
-      env: MPI=YES
-           NPROCS=2
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - mkdir ${TRAVIS_BUILD_DIR}/build
-        - cd ${TRAVIS_BUILD_DIR}/build
-        - cmake ..
-             -DMFEM_USE_MPI=ON
-             -DHYPRE_DIR=${TRAVIS_BUILD_DIR}/../hypre-2.10.0b/src/hypre
-             -DMFEM_MPI_NP=$NPROCS
-        - make -j3 mfem examples
-        - cd ${TRAVIS_BUILD_DIR}/build/tests/unit
-        - make -j3
-        - ctest --output-on-failure
-      cache:
-        directories:
-          - $TRAVIS_BUILD_DIR/../hypre-2.10.0b/src/hypre/lib
-          - $TRAVIS_BUILD_DIR/../hypre-2.10.0b/src/hypre/include
-          - $TRAVIS_BUILD_DIR/../metis-4.0
-      before_cache:
-        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
-
-    # ========================
-    #      Mac OS X tests
-    # ========================
-    # - serial + debug
-    # - serial
-    # - parallel + debug
-    # - parallel
-
+          mv libmetis.a ..; rm -rf *; mv ../libmetis.a .
+    #
+    # Mac OS X
+    #
     - os: osx
       # osx_image: xcode7.3
       compiler: clang
-      name: "Mac: Serial + Debug"
       env: DEBUG=YES
            MPI=NO
            CODECOV=NO
            MFEM_TEST_TARGET=check
-
+    #
     - os: osx
       # osx_image: xcode7.3
       compiler: clang
-      name: "Mac: Serial"
       env: DEBUG=NO
            MPI=NO
            CODECOV=NO
            MFEM_TEST_TARGET=test
-
+    #
     - os: osx
       # osx_image: xcode7.3
       compiler: clang
-      name: "Mac: Parallel + Debug"
       env: DEBUG=YES
            MPI=YES
            CODECOV=NO
@@ -255,13 +114,11 @@ jobs:
           - $HOME/local-cached
       before_cache:
         - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
-
+          mv libmetis.a ..; rm -rf *; mv ../libmetis.a .
+    #
     - os: osx
       # osx_image: xcode7.3
       compiler: clang
-      name: "Mac: Parallel"
       env: DEBUG=NO
            MPI=YES
            CODECOV=YES
@@ -276,8 +133,8 @@ jobs:
           - $HOME/local-cached
       before_cache:
         - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
-          rm -f Lib/*.{c,o}
+          mv libmetis.a ..; rm -rf *; mv ../libmetis.a .
+
 
 before_install:
    # No addon for brew yet, have to install OSX packages this way.
@@ -348,7 +205,6 @@ install:
         else
             echo "Reusing cached hypre-2.10.0b/";
         fi;
-        ln -s hypre-2.10.0b hypre;
      else
         echo "Serial build, not using hypre";
      fi

CHANGELOG

@@ -8,500 +8,17 @@
                                http://mfem.org
 
 
-Version 4.1.1 (development)
+Version 3.4.1 (development)
 ===========================
-
-Meshing improvements
---------------------
-- The graph linear ordering library Gecko, previously an external dependency, is
-  now included directly in MFEM. As a result, Mesh::GetGeckoElementOrdering is
-  always available. The interface has also been improved, see for example the
-  mesh-explorer miniapp.
-
-- Added support for finite difference-based gradient and Hessian approximation
-  in the TMOP mesh optimization algorithms. This improves the accuracy of the
-  Hessian for r-adaptivity using discrete fields, and allows use of skewness
-  and orientation based metrics.
-
-Improved GPU capabilities
--------------------------
-- Added support for Chebyshev accelerated polynomial smoother on GPU.
-
-Discretization improvements
----------------------------
-- Added support for matrix-free interpolation and restriction operators between
-  continuous H1 finite element spaces of different order on the same mesh or
-  with the same order on uniformly refined meshes.
-
-- Added support for simplices in GSLIB-FindPoints.
-
-Linear and nonlinear solvers
-----------------------------
-- Added power method to iteratively estimate the largest eigenvalue and the
-  corresponding eigenvector of an operator.
-
-- Added initial support for h- and p-multigrid solvers and preconditioners for
-  matrix-based and matrix-free discretizations with basic GPU capability.
-
-New and updated examples and miniapps
--------------------------------------
-- Added a new example, Example 25/25p, to demonstrate the use of a Perfectly
-  Matched Layer (PML) for the simulation of electromagnetic wave propagation.
-  The example defines and solves several indefinite Maxwell problems.
-
-- Added a new Example 26/26p to demonstrate the construction of a matrix-free
-  geometric and p-multigrid preconditioner for the Laplace problem.
-
-- Added a new example, Example 27/27p, to demonstrate the enforcement of
-  various boundary conditions with the Laplace operator.  The example shows the
-  procedures for applying Dirichlet, Neumann (both homogeneous and
-  inhomogeneous), Robin, and periodic boundary conditions with either H1 or DG
-  discretizations.
-
-- Added a simple meshing miniapp, Twist, which demonstrates MFEM's strategy of
-  stitching together opposite surfaces of a mesh to create a topologically
-  periodic mesh.
-
-- Added a new meshing miniapp, Minimal Surface, which solves Plateau's problem:
-  the Dirichlet problem for the minimal surface equation.
-
-Improved testing
-----------------
-- Added a GitLab pipeline that automates PR testing on supercomputing systems
-  and Linux clusters at Lawrence Livermore National Lab (LLNL). This can be
-  triggered only by LLNL developers, see .gitlab-ci.yml, the .gitlab directory
-  and the updated CONTRIBUTING.md file.
-
-Miscellaneous
--------------
-- In SLISolver, changed the residual inner product from (Br,r) to (Br,Br) so the
-  solver can work with non-SPD preconditioner B.
-
-- Added support for ADIOS2 for parallel I/O with ParaView visualization. The
-  classes adios2stream and ADIOS2DataCollection are introduced in mfem as the
-  interfaces to generate ADIOS2 Binary Pack (BP4) directory datasets for the
-  entire spatial and temporal data. In addition, ADIOS2 allows for setting a
-  user-defined number of data substreams/subfiles. See examples 5, 9, 12, 16.
-
-
-Version 4.1, released on March 10, 2020
-=======================================
-
-Starting with this version, the MFEM open source license is changed to BSD-3.
-
-Improved GPU capabilities
--------------------------
-- Added initial support for AMD GPUs based on HIP: a C++ runtime API and kernel
-  language that can run on both AMD and NVIDIA hardware.
-
-- Added support for Umpire, a resource management library that allows the
-  discovery, provision, and management of memory on machines with multiple
-  memory devices like NUMA and GPUs, see https://github.com/LLNL/Umpire.
-
-- GPU acceleration is now available in 3 additional examples: 3, 9 and 24.
-
-- Improved RAJA backend and multi-GPU MPI communications.
-
-- Added a "debug" device designed specifically to aid in debugging GPU code by
-  following the "device" code path (using separate host/device memory spaces and
-  host <-> device transfers) without any GPU hardware.
-
-- Added support for matrix-free diagonal smoothers on GPUs.
-
-- The current list of available device backends is: "ceed-cuda", "occa-cuda",
-  "raja-cuda", "cuda", "hip", "debug", "occa-omp", "raja-omp", "omp",
-  "ceed-cpu", "occa-cpu", "raja-cpu", and "cpu".
-
-- The MFEM memory manager now supports different memory types, associated with
-  the following memory backends:
-  * Default host memory, using standard C++ new and delete,
-  * CUDA pointers, using cudaMalloc and HIP pointers, using hipMalloc,
-  * Managed CUDA/HIP memory (UVM), using cudaMallocManaged/hipMallocManaged,
-  * Umpire-managed memory, including memory pools,
-  * 32- or 64-byte aligned memory, using posix_memalign (WIN32 also supported),
-  * Debug memory with mmap/mprotect protection used by the new "debug" device.
-
-libCEED support
----------------
-- Added support for libCEED, the portable library for high-order operator
-  evaluation developed by the Center for Efficient Exascale Discretizations in
-  the Exascale Computing Project, https://github.com/CEED/libCEED.
-
-- This initial integration includes Mass and Diffusion integrators. libCEED GPU
-  backends can be used without specific MFEM configuration, however it is highly
-  recommended to use the "cuda" build option to minimize memory transfers.
-
-- Both CPU and GPU modes are available as MFEM device backends (ceed-cpu and
-  ceed-cuda), using some of the best performing CPU and GPU backends from
-  libCEED, see the sample runs in examples 1 and 6.
-
-- NOTE: The current default libCEED GPU backend (ceed-cuda) uses atomics and
-  therefore is non-deterministic.
-
-Partial assembly and matrix-free discretizations
-------------------------------------------------
-- The support for matrix-free methods on both CPU and GPU devices based on a
-  partially assembled operator decomposition was extended to include:
-  * DG integrators, (for now only in the Gauss-Lobatto basis), see Example 9,
-  * H(curl) bilinear forms, see Example 3,
-  * vector mass and vector diffusion bilinear integrators,
-  * convection integrator with improved performance,
-  * gradient and vector divergence integrators for Stokes problems,
-  * initial partial assembly mode for NonlinearForms.
-
-- Diagonals of partially assembled operators can now be computed efficiently.
-  See the new methods AssembleDiagonal in BilinearForm, AssembleDiagonalPA in
-  BilinearFormIntegrator and the implementations in fem/bilininteg_*.cpp.
-
-- In many examples, the partial assembly algorithms provide significantly
-  improved performance, particularly in high-order 3D runs on GPUs.
-
-Meshing improvements
---------------------
-- The algorithms for mesh element numbering were changed to have significantly
-  better caching and parallel partitioning properties. Both initial (see e.g.
-  Mesh::GetHilbertElementOrdering) and ordering after uniform refinement were
-  improved. NOTE: new ordering can have a round-off effect on solver results.
-
-- Added support for non-conforming AMR on both prisms and tetrahedra, including
-  coarsening and parallel load balancing. Anisotropic prism refinement is only
-  available in the serial version at the moment.
-
-- The TMOP mesh optimization algorithms were extended to support r-adaptivity.
-  Target matrices can now be constructed either via a given analytical function
-  (e.g. spatial dependence of size, aspect ratio, etc., for each element) or via
-  a (Par)GridFunction specified on the original mesh.
-
-- The TMOP algorithms were also improved to support non-conforming AMR meshes.
-
-- Added support for creating refined versions of periodic meshes, making use of
-  the new L2ElementRestriction class. This class also allows for computing
-  geometric factors on periodic meshes using partial assembly.
-
-Discretization improvements
----------------------------
-- Added support for GSLIB-FindPoints, a general high-order interpolation utility
-  that can robustly evaluate a GridFunction in an arbitrary collection of points
-  in physical space. See INSTALL for details on building MFEM with GSLIB, and
-  miniapps/gslib for examples of how to use this feature.
-
-- Added support for complex-valued finite element operators and fields using a
-  2x2 block structured linear system to mimic complex arithmetic. New classes
-  include: ComplexGridFunction, SesquilinearForm, ComplexLinearForm, and their
-  parallel counterparts.
-
-- Added second order derivatives of NURBS shape functions.
-
-- Added support for serendipity elements of arbitrary order on affinely-mapped
-  square elements. Basis functions for these elements can be visualized using
-  an option in the display-basis miniapp.
-
-- Two integrators related to Stokes problems, (Q grad u, v) and (Q div v, u),
-  where u and the components of v are in H1, were added/modified to support full
-  and partial assembly modes. See the new GradientIntegrator and the updated
-  VectorDivergenceIntegrator classes in fem/bilininteg.hpp, as well as the PA
-  kernels in fem/bilininteg_gradient.cpp and fem/bilininteg_divergence.cpp.
-
-- Added a nonlinear vector valued convection integrator (Q u \cdot grad u, v)
-  where u_i and v_i are in H1. This form occurs e.g. in the Navier-Stokes
-  equations. The integrator supports the partial assembly mode for its
-  action. In full assembly mode we also provide the GetGradient method that
-  computes the linearized version of the integrator.
-
-- Added a new method, MixedBilinearForm::FormRectangularLinearSystem, that can
-  be used to impose boundary conditions on the non-square off-diagonal blocks of
-  a block operator (similar to FormLinearSystem in the square case).
-
-Linear and nonlinear solvers
-----------------------------
-- Added support for Ginkgo, a high-performance linear algebra library for GPU
-  and manycore nodes, with a focus on sparse solution of linear systems. For
-  more details see linalg/ginkgo.hpp and the example code in examples/gingko.
-
-- Added support for HiOp, a lightweight HPC solver for nonlinear optimization
-  problems, see class HiOpNLPOptimizer and the example codes in examples/hiop.
-
-- Added a general interface for specifying and solving nonlinear constrained
-  optimization problems through the new classes OptimizationProblem and
-  OptimizationSolver, see linalg/solver.hpp.
-
-- Added a block ILU(0) preconditioner for DG-type discretizations. Example 9
-  (DG advection) now takes advantage of this for implicit time integration.
-
-- New time integrators: Adams-Bashforth, Adams-Moulton and several integrators
-  for 2nd order ODEs, see the new Example 23.
-
-- Added a LinearSolve(A,X) convenience method to solve dense linear systems. In
-  the trivial cases, i.e., square matrices of size 1 or 2, the system is solved
-  directly, otherwise, LU factorization is employed.
-
-New and updated examples and miniapps
--------------------------------------
-- Added a collection of 7 playful miniapps in miniapps/toys that illustrate the
-  meshing and visualization features of the library in more relaxed settings.
-  The toys include simulations of cellular automata, Rubik's cube, Mandelbrot
-  set, a tool to convert any image to mfem mesh, and more.
-
-- Added 8 new example codes:
-  * Example 22/22p demonstrates the use of the new complex-valued finite element
-    operators by defining and solving a family of time-harmonic PDEs related to
-    damped harmonic oscillators.
-  * Example 23 solves a simple 2D/3D wave equation with the new second order
-    time integrators.
-  * Example 24/24p demonstrates usage of mixed finite element spaces in bilinear
-    forms. Partial assembly is supported in this example.
-  * A version of Example 1 in examples/ginkgo demonstrating the use of the
-    Gingko interface to solve a linear system.
-  * A version of Example 9/9p in examples/hiop demonstrating the nonlinear
-    constrained optimization interface and use of the SLBQP and HiOp solvers.
-
-- Added two new miniapps: Find Points and Field Diff in miniapps/gslib that show
-  how GSLIB-FindPoints can be used to interpolate a (Par) GridFunction in an
-  arbitrary number of physical space points in 2D and 3D. The GridFunction must
-  be in H1 and in the same space as the mesh that is used to find the points.
-
-- Added a simple miniapp, Get Values, that extracts field values at a set of
-  points, from previously saved data via DataCollection classes.
-
-- Several examples and miniapps were updated:
-  * Added device support in Example 3/3p and Example 9/9p.
-  * Example 1/1p and Example 3/3p now use diagonal preconditioning in partial
-    assembly mode.
-  * Example 9/9p now supports implicit time integration, using the new block
-    ILU(0) solvers as preconditioners for the linear system.
-  * The mesh-optimizer and pmesh-optimizer miniapps now include the new
-    r-adaptivity capabilities of TMOP. They were also updated to support mesh
-    optimization on non-conforming AMR meshes.
-  * New options to reorder and partition the mesh and boundary attribute
-    visualization (key 'b') are now available in the mesh-explorer miniapp.
-
-- Collected object files from the miniapps/common directory into a new library,
-  libmfem-common for the convenience of application developers. The new library
-  is now used in several miniapps in the electromagnetic and tools directories.
-
-Improved testing
-----------------
-- Added a large number of unit tests in the tests/unit directory, including
-  several parallel unit tests.
-
-- Added a new directory, tests/scripts, with several shell scripts that perform
-  simple checks on the code including: code styling, documentation formatting,
-  proper use of .gitignore, and preventing the accidental commit of large files.
-
-- It is recommended that developers run the above tests scripts (via the runtest
-  script) before pushing to GitHub. See the README file in tests/scripts.
-
-- The Travis CI settings have been updated to include an initial Checks stage
-  which currently runs the code-style, documentation and gitignore test scripts,
-  as well as a final stage for optional checks/tests which currently runs the
-  branch-history script.
-
-Miscellaneous
--------------
-- Added support for output in the ParaView XML format. Both low-order and
-  high-order Lagrange elements are supported. Output can be in ASCII or binary
-  format. The binary output can be compressed if MFEM is compiled with zlib
-  support (MFEM_USE_ZLIB). See the new ParaViewDataCollection class and the
-  updated Examples 5/5p and 9/9p.
-
-- Upgraded the SUNDIALS interface to utilize SUNDIALS 5.0. This necessitated a
-  complete rework of the interface and requires changes at the application
-  level. Example usage of the new interface can be found in examples/sundials.
-
-- Switched from gzstream to zstr for the implementation of zlib-compressed C++
-  output stream. The build system definition now uses MFEM_USE_ZLIB instead of
-  MFEM_USE_GZSTREAM, but the code interface (e.g. ofgzstream) remains the same.
-
-- Various other simplifications, extensions, and bugfixes in the code.
-
-API changes
------------
-- In the enum classes MemoryType and MemoryClass, "CUDA" was renamed to "DEVICE"
-  which now denotes either "CUDA" or "HIP" depending on the build configuration.
-  In the same enum classes, "CUDA_UVM" was renamed to "MANAGED".
-
-
-Version 4.0, released on May 24, 2019
-=====================================
-
-Unlike previous MFEM releases, this version requires a C++11 compiler.
-
-GPU support
------------
-- Added initial support for hardware devices, such as GPUs, and programming
-  models, such as CUDA, OCCA, RAJA and OpenMP.
-
-- The GPU/device support is based on MFEM's new backends and kernels working
-  seamlessly with a new lightweight device/host memory manager. The kernels can
-  be implemented either in OCCA, or as a simple wrapper around for-loops, which
-  can then be dispatched to RAJA and native backends. See the files forall.hpp
-  and mem_manager.hpp in the general/ directory for more details.
-
-- Several of the MFEM example codes (ex1, ex1p, ex6, and ex6p) can now take
-  advantage of GPU acceleration with the backend selectable at runtime. Many of
-  the linear algebra and finite element operations (e.g. partially assembled
-  bilinear forms) have been extended to take advantage of kernel acceleration by
-  simply replacing loops with the MFEM_FORALL() macro.
-
-- In addition to native CUDA kernels, the library currently supports OCCA, RAJA
-  and OpenMP kernels, which could be mixed and matched in different parts of the
-  same application. We plan on adding support for more programming models and
-  devices in the future, without the need for significant modifications in user
-  code. The list of current backends is: "occa-cuda", "raja-cuda", "cuda",
-  "occa-omp", "raja-omp", "omp", "occa-cpu", "raja-cpu", and "cpu".
-
-- GPU-related limitations:
-  * Hypre preconditioners are not yet available in GPU mode, and in particular
-    hypre must be built in CPU mode.
-  * Only constant coefficients are currently supported on GPUs.
-  * Optimized element assembly, and matrix-free bilinear forms are not
-    implemented yet. Element batching is currently ignored.
-  * In device mode, full assembly is performed on the host (but the matvec
-    action is performed on the device).
-  * Partial assembly kernels are not implemented yet for simplices.
-
-Discretization improvements
----------------------------
-- Partial assembled finite element operators are now available in the core
-  library, based on the new classes PABilinearFormExtension, ElementRestriction,
-  DofToQuad and GeometricFactors (associated with the classes BilinearForm,
-  FiniteElementSpace, FiniteElement and Mesh, respectively). The kernels for
-  partial assembled Setup/Assembly and Action/Mult are implemented in the
-  BilinearFormIntegrator methods AssemblePA and AddMultPA.
-
-- Added support for a general "low-order refined"-to-"high-order" transfer of
-  GridFunction data from a "low-order refined" (LOR) space defined on a refined
-  mesh to a "high-order" (HO) finite element space defined on a coarse mesh. See
-  the new classes InterpolationGridTransfer and L2ProjectionGridTransfer and the
-  new LOR Transfer miniapp: miniapps/tools/lor-transfer.cpp.
-
-- Added element flux, and flux energy computation in class ElasticityIntegrator,
-  allowing for the use of Zienkiewicz-Zhu type error estimators with the
-  integrator. For an illustration of this addition, see the new Example 21.
-
-- Added support for derefinement of vector (RT + ND) spaces.
-
-- Added a variety of coefficients which are sums or products of existing
-  coefficients as well as grid function coefficients which return the
-  divergence, gradient, or curl of their GridFunctions.
-
-Support for wedge elements and meshes with mixed element types
---------------------------------------------------------------
-- Added support for wedge-shaped mesh elements of arbitrary order (with Geometry
-  type PRISM) which have two triangular faces and three quadrilateral faces.
-  Several examples of such meshes can be found in the data/ directory.
-
-- Added support for mixed meshes containing triangles and quadrilaterals in 2D
-  or tetrahedra, wedges, and hexahedra in 3D. This includes support for uniform
-  refinement of such meshes. Several examples of such meshes can be found in the
-  data/ directory.
-
-- Added H1 and L2 finite elements of arbitrary order for Wedge elements.
-
-- Added support for reading and writing linear and quadratic meshes containing
-  wedge elements in VTK mesh format. Several examples of such meshes can be
-  found in the data/ directory.
-
-Other meshing improvements
---------------------------
-- Improved the uniform refinement of tetrahedral meshes (also part of the
-  uniform refinement of mixed 3D meshes). The previous refinement algorithm is
-  still available as an option in Mesh::UniformRefinement. Both can be used in
-  the updated Mesh Explorer miniapp.
-
-- The local tetrahedral mesh refinement algorithm in serial and in parallel now
-  follows precisely the paper:
-
-     D. Arnold, A. Mukherjee, and L. Pouly, "Locally Adapted Tetrahedral Meshes
-     Using Bisection", SIAM J. Sci. Comput. 22 (2000), 431–448.
-
-  This guarantees that the shape regularity of the elements will be preserved
-  under refinement.
-
-- The TMOP mesh optimization algorithms were extended to support user-defined
-  space-dependent limiting terms. Improved the TMOP objective functions by more
-  accurate normalization of the different terms.
-
-- Added support for parallel communication groups on non-conforming meshes.
-
-- Improved parallel partitioning of non-conforming meshes. If the coarse mesh
-  elements are ordered as a sequence of face-neighbors, the parallel partitions
-  are now guaranteed to be continuous. To that end, inline quadrilateral and
-  hexahedral meshes are now by default ordered along a space-filling curve.
-
-- A boundary in a NURBS mesh can now be connected with another boundary. Such a
-  periodic NURBS mesh is a simple way to impose periodic boundary conditions.
-
 - Added support for reading linear and quadratic 2D quadrilateral and triangular
   Cubit meshes.
 
-New and updated examples and miniapps
--------------------------------------
-- Added a new meshing miniapp, Toroid, which can produce a variety of torus
-  shaped meshes by twisting a stack of wedges or hexahedra.
-
-- Added a new meshing miniapp, Extruder, that demonstrates the capability to
-  produce 3D meshes by extruding 2D meshes.
-
-- Added a simple miniapp, LOR Transfer, for visualizing the actions of the
-  transfer operators between a high-order and a low-order refined spaces.
-
-- Added a new example, Example 20/20p, that solves a system of 1D ODEs derived
-  from a Hamiltonian. The example demonstrates the use of the variable order,
-  symplectic integration algorithm implemented in class SIAVSolver.
-
-- Added a new example, Example 21/21p, that illustrates the use of AMR to solve
-  a linear elasticity problem. This is an extension of Example 2/2p.
-
-New and improved solvers and preconditioners
---------------------------------------------
-- Added support for parallel ILU preconditioning via hypre's Euclid solver.
-
-- Added support for STRUMPACK v3 with a small API change in the class
-  STRUMPACKSolver, see "API changes" below.
-
-Miscellaneous
--------------
-- Added unit tests based on the Catch++ library in the test/ directory.
-
-- Renamed the option MFEM_USE_OPENMP to MFEM_USE_LEGACY_OPENMP. This legacy
-  option is deprecated and planned for removal in a future release. The original
-  option name, MFEM_USE_OPENMP, is now used to enable the new OpenMP backends in
-  the new kernels.
-
-- In SparseMatrix added the option to perform MultTranspose() by matvec with
-  computed and stored transpose matrix. This is required for deterministic
-  results when using devices such as CUDA and OpenMP.
-
-- Altered the way FGMRES counts its iterations so that it matches GMRES.
-
-- Various other simplifications, extensions, and bugfixes in the code.
-
-- Construct abstract parallel rectangular truedof-to-truedof operators via
-  Operator::FormDiscreteOperator().
-
-API changes
------------
-- In multiple places, use Geometry::Type instead of int, where appropriate.
-- In multiple places, use Element::Type instead of int, where appropriate.
-- The Mesh methods GetElementBaseGeometry and GetBdrElementBaseGeometry no
-  longer have a default value for their parameter, they only work with an
-  explicitly given index.
-- In class Mesh, added methods useful for queries regarding the types of
-  elements present in the mesh: HasGeometry, GetNumGeometries, GetGeometries,
-  and class Mesh::GeometryList.
-- The struct CoarseFineTransformations (returned by the Mesh method
-  GetRefinementTransforms) now stores the embedding matrices separately for each
-  Geometry::Type.
-- In class ParMesh, replaced the method GroupNFaces with two new methods:
-  GroupNTriangles and GroupNQuadrilaterals. Also, replaced GroupFace with two
-  methods: GroupTriangle and GroupQuadrilateral.
-- In class ParMesh, made the two RefineGroups methods protected.
-- Removed the virtual method Element::GetRefinementFlag, it is only used by the
-  derived class Tetrahedron.
-- Added new methods: Array::CopyTo, Tetrahedron::Init.
-- In class STRUMPACKSolver, the method SetMC64Job() was replaced by the new
-  methods: DisableMatching(), EnableMatching(), and EnableParallelMatching().
+- The tetrahedral mesh refinement algorithm in serial and in parallel now
+  follows precisely the paper:
+     D. Arnold, A. Mukherjee, and L. Pouly, "Locally Adapted Tetrahedral Meshes
+     Using Bisection", SIAM J. Sci. Comput., 22(2), 431–448.
+  This guarantees that the shape regularity of the elements will be preserved
+  under refinement.
 
 
 Version 3.4, released on May 29, 2018
@@ -572,9 +89,6 @@ New and updated examples and miniapps
   incompressible hyperelastic equations. The example demonstrates the use of
   block nonlinear forms as well as custom block preconditioners.
 
-- Added a new serial example (ex23) to demonstrate the use of second order
-  time integration to solve the wave equation.
-
 - Added a new electromagnetics miniapp, Maxwell, for simulating time-domain
   electromagnetics phenomena as a coupled first order system of equations.
 

CMakeLists.txt

@@ -1,23 +1,18 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 cmake_minimum_required(VERSION 2.8.11)
 set(USER_CONFIG "${CMAKE_CURRENT_SOURCE_DIR}/config/user.cmake" CACHE PATH
   "Path to optional user configuration file.")
 
-# Require C++11 and disable compiler-specific extensions
-set(CMAKE_CXX_STANDARD 11)
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_EXTENSIONS OFF)
-
 # Load user settings before the defaults - this way the defaults will not
 # overwrite the user set options. If the user has not set all options, we still
 # have the defaults.
@@ -50,7 +45,7 @@ project(mfem NONE)
 # Current version of MFEM, see also `makefile`.
 #   mfem_VERSION = (string)
 #   MFEM_VERSION = (int)   [automatically derived from mfem_VERSION]
-set(${PROJECT_NAME}_VERSION 4.1.1)
+set(${PROJECT_NAME}_VERSION 3.4.1)
 
 # Prohibit in-source build
 if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
@@ -86,13 +81,6 @@ include("${CMAKE_CURRENT_SOURCE_DIR}/config/XSDKDefaults.cmake")
 
 # Enable languages.
 enable_language(CXX)
-if (MFEM_USE_CUDA)
-   # MFEM_USE_CUDA requires CMake 3.8 or newer (for direct CUDA support)
-   cmake_minimum_required(VERSION 3.8 FATAL_ERROR)
-   enable_language(CUDA)
-   message(STATUS "Using CUDA architecture: ${CUDA_ARCH}")
-endif()
-
 if (XSDK_ENABLE_C)
    enable_language(C)
 endif()
@@ -164,17 +152,8 @@ if (MFEM_USE_METIS)
   find_package(METIS REQUIRED)
 endif()
 
-if (MFEM_USE_GINKGO)
-  find_package(Ginkgo REQUIRED)
-  if (Ginkgo_FOUND)
-    get_target_property(Ginkgo_INCLUDE_DIRS
-      Ginkgo::ginkgo INTERFACE_INCLUDE_DIRECTORIES)
-    set(Ginkgo_LIBRARIES Ginkgo::ginkgo)
-  endif()
-endif()
-
-# zlib
-if (MFEM_USE_ZLIB)
+# GZSTREAM -> zlib
+if (MFEM_USE_GZSTREAM)
   find_package(ZLIB REQUIRED)
 endif()
 
@@ -191,11 +170,12 @@ if (MFEM_USE_LAPACK)
 endif()
 
 # OpenMP
-if (MFEM_USE_OPENMP OR MFEM_USE_LEGACY_OPENMP)
-  if (NOT MFEM_THREAD_SAFE AND MFEM_USE_LEGACY_OPENMP)
-    message(FATAL_ERROR " *** MFEM_USE_LEGACY_OPENMP requires MFEM_THREAD_SAFE=ON.")
+if (MFEM_USE_OPENMP)
+  if (MFEM_THREAD_SAFE)
+    find_package(OpenMP REQUIRED)
+  else()
+    message(FATAL_ERROR " *** MFEM_USE_OPENMP requires MFEM_THREAD_SAFE=ON.")
   endif()
-  find_package(OpenMP REQUIRED)
 endif()
 
 # SuiteSparse (before SUNDIALS which may depend on KLU)
@@ -237,16 +217,16 @@ if (MFEM_USE_STRUMPACK)
   endif()
 endif()
 
+# Gecko
+if (MFEM_USE_GECKO)
+  find_package(Gecko REQUIRED)
+endif()
+
 # GnuTLS
 if (MFEM_USE_GNUTLS)
   find_package(_GnuTLS REQUIRED)
 endif()
 
-# GSLIB
-if (MFEM_USE_GSLIB)
-  find_package(GSLIB REQUIRED)
-endif()
-
 # NetCDF
 if (MFEM_USE_NETCDF)
   find_package(NetCDF REQUIRED)
@@ -257,17 +237,13 @@ if (MFEM_USE_MPFR)
   find_package(MPFR REQUIRED)
 endif()
 
-if (MFEM_USE_CEED)
-  find_package(libCEED REQUIRED)
-endif()
-
 if (MFEM_USE_CONDUIT)
     find_package(Conduit REQUIRED conduit relay blueprint )
 endif()
 
 # Axom/Sidre
 if (MFEM_USE_SIDRE)
-  find_package(Axom REQUIRED Axom)
+  find_package(Axom REQUIRED Sidre SLIC axom_utils)
 endif()
 
 # PUMI
@@ -286,48 +262,6 @@ if (MFEM_USE_PUMI)
   endif()
 endif()
 
-# HiOp optimizer
-if (MFEM_USE_HIOP)
-  find_package(HIOP REQUIRED)
-  # find_package updates HIOP_FOUND, HIOP_INCLUDE_DIRS, HIOP_LIBRARIES
-endif()
-
-# CUDA
-if (MFEM_USE_CUDA)
-   set(CMAKE_CUDA_STANDARD 11)
-   set(CMAKE_CUDA_STANDARD_REQUIRED ON)
-   set(CMAKE_CUDA_EXTENSIONS OFF)
-   set(CMAKE_CUDA_FLAGS "-arch=${CUDA_ARCH} --expt-extended-lambda"
-       CACHE STRING "CUDA flags set for MFEM" FORCE)
-   if (MFEM_USE_MPI)
-      set(CUDA_CCBIN_COMPILER ${MPI_CXX_COMPILER})
-   else()
-      set(CUDA_CCBIN_COMPILER ${CMAKE_CXX_COMPILER})
-   endif()
-   string(APPEND CMAKE_CUDA_FLAGS " -ccbin ${CUDA_CCBIN_COMPILER}")
-   set(CMAKE_CUDA_HOST_LINK_LAUNCHER ${CUDA_CCBIN_COMPILER})
-endif()
-
-# OCCA
-if (MFEM_USE_OCCA)
-   find_package(OCCA REQUIRED)
-endif()
-
-# RAJA
-if (MFEM_USE_RAJA)
-   find_package(RAJA REQUIRED)
-endif()
-
-# UMPIRE
-if (MFEM_USE_UMPIRE)
-   find_package(UMPIRE REQUIRED)
-endif()
-
-# ADIOS2 for parallel I/O
-if (MFEM_USE_ADIOS2)
-   find_package(ADIOS2 REQUIRED)
-endif()
-
 # MFEM_TIMER_TYPE
 if (NOT DEFINED MFEM_TIMER_TYPE)
   if (APPLE)
@@ -352,8 +286,8 @@ endif()
 #    integers, the METIS header (with 32-bit indices, as used by mfem) needs to
 #    be before SuiteSparse.
 set(MFEM_TPLS MPI_CXX OPENMP BLAS LAPACK METIS HYPRE SuiteSparse SUNDIALS PETSC
-    MESQUITE SuperLUDist STRUMPACK AXOM CONDUIT Ginkgo GNUTLS GSLIB NETCDF
-    MPFR PUMI HIOP POSIXCLOCKS MFEMBacktrace ZLIB OCCA CEED RAJA UMPIRE ADIOS2)
+    MESQUITE SuperLUDist STRUMPACK AXOM CONDUIT GECKO GNUTLS NETCDF MPFR PUMI
+    POSIXCLOCKS MFEMBacktrace ZLIB)
 # Add all *_FOUND libraries in the variable TPL_LIBRARIES.
 set(TPL_LIBRARIES "")
 set(TPL_INCLUDE_DIRS "")
@@ -378,6 +312,9 @@ message(STATUS "MFEM build type: CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
 message(STATUS "MFEM version: v${MFEM_VERSION_STRING}")
 message(STATUS "MFEM git string: ${MFEM_GIT_STRING}")
 
+# Windows specific
+set(_USE_MATH_DEFINES ${WIN32})
+
 #-------------------------------------------------------------------------------
 # Define and configure the MFEM library
 #-------------------------------------------------------------------------------
@@ -389,13 +326,6 @@ set(MFEM_SOURCE_DIRS general linalg mesh fem)
 foreach(DIR IN LISTS MFEM_SOURCE_DIRS)
   add_subdirectory(${DIR})
 endforeach()
-
-if (MFEM_USE_CUDA)
-   foreach(file IN LISTS SOURCES)
-      set_property(SOURCE ${file} PROPERTY LANGUAGE CUDA)
-   endforeach()
-endif()
-
 add_subdirectory(config)
 set(MASTER_HEADERS
   ${PROJECT_SOURCE_DIR}/mfem.hpp
@@ -406,11 +336,6 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON CACHE BOOL "")
 set(CMAKE_INSTALL_RPATH "${_lib_path}" CACHE PATH "")
 set(CMAKE_INSTALL_NAME_DIR "${_lib_path}" CACHE PATH "")
 
-set(MFEM_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR} CACHE PATH
-    "The MFEM source directory" FORCE)
-set(MFEM_INSTALL_DIR ${CMAKE_INSTALL_PREFIX} CACHE PATH
-    "The MFEM install directory" FORCE)
-
 # Declaring the library
 add_library(mfem ${SOURCES} ${HEADERS} ${MASTER_HEADERS})
 # message(STATUS "TPL_LIBRARIES = ${TPL_LIBRARIES}")
@@ -425,11 +350,11 @@ endif()
 set_target_properties(mfem PROPERTIES VERSION "${mfem_VERSION}")
 set_target_properties(mfem PROPERTIES SOVERSION "${mfem_VERSION}")
 
-# If building out-of-source, define MFEM_CONFIG_FILE to point to the config file
-# inside the build directory.
+# If building out-of-source, define MFEM_BUILD_DIR to point to the build
+# directory.
 if (NOT ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}"))
   target_compile_definitions(mfem PRIVATE
-    "MFEM_CONFIG_FILE=\"${PROJECT_BINARY_DIR}/config/_config.hpp\"")
+    "MFEM_BUILD_DIR=${PROJECT_BINARY_DIR}")
 endif()
 
 # Generate configuration file in the build directory: config/_config.hpp.
@@ -445,7 +370,7 @@ if (NOT ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}"))
       "Writing substitute header --> \"${Header}\"")
     file(WRITE "${PROJECT_BINARY_DIR}/${Header}"
 "// Auto-generated file.
-#define MFEM_CONFIG_FILE \"${PROJECT_BINARY_DIR}/config/_config.hpp\"
+#define MFEM_BUILD_DIR ${PROJECT_BINARY_DIR}
 #include \"${PROJECT_SOURCE_DIR}/${Header}\"
 ")
     # This version will be installed in the top include directory:
@@ -463,9 +388,6 @@ endif()
 # Enable testing if required
 if (MFEM_ENABLE_TESTING)
   enable_testing()
-  set(MFEM_ALL_TESTS_TARGET_NAME tests)
-  add_mfem_target(${MFEM_ALL_TESTS_TARGET_NAME} OFF)
-  add_subdirectory(tests EXCLUDE_FROM_ALL)
 endif()
 
 # Define a target that all examples and miniapps will depend on.
@@ -485,9 +407,7 @@ add_subdirectory(miniapps EXCLUDE_FROM_ALL)
 # Target to build all executables, i.e. everything.
 add_custom_target(exec)
 add_dependencies(exec
-  ${MFEM_ALL_EXAMPLES_TARGET_NAME}
-  ${MFEM_ALL_MINIAPPS_TARGET_NAME}
-  ${MFEM_ALL_TESTS_TARGET_NAME})
+  ${MFEM_ALL_EXAMPLES_TARGET_NAME} ${MFEM_ALL_MINIAPPS_TARGET_NAME})
 # Here, we want to "add_dependencies(test exec)". However, dependencies for
 # 'test' (and other built-in targets) can not be added with add_dependencies():
 #  - https://gitlab.kitware.com/cmake/cmake/issues/8438
@@ -508,12 +428,12 @@ endif()
 # Add 'check' target - quick test
 if (NOT MFEM_USE_MPI)
   add_custom_target(check
-    ${CMAKE_CTEST_COMMAND} -R \"^ex1_ser\" -C ${CMAKE_CFG_INTDIR}
+    ${CMAKE_CTEST_COMMAND} -R '^ex1_ser' -C ${CMAKE_CFG_INTDIR}
     USES_TERMINAL)
   add_dependencies(check ex1)
 else()
   add_custom_target(check
-    ${CMAKE_CTEST_COMMAND} -R \"^ex1p\" -C ${CMAKE_CFG_INTDIR}
+    ${CMAKE_CTEST_COMMAND} -R '^ex1p' -C ${CMAKE_CFG_INTDIR}
     USES_TERMINAL)
   add_dependencies(check ex1p)
 endif()
@@ -558,20 +478,6 @@ install(DIRECTORY ${MFEM_SOURCE_DIRS}
   DESTINATION ${INSTALL_INCLUDE_DIR}/mfem
   FILES_MATCHING PATTERN "*.hpp")
 
-# Install the okl files
-if (MFEM_USE_OCCA)
-  install(DIRECTORY ${MFEM_SOURCE_DIRS}
-    DESTINATION ${INSTALL_INCLUDE_DIR}/mfem
-    FILES_MATCHING PATTERN "*.okl")
-endif()
-
-# Install the libCEED files
-if (MFEM_USE_CEED)
-  install(DIRECTORY ${MFEM_SOURCE_DIRS}
-    DESTINATION ${INSTALL_INCLUDE_DIR}/mfem
-    FILES_MATCHING PATTERN "fem/libceed/*.h")
-endif()
-
 # Install ${HEADERS}
 # ---
 # foreach (HDR ${HEADERS})
@@ -637,10 +543,3 @@ install(FILES
 # Install the export set for use with the install-tree
 install(EXPORT ${PROJECT_NAME_UC}Targets
     DESTINATION ${INSTALL_CMAKE_DIR})
-
-#-------------------------------------------------------------------------------
-# Create 'config.mk' from 'config.mk.in' for the build and install locations and
-# define install rules for 'config.mk' and 'test.mk'
-#-------------------------------------------------------------------------------
-
-mfem_export_mk_files()

CONTRIBUTING.md

@@ -3,7 +3,7 @@
 </p>
 
 <p align="center">
-<a href="https://github.com/mfem/mfem/blob/master/LICENSE"><img alt="License" src="https://img.shields.io/badge/License-BSD-brightgreen.svg"></a>
+<a href="https://github.com/mfem/mfem/blob/master/COPYRIGHT"><img alt="License" src="https://img.shields.io/badge/License-LGPL--2.1-brightgreen.svg"></a>
 <a href="https://travis-ci.org/mfem/mfem"><img alt="Build Status" src="https://travis-ci.org/mfem/mfem.svg?branch=master"></a>
 <a href="https://ci.appveyor.com/project/mfem/mfem"><img alt="Build Status" src="https://ci.appveyor.com/api/projects/status/19non9sqm6msi2wy?svg=true"></a>
 <a href="http://mfem.github.io/doxygen/html/index.html"><img alt="Doxygen" src="https://img.shields.io/badge/code-documented-brightgreen.svg"></a>
@@ -12,28 +12,22 @@
 
 # How to Contribute
 
-The MFEM team welcomes contributions at all levels: bugfixes; code improvements;
-simplifications; new mesh, discretization or solver capabilities; improved
-documentation; new examples and miniapps; HPC performance improvements; etc.
+The MFEM team welcomes contributions at all levels: bugfixes; code
+improvements; simplifications; new mesh, discretization or solver
+capabilities; improved documentation; new examples and miniapps;
+HPC performance improvements; ...
 
-MFEM is distributed under the terms of the BSD-3 license. All new contributions
-must be made under this license.
-
-If you plan on contributing to MFEM, consider reviewing the
-[issue tracker](https://github.com/mfem/mfem/issues) first to check if a thread
-already exists for your desired feature or the bug you ran into. Use a pull
-request (PR) toward the `mfem:master` branch to propose your contribution. If
-you are planning significant code changes or have questions, you may want to
-open an [issue](https://github.com/mfem/mfem/issues) before issuing a PR. In
-addition to technical contributions, we are also interested in your results and
-[simulation images](http://mfem.org/gallery/), which you can share via a pull
-request in the [mfem/web](https://github.com/mfem/web) repo.
+Use a pull request (PR) toward the `mfem:master` branch to propose your
+contribution. If you are planning significant code changes, or have any
+questions, you can also open an [issue](https://github.com/mfem/mfem/issues)
+before issuing a PR.  We also welcome your [simulation
+images](http://mfem.org/gallery/), which you can submit via a pull request in
+[mfem/web](https://github.com/mfem/web).
 
 See the [Quick Summary](#quick-summary) section for the main highlights of our
 GitHub workflow. For more details, consult the following sections and refer
 back to them before issuing pull requests:
 
-- [Quick Summary](#quick-summary)
 - [Code Overview](#code-overview)
 - [GitHub Workflow](#github-workflow)
   - [MFEM Organization](#mfem-organization)
@@ -65,12 +59,6 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
   with regards to documentation and code styling.
 - 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
-  reviewers to evaluate the changes.
-- The reviewers have 3 weeks to evaluate the PR and work with the author to
-  fix issues and implement improvements.
 - After approval, MFEM developers merge the PR manually in the [mfem:next branch](#masternext-workflow).
 - After a week of testing in `mfem:next`, the original PR is merged in `mfem:master`.
 - We use [milestones](https://github.com/mfem/mfem/milestones) to coordinate the
@@ -80,15 +68,12 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
 
 ### Code Overview
 
-#### Source code structure:
+- The MFEM library uses object-orient design principles which reflect, in code,
+  the independent mathematical concepts of meshing, linear algebra and finite
+  element spaces and operators.
 
-The MFEM library uses object-oriented design principles which reflect, in code,
-the independent mathematical concepts of meshing, linear algebra and finite
-element spaces and operators.
-
-The MFEM source code has the following structure:
-
-```
+- The MFEM source code has the following structure:
+  ```
   .
   ├── config
   │   └── cmake
@@ -98,37 +83,25 @@ The MFEM source code has the following structure:
   │   └── web
   │       └── examples
   ├── examples
-  │   ├── ginkgo
-  │   ├── hiop
   │   ├── petsc
   │   ├── pumi
   │   └── sundials
   ├── fem
-  │   └── libceed
   ├── general
   ├── linalg
   ├── mesh
-  ├── miniapps
-  │   ├── common
-  │   ├── electromagnetics
-  │   ├── gslib
-  │   ├── meshing
-  │   ├── nurbs
-  │   ├── performance
-  │   ├── tools
-  │   └── toys
-  └── tests
-      ├── scripts
-      ├── unit
-      │   ├── ...
-      └── ...
-```
+  └── miniapps
+      ├── common
+      ├── electromagnetics
+      ├── meshing
+      ├── nurbs
+      ├── performance
+      └── tools
+  ```
 
-#### Main directories and classes
-
-The main directories are `fem/`, `mesh/` and `linalg/` containing the C++
-classes implementing the finite element, mesh and linear algebra concepts
-respectively.
+- The main directories are `fem/`, `mesh/` and `linalg/` containing the C++
+  classes implementing the finite element, mesh and linear algebra concepts
+  respectively.
 
 - The main mesh classes are:
   + [`Mesh`](http://mfem.github.io/doxygen/html/classmfem_1_1Mesh.html)
@@ -150,12 +123,10 @@ respectively.
   + [`DenseMatrix`](http://mfem.github.io/doxygen/html/classmfem_1_1DenseMatrix.html) and [`SparseMatrix`](http://mfem.github.io/doxygen/html/classmfem_1_1SparseMatrix.html)
   + Sparse [smoothers](http://mfem.github.io/doxygen/html/sparsesmoothers_8hpp.html) and linear [solvers](http://mfem.github.io/doxygen/html/solvers_8hpp.html)
 
-#### Parallel implementation
-
-Parallel MPI objects in MFEM inherit their serial counterparts, so a parallel
-mesh for example is just a serial mesh on each task plus the information on
-shared geometric entities between different tasks. The parallel source files
-have a `p` prefix, e.g. `pmesh.cpp` vs. the serial `mesh.cpp`.
+- Parallel MPI objects in MFEM inherit their serial counterparts, so a parallel
+  mesh for example is just a serial mesh on each task plus the information on
+  shared geometric entities between different tasks. The parallel source files
+  have a `p` prefix, e.g. `pmesh.cpp` vs. the serial `mesh.cpp`.
 
 - The main parallel classes are
   + [`ParMesh`](http://mfem.github.io/doxygen/html/solvers_8hpp.html)
@@ -166,43 +137,29 @@ have a `p` prefix, e.g. `pmesh.cpp` vs. the serial `mesh.cpp`.
   + [`HypreParMatrix`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreParMatrix.html) and [`HypreParVector`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreParVector.html)
   + [`HypreSolver`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreSolver.html) and other [hypre classes](http://mfem.github.io/doxygen/html/hypre_8hpp.html)
 
-#### GPU and general device support
-
-GPU and multi-core CPU support is based on device kernels supporting different
-backends (CUDA, OCCA, RAJA, OpenMP, etc.) and an internal lightweight
-device/host memory manager.
-
-- The main device-relevant classes and sources are:
-  + [`Device`](http://mfem.github.io/doxygen/html/device_8hpp.html)
-  + [`MemoryManager`](http://mfem.github.io/doxygen/html/mem_manager_8hpp.html)
-  + the [`MFEM_FORALL`](http://mfem.github.io/doxygen/html/forall_8hpp.html) macro
-  + the [`cuda.hpp`](http://mfem.github.io/doxygen/html/cuda_8hpp.html) and [`occa.hpp`](http://mfem.github.io/doxygen/html/occa_8hpp.html) files
-
-#### Utilities, building and documentation
 - The `general/` directory contains C++ classes that serve as utilities for
   communication, error handling, arrays, (Boolean) tables, timing, etc.
+
 - The `config/` directory contains build-related files, both for the plain
   Makefile and the CMake build options.
+
 - The `doc/` directory contains configuration for the Doxygen code documentation
-  that can either be built locally or browsed online at
+  that can either be build locally, or browsed online at
   http://mfem.github.io/doxygen/html/index.html.
 
-#### Examples and tests
-- `examples` and `miniapps` respectively gather simple and more fully-featured
-  demonstrations of the usage on MFEM. They both rely on `data/` for the
-  collection of meshes.
-- The `tests/` directory contains a unit test suite and will later contain more
-  tests that run example codes.
+- The `data/` directory contains a collection of small mesh files, that are used
+  in the simple example codes and more fully-featured mini applications in the
+  `examples/` and `miniapps/` directories.
 
-See also the [code overview](http://mfem.org/code-overview/) section on the MFEM
-website.
+- See also the [code overview](http://mfem.org/code-overview/) section on the
+  MFEM website.
 
 ## GitHub Workflow
 
-The MFEM GitHub organization: https://github.com/mfem, is the main developer hub
-for the MFEM project.
+The GitHub organization, https://github.com/mfem, is the main developer hub for
+the MFEM project.
 
-If you plan to make contributions or would like to stay up-to-date with changes
+If you plan to make contributions or will like to stay up-to-date with changes
 in the code, *we strongly encourage you to [join the MFEM organization](#mfem-organization)*.
 
 This will simplify the workflow (by providing you additional permissions), and
@@ -211,31 +168,34 @@ will allow us to reach you directly with project announcements.
 
 ### MFEM Organization
 
-#### Getting started (GitHub)
-Before you can start, you need a GitHub account, here are a few suggestions:
-  + Create the account at: [github.com/join](https://github.com/join).
-  + For easy identification, please add your full name and maybe a picture of you at:
-    https://github.com/settings/profile.
+- Before you can start, you need a GitHub account, here are a few suggestions:
+  + Create the account at: github.com/join.
+  + For easy identification, please add your name and maybe a picture of you at: https://github.com/settings/profile.
   + To receive notification, set a primary email at: https://github.com/settings/emails.
   + For password-less pull/push over SSH, add your SSH keys at: https://github.com/settings/keys.
 
-#### Joining
 - [Contact us](#contact-information) for an invitation to join the MFEM GitHub
-  organization. You will receive an invitation email, which you can directly accept.
+  organization.
+
+- You should receive an invitation email, which you can directly accept.
   Alternatively, *after logging into GitHub*, you can accept the invitation at
   the top of https://github.com/mfem.
+
 - Consider making your membership public by going to https://github.com/orgs/mfem/people
-  and clicking on the organization visibility drop box next to your name.
+  and clicking on the organization visibility dropbox next to your name.
+
 - Project discussions and announcements will be posted at
   https://github.com/orgs/mfem/teams/everyone.
 
-#### Structure
 - The MFEM source code is in the [mfem](https://github.com/mfem/mfem)
   repository.
+
 - The website and corresponding documentation are in the
   [web](https://github.com/mfem/web) repository.
+
 - The [PyMFEM](https://github.com/mfem/PyMFEM) repository contains a Python
   wrapper for MFEM.
+
 - The [data](https://github.com/mfem/data) repository contains additional
   (large) datafiles for MFEM.
 
@@ -243,9 +203,9 @@ Before you can start, you need a GitHub account, here are a few suggestions:
 ### New Feature Development
 
 - A new feature should be important enough that at least one person, the
-  author, is willing to work on it and be its champion.
+  proposer, is willing to work on it and be its champion.
 
-- The author creates a branch for the new feature (with suffix `-dev`), off
+- The proposer creates a branch for the new feature (with suffix `-dev`), off
   the `master` branch, or another existing feature branch, for example:
 
   ```
@@ -288,13 +248,12 @@ Before you can start, you need a GitHub account, here are a few suggestions:
   - Lean code base is easier to understand by new collaborators.
   - New features should be added only if they are necessary or generally useful.
   - Introduction of language constructions not currently used in MFEM should be
-    justified and generally avoided (to maintain portability to various systems
-    and compilers, including early access hardware).
+    justified and generally avoided (so we can build on cutting-edge systems).
   - We prefer basic C++ and the C++03 standard, to keep the code readable by
     a large audience and to make sure it compiles anywhere.
 
 - *Keep the code general and reasonably efficient*
-  - The main goal is fast prototyping for research and application development.
+  - Main goal is fast prototyping for research.
   - When in doubt, generality wins over efficiency.
   - Respect the needs of different users (current and/or future).
 
@@ -337,41 +296,15 @@ Before you can start, you need a GitHub account, here are a few suggestions:
 
      `[DISCUSS] Hybridized DG [hdg-dev]`
 
-- If the PR is still a work in progress, add the `WIP` label to it and
-  optionally the `[WIP]` prefix in the title.
-
 - Add a description, appropriate labels and assign yourself to the PR. The MFEM
   team will add reviewers as appropriate.
 
 - List outstanding TODO items in the description, see PR #222 for an example.
 
-- 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 reviewers to evaluate the changes. The reviewers have 3 weeks to evaluate
-  the PR and work with the author to implement improvements and fix issues.
-
-- After approval, the PR is [tested](#masternext-workflow) for a week with
-  other approved PRs in the `mfem:next` branch.
-
-- Consider manually running the tests in `tests/scripts` before merging in
-  `mfem:next`, see the [README](tests/scripts/README) file in that directory
-  for more details.
-
 - Track the Travis CI and Appveyor [continuous integration](#automated-testing)
-  builds at the end of the PR. These should generally run clean, so address any
-  errors as soon as possible. Please ask if you are unsure how to do that.
+  builds at the end of the PR. These should run clean, so address any errors as
+  soon as possible.
 
-- Note that some tests, such as the `branch-history` check in Travis are
-  safeguards that are allowed to fail in certain cases.
-
-- Other tests, such as the `code-style`, `documentation` and `gitignore`
-  checks in Travis enforce MFEM-specific rules which are explained in the
-  error messages and the `tests/scripts` directory.
-
-- If triggered, track the status of the LLNL GitLab tests. If failing, ask
-  one of the _LLNL developers_ for details.
 
 ### Pull Request Checklist
 
@@ -383,18 +316,14 @@ Before a PR can be merged, it should satisfy the following:
     - [ ] Is this a new feature users need to be aware of? New or updated example or miniapp?
     - [ ] Does it make sense to create a new section in the `CHANGELOG` to group with other related features?
 - [ ] Update `INSTALL`:
-    - [ ] Had a new optional library been added? If so, what range of versions of this library are required? (*Make sure the external library is compatible with our BSD license, e.g. it is not licensed under GPL!*)
-    - [ ] Have the version ranges for any required or optional libraries changed?
+    - [ ] Has a new optional library been added? (*Make sure the external library is licensed under LGPL, not GPL!*)
     - [ ] Does `make` or `cmake` have a new target?
-    - [ ] Did the requirements or the installation process change? *(rare)*
-- [ ] Update continuous integration server configurations if necessary (e.g. with new version requirements for each of MFEM's dependencies)
-    - [ ] `.travis.yml`
-    - [ ] `.appveyor.yml`
+    - [ ] Did the requirements or the installation process change? *(rare)*.
 - [ ] Update `.gitignore`:
-    - [ ] Check if `make distclean; git status` shows any files that were generated from the source by the project (not an IDE) but we don't want to track in the repository.
+    - [ ] Check if `make distclean; git status` shows any files that are generated from the source but we don't want to track in the repository.
     - [ ] Add new patterns (just for the new files above) and re-run the above test.
 - [ ] New examples:
-    - [ ] All sample runs at the top of the example source file work.
+    - [ ] All sample runs at the top of the example work.
     - [ ] Update `examples/makefile`:
       - [ ] Add the example code to the appropriate `SEQ_EXAMPLES` and `PAR_EXAMPLES` variables.
       - [ ] Add any files generated by it to the `clean` target.
@@ -403,14 +332,13 @@ Before a PR can be merged, it should satisfy the following:
       - [ ] Add the example code to the `ALL_EXE_SRCS` variable.
       - [ ] Make sure `THIS_TEST_OPTIONS` is set correctly for the new example.
    - [ ] List the new example in `doc/CodeDocumentation.dox`.
-   - [ ] If new examples directory (e.g.`examples/pumi`), list it in `doc/CodeDocumentation.conf.in`
    - [ ] Companion pull request for documentation in [mfem/web](https://github.com/mfem/web) repo:
       - [ ] Update or add example-specific documentation, see e.g. the `src/examples.md`.
       - [ ] Add the description, labels and screenshots in `src/examples.md` and `src/img`.
       - [ ] In `examples.md`, list the example under the appropriate categories, add new categories if necessary.
       - [ ] Add a short description of the example in the "Extensive Examples" section of `features.md`.
 - [ ] New miniapps:
-   - [ ] All sample runs at the top of the miniapp source file work.
+   - [ ] All sample runs at the top of the miniapp work.
    - [ ] Update top-level `makefile` and `makefile` in corresponding miniapp directory.
    - [ ] Add the miniapp binary and any files generated by it to the top-level `.gitignore` file.
    - [ ] Update CMake build system:
@@ -418,7 +346,6 @@ Before a PR can be merged, it should satisfy the following:
       - [ ] Add/update the `CMakeLists.txt` file in the new miniapp directory.
       - [ ] Consider adding a new test for the new miniapp.
    - [ ] List the new miniapp in `doc/CodeDocumentation.dox`
-   - [ ] If new miniapps directory (e.g.`miniapps/nurbs`), list it in `doc/CodeDocumentation.conf.in`
    - [ ] Companion pull request for documentation in [mfem/web](https://github.com/mfem/web) repo:
      - [ ] Update or add miniapp-specific documentation, see e.g. the `src/meshing.md` and `src/electromagnetics.md` files.
      - [ ] Add the description, labels and screenshots in `src/examples.md` and `src/img`.
@@ -428,14 +355,18 @@ Before a PR can be merged, it should satisfy the following:
    - [ ] 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)*.
+   - [ ] If this is a major new feature, consider mentioning in the short summary inside `README` *(rare)*.
    - [ ] List major new classes in `doc/CodeDocumentation.dox` *(rare)*.
 - [ ] Update this checklist, if the new pull request affects it.
-- [ ] Run `make unittest` to make sure all unit tests pass.
-- [ ] Run the tests in `tests/scripts`.
+- [ ] (LLNL only) Clone the `tests` repository and run the following tests, see `mfem/tests/README.md`:
+   - [ ] `compilers`
+   - [ ] `memcheck`
+   - [ ] `unit-test`
+   - [ ] `documentation`
 - [ ] (LLNL only) After merging:
    - [ ] Regenerate `README.html` files from companion documentation pull requests.
-   - [ ] Update internal tests to include the new features.
+   - [ ] Update the `baseline` and `compiler` tests, add new tests if necessary.
+   - [ ] Consider updating the script `mfem/tests/sample-runs` (`sample-runs-serial` and `sample-runs-parallel`).
 
 ### Master/Next Workflow
 
@@ -494,7 +425,7 @@ MFEM uses a `master`/`next`-branch workflow as described below:
   (replace `3.3.2` with current release):
   - Rename the current `next` branch to `next-pre-v3.3.2`.
   - Create a new `next` branch starting from the `v3.3.2` release.
-  - Local copies of `next` can then be updated with `git fetch origin next && git checkout -B next origin/next`.
+  - Local copies of `next` can then be updated with `git checkout -B next origin/next`.
 
 ### Release Checklist
 
@@ -503,10 +434,6 @@ MFEM uses a `master`/`next`-branch workflow as described below:
     - [ ] `makefile`
     - [ ] `CMakeLists.txt`
     - [ ] `doc/CodeDocumentation.conf.in`
-- [ ] Check that version requirements for each of MFEM's dependencies are documented in `INSTALL` and up-to-date
-- [ ] Check that continuous integration server configurations reflect the dependency version requirements of the new release
-    - [ ] `.travis.yml`
-    - [ ] `.appveyor.yml`
 - [ ] (LLNL only) Make sure all `README.html` files in the source repo are up to date.
 - [ ] Tag the repository:
 
@@ -517,9 +444,9 @@ MFEM uses a `master`/`next`-branch workflow as described below:
 - [ ] Create the release tarball and push to `mfem/releases`.
 - [ ] Recreate the `next` branch as described in previous section.
 - [ ] Update and push documentation  to `mfem/doxygen`.
-- [ ] Update URL shortlinks:
-    - [ ] Create a shortlink at [http://bit.ly/](http://bit.ly/) for the release tarball, e.g. http://mfem.github.io/releases/mfem-3.1.tgz.
-    - [ ] (LLNL only) Add and commit the new shortlink in the `links` and `links-mfem` files of the internal `mfem/downloads` repo.
+- [ ] Update URL shorlinks:
+    - [ ] Create a shortlink at [https://goo.gl/](https://goo.gl/) for the release tarball, e.g. http://mfem.github.io/releases/mfem-3.1.tgz.
+    - [ ] (LLNL only) Add and commit the new shorlink in the `links` and `links-mfem` files of the internal `mfem/downloads` repo.
     - [ ] Add the new shortlinks to the MFEM packages in `spack`, `homebrew/science`, `VisIt`, etc.
 - [ ] Update website in `mfem/web` repo:
     - Update version and shortlinks in `src/index.md` and `src/download.md`.
@@ -528,8 +455,6 @@ MFEM uses a `master`/`next`-branch workflow as described below:
 
 ## LLNL Workflow
 
-### Mirroring on Bitbucket
-
 - The GitHub `master` and `next` branches are mirrored to the LLNL institutional
   Bitbucket repository as `gh-master` and `gh-next`.
 
@@ -547,16 +472,6 @@ 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
-  GitHub pull request.
-
-- No change can be made on this instance.
 
 ## Automated Testing
 
@@ -584,15 +499,11 @@ 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
+At LLNL, we mirror the `master` and `next` branches internally (to `gh-master`
+and `gh-next`) and run longer nightly tests via cron. On the weekends, a more
+extensive test is run which extracts and executes all the different sample runs
+from each example.
 
-- We mirror the `master` and `next` branches internally (to `gh-master` and
-  `gh-next`) and run longer nightly tests via cron. On the weekends, a more
-  extensive test is run which extracts and executes all the different sample
-  runs from each example.
-
-- We also mirror PRs on the LLNL GitLab instance. PR mirroring can only be
-  triggered by _LLNL developers_, but test status is publicly available. Only
-  _LLNL developers_ can access the detailed test report.
 
 ## Contact Information
 

COPYRIGHT

@@ -0,0 +1,64 @@
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability see http://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
+
+COPYRIGHT
+
+The following copyright applies to each file in the MFEM distribution, unless
+otherwise stated in the file:
+
+Copyright (c) 2010, Lawrence Livermore National Security, LLC.  Produced at the
+Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344 with
+the DOE.
+
+Neither the United States Government nor Lawrence Livermore National Security,
+LLC nor any of their employees, makes any warranty, express or implied, or
+assumes any liability or responsibility for the accuracy, completeness, or
+usefulness of any information, apparatus, product, or process disclosed, or
+represents that its use would not infringe privately-owned rights.
+
+Also, reference herein to any specific commercial products, process, or services
+by trade name, trademark, manufacturer or otherwise does not necessarily
+constitute or imply its endorsement, recommendation, or favoring by the United
+States Government or Lawrence Livermore National Security, LLC. The views and
+opinions of authors expressed herein do not necessarily state or reflect those
+of the United States Government or Lawrence Livermore National Security, LLC,
+and shall not be used for advertising or product endorsement purposes.
+
+
+LICENSE
+
+MFEM is free software; you can redistribute it and/or modify it under the terms
+of the GNU Lesser General Public License (as published by the Free Software
+Foundation) version 2.1 dated February 1999, with the following EXCEPTIONS:
+
+   1. Subclasses of MFEM classes do not constitute a derivative work.
+
+   2. Static linking of applications to the MFEM library does not constitute a
+      derivative work and does not require the author to provide source code for
+      the application, use the shared MFEM library, or link their applications
+      against a user-supplied version of MFEM.
+
+MFEM is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE.  See the terms and conditions of the GNU Lesser General
+Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License along
+with this library (file LICENSE); if not, write to the Free Software Foundation,
+Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+
+CONTACT INFORMATION
+
+The software is released under LLNL-CODE-443211. Please see
+
+                   http://mfem.org
+
+for more information and source code availability.

INSTALL

@@ -13,42 +13,14 @@ of MFEM is a (modern) C++ compiler, such as g++. The parallel version of MFEM
 requires an MPI C++ compiler, as well as the following external libraries:
 
 - hypre (a library of high-performance preconditioners)
-  https://github.com/hypre-space/hypre
+  http://www.llnl.gov/CASC/hypre
 
 - METIS (a family of multilevel partitioning algorithms)
   http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
 
-The hypre dependency can be downloaded as a tarball from GitHub or from the
-project webpage https://www.llnl.gov/casc/hypre. For example, the 2.16.0 release
-of hypre is available at
-
-   https://github.com/hypre-space/hypre/archive/v2.16.0.tar.gz
-
 The METIS dependency can be disabled but that is not generally recommended, see
 the option MFEM_USE_METIS.
 
-MFEM also includes support for devices such as GPUs, and programming models such
-as CUDA, HIP, OCCA, OpenMP and RAJA.
-
-- Starting with version 4.0, MFEM requires a C++11 compiler. We recommend using
-  a newer compiler, e.g. GCC version 4.9 or higher.
-
-- CUDA support requires an NVIDIA GPU and an installation of the CUDA Toolkit
-  https://developer.nvidia.com/cuda-toolkit
-
-- HIP support requires an AMD GPU and an installation of the ROCm software stack
-  https://rocm.github.io/ROCmInstall.html#installing-from-amd-rocm-repositories
-
-- OCCA support requires the OCCA library
-  https://libocca.org
-
-- OpenMP support requires a compiler implementing the OpenMP API
-  https://www.openmp.org
-
-- RAJA support requires installation of the RAJA performance portability layer
-  with (optionally) support for CUDA and OpenMP
-  https://github.com/LLNL/RAJA
-
 The library supports two build systems: one based on GNU make, and a second one
 based on CMake. Both build systems are described below. Some hints for building
 without GNU make or CMake can be found at the end of this file.
@@ -58,7 +30,7 @@ following package managers:
 
 - Spack, https://github.com/spack/spack
 - OpenHPC, http://openhpc.community
-- Homebrew/Science, https://github.com/Homebrew/homebrew-science (deprecated)
+- Homebrew/Science, https://github.com/Homebrew/homebrew-science
 
 We also recommend downloading and building the MFEM-based GLVis visualization
 tool which can be used to visualize the meshes and solution in MFEM's examples
@@ -70,19 +42,11 @@ Serial build:
    make serial -j 4
 
 Parallel build:
-   (download hypre and METIS 4 from above URLs)
+   (download hypre 2.10.0b and METIS 4 from above URLs)
    (build METIS 4 in ../metis-4.0 relative to mfem/)
-   (build hypre in ../hypre relative to mfem/)
+   (build hypre 2.10.0b in ../hypre-2.10.0b relative to mfem/)
    make parallel -j 4
 
-CUDA build:
-   make cuda -j 4
-   (build for a specific compute capability: 'make cuda -j 4 CUDA_ARCH=sm_30')
-
-HIP build:
-   make hip -j 4
-   (build for a specific AMD GPU chip: 'make hip -j 4 HIP_ARCH=gfx900')
-
 Example codes (serial/parallel, depending on the build):
    cd examples
    make -j 4
@@ -93,6 +57,7 @@ Build everything (library, examples and miniapps) with current configuration:
 Quick-check the build by running Example 1/1p (optional):
    make check
 
+
 Quick start with CMake
 ======================
 Serial build:
@@ -101,19 +66,13 @@ Serial build:
    make -j 4   (assuming "UNIX Makefiles" generator)
 
 Parallel build:
-   (download hypre and METIS 4 from above URLs)
+   (download hypre 2.10.0b and METIS 4 from above URLs)
    (build METIS 4 in ../metis-4.0 relative to mfem/)
-   (build hypre in ../hypre relative to mfem/)
+   (build hypre 2.10.0b in ../hypre-2.10.0b relative to mfem/)
    mkdir <mfem-build-dir> ; cd <mfem-build-dir>
    cmake <mfem-source-dir> -DMFEM_USE_MPI=YES
    make -j 4
 
-CUDA build:
-   (this build requires CMake 3.8 or newer)
-   mkdir <mfem-build-dir> ; cd <mfem-build-dir>
-   cmake <mfem-source-dir> -DMFEM_USE_CUDA=YES
-   make -j 4
-
 Example codes (serial/parallel, depending on the build):
    make examples -j 4
 
@@ -169,18 +128,10 @@ Note that re-configuration is only needed to change the currently configured
 options. Several shortcut targets combining (re-)configuration and compilation
 are also defined:
 
-   make serial    -> Builds serial optimized version of the library
-   make parallel  -> Builds parallel optimized version of the library
-   make debug     -> Builds serial debug version of the library
-   make pdebug    -> Builds parallel debug version of the library
-   make cuda      -> Builds serial cuda optimized version of the library
-   make pcuda     -> Builds parallel cuda optimized version of the library
-   make cudebug   -> Builds serial cuda debug version of the library
-   make pcudebug  -> Builds parallel cuda debug version of the library
-   make hip       -> Builds serial hip optimized version of the library
-   make phip      -> Builds parallel hip optimized version of the library
-   make hipdebug  -> Builds serial hip debug version of the library
-   make phipdebug -> Builds parallel hip debug version of the library
+   make serial   -> Builds serial optimized version of the library
+   make parallel -> Builds parallel optimized version of the library
+   make debug    -> Builds serial debug version of the library
+   make pdebug   -> Builds parallel debug version of the library
 
 Note that any of the above shortcuts accept configuration options, either at the
 command line or through a user configuration file.
@@ -242,9 +193,8 @@ Configuration options (GNU make)
 See the configuration file config/defaults.mk for the default settings.
 
 Compilers:
-   CXX      - C++ compiler, serial build
-   MPICXX   - MPI C++ compiler, parallel build
-   CUDA_CXX - The CUDA compiler, 'nvcc'
+   CXX    - C++ compiler, serial build
+   MPICXX - MPI C++ compiler, parallel build
 
 Compiler options:
    OPTIM_FLAGS - Options for optimized build
@@ -280,7 +230,7 @@ MFEM_DEBUG = YES/NO
    and consistency checks that may simplify bug-hunting.
 
 MFEM_USE_EXCEPTIONS = YES/NO
-   Enable the use of exceptions. In particular, modifies the default behavior
+   Enable the use of exceptions. In particular, modifies the default bahavior
    when errors are encountered: throw an exception, instead of aborting.
 
 MFEM_USE_LIBUNWIND = YES/NO
@@ -300,12 +250,8 @@ MFEM_THREAD_SAFE = YES/NO
    Use thread-safe implementation for some classes/methods. This comes at the
    cost of extra memory allocation and de-allocation.
 
-MFEM_USE_LEGACY_OPENMP = YES/NO
-   Enable (basic) experimental OpenMP support. Requires MFEM_THREAD_SAFE.
-   This option is deprecated.
-
 MFEM_USE_OPENMP = YES/NO
-   Enable the OpenMP backend.
+   Enable (basic) experimental OpenMP support. Requires MFEM_THREAD_SAFE.
 
 MFEM_USE_MEMALLOC = YES/NO
    Internal MFEM option: enable batch allocation for some small objects.
@@ -350,12 +296,6 @@ MFEM_USE_STRUMPACK = YES/NO
    classes. When enabled, this option uses the STRUMPACK_* library options, see
    below.
 
-MFEM_USE_GINKGO = YES/NO
-   Enable MFEM functionality based on the Ginkgo library, which provides
-   iterative linear solvers and preconditioners with OpenMP, CUDA backends, see
-   https://github.com/ginkgo-project/ginkgo. When enabled, the user can use
-   Ginkgo's solvers and preconditioners as shown in examples/ginkgo/.
-
 MFEM_USE_GNUTLS = YES/NO
    Enable secure socket support in class socketstream, using the auxiliary
    GnuTLS_* classes, based on the GnuTLS library. This option may be useful in
@@ -390,11 +330,11 @@ MFEM_USE_MPFR = YES/NO
    see below.
 
 MFEM_USE_SIDRE = YES/NO
-   Sidre is a component of LLNL's axom project, https://github.com/LLNL/axom,
-   that provides an HDF5-based file format for visualization or restart
-   capability following the Conduit (https://github.com/LLNL/conduit) mesh
-   blueprint specification. When enabled, this option requires installation of
-   HDF5 (see also MFEM_USE_NETCDF), Conduit and LLNL's axom project.
+   Sidre is a component of LLNL's axom project, http://goo.gl/cZyJdn, that
+   provides an HDF5-based file format for visualization or restart capability
+   following the Conduit (https://github.com/LLNL/conduit) mesh blueprint
+   specification. When enabled, this option requires installation of HDF5 (see
+   also MFEM_USE_NETCDF), Conduit and LLNL's axom project.
 
 MFEM_USE_CONDUIT = YES/NO
    Enables support for converting MFEM Mesh and Grid Function objects to and
@@ -403,15 +343,10 @@ MFEM_USE_CONDUIT = YES/NO
    an installation of Conduit. If Conduit was built with HDF5 support, it also
    requires an installation of HDF5 (see also MFEM_USE_NETCDF).
 
-MFEM_USE_ADIOS2 = YES/NO
-   Enables support for ADIOS2, version 2 of the adaptable input output system
-   for scientific data management. In MFEM, ADIOS2 provides parallel I/O with
-   ParaView visualization.
-
-MFEM_USE_ZLIB = YES/NO
+MFEM_USE_GZSTREAM = YES/NO
    Enables use of on-the-fly gzip compressed streams. With this feature enabled
    (YES), MFEM can compress its output files on-the-fly. In addition, it can
-   read back files compressed with zlib (or any compression utility capable
+   read back files compressed with gzstream (or any compression utility capable
    of creating a gzip-compatible output such as gzip).
    MFEM will write compressed files if the mode argument in the constructor
    includes a 'z' character. With this feature disabled (NO), MFEM will not be
@@ -427,53 +362,6 @@ MFEM_USE_PUMI = YES/NO
    models and effectively supports automated adaptive analysis. PUMI enables
    support for parallel unstructured mesh modifications in MFEM.
 
-MFEM_USE_UMPIRE = YES/NO
-   Enables support for Umpire, a resource management library that allows the
-   discovery, provision, and management of memory on machines with multiple
-   memory devices like NUMA and GPUs.
-
-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_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
-   units (GPUs). The variable CUDA_ARCH is used to specify the CUDA compute
-   capability used during compilation (by default, CUDA_ARCH=sm_60). When
-   enabled, this option uses the CUDA_* build options, see below.
-
-MFEM_USE_HIP = YES/NO
-   Enables support for AMD devices in MFEM. HIP is a heterogeneous-compute
-   interface for portability developed by AMD that can target both AMD and
-   NVIDIA GPUs. The variable HIP_ARCH is used to specify the AMD GPU processor
-   used during compilation (by default, HIP_ARCH=gfx900).  When enabled, this
-   option uses the HIP_* build options, see below.
-
-MFEM_USE_RAJA = YES/NO
-   Enable support for the RAJA performance portability layer in MFEM. RAJA
-   provides a portable abstraction for loops, supporting different programming
-   model backends. When using RAJA built with CUDA support, CUDA support must be
-   also enabled in MFEM, i.e. MFEM_USE_CUDA=YES must be set.
-
-MFEM_USE_OCCA = YES/NO
-   Enables support for the OCCA library in MFEM. OCCA is an open-source library
-   which aims to make it easy to program different types of devices (e.g. CPU,
-   GPU, FPGA) by providing an unified API for interacting with JIT-compiled
-   backends. In order to use the OCCA CUDA backend, CUDA support must be enabled
-   in MFEM as well, i.e. MFEM_USE_CUDA=YES must be set.
-
-MFEM_USE_GSLIB = YES/NO
-   Enables MFEM functionality based on the GSLIB library, and specifically its
-   FindPoints component, which provides a robust algorithms to evaluate finite
-   element functions in a collection of points in physical space. When enabled,
-   the user can use the GSLIB-FindPoints methods as shown in miniapps/gslib.
-
-MFEM_USE_CEED = YES/NO
-   Enables support for the libCEED library in MFEM. libCEED is a portable
-   library for performant high-order operator evaluation developed by the Center
-   for Efficient Exascale Discretizations in the Exascale Computing Project.
-
 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.
@@ -495,15 +383,13 @@ directory and use the string @MFEM_DIR@, e.g. HYPRE_OPT = -I@MFEM_DIR@/../hypre.
 The specific libraries and their options are:
 
 - HYPRE, required for the parallel build, i.e. when MFEM_USE_MPI = YES.
-  URL: https://github.com/hypre-space/hypre and https://www.llnl.gov/casc/hypre
+  URL: http://www.llnl.gov/CASC/hypre
   Options: HYPRE_OPT, HYPRE_LIB.
-  Versions: HYPRE >= 2.10.0b.
 
 - METIS, used when MFEM_USE_METIS = YES. If using METIS 5, set
   MFEM_USE_METIS_5 = YES (default is to use METIS 4).
   URL: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
   Options: METIS_OPT, METIS_LIB.
-  Versions: METIS 4.0.3 or 5.1.0.
 
 - LAPACK (optional), used when MFEM_USE_LAPACK = YES. Alternative, optimized
   implementations can also be used, e.g. the ATLAS project.
@@ -511,8 +397,7 @@ The specific libraries and their options are:
        http://math-atlas.sourceforge.net (ATLAS)
   Options: LAPACK_OPT (currently not used/needed), LAPACK_LIB.
 
-- OpenMP (optional), usually part of compiler, used when either MFEM_USE_OPENMP
-  or MFEM_USE_LEGACY_OPENMP is set to YES.
+- OpenMP (optional), usually part of compiler, used when MFEM_USE_OPENMP = YES.
   Options: OPENMP_OPT, OPENMP_LIB.
 
 - High-resolution POSIX clocks: when using MFEM_TIMER_TYPE = 2, it may be
@@ -522,12 +407,10 @@ The specific libraries and their options are:
 - SUNDIALS (optional), used when MFEM_USE_SUNDIALS = YES.
   Beginning with MFEM v3.3, SUNDIALS v2.7.0 is supported.
   Beginning with MFEM v3.3.2, SUNDIALS v3.0.0 is also supported.
-  Beginning with MFEM v4.1, only SUNDIALS v5.0.0+ is supported.
   If MFEM_USE_MPI is enabled, we expect that SUNDIALS is built with support for
   both MPI and hypre.
   URL: http://computation.llnl.gov/projects/sundials/sundials-software
   Options: SUNDIALS_OPT, SUNDIALS_LIB.
-  Versions: SUNDIALS >= 5.0.0.
 
 - Mesquite (optional), used when MFEM_USE_MESQUITE = YES.
   URL: http://trilinos.org/oldsite/packages/mesquite
@@ -536,7 +419,6 @@ The specific libraries and their options are:
 - SuiteSparse (optional), used when MFEM_USE_SUITESPARSE = YES.
   URL: http://faculty.cse.tamu.edu/davis/suitesparse.html
   Options: SUITESPARSE_OPT, SUITESPARSE_LIB.
-  Versions: SuiteSparse >= 4.5.4, older versions may work too.
 
 - SuperLU_DIST (optional), used when MFEM_USE_SUPERLU = YES. Note that
   SuperLU_DIST requires ParMETIS, which includes METIS 5 in its distribution.
@@ -544,30 +426,20 @@ The specific libraries and their options are:
   same location.
   URL: http://crd-legacy.lbl.gov/~xiaoye/SuperLU
   Options: SUPERLU_OPT, SUPERLU_LIB.
-  Versions: SuperLU_DIST >= 5.1.0.
 
 - STRUMPACK (optional), used when MFEM_USE_STRUMPACK = YES. Note that STRUMPACK
   requires the PT-Scotch and Scalapack libraries as well as ParMETIS, which
-  includes METIS 5 in its distribution. Starting with STRUMPACK v2.2.0, ParMETIS
-  and PT-Scotch are optional dependencies.
+  includes METIS 5 in its distribution.
   The support for STRUMPACK was added in MFEM v3.3.2 and it requires STRUMPACK
   2.0.0 or later.
   URL: http://portal.nersc.gov/project/sparse/strumpack
   Options: STRUMPACK_OPT, STRUMPACK_LIB.
-  Versions: STRUMPACK >= 3.0.0, requires HYPRE < 2.16.0.
-
-- Ginkgo (optional), used when MFEM_USE_GINKGO = YES. Note that Ginkgo needs a
-  C++ compiler that supports the C++-11 standard. For additional requirements
-  and dependencies of specific modules see the Ginkgo webpage below.
-  URL: https://ginkgo-project.github.io
-  Options: GINKGO_OPT (Not used), GINKGO_LIB.
 
 - GnuTLS (optional), used when MFEM_USE_GNUTLS = YES. On most Linux systems,
   GnuTLS is available as a development package, e.g. gnutls-devel. On Mac OS X,
   one can get the library through the Homebrew package manager (http://brew.sh).
   URL: http://gnutls.org
   Options: GNUTLS_OPT, GNUTLS_LIB.
-  Versions: GnuTLS >= 2.12.0, older versions may work too.
 
 - NetCDF (optional), used when MFEM_USE_NETCDF = YES, required for reading Cubit
   mesh files. Also requires installation of HDF5 and ZLIB, as explained at the
@@ -575,7 +447,6 @@ The specific libraries and their options are:
   don't need the C++ or parallel versions.
   URL: www.unidata.ucar.edu/software/netcdf
   Options: NETCDF_OPT, NETCDF_LIB.
-  Versions: NetCDF >= 4.4.0.
 
 - PETSc (optional), used when MFEM_USE_PETSC = YES. Version 3.8 or higher of
   the PETSC dev branch is required. The MFEM and PETSc builds can share common
@@ -587,76 +458,22 @@ The specific libraries and their options are:
                 --with-shared-libraries=0
   URL: https://www.mcs.anl.gov/petsc
   Options: PETSC_OPT, PETSC_LIB.
-  Versions: PETSc >= 3.8.0.
 
 - Sidre (optional), part of LLNL's axom project, used when MFEM_USE_SIDRE = YES.
-  Starting with MFEM v4.1, Axom version 0.3.1 or later is required.
-  URL: https://github.com/LLNL/axom
+  URL: http://goo.gl/cZyJdn (axom, to be released)
        https://github.com/LLNL/conduit (Conduit)
        https://support.hdfgroup.org/HDF5 (HDF5)
   Options: SIDRE_OPT, SIDRE_LIB.
-  Versions: Axom >= 0.3.1.
 
-- Conduit (optional), used when MFEM_USE_CONDUIT = YES. Conduit Mesh Blueprint
+- Conduit, used when MFEM_USE_CONDUIT = YES. Direct Conduit Mesh Blueprint
   support requires Conduit >= v0.3.1 and VisIt >= v2.13.1 to read the output.
   URL: https://github.com/LLNL/conduit (Conduit)
        https://support.hdfgroup.org/HDF5 (HDF5)
   Options: CONDUIT_OPT, CONDUIT_LIB.
-  Versions: Conduit >= 0.3.1.
 
-- ADIOS2 (optional) used when MFEM_USE_ADIOS2 = YES.
-  URL: https://adios2.readthedocs.io/
-
-- PUMI (optional), used when MFEM_USE_PUMI = YES.
+- PUMI, used when MFEM_USE_PUMI = YES.
   URL: https://scorec.rpi.edu/pumi
   Options: PUMI_OPT, PUMI_LIB.
-  Versions: PUMI >= 2.2.0.
-
-- HiOp (optional), used when MFEM_USE_HIOP = YES.
-  URL: https://github.com/LLNL/hiop
-  Options: HIOP_OPT, HIOP_LIB.
-
-- GSLIB (optional), used when MFEM_USE_GSLIB = YES. The gslib library must be
-  built prior to the MFEM build, as follows: download gslib-1.0.5, untar it at
-  the same level as MFEM and create a symbolic link: "ln -s gslib-1.0.5 gslib".
-  Build gslib in parallel or in serial based on the desired MFEM build: "make
-  clean; make CC=mpicc" or "make clean; make CC=gcc MPI=0". Build MFEM with
-  MFEM_USE_GSLIB=YES.
-  URL: https://github.com/gslib/gslib/archive/v1.0.5.tar.gz
-  Options: GSLIB_OPT, GSLIB_LIB.
-  Versions: GSLIB >= 1.0.5.
-
-- CUDA (optional), used when MFEM_USE_CUDA = YES.
-  URL: https://developer.nvidia.com/cuda-toolkit
-  Options: CUDA_CXX, CUDA_ARCH, CUDA_OPT, CUDA_LIB.
-  Versions: CUDA >= 9.1, older versions may work too.
-
-- HIP (optional), used when MFEM_USE_HIP = YES.
-  URL: https://rocm.github.io/ROCmInstall.html
-  Options: HIP_CXX, HIP_ARCH, HIP_OPT, HIP_LIB.
-
-- OCCA (optional), used when MFEM_USE_OCCA = YES.
-  URL: https://libocca.org
-  Options: OCCA_DIR, OCCA_OPT, OCCA_LIB.
-  Versions: OCCA >= 1.0.9.
-
-- libCEED (optional), used when MFEM_USE_CEED = YES. Requires libCEED v0.6
-  or later version, specifically, git-hash 3d05795 or later.
-  URL: https://github.com/CEED/libCEED
-       https://ceed.exascaleproject.org/libceed
-  Options: CEED_DIR, CEED_OPT, CEED_LIB.
-  Versions: libCEED >= 0.6.
-
-- RAJA (optional), used when MFEM_USE_RAJA = YES.
-  Beginning with MFEM v4.1, only RAJA v0.10.0+ is supported.
-  URL: https://github.com/LLNL/RAJA
-  Options: RAJA_DIR, RAJA_OPT, RAJA_LIB.
-  Versions: RAJA >= 0.10.0.
-
-- Umpire, used when MFEM_USE_UMPIRE = YES.
-  URL: https://github.com/LLNL/Umpire
-  Options: UMPIRE_DIR, UMPIRE_OPT, UMPIRE_LIB.
-  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
@@ -668,11 +485,12 @@ The specific libraries and their options are:
   URL: http://www.nongnu.org/libunwind
   Options: LIBUNWIND_OPT, LIBUNWIND_LIB.
 
-- ZLIB (optional), used when MFEM_USE_ZLIB = YES, or when MFEM_USE_NETCDF =
+- ZLIB (optional), used when MFEM_USE_GZSTREAM = YES, or when MFEM_USE_NETCDF =
   YES (in the default settings for NETCDF_OPT and NETCDF_LIB).
   URL: https://zlib.net
   Options: ZLIB_OPT, ZLIB_LIB.
 
+
 Building with CMake
 ===================
 The MFEM build system consists of two steps: configuration and compilation.
@@ -761,8 +579,6 @@ Configuration variables (CMake)
 ===============================
 See the configuration file config/defaults.cmake for the default settings.
 
-Note: the option MFEM_USE_CUDA requires CMake version 3.8 or newer!
-
 Non-standard CMake variables for compilers:
    CXX    - If set, overwrite the auto-detected C++ compiler, serial build
    MPICXX - If set, overwrite the auto-detected MPI C++ compiler, parallel build
@@ -780,7 +596,6 @@ MFEM_USE_METIS - Set to ${MFEM_USE_MPI}, can be overwritten.
 MFEM_USE_LIBUNWIND
 MFEM_USE_LAPACK
 MFEM_THREAD_SAFE
-MFEM_USE_LEGACY_OPENMP
 MFEM_USE_OPENMP
 MFEM_USE_MEMALLOC
 MFEM_TIMER_TYPE - Set automatically, can be overwritten.
@@ -788,19 +603,11 @@ MFEM_USE_MESQUITE
 MFEM_USE_SUITESPARSE
 MFEM_USE_SUPERLU
 MFEM_USE_STRUMPACK
-MFEM_USE_GINKGO
 MFEM_USE_GNUTLS
 MFEM_USE_NETCDF
 MFEM_USE_MPFR
-MFEM_USE_ZLIB
+MFEM_USE_GZSTREAM
 MFEM_USE_PUMI
-MFEM_USE_HIOP
-MFEM_USE_CUDA
-MFEM_USE_OCCA
-MFEM_USE_CEED
-MFEM_USE_RAJA
-MFEM_USE_UMPIRE
-MFEM_USE_SIDRE
 
 The following options are CMake specific:
 
@@ -841,18 +648,12 @@ The CMake build system adds auto-detection for the following packages/libraries:
  - SuiteSparse
  - SuperLUDist, STRUMPACK
  - ParMETIS
- - Ginkgo
  - GNUTLS - Extends the built-in CMake support, to search GNUTLS_DIR as well.
  - NETCDF
  - MPFR
  - LIBUNWIND
  - POSIXCLOCKS
  - PUMI
- - HIOP
- - OCCA
- - RAJA
- - UMPIRE
- - AXOM - Used when MFEM_USE_SIDRE is enabled
 
 The following built-in CMake packages are also used:
 

LICENSE

@@ -1,29 +1,504 @@
-BSD 3-Clause License
+		  GNU LESSER GENERAL PUBLIC LICENSE
+		       Version 2.1, February 1999
 
-Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC
-All rights reserved.
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
 
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+[This is the first released version of the Lesser GPL.  It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
 
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
+			    Preamble
 
-* Redistributions in binary form must reproduce the above copyright notice,
-  this list of conditions and the following disclaimer in the documentation
-  and/or other materials provided with the distribution.
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
+  This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it.  You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations below.
+
+  When we speak of free software, we are referring to freedom of use,
+not price.  Our General Public Licenses are designed to make sure that
+you have the freedom to distribute copies of free software (and charge
+for this service if you wish); that you receive source code or can get
+it if you want it; that you can change the software and use pieces of
+it in new free programs; and that you are informed that you can do
+these things.
+
+  To protect your rights, we need to make restrictions that forbid
+distributors to deny you these rights or to ask you to surrender these
+rights.  These restrictions translate to certain responsibilities for
+you if you distribute copies of the library or if you modify it.
+
+  For example, if you distribute copies of the library, whether gratis
+or for a fee, you must give the recipients all the rights that we gave
+you.  You must make sure that they, too, receive or can get the source
+code.  If you link other code with the library, you must provide
+complete object files to the recipients, so that they can relink them
+with the library after making changes to the library and recompiling
+it.  And you must show them these terms so they know their rights.
+
+  We protect your rights with a two-step method: (1) we copyright the
+library, and (2) we offer you this license, which gives you legal
+permission to copy, distribute and/or modify the library.
+
+  To protect each distributor, we want to make it very clear that
+there is no warranty for the free library.  Also, if the library is
+modified by someone else and passed on, the recipients should know
+that what they have is not the original version, so that the original
+author's reputation will not be affected by problems that might be
+introduced by others.
+
+  Finally, software patents pose a constant threat to the existence of
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+
+That's all there is to it!
 
-* Neither the name of the copyright holder nor the names of its
-  contributors may be used to endorse or promote products derived from
-  this software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

NOTICE

@@ -1,31 +0,0 @@
-This work was produced under the auspices of the U.S. Department of Energy by
-Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
-
-This work was prepared as an account of work sponsored by an agency of
-the United States Government. Neither the United States Government nor
-Lawrence Livermore National Security, LLC, nor any of their employees
-makes any warranty, expressed or implied, or assumes any legal liability
-or responsibility for the accuracy, completeness, or usefulness of any
-information, apparatus, product, or process disclosed, or represents that
-its use would not infringe privately owned rights.
-
-Reference herein to any specific commercial product, process, or service
-by trade name, trademark, manufacturer, or otherwise does not necessarily
-constitute or imply its endorsement, recommendation, or favoring by the
-United States Government or Lawrence Livermore National Security, LLC.
-
-The views and opinions of authors expressed herein do not necessarily
-state or reflect those of the United States Government or Lawrence
-Livermore National Security, LLC, and shall not be used for advertising
-or product endorsement purposes.
-
-Inclusion of external software:
-
-This project distributes the sources of several external software products with
-their own respective licenses which can be found in their code and attached
-license files. These software products and their licenses are as follows:
-
-* Gecko (general/gecko.{cpp,hpp}) -- BSD 3-clause license
-* Picojson (fem/picojson.h) -- Custom 2-clause license
-* Catch++  (tests/unit/catch.hpp) -- Boost 1.0 license
-* Zstr (general/zstr.hpp) -- MIT license

README

@@ -8,13 +8,13 @@
                                http://mfem.org
 
 MFEM is a modular parallel C++ library for finite element methods. Its goal is
-to enable high-performance scalable finite element discretization research and
-application development on a wide variety of platforms, ranging from laptops to
-supercomputers.
+to enable the research and development of scalable finite element discretization
+and solver algorithms through general finite element abstractions, accurate and
+flexible visualization, and tight integration with the hypre library.
 
 * For building instructions, see the file INSTALL, or type "make help".
 
-* Copyright and licensing information can be found in files LICENSE and NOTICE.
+* Copyright and licensing information can be found in the file COPYRIGHT.
 
 * The best starting point for new users interested in MFEM's features is the
   interactive documentation in examples/README.html.
@@ -39,31 +39,29 @@ conforming and non-conforming (AMR) adaptive refinement. Arbitrary element
 transformations, allowing for high-order mesh elements with curved boundaries,
 are also supported.
 
-When used as a "finite element to linear algebra translator", MFEM can take a
-problem described in terms of finite element-type objects, and produce the
-corresponding linear algebra vectors and fully or partially assembled operators,
-e.g. in the form of global sparse matrices or matrix-free operators. The library
-includes simple smoothers and Krylov solvers, such as PCG, MINRES and GMRES, as
-well as support for sequential sparse direct solvers from the SuiteSparse
+MFEM is commonly used as a "finite element to linear algebra translator", since
+it can take a problem described in terms of finite element-type objects, and
+produce the corresponding linear algebra vectors and sparse matrices. In order
+to facilitate this, MFEM uses compressed sparse row (CSR) sparse matrix storage
+and includes simple smoothers and Krylov solvers, such as PCG, MINRES and GMRES,
+as well as support for sequential sparse direct solvers from the SuiteSparse
 library. Nonlinear solvers (the Newton method), eigensolvers (LOBPCG), and
 several explicit and implicit Runge-Kutta time integrators are also available.
 
 MFEM supports MPI-based parallelism throughout the library, and can readily be
-used as a scalable unstructured finite element problem generator. As of version
-4.0, MFEM offers initial support for GPU acceleration, and programming models,
-such as CUDA, OCCA, RAJA and OpenMP. MFEM-based applications require minimal
-changes to switch from a serial to a high-performing MPI-parallel version of the
-code, where they can take advantage of the integrated linear solvers from the
-hypre library.  Comprehensive support for other external packages, e.g. PETSc
-and SUNDIALS is also included, giving access to many additional linear and
-nonlinear solvers, preconditioners, time integrators, etc.
+used as a scalable unstructured finite element problem generator. MFEM-based
+applications require minimal changes to transition from a serial to a
+high-performing parallel version of the code, where they can take advantage of
+the integrated scalable linear solvers from the hypre library. Comprehensive
+support for other external packages, e.g. PETSc and SUNDIALS is also included,
+giving access to many additional linear and nonlinear solvers, preconditioners,
+time integrators, etc.
 
 For examples of using MFEM, see the examples/ and miniapps/ directories, as well
 as the OpenGL visualization tool GLVis which is available at http://glvis.org.
 
-MFEM is distributed under the terms of the BSD-3 license. All new contributions
-must be made under this license. See LICENSE and NOTICE for details.
+This project is released under the LGPL v2.1 license with static linking
+exception. See files COPYRIGHT and LICENSE file for full details.
 
-SPDX-License-Identifier: BSD-3-Clause
-LLNL Release Number: LLNL-CODE-806117
+LLNL Release Number: LLNL-CODE-443211
 DOI: 10.11578/dc.20171025.1248

config/CMakeLists.txt

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 set(HDRS
  config.hpp

config/XSDKDefaults.cmake

@@ -74,7 +74,7 @@
 
 IF (NOT COMMAND PRINT_VAR)
   FUNCTION(PRINT_VAR  VAR_NAME)
-    MESSAGE(STATUS "${VAR_NAME} = '${${VAR_NAME}}'")
+    MESSAGE("-- " "${VAR_NAME} = '${${VAR_NAME}}'")
   ENDFUNCTION()
 ENDIF()
 
@@ -166,112 +166,17 @@ IF (USE_XSDK_DEFAULTS)
     ENDIF()
     XSDK_HANDLE_LANG_DEFAULTS(Fortran  FC  "FFLAGS;FCFLAGS")
   ENDIF()
-
+  
   # Set XSDK defaults for other CMake variables
-
+  
   IF ("${BUILD_SHARED_LIBS}"  STREQUAL  "")
     MESSAGE("-- " "XSDK: Setting default BUILD_SHARED_LIBS=TRUE")
     SET(BUILD_SHARED_LIBS  TRUE  CACHE  BOOL  "Set by default in XSDK mode")
   ENDIF()
-
+  
   IF ("${CMAKE_BUILD_TYPE}"  STREQUAL  "")
     MESSAGE("-- " "XSDK: Setting default CMAKE_BUILD_TYPE=DEBUG")
     SET(CMAKE_BUILD_TYPE  DEBUG  CACHE  STRING  "Set by default in XSDK mode")
   ENDIF()
 
 ENDIF()
-
-
-##################################################################################
-#
-#               MFEM-specific additions: set TPL MFEM_USE_* defaults
-#
-##################################################################################
-
-IF (DEFINED TPL_ENABLE_MPI)
-  SET(MFEM_USE_MPI ${TPL_ENABLE_MPI} CACHE BOOL "Enable MPI parallel build" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_METIS)
-  SET(MFEM_USE_METIS ${TPL_ENABLE_METIS} CACHE BOOL "Enable METIS usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_ZLIB)
-  SET(MFEM_USE_ZLIB ${TPL_ENABLE_ZLIB} CACHE BOOL "Enable zlib for compressed data streams." FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_LIBUNWIND)
-  SET(MFEM_USE_LIBUNWIND ${TPL_ENABLE_LIBUNWIND} CACHE BOOL "Enable backtrace for errors." FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_LAPACK)
-  SET(MFEM_USE_LAPACK ${TPL_ENABLE_LAPACK} CACHE BOOL "Enable LAPACK usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_SUNDIALS)
-  SET(MFEM_USE_SUNDIALS ${TPL_ENABLE_SUNDIALS} CACHE BOOL "Enable SUNDIALS usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_MESQUITE)
-  SET(MFEM_USE_MESQUITE ${TPL_ENABLE_MESQUITE} CACHE BOOL "Enable MESQUITE usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_SUITESPARSE)
-  SET(MFEM_USE_SUITESPARSE ${TPL_ENABLE_SUITESPARSE} CACHE BOOL "Enable SuiteSparse usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_SUPERLU)
-  SET(MFEM_USE_SUPERLU ${TPL_ENABLE_SUPERLU} CACHE BOOL "Enable SuperLU_DIST usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_STRUMPACK)
-  SET(MFEM_USE_STRUMPACK ${TPL_ENABLE_STRUMPACK} CACHE BOOL "Enable STRUMPACK usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_GINKGO)
-  SET(MFEM_USE_GINKGO ${TPL_ENABLE_GINKGO} CACHE BOOL "Enable GINKGO usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_GNUTLS)
-  SET(MFEM_USE_GNUTLS ${TPL_ENABLE_GNUTLS} CACHE BOOL "Enable GNUTLS usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_NETCDF)
-  SET(MFEM_USE_NETCDF ${TPL_ENABLE_NETCDF} CACHE BOOL "Enable NETCDF usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_PETSC)
-  SET(MFEM_USE_PETSC ${TPL_ENABLE_PETSC} CACHE BOOL "Enable PETSc support." FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_MPFR)
-  SET(MFEM_USE_MPFR ${TPL_ENABLE_MPFR} CACHE BOOL "Enable MPFR usage." FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_SIDRE)
-  SET(MFEM_USE_SIDRE ${TPL_ENABLE_SIDRE} CACHE BOOL "Enable Axom/Sidre usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_CONDUIT)
-  SET(MFEM_USE_CONDUIT ${TPL_ENABLE_CONDUIT} CACHE BOOL "Enable Conduit usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_PUMI)
-  SET(MFEM_USE_PUMI ${TPL_ENABLE_PUMI} CACHE BOOL "Enable PUMI" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_CUDA)
-  SET(MFEM_USE_CUDA ${TPL_ENABLE_CUDA} CACHE BOOL "Enable CUDA" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_OCCA)
-  SET(MFEM_USE_OCCA ${TPL_ENABLE_OCCA} CACHE BOOL "Enable OCCA" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_RAJA)
-  SET(MFEM_USE_RAJA ${TPL_ENABLE_RAJA} CACHE BOOL "Enable RAJA" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_UMPIRE)
-  SET(MFEM_USE_UMPIRE ${TPL_ENABLE_UMPIRE} CACHE BOOL "Enable Umpire" FORCE)
-ENDIF()

config/cmake/MFEMConfig.cmake.in

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at
+# the Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights
+# reserved. See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 include(${CMAKE_CURRENT_LIST_DIR}/MFEMConfigVersion.cmake)
 
@@ -20,12 +20,11 @@ set(MFEM_USE_METIS @MFEM_USE_METIS@)
 set(MFEM_USE_METIS_5 @MFEM_USE_METIS_5@)
 set(MFEM_DEBUG @MFEM_DEBUG@)
 set(MFEM_USE_EXCEPTIONS @MFEM_USE_EXCEPTIONS@)
-set(MFEM_USE_ZLIB @MFEM_USE_ZLIB@)
+set(MFEM_USE_GZSTREAM @MFEM_USE_GZSTREAM@)
 set(MFEM_USE_LIBUNWIND @MFEM_USE_LIBUNWIND@)
 set(MFEM_USE_LAPACK @MFEM_USE_LAPACK@)
 set(MFEM_THREAD_SAFE @MFEM_THREAD_SAFE@)
 set(MFEM_USE_OPENMP @MFEM_USE_OPENMP@)
-set(MFEM_USE_LEGACY_OPENMP @MFEM_USE_LEGACY_OPENMP@)
 set(MFEM_USE_MEMALLOC @MFEM_USE_MEMALLOC@)
 set(MFEM_TIMER_TYPE @MFEM_TIMER_TYPE@)
 set(MFEM_USE_SUNDIALS @MFEM_USE_SUNDIALS@)
@@ -33,21 +32,14 @@ set(MFEM_USE_MESQUITE @MFEM_USE_MESQUITE@)
 set(MFEM_USE_SUITESPARSE @MFEM_USE_SUITESPARSE@)
 set(MFEM_USE_SUPERLU @MFEM_USE_SUPERLU@)
 set(MFEM_USE_STRUMPACK @MFEM_USE_STRUMPACK@)
-set(MFEM_USE_GINKGO @MFEM_USE_GINKGO@)
+set(MFEM_USE_GECKO @MFEM_USE_GECKO@)
 set(MFEM_USE_GNUTLS @MFEM_USE_GNUTLS@)
-set(MFEM_USE_GSLIB @MFEM_USE_GSLIB@)
 set(MFEM_USE_NETCDF @MFEM_USE_NETCDF@)
 set(MFEM_USE_PETSC @MFEM_USE_PETSC@)
 set(MFEM_USE_MPFR @MFEM_USE_MPFR@)
 set(MFEM_USE_SIDRE @MFEM_USE_SIDRE@)
 set(MFEM_USE_CONDUIT @MFEM_USE_CONDUIT@)
 set(MFEM_USE_PUMI @MFEM_USE_PUMI@)
-set(MFEM_USE_CUDA @MFEM_USE_CUDA@)
-set(MFEM_USE_OCCA @MFEM_USE_OCCA@)
-set(MFEM_USE_RAJA @MFEM_USE_RAJA@)
-set(MFEM_USE_CEED @MFEM_USE_CEED@)
-set(MFEM_USE_UMPIRE @MFEM_USE_UMPIRE@)
-set(MFEM_USE_ADIOS2 @MFEM_USE_ADIOS2@)
 
 set(MFEM_CXX_COMPILER "@CMAKE_CXX_COMPILER@")
 set(MFEM_CXX_FLAGS "@CMAKE_CXX_FLAGS@")

config/cmake/config.hpp.in

@@ -1,13 +1,13 @@
-// Copyright (c) 2010-2020, 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.
+// Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at
+// the Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights
+// reserved. See file COPYRIGHT for details.
 //
 // This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
+// availability see http://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.
+// terms of the GNU Lesser General Public License (as published by the Free
+// Software Foundation) version 2.1 dated February 1999.
 
 #ifndef MFEM_CONFIG_HEADER
 #define MFEM_CONFIG_HEADER
@@ -30,12 +30,6 @@
 #define MFEM_VERSION_MINOR (((MFEM_VERSION)/100)%100)
 #define MFEM_VERSION_PATCH ((MFEM_VERSION)%100)
 
-// MFEM source directory.
-#define MFEM_SOURCE_DIR "@MFEM_SOURCE_DIR@"
-
-// MFEM install directory.
-#define MFEM_INSTALL_DIR "@MFEM_INSTALL_DIR@"
-
 // Description of the git commit used to build MFEM.
 #cmakedefine MFEM_GIT_STRING "@MFEM_GIT_STRING@"
 
@@ -49,8 +43,8 @@
 // Throw an exception on errors.
 #cmakedefine MFEM_USE_EXCEPTIONS
 
-// Enable zlib in MFEM.
-#cmakedefine MFEM_USE_ZLIB
+// Enable gzstream in MFEM.
+#cmakedefine MFEM_USE_GZSTREAM
 
 // Enable backtraces for mfem_error through libunwind.
 #cmakedefine MFEM_USE_LIBUNWIND
@@ -68,12 +62,9 @@
 // allocation and de-allocation.
 #cmakedefine MFEM_THREAD_SAFE
 
-// Enable the OpenMP backend.
+// Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
 #cmakedefine MFEM_USE_OPENMP
 
-// [Deprecated] Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
-#cmakedefine MFEM_USE_LEGACY_OPENMP
-
 // Enable MFEM functionality based on the Mesquite library.
 #cmakedefine MFEM_USE_MESQUITE
 
@@ -89,15 +80,12 @@
 // Internal MFEM option: enable group/batch allocation for some small objects.
 #cmakedefine MFEM_USE_MEMALLOC
 
-// Enable functionality based on the Ginkgo library
-#cmakedefine MFEM_USE_GINKGO
+// Enable functionality based on the Gecko library
+#cmakedefine MFEM_USE_GECKO
 
 // Enable MFEM functionality based on the GnuTLS library
 #cmakedefine MFEM_USE_GNUTLS
 
-// Enable MFEM functionality based on the GSLIB library
-#cmakedefine MFEM_USE_GSLIB
-
 // Enable MFEM functionality based on the NetCDF library
 #cmakedefine MFEM_USE_NETCDF
 
@@ -113,28 +101,6 @@
 // Enable MFEM functionality based on the PUMI library
 #cmakedefine MFEM_USE_PUMI
 
-// Enable MFEM functionality based on the HiOp library
-#cmakedefine MFEM_USE_HIOP
-
-// Build the GPU/CUDA-enabled version of the MFEM library.
-// Requires a CUDA compiler (nvcc).
-#cmakedefine MFEM_USE_CUDA
-
-// Enable MFEM functionality based on the RAJA library
-#cmakedefine MFEM_USE_RAJA
-
-// Enable MFEM functionality based on the OCCA library
-#cmakedefine MFEM_USE_OCCA
-
-// Enable MFEM functionality based on the libCEED library
-#cmakedefine MFEM_USE_CEED
-
-// Enable MFEM functionality based on the Umpire library
-#cmakedefine MFEM_USE_UMPIRE
-
-// Enable MFEM functionality based on the ADIOS2 library
-#cmakedefine MFEM_USE_ADIOS2
-
 // Which library functions to use in class StopWatch for measuring time.
 // For a list of the available options, see INSTALL.
 // If not defined, an option is selected automatically.
@@ -143,6 +109,10 @@
 // Enable MFEM functionality based on the SUNDIALS libraries.
 #cmakedefine MFEM_USE_SUNDIALS
 
+// Windows specific options
+// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
+#cmakedefine _USE_MATH_DEFINES
+
 // Version of HYPRE used for building MFEM.
 #cmakedefine MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@
 

config/cmake/modules/FindADIOS2.cmake

@@ -1,52 +0,0 @@
-#------------------------------------------------------------------------------#
-# Distributed under the OSI-approved Apache License, Version 2.0.  See
-# accompanying file Copyright.txt for details.
-#------------------------------------------------------------------------------#
-#
-# FindADIOS2
-# -----------
-#
-# Try to find the ADIOS2 library
-#
-# This module defines the following variables:
-#
-#   ADIOS2_FOUND        - System has ADIOS2
-#   ADIOS2_INCLUDE_DIRS - The ADIOS2 include directory
-#   ADIOS2_LIBRARIES    - Link these to use ADIOS2
-#
-# and the following imported targets:
-#   ADIOS2::ADIOS2 - The ADIOS2 compression library target
-#
-# You can also set the following variable to help guide the search:
-#   ADIOS2_DIR - The install prefix for ADIOS2 containing the
-#              include and lib folders
-#              Note: this can be set as a CMake variable or an
-#                    environment variable.  If specified as a CMake
-#                    variable, it will override any setting specified
-#                    as an environment variable.
-
-if(NOT ADIOS2_FOUND)
-  if((NOT ADIOS2_DIR) AND (NOT (ENV{ADIOS2_DIR} STREQUAL "")))
-    set(ADIOS2_DIR "$ENV{ADIOS2_DIR}")
-  endif()
-  if(ADIOS2_DIR)
-    set(ADIOS2_INCLUDE_OPTS HINTS ${ADIOS2_DIR}/include NO_DEFAULT_PATHS)
-    set(ADIOS2_LIBRARY_OPTS
-      HINTS ${ADIOS2_DIR}/lib ${ADIOS2_DIR}/lib64
-      NO_DEFAULT_PATHS
-    )
-  endif()
-
-  find_path(ADIOS2_INCLUDE_DIR adios2.h ${ADIOS2_INCLUDE_OPTS})
-  find_library(ADIOS2_LIBRARY NAMES adios2 ${ADIOS2_LIBRARY_OPTS}) 
-
-  include(FindPackageHandleStandardArgs)
-  find_package_handle_standard_args(ADIOS2
-    FOUND_VAR ADIOS2_FOUND
-    REQUIRED_VARS ADIOS2_LIBRARY ADIOS2_INCLUDE_DIR
-  )
-  if(ADIOS2_FOUND)
-    set(ADIOS2_INCLUDE_DIRS ${ADIOS2_INCLUDE_DIR})
-    set(ADIOS2_LIBRARIES ${ADIOS2_LIBRARY})
-  endif()
-endif()

config/cmake/modules/FindAxom.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Defines the following variables:
 #   - AXOM_FOUND
@@ -18,4 +18,6 @@ include(MfemCmakeUtilities)
 # Note: components are enabled based on the find_package() parameters.
 mfem_find_package(Axom AXOM AXOM_DIR "include" "" "lib" ""
   "Paths to headers required by Axom." "Libraries required by Axom."
-  ADD_COMPONENT Axom "include" axom/config.hpp "lib" axom)
+  ADD_COMPONENT Sidre "include" sidre/sidre.hpp "lib" sidre
+  ADD_COMPONENT SLIC "include" slic/slic.hpp "lib" slic
+  ADD_COMPONENT axom_utils "include" axom_utils/Utilities.hpp "lib" axom_utils)

config/cmake/modules/FindCXXABIDemangle.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Check for "abi::__cxa_demangle" in <cxxabi.h>.
 # Defines the variables:

config/cmake/modules/FindConduit.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Defines the following variables:
 #   - CONDUIT_FOUND

config/cmake/modules/FindGSLIB.cmake

@@ -1,19 +0,0 @@
-# Copyright (c) 2010-2020, 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:
-#   - GSLIB_FOUND
-#   - GSLIB_LIBRARIES
-#   - GSLIB_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(gslib GSLIB GSLIB_DIR "include" gslib.h "lib" gs
-  "Paths to headers required by GSLIB." "Libraries required by GSLIB.")

config/cmake/modules/FindGecko.cmake

@@ -0,0 +1,19 @@
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability see http://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
+
+# Defines the following variables:
+#   - GECKO_FOUND
+#   - GECKO_LIBRARIES
+#   - GECKO_INCLUDE_DIRS
+
+include(MfemCmakeUtilities)
+mfem_find_package(Gecko GECKO GECKO_DIR "include;inc" graph.h "lib" gecko
+  "Paths to headers required by Gecko." "Libraries required by Gecko.")

config/cmake/modules/FindHIOP.cmake

@@ -1,36 +0,0 @@
-# Copyright (c) 2010-2020, 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.
-
-# Sets the following variables:
-#   - HIOP_FOUND
-#   - HIOP_INCLUDE_DIRS
-#   - HIOP_LIBRARIES
-
-include(MfemCmakeUtilities)
-mfem_find_package(HIOP HIOP HIOP_DIR
-  "include" "hiopInterface.hpp"
-  "lib" "hiop"
-  "Paths to headers required by HIOP."
-  "Libraries required by HIOP.")
-
-# this test fails with parallel MFEM since mpi.h is not available (cxx compiler is used for some reason)
-#  CHECK_BUILD HIOP_VERSION_OK TRUE
-#"
-##include <hiopInterface.hpp>
-#using namespace hiop;
-#int main(int argc, char *argv[])
-#{
-#   MPI_Init(&argc, &argv);
-#   MPI_Comm comm = MPI_COMM_WORLD;
-#
-#   return 0;
-#}
-#")

config/cmake/modules/FindHYPRE.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Defines the following variables:
 #   - HYPRE_FOUND

config/cmake/modules/FindLIBDL.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Find libdl.
 # Defines:

config/cmake/modules/FindLibunwind.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Find libunwind.
 # Defines the following variables:

config/cmake/modules/FindMETIS.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Defines the following variables:
 #   - METIS_FOUND

config/cmake/modules/FindMFEMBacktrace.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Find the libraries needed for backtrace in MFEM. This is a "meta-package",
 # i.e. it simply combines all packages from MFEMBacktrace_REQUIRED_PACKAGES.

config/cmake/modules/FindMPFR.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Find MPFR.
 # Defines the following variables:

config/cmake/modules/FindMesquite.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Defines the following variables:
 #   - MESQUITE_FOUND

config/cmake/modules/FindNetCDF.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Defines the following variables:
 #   - NETCDF_FOUND

config/cmake/modules/FindOCCA.cmake

@@ -1,19 +0,0 @@
-# Copyright (c) 2010-2020, 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:
-#   - OCCA_FOUND
-#   - OCCA_LIBRARIES
-#   - OCCA_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(OCCA OCCA OCCA_DIR "include" "occa.hpp" "lib" "occa"
-  "Paths to headers required by OCCA." "Libraries required by OCCA.")

config/cmake/modules/FindPOSIXClocks.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Find POSIX clocks.
 # Defines:

config/cmake/modules/FindParMETIS.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Sets the following variables
 #   - ParMETIS_FOUND

config/cmake/modules/FindRAJA.cmake

@@ -1,30 +0,0 @@
-# Copyright (c) 2010-2020, 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:
-#   - RAJA_FOUND
-#   - RAJA_LIBRARIES
-#   - RAJA_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(RAJA RAJA RAJA_DIR "include" "RAJA/RAJA.hpp" "lib" "RAJA"
-  "Paths to headers required by RAJA." "Libraries required by RAJA.")
-
-if (NOT RAJA_CONFIG_CMAKE)
-   set(RAJA_CONFIG_CMAKE "${RAJA_DIR}/share/raja/cmake/raja-config.cmake")
-endif()
-if (EXISTS "${RAJA_CONFIG_CMAKE}")
-   include("${RAJA_CONFIG_CMAKE}")
-   if (ENABLE_CUDA AND NOT MFEM_USE_CUDA)
-      message(FATAL_ERROR
-         "RAJA is built with CUDA: MFEM_USE_CUDA=YES is required")
-   endif()
-endif()

config/cmake/modules/FindSTRUMPACK.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Sets the following variables:
 #   - STRUMPACK_FOUND

config/cmake/modules/FindSUNDIALS.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Defines the following variables:
 #   - SUNDIALS_FOUND

config/cmake/modules/FindScotch.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Sets the following variables:
 #   - Scotch_FOUND

config/cmake/modules/FindSuiteSparse.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Sets the following variables
 #   - SuiteSparse_FOUND

config/cmake/modules/FindSuperLUDist.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Sets the following variables:
 #   - SuperLUDist_FOUND

config/cmake/modules/FindUMPIRE.cmake

@@ -1,19 +0,0 @@
-# Copyright (c) 2010-2020, 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:
-#   - UMPIRE_FOUND
-#   - UMPIRE_LIBRARIES
-#   - UMPIRE_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(UMPIRE UMPIRE UMPIRE_DIR "include" "umpire/Umpire.hpp" "lib" "umpire"
-  "Paths to headers required by UMPIRE." "Libraries required by UMPIRE.")

config/cmake/modules/Find_GnuTLS.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Find GnuTLS, searching ${GNUTLS_DIR} first. If not successful, tries the
 # standard FindGnuTLS.cmake. Defines:

config/cmake/modules/FindlibCEED.cmake

@@ -1,19 +0,0 @@
-# Copyright (c) 2010-2020, 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:
-#   - CEED_FOUND
-#   - CEED_LIBRARIES
-#   - CEED_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(libCEED CEED CEED_DIR "include" ceed.h "lib" ceed
-  "Paths to headers required by libCEED." "Libraries required by libCEED.")

config/cmake/modules/MfemCmakeUtilities.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Function that converts a version string of the form 'major[.minor[.patch]]' to
 # the integer ((major * 100) + minor) * 100 + patch.
@@ -70,11 +70,6 @@ function(add_mfem_examples EXE_SRCS)
     endif()
   endif()
   foreach(SRC_FILE IN LISTS ${EXE_SRCS})
-    # If CUDA is enabled, tag source files to be compiled with nvcc.
-    if (MFEM_USE_CUDA)
-      set_property(SOURCE ${SRC_FILE} PROPERTY LANGUAGE CUDA)
-    endif()
-
     get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
 
     string(REPLACE ".cpp" "" EXE_NAME "${EXE_PREFIX}${SRC_FILENAME}")
@@ -124,13 +119,6 @@ function(add_mfem_miniapp MFEM_EXE_NAME)
     endif()
   endforeach()
 
-  # If CUDA is enabled, tag source files to be compiled with nvcc.
-  if (MFEM_USE_CUDA)
-    set_property(SOURCE ${MAIN_LIST} ${EXTRA_SOURCES_LIST}
-      PROPERTY LANGUAGE CUDA)
-    list(TRANSFORM EXTRA_OPTIONS_LIST PREPEND "-Xcompiler=")
-  endif()
-
   # Actually add the executable
   add_executable(${MFEM_EXE_NAME} ${MAIN_LIST}
     ${EXTRA_SOURCES_LIST} ${EXTRA_HEADERS_LIST})
@@ -241,17 +229,6 @@ endfunction(mfem_find_component)
 function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
          Lib IncDoc LibDoc)
 
-  # If we have the TPL_ versions of _INCLUDE_DIRS and _LIBRARIES then set the
-  # standard ${Prefix} versions
-  if (TPL_${Prefix}_INCLUDE_DIRS)
-    set(${Prefix}_INCLUDE_DIRS ${TPL_${Prefix}_INCLUDE_DIRS} CACHE STRING
-      "TPL_${Prefix}_INCLUDE_DIRS was found." FORCE)
-  endif()
-  if (TPL_${Prefix}_LIBRARIES)
-    set(${Prefix}_LIBRARIES ${TPL_${Prefix}_LIBRARIES} CACHE STRING
-      "TPL_${Prefix}_LIBRARIES was found." FORCE)
-  endif()
-
   # Quick return
   if (${Prefix}_FOUND)
     return()
@@ -708,164 +685,3 @@ function(mfem_find_library Name Prefix Lib LibDoc CheckVar CheckSrc)
   endif()
 
 endfunction(mfem_find_library)
-
-
-#
-#   Function that creates 'config.mk' from 'config.mk.in' for the both the
-#   build- and the install-locations and define install rules for 'config.mk'
-#   and 'test.mk'.
-#
-function(mfem_export_mk_files)
-
-  # Define a few auxiliary variables (not written to 'config.mk')
-  string(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE)
-  # CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG -> '-Wl,-rpath,'
-  set(shared_link_flag ${CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG})
-  if (NOT shared_link_flag)
-    set(shared_link_flag "-Wl,-rpath,")
-  endif()
-
-  # Convert Boolean vars to YES/NO without writting the values to cache
-  set(CONFIG_MK_BOOL_VARS MFEM_USE_MPI MFEM_USE_METIS MFEM_USE_METIS_5
-      MFEM_DEBUG MFEM_USE_EXCEPTIONS MFEM_USE_ZLIB MFEM_USE_LIBUNWIND
-      MFEM_USE_LAPACK MFEM_THREAD_SAFE MFEM_USE_OPENMP MFEM_USE_LEGACY_OPENMP
-      MFEM_USE_MEMALLOC MFEM_USE_SUNDIALS MFEM_USE_MESQUITE MFEM_USE_SUITESPARSE
-      MFEM_USE_SUPERLU MFEM_USE_STRUMPACK MFEM_USE_GNUTLS
-      MFEM_USE_GSLIB MFEM_USE_NETCDF MFEM_USE_PETSC MFEM_USE_MPFR MFEM_USE_SIDRE
-      MFEM_USE_CONDUIT MFEM_USE_PUMI MFEM_USE_CUDA MFEM_USE_OCCA MFEM_USE_RAJA
-      MFEM_USE_UMPIRE)
-  foreach(var ${CONFIG_MK_BOOL_VARS})
-    if (${var})
-      set(${var} YES)
-    else()
-      set(${var} NO)
-    endif()
-  endforeach()
-  # TODO: Add support for MFEM_USE_CUDA=YES
-  set(MFEM_CXX ${CMAKE_CXX_COMPILER})
-  set(MFEM_CPPFLAGS "")
-  string(STRIP "${CMAKE_CXX_FLAGS_${BUILD_TYPE}} ${CMAKE_CXX_FLAGS}"
-         MFEM_CXXFLAGS)
-  set(MFEM_TPLFLAGS "")
-  foreach(dir ${MFEM_TPL_INCLUDE_DIRS})
-    set(MFEM_TPLFLAGS "${MFEM_TPLFLAGS} -I${dir}")
-  endforeach()
-  # TODO: MFEM_TPLFLAGS: add other TPL flags, in addition to the -I flags.
-  set(MFEM_INCFLAGS "-I\$(MFEM_INC_DIR) \$(MFEM_TPLFLAGS)")
-  set(MFEM_PICFLAG "")
-  if (BUILD_SHARED_LIBS)
-    set(MFEM_PICFLAG "${CMAKE_SHARED_LIBRARY_CXX_FLAGS}")
-  endif()
-  set(MFEM_FLAGS "\$(MFEM_CPPFLAGS) \$(MFEM_CXXFLAGS) \$(MFEM_INCFLAGS)")
-  # TPL link flags: set below
-  set(MFEM_EXT_LIBS "")
-  if (BUILD_SHARED_LIBS)
-    set(MFEM_LIBS "${shared_link_flag}\$(MFEM_LIB_DIR) -L\$(MFEM_LIB_DIR)")
-    set(MFEM_LIBS "${MFEM_LIBS} -lmfem \$(MFEM_EXT_LIBS)")
-    if (APPLE)
-      set(SO_VER ".${mfem_VERSION}${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    else()
-      set(SO_VER "${CMAKE_SHARED_LIBRARY_SUFFIX}.${mfem_VERSION}")
-    endif()
-    set(MFEM_LIB_FILE "\$(MFEM_LIB_DIR)/libmfem${SO_VER}")
-    set(MFEM_SHARED YES)
-    set(MFEM_STATIC NO)
-  else()
-    set(MFEM_LIBS "-L\$(MFEM_LIB_DIR) -lmfem \$(MFEM_EXT_LIBS)")
-    set(MFEM_LIB_FILE "\$(MFEM_LIB_DIR)/libmfem.a")
-    set(MFEM_SHARED NO)
-    set(MFEM_STATIC YES)
-  endif()
-  set(MFEM_BUILD_TAG "${CMAKE_SYSTEM}")
-  set(MFEM_PREFIX "${CMAKE_INSTALL_PREFIX}")
-  # For the next 4 variable, these are the values for the build-tree version of
-  # 'config.mk'
-  set(MFEM_INC_DIR "${PROJECT_BINARY_DIR}")
-  set(MFEM_LIB_DIR "${PROJECT_BINARY_DIR}")
-  set(MFEM_TEST_MK "${PROJECT_SOURCE_DIR}/config/test.mk")
-  set(MFEM_CONFIG_EXTRA "MFEM_BUILD_DIR ?= ${PROJECT_BINARY_DIR}")
-  set(MFEM_MPIEXEC ${MPIEXEC})
-  if (NOT MFEM_MPIEXEC)
-    set(MFEM_MPIEXEC "mpirun")
-  endif()
-  set(MFEM_MPIEXEC_NP ${MPIEXEC_NUMPROC_FLAG})
-  if (NOT MFEM_MPIEXEC_NP)
-    set(MFEM_MPIEXEC_NP "-np")
-  endif()
-  # MFEM_MPI_NP is already set
-  # Define the variable 'MFEM_EXT_LIBS': handle PUMI libs
-  if ("${MFEM_USE_PUMI}" STREQUAL "YES")
-    message(STATUS "simmodsuite_dir = '${SIMMODSUITE_DIR}'")
-    get_target_property(liblist ${PUMI_LIBRARIES} INTERFACE_LINK_LIBRARIES)
-    set(pumi_dep_libs "${liblist}")
-    foreach(pumilib ${liblist})
-      get_target_property(libdeps ${pumilib} INTERFACE_LINK_LIBRARIES)
-      if (NOT "${libdeps}" MATCHES "libdeps-NOTFOUND")
-        list(APPEND pumi_dep_libs ${libdeps})
-      endif()
-    endforeach()
-    list(REMOVE_DUPLICATES pumi_dep_libs)
-    foreach(pumilib ${pumi_dep_libs})
-      unset(lib CACHE)
-      string(REGEX REPLACE "^SCOREC::" "" libname ${pumilib})
-      string(FIND "${pumilib}" ".a" staticlib)
-      string(FIND "${pumilib}" ".so" sharedlib)
-      find_library(lib ${libname} PATHS ${PUMI_DIR}/lib NO_DEFUALT_PATH)
-      if (NOT "${sharedlib}" MATCHES "-1" OR
-          NOT "${staticlib}" MATCHES "-1"   )
-        set(MFEM_EXT_LIBS "${pumilib} ${MFEM_EXT_LIBS}")
-      elseif (NOT "${lib}" MATCHES "lib-NOTFOUND")
-        set(MFEM_EXT_LIBS "${lib} ${MFEM_EXT_LIBS}")
-      elseif ("${lib}" MATCHES "lib-NOTFOUND" AND
-              NOT "${libname}" MATCHES "can" AND
-              NOT "${libname}" MATCHES "pthread")
-        message(FATAL_ERROR "SCOREC lib ${libname} not found")
-      endif()
-    endforeach()
-  endif()
-  # Define the variable 'MFEM_EXT_LIBS': handle other (not PUMI) libs
-  foreach(lib ${TPL_LIBRARIES})
-    get_filename_component(suffix ${lib} EXT)
-    # handle interfaces (e.g., SCOREC::apf)
-    if ("${lib}" MATCHES "SCOREC::.*" OR "${lib}" MATCHES "Ginkgo::.*")
-    elseif (NOT "${lib}" MATCHES "SCOREC::.*" AND "${lib}" MATCHES ".*::.*")
-      message(FATAL_ERROR "***** interface lib found ... exiting *****")
-      # handle static and shared libs
-    elseif ("${suffix}" STREQUAL "${CMAKE_SHARED_LIBRARY_SUFFIX}")
-      get_filename_component(dir ${lib} DIRECTORY)
-      get_filename_component(fullLibName ${lib} NAME_WE)
-      string(REGEX REPLACE "^lib" "" libname ${fullLibName})
-      set(MFEM_EXT_LIBS
-          "${MFEM_EXT_LIBS} ${shared_link_flag}${dir} -L${dir} -l${libname}")
-    else()
-      set(MFEM_EXT_LIBS "${MFEM_EXT_LIBS} ${lib}")
-    endif()
-  endforeach()
-
-  # Create the build-tree version of 'config.mk'
-  configure_file(
-    "${PROJECT_SOURCE_DIR}/config/config.mk.in"
-    "${PROJECT_BINARY_DIR}/config/config.mk")
-  # Copy 'test.mk' from the source-tree to the build-tree
-  configure_file(
-    "${PROJECT_SOURCE_DIR}/config/test.mk"
-    "${PROJECT_BINARY_DIR}/config/test.mk" COPYONLY)
-
-  # Update variables for the install-tree version of 'config.mk'
-  set(MFEM_INC_DIR "${CMAKE_INSTALL_PREFIX}/include")
-  set(MFEM_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib")
-  set(MFEM_TEST_MK "${CMAKE_INSTALL_PREFIX}/share/mfem/test.mk")
-  set(MFEM_CONFIG_EXTRA "")
-
-  # Create the install-tree version of 'config.mk'
-  configure_file(
-    "${PROJECT_SOURCE_DIR}/config/config.mk.in"
-    "${PROJECT_BINARY_DIR}/config/config-install.mk")
-
-  # Install rules for 'config.mk' and 'test.mk'
-  install(FILES ${PROJECT_SOURCE_DIR}/config/test.mk
-    DESTINATION ${CMAKE_INSTALL_PREFIX}/share/mfem/)
-  install(FILES ${PROJECT_BINARY_DIR}/config/config-install.mk
-    DESTINATION ${CMAKE_INSTALL_PREFIX}/share/mfem/ RENAME config.mk)
-
-endfunction()

config/config.hpp

@@ -1,40 +1,28 @@
-// Copyright (c) 2010-2020, 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.
+// Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at
+// the Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights
+// reserved. See file COPYRIGHT for details.
 //
 // This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
+// availability see http://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.
+// terms of the GNU Lesser General Public License (as published by the Free
+// Software Foundation) version 2.1 dated February 1999.
 
 
-// Support out-of-source builds: if MFEM_CONFIG_FILE is defined, include it.
+// Support out-of-source builds: if MFEM_BUILD_DIR is defined, load the config
+// file MFEM_BUILD_DIR/config/_config.hpp.
 //
 // Otherwise, use the local file: _config.hpp.
 
-#ifndef MFEM_CONFIG_HPP
-#define MFEM_CONFIG_HPP
-
-#ifdef MFEM_CONFIG_FILE
-#include MFEM_CONFIG_FILE
+#ifdef MFEM_BUILD_DIR
+#define MFEM_QUOTE(a) #a
+#define MFEM_MAKE_PATH(x,y) MFEM_QUOTE(x/y)
+#include MFEM_MAKE_PATH(MFEM_BUILD_DIR,config/_config.hpp)
 #else
 #include "_config.hpp"
 #endif
 
-// Common configuration macros
-
-#if (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 7)) || defined(__clang__)
-#define MFEM_HAVE_GCC_PRAGMA_DIAGNOSTIC
-#endif
-
-// Windows specific options
-#ifdef _WIN32
-// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
-#define _USE_MATH_DEFINES
-#endif
-
 // Check dependencies:
 
 // Options that require MPI
@@ -52,5 +40,3 @@
 #error Building with PUMI (MFEM_USE_PUMI=YES) requires MPI (MFEM_USE_MPI=YES)
 #endif
 #endif // MFEM_USE_MPI not defined
-
-#endif // MFEM_CONFIG_HPP

config/config.hpp.in

@@ -1,13 +1,13 @@
-// Copyright (c) 2010-2020, 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.
+// Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at
+// the Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights
+// reserved. See file COPYRIGHT for details.
 //
 // This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
+// availability see http://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.
+// terms of the GNU Lesser General Public License (as published by the Free
+// Software Foundation) version 2.1 dated February 1999.
 
 #ifndef MFEM_CONFIG_HEADER
 #define MFEM_CONFIG_HEADER
@@ -30,12 +30,6 @@
 #define MFEM_VERSION_MINOR (((MFEM_VERSION)/100)%100)
 #define MFEM_VERSION_PATCH ((MFEM_VERSION)%100)
 
-// The absolute path of the MFEM source prefix
-// #define MFEM_SOURCE_DIR "@MFEM_SOURCE_DIR@"
-
-// The absolute path of the MFEM installation prefix
-// #define MFEM_INSTALL_DIR "@MFEM_INSTALL_DIR@"
-
 // Description of the git commit used to build MFEM.
 // #define MFEM_GIT_STRING "@MFEM_GIT_STRING@"
 
@@ -49,8 +43,8 @@
 // Throw an exception on errors.
 // #define MFEM_USE_EXCEPTIONS
 
-// Enable zlib in MFEM.
-// #define MFEM_USE_ZLIB
+// Enable gzstream in MFEM.
+// #define MFEM_USE_GZSTREAM
 
 // Enable backtraces for mfem_error through libunwind.
 // #define MFEM_USE_LIBUNWIND
@@ -68,12 +62,9 @@
 // allocation and de-allocation.
 // #define MFEM_THREAD_SAFE
 
-// Enable the OpenMP backend.
+// Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
 // #define MFEM_USE_OPENMP
 
-// [Deprecated] Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
-// #define MFEM_USE_LEGACY_OPENMP
-
 // Internal MFEM option: enable group/batch allocation for some small objects.
 // #define MFEM_USE_MEMALLOC
 
@@ -97,8 +88,8 @@
 // Enable MFEM functionality based on the STRUMPACK library.
 // #define MFEM_USE_STRUMPACK
 
-// Enable MFEM features based on the Ginkgo library
-// #define MFEM_USE_GINKGO
+// Enable functionality based on the Gecko library
+// #define MFEM_USE_GECKO
 
 // Enable secure socket streams based on the GNUTLS library
 // #define MFEM_USE_GNUTLS
@@ -121,34 +112,11 @@
 // Enable MFEM functionality based on the PUMI library
 // #define MFEM_USE_PUMI
 
-// Enable MFEM functionality based on the HIOP library.
-// #define MFEM_USE_HIOP
-
-// Enable MFEM functionality based on the GSLIB library
-// #define MFEM_USE_GSLIB
-
-// Build the NVIDIA GPU/CUDA-enabled version of the MFEM library.
-// Requires a CUDA compiler (nvcc).
-// #define MFEM_USE_CUDA
-
-// Build the AMD GPU/HIP-enabled version of the MFEM library.
-// Requires a HIP compiler (hipcc).
-// #define MFEM_USE_HIP
-
-// Enable functionality based on the RAJA library.
-// #define MFEM_USE_RAJA
-
-// Enable functionality based on the OCCA library.
-// #define MFEM_USE_OCCA
-
-// Enable functionality based on the libCEED library.
-// #define MFEM_USE_CEED
-
-// Enable functionality based on the Umpire library.
-// #define MFEM_USE_UMPIRE
-
-// Enable IO functionality based on the ADIOS2 library.
-// #define MFEM_USE_ADIOS2
+// Windows specific options
+#ifdef _WIN32
+// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
+#define _USE_MATH_DEFINES
+#endif
 
 // Version of HYPRE used for building MFEM.
 // #define MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@

config/config.mk.in

@@ -1,55 +1,43 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Variables corresponding to defines in config.hpp (YES, NO, or value)
-MFEM_VERSION           = @MFEM_VERSION@
-MFEM_VERSION_STRING    = @MFEM_VERSION_STRING@
-MFEM_SOURCE_DIR        = @MFEM_SOURCE_DIR@
-MFEM_INSTALL_DIR       = @MFEM_INSTALL_DIR@
-MFEM_GIT_STRING        = @MFEM_GIT_STRING@
-MFEM_USE_MPI           = @MFEM_USE_MPI@
-MFEM_USE_METIS         = @MFEM_USE_METIS@
-MFEM_USE_METIS_5       = @MFEM_USE_METIS_5@
-MFEM_DEBUG             = @MFEM_DEBUG@
-MFEM_USE_EXCEPTIONS    = @MFEM_USE_EXCEPTIONS@
-MFEM_USE_ZLIB          = @MFEM_USE_ZLIB@
-MFEM_USE_LIBUNWIND     = @MFEM_USE_LIBUNWIND@
-MFEM_USE_LAPACK        = @MFEM_USE_LAPACK@
-MFEM_THREAD_SAFE       = @MFEM_THREAD_SAFE@
-MFEM_USE_LEGACY_OPENMP = @MFEM_USE_LEGACY_OPENMP@
-MFEM_USE_OPENMP        = @MFEM_USE_OPENMP@
-MFEM_USE_MEMALLOC      = @MFEM_USE_MEMALLOC@
-MFEM_TIMER_TYPE        = @MFEM_TIMER_TYPE@
-MFEM_USE_SUNDIALS      = @MFEM_USE_SUNDIALS@
-MFEM_USE_MESQUITE      = @MFEM_USE_MESQUITE@
-MFEM_USE_SUITESPARSE   = @MFEM_USE_SUITESPARSE@
-MFEM_USE_SUPERLU       = @MFEM_USE_SUPERLU@
-MFEM_USE_STRUMPACK     = @MFEM_USE_STRUMPACK@
-MFEM_USE_GINKGO        = @MFEM_USE_GINKGO@
-MFEM_USE_GNUTLS        = @MFEM_USE_GNUTLS@
-MFEM_USE_NETCDF        = @MFEM_USE_NETCDF@
-MFEM_USE_PETSC         = @MFEM_USE_PETSC@
-MFEM_USE_MPFR          = @MFEM_USE_MPFR@
-MFEM_USE_SIDRE         = @MFEM_USE_SIDRE@
-MFEM_USE_CONDUIT       = @MFEM_USE_CONDUIT@
-MFEM_USE_PUMI          = @MFEM_USE_PUMI@
-MFEM_USE_HIOP          = @MFEM_USE_HIOP@
-MFEM_USE_GSLIB         = @MFEM_USE_GSLIB@
-MFEM_USE_CUDA          = @MFEM_USE_CUDA@
-MFEM_USE_HIP           = @MFEM_USE_HIP@
-MFEM_USE_RAJA          = @MFEM_USE_RAJA@
-MFEM_USE_OCCA          = @MFEM_USE_OCCA@
-MFEM_USE_CEED          = @MFEM_USE_CEED@
-MFEM_USE_UMPIRE        = @MFEM_USE_UMPIRE@
-MFEM_USE_ADIOS2        = @MFEM_USE_ADIOS2@
+MFEM_VERSION         = @MFEM_VERSION@
+MFEM_VERSION_STRING  = @MFEM_VERSION_STRING@
+MFEM_GIT_STRING      = @MFEM_GIT_STRING@
+MFEM_USE_MPI         = @MFEM_USE_MPI@
+MFEM_USE_METIS       = @MFEM_USE_METIS@
+MFEM_USE_METIS_5     = @MFEM_USE_METIS_5@
+MFEM_DEBUG           = @MFEM_DEBUG@
+MFEM_USE_EXCEPTIONS  = @MFEM_USE_EXCEPTIONS@
+MFEM_USE_GZSTREAM    = @MFEM_USE_GZSTREAM@
+MFEM_USE_LIBUNWIND   = @MFEM_USE_LIBUNWIND@
+MFEM_USE_LAPACK      = @MFEM_USE_LAPACK@
+MFEM_THREAD_SAFE     = @MFEM_THREAD_SAFE@
+MFEM_USE_OPENMP      = @MFEM_USE_OPENMP@
+MFEM_USE_MEMALLOC    = @MFEM_USE_MEMALLOC@
+MFEM_TIMER_TYPE      = @MFEM_TIMER_TYPE@
+MFEM_USE_SUNDIALS    = @MFEM_USE_SUNDIALS@
+MFEM_USE_MESQUITE    = @MFEM_USE_MESQUITE@
+MFEM_USE_SUITESPARSE = @MFEM_USE_SUITESPARSE@
+MFEM_USE_SUPERLU     = @MFEM_USE_SUPERLU@
+MFEM_USE_STRUMPACK   = @MFEM_USE_STRUMPACK@
+MFEM_USE_GECKO       = @MFEM_USE_GECKO@
+MFEM_USE_GNUTLS      = @MFEM_USE_GNUTLS@
+MFEM_USE_NETCDF      = @MFEM_USE_NETCDF@
+MFEM_USE_PETSC       = @MFEM_USE_PETSC@
+MFEM_USE_MPFR        = @MFEM_USE_MPFR@
+MFEM_USE_SIDRE       = @MFEM_USE_SIDRE@
+MFEM_USE_CONDUIT     = @MFEM_USE_CONDUIT@
+MFEM_USE_PUMI        = @MFEM_USE_PUMI@
 
 # Compiler, compile options, and link options
 MFEM_CXX       = @MFEM_CXX@
@@ -77,8 +65,5 @@ MFEM_MPIEXEC    = @MFEM_MPIEXEC@
 MFEM_MPIEXEC_NP = @MFEM_MPIEXEC_NP@
 MFEM_MPI_NP     = @MFEM_MPI_NP@
 
-# The NVCC compiler cannot link with -x=cu
-MFEM_LINK_FLAGS := $(filter-out -x=cu, $(MFEM_FLAGS))
-
 # Optional extra configuration
 @MFEM_CONFIG_EXTRA@

config/defaults.cmake

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # See the file INSTALL for description of the configuration options.
 
@@ -22,36 +22,25 @@ endif()
 option(MFEM_USE_MPI "Enable MPI parallel build" OFF)
 option(MFEM_USE_METIS "Enable METIS usage" ${MFEM_USE_MPI})
 option(MFEM_USE_EXCEPTIONS "Enable the use of exceptions" OFF)
-option(MFEM_USE_ZLIB "Enable zlib for compressed data streams." OFF)
+option(MFEM_USE_GZSTREAM "Enable gzstream for compressed data streams." OFF)
 option(MFEM_USE_LIBUNWIND "Enable backtrace for errors." OFF)
 option(MFEM_USE_LAPACK "Enable LAPACK usage" OFF)
 option(MFEM_THREAD_SAFE "Enable thread safety" OFF)
-option(MFEM_USE_OPENMP "Enable the OpenMP backend" OFF)
-option(MFEM_USE_LEGACY_OPENMP "Enable legacy OpenMP usage" OFF)
+option(MFEM_USE_OPENMP "Enable OpenMP usage" OFF)
 option(MFEM_USE_MEMALLOC "Enable the internal MEMALLOC option." ON)
 option(MFEM_USE_SUNDIALS "Enable SUNDIALS usage" OFF)
 option(MFEM_USE_MESQUITE "Enable MESQUITE usage" OFF)
 option(MFEM_USE_SUITESPARSE "Enable SuiteSparse usage" OFF)
 option(MFEM_USE_SUPERLU "Enable SuperLU_DIST usage" OFF)
 option(MFEM_USE_STRUMPACK "Enable STRUMPACK usage" OFF)
-option(MFEM_USE_GINKGO "Enable Ginkgo usage" OFF)
+option(MFEM_USE_GECKO "Enable GECKO usage" OFF)
 option(MFEM_USE_GNUTLS "Enable GNUTLS usage" OFF)
-option(MFEM_USE_GSLIB "Enable GSLIB usage" OFF)
 option(MFEM_USE_NETCDF "Enable NETCDF usage" OFF)
 option(MFEM_USE_PETSC "Enable PETSc support." OFF)
 option(MFEM_USE_MPFR "Enable MPFR usage." OFF)
 option(MFEM_USE_SIDRE "Enable Axom/Sidre usage" OFF)
 option(MFEM_USE_CONDUIT "Enable Conduit usage" OFF)
 option(MFEM_USE_PUMI "Enable PUMI" OFF)
-option(MFEM_USE_HIOP "Enable HiOp" OFF)
-option(MFEM_USE_CUDA "Enable CUDA" OFF)
-option(MFEM_USE_OCCA "Enable OCCA" OFF)
-option(MFEM_USE_RAJA "Enable RAJA" OFF)
-option(MFEM_USE_CEED "Enable CEED" OFF)
-option(MFEM_USE_UMPIRE "Enable Umpire" OFF)
-option(MFEM_USE_ADIOS2 "Enable ADIOS2" OFF)
-
-set(MFEM_MPI_NP 4 CACHE STRING "Number of processes used for MPI tests")
 
 # Allow a user to disable testing, examples, and/or miniapps at CONFIGURE TIME
 # if they don't want/need them (e.g. if MFEM is "just a dependency" and all they
@@ -67,16 +56,13 @@ option(MFEM_ENABLE_MINIAPPS "Build all of the miniapps" OFF)
 # set(CXX g++)
 # set(MPICXX mpicxx)
 
-# Set the target CUDA architecture
-set(CUDA_ARCH "sm_60" CACHE STRING "Target CUDA architecture.")
-
 set(MFEM_DIR ${CMAKE_CURRENT_SOURCE_DIR})
 
 # The *_DIR paths below will be the first place searched for the corresponding
 # headers and library. If these fail, then standard cmake search is performed.
 # Note: if the variables are already in the cache, they are not overwritten.
 
-set(HYPRE_DIR "${MFEM_DIR}/../hypre/src/hypre" CACHE PATH
+set(HYPRE_DIR "${MFEM_DIR}/../hypre-2.10.0b/src/hypre" CACHE PATH
     "Path to the hypre library.")
 # If hypre was compiled to depend on BLAS and LAPACK:
 # set(HYPRE_REQUIRED_PACKAGES "BLAS" "LAPACK" CACHE STRING
@@ -86,7 +72,7 @@ set(METIS_DIR "${MFEM_DIR}/../metis-4.0" CACHE PATH "Path to the METIS library."
 
 set(LIBUNWIND_DIR "" CACHE PATH "Path to Libunwind.")
 
-set(SUNDIALS_DIR "${MFEM_DIR}/../sundials-5.0.0/instdir" CACHE PATH
+set(SUNDIALS_DIR "${MFEM_DIR}/../sundials-3.0.0" CACHE PATH
     "Path to the SUNDIALS library.")
 # The following may be necessary, if SUNDIALS was built with KLU:
 # set(SUNDIALS_REQUIRED_PACKAGES "SuiteSparse/KLU/AMD/BTF/COLAMD/config"
@@ -114,7 +100,6 @@ set(SuperLUDist_REQUIRED_PACKAGES "MPI" "BLAS" "ParMETIS" CACHE STRING
 set(STRUMPACK_DIR "${MFEM_DIR}/../STRUMPACK-build" CACHE PATH
     "Path to the STRUMPACK library.")
 # STRUMPACK may also depend on "OpenMP", depending on how it was compiled.
-# Starting with v2.2.0 of STRUMPACK, ParMETIS and Scotch are optional.
 set(STRUMPACK_REQUIRED_PACKAGES "MPI" "MPI_Fortran" "ParMETIS" "METIS"
     "ScaLAPACK" "Scotch/ptscotch/ptscotcherr/scotch/scotcherr" CACHE STRING
     "Additional packages required by STRUMPACK.")
@@ -122,8 +107,7 @@ set(STRUMPACK_REQUIRED_PACKAGES "MPI" "MPI_Fortran" "ParMETIS" "METIS"
 # set(STRUMPACK_REQUIRED_LIBRARIES "gfortran" "mpi_mpifh" CACHE STRING
 #     "Additional libraries required by STRUMPACK.")
 
-# The Scotch library, required by STRUMPACK <= v2.1.0, optional in STRUMPACK >=
-# v2.2.0.
+# The Scotch library, required by STRUMPACK
 set(Scotch_DIR "${MFEM_DIR}/../scotch_6.0.4" CACHE PATH
     "Path to the Scotch and PT-Scotch libraries.")
 set(Scotch_REQUIRED_PACKAGES "Threads" CACHE STRING
@@ -139,12 +123,10 @@ set(ScaLAPACK_TARGET_NAMES scalapack)
 # set(ScaLAPACK_TARGET_FORCE)
 # set(ScaLAPACK_IMPORT_CONFIG DEBUG)
 
-set(Ginkgo_DIR "${MFEM_DIR}/../ginkgo" CACHE PATH "Path to the Ginkgo library.")
+set(GECKO_DIR "${MFEM_DIR}/../gecko" CACHE PATH "Path to the Gecko library.")
 
 set(GNUTLS_DIR "" CACHE PATH "Path to the GnuTLS library.")
 
-set(GSLIB_DIR "" CACHE PATH "Path to the GSLIB library.")
-
 set(NETCDF_DIR "" CACHE PATH "Path to the NetCDF library.")
 # May need to add "HDF5" as requirement.
 set(NetCDF_REQUIRED_PACKAGES "" CACHE STRING
@@ -161,22 +143,12 @@ set(CONDUIT_DIR "${MFEM_DIR}/../conduit" CACHE PATH
 
 set(AXOM_DIR "${MFEM_DIR}/../axom" CACHE PATH "Path to the Axom library.")
 # May need to add "Boost" as requirement.
-set(Axom_REQUIRED_PACKAGES "Conduit/relay/blueprint" CACHE STRING
+set(Axom_REQUIRED_PACKAGES "Conduit/relay" CACHE STRING
     "Additional packages required by Axom.")
 
 set(PUMI_DIR "${MFEM_DIR}/../pumi-2.1.0" CACHE STRING
     "Directory where PUMI is installed")
 
-set(HIOP_DIR "${MFEM_DIR}/../hiop/install" CACHE STRING
-    "Directory where HiOp is installed")
-set(HIOP_REQUIRED_PACKAGES "BLAS" "LAPACK" CACHE STRING
-    "Packages that HiOp depends on.")
-
-set(OCCA_DIR "${MFEM_DIR}/../occa" CACHE PATH "Path to OCCA")
-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(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.")

config/defaults.mk

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # This file describes the default MFEM build options.
 #
@@ -21,13 +21,8 @@ NOTMAC := $(subst Darwin,,$(shell uname -s))
 CXX = g++
 MPICXX = mpicxx
 
-BASE_FLAGS  = -std=c++11
-OPTIM_FLAGS = -O3 $(BASE_FLAGS)
-DEBUG_FLAGS = -g $(XCOMPILER)-Wall $(BASE_FLAGS)
-
-# Prefixes for passing flags to the compiler and linker when using CXX or MPICXX
-CXX_XCOMPILER =
-CXX_XLINKER   = -Wl,
+OPTIM_FLAGS = -O3
+DEBUG_FLAGS = -g -Wall
 
 # Destination location of make install
 # PREFIX = $(HOME)/mfem
@@ -38,49 +33,33 @@ INSTALL = /usr/bin/install
 STATIC = YES
 SHARED = NO
 
-# CUDA configuration options
-CUDA_CXX = nvcc
-CUDA_ARCH = sm_60
-CUDA_FLAGS = -x=cu --expt-extended-lambda -arch=$(CUDA_ARCH)
-# Prefixes for passing flags to the host compiler and linker when using CUDA_CXX
-CUDA_XCOMPILER = -Xcompiler=
-CUDA_XLINKER   = -Xlinker=
-
-# HIP configuration options
-HIP_CXX = hipcc
-# The HIP_ARCH option specifies the AMD GPU processor, similar to CUDA_ARCH. For
-# example: gfx600 (tahiti), gfx700 (kaveri), gfx701 (hawaii), gfx801 (carrizo),
-# gfx900, gfx1010, etc.
-HIP_ARCH = gfx900
-HIP_FLAGS = --amdgpu-target=$(HIP_ARCH)
-
 ifneq ($(NOTMAC),)
    AR      = ar
    ARFLAGS = cruv
    RANLIB  = ranlib
-   PICFLAG = $(XCOMPILER)-fPIC
+   PICFLAG = -fPIC
    SO_EXT  = so
    SO_VER  = so.$(MFEM_VERSION_STRING)
-   BUILD_SOFLAGS = -shared $(XLINKER)-soname,libmfem.$(SO_VER)
-   BUILD_RPATH = $(XLINKER)-rpath,$(BUILD_REAL_DIR)
+   BUILD_SOFLAGS = -shared -Wl,-soname,libmfem.$(SO_VER)
+   BUILD_RPATH = -Wl,-rpath,$(BUILD_REAL_DIR)
    INSTALL_SOFLAGS = $(BUILD_SOFLAGS)
-   INSTALL_RPATH = $(XLINKER)-rpath,@MFEM_LIB_DIR@
+   INSTALL_RPATH = -Wl,-rpath,@MFEM_LIB_DIR@
 else
    # Silence "has no symbols" warnings on Mac OS X
    AR      = ar
    ARFLAGS = Scruv
    RANLIB  = ranlib -no_warning_for_no_symbols
-   PICFLAG = $(XCOMPILER)-fPIC
+   PICFLAG = -fPIC
    SO_EXT  = dylib
    SO_VER  = $(MFEM_VERSION_STRING).dylib
-   MAKE_SOFLAGS = $(XLINKER)-dylib,-install_name,$(1)/libmfem.$(SO_VER),\
+   MAKE_SOFLAGS = -Wl,-dylib,-install_name,$(1)/libmfem.$(SO_VER),\
       -compatibility_version,$(MFEM_VERSION_STRING),\
       -current_version,$(MFEM_VERSION_STRING),\
       -undefined,dynamic_lookup
    BUILD_SOFLAGS = $(subst $1 ,,$(call MAKE_SOFLAGS,$(BUILD_REAL_DIR)))
-   BUILD_RPATH = $(XLINKER)-undefined,dynamic_lookup
+   BUILD_RPATH = -Wl,-undefined,dynamic_lookup
    INSTALL_SOFLAGS = $(subst $1 ,,$(call MAKE_SOFLAGS,$(MFEM_LIB_DIR)))
-   INSTALL_RPATH = $(XLINKER)-undefined,dynamic_lookup
+   INSTALL_RPATH = -Wl,-undefined,dynamic_lookup
 endif
 
 # Set CXXFLAGS to overwrite the default selection of DEBUG_FLAGS/OPTIM_FLAGS
@@ -103,41 +82,31 @@ MFEM_MPI_NP = 4
 # config.hpp. The values below are the defaults for generating the actual values
 # in config.mk and config.hpp.
 
-MFEM_USE_MPI           = NO
-MFEM_USE_METIS         = $(MFEM_USE_MPI)
-MFEM_USE_METIS_5       = NO
-MFEM_DEBUG             = NO
-MFEM_USE_EXCEPTIONS    = NO
-MFEM_USE_ZLIB          = NO
-MFEM_USE_LIBUNWIND     = NO
-MFEM_USE_LAPACK        = NO
-MFEM_THREAD_SAFE       = NO
-MFEM_USE_OPENMP        = NO
-MFEM_USE_LEGACY_OPENMP = NO
-MFEM_USE_MEMALLOC      = YES
-MFEM_TIMER_TYPE        = $(if $(NOTMAC),2,4)
-MFEM_USE_SUNDIALS      = NO
-MFEM_USE_MESQUITE      = NO
-MFEM_USE_SUITESPARSE   = NO
-MFEM_USE_SUPERLU       = NO
-MFEM_USE_STRUMPACK     = NO
-MFEM_USE_GINKGO        = NO
-MFEM_USE_GNUTLS        = NO
-MFEM_USE_NETCDF        = NO
-MFEM_USE_PETSC         = NO
-MFEM_USE_MPFR          = NO
-MFEM_USE_SIDRE         = NO
-MFEM_USE_CONDUIT       = NO
-MFEM_USE_PUMI          = NO
-MFEM_USE_HIOP          = NO
-MFEM_USE_GSLIB         = NO
-MFEM_USE_CUDA          = NO
-MFEM_USE_HIP           = NO
-MFEM_USE_RAJA          = NO
-MFEM_USE_OCCA          = NO
-MFEM_USE_CEED          = NO
-MFEM_USE_UMPIRE        = NO
-MFEM_USE_ADIOS2        = NO
+MFEM_USE_MPI         = NO
+MFEM_USE_METIS       = $(MFEM_USE_MPI)
+MFEM_USE_METIS_5     = NO
+MFEM_DEBUG           = NO
+MFEM_USE_EXCEPTIONS  = NO
+MFEM_USE_GZSTREAM    = NO
+MFEM_USE_LIBUNWIND   = NO
+MFEM_USE_LAPACK      = NO
+MFEM_THREAD_SAFE     = NO
+MFEM_USE_OPENMP      = NO
+MFEM_USE_MEMALLOC    = YES
+MFEM_TIMER_TYPE      = $(if $(NOTMAC),2,4)
+MFEM_USE_SUNDIALS    = NO
+MFEM_USE_MESQUITE    = NO
+MFEM_USE_SUITESPARSE = NO
+MFEM_USE_SUPERLU     = NO
+MFEM_USE_STRUMPACK   = NO
+MFEM_USE_GECKO       = NO
+MFEM_USE_GNUTLS      = NO
+MFEM_USE_NETCDF      = NO
+MFEM_USE_PETSC       = NO
+MFEM_USE_MPFR        = NO
+MFEM_USE_SIDRE       = NO
+MFEM_USE_CONDUIT     = NO
+MFEM_USE_PUMI        = NO
 
 # Compile and link options for zlib.
 ZLIB_DIR =
@@ -149,7 +118,7 @@ LIBUNWIND_OPT = -g
 LIBUNWIND_LIB = $(if $(NOTMAC),-lunwind -ldl,)
 
 # HYPRE library configuration (needed to build the parallel version)
-HYPRE_DIR = @MFEM_DIR@/../hypre/src/hypre
+HYPRE_DIR = @MFEM_DIR@/../hypre-2.10.0b/src/hypre
 HYPRE_OPT = -I$(HYPRE_DIR)/include
 HYPRE_LIB = -L$(HYPRE_DIR)/lib -lHYPRE
 
@@ -167,8 +136,6 @@ ifeq ($(MFEM_USE_SUPERLU)$(MFEM_USE_STRUMPACK),NONO)
 else
    # ParMETIS: currently needed by SuperLU or STRUMPACK. We assume that METIS 5
    # (included with ParMETIS) is installed in the same location.
-   # Starting with STRUMPACK v2.2.0, ParMETIS is an optional dependency while
-   # METIS is still required.
    METIS_DIR = @MFEM_DIR@/../parmetis-4.0.3
    METIS_OPT = -I$(METIS_DIR)/include
    METIS_LIB = -L$(METIS_DIR)/lib -lparmetis -lmetis
@@ -180,16 +147,16 @@ LAPACK_OPT =
 LAPACK_LIB = $(if $(NOTMAC),-llapack -lblas,-framework Accelerate)
 
 # OpenMP configuration
-OPENMP_OPT = $(XCOMPILER)-fopenmp
+OPENMP_OPT = -fopenmp
 OPENMP_LIB =
 
 # Used when MFEM_TIMER_TYPE = 2
 POSIX_CLOCKS_LIB = -lrt
 
 # SUNDIALS library configuration
-SUNDIALS_DIR = @MFEM_DIR@/../sundials-5.0.0/instdir
+SUNDIALS_DIR = @MFEM_DIR@/../sundials-3.0.0
 SUNDIALS_OPT = -I$(SUNDIALS_DIR)/include
-SUNDIALS_LIB = -Wl,-rpath,$(SUNDIALS_DIR)/lib64 -L$(SUNDIALS_DIR)/lib64\
+SUNDIALS_LIB = -Wl,-rpath,$(SUNDIALS_DIR)/lib -L$(SUNDIALS_DIR)/lib\
  -lsundials_arkode -lsundials_cvode -lsundials_nvecserial -lsundials_kinsol
 
 ifeq ($(MFEM_USE_MPI),YES)
@@ -214,10 +181,9 @@ SUITESPARSE_LIB = -Wl,-rpath,$(SUITESPARSE_DIR)/lib -L$(SUITESPARSE_DIR)/lib\
 # SuperLU library configuration
 SUPERLU_DIR = @MFEM_DIR@/../SuperLU_DIST_5.1.0
 SUPERLU_OPT = -I$(SUPERLU_DIR)/SRC
-SUPERLU_LIB = -Wl,-rpath,$(SUPERLU_DIR)/lib -L$(SUPERLU_DIR)/lib -lsuperlu_dist_5.1.0
+SUPERLU_LIB = -Wl,-rpath,$(SUPERLU_DIR)/SRC -L$(SUPERLU_DIR)/SRC -lsuperlu_dist
 
-# SCOTCH library configuration (required by STRUMPACK <= v2.1.0, optional in
-# STRUMPACK >= v2.2.0)
+# SCOTCH library configuration (required by STRUMPACK)
 SCOTCH_DIR = @MFEM_DIR@/../scotch_6.0.4
 SCOTCH_OPT = -I$(SCOTCH_DIR)/include
 SCOTCH_LIB = -L$(SCOTCH_DIR)/lib -lptscotch -lptscotcherr -lscotch -lscotcherr\
@@ -244,10 +210,10 @@ STRUMPACK_OPT = -I$(STRUMPACK_DIR)/include $(SCOTCH_OPT)
 STRUMPACK_LIB = -L$(STRUMPACK_DIR)/lib -lstrumpack $(MPI_FORTRAN_LIB)\
  $(SCOTCH_LIB) $(SCALAPACK_LIB)
 
-# Ginkgo library configuration (currently not needed)
-GINKGO_DIR = @MFEM_DIR@/../ginkgo/install
-GINKGO_OPT = -isystem $(GINKGO_DIR)/include
-GINKGO_LIB = $(XLINKER)-rpath,$(GINKGO_DIR)/lib -L$(GINKGO_DIR)/lib -lginkgo -lginkgo_omp -lginkgo_cuda -lginkgo_reference
+# Gecko library configuration
+GECKO_DIR = @MFEM_DIR@/../gecko
+GECKO_OPT = -I$(GECKO_DIR)/inc
+GECKO_LIB = -L$(GECKO_DIR)/lib -lgecko
 
 # GnuTLS library configuration
 GNUTLS_OPT =
@@ -304,7 +270,7 @@ SIDRE_LIB = \
    -Wl,-rpath,$(SIDRE_DIR)/lib -L$(SIDRE_DIR)/lib \
    -Wl,-rpath,$(CONDUIT_DIR)/lib -L$(CONDUIT_DIR)/lib \
    -Wl,-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib \
-   -laxom -lconduit -lconduit_relay -lconduit_blueprint -lhdf5 $(ZLIB_LIB) -ldl
+   -lsidre -lslic -laxom_utils -lconduit -lconduit_relay -lhdf5 $(ZLIB_LIB) -ldl
 
 # PUMI
 # Note that PUMI_DIR is needed -- it is used to check for gmi_sim.h
@@ -313,47 +279,6 @@ PUMI_OPT = -I$(PUMI_DIR)/include
 PUMI_LIB = -L$(PUMI_DIR)/lib -lpumi -lcrv -lma -lmds -lapf -lpcu -lgmi -lparma\
    -llion -lmth -lapf_zoltan -lspr
 
-# HIOP
-HIOP_DIR = @MFEM_DIR@/../hiop/install
-HIOP_OPT = -I$(HIOP_DIR)/include
-HIOP_LIB = -L$(HIOP_DIR)/lib -lhiop $(LAPACK_LIB)
-
-# GSLIB library
-GSLIB_DIR = @MFEM_DIR@/../gslib/build
-GSLIB_OPT = -I$(GSLIB_DIR)/include
-GSLIB_LIB = -L$(GSLIB_DIR)/lib -lgs
-
-# CUDA library configuration (currently not needed)
-CUDA_OPT =
-CUDA_LIB =
-
-# HIP library configuration (currently not needed)
-HIP_OPT =
-HIP_LIB =
-
-# OCCA library configuration
-OCCA_DIR = @MFEM_DIR@/../occa
-OCCA_OPT = -I$(OCCA_DIR)/include
-OCCA_LIB = $(XLINKER)-rpath,$(OCCA_DIR)/lib -L$(OCCA_DIR)/lib -locca
-
-# libCEED library configuration
-CEED_DIR ?= @MFEM_DIR@/../libCEED
-CEED_OPT = -I$(CEED_DIR)/include
-CEED_LIB = $(XLINKER)-rpath,$(CEED_DIR)/lib -L$(CEED_DIR)/lib -lceed
-
-# RAJA library configuration
-RAJA_DIR = @MFEM_DIR@/../raja
-RAJA_OPT = -I$(RAJA_DIR)/include
-ifdef CUB_DIR
-   RAJA_OPT += -I$(CUB_DIR)
-endif
-RAJA_LIB = $(XLINKER)-rpath,$(RAJA_DIR)/lib -L$(RAJA_DIR)/lib -lRAJA
-
-# UMPIRE library configuration
-UMPIRE_DIR = @MFEM_DIR@/../umpire
-UMPIRE_OPT = -I$(UMPIRE_DIR)/include
-UMPIRE_LIB = -L$(UMPIRE_DIR)/lib -lumpire
-
 # If YES, enable some informational messages
 VERBOSE = NO
 

config/get_hypre_version.cpp

@@ -1,13 +1,13 @@
-// Copyright (c) 2010-2020, 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.
+// Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at
+// the Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights
+// reserved. See file COPYRIGHT for details.
 //
 // This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
+// availability see http://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.
+// terms of the GNU Lesser General Public License (as published by the Free
+// Software Foundation) version 2.1 dated February 1999.
 
 #include "HYPRE_config.h"
 #include <cstdio>

config/makefile

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 SRC = $(if $(MFEM_DIR),$(MFEM_DIR)/config/,)
 
@@ -36,7 +36,6 @@ CONFIG_MK = config.mk
 all: header config-mk
 
 MPI = $(MFEM_USE_MPI:NO=)
-GHV_CXX ?= $(MFEM_CXX)
 GHV = get_hypre_version
 GHV_FLAGS = $(subst @MFEM_DIR@,$(if $(MFEM_DIR),$(MFEM_DIR),..),$(HYPRE_OPT))
 SMX = $(if $(MFEM_USE_PUMI:NO=),MFEM_USE_SIMMETRIX)
@@ -45,7 +44,7 @@ SMX_FILE = $(subst @MFEM_DIR@,$(if $(MFEM_DIR),$(MFEM_DIR),..),$(SMX_PATH))
 
 $(GHV): $(SRC)$(GHV).cpp
 	$(call mfem-info, Determining HYPRE version ...)
-	$(GHV_CXX) ${GHV_FLAGS} $(SRC)$(GHV).cpp -o $(GHV)
+	$(MFEM_CXX) ${GHV_FLAGS} $(SRC)$(GHV).cpp -o $(GHV)
 $(GHV).out: $(GHV)
 	./$(GHV) > $(GHV).out
 .INTERMEDIATE: $(GHV) $(GHV).out

config/sample-runs.sh

@@ -1,15 +1,15 @@
 #!/bin/bash
 
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 make="${MAKE:-make}"
 mpiexec="${MPIEXEC:-mpirun}"
@@ -18,8 +18,6 @@ run_prefix=""
 run_vg="valgrind --leak-check=full --show-reachable=yes --track-origins=yes"
 run_suffix="-no-vis"
 skip_gen_meshes="yes"
-# filter-out device runs ("no") or non-device runs ("yes"):
-device_runs="no"
 cur_dir="${PWD}"
 mfem_dir="$(cd "$(dirname "$0")"/.. && pwd)"
 mfem_build_dir=""
@@ -32,7 +30,7 @@ groups_serial=(
 '"examples"
    "Examples:"
    "examples"
-   "ex{,1,2}[0-9].cpp"'
+   "ex{,1}[0-9].cpp"'
 #   "ex1.cpp"'
 '"sundials"
    "SUNDIALS examples:"
@@ -46,15 +44,14 @@ groups_serial=(
 '"meshing"
    "Meshing miniapps:"
    "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
-    mesh-optimizer.cpp minimal-surface.cpp"'
+   "mobius-strip.cpp klein-bottle.cpp mesh-optimizer.cpp"'
 )
 # Parallel groups
 groups_parallel=(
 '"examples"
    "Examples:"
    "examples"
-   "ex{,1,2}[0-9]p.cpp"'
+   "ex{,1}[0-9]p.cpp"'
 #   "ex1p.cpp"'
 '"sundials"
    "SUNDIALS examples:"
@@ -72,7 +69,7 @@ groups_parallel=(
 '"meshing"
    "Meshing miniapps:"
    "miniapps/meshing"
-   "pmesh-optimizer.cpp pminimal-surface.cpp"'
+   "pmesh-optimizer.cpp"'
 '"electromagnetics"
    "Electromagnetics miniapps:"
    "miniapps/electromagnetics"
@@ -84,7 +81,7 @@ groups_all=(
 '"examples"
    "Examples:"
    "examples"
-   "ex\"{,1,2}[0-9]\"{,p}.cpp"'
+   "ex\"{,1}[0-9]\"{,p}.cpp"'
 '"sundials"
    "SUNDIALS examples:"
    "examples/sundials"
@@ -100,8 +97,7 @@ groups_all=(
 '"meshing"
    "Meshing miniapps:"
    "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
-    {,p}mesh-optimizer.cpp {,p}minimal-surface.cpp"'
+   "mobius-strip.cpp klein-bottle.cpp {,p}mesh-optimizer.cpp"'
 '"electromagnetics"
    "Electromagnetics miniapps:"
    "miniapps/electromagnetics"
@@ -150,20 +146,6 @@ function extract_sample_runs()
    if [ "$skip_gen_meshes" == "yes" ]; then
       runs=`printf "%s" "$runs" | grep -v ".* -m .*\.gen"`
    fi
-   if [ "$device_runs" == "yes" ]; then
-      runs=`printf "%s" "$runs" | grep ".* -d .*"`
-      if [ "$have_occa" == "no" ]; then
-         runs=`printf "%s" "$runs" | grep -v ".* -d occa-.*"`
-      fi
-      if [ "$have_raja" == "no" ]; then
-         runs=`printf "%s" "$runs" | grep -v ".* -d raja-.*"`
-      fi
-      if [ "$have_ceed" == "no" ]; then
-         runs=`printf "%s" "$runs" | grep -v ".* -d ceed-.*"`
-      fi
-   else
-      runs=`printf "%s" "$runs" | grep -v ".* -d .*"`
-   fi
    IFS=$'\n'
    runs=(${runs})
    IFS="${old_IFS}"
@@ -185,15 +167,9 @@ function help_message()
       -g <dir> <pattern>
                   Specify explicitly a group (dir + file pattern) to run; This
                   option can be used multiple times to define multiple groups
-      -dev        configure only sample runs using devices.
-                  To test with a parallel build, the parallel (-p|-par) option
-                  should be set first on the command line.
       -v          Enable valgrind
       -o <dir>    [${output_dir:-"<empty>: output goes to stdout"}]
                   If not empty, save output to files inside <dir>
-      -d <dir>    [${mfem_build_dir}]
-                  If <dir> is different from <mfem_dir> then use an
-                  out-of-source build in <dir>
       -j <np>     [${make_j}] Specify the number of jobs to use for building
       -c|-color   Always use colors for the status messages: OK, FAILED, etc
       -b|-built   Do NOT rebuild the library and the executables
@@ -201,11 +177,11 @@ function help_message()
       -s|-show    Show all configured sample runs and exit
       -n          Dry run: replace "\$sample_run" with "echo \$sample_run"
       <var>=<value>
-                  Set a shell script variable; see below for valid variables
+                  Set a shell script varible; see below for valid variables
        *          Any other parameter is treated as <mfem_dir>
       <mfem_dir>  [${mfem_dir}] is the MFEM source directory
 
-   This script tests all the sample runs listed in the beginning comments of
+   This script tests all the sample runs listed in the begining comments of
    MFEM's serial or parallel example and miniapp codes. The list of sample runs
    is auto-generated and can be viewed with the -s|-show option.
 
@@ -220,8 +196,8 @@ function help_message()
          Their values can also set using the respective uppercase environment
          variable
       mfem_build_dir [${mfem_build_dir}]
-         Same as '-d': set this variable to something different from <mfem_dir>
-         to use an out-of-source build
+         Set this variable to something different from <mfem_dir> to use an
+         out-of-source build
 
    For other valid variables, see the script source.
 
@@ -272,7 +248,7 @@ case "$1" in
    -h|-help)
       opt_help="yes"
       ;;
-   -p|-par)
+   -p|-parallel)
       mfem_config="MFEM_USE_MPI=YES MFEM_DEBUG=NO"
       ;;
    -g)
@@ -283,11 +259,6 @@ case "$1" in
       groups=("${groups[@]}" "${test_group}")
       shift 2
       ;;
-   -dev)
-       device_runs="yes"
-       mfem_config+=" MFEM_USE_CUDA=YES MFEM_USE_OPENMP=YES"
-       # OCCA, RAJA, libCEED are enabled below, if available
-      ;;
    -v)
       valgrind="yes"
       ;;
@@ -295,10 +266,6 @@ case "$1" in
       shift
       output_dir="$1"
       ;;
-   -d)
-      shift
-      mfem_build_dir="$1"
-      ;;
    -j)
       shift
       make_j="-j $1"
@@ -318,10 +285,6 @@ case "$1" in
    -n)
       run_prefix="echo"
       ;;
-   -*)
-      echo "unknown option: '$1'"
-      exit 1
-      ;;
    *=*)
       eval $1
       ;;
@@ -467,30 +430,6 @@ fi
 
 TIMEFORMAT="${base_timeformat}"
 
-# Setup optional libraries when not using externally built MFEM:
-if [ "${built}" == "no" ]; then
-   have_occa="no"
-   have_raja="no"
-   have_ceed="no"
-   if [ "${device_runs}" == "yes" ]; then
-      if [ -n "${CUDA_ARCH}" ]; then
-         mfem_config+=" CUDA_ARCH=${CUDA_ARCH}"
-      fi
-      if [ -d "${mfem_dir}/../occa" ]; then
-         mfem_config+=" MFEM_USE_OCCA=YES"
-         have_occa="yes"
-      fi
-      if [ -d "${mfem_dir}/../raja" ]; then
-         mfem_config+=" MFEM_USE_RAJA=YES"
-         have_raja="yes"
-      fi
-      if [ -d "${mfem_dir}/../libCEED" ]; then
-         mfem_config+=" MFEM_USE_CEED=YES"
-         have_ceed="yes"
-      fi
-   fi
-fi
-
 function set_echo_log()
 {
    local dirname=`dirname "$1"`

config/tconfig.hpp

@@ -1,13 +1,13 @@
-// Copyright (c) 2010-2020, 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.
+// Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at
+// the Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights
+// reserved. See file COPYRIGHT for details.
 //
 // This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
+// availability see http://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.
+// terms of the GNU Lesser General Public License (as published by the Free
+// Software Foundation) version 2.1 dated February 1999.
 
 #ifndef MFEM_TEMPLATE_CONFIG
 #define MFEM_TEMPLATE_CONFIG
@@ -43,14 +43,15 @@
 #define MFEM_ALIGN_SIZE(size,type) \
    MFEM_ROUNDUP(size,(MFEM_SIMD_SIZE)/sizeof(type))
 
-#ifdef MFEM_COUNT_FLOPS
 namespace mfem
 {
 namespace internal
 {
-extern long long flop_count;
+long long flop_count;
 }
 }
+
+#ifdef MFEM_COUNT_FLOPS
 #define MFEM_FLOPS_RESET() (mfem::internal::flop_count = 0)
 #define MFEM_FLOPS_ADD(cnt) (mfem::internal::flop_count += (cnt))
 #define MFEM_FLOPS_GET() (mfem::internal::flop_count)

config/test.mk

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 # Utilities for the "make test" and "make check" targets.
 
@@ -38,7 +38,7 @@ export TIME='%es %MkB %x'; \
 set -- $$($(1) $(SHELL) -c "$(2)" 2>&1); while [ "$$#" -gt 3 ]; do shift; done
 endef
 define TIMECMD.NOTGNU
-set -- $$($(1) -l $(SHELL) -c "{ $(2); } > /dev/null 2>&1" 2>&1; echo $$?); \
+set -- $$($(1) -l $(SHELL) -c "$(2)" 2>&1; echo $$?); \
 set -- "$$1"s "$$(($$7/1024))"kB "$${60}"
 endef
 define TIMECMD.BASH
@@ -60,8 +60,7 @@ endif
 # Test runs of the examples/miniapps with parameters - check exit code
 mfem-test = \
    printf "   $(3) [$(2) $(1) ... ]: "; \
-   $(call $(TIMEFUN),$(TIMECMD),$(2) ./$(1) $(if $(5),,-no-vis )$(4) \
-     > $(1).stderr 2>&1); \
+   $(call $(TIMEFUN),$(TIMECMD),$(2) ./$(1) -no-vis $(4) > $(1).stderr 2>&1); \
    if [ "$$3" = 0 ]; \
    then $(PRINT_OK); else $(PRINT_FAILED); cat $(1).stderr; fi; \
    rm -f $(1).stderr; exit $$3
@@ -70,10 +69,9 @@ mfem-test = \
 mfem-test-file = \
    printf "   $(3) [$(2) $(1) ... ]: "; \
    $(call $(TIMEFUN),$(TIMECMD),$(2) ./$(1) -no-vis > $(1).stderr 2>&1); \
-   err="$$3"; \
    if [ "$$3" = 0 ] && [ -e $(4) ]; \
-   then $(PRINT_OK); else $(PRINT_FAILED); cat $(1).stderr; err=64; fi; \
-   rm -f $(1).stderr; exit $$err
+   then $(PRINT_OK); else $(PRINT_FAILED); cat $(1).stderr; fi; \
+   rm -f $(1).stderr; exit $$3
 
 .PHONY: test test-par-YES test-par-NO test-ser test-par test-clean test-print
 
@@ -83,10 +81,8 @@ test-par-NO:  $(SEQ_$(MFEM_TESTS):=-test-seq)
 test-ser:     test-par-NO
 test-par:     test-par-YES
 test:         all test-par-$(MFEM_USE_MPI) clean-exec
-test-noclean: all test-par-$(MFEM_USE_MPI)
 test-clean: ; @rm -f *.stderr
-test-print: \
- mfem-test=printf "   $(3) [$(2) ./$(1) $(if $(5),,-no-vis )$(if $(4),$(4) )]\n"
+test-print: mfem-test=printf "   $(3) [$(2) ./$(1) -no-vis $(if $(4),$(4) )]\n"
 test-print: mfem-test-file=printf "   $(3) [$(2) ./$(1) -no-vis ]\n"
 test-print: test-par-$(MFEM_USE_MPI)
 ifeq ($(MAKECMDGOALS),test-print)

data/beam-wedge.mesh

@@ -1,87 +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
-8
-1 6  0  9 18  1 10 19
-1 6  1 10 19  2 11 20
-1 6  2 11 20  3 12 21
-1 6  3 12 21  4 13 22
-2 6  4 13 22  5 14 23
-2 6  5 14 23  6 15 24
-2 6  6 15 24  7 16 25
-2 6  7 16 25  8 17 26
-
-boundary
-26
-1 2  0 18  9
-2 2  8 17 26
-3 3  0  9 10  1
-3 3  1 10 11  2
-3 3  2 11 12  3
-3 3  3 12 13  4
-3 3  4 13 14  5
-3 3  5 14 15  6
-3 3  6 15 16  7
-3 3  7 16 17  8
-3 3 18  0  1 19
-3 3 19  1  2 20
-3 3 20  2  3 21
-3 3 21  3  4 22
-3 3 22  4  5 23
-3 3 23  5  6 24
-3 3 24  6  7 25
-3 3 25  7  8 26
-3 3  9 18 19 10
-3 3 10 19 20 11
-3 3 11 20 21 12
-3 3 12 21 22 13
-3 3 13 22 23 14
-3 3 14 23 24 15
-3 3 15 24 25 16
-3 3 16 25 26 17
-
-vertices
-27
-3
-0 0 0
-1 0 0
-2 0 0
-3 0 0
-4 0 0
-5 0 0
-6 0 0
-7 0 0
-8 0 0
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-1 1 0
-2 1 0
-3 1 0
-4 1 0
-5 1 0
-6 1 0
-7 1 0
-8 1 0
-0 0.5 1
-1 0.5 1
-2 0.5 1
-3 0.5 1
-4 0.5 1
-5 0.5 1
-6 0.5 1
-7 0.5 1
-8 0.5 1

data/beam-wedge.vtk

@@ -1,61 +0,0 @@
-# vtk DataFile Version 3.0
-Generated by MFEM
-ASCII
-DATASET UNSTRUCTURED_GRID
-POINTS 27 double
-0 0 0
-1 0 0
-2 0 0
-3 0 0
-4 0 0
-5 0 0
-6 0 0
-7 0 0
-8 0 0
-0 1 0
-1 1 0
-2 1 0
-3 1 0
-4 1 0
-5 1 0
-6 1 0
-7 1 0
-8 1 0
-0 0.5 1
-1 0.5 1
-2 0.5 1
-3 0.5 1
-4 0.5 1
-5 0.5 1
-6 0.5 1
-7 0.5 1
-8 0.5 1
-CELLS 8 56
-6 0 9 18 1 10 19
-6 1 10 19 2 11 20
-6 2 11 20 3 12 21
-6 3 12 21 4 13 22
-6 4 13 22 5 14 23
-6 5 14 23 6 15 24
-6 6 15 24 7 16 25
-6 7 16 25 8 17 26
-CELL_TYPES 8
-13
-13
-13
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-13
-13
-13
-13
-CELL_DATA 8
-SCALARS material int
-LOOKUP_TABLE default
-1
-1
-1
-1
-2
-2
-2
-2

data/fichera-mixed-p2.mesh

@@ -1,192 +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 15 13 21 12
-1 4 21 13 25 22
-1 4 15 21 25 24
-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 6 4 3
-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 10 18 9
-7 2 18 10 19
-8 3 8 9 18 17
-9 3 1 4 13 10
-10 3 4 7 16 13
-11 2 25 13 16
-11 2 13 25 22
-12 3 10 13 22 19
-13 3 7 6 15 16
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-16 2 15 25 16
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-17 3 5 2 11 14
-18 3 3 0 9 12
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-20 2 20 14 11
-20 2 14 20 23
-21 3 17 18 21 20
-22 3 18 19 22 21
-23 2 25 21 22
-23 2 21 25 24
-24 3 20 21 24 23
-
-vertices
-26
-
-nodes
-FiniteElementSpace
-FiniteElementCollection: H1_3D_P2
-VDim: 3
-Ordering: 1
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data/fichera-mixed-p2.vtk

@@ -1,168 +0,0 @@
-# vtk DataFile Version 3.0
-Generated by MFEM
-ASCII
-DATASET UNSTRUCTURED_GRID
-POINTS 116 double
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data/fichera-mixed.mesh

@@ -1,96 +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
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-
-boundary
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- 2 2  3  6  4
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data/fichera.mesh

@@ -19,10 +19,10 @@ elements
 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 11 12 15 14 20 21 24 23
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-1 5 9 10 13 12 18 19 22 21
 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

data/inline-wedge.mesh

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

data/mixed-ele-meshes/annulus-trans-24.mesh

@@ -0,0 +1,218 @@
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data/mixed-ele-meshes/annulus-trans-6.mesh

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data/mixed-ele-meshes/circInSquare.py

@@ -0,0 +1,924 @@
+#Title:circInSquare.py
+#Author:T. M. McManus
+#Date:10-7-18
+#Purpose: Fill a circular sector with triangles and a bounding region,
+#defined by 3 nodes, with quads.  Then reflect/preserve QuadI twice to
+#create a complete disc bounded in a square.
+
+import scipy as sp
+import argparse
+import sys
+import subprocess
+import time
+
+parser=argparse.ArgumentParser(description='Fill a circular sector with triangles and a bounding region,\
+defined by 3 nodes, with quads.  Then reflect/preserve QuadI twice to create a complete disc bounded in a square.'
+,epilog='Sample run: python circInSquare.py -r 1 -e 2 -n 8 -g ../../../glvis/glvis')
+
+parser.add_argument('-r','--circRad', nargs='?',const=1, default = 1.0, type=float, help='Radius of circle')
+parser.add_argument('-e','--edgeLength', nargs='?',const=1,default=2.0,type=float,help='Edge-length of bounding square')
+parser.add_argument('-n','--numEdges',nargs='?',const=1,default=6,type=int,help='n-gon approximation of internal circle')
+parser.add_argument('-o','--outputFile',nargs='?',const=1,default='circInSquare', help='Output file name.')
+parser.add_argument('-g','--glvis',nargs='?',const=1,default='',type=str,help='Abs. or rel. path of glvis binary.')
+args=parser.parse_args()
+
+r=args.circRad 
+edgeLength=args.edgeLength
+numEdges=args.numEdges
+outputName=args.outputFile
+glvis=args.glvis
+
+visMesh=False;
+
+if glvis!='':
+    visMesh=True
+
+if r >= edgeLength:
+    print("Circle radius must be less than bounding square edge length")
+    sys.exit(1)
+
+if sp.mod(numEdges,2) != 0:
+    print("Currently this mixed element generator only supports an even numbers of edges.")
+    sys.exit(1)
+
+    
+#The basic idea:
+#1. Construct topology for regions
+#2. Combine topologies
+#3. Construct boundary
+#4. Construct geometry for regions
+#5. Combine geometries
+#6. Output
+
+def eleMatCirc(numEdges):
+    
+    nNodesSeq=sp.zeros([numEdges])
+    nNodesSeq[0]=3
+    if numEdges != 1:
+        for n in range(1,numEdges):
+            nNodesSeq[n]=nNodesSeq[n-1]+(2+n)
+            
+    numCircNodesTot =int(((numEdges+1)*(numEdges+2))/2)
+    
+    b=range(numCircNodesTot)
+    row_size=1
+    A=sp.zeros([numEdges+1,numEdges+1])
+    start=0;stop=1;
+    for m in range(numEdges+1):
+        if m==0:
+            A[m,range(m+1)]=b[0:1]
+            start=0
+            stop=1
+        else:
+            start=stop
+            stop=stop+m+1
+            A[m,range(m+1)]=b[start:stop]
+
+    M=sp.ones([numEdges**2,5])
+    m_row=0
+    for m in range(numEdges):
+        if m==0:
+            M[0,:]=[1,2,0,1,2]
+            m_row+=1
+        else:
+           holder=sp.size(sp.nonzero(A[m,:]))
+           for n in range(holder):
+               if n!=holder-1:
+                   M[m_row,:]=[1,2,A[m,n],A[m,n+1],A[m+1,n+1]]
+                   m_row+=1
+                   M[m_row,:]=[1,2,A[m,n],A[m+1,n],A[m+1,n+1]]
+                   m_row+=1
+               else:
+                   M[m_row,:]=[1,2,A[m,n],A[m+1,n],A[m+1,n+1]]
+                   m_row+=1
+            
+    return M.astype(int),numCircNodesTot
+
+def eleMatQuad(numEdges):
+    S0=numEdges*(numEdges+1)/(2.0)
+    A=sp.linspace(S0,(S0+(numEdges+1)**2)-1,(numEdges+1)**2)
+    A=A.reshape([numEdges+1,numEdges+1])
+    quadNode=sp.delete(A,-1,1)
+    quadNode=sp.delete(quadNode,-1,0)
+    quadNode=quadNode.flatten()
+    M=sp.zeros([numEdges**2,6])
+    for n in range(numEdges**2):
+        M[n,:]=[2,3,quadNode[n],quadNode[n]+1,quadNode[n]+numEdges+2,quadNode[n]+numEdges+1]
+    return M.astype(int)
+
+def boundMatTot(numEdges):
+    triS1=sp.zeros(numEdges+1)
+    triS3=sp.zeros(numEdges+1)
+    quadS1=sp.zeros(numEdges)
+    quadS2=sp.zeros(numEdges-1)
+    quadS3=sp.zeros(numEdges)
+
+    triS1[0]=0;
+    triS3[0]=0;
+    for n in range(1,numEdges+1):
+        triS1[n]=triS1[n-1]+n
+        triS3[n]=triS1[n]+n
+    ref1=triS3
+    
+    triS3=sp.flipud(triS3)
+    quadS1[0]=triS1[-1]+numEdges+1
+    quadS3[0]=triS1[-1]+2*numEdges+1
+
+    for n in range(1,numEdges):
+        quadS1[n]=quadS1[n-1]+(numEdges+1)
+        quadS3[n]=quadS3[n-1]+(numEdges+1)    
+    ref2=quadS3
+    xAxisRootRef=sp.concatenate([triS1.copy(),quadS1],axis=0)
+    quadS3=sp.flipud(quadS3)
+    quadS2=range(int(quadS1[-1]+1),int(quadS3[0]),1)
+    STOT=sp.concatenate([triS1,quadS1,quadS2,quadS3,triS3],axis=0)
+
+    filler=sp.zeros(1)
+    filler[0]=quadS3[0]
+    fillerFirst=sp.zeros(1)
+    fillerFirst[0]=quadS1[-1]
+    sTotRef=sp.concatenate([triS1,quadS1,quadS2,filler],axis=0)
+    newsTotRef=sp.concatenate([fillerFirst,quadS2,filler],axis=0)
+    boundMat=sp.zeros([STOT.size-1,4])
+    boundMatRef=sp.zeros([sTotRef.size-1,4])
+    new_boundMat_ref=sp.zeros([newsTotRef.size-1,4])
+    
+    for n in range(STOT.size-1):
+        boundMat[n,:]=[1,1,STOT[n],STOT[n+1]]
+    for n in range(sTotRef.size-1):
+        boundMatRef[n,:]=[1,1,sTotRef[n],sTotRef[n+1]]
+    for n in range(newsTotRef.size-1):
+        new_boundMat_ref[n,:]=[1,1,newsTotRef[n],newsTotRef[n+1]]
+        
+    ref=sp.concatenate([ref1,ref2],axis=0).astype(int)
+    return boundMat.astype(int),ref,boundMatRef.astype(int),xAxisRootRef.astype(int),new_boundMat_ref.astype(int)
+
+def vertMatCirc(numEdges):
+    r_o=sp.linspace(0,r,numEdges+1)
+    counter=0
+    vertMat=sp.zeros([numCircNodesTot,2])
+    for m in range(numEdges+1):
+        theta=sp.linspace(0,sp.pi/2.0,m+1)
+        for n in range(sp.size(theta)):
+            vertMat[counter,:]=[r_o[m]*sp.cos(theta[n]),r_o[m]*sp.sin(theta[n])]
+            counter+=1
+    return vertMat
+
+def vertMatQuad(numEdges):
+
+    theta=sp.linspace(0,sp.pi/2.0,numEdges+1)
+    AX=sp.zeros([numEdges+1,numEdges+1])
+    AY=sp.zeros([numEdges+1,numEdges+1])
+    AX[0,:]=r*sp.cos(theta)
+    AY[0,:]=r*sp.sin(theta)
+
+    vertLinSpace=sp.linspace(0,edgeLength,(numEdges/2)+1)
+    horzLineSpace=sp.linspace(edgeLength,0,(numEdges/2)+1)
+
+    #Assigning node locations along the boundary
+    vertCount=0
+    horzCount=1
+    for n in range(numEdges+1):
+        if n < (numEdges/2):
+            AX[-1,n]=edgeLength
+            AY[-1,n]=vertLinSpace[vertCount]
+            vertCount+=1
+        elif n == int(numEdges/2):
+            AX[-1,n]=edgeLength
+            AY[-1,n]=edgeLength
+        else:
+            AX[-1,n]=horzLineSpace[horzCount]
+            AY[-1,n]=edgeLength
+            horzCount+=1
+
+    #Linearly spacing nodes between the inner/outer boundaries
+    #One could then smooth this via r-based adaptivity
+    for col in range(numEdges+1):
+        for row in range(1,numEdges):
+            AX[row,col]=sp.linspace(AX[0,col],AX[-1,col],numEdges+1)[row]
+            AY[row,col]=sp.linspace(AY[0,col],AY[-1,col],numEdges+1)[row]
+
+    AX=sp.delete(AX,0,0)
+    AY=sp.delete(AY,0,0)
+    AX=AX.flatten()
+    AY=AY.flatten()
+    AX_reshape = AX.flatten()
+    
+    numQuadNodesTot=numEdges*(numEdges+1)
+    vertMat=sp.zeros([numQuadNodesTot,2])
+    for n in range(numQuadNodesTot):
+        vertMat[n,:]=[AX[n],AY[n]]    
+    return vertMat
+
+def orient(A):
+    aOrient=sp.zeros([A.shape[0],A.shape[1]])
+    triCounter=0
+    quadCounter=0
+    #Determine the number of triangle and quad elments in the given element matrix
+    for n in range(A.shape[0]):
+        if A[n,1]==2:
+            triCounter+=1
+        else:
+            quadCounter+=1
+    edgeMatTotal=sp.zeros([3*triCounter+4*quadCounter,2])
+    counter=0
+    for n in range(A.shape[0]):
+        detected=0
+        if A[n,1]==2:
+            for m in range(edgeMatTotal.shape[0]):
+                if detected != 1:
+                    if edgeMatTotal[m,0]==A[n,2] and edgeMatTotal[m,1]==A[n,3]:
+                        aOrient[n,:]=[1,2,A[n,2],A[n,4],A[n,3],0]
+                        detected=1
+                        #print("reorder:[{} {} {}] to [{} {} {}]".format(A[n,2],A[n,3],A[n,4],int(aOrient[n,2]),int(aOrient[n,3]),int(aOrient[n,4])))
+                    elif edgeMatTotal[m,0]==A[n,4] and edgeMatTotal[m,1]==A[n,2]:
+                        aOrient[n,:]=[1,2,A[n,2],A[n,4],A[n,3],0]
+                        detected=1
+                    else:
+                        aOrient[n,:]=A[n,:]
+
+            edgeMatTotal[counter,:]=[aOrient[n,2],aOrient[n,3]]
+            counter+=1
+            edgeMatTotal[counter,:]=[aOrient[n,3],aOrient[n,4]]
+            counter+=1
+            edgeMatTotal[counter,:]=[aOrient[n,4],aOrient[n,2]]
+            counter+=1
+        else:
+            for m in range(edgeMatTotal.shape[0]):
+                if detected != 1: 
+                    if edgeMatTotal[m,0]==A[n,2] and edgeMatTotal[m,1]==A[n,3]:
+                        aOrient[n,:]=[2,3,A[n,2],A[n,5],A[n,4],A[n,3]]
+                        detected=1
+                        #print("reorder:[{} {} {} {}] to [{} {} {} {}]".format(A[n,2],A[n,3],A[n,4],A[n,5],int(aOrient[n,2]),int(aOrient[n,3]),int(aOrient[n,4]),int(aOrient[n,5])))
+                    elif edgeMatTotal[m,0]==A[n,5] and edgeMatTotal[m,1]==A[n,2]:
+                        aOrient[n,:]=[2,3,A[n,2],A[n,5],A[n,4],A[n,3]]
+                        detected=1
+                    else:
+                        aOrient[n,:]=A[n,:]
+            edgeMatTotal[counter,:]=[aOrient[n,2],aOrient[n,3]]
+            counter+=1
+            edgeMatTotal[counter,:]=[aOrient[n,3],aOrient[n,4]]
+            counter+=1
+            edgeMatTotal[counter,:]=[aOrient[n,4],aOrient[n,5]]
+            counter+=1
+            edgeMatTotal[counter,:]=[aOrient[n,5],aOrient[n,2]]
+            counter+=1
+    return aOrient.astype(int)
+
+def gVis(_glvis,_meshFile):
+
+    if(_glvis==''):
+        print("Failure: Set glvis location via -g switch")
+        sys.exit(1)
+
+    colFuncFileName=_meshFile.replace('.mesh','.gf')
+    glvsScriptFileName=_meshFile.replace('.mesh','.glvs')
+    imageFileName=_meshFile.replace('.mesh','.png')
+    
+    #Create Coloring Function for mesh
+    _colFuncCommand=_glvis+ ' -m '+ _meshFile +' -sc -k q'
+    args=_colFuncCommand.split()
+    p=subprocess.Popen(args)#Create 'GLVis_coloring.gf'
+
+    _renameCommand='mv GLVis_coloring.gf {}'.format(colFuncFileName)
+    args=_renameCommand.split()
+    p=subprocess.Popen(args)
+
+    #Glvis script template
+    f=open(glvsScriptFileName,'w')
+    f.write('window 0 0 800 800\n'+'\n')
+    f.write('solution {} {}\n'.format(_meshFile,colFuncFileName)+'\n')
+    f.write('{\n'+'perspective off\n'+'zoom 1.5\n'+'keys gAeeRM\n'+'solution {} {} screenshot {}\n'.format(_meshFile,colFuncFileName,imageFileName)+'keys q\n'+'}\n')
+    f.close()
+
+    _runGlvisCommand=_glvis+' -run {}'.format(glvsScriptFileName)
+    args=_runGlvisCommand.split()
+    p=subprocess.Popen(args)
+    p.wait()
+    
+    return 0
+def quadInterDof(_edge,_linEleMat,_linVertMatRound):
+    _state=False
+    for n in range(_linEleMat.shape[0]):
+        if _linEleMat[n,1]==3:
+            if sp.any(_edge[0]==_linEleMat[n,2:6]) and sp.any(_edge[1]==_linEleMat[n,2:6]):
+                print("{} is possibly in {}".format(_edge,_linEleMat[n,2:6]))
+                _n1Loc=sp.where(_edge[0]==_linEleMat[n,2:6])[0][0]
+                _n2Loc=sp.where(_edge[1]==_linEleMat[n,2:6])[0][0]
+                if _n1Loc==sp.mod(_n2Loc+1,4) or _n1Loc==sp.mod(_n2Loc-1,4):
+                    _state=True
+                    xcent=(_linVertMatRound[_linEleMat[n,2],0]+_linVertMatRound[_linEleMat[n,3],0]+_linVertMatRound[_linEleMat[n,4],0]+_linVertMatRound[_linEleMat[n,5],0])/4.0
+                    ycent=(_linVertMatRound[_linEleMat[n,2],1]+_linVertMatRound[_linEleMat[n,3],1]+_linVertMatRound[_linEleMat[n,4],1]+_linVertMatRound[_linEleMat[n,5],1])/4.0
+                    _interDof=sp.zeros(2)
+                    _interDof[0]=sp.round_((_linVertMatRound[_edge[0],0]+_linVertMatRound[_edge[1],0]+xcent)/3.0,5)
+                    _interDof[1]=sp.round_((_linVertMatRound[_edge[0],1]+_linVertMatRound[_edge[1],1]+ycent)/3.0,5)
+                    print("dof loc is {},{}".format(_interDof[0],_interDof[1]))
+                    return(_state,_interDof[0],_interDof[1])
+
+    return(_state,0,0)
+
+[eleMatTriHolder,numCircNodesTot]=eleMatCirc(numEdges) #Construct tri element matrix for the region inside circular sector
+eleMatQuadHolder=eleMatQuad(numEdges) #Construct quad element matrix for region outside the circular sector
+
+#Combining eleMatTriHolder and eleMatQuadHolder
+linEleMat=sp.zeros([eleMatTriHolder.shape[0]+eleMatQuadHolder.shape[0],6])
+counter=0
+for n in range(eleMatTriHolder.shape[0]):
+    linEleMat[n,[0,1,2,3,4]]=eleMatTriHolder[n,:]
+    counter+=1
+for n in range(eleMatQuadHolder.shape[0]):
+    linEleMat[counter+n,:]=eleMatQuadHolder[n,:]
+
+linEleMat=linEleMat.astype(int)
+linBoundMat=boundMatTot(numEdges)[0] #Construct the boundary
+vertMatCircHolder = vertMatCirc(numEdges) #Construct vertex matrix for triang region
+vertMatQuadHolder = vertMatQuad(numEdges) #Construct vertex matrix for the quad region
+
+
+#Combining the two vertex matrices in Quadrant I (q1)
+linVertMat=sp.zeros([vertMatCircHolder.shape[0]+vertMatQuadHolder.shape[0],2])
+counter=0
+for n in range(vertMatCircHolder.shape[0]):
+    linVertMat[n,:]=vertMatCircHolder[n,:]
+    counter+=1
+for n in range(vertMatQuadHolder.shape[0]):
+    linVertMat[counter+n,:]=vertMatQuadHolder[n,:]
+
+#Outputting P1/Q1 mesh to a .mesh file
+g=open(outputName+'Lin.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(linEleMat.shape[0]))
+for n in range(linEleMat.shape[0]):
+    if linEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4],linEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(linBoundMat.shape[0]))
+for n in range(linBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(linBoundMat[n,0],linBoundMat[n,1],linBoundMat[n,2],linBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(linVertMat.shape[0])+'2\n')
+for n in range(linVertMat.shape[0]):
+    g.write('{} {}\n'.format(linVertMat[n,0],linVertMat[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'Lin.mesh')
+
+#Quadratic (P2/Q2) Element Generation
+
+#1.)Create Edge list from previously generated linear elements
+edgeMat=sp.zeros([3*eleMatTriHolder.shape[0]+4*eleMatQuadHolder.shape[0],2])
+linEleMat=orient(linEleMat)#Make sure that element orientation is in agreement with MFEM requirements
+
+counter=0
+for n in range(linEleMat.shape[0]):
+    if linEleMat[n,1]==2:
+        edgeMat[counter,:]=[linEleMat[n,2],linEleMat[n,3]]
+        counter+=1
+        edgeMat[counter,:]=[linEleMat[n,3],linEleMat[n,4]]
+        counter+=1
+        edgeMat[counter,:]=[linEleMat[n,4],linEleMat[n,2]]
+        counter+=1
+    else:
+        edgeMat[counter,:]=[linEleMat[n,2],linEleMat[n,3]]
+        counter+=1
+        edgeMat[counter,:]=[linEleMat[n,3],linEleMat[n,4]]
+        counter+=1
+        edgeMat[counter,:]=[linEleMat[n,4],linEleMat[n,5]]
+        counter+=1
+        edgeMat[counter,:]=[linEleMat[n,5],linEleMat[n,2]]
+        counter+=1
+
+#Remove duplicates
+holder=[]
+for n in range(edgeMat.shape[0]):
+    counter=0
+    for m in range(edgeMat.shape[0]):
+        if edgeMat[n,0]==edgeMat[m,0] and edgeMat[n,1]==edgeMat[m,1] and m!=n:
+            holder.append([n,m])
+        elif edgeMat[n,1]==edgeMat[m,0] and edgeMat[n,0]==edgeMat[m,1] and m!=n:
+            holder.append([n,m])
+
+removeIndices=sp.zeros(len(holder))
+for n in range(len(holder)):
+    if holder[n][0]>holder[n][1]:
+        removeIndices[n]=holder[n][0]
+    else:
+        removeIndices[n]=holder[n][1]
+removeIndices=sp.unique(removeIndices).astype(int)
+edgeMat=sp.delete(edgeMat,removeIndices,0)
+edgeMat=edgeMat.astype(int)
+
+edgeDofMat=sp.zeros([edgeMat.shape[0],2])#These will be the new DoFs that appear after the Element Vertices within the .mesh file
+linVertMatRound=sp.round_(linVertMat,5) 
+ 
+counter=0
+
+for n in edgeMat:
+    if linVertMatRound[n[0],1] == linVertMatRound[n[1],1]:
+        xmid=(linVertMatRound[n[0],0]+linVertMatRound[n[1],0])/2.0
+        ymid=linVertMatRound[n[0],1]
+        edgeDofMat[counter,:]=[xmid,ymid]
+    elif linVertMatRound[n[0],0] == linVertMatRound[n[1],0]:
+        xmid=linVertMatRound[n[0],0]
+        ymid=(linVertMatRound[n[0],1]+linVertMatRound[n[1],1])/2.0
+        edgeDofMat[counter,:]=[xmid,ymid]
+    else:
+        r0=sp.sqrt(linVertMatRound[n[0],0]**2+linVertMatRound[n[0],1]**2)
+        r1=sp.sqrt(linVertMatRound[n[1],0]**2+linVertMatRound[n[1],1]**2)
+        rmid = (r0+r1)/2.0 #should not be needed
+        xmidOld=(linVertMatRound[n[0],0]+linVertMatRound[n[1],0])/2.0
+        ymidOld=(linVertMatRound[n[0],1]+linVertMatRound[n[1],1])/2.0
+        midtheta=sp.arctan(ymidOld/xmidOld)
+        xmid=rmid*sp.cos(midtheta)
+        ymid=rmid*sp.sin(midtheta)
+        edgeDofMat[counter,:]=[xmid,ymid]
+    counter+=1
+edgeDofMat = sp.round_(edgeDofMat,5)
+
+#Determine midpoints of all Q1 elements:
+quadCentroidLoc=sp.zeros([eleMatQuadHolder.shape[0],2])
+for n in range(eleMatQuadHolder.shape[0]):
+    quadCentroidLoc[n,0]=(linVertMatRound[eleMatQuadHolder[n,2],0]+linVertMatRound[eleMatQuadHolder[n,3],0]+linVertMatRound[eleMatQuadHolder[n,4],0]+linVertMatRound[eleMatQuadHolder[n,5],0])/4.0
+    quadCentroidLoc[n,1]=(linVertMatRound[eleMatQuadHolder[n,2],1]+linVertMatRound[eleMatQuadHolder[n,3],1]+linVertMatRound[eleMatQuadHolder[n,4],1]+linVertMatRound[eleMatQuadHolder[n,5],1])/4.0
+
+quadCentroidLoc = sp.round_(quadCentroidLoc,5)
+
+#3.)Populate nodes section
+g=open(outputName+'Quad.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(linEleMat.shape[0]))
+for n in range(linEleMat.shape[0]):
+    if linEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4],linEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(linBoundMat.shape[0]))
+for n in range(linBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(linBoundMat[n,0],linBoundMat[n,1],linBoundMat[n,2],linBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(linVertMat.shape[0]))
+g.write('\n'+'nodes'+'\n'+'FiniteElementSpace'+'\n'+'FiniteElementCollection: H1_2D_P2'+'\n'+'VDim: 2'+'\n'+'Ordering: 1' +'\n\n')
+for n in range(linVertMatRound.shape[0]):
+    g.write('{} {}\n'.format(linVertMatRound[n,0],linVertMatRound[n,1]))
+for n in range(edgeDofMat.shape[0]):
+    g.write('{} {}\n'.format(edgeDofMat[n,0],edgeDofMat[n,1]))
+for n in range(quadCentroidLoc.shape[0]):
+    g.write('{} {}\n'.format(quadCentroidLoc[n,0],quadCentroidLoc[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'Quad.mesh')
+
+#Cubic (P3/Q3) Element Generation
+
+cubeDofMat=sp.zeros([2*edgeMat.shape[0],2])#These will be the new DoFs that appear after the Element Vertices within the .mesh file
+
+counter=0
+for n in edgeMat: #Here DoF ordering matters. 
+    if linVertMatRound[n[0],1] == linVertMatRound[n[1],1]:
+        xmid=(linVertMatRound[n[0],0]+linVertMatRound[n[1],0])/2.0
+        ymid=linVertMatRound[n[0],1]
+        xmid1=(linVertMatRound[n[0],0]+xmid)/2.0
+        ymid1=linVertMatRound[n[0],1]
+        xmid2=(linVertMatRound[n[1],0]+xmid)/2.0
+        ymid2=linVertMatRound[n[0],1]
+        if n[0] > n[1]:
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+        else:
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+            
+    elif linVertMatRound[n[0],0] == linVertMatRound[n[1],0]:
+        xmid=linVertMatRound[n[0],0]
+        ymid=(linVertMatRound[n[0],1]+linVertMatRound[n[1],1])/2.0
+        xmid1=linVertMatRound[n[0],0]
+        ymid1=(linVertMatRound[n[0],1]+ymid)/2.0
+        xmid2=linVertMatRound[n[0],0]
+        ymid2=(linVertMatRound[n[1],1]+ymid)/2.0
+        if n[0] > n[1]:
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+        else:
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+    else:
+        r0=sp.sqrt(linVertMatRound[n[0],0]**2+linVertMatRound[n[0],1]**2)
+        r1=sp.sqrt(linVertMatRound[n[1],0]**2+linVertMatRound[n[1],1]**2)
+        rmid = (r0+r1)/2.0 #should not be needed
+        xmidOld=(linVertMatRound[n[0],0]+linVertMatRound[n[1],0])/2.0
+        ymidOld=(linVertMatRound[n[0],1]+linVertMatRound[n[1],1])/2.0
+        midtheta=sp.arctan(ymidOld/xmidOld)
+        xmid=rmid*sp.cos(midtheta)
+        ymid=rmid*sp.sin(midtheta)
+        xmid1=(linVertMatRound[n[0],0]+xmid)/2.0
+        ymid1=(linVertMatRound[n[0],1]+ymid)/2.0
+        xmid2=(linVertMatRound[n[1],0]+xmid)/2.0
+        ymid2=(linVertMatRound[n[1],1]+ymid)/2.0
+        if n[0] > n[1]:
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+        else:
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+            
+cubeDofMat = sp.round_(cubeDofMat,5)
+
+triCentroidLoc=sp.zeros([eleMatTriHolder.shape[0],2])
+
+for n in range(eleMatTriHolder.shape[0]):
+    triCentroidLoc[n,0]=(linVertMatRound[eleMatTriHolder[n,2],0]+linVertMatRound[eleMatTriHolder[n,3],0]+linVertMatRound[eleMatTriHolder[n,4],0])/3.0
+    triCentroidLoc[n,1]=(linVertMatRound[eleMatTriHolder[n,2],1]+linVertMatRound[eleMatTriHolder[n,3],1]+linVertMatRound[eleMatTriHolder[n,4],1])/3.0
+
+quadCentroidLocCubic=sp.zeros([4*eleMatQuadHolder.shape[0],2])
+
+counter=0
+for n in range(eleMatQuadHolder.shape[0]):
+    xcent=quadCentroidLoc[n,0];ycent=quadCentroidLoc[n,1]
+    a=eleMatQuadHolder[n,2:6]
+    aMinIndex=sp.where(a[:]==a.min())[0][0]
+    dof0=0.5*sp.array([xcent+linVertMatRound[a[aMinIndex],0],ycent+linVertMatRound[a[aMinIndex],1]])
+    quadCentroidLocCubic[counter,:]=dof0
+    counter+=1
+    if aMinIndex==0:
+        aLeft=-1
+        aRight=1
+        aLast=2
+    else:
+        aLeft=aMinIndex-1
+        aRight=aMinIndex+1
+        aLast=sp.delete(a,[aMinIndex,aLeft,aRight])[0]
+    edge1=[a[aMinIndex], a[aLeft]]
+    edge2=[a[aMinIndex], a[aRight]]
+    edge1Index=0
+    edge2Index=0
+    edgeCounter=0
+    for edge in edgeMat:
+        if(edge[0]==edge1[0] and edge[1]==edge1[1]) or (edge[1]==edge1[0] and edge[0]==edge1[1]):
+            edge1Index=edgeCounter
+        if(edge[0]==edge2[0] and edge[1]==edge2[1]) or (edge[1]==edge2[0] and edge[0]==edge2[1]):
+            edge2Index=edgeCounter
+        edgeCounter+=1
+
+    if (edge1Index > edge2Index):
+        dof1=0.5*sp.array([xcent+linVertMatRound[a[aLeft],0],ycent+linVertMatRound[a[aLeft],1]])
+        quadCentroidLocCubic[counter,:]=dof1
+        counter+=1
+        dof2=0.5*sp.array([xcent+linVertMatRound[a[aRight],0],ycent+linVertMatRound[a[aRight],1]])
+        quadCentroidLocCubic[counter,:]=dof2
+        counter+=1
+        dof3=0.5*sp.array([xcent+linVertMatRound[a[aLast],0],ycent+linVertMatRound[a[aLast],1]])
+        quadCentroidLocCubic[counter,:]=dof3
+        counter+=1
+    else:
+        dof1=0.5*sp.array([xcent+linVertMatRound[a[aRight],0],ycent+linVertMatRound[a[aRight],1]])
+        quadCentroidLocCubic[counter,:]=dof1
+        counter+=1
+        dof2=0.5*sp.array([xcent+linVertMatRound[a[aLeft],0],ycent+linVertMatRound[a[aLeft],1]])
+        quadCentroidLocCubic[counter,:]=dof2
+        counter+=1
+        dof3=0.5*sp.array([xcent+linVertMatRound[a[aLast],0],ycent+linVertMatRound[a[aLast],1]])
+        quadCentroidLocCubic[counter,:]=dof3
+        counter+=1
+        
+truCentroidLoc=sp.round_(triCentroidLoc,5)
+    
+#3.)Populate nodes section
+g=open(outputName+'Cub.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(linEleMat.shape[0]))
+for n in range(linEleMat.shape[0]):
+    if linEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4],linEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(linBoundMat.shape[0]))
+for n in range(linBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(linBoundMat[n,0],linBoundMat[n,1],linBoundMat[n,2],linBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(linVertMat.shape[0]))
+g.write('\n'+'nodes'+'\n'+'FiniteElementSpace'+'\n'+'FiniteElementCollection: H1_2D_P3'+'\n'+'VDim: 2'+'\n'+'Ordering: 1' +'\n\n')
+for n in range(linVertMatRound.shape[0]):
+    g.write('{} {}\n'.format(linVertMatRound[n,0],linVertMatRound[n,1]))
+for n in range(cubeDofMat.shape[0]):
+    g.write('{} {}\n'.format(cubeDofMat[n,0],cubeDofMat[n,1]))
+for n in range(triCentroidLoc.shape[0]):
+    g.write('{} {}\n'.format(triCentroidLoc[n,0],triCentroidLoc[n,1]))
+for n in range(quadCentroidLocCubic.shape[0]):
+    g.write('{} {}\n'.format(quadCentroidLocCubic[n,0],quadCentroidLocCubic[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'Cub.mesh')
+#raw_input()
+#'Reflecting' topology about one of its edges and append it to itself
+upperPlaneEleMat = sp.zeros([2*linEleMat.shape[0],6])
+for n in range(linEleMat.shape[0]):
+    upperPlaneEleMat[n,:]=linEleMat[n,:]
+    
+#Create ele_mat_holder.shape[0]x2 matrix for mapping
+refEdge=boundMatTot(numEdges)[1]
+q1NumNodes=linVertMat.shape[0]
+
+mapping = sp.zeros([q1NumNodes])
+counter=0
+for n in range(q1NumNodes):
+     if (sp.any(refEdge == n)):
+         mapping[n]=n
+     else:
+         mapping[n]=counter+q1NumNodes
+         counter+=1
+
+mapping=mapping.astype(int)
+#Implement mapping
+
+counter=0
+for n in range(linEleMat.shape[0],2*linEleMat.shape[0]):
+    upperPlaneEleMat[n,0]=linEleMat[counter,0]
+    upperPlaneEleMat[n,1]=linEleMat[counter,1]
+    upperPlaneEleMat[n,2]=mapping[linEleMat[counter,2]]
+    upperPlaneEleMat[n,3]=mapping[linEleMat[counter,3]]
+    upperPlaneEleMat[n,4]=mapping[linEleMat[counter,4]]
+    upperPlaneEleMat[n,5]=mapping[linEleMat[counter,5]]
+    counter+=1
+    
+upperPlaneEleMat = upperPlaneEleMat.astype(int)
+
+#Reflecting boundary matrix
+origBound=boundMatTot(numEdges)[2]
+upperPlaneBoundMat=sp.zeros([2*origBound.shape[0],4])
+for n in range(origBound.shape[0]):
+    upperPlaneBoundMat[n,:]=origBound[n,:]
+counter=0
+newOrigBound=origBound.copy()
+newOrigBound[:,2]=sp.flipud(origBound[:,3])
+newOrigBound[:,3]=sp.flipud(origBound[:,2])
+for n in range(newOrigBound.shape[0],upperPlaneBoundMat.shape[0]):
+    upperPlaneBoundMat[n,0]=newOrigBound[counter,0]
+    upperPlaneBoundMat[n,1]=newOrigBound[counter,1]
+    upperPlaneBoundMat[n,2]=mapping[newOrigBound[counter,2]]
+    upperPlaneBoundMat[n,3]=mapping[newOrigBound[counter,3]]
+    counter+=1
+upperPlaneBoundMat=upperPlaneBoundMat.astype(int)
+
+#Reflecting vertex matrix about the y-axis and appending it to itself
+upperPlaneNumNodes=q1NumNodes+(q1NumNodes-refEdge.shape[0])
+upperPlaneVertMat = sp.zeros([upperPlaneNumNodes,2])
+for n in range(linVertMat.shape[0]):
+    upperPlaneVertMat[n,:]=linVertMat[n,:]
+counter=0
+for n in range(linVertMat.shape[0],upperPlaneNumNodes):
+        upperPlaneVertMat[n,0]=-1.0*linVertMat[sp.where(mapping==n)[0][0],0]
+        upperPlaneVertMat[n,1]=linVertMat[sp.where(mapping==n)[0][0],1]
+        counter+=1
+
+upperPlaneEleMat=orient(upperPlaneEleMat)
+g=open(outputName+'UpperPlaneLin.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(upperPlaneEleMat.shape[0]))
+for n in range(upperPlaneEleMat.shape[0]):
+    if upperPlaneEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(upperPlaneEleMat[n,0],upperPlaneEleMat[n,1],upperPlaneEleMat[n,2],upperPlaneEleMat[n,3],upperPlaneEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(upperPlaneEleMat[n,0],upperPlaneEleMat[n,1],upperPlaneEleMat[n,2],upperPlaneEleMat[n,3],upperPlaneEleMat[n,4],upperPlaneEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(upperPlaneBoundMat.shape[0]))
+for n in range(upperPlaneBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(upperPlaneBoundMat[n,0],upperPlaneBoundMat[n,1],upperPlaneBoundMat[n,2],upperPlaneBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(upperPlaneVertMat.shape[0])+'2\n')
+for n in range(upperPlaneVertMat.shape[0]):
+    g.write('{} {}\n'.format(upperPlaneVertMat[n,0],upperPlaneVertMat[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'UpperPlaneLin.mesh')
+
+#'Reflecting' topology about one of its edges and append it to itself
+wholePlaneEleMat = sp.zeros([2*upperPlaneEleMat.shape[0],6])
+for n in range(upperPlaneEleMat.shape[0]):
+    wholePlaneEleMat[n,:]=upperPlaneEleMat[n,:]
+
+quad1Edge=boundMatTot(numEdges)[3]
+newRefEdge=sp.zeros(2*quad1Edge.shape[0]-1)
+for n in range(quad1Edge.shape[0]):
+    newRefEdge[n]=quad1Edge[n]
+counter=0
+for n in range(quad1Edge.shape[0],newRefEdge.shape[0]):
+    newRefEdge[n]=mapping[quad1Edge[counter]]
+    counter+=1
+newRefEdge=sp.unique(newRefEdge)
+newRefEdge=newRefEdge.astype(int)
+newTotNumNodes=upperPlaneVertMat.shape[0]
+
+newMapping=sp.zeros([newTotNumNodes])
+counter=0
+for n in range(newTotNumNodes):
+    if (sp.any(newRefEdge == n)):
+        newMapping[n]=n
+    else:
+        newMapping[n]=counter+newTotNumNodes
+        counter+=1
+newMapping=newMapping.astype(int)
+
+counter=0
+for n in range(upperPlaneEleMat.shape[0],2*upperPlaneEleMat.shape[0]):
+    wholePlaneEleMat[n,0]=upperPlaneEleMat[counter,0]
+    wholePlaneEleMat[n,1]=upperPlaneEleMat[counter,1]
+    wholePlaneEleMat[n,2]=newMapping[upperPlaneEleMat[counter,2]]
+    wholePlaneEleMat[n,3]=newMapping[upperPlaneEleMat[counter,3]]
+    wholePlaneEleMat[n,4]=newMapping[upperPlaneEleMat[counter,4]]
+    wholePlaneEleMat[n,5]=newMapping[upperPlaneEleMat[counter,5]]
+    counter+=1
+
+wholePlaneEleMat=wholePlaneEleMat.astype(int)
+
+#Reflecting boundary matrix
+newOrigBoundQuad1=boundMatTot(numEdges)[4]
+newFirstBoundMatHolder=sp.zeros([2*newOrigBoundQuad1.shape[0],4])
+for n in range(newOrigBoundQuad1.shape[0]):
+    newFirstBoundMatHolder[n,:]=newOrigBoundQuad1[n,:]
+
+newNewOrigBoundQuad1=newOrigBoundQuad1.copy()
+newNewOrigBoundQuad1[:,2]=sp.flipud(newOrigBoundQuad1[:,3])
+newNewOrigBoundQuad1[:,3]=sp.flipud(newOrigBoundQuad1[:,2])
+counter=0
+for n in range(newOrigBoundQuad1.shape[0],newFirstBoundMatHolder.shape[0]):
+    newFirstBoundMatHolder[n,0]=newNewOrigBoundQuad1[counter,0]
+    newFirstBoundMatHolder[n,1]=newNewOrigBoundQuad1[counter,1]
+    newFirstBoundMatHolder[n,2]=mapping[newNewOrigBoundQuad1[counter,2]]
+    newFirstBoundMatHolder[n,3]=mapping[newNewOrigBoundQuad1[counter,3]]
+    counter+=1
+
+upperQuadMat=newFirstBoundMatHolder.copy()
+wholePlaneBoundMat=sp.zeros([2*upperQuadMat.shape[0],4])
+for n in range(upperQuadMat.shape[0]):
+    wholePlaneBoundMat[n,:]=upperQuadMat[n,:]
+
+counter=0
+newNewOrigBound=upperQuadMat.copy()
+newNewOrigBound[:,2]=sp.flipud(upperQuadMat[:,3])
+newNewOrigBound[:,3]=sp.flipud(upperQuadMat[:,2])
+newNewOrigBound=newNewOrigBound.astype(int)
+for n in range(newNewOrigBound.shape[0],wholePlaneBoundMat.shape[0]):
+    wholePlaneBoundMat[n,0]=newNewOrigBound[counter,0]
+    wholePlaneBoundMat[n,1]=newNewOrigBound[counter,1]
+    wholePlaneBoundMat[n,2]=newMapping[newNewOrigBound[counter,2]]
+    wholePlaneBoundMat[n,3]=newMapping[newNewOrigBound[counter,3]]
+    counter+=1
+wholePlaneBoundMat=wholePlaneBoundMat.astype(int)
+
+wholePlaneNumNodes=newTotNumNodes+(newTotNumNodes-newRefEdge.shape[0])
+wholePlaneVertMat = sp.zeros([wholePlaneNumNodes,2])
+for n in range(upperPlaneVertMat.shape[0]):
+    wholePlaneVertMat[n,:]=upperPlaneVertMat[n,:]
+counter=0
+for n in range(upperPlaneVertMat.shape[0],wholePlaneNumNodes):
+        wholePlaneVertMat[n,0]=upperPlaneVertMat[sp.where(newMapping==n)[0][0],0]
+        wholePlaneVertMat[n,1]=-1.0*upperPlaneVertMat[sp.where(newMapping==n)[0][0],1]
+        counter+=1
+
+g=open(outputName+'WholePlaneLin.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(wholePlaneEleMat.shape[0]))
+for n in range(wholePlaneEleMat.shape[0]):
+    if wholePlaneEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(wholePlaneEleMat[n,0],wholePlaneEleMat[n,1],wholePlaneEleMat[n,2],wholePlaneEleMat[n,3],wholePlaneEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(wholePlaneEleMat[n,0],wholePlaneEleMat[n,1],wholePlaneEleMat[n,2],wholePlaneEleMat[n,3],wholePlaneEleMat[n,4],wholePlaneEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(wholePlaneBoundMat.shape[0]))
+for n in range(wholePlaneBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(wholePlaneBoundMat[n,0],wholePlaneBoundMat[n,1],wholePlaneBoundMat[n,2],wholePlaneBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(wholePlaneVertMat.shape[0])+'2\n')
+for n in range(wholePlaneVertMat.shape[0]):
+    g.write('{} {}\n'.format(wholePlaneVertMat[n,0],wholePlaneVertMat[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'WholePlaneLin.mesh')
+
+#1.)Create Edge list from elements
+wholePlaneEleMat=orient(wholePlaneEleMat)
+triCounter=0;quadCounter=0;
+for n in range(wholePlaneEleMat.shape[0]):
+    if wholePlaneEleMat[n,1]==2:
+        triCounter+=1
+    else:
+        quadCounter+=1
+edgeMat=sp.zeros([3*triCounter+4*quadCounter,2])
+counter=0
+for n in range(wholePlaneEleMat.shape[0]):
+    if wholePlaneEleMat[n,1]==2:
+        edgeMat[counter,:]=[wholePlaneEleMat[n,2],wholePlaneEleMat[n,3]]
+        counter+=1
+        edgeMat[counter,:]=[wholePlaneEleMat[n,3],wholePlaneEleMat[n,4]]
+        counter+=1
+        edgeMat[counter,:]=[wholePlaneEleMat[n,4],wholePlaneEleMat[n,2]]
+        counter+=1
+    else:
+        edgeMat[counter,:]=[wholePlaneEleMat[n,2],wholePlaneEleMat[n,3]]
+        counter+=1
+        edgeMat[counter,:]=[wholePlaneEleMat[n,3],wholePlaneEleMat[n,4]]
+        counter+=1
+        edgeMat[counter,:]=[wholePlaneEleMat[n,4],wholePlaneEleMat[n,5]]
+        counter+=1
+        edgeMat[counter,:]=[wholePlaneEleMat[n,5],wholePlaneEleMat[n,2]]
+        counter+=1
+
+#Remove duplicates
+holder=[]
+for n in range(edgeMat.shape[0]):
+    counter=0
+    for m in range(edgeMat.shape[0]):
+        if edgeMat[n,0]==edgeMat[m,0] and edgeMat[n,1]==edgeMat[m,1] and m!=n:
+            holder.append([n,m])
+        elif edgeMat[n,1]==edgeMat[m,0] and edgeMat[n,0]==edgeMat[m,1] and m!=n:
+            holder.append([n,m])
+removeIndices=sp.zeros(len(holder))
+for n in range(len(holder)):
+    if holder[n][0]>holder[n][1]:
+        removeIndices[n]=holder[n][0]
+    else:
+        removeIndices[n]=holder[n][1]
+removeIndices=sp.unique(removeIndices).astype(int)
+edgeMat=sp.delete(edgeMat,removeIndices,0)
+edgeMat=edgeMat.astype(int)
+
+edgeDofMat=sp.zeros([edgeMat.shape[0],2])
+
+wholePlaneVertMatRound=sp.round_(wholePlaneVertMat,5)
+
+counter=0
+for n in edgeMat:
+    if wholePlaneVertMatRound[n[0],1] == wholePlaneVertMatRound[n[1],1]:
+        xmid=(wholePlaneVertMatRound[n[0],0]+wholePlaneVertMatRound[n[1],0])/2.0
+        ymid=wholePlaneVertMatRound[n[0],1]
+        edgeDofMat[counter,:]=[xmid,ymid]
+    elif wholePlaneVertMatRound[n[0],0] == wholePlaneVertMatRound[n[1],0]:
+        xmid=wholePlaneVertMatRound[n[0],0]
+        ymid=(wholePlaneVertMatRound[n[0],1]+wholePlaneVertMatRound[n[1],1])/2.0
+        edgeDofMat[counter,:]=[xmid,ymid]
+    else:
+        r0=sp.sqrt(wholePlaneVertMatRound[n[0],0]**2+wholePlaneVertMatRound[n[0],1]**2)
+        r1=sp.sqrt(wholePlaneVertMatRound[n[1],0]**2+wholePlaneVertMatRound[n[1],1]**2)
+        rmid = (r0+r1)/2.0 #should not be needed
+        xmidOld=(wholePlaneVertMatRound[n[0],0]+wholePlaneVertMatRound[n[1],0])/2.0
+        ymidOld=(wholePlaneVertMatRound[n[0],1]+wholePlaneVertMatRound[n[1],1])/2.0
+        midtheta=sp.arctan2(ymidOld,xmidOld)
+        xmid=rmid*sp.cos(midtheta)
+        ymid=rmid*sp.sin(midtheta)
+        edgeDofMat[counter,:]=[xmid,ymid]
+    counter+=1
+edgeDofMat = sp.round_(edgeDofMat,5)
+
+#2.)Create correct dof locations
+#Determine midpoints of all quads:
+quadCentroidLoc=sp.zeros([quadCounter,2])
+counter=0
+for n in range(wholePlaneEleMat.shape[0]):
+    if wholePlaneEleMat[n,1]==3:
+        quadCentroidLoc[counter,0]=(wholePlaneVertMatRound[wholePlaneEleMat[n,2],0]+wholePlaneVertMatRound[wholePlaneEleMat[n,3],0]+wholePlaneVertMatRound[wholePlaneEleMat[n,4],0]+wholePlaneVertMatRound[wholePlaneEleMat[n,5],0])/4.0
+        quadCentroidLoc[counter,1]=(wholePlaneVertMatRound[wholePlaneEleMat[n,2],1]+wholePlaneVertMatRound[wholePlaneEleMat[n,3],1]+wholePlaneVertMatRound[wholePlaneEleMat[n,4],1]+wholePlaneVertMatRound[wholePlaneEleMat[n,5],1])/4.0
+        counter+=1
+
+quadCentroidLoc = sp.round_(quadCentroidLoc,5)
+
+#3.)Populate nodes section
+g=open(outputName+'WholePlaneQuad.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(wholePlaneEleMat.shape[0]))
+for n in range(wholePlaneEleMat.shape[0]):
+    if wholePlaneEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(wholePlaneEleMat[n,0],wholePlaneEleMat[n,1],wholePlaneEleMat[n,2],wholePlaneEleMat[n,3],wholePlaneEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(wholePlaneEleMat[n,0],wholePlaneEleMat[n,1],wholePlaneEleMat[n,2],wholePlaneEleMat[n,3],wholePlaneEleMat[n,4],wholePlaneEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(wholePlaneBoundMat.shape[0]))
+for n in range(wholePlaneBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(wholePlaneBoundMat[n,0],wholePlaneBoundMat[n,1],wholePlaneBoundMat[n,2],wholePlaneBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(wholePlaneVertMat.shape[0]))
+g.write('\n'+'nodes'+'\n'+'FiniteElementSpace'+'\n'+'FiniteElementCollection: H1_2D_P2'+'\n'+'VDim: 2'+'\n'+'Ordering: 1' +'\n\n')
+for n in range(wholePlaneVertMatRound.shape[0]):
+    g.write('{} {}\n'.format(wholePlaneVertMatRound[n,0],wholePlaneVertMatRound[n,1]))
+for n in range(edgeDofMat.shape[0]):
+    g.write('{} {}\n'.format(edgeDofMat[n,0],edgeDofMat[n,1]))
+for n in range(quadCentroidLoc.shape[0]):
+    g.write('{} {}\n'.format(quadCentroidLoc[n,0],quadCentroidLoc[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'WholePlaneQuad.mesh')

data/mixed-ele-meshes/comp_tri_quad_4_edges.mesh

@@ -0,0 +1,264 @@
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+
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data/mixed-ele-meshes/spec-3-mixed-type.mesh

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data/mixed-ele-meshes/spec-3-type-1-trans-5.mesh

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data/mixed-ele-meshes/spec-3-type-1.mesh

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data/mixed-ele-meshes/spec-3-type-2.mesh

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data/mixed-ele-meshes/tri_circ_sect_4.mesh

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data/toroid-wedge.mesh

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-1 3 11 9 12 14
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-1 3 15 16 1 0
-1 3 16 17 2 1
-1 3 17 15 0 2
-
-vertices
-18
-
-nodes
-FiniteElementSpace
-FiniteElementCollection: H1_3D_P3
-VDim: 3
-Ordering: 1
-
-0.6 -1.4695762e-16 -9.7971744e-17
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-0.4 0.69282032 0.34641016
-0.7 1.2124356 2.7755576e-17
-0.4 0.69282032 -0.34641016
--0.6 1.0392305 0.34641016
--0.6 1.0392305 -0.34641016
--0.3 0.51961524 -3.8651415e-16
--1.4 1.7145055e-16 4.8985872e-17
--0.8 9.7971744e-17 -0.34641016
--0.8 4.5324311e-16 0.34641016
--0.6 -1.0392305 -0.34641016
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--0.6 1.0392305 0.15491933
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-0.48291796 -0.83643844 -0.25066475
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--0.25356098 -1.0629872 -0.38908379
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--0.1430764 -0.59980988 0.11416557
-0.16461091 -0.69008761 0.27491822
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-0.65062668 0.6156201 0.23048728
-0.86954463 0.8227593 0.15859651
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-0.75456149 0.71396276 -0.24998909
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-0.71712515 0.2135607 -0.024929133
-0.61926276 0.5859437 -0.20555815
-0.55502751 0.52516459 0.091392579
--0.5 0.8660254 5.1344633e-17
-0.24102914 1.0104508 0.24998909
-0.29043935 1.21759 0.024929133
--0.26624219 1.1161498 0.20555815
--0.28676082 1.2021687 -0.091392579
-0.27775814 1.1644274 -0.15859651
-0.20782931 0.87126929 -0.23048728
--0.25622363 1.0741497 -0.23048728
--0.1862948 0.78099155 -0.15859651
-0.17729212 0.74325022 -0.091392579
-0.19781075 0.82926913 0.20555815
--0.17361359 0.72782894 0.024929133
--0.22302379 0.93496814 0.24998909
--1 -1.2098029e-15 1.3788671e-16
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--0.833493 0.78864741 -0.20555815
--1.1996835 0.35726714 -0.024929133
--0.99559063 0.29648804 -0.24998909
--0.69819427 0.66062834 -0.24998909
--0.54351156 0.51426825 -0.024929133
--0.8170735 0.24332543 -0.20555815
--0.73231963 0.21808563 0.091392579
--0.58321113 0.5518318 0.15859651
--0.80212907 0.758971 0.23048728
--0.85845599 0.25564918 0.23048728
--1.1473028 0.34166809 0.15859651
--0.5 -0.8660254 8.6542076e-17
--1.1473028 -0.34166809 -0.15859651
--0.85845599 -0.25564918 -0.23048728
--0.80212907 -0.758971 -0.23048728
--0.58321113 -0.5518318 -0.15859651
--0.73231963 -0.21808563 -0.091392579
--0.8170735 -0.24332543 0.20555815
--0.54351156 -0.51426825 0.024929133
--0.69819427 -0.66062834 0.24998909
--0.99559063 -0.29648804 0.24998909
--1.1996835 -0.35726714 0.024929133
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--0.89772824 -0.84942651 -0.091392579
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--0.72637788 -0.68729555 1.1412456e-16
--0.23202647 -0.97270947 5.1760042e-17
-0.23202647 -0.97270947 -1.2226691e-17
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-0.95840435 -0.28541392 -1.2635125e-16

doc/CMakeLists.txt

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 find_package(Doxygen)
 

doc/CodeDocumentation.conf.in

@@ -38,7 +38,7 @@ PROJECT_NAME           = "MFEM"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v4.1.1
+PROJECT_NUMBER         = v3.4.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -768,17 +768,13 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/examples \
                          @MFEM_SOURCE_DIR@/examples/petsc \
                          @MFEM_SOURCE_DIR@/examples/pumi \
-                         @MFEM_SOURCE_DIR@/examples/hiop \
                          @MFEM_SOURCE_DIR@/examples/sundials \
                          @MFEM_SOURCE_DIR@/miniapps/common \
-                         @MFEM_SOURCE_DIR@/miniapps/electromagnetics \
-                         @MFEM_SOURCE_DIR@/miniapps/gslib \
                          @MFEM_SOURCE_DIR@/miniapps/meshing \
-                         @MFEM_SOURCE_DIR@/miniapps/navier \
-                         @MFEM_SOURCE_DIR@/miniapps/nurbs \
-                         @MFEM_SOURCE_DIR@/miniapps/performance \
                          @MFEM_SOURCE_DIR@/miniapps/tools \
-                         @MFEM_SOURCE_DIR@/miniapps/toys
+                         @MFEM_SOURCE_DIR@/miniapps/nurbs \
+                         @MFEM_SOURCE_DIR@/miniapps/electromagnetics \
+                         @MFEM_SOURCE_DIR@/miniapps/performance
 
 # 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
@@ -842,7 +838,7 @@ EXCLUDE_PATTERNS       =
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories use the pattern */test/*
 
-EXCLUDE_SYMBOLS        = mfem::internal mfem::kernels::internal
+EXCLUDE_SYMBOLS        = mfem::internal
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or directories
 # that contain example code fragments that are included (see the \include

doc/CodeDocumentation.dox

@@ -35,12 +35,6 @@ namespace mfem {
  * - HypreParMatrix and HypreParVector
  * - HypreSolver and other \link hypre.hpp hypre classes\endlink
  *
- * <H3>Main GPU classes</H3>
- * - Device
- * - Memory
- * - MemoryManager
- * - MFEM_FORALL macro in forall.hpp
- *
  * <H3>Example codes</H3>
  * - <a class="el" href="examples_2ex1_8cpp_source.html">Example 1</a>: nodal H1 FEM for the Laplace problem
  * - <a class="el" href="examples_2ex1p_8cpp_source.html">Example 1p</a>: parallel nodal H1 FEM for the Laplace problem
@@ -77,19 +71,6 @@ namespace mfem {
  * - <a class="el" href="ex18p_8cpp_source.html">Example 18p</a>: parallel Discontinuous Galerkin (DG) for the Euler equations
  * - <a class="el" href="ex19_8cpp_source.html">Example 19</a>: incompressible nonlinear elasticity
  * - <a class="el" href="ex19p_8cpp_source.html">Example 19p</a>: parallel incompressible nonlinear elasticity
- * - <a class="el" href="ex20_8cpp_source.html">Example 20</a>: symplectic ODE integration
- * - <a class="el" href="ex20p_8cpp_source.html">Example 20p</a>: parallel symplectic ODE integration
- * - <a class="el" href="ex21_8cpp_source.html">Example 21</a>: adaptive mesh refinement for linear elasticity
- * - <a class="el" href="ex21p_8cpp_source.html">Example 21p</a>: parallel adaptive mesh refinement for linear elasticity
- * - <a class="el" href="ex22_8cpp_source.html">Example 22</a>: complex-valued linear systems for damped harmonic oscillators
- * - <a class="el" href="ex22p_8cpp_source.html">Example 22p</a>: parallel complex-valued linear systems for damped harmonic oscillators
- * - <a class="el" href="ex23_8cpp_source.html">Example 23</a>: second order in time wave equation
- * - <a class="el" href="ex24_8cpp_source.html">Example 24</a>: mixed finite element spaces and interpolators
- * - <a class="el" href="ex24p_8cpp_source.html">Example 24p</a>: parallel mixed finite element spaces and interpolators
- * - <a class="el" href="ex25_8cpp_source.html">Example 25</a>: simulation of electromagnetic wave propagation using a Perfectly Matched Layer (PML)
- * - <a class="el" href="ex25p_8cpp_source.html">Example 25p</a>: parallel simulation of electromagnetic wave propagation using a Perfectly Matched Layer (PML)
- * - <a class="el" href="ex26_8cpp_source.html">Example 26</a>: multigrid preconditioner for the Laplace problem using nodal H1 FEM 
- * - <a class="el" href="ex26p_8cpp_source.html">Example 26p</a>: parallel multigrid preconditioner for the Laplace problem using nodal H1 FEM 
  *
  * <H4>SUNDIALS Examples</H4>
  * - Variants of Examples
@@ -124,17 +105,6 @@ namespace mfem {
  *   <a class="el" href="pumi_2ex6p_8cpp_source.html">6p</a>
  *   demonstrating the use of MFEM's \link pumi.hpp PUMI classes\endlink
  *
- * <H4>HiOp Examples</H4>
- * - Variants of Examples
- *   <a class="el" href="hiop_2ex9_8cpp_source.html">9</a> and
- *   <a class="el" href="hiop_2ex9p_8cpp_source.html">9p</a>,
- *   demonstrating the use of MFEM's \link hiop.hpp HiOp classes\endlink
- *
- * <H4>Ginkgo Examples</H4>
- * - Variants of Example
- *   <a class="el" href="ginkgo_2ex1_8cpp_source.html">1</a>
- *   demonstrating the use of MFEM's \link ginkgo.hpp Ginkgo classes\endlink
- *
  * <H3>Miniapps</H3>
  * - <a class="el" href="volta_8cpp_source.html">Volta</a>: simple electrostatics simulation code
  * - <a class="el" href="tesla_8cpp_source.html">Tesla</a>: simple magnetostatics simulation code
@@ -142,21 +112,12 @@ namespace mfem {
  * - <a class="el" href="joule_8cpp_source.html">Joule</a>: transient magnetics and Joule heating miniapp
  * - <a class="el" href="mobius-strip_8cpp_source.html">Mobius Strip</a>: generate various Mobius strip-like meshes
  * - <a class="el" href="klein-bottle_8cpp_source.html">Klein Bottle</a>: generate three types of Klein bottle surfaces
- * - <a class="el" href="toroid_8cpp_source.html">Toroid</a>: generate simple toroidal meshes
- * - <a class="el" href="twist_8cpp_source.html">Twist</a>: generate simple periodic meshes
- * - <a class="el" href="minimal-surface_8cpp_source.html">Minimal Surface</a>: compute minimal surfaces, <a class="el" href="minimal-surface_8cpp_source.html">serial</a> and <a class="el" href="pminimal-surface_8cpp_source.html">parallel</a> versions
  * - <a class="el" href="shaper_8cpp_source.html">Shaper</a>: resolve material interfaces by mesh refinement
- * - <a class="el" href="extruder_8cpp_source.html">Extruder</a>: extrude a low-dimensional mesh into a higher dimension
  * - <a class="el" href="mesh-explorer_8cpp_source.html">Mesh Explorer</a>: visualize and manipulate meshes
  * - <a class="el" href="mesh-optimizer_8cpp_source.html">Mesh Optimizer</a>: optimize high-order meshes, <a class="el" href="mesh-optimizer_8cpp_source.html">serial</a> and <a class="el" href="pmesh-optimizer_8cpp_source.html">parallel</a> versions
  * - <a class="el" href="display-basis_8cpp_source.html">Display Basis</a>: visualize finite element basis functions
- * - <a class="el" href="get-values_8cpp_source.html">Get Values</a>: extract field values via DataCollection classes
  * - <a class="el" href="load-dc_8cpp_source.html">Load DC</a>: visualize fields saved via DataCollection classes
- * - <a class="el" href="convert-dc_8cpp_source.html">Convert DC</a>: convert between different DataCollection formats
- * - <a class="el" href="lor-transfer_8cpp_source.html">LOR Transfer</a>: map functions between high-order and low-order refined spaces
- * - <a class="el" href="findpts_8cpp_source.html">Find Points</a>: evaluate grid function in physical space, <a class="el" href="findpts_8cpp_source.html">serial</a> and <a class="el" href="pfindpts_8cpp_source.html">parallel</a> versions
- * - <a class="el" href="field-diff_8cpp_source.html">Field Diff</a>: compare grid functions on different meshes
- * - <a class="el" href="classmfem_1_1navier_1_1NavierSolver.html">Navier</a>: solve the transient incompressible Navier-Stokes equations
+ * - <a class="el" href="convert-dc_8cpp_source.html">Convert DC</a>: convert between diffirent DataCollection formats
  * - <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
  *

doc/makefile

@@ -1,13 +1,13 @@
-# Copyright (c) 2010-2020, 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.
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
 #
 # This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
+# availability see http://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.
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
 
 MFEM_DIR ?= ..
 DOXYGEN_CONF = CodeDocumentation.conf