Improved the Jz computation.

cleanup.

.appveyor.yml

@@ -1,49 +0,0 @@
-version: '{build}'
-
-# https://www.appveyor.com/docs/build-environment/#build-worker-images
-image: Visual Studio 2017
-
-install:
-
-# Install MS-MPI
-- ps: Start-FileDownload 'https://download.microsoft.com/download/B/2/E/B2EB83FE-98C2-4156-834A-E1711E6884FB/MSMpiSetup.exe'
-- MSMpiSetup.exe -unattend
-- set PATH=C:\Program Files\Microsoft MPI\Bin;%PATH%
-
-# Install MS-MPI SDK
-- ps: Start-FileDownload 'https://download.microsoft.com/download/B/2/E/B2EB83FE-98C2-4156-834A-E1711E6884FB/msmpisdk.msi'
-- msmpisdk.msi /passive
-- set PATH=C:\Program Files\Microsoft MPI\Bin;%PATH%
-
-# Install METIS
-- ps: Start-FileDownload 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz'
-- 7z x metis-5.1.0.tar.gz -so | 7z x -si -ttar > nul
-- cd metis-5.1.0
-- ps: ( get-content "GKlib\gk_arch.h") | % { If ($_.ReadCount -ge 52) {$_ -replace "#ifdef __MSC__","#ifdef DISABLE_THIS_ANCIENT_MSC_CHECK"} Else {$_} } | set-content "GKlib\gk_arch.h"
-- cmake -H. -Bbuild
-# -DCMAKE_BUILD_TYPE=Release
-- cmake --build build
-- cd ..
-
-# Install hypre
-- 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\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
-- cmake --build build_serial
-
-after_build:
-# - cmake --build build_parallel --target check
-- cmake --build build_serial --target check

.gitignore

@@ -1,185 +0,0 @@
-# ------------------------------------------------------------------------------
-# Ignore files that are generated from the repository sources by either building
-# the code or running it. These should be the same as the files erased by
-# `make distclean`.
-#
-# Also ignore OS-specific files like .DS_Store on Mac
-# ------------------------------------------------------------------------------
-
-# Object and library files
-*.o
-/libmfem.*
-
-# CMake generated files
-CMakeCache.txt
-CMakeFiles/
-
-# Backup files
-*~
-
-# Default install location
-/mfem/
-
-# Generated files in main directory, config/ and docs/
-/deps.mk
-config/_config.hpp
-config/config.mk
-config/sample-runs-build.log
-doc/CodeDocumentation.conf
-doc/CodeDocumentation.html
-doc/CodeDocumentation
-
-# Temporary files created by the tests.
-*.stderr
-
-# Totalview breakpoint files
-*.TVD.*breakpoints
-
-# OS-specific: Mac
-*.dSYM
-.DS_Store
-
-# Example and miniapp binaries and outputs
-
-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/Example9*
-examples/Example15*
-examples/Example16*
-examples/sphere_refined.*
-examples/sol.*
-examples/sol_u.*
-examples/sol_p.*
-examples/ex9.mesh
-examples/ex9-mesh.*
-examples/ex9-init.*
-examples/ex9-final.*
-examples/deformed.*
-examples/velocity.*
-examples/elastic_energy.*
-examples/mode_*
-examples/ex16.mesh
-examples/ex16-mesh.*
-examples/ex16-init.*
-examples/ex16-final.*
-examples/vortex-mesh.*
-examples/vortex.mesh
-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/ex22*.mesh
-examples/ex22*.sol
-examples/ex22p_*.*
-
-examples/sundials/ex9
-examples/sundials/ex1[06]
-examples/sundials/ex9p
-examples/sundials/ex1[06]p
-
-examples/sundials/ex9.mesh
-examples/sundials/ex9-mesh.*
-examples/sundials/ex9-init.*
-examples/sundials/ex9-final.*
-examples/sundials/Example9*
-examples/sundials/deformed.*
-examples/sundials/velocity.*
-examples/sundials/elastic_energy.*
-examples/sundials/ex16.mesh
-examples/sundials/ex16-mesh.*
-examples/sundials/ex16-init.*
-examples/sundials/ex16-final.*
-examples/sundials/Example16*
-
-examples/petsc/ex[1-69]p
-examples/petsc/ex10p
-
-examples/petsc/mesh.*
-examples/petsc/sol.*
-examples/petsc/sol_p.*
-examples/petsc/sol_u.*
-examples/petsc/Example5*
-examples/petsc/ex9-mesh.*
-examples/petsc/ex9-init.*
-examples/petsc/ex9-final.*
-examples/petsc/Example9*
-examples/petsc/deformed.*
-examples/petsc/velocity.*
-examples/petsc/elastic_energy.*
-
-examples/pumi/ex1
-examples/pumi/ex[126]p
-
-examples/pumi/refined.mesh
-examples/pumi/sol.gf
-examples/pumi/mesh.*
-examples/pumi/sol.*
-examples/pumi/displaced.mesh
-
-miniapps/electromagnetics/volta
-miniapps/electromagnetics/tesla
-miniapps/electromagnetics/maxwell
-miniapps/electromagnetics/joule
-
-miniapps/electromagnetics/Volta-AMR*
-miniapps/electromagnetics/Tesla-AMR*
-miniapps/electromagnetics/Maxwell-Parallel*
-miniapps/electromagnetics/Joule_*
-
-miniapps/meshing/mobius-strip
-miniapps/meshing/klein-bottle
-miniapps/meshing/toroid
-miniapps/meshing/mesh-explorer
-miniapps/meshing/shaper
-miniapps/meshing/extruder
-miniapps/meshing/mesh-optimizer
-miniapps/meshing/pmesh-optimizer
-
-miniapps/meshing/mobius-strip.mesh
-miniapps/meshing/klein-bottle.mesh
-miniapps/meshing/toroid-*.mesh
-miniapps/meshing/mesh-explorer.mesh
-miniapps/meshing/partitioning.txt
-miniapps/meshing/shaper.mesh
-miniapps/meshing/extruder.mesh
-miniapps/meshing/optimized*
-miniapps/meshing/perturbed*
-
-miniapps/performance/ex1
-miniapps/performance/ex1p
-
-miniapps/performance/refined.mesh
-miniapps/performance/mesh.*
-miniapps/performance/sol.*
-
-miniapps/tools/display-basis
-miniapps/tools/load-dc
-miniapps/tools/convert-dc
-miniapps/tools/lor-transfer
-
-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*
-
-# Unit test binary and outputs
-tests/unit/output_meshes
-tests/unit/unit_tests

.travis.yml

@@ -1,207 +1,55 @@
-sudo: false
-
 language: cpp
 
-matrix:
-  include:
-    #
-    # Linux
-    #
-    - os: linux
-      compiler: gcc
-      env: DEBUG=YES
-           MPI=NO
-           CODECOV=NO
-           MFEM_TEST_TARGET=check
-    #
-    - os: linux
-      compiler: gcc
-      env: DEBUG=NO
-           MPI=NO
-           CODECOV=NO
-           MFEM_TEST_TARGET=test
-    #
-    - os: linux
-      compiler: gcc
-      addons:
-        apt:
-          # sources:
-            # - ubuntu-toolchain-r-test
-          packages:
-            # GCC 4.9
-            # - g++-4.9
-            # MPICH
-            - mpich
-            - libmpich-dev
-            # OpenMPI
-            # - openmpi-bin
-            # - libopenmpi-dev
-      env: DEBUG=YES
-           MPI=YES
-           CODECOV=NO
-           MFEM_TEST_TARGET=check
-           NPROCS=2
-      cache:
-        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 ..; rm -rf *; mv ../libmetis.a .
-    #
-    - os: linux
-      compiler: gcc
-      addons:
-        apt:
-          # sources:
-            # - ubuntu-toolchain-r-test
-          packages:
-            # GCC 4.9
-            # - g++-4.9
-            # MPICH
-            - mpich
-            - libmpich-dev
-            # OpenMPI
-            # - openmpi-bin
-            # - libopenmpi-dev
-      env: DEBUG=NO
-           MPI=YES
-           CODECOV=YES
-           MFEM_TEST_TARGET=test
-           NPROCS=2
-      cache:
-        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 ..; rm -rf *; mv ../libmetis.a .
-    #
-    # Mac OS X
-    #
-    - os: osx
-      # osx_image: xcode7.3
-      compiler: clang
-      env: DEBUG=YES
-           MPI=NO
-           CODECOV=NO
-           MFEM_TEST_TARGET=check
-    #
-    - os: osx
-      # osx_image: xcode7.3
-      compiler: clang
-      env: DEBUG=NO
-           MPI=NO
-           CODECOV=NO
-           MFEM_TEST_TARGET=test
-    #
-    - os: osx
-      # osx_image: xcode7.3
-      compiler: clang
-      env: DEBUG=YES
-           MPI=YES
-           CODECOV=NO
-           MFEM_TEST_TARGET=check
-           NPROCS=4
-           TMPDIR=/tmp
-      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
-          - $HOME/local-cached
-      before_cache:
-        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a ..; rm -rf *; mv ../libmetis.a .
-    #
-    - os: osx
-      # osx_image: xcode7.3
-      compiler: clang
-      env: DEBUG=NO
-           MPI=YES
-           CODECOV=YES
-           MFEM_TEST_TARGET=test
-           NPROCS=4
-           TMPDIR=/tmp
-      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
-          - $HOME/local-cached
-      before_cache:
-        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
-          mv libmetis.a ..; rm -rf *; mv ../libmetis.a .
+compiler:
+   - gcc
+   - clang
 
+os:
+   - linux
+   - osx
+
+env:
+   - DEBUG=YES MPI=YES TMPDIR=/tmp
+   - DEBUG=NO MPI=YES TMPDIR=/tmp
+   - DEBUG=YES MPI=NO
+   - DEBUG=NO MPI=NO
+
+# Test with GCC on Linux an Clang on Mac
+matrix:
+   exclude:
+      - compiler: clang
+        os: linux
+      - compiler: gcc
+        os: osx
 
 before_install:
-   # No addon for brew yet, have to install OSX packages this way.
-   # - if [ $TRAVIS_OS_NAME == "osx" ] && [ $MPI == "YES" ]; then
-   #      brew install open-mpi;
-   #   fi
-
-   # On Mac OS X, build and cache OpenMPI 2.1.1:
-   - if [ $TRAVIS_OS_NAME == "osx" ] && [ $MPI == "YES" ]; then
-        if [ ! -e $HOME/local-cached/bin/mpicc ]; then
-           mkdir -p $HOME/builds && cd $HOME/builds &&
-           wget https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.bz2 &&
-           tar jxf openmpi-2.1.1.tar.bz2 &&
-           mkdir openmpi-build && cd openmpi-build &&
-           ../openmpi-2.1.1/configure --prefix=$HOME/local-cached &&
-           make -j3 all && make install;
-        fi;
-        PATH=$HOME/local-cached/bin:$PATH;
-        cd $TRAVIS_BUILD_DIR;
-     fi
-
-   # Update environment to find g++ 4.9 installation first.
-   # - if [ $TRAVIS_OS_NAME == "linux" ]; then
-   #      mkdir -p latest-gcc-symlinks;
-   #      ln -s /usr/bin/g++-4.9 latest-gcc-symlinks/g++;
-   #      ln -s /usr/bin/gcc-4.9 latest-gcc-symlinks/gcc;
-   #      ln -s /usr/bin/gcov-4.9 latest-gcc-symlinks/gcov;
-   #      export PATH=$PWD/latest-gcc-symlinks:$PATH;
-   #   fi
-
-   # Install tool to upload code coverage reports to coveralls.io
-   - if [ "$CODECOV" == "YES" ]; then
-        export PYTHONUSERBASE=$HOME/local;
-        pip install --user cpp-coveralls;
-        pip install --user pyyaml;
-        PATH=$HOME/local/bin:$PATH;
-     fi
+   - if [ $TRAVIS_OS_NAME == "linux" -a "$CXX" == "g++" ]; then sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test; fi
+   - if [ $TRAVIS_OS_NAME == "linux" ]; then sudo apt-get update; fi || true
 
 install:
-   # Set MPI compilers, print compiler version
-   - if [ $MPI == "YES" ]; then
-        if [ "$TRAVIS_OS_NAME" == "linux" ]; then
-           export MPICH_CC="$CC";
-           export MPICH_CXX="$CXX";
-        else
-           export OMPI_CC="$CC";
-           export OMPI_CXX="$CXX";
-           mpic++ --showme:version;
-        fi;
-        mpic++ -v;
-     else
-        $CXX -v;
-     fi
+   # g++-4.9
+   - if [ $TRAVIS_OS_NAME == "linux" -a "$CXX" == "g++" ]; then sudo apt-get install -qq g++-4.9; fi
+   - if [ $TRAVIS_OS_NAME == "linux" -a "$CXX" == "g++" ]; then export CXX="g++-4.9"; fi
 
    # Back out of the mfem directory to install the libraries
    - cd ..
 
+   # OpenMPI
+   - if [ $TRAVIS_OS_NAME == "linux" ]; then
+        sudo apt-get install openmpi-bin openmpi-common openssh-client openssh-server libopenmpi1.3 libopenmpi-dbg libopenmpi-dev;
+     else
+        travis_wait brew install open-mpi;
+     fi
+
    # hypre
    - if [ $MPI == "YES" ]; then
-        if [ ! -e hypre-2.10.0b/src/hypre/lib/libHYPRE.a ]; then
-           wget https://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz --no-check-certificate;
-           rm -rf hypre-2.10.0b;
-           tar xvzf hypre-2.10.0b.tar.gz;
-           cd hypre-2.10.0b/src;
-           ./configure --disable-fortran --without-fei CC=mpicc CXX=mpic++;
-           make -j3;
-           cd ../..;
+        if [ ! -d hypre-2.10.0b ]; then
+            wget https://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz --no-check-certificate;
+            tar xvzf hypre-2.10.0b.tar.gz;
+            cd hypre-2.10.0b/src;
+            ./configure --disable-fortran --without-fei CC=mpicc CXX=mpic++;
+            make -j 4;
+            cd ../..;
         else
             echo "Reusing cached hypre-2.10.0b/";
         fi;
@@ -210,54 +58,43 @@ install:
      fi
 
    # METIS
-   - if [ $MPI == "YES" ]; then
-        if [ ! -e metis-4.0/libmetis.a ]; then
-           wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.3.tar.gz;
-           tar xvzf metis-4.0.3.tar.gz;
-           make -j3 -C metis-4.0.3/Lib CC="$CC" OPTFLAGS="-O2";
-           rm -rf metis-4.0;
-           mv metis-4.0.3 metis-4.0;
-        else
-           echo "Reusing cached metis-4.0/";
-        fi;
+   - if [ ! -d metis-4.0 ]; then
+        wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.3.tar.gz;
+        tar xvzf metis-4.0.3.tar.gz;
+        cd metis-4.0.3;
+        make -j 4;
+        cd ..;
+        mv metis-4.0.3 metis-4.0;
+     else
+        echo "Reusing cached metis-4.0/";
      fi
 
+# # Delete an expired cache here: https://travis-ci.org/mfem/mfem/caches
+# cache:
+#   directories:
+#     - $TRAVIS_BUILD_DIR/../hypre-2.10.0b
+#     - $TRAVIS_BUILD_DIR/../metis-4.0
+
 script:
    # Compiler
    - if [ $MPI == "YES" ]; then
         export MYCXX=mpic++;
+        export OMPI_CXX="$CXX";
+        $MYCXX --showme:version;
      else
         export MYCXX="$CXX";
      fi
-
    # Print the compiler version
    - $MYCXX -v
-
-   # Set some variables
-   - cd $TRAVIS_BUILD_DIR;
-     CPPFLAGS="";
-     SKIP_TEST_DIRS="";
-     if [ "$CODECOV" == "YES" ]; then
-        CPPFLAGS="--coverage -g";
-     fi;
-     if [ "$CXX" == "clang++" ]; then
-        export MFEM_PERF_SW=clang;
-     fi
-
-   # Configure the library
-   - make config MFEM_USE_MPI=$MPI MFEM_DEBUG=$DEBUG MFEM_CXX="$MYCXX"
-        MFEM_MPI_NP=$NPROCS CPPFLAGS="$CPPFLAGS"
-   # Show the configuration
-   - make info
-   # Build the library
-   - make -j3
-   # Build the examples and the miniapps
-   - make -j3 all
-   # Run tests
-   - make $MFEM_TEST_TARGET SKIP_TEST_DIRS="$SKIP_TEST_DIRS"
-
-after_success:
-   - if [ "$CODECOV" == "YES" ]; then
-        coveralls --include fem --include general --include linalg --include
-           mesh --exclude /usr --gcov-options '\-lp' --root $TRAVIS_BUILD_DIR;
+   # Build the code and do a quick check (debug mode) or a full tests run (non-debug mode)
+   - if [ $DEBUG == "NO" ]; then
+        export MFEM_TEST_TARGET="test";
+     else
+        export MFEM_TEST_TARGET="check";
      fi
+   # Build and check/test MFEM, its examples and miniapps
+   - cd $TRAVIS_BUILD_DIR &&
+     make config MFEM_USE_MPI=$MPI MFEM_DEBUG=$DEBUG MFEM_CXX="$MYCXX" &&
+     make info &&
+     make all -j 4 &&
+     make $MFEM_TEST_TARGET

CHANGELOG

@@ -8,462 +8,16 @@
                                http://mfem.org
 
 
-Version 4.0-RC1, Apr 11, 2019
-=============================
-
-Requirements and Limitations
-----------------------------
-- This is a release candidate for mfem-4.0.
-- Use at your own risk -- not everything will work, the API may change.
-- We are looking for feedback from friendly users.
-- Unlike previous MFEM releases, this version requires a C++11 compiler.
-
-- GPU-related limitations:
-  * NVCC is not supported in the CMake build system yet.
-  * Element batching is currently ignored.
-  * Full-assembly (on device), element assembly, and matrix-free bilinear forms
-    are not supported yet.
-  * FunctionCoefficients do not currently work on GPUs.
-  * Partial assembly kernels are not implemented yet for simplices.
-
-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.
-
-- 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 pure CUDA, 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".
-
-Discretization improvements
----------------------------
-- 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 support for derefinement of vector (RT + ND) spaces.
-
-- 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 22.
-
-- 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 H1 and L2 finite elements of arbitrary order for Wedge elements.
-
-- 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 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.
-
-- 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.
-
-- 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.
-
-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 22/22p, 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.
-
-- 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.
-
-- Altered the way FGMRES counts its iterations so that it matches GMRES.
-
-- Various other simplifications, extensions, and bugfixes in the code.
-
-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().
-
-
-Version 3.4, released on May 29, 2018
+Development version, not released yet
 =====================================
 
-More general and efficient mesh adaptivity
-------------------------------------------
-- Added support for PUMI, the Parallel Unstructured Mesh Infrastructure from
-  https://scorec.rpi.edu/pumi. PUMI is an unstructured, distributed mesh data
-  management system that is capable of handling general non-manifold models and
-  effectively supports automated adaptive analysis. PUMI enables for the first
-  time support for parallel unstructured modifications of MFEM meshes.
-
-- Significantly reduced MPI communication in the construction of the parallel
-  prolongation matrix in ParFiniteElementSpace, for much improved parallel
-  scaling of non-conforming AMR on hundreds of thousands of MPI tasks. The
-  memory footprint of the ParNCMesh class has also been reduced.
-
-- In FiniteElementSpace, the fully assembled refinement matrix is now replaced
-  by default by a specialized refinement operator. The operator option is both
-  faster and more memory efficient than using the fully assembled matrix. The
-  old approach is still available and can be enabled, if needed, using the new
-  method FiniteElementSpace::SetUpdateOperatorType().
-
-Discretization improvements
----------------------------
-- Added support for a general "high-order"-to-"low-order refined" transfer of
-  GridFunction and true-dof data from a "high-order" finite element space
-  defined on a coarse mesh, to a "low-order refined" space defined on a refined
-  mesh. The new methods, GetTransferOperator and GetTrueTransferOperator in the
-  FiniteElementSpace classes, work in both serial and parallel and support
-  matrix-based as well as matrix-free transfer operator representations. They
-  use a new method, GetTransferMatrix, in the FiniteElement class similar to
-  GetLocalInterpolation, that allows the coarse FiniteElement to be different
-  from the fine FiniteElement.
-
-- Added class ComplexOperator, that implements the action of a complex operator
-  through the equivalent 2x2 real formulation. Both symmetric and antisymmetric
-  block structures are supported.
-
-- Added classes for general block nonlinear finite element operators (deriving
-  from BlockNonlinearForm and ParBlockNonlinearForm) enabling solution of
-  nonlinear systems with multiple unknowns in different function spaces. Such
-  operators have assemble-based action and also support assembly of the gradient
-  operator to enable inversion with Newton iteration.
-
-- Added variable order NURBS: for each space each knot vector in the mesh can
-  have a different order. The order information is now part of the finite
-  element space header in the NURBS mesh output, so NURBS meshes in the old
-  format need to be updated.
-
-- In the classes NonlinearForm and ParNonlinearForm, added support for
-  non-conforming AMR meshes; see also the "API changes" section.
-
-- New specialized time integrators: symplectic integrators of orders 1-4 for
-  systems of first order ODEs derived from a Hamiltonian and generalized-alpha
-  ODE solver for the filtered Navier–Stokes equations with stabilization. See
-  classes SIASolver and GeneralizedAlphaSolver in linalg/ode.hpp.
-
-- Inherit finite element classes from the new base class TensorBasisElement,
-  whenever the basis can be represented by a tensor product of 1D bases.
-
-- Added support for elimination of boundary conditions in block matrices.
-
-New and updated examples and miniapps
--------------------------------------
-- Added a new serial and parallel example (ex19) that solves the quasi-static
-  incompressible hyperelastic equations. The example demonstrates the use of
-  block nonlinear forms as well as custom block preconditioners.
-
-- Added a new electromagnetics miniapp, Maxwell, for simulating time-domain
-  electromagnetics phenomena as a coupled first order system of equations.
-
-- A simple local refinement option has been added to the mesh-explorer miniapp
-  (menu option 'r', sub-option 'l') that selects elements for refinement based
-  on their spatial location - see the function 'region()' in the source file.
-
-- Added a set of miniapps specifically focused on Isogeometric Analysis (IGA) on
-  NURBS meshes in the miniapps/nurbs directory. Currently the directory contains
-  variable order NURBS versions of examples 1, 1p and 11p.
-
-- Added PUMI versions of examples ex1, ex1p, ex2 and ex6p in a new examples/pumi
-  directory. The new examples demonstrate the PUMI APIs for parallel and serial
-  mesh loading (ex1 and ex1p), applying BCs using classification (ex2), and
-  performing parallel mesh adaptation (ex6p).
-
-- Added two new miniapps related to DataCollection I/O in miniapps/tools:
-  load-dc.cpp can be used to visualize fields saved via DataCollection classes;
-  convert-dc.cpp demonstrates how to convert between MFEM's different concrete
-  DataCollection options.
-
-- Example 10p with its SUNDIALS and PETSc versions have been updated to reflect
-  the change in the behavior of the method ParNonlinearForm::GetLocalGradient()
-  (see the "API changes" section) and now works correctly on non-conforming AMR
-  meshes. Example 10 and its SUNDIALS version have also been updated to support
-  non-conforming ARM meshes.
-
-Miscellaneous
--------------
-- Documented project workflow and provided contribution guidelines in the new
-  top-level file, CONTRIBUTING.md.
-
-- Added (optional) Conduit Mesh Blueprint support of MFEM data for both in-core
-  and I/O use cases. This includes a new ConduitDataCollection that provides
-  json, simple binary, and HDF5-based I/O. Support requires Conduit >= v0.3.1
-  and VisIt >= v2.13.1 will read the new Data Collection outputs.
-
-- Added a new developer tool, config/sample-runs.sh, that extracts the sample
-  runs from all examples and miniapps and runs them. Optionally, it can save the
-  output from the execution to files, allowing comparison between different
-  versions and builds of the library.
-
-- Support for building a shared version of the MFEM library with GNU make.
-
-- Added a build option, MFEM_USE_EXCEPTIONS=YES, to throw an exception instead
-  of calling abort on mfem errors.
-
-- When building with the GnuTLS library, switch to using X.509 certificates for
-  secure socket authentication. Support for the previously used OpenPGP keys has
-  been deprecated in GnuTLS 3.5.x and removed in 3.6.0. For secure communication
-  with the visualization tool GLVis, a new set of certificates can be generated
-  using the latest version of the script 'glvis-keygen.sh' from GLVis.
-
-- Upgraded MFEM to support Axom 0.2.8. Prior versions are no longer supported.
-
-API changes
------------
-- Introduced a new enum, Matrix::DiagonalPolicy, that replaces the integer
-  parameters in many methods that perform elimination of rows and/or columns in
-  matrices. Some examples of such methods are:
-  * class SparseMatrix: EliminateRow(), EliminateCol(), EliminateRowCol(), ...
-  * class BilinearForm: EliminateEssentialBC(), EliminateVDofs(), ...
-  * class StaticCondensation: EliminateReducedTrueDofs()
-  * class BlockMatrix: EliminateRowCol()
-  Calling these methods with an explicitly given (integer) constants, will now
-  generate compilation errors, please use one of the new enum constants instead.
-
-- Modified the virtual method AbstractSparseMatrix::EliminateZeroRows() and its
-  implementations in derived classes, to accept an optional 'threshold'
-  parameter, replacing previously hard-coded threshold values.
-
-- In the classes NonlinearForm and ParNonlinearForm:
-  * The method GetLocalGradient() no longer imposes boundary conditions. The
-    motivation for the change is that, in the case of non-conforming AMR,
-    performing the elimination at the local level is incorrect - it must be
-    applied at the true-dof level.
-  * The method SetEssentialVDofs() is now deprecated.
-
-
-Version 3.3.2, released on Nov 10, 2017
-=======================================
-
-High-order mesh optimization
-----------------------------
-- Added support for mesh optimization via node-movement based on the Target-
-  Matrix Optimization Paradigm (TMOP) developed by P.Knupp et al. A variety of
-  mesh quality metrics, with their first and second derivatives have been
-  implemented. The combination of targets & quality metrics is used to optimize
-  the physical node positions, i.e., they must be as close as possible to the
-  shape, size and/or alignment of their targets. The optimization of arbitrary
-  high-order meshes in 2D, 3D, serial and parallel is supported.
-
-- The new Mesh Optimizer miniapp can be used to perform mesh optimization with
-  TMOP in serial and parallel versions. The miniapp also demonstrates the use of
-  nonlinear operators and their coupling to Newton methods for solving
-  minimization problems.
-
-New and improved solvers and preconditioners
---------------------------------------------
-- MFEM is now included in the xSDK project, the Extreme-scale Scientific
-  Software Development Kit, as of xSDK-0.3.0. Various changes were made to
-  comply with xSDK's community policies, https://xsdk.info/policies, including:
-  xSDK-specific options in CMake, support for user-provided MPI communicators,
-  runtime API for version number, and the ability to disable/redirect output.
-  For more details, see general/globals.hpp and in particular the mfem::err and
-  mfem::out streams replacing std::err and std::out respectively.
-
-- Added (optional) support for the STRUMPACK parallel sparse direct solver and
-  preconditioner. STRUMPACK uses Hierarchically Semi-Separable (HSS) compression
-  in a fully algebraic manner, with interface similar to SuperLU_DIST. See
-  http://portal.nersc.gov/project/sparse/strumpack for more details.
-
-- Added a block lower triangular preconditioner based (only) on the actions of
-  each block, see class BlockLowerTriangularPreconditioner.
-
-- Added an optional operator in LOBPCG to projects vectors onto a desired
-  subspace (e.g. divergence-free). Other small changes in LOBPCG include the
-  ability to set the starting vectors and support for relative tolerance.
-
-- The Newton solver supports an optional scaling factor, that can limit the
-  increment in the Newton step, see e.g. the Mesh Optimizer miniapp.
-
-- Updated MFEM integration to support the new SUNDIALS 3.0.0 interface.
-
-New and updated examples and miniapps
--------------------------------------
-- Added a new serial and parallel example (ex18) that solves the transient Euler
-  equations on a periodic domain with explicit time integrators. In the process
-  extended the NonlinearForm class to allow for integrals over faces and
-  exchanging face-neighbor data in parallel.
-
-- Added a new meshing miniapp, Shaper, that can be used to resolve complicated
-  material interfaces by mesh refinement, e.g. as a tool for initial mesh
-  generation from prescribed "material()" function.  Both conforming and
-  non-conforming (isotropic and anisotropic) refinements are supported.
-
-- Added a new meshing miniapp, Mesh Optimizer, that demonstrates the use of TMOP
-  for mesh optimization (serial and parallel version.)
-
-- Added SUNDIALS version of Example 16/16p.
-
-Discretization improvements
----------------------------
-- Added a FindPoints method of the Mesh and ParMesh classes that returns the
-  elements that contain a given set of points, together with the coordinates of
-  the points in the reference space of the corresponding element.  In parallel,
-  if a point is shared by multiple processors, only one of them will mark that
-  point as found. Note that the current implementation of this method is not
-  optimal and/or 100% reliable. See the mesh-explorer miniapp for an example.
-
-- Added a new class InverseElementTransformation, that supports a number of
-  algorithms for inversion of general ElementTransformations. This class can be
-  used as a more flexible and extensible alternative to ElementTransformation's
-  TransformBack method. It is also used in the FindPoints methods as a tunable
-  and customizable inversion algorithm.
-
-- Memory optimizations in the NCMesh class, which now uses 50% less memory than
-  before. The average cost of an element in a uniformly refined mesh (including
-  the refinement hierarchy, but excluding the temporary face_list and edge_list)
+- Memory optimizations in the NCMesh class, which now uses 50% less memory.
+  The average cost of an NC element in a uniformly refined mesh (including the
+  refinement hierarchy, but excluding the temporary face_list and edge_list)
   is now only about 290 bytes. This also makes the class faster.
 
-- Added the ability to integrate delta functions on the right-hand side (by
-  sampling the test function at the center of the delta coefficient). Currently
-  this is supported in the DomainLFIntegrator, VectorDomainLFIntegrator and
-  VectorFEDomainLFIntegrator classes.
-
-- Added five new linear interpolators in fem/bilininteg.cpp to compute products
-  of scalar and vector fields or products with arbitrary coefficients.
-
-- Added matrix coefficient support to CurlCurlIntegrator.
-
-- Extend the method NodalFiniteElement::Project for VectorCoefficient to work
-  with arbitrary number of vector components.
-
-Miscellaneous
--------------
-- Added a .gitignore file that ignores all files erased by "make distclean",
-  i.e. the files that can be generated from the source but we don't want to
-  track in the repository, as well as a few platform-specific files.
-
-- Added Linux, Mac and Windows CI testing on GitHub with Travis CI and Appveyor.
-
-- Added a new macro, MFEM_VERSION, defined as a single integer of the form
-  (major*100 + minor)*100 + patch. The convention is that an even number
-  (i.e. even patch number) denotes a "release" version, while an odd number
-  denotes a "development" version. See config/config.hpp.in.
-
-- Added an option for building in parallel without a METIS dependency. This is
-  used for example the Laghos miniapp, https://github.com/CEED/Laghos.
-
-- Modified the installation layout: all headers, except the master headers
-  (mfem.hpp and mfem-performance.hpp), are installed in <PREFIX>/include/mfem;
-  the master headers are installed in both <PREFIX>/include/mfem and in
-  <PREFIX>/include. The mfem configuration and testing makefiles (config.mk and
-  test.mk) are installed in <PREFIX>/share/mfem, instead of <PREFIX>.
-
-- Add three more options for MFEM_TIMER_TYPE.
-
-- Support independent number of digits for cycle and rank in DataCollection.
-
-- Converted Sidre usage from "asctoolkit" to "axom" namespace.
-
-- Various small fixes and styling updates.
-
-API changes
------------
-- The methods GetCoeff of VectorArrayCoefficient and MatrixArrayCoefficient now
-  return a pointer to Coefficient (instead of reference). Note that NULL pointer
-  is a valid entry for these two classes - it is treated as the zero function.
-
-- When building with PETSc, the required PETSc version is now 3.8.0. Newer
-  versions may work too, as long as there are no interface changes in PETSc.
-
-- The class GeometryRefiner now uses the enum in Quadrature1D for its type
-  specification. In particular, this will affect older versions of GLVis. A
-  simple upgrade to the latest version of GLVis should resolve this issue.
+- Add a block lower triangular preconditioner in using a matrix-free
+  implementation, see class BlockLowerTriangularPreconditioner.
 
 
 Version 3.3, released on Jan 28, 2017
@@ -619,7 +173,7 @@ Improved file output
 - Added experimental support for an HDF5-based output file format following the
   Conduit (https://github.com/LLNL/conduit) mesh blueprint specification for
   visualization and/or restart capability. This functionality is aimed primarily
-  at user of LLNL's axom project (Sidre component) that run problems at extreme
+  at user of LLNL's ASC Toolkit (Sidre component) that run problems at extreme
   scales. Users desiring a small scale binary format may want to look at the
   gzstream functionality instead.
 

CMakeLists.txt

@@ -13,11 +13,6 @@ 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.
@@ -43,14 +38,8 @@ if (NOT CMAKE_CXX_COMPILER)
   endif()
 endif()
 
-#-------------------------------------------------------------------------------
-# Project name and version
-#-------------------------------------------------------------------------------
-project(mfem NONE)
-# Current version of MFEM, see also `makefile`.
-#   mfem_VERSION = (string)
-#   MFEM_VERSION = (int)   [automatically derived from mfem_VERSION]
-set(${PROJECT_NAME}_VERSION 3.4.1)
+project(mfem CXX)
+set(${PROJECT_NAME}_VERSION 3.3)
 
 # Prohibit in-source build
 if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
@@ -58,65 +47,18 @@ if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
     "MFEM does not support in-source CMake builds at this time.")
 endif (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
 
-# Set xSDK defaults.
-set(USE_XSDK_DEFAULTS_DEFAULT OFF)
-set(XSDK_ENABLE_CXX ON)
-set(XSDK_ENABLE_C OFF)
-set(XSDK_ENABLE_Fortran OFF)
-
-# Check if we need to enable C or Fortran.
-if (CMAKE_VERSION VERSION_LESS 3.2 OR
-    MFEM_USE_CONDUIT OR
-    MFEM_USE_SIDRE OR
-    MFEM_USE_PETSC)
+if (CMAKE_VERSION VERSION_LESS 3.2 OR MFEM_USE_SIDRE)
    # This seems to be needed by:
    #  * find_package(BLAS REQUIRED) and
    #  * find_package(HDF5 REQUIRED) needed, in turn, by:
-   #    - find_package(AXOM REQUIRED)
-   #  * find_package(PETSc REQUIRED)
-   set(XSDK_ENABLE_C ON)
-endif()
-if (MFEM_USE_STRUMPACK)
-  # Just needed to find the MPI_Fortran libraries to link with
-  set(XSDK_ENABLE_Fortran ON)
-endif()
-
-# Include xSDK default CMake file.
-include("${CMAKE_CURRENT_SOURCE_DIR}/config/XSDKDefaults.cmake")
-
-# Enable languages.
-enable_language(CXX)
-if (XSDK_ENABLE_C)
+   #    - find_package(ATK REQUIRED)
    enable_language(C)
 endif()
-if (XSDK_ENABLE_Fortran)
-   enable_language(Fortran)
-endif()
-
-# Suppress warnings about MACOSX_RPATH
-set(CMAKE_MACOSX_RPATH OFF CACHE BOOL "")
 
 # CMake needs to know where to find things
 set(MFEM_CMAKE_PATH ${PROJECT_SOURCE_DIR}/config)
 set(CMAKE_MODULE_PATH ${MFEM_CMAKE_PATH}/cmake/modules)
 
-# Load MFEM CMake utilities.
-include(MfemCmakeUtilities)
-
-string(TOUPPER "${PROJECT_NAME}" PROJECT_NAME_UC)
-mfem_version_to_int(${${PROJECT_NAME}_VERSION} ${PROJECT_NAME_UC}_VERSION)
-set(${PROJECT_NAME_UC}_VERSION_STRING ${${PROJECT_NAME}_VERSION})
-if (EXISTS ${PROJECT_SOURCE_DIR}/.git)
-   execute_process(
-     COMMAND git describe --all --long --abbrev=40 --dirty --always
-     WORKING_DIRECTORY "${PROJECT_SOURCE_DIR}"
-     OUTPUT_VARIABLE ${PROJECT_NAME_UC}_GIT_STRING
-     ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
-endif()
-if (NOT ${PROJECT_NAME_UC}_GIT_STRING)
-   set(${PROJECT_NAME_UC}_GIT_STRING "(unknown)")
-endif()
-
 #-------------------------------------------------------------------------------
 # Process configuration options
 #-------------------------------------------------------------------------------
@@ -128,23 +70,25 @@ else()
   set(MFEM_DEBUG OFF)
 endif()
 
-# MPI -> hypre; PETSc (optional)
+# MPI -> hypre, METIS
 if (MFEM_USE_MPI)
   find_package(MPI REQUIRED)
-  set(MPI_CXX_INCLUDE_DIRS ${MPI_CXX_INCLUDE_PATH})
-  # Parallel MFEM depends on hypre
+  include_directories(${MPI_CXX_INCLUDE_PATH})
+  # Parallel MFEM depends on hypre and METIS
   find_package(HYPRE REQUIRED)
-  set(MFEM_HYPRE_VERSION ${HYPRE_VERSION})
+  include_directories(${HYPRE_INCLUDE_DIRS})
+  find_package(METIS REQUIRED)
+  include_directories(${METIS_INCLUDE_DIRS})
   if (MFEM_USE_PETSC)
     find_package(PETSc REQUIRED)
     message(STATUS "Found PETSc version ${PETSC_VERSION}")
-    if (PETSC_VERSION AND (PETSC_VERSION VERSION_LESS 3.8.0))
-      message(FATAL_ERROR "PETSc version >= 3.8.0 is required")
+    if (PETSC_VERSION AND (PETSC_VERSION VERSION_LESS 3.7.5.99))
+      message(FATAL_ERROR "PETSc version >= 3.7.5.99 is required")
     endif()
-    set(PETSC_INCLUDE_DIRS ${PETSC_INCLUDES})
+    include_directories(${PETSC_INCLUDES})
   endif()
 else()
-  set(PKGS_NEED_MPI SUPERLU PETSC STRUMPACK PUMI)
+  set(PKGS_NEED_MPI SUPERLU PETSC)
   foreach(PKG IN LISTS PKGS_NEED_MPI)
     if (MFEM_USE_${PKG})
       message(STATUS "Disabling package ${PKG} - requires MPI")
@@ -153,19 +97,17 @@ else()
   endforeach()
 endif()
 
-if (MFEM_USE_METIS)
-  find_package(METIS REQUIRED)
-endif()
-
 # GZSTREAM -> zlib
 if (MFEM_USE_GZSTREAM)
   find_package(ZLIB REQUIRED)
+  include_directories(${ZLIB_INCLUDE_DIRS})
 endif()
 
 # Backtrace with libunwind
 if (MFEM_USE_LIBUNWIND)
   set(MFEMBacktrace_REQUIRED_PACKAGES "Libunwind" "LIBDL" "CXXABIDemangle")
   find_package(MFEMBacktrace REQUIRED)
+  include_directories(${LIBUNWIND_INCLUDE_DIRS})
 endif()
 
 # BLAS, LAPACK
@@ -175,17 +117,19 @@ 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)
 if (MFEM_USE_SUITESPARSE)
   find_package(SuiteSparse REQUIRED
     UMFPACK KLU AMD BTF CHOLMOD COLAMD CAMD CCOLAMD config)
+  include_directories(${SuiteSparse_INCLUDE_DIRS})
 endif()
 
 # SUNDIALS
@@ -196,82 +140,63 @@ if (MFEM_USE_SUNDIALS)
     find_package(SUNDIALS REQUIRED
       NVector_Serial NVector_Parallel NVector_ParHyp CVODE ARKODE KINSOL)
   endif()
+  include_directories(${SUNDIALS_INCLUDE_DIRS})
 endif()
 
 # Mesquite
 if (MFEM_USE_MESQUITE)
   find_package(Mesquite REQUIRED)
+  include_directories(${MESQUITE_INCLUDE_DIRS})
 endif()
 
-# SuperLU_DIST can only be enabled in parallel
+# SuperLU_DIST can only be enabled if parallel
 if (MFEM_USE_SUPERLU)
   if (MFEM_USE_MPI)
     find_package(SuperLUDist REQUIRED)
+    include_directories(${SuperLUDist_INCLUDE_DIRS})
   else()
     message(FATAL_ERROR " *** SuperLU_DIST requires that MPI be enabled.")
   endif()
 endif()
 
-# STRUMPACK can only be enabled in parallel
-if (MFEM_USE_STRUMPACK)
-  if (MFEM_USE_MPI)
-    find_package(STRUMPACK REQUIRED)
-  else()
-    message(FATAL_ERROR " *** STRUMPACK requires that MPI be enabled.")
-  endif()
-endif()
-
 # Gecko
 if (MFEM_USE_GECKO)
   find_package(Gecko REQUIRED)
+  include_directories(${GECKO_INCLUDE_DIRS})
 endif()
 
 # GnuTLS
 if (MFEM_USE_GNUTLS)
   find_package(_GnuTLS REQUIRED)
+  include_directories(${GNUTLS_INCLUDE_DIRS})
 endif()
 
 # NetCDF
 if (MFEM_USE_NETCDF)
   find_package(NetCDF REQUIRED)
+  include_directories(${NETCDF_INCLUDE_DIRS})
 endif()
 
 # MPFR
 if (MFEM_USE_MPFR)
   find_package(MPFR REQUIRED)
-endif()
-
-if (MFEM_USE_CONDUIT)
-    find_package(Conduit REQUIRED conduit relay blueprint )
+  include_directories(${MPFR_INCLUDE_DIRS})
 endif()
 
 # Axom/Sidre
 if (MFEM_USE_SIDRE)
-  find_package(Axom REQUIRED Sidre SLIC axom_utils)
-endif()
-
-# PUMI
-if (MFEM_USE_PUMI)
-  # If PUMI_DIR was specified, only link to that directory,
-  # i.e. don't link to another installation in /usr/lib by mistake
-  find_package(SCOREC 2.1.0 REQUIRED OPTIONAL_COMPONENTS gmi_sim
-    CONFIG PATHS ${PUMI_DIR} NO_DEFAULT_PATH)
-  if (SCOREC_FOUND)
-    # Define a header file with the MFEM_USE_SIMMETRIX preprocessor variable
-    set(MFEM_USE_SIMMETRIX ${SCOREC_gmi_sim_FOUND})
-    set(PUMI_FOUND ${SCOREC_FOUND})
-    get_target_property(PUMI_INCLUDE_DIRS
-      SCOREC::apf INTERFACE_INCLUDE_DIRECTORIES)
-    set(PUMI_LIBRARIES SCOREC::core)
+  if (NOT MFEM_USE_MPI)
+    find_package(ATK REQUIRED Sidre SLIC common)
+  else()
+    find_package(ATK REQUIRED Sidre SPIO SLIC common)
   endif()
+  include_directories(${ATK_INCLUDE_DIRS})
 endif()
 
 # MFEM_TIMER_TYPE
 if (NOT DEFINED MFEM_TIMER_TYPE)
   if (APPLE)
-    # use std::clock from <ctime> for UserTime and
-    # use mach_absolute_time from <mach/mach_time.h> for RealTime
-    set(MFEM_TIMER_TYPE 4)
+    set(MFEM_TIMER_TYPE 0) # use std::clock from <ctime>
   elseif (WIN32)
     set(MFEM_TIMER_TYPE 3) # QueryPerformanceCounter from <windows.h>
   else()
@@ -285,27 +210,17 @@ if (NOT DEFINED MFEM_TIMER_TYPE)
 endif()
 
 # List all possible libraries in order of dependencies.
-# [METIS < SuiteSparse]:
-#    With newer versions of SuiteSparse which include METIS header using 64-bit
-#    integers, the METIS header (with 32-bit indices, as used by mfem) needs to
-#    be before SuiteSparse.
-set(MFEM_TPLS MPI_CXX OPENMP BLAS LAPACK METIS HYPRE SuiteSparse SUNDIALS PETSC
-    MESQUITE SuperLUDist STRUMPACK AXOM CONDUIT GECKO GNUTLS NETCDF MPFR PUMI
-    POSIXCLOCKS MFEMBacktrace ZLIB)
+set(MFEM_TPLS HYPRE OPENMP SUNDIALS MESQUITE SuiteSparse SuperLUDist
+    ParMETIS METIS LAPACK BLAS GECKO GNUTLS NETCDF PETSC MPFR ATK POSIXCLOCKS
+    MFEMBacktrace ZLIB)
 # Add all *_FOUND libraries in the variable TPL_LIBRARIES.
 set(TPL_LIBRARIES "")
-set(TPL_INCLUDE_DIRS "")
 foreach(TPL IN LISTS MFEM_TPLS)
   if (${TPL}_FOUND)
     message(STATUS "MFEM: using package ${TPL}")
     list(APPEND TPL_LIBRARIES ${${TPL}_LIBRARIES})
-    list(APPEND TPL_INCLUDE_DIRS ${${TPL}_INCLUDE_DIRS})
   endif()
 endforeach(TPL)
-list(REMOVE_DUPLICATES TPL_LIBRARIES)
-list(REMOVE_DUPLICATES TPL_INCLUDE_DIRS)
-# message(STATUS "TPL_INCLUDE_DIRS = ${TPL_INCLUDE_DIRS}")
-include_directories(${TPL_INCLUDE_DIRS})
 
 if (OPENMP_FOUND)
   message(STATUS "MFEM: using package OpenMP")
@@ -313,14 +228,16 @@ if (OPENMP_FOUND)
 endif()
 
 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
 #-------------------------------------------------------------------------------
 
 # Headers and sources
+include(MfemCmakeUtilities)
 set(SOURCES "")
 set(HEADERS "")
 set(MFEM_SOURCE_DIRS general linalg mesh fem)
@@ -332,30 +249,21 @@ set(MASTER_HEADERS
   ${PROJECT_SOURCE_DIR}/mfem.hpp
   ${PROJECT_SOURCE_DIR}/mfem-performance.hpp)
 
-set(_lib_path "${CMAKE_INSTALL_PREFIX}/lib")
-set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON CACHE BOOL "")
-set(CMAKE_INSTALL_RPATH "${_lib_path}" CACHE PATH "")
-set(CMAKE_INSTALL_NAME_DIR "${_lib_path}" CACHE PATH "")
-
 # Declaring the library
 add_library(mfem ${SOURCES} ${HEADERS} ${MASTER_HEADERS})
-# message(STATUS "TPL_LIBRARIES = ${TPL_LIBRARIES}")
+list(REMOVE_DUPLICATES TPL_LIBRARIES)
+# message(STATUS " TPL_LIBRARIES = ${TPL_LIBRARIES}")
 if (CMAKE_VERSION VERSION_GREATER 2.8.11)
   target_link_libraries(mfem PUBLIC ${TPL_LIBRARIES})
 else()
   target_link_libraries(mfem ${TPL_LIBRARIES})
 endif()
-if (MINGW)
-  target_link_libraries(mfem ws2_32)
-endif()
-set_target_properties(mfem PROPERTIES VERSION "${mfem_VERSION}")
-set_target_properties(mfem PROPERTIES SOVERSION "${mfem_VERSION}")
 
 # 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_BUILD_DIR=${PROJECT_BINARY_DIR}")
+    "-DMFEM_BUILD_DIR=${PROJECT_BINARY_DIR}")
 endif()
 
 # Generate configuration file in the build directory: config/_config.hpp.
@@ -373,11 +281,6 @@ if (NOT ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}"))
 "// Auto-generated file.
 #define MFEM_BUILD_DIR ${PROJECT_BINARY_DIR}
 #include \"${PROJECT_SOURCE_DIR}/${Header}\"
-")
-    # This version will be installed in the top include directory:
-    file(WRITE "${PROJECT_BINARY_DIR}/InstallHeaders/${Header}"
-"// Auto-generated file.
-#include \"mfem/${Header}\"
 ")
   endforeach()
 endif()
@@ -389,9 +292,6 @@ 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.
@@ -411,9 +311,7 @@ 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
@@ -434,12 +332,12 @@ 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 -E performance -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 -E performance -C ${CMAKE_CFG_INTDIR}
     USES_TERMINAL)
   add_dependencies(check ex1p)
 endif()
@@ -454,6 +352,7 @@ add_subdirectory(doc)
 #-------------------------------------------------------------------------------
 
 message(STATUS "CMAKE_INSTALL_PREFIX = ${CMAKE_INSTALL_PREFIX}")
+string(TOUPPER "${PROJECT_NAME}" PROJECT_NAME_UC)
 set(INSTALL_INCLUDE_DIR include
   CACHE PATH "Relative path for installing header files.")
 set(INSTALL_LIB_DIR lib
@@ -473,15 +372,11 @@ install(TARGETS ${PROJECT_NAME}
   DESTINATION ${INSTALL_LIB_DIR})
 
 # Install the master headers
-foreach(Header mfem.hpp mfem-performance.hpp)
-  install(FILES ${PROJECT_BINARY_DIR}/InstallHeaders/${Header}
-    DESTINATION ${INSTALL_INCLUDE_DIR})
-endforeach()
-install(FILES ${MASTER_HEADERS} DESTINATION ${INSTALL_INCLUDE_DIR}/mfem)
+install(FILES ${MASTER_HEADERS} DESTINATION ${INSTALL_INCLUDE_DIR})
 
 # Install the headers; currently, the miniapps headers are excluded
 install(DIRECTORY ${MFEM_SOURCE_DIRS}
-  DESTINATION ${INSTALL_INCLUDE_DIR}/mfem
+  DESTINATION ${INSTALL_INCLUDE_DIR}
   FILES_MATCHING PATTERN "*.hpp")
 
 # Install ${HEADERS}
@@ -494,11 +389,11 @@ install(DIRECTORY ${MFEM_SOURCE_DIRS}
 
 # Install the configuration header files
 install(FILES ${PROJECT_BINARY_DIR}/config/_config.hpp
-  DESTINATION ${INSTALL_INCLUDE_DIR}/mfem/config
+  DESTINATION ${INSTALL_INCLUDE_DIR}/config
   RENAME config.hpp)
 
 install(FILES ${PROJECT_SOURCE_DIR}/config/tconfig.hpp
-  DESTINATION ${INSTALL_INCLUDE_DIR}/mfem/config)
+  DESTINATION ${INSTALL_INCLUDE_DIR}/config)
 
 # Package the whole thing up nicely
 include(CMakePackageConfigHelpers)
@@ -508,15 +403,11 @@ export(TARGETS ${PROJECT_NAME}
   FILE "${PROJECT_BINARY_DIR}/MFEMTargets.cmake")
 
 # Export the package for use from the build-tree (this registers the build-tree
-# with the CMake user package registry.)
-# TODO: How do we register the install-tree? Replacing the build-tree?
+# with a global CMake-registry)
 export(PACKAGE ${PROJECT_NAME})
 
 # Extract the include directories required to use MFEM
 get_target_property(MFEM_TPL_INCLUDE_DIRS mfem INCLUDE_DIRECTORIES)
-if (NOT MFEM_TPL_INCLUDE_DIRS)
-  set(MFEM_TPL_INCLUDE_DIRS "")
-endif()
 
 # This is the build-tree version
 set(INCLUDE_INSTALL_DIRS ${PROJECT_BINARY_DIR} ${MFEM_TPL_INCLUDE_DIRS})
@@ -549,10 +440,3 @@ 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

@@ -1,545 +0,0 @@
-<p align="center">
-<a href="http://mfem.org/"><img alt="mfem" src="http://mfem.org/img/logo-300.png"></a>
-</p>
-
-<p align="center">
-<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>
-</p>
-
-
-# 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; ...
-
-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:
-
-- [Code Overview](#code-overview)
-- [GitHub Workflow](#github-workflow)
-  - [MFEM Organization](#mfem-organization)
-  - [New Feature Development](#new-feature-development)
-  - [Developer Guidelines](#developer-guidelines)
-  - [Pull Requests](#pull-requests)
-  - [Pull Request Checklist](#pull-request-checklist)
-  - [Master/Next Workflow](#masternext-workflow)
-  - [Releases](#releases)
-  - [Release Checklist](#release-checklist)
-- [LLNL Workflow](#llnl-workflow)
-- [Automated Testing](#automated-testing)
-- [Contact Information](#contact-information)
-
-Contributing to MFEM requires knowledge of Git and, likely, finite elements. If
-you are new to Git, see the [GitHub learning
-resources](https://help.github.com/articles/git-and-github-learning-resources/).
-To learn more about the finite element method, see our [FEM page](http://mfem.org/fem).
-
-*By submitting a pull request, you are affirming the [Developer's Certificate of
-Origin](#developers-certificate-of-origin-11) at the end of this file.*
-
-
-## Quick Summary
-
-- We encourage you to [join the MFEM organization](#mfem-organization) and create
-  development branches off `mfem:master`.
-- Please follow the [developer guidelines](#developer-guidelines), in particular
-  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).
-- 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
-  work on different PRs toward a release.
-- Don't hesitate to [contact us](#contact-information) if you have any questions.
-
-
-### Code Overview
-
-- 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 source code has the following structure:
-  ```
-  .
-  ├── config
-  │   └── cmake
-  │       └── modules
-  ├── data
-  ├── doc
-  │   └── web
-  │       └── examples
-  ├── examples
-  │   ├── petsc
-  │   ├── pumi
-  │   └── sundials
-  ├── fem
-  ├── general
-  ├── linalg
-  ├── mesh
-  ├── miniapps
-  │   ├── common
-  │   ├── electromagnetics
-  │   ├── meshing
-  │   ├── nurbs
-  │   ├── performance
-  │   └── tools
-  └── tests
-      ├── unit
-      │   ├── ...
-      └── ...
-
-  ```
-
-- 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)
-  + [`NCMesh`](http://mfem.github.io/doxygen/html/classmfem_1_1NCMesh.html)
-  + [`Element`](http://mfem.github.io/doxygen/html/classmfem_1_1Element.html)
-  + [`ElementTransformation`](http://mfem.github.io/doxygen/html/classmfem_1_1ElementTransformation.html)
-
-- The main finite element classes are:
-  + [`FiniteElement`](http://mfem.github.io/doxygen/html/classmfem_1_1FiniteElement.html)
-  + [`FiniteElementCollection`](http://mfem.github.io/doxygen/html/classmfem_1_1FiniteElement.html)
-  + [`FiniteElementSpace`](http://mfem.github.io/doxygen/html/classmfem_1_1FiniteElementSpace.html)
-  + [`GridFunction`](http://mfem.github.io/doxygen/html/classmfem_1_1GridFunction.html)
-  + [`BilinearFormIntegrator`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearFormIntegrator.html) and [`LinearFormIntegrator`](http://mfem.github.io/doxygen/html/classmfem_1_1LinearFormIntegrator.html)
-  + [`LinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1LinearFormIntegrator.html), [`BilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html) and [`MixedBilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1MixedBilinearForm.html)
-
-- The main linear algebra classes and sources are
-  + [`Operator`](http://mfem.github.io/doxygen/html/classmfem_1_1Operator.html) and [`BilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html)
-  + [`Vector`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html) and [`LinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1LinearForm.html)
-  + [`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 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)
-  + [`ParNCMesh`](http://mfem.github.io/doxygen/html/classmfem_1_1ParMesh.html)
-  + [`ParFiniteElementSpace`](http://mfem.github.io/doxygen/html/classmfem_1_1ParFiniteElementSpace.html)
-  + [`ParGridFunction`](http://mfem.github.io/doxygen/html/classmfem_1_1ParGridFunction.html)
-  + [`ParBilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1ParBilinearForm.html) and [`ParLinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1ParLinearForm.html)
-  + [`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)
-
-- 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 build locally, or browsed online at
-  http://mfem.github.io/doxygen/html/index.html.
-
-- 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.
-
-- The `tests/` directory contains a unit test suite and will later contain more
-  tests that run example codes.
-
-- See also the [code overview](http://mfem.org/code-overview/) section on the
-  MFEM website.
-
-## GitHub Workflow
-
-The GitHub organization, https://github.com/mfem, is the main developer hub for
-the MFEM project.
-
-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
-will allow us to reach you directly with project announcements.
-
-
-### MFEM Organization
-
-- 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.
-
-- [Contact us](#contact-information) for an invitation to join the MFEM GitHub
-  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 dropbox next to your name.
-
-- Project discussions and announcements will be posted at
-  https://github.com/orgs/mfem/teams/everyone.
-
-- 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.
-
-
-### New Feature Development
-
-- A new feature should be important enough that at least one person, the
-  proposer, is willing to work on it and be its champion.
-
-- The proposer creates a branch for the new feature (with suffix `-dev`), off
-  the `master` branch, or another existing feature branch, for example:
-
-  ```
-  # Clone assuming you have setup your ssh keys on GitHub:
-  git clone git@github.com:mfem/mfem.git
-
-  # Alternatively, clone using the "https" protocol:
-  git clone https://github.com/mfem/mfem.git
-
-  # Create a new feature branch starting from "master":
-  git checkout master
-  git pull
-  git checkout -b feature-dev
-
-  # Work on "feature-dev", add local commits
-  # ...
-
-  # (One time only) push the branch to github and setup your local
-  # branch to track the github branch (for "git pull"):
-  git push -u origin feature-dev
-
-  ```
-
-- **We prefer that you create the new feature branch inside the MFEM organization
-  as opposed to in a fork.** This allows everyone in the community to collaborate
-  in one central place.
-
-  - If you prefer to work in your fork, please [enable upstream edits](https://help.github.com/articles/allowing-changes-to-a-pull-request-branch-created-from-a-fork/).
-
-  - Never use the `next` branch to start a new feature branch!
-
-- The typical feature branch name is `new-feature-dev`, e.g. `pumi-dev`. While
-  not frequent in MFEM, other suffixes are possible, e.g. `-fix`, `-doc`, etc.
-
-
-### Developer Guidelines
-
-- *Keep the code lean and as simple as possible*
-  - Well-designed simple code is frequently more general and powerful.
-  - 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 (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*
-  - Main goal is fast prototyping for research.
-  - When in doubt, generality wins over efficiency.
-  - Respect the needs of different users (current and/or future).
-
-- *Keep things separate and logically organized*
-  - General usage features go in MFEM (implemented in as much generality as
-    possible), non-general features go into external apps.
-  - Inside MFEM, compartmentalize between linalg, fem, mesh, GLVis, etc.
-  - Contributions that are project-specific or have external dependencies are
-    allowed (if they are of broader interest), but should be `#ifdef`-ed and not
-    change the code by default.
-
-- Code specifics
-  - All significant new classes, methods and functions have Doxygen-style
-    documentation in source comments.
-  - Consistent code styling is enforced with `make style` in the top-level
-    directory. This requires [Artistic Style](http://astyle.sourceforge.net) (we
-    specifically use version 2.05.1). See also the file `config/mfem.astylerc`.
-  - Use `mfem::out` and `mfem::err` instead of `std::cout` and `std::cerr` in
-    internal library code. (You can use `std` in examples and miniapps.)
-  - When manually resolving conflicts during a merge, make sure to mention the
-    conflicted files in the commit message.
-
-### Pull Requests
-
-- When your branch is ready for other developers to review / comment on
-  the code, create a pull request towards `mfem:master`.
-
-- Pull request typically have titles like:
-
-     `Description [new-feature-dev]`
-
-  for example:
-
-     `Parallel Unstructured Mesh Infrastructure (PUMI) integration [pumi-dev]`
-
-  Note the branch name suffix (in square brackets).
-
-- Titles may contain a prefix in square brackets to emphasize the type of PR.
-  Common choices are: `[DON'T MERGE]`, `[WIP]` and `[DISCUSS]`, for example:
-
-     `[DISCUSS] Hybridized DG [hdg-dev]`
-
-- 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.
-
-- Track the Travis CI and Appveyor [continuous integration](#automated-testing)
-  builds at the end of the PR. These should run clean, so address any errors as
-  soon as possible.
-
-
-### Pull Request Checklist
-
-Before a PR can be merged, it should satisfy the following:
-
-- [ ] Code builds.
-- [ ] Code passes `make style`.
-- [ ] Update `CHANGELOG`:
-    - [ ] 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? (*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 `.gitignore`:
-    - [ ] 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 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.
-      - [ ] Add the example binary and any files generated by it to the top-level `.gitignore` file.
-    - [ ] Update `examples/CMakeLists.txt`:
-      - [ ] 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`.
-   - [ ] 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 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:
-      - [ ] Update the `CMakeLists.txt` file in the `miniapps` directory, if the new miniapp is in a new directory.
-      - [ ] 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`
-   - [ ] 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`.
-     - [ ] The miniapps go at the end of the page, and are usually listed only under a specific "Application (PDE)" category.
-     - [ ] Add a short description of the miniapp in the "Extensive Examples" section of `features.md`.
-- [ ] New capability:
-   - [ ] All 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 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 the unit tests and make sure they all pass `make unittest`.
-- [ ] (LLNL only) Clone the `tests` repository and run the following tests, see `mfem/tests/README.md`:
-   - [ ] `compilers`
-   - [ ] `memcheck`
-   - [ ] `documentation`
-- [ ] (LLNL only) After merging:
-   - [ ] Regenerate `README.html` files from companion documentation pull requests.
-   - [ ] 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
-
-MFEM uses a `master`/`next`-branch workflow as described below:
-
-- The `master` branch should always be of release quality and changes should not
-  be merged until they have been fully tested. This branch is protected, and
-  changes can only be made through pull requests.
-
-- After approval, a pull request is merged manually (by MFEM developers) in the
-  `next` branch for testing and the `in-next` label is added to the PR.
-  This can be done as follows:
-
-  ```
-  # Pull the latest version of the "feature-dev" branch
-  git checkout feature-dev
-  git pull
-
-  # Pull the latest version of the "next" branch
-  git checkout next
-  git pull
-
-  # Merge "feature-dev" into "next", resolving conflicts, if necessary.
-  # Use the "--no-ff" flag to create a new commit with merge message.
-  git merge --no-ff feature-dev
-
-  # Push the "next" branch to the server
-  git push
-  ```
-
-- After a week of testing in `next` (excluding bugfixes), both on GitHub, as
-  well as [internally](#tests-at-llnl) at LLNL, the original PR is merged into
-  `master` (provided there are no issues).
-
-- After the merge, the feature branch is deleted (unless it is a long-term
-  project with periodic PRs).
-
-- The `next` branch is used just for integrated testing of all PRs approved for
-  merging into `master` to verify that each works individually and that all of
-  them work as a group. This branch can be discarded at any time, though we
-  typically do that only at the end of a [release cycle](#releases).
-
-
-### Releases
-
-- Releases are just tags in the `master` branch, e.g. https://github.com/mfem/mfem/releases/tag/v3.3.2,
-  and have a version that ends in an even "patch" number, e.g. `v3.2.2` or
-  `v3.4` (by convention `v3.4` is the same as `v3.4.0`.)  Between releases, the
-  version ends in an odd "patch" number, e.g. `v3.3.3`.
-
-- We use [milestones](https://github.com/mfem/mfem/milestones) to coordinate the
-  work on different PRs toward a release, see for example the
-  [v3.3.2 release](https://github.com/mfem/mfem/milestone/1?closed=1).
-
-- After a release is complete, the `next` branch is recreated, e.g. as follows
-  (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 checkout -B next origin/next`.
-
-### Release Checklist
-
-- [ ] Update the MFEM version in the following files:
-    - [ ] `CHANGELOG`
-    - [ ] `makefile`
-    - [ ] `CMakeLists.txt`
-    - [ ] `doc/CodeDocumentation.conf.in`
-- [ ] (LLNL only) Make sure all `README.html` files in the source repo are up to date.
-- [ ] Tag the repository:
-
-  ```
-  git tag -a v3.1 -m "Official release v3.1"
-  git push origin v3.1
-  ```
-- [ ] 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 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`.
-    -  Use [cloc-1.62.pl](http://cloc.sourceforge.net/) and `ls -lh` to estimate the SLOC and the tarball size in `src/download.md`.
-
-
-## LLNL Workflow
-
-- The GitHub `master` and `next` branches are mirrored to the LLNL institutional
-  Bitbucket repository as `gh-master` and `gh-next`.
-
-- `gh-master` is merged into LLNL's internal `master` through pull requests; write
-  permissions to `master` are restricted to ensure this is the only way in which it
-  gets updated.
-
-- We never push directly from LLNL to GitHub.
-
-- Versions of the code on LLNL's internal server, from most to least stable:
-  - MFEM official release on mfem.org -- Most stable, tested in many apps.
-  - `mfem:master` -- Recent development version, guaranteed to work.
-  - `mfem:gh-master` -- Stable development version, passed testing, you can use
-     it to build your code between releases.
-  - `mfem:gh-next` -- Bleeding-edge development version, may be broken, use at
-     your own risk.
-
-## Automated Testing
-
-MFEM has several levels of automated testing running on GitHub, as well as on
-local Mac and Linux workstations, and Livermore Computing clusters at LLNL.
-
-### Linux and Mac smoke tests
-We use Travis CI to drive the default tests on the `master` and `next`
-branches. See the `.travis` file and the logs at
-[https://travis-ci.org/mfem/mfem](https://travis-ci.org/mfem/mfem).
-
-Testing using Travis CI should be kept lightweight, as there is a 50 minute time
-constraint on jobs. Two virtual machines are configured - Mac (OS X) and Linux.
-
-- Tests on the `master` branch are triggered whenever a PR is issued on this branch.
-- Tests on the `next` branch are currently scheduled to run each night.
-
-### Windows smoke test
-We use Appveyor to test building with the MS Visual C++ compiler in a Windows
-environment, as well as to test the CMake build. See the `.appveyor` file and the
-build logs at
-[https://ci.appveyor.com/project/mfem/mfem](https://ci.appveyor.com/project/mfem/mfem).
-
-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.
-
-
-## Contact Information
-
-- Contact the MFEM team by posting to the [GitHub issue tracker](https://github.com/mfem/mfem).
-  Please perform a search to make sure your question has not been answered already.
-
-- Email communications should be sent to the MFEM developers mailing list,
-  mfem-dev@llnl.gov.
-
-
-## [Developer's Certificate of Origin 1.1](https://developercertificate.org/)
-
-By making a contribution to this project, I certify that:
-
-(a) The contribution was created in whole or in part by me and I have the right
-    to submit it under the open source license indicated in the file; or
-
-(b) The contribution is based upon previous work that, to the best of my
-    knowledge, is covered under an appropriate open source license and I have
-    the right under that license to submit that work with modifications, whether
-    created in whole or in part by me, under the same open source license
-    (unless I am permitted to submit under a different license), as indicated in
-    the file; or
-
-(c) The contribution was provided directly to me by some other person who
-    certified (a), (b) or (c) and I have not modified it.
-
-(d) I understand and agree that this project and the contribution are public and
-    that a record of the contribution (including all personal information I
-    submit with it, including my sign-off) is maintained indefinitely and may be
-    redistributed consistent with this project or the open source license(s)
-    involved.

INSTALL

@@ -18,41 +18,14 @@ requires an MPI C++ compiler, as well as the following external libraries:
 - METIS (a family of multilevel partitioning algorithms)
   http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
 
-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, OCCA, OpenMP and RAJA.
-
-- Starting with version 4.0, MFEM requires a C++11 compiler
-
-- CUDA support requires an NVIDIA GPU and an installation of the CUDA Toolkit
-  https://developer.nvidia.com/cuda-toolkit
-
-- 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.
 
-In addition to the native build systems, MFEM packages are also available in the
-following package managers:
+In addition to the native build systems, MFEM packages are also available in
+the Homebrew/Science, https://github.com/Homebrew/homebrew-science, and the
+Spack, https://github.com/LLNL/spack, package managers.
 
-- Spack, https://github.com/spack/spack
-- OpenHPC, http://openhpc.community
-- 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
-and miniapps. See http://glvis.org and http://mfem.org/building.
 
 Quick start with GNU make
 =========================
@@ -65,10 +38,6 @@ Parallel build:
    (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')
-
 Example codes (serial/parallel, depending on the build):
    cd examples
    make -j 4
@@ -79,6 +48,7 @@ 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:
@@ -153,10 +123,6 @@ are also defined:
    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
 
 Note that any of the above shortcuts accept configuration options, either at the
 command line or through a user configuration file.
@@ -172,7 +138,7 @@ check the results from all the serial/parallel MFEM examples and miniapps use:
 
 Note that by default MFEM uses "mpirun -np" in its test runs (this is also what
 is used in the sample runs of its examples and miniapps). The MPI launcher can
-be changed by the user as described in the "Specifying an MPI job launcher"
+be changed by the user as described in the "Specifying a MPI job launcher"
 section at the end of this file.
 
 Running all the tests may take a while. Implementation details about the check
@@ -184,8 +150,8 @@ An optional installation of the library and the headers can be performed with
    make install [PREFIX=<dir>]
 
 The library will be installed in $(PREFIX)/lib, the headers in
-$(PREFIX)/include, and the configuration makefile (config.mk) in
-$(PREFIX)/share/mfem. The PREFIX option can also be set during configuration.
+$(PREFIX)/include, and the configuration makefile (config.mk) in $(PREFIX).
+The PREFIX option can also be set during configuration.
 
 Information about the current build configuration can be viewed using
 
@@ -215,12 +181,9 @@ examples/ directory.
 
 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
@@ -228,14 +191,10 @@ Compiler options:
    CXXFLAGS    - If not set, defined based on the above optimized/debug flags
    CPPFLAGS    - Additional compiler options
 
-Build options:
-   STATIC - Build a static version of the library (YES/NO), default = YES
-   SHARED - Build a shared version of the library (YES/NO), default = NO
-
 Installation options:
    PREFIX  - Specify the installation directory. The library (libmfem.a) will be
              installed in $(PREFIX)/lib, the headers in $(PREFIX)/include, and
-             the configuration makefile (config.mk) in $(PREFIX)/share/mfem.
+             the configuration makefile (config.mk) in $(PREFIX).
    INSTALL - Specify the install program, e.g /usr/bin/install
 
 MFEM library features/options (GNU make)
@@ -244,21 +203,10 @@ MFEM_USE_MPI = YES/NO
    Choose parallel/serial build. The parallel build requires proper setup of the
    HYPRE_* and METIS_* library options, see below.
 
-MFEM_USE_METIS = YES/NO
-   Enable/disable the use of the METIS library. By default, this option is set
-   to the value of MFEM_USE_MPI. If this option is explicitly disabled in a
-   parallel build, then the only parallel partitioning (domain decomposition)
-   option in the library will be Cartesian partitioning with box meshes, and
-   thus most of the parallel examples and miniapps will fail.
-
 MFEM_DEBUG = YES/NO
    Choose debug/optimized build. The debug build enables a number of messages
    and consistency checks that may simplify bug-hunting.
 
-MFEM_USE_EXCEPTIONS = YES/NO
-   Enable the use of exceptions. In particular, modifies the default behavior
-   when errors are encountered: throw an exception, instead of aborting.
-
 MFEM_USE_LIBUNWIND = YES/NO
    Use libunwind to print a stacktrace whenever mfem_error is raised. The
    information printed is enough to determine the line numbers where the
@@ -276,26 +224,20 @@ 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.
-
 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.
    Recommended value is YES.
 
-MFEM_TIMER_TYPE = 0/1/2/3/4/5/6/NO
+MFEM_TIMER_TYPE = 0/1/2/3/NO
    Specify which library functions to use in the class StopWatch used for
    measuring time. The available options are:
       0  - use std::clock from <ctime>, standard C++
       1  - use times from <sys/times.h>
       2  - use high-resolution POSIX clocks (see option POSIX_CLOCKS_LIB)
       3  - use QueryPerformanceCounter from <windows.h>
-      4  - use mach_absolute_time from <mach/mach_time.h> + std::clock (Mac)
-      5  - use gettimeofday from <sys/time.h>
-      6  - use MPI_Wtime from <mpi.h>
       NO - use option 3 if the compiler macro _WIN32 is defined, 0 otherwise
 
 MFEM_USE_SUNDIALS = YES/NO
@@ -319,12 +261,6 @@ MFEM_USE_SUPERLU = YES/NO
    SuperLURowLocMatrix a distributed CSR matrix class needed by SuperLU. When
    enabled, this option uses the SUPERLU_* library options, see below.
 
-MFEM_USE_STRUMPACK = YES/NO
-   Enable MFEM functionality based on the STRUMPACK sparse direct solver and
-   preconditioner through the STRUMPACKSolver and STRUMPACKRowLocMatrix
-   classes. When enabled, this option uses the STRUMPACK_* library options, see
-   below.
-
 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
@@ -336,9 +272,6 @@ MFEM_USE_GNUTLS = YES/NO
    the script 'glvis-keygen.sh' in the main GLVis directory can be used to do
    that:
       bash glvis-keygen.sh ["Your Name"] ["Your Email"]
-   In MFEM v3.3.2 and earlier, the secure authentication is based on OpenPGP
-   keys, while later versions use X.509 certificates. The latest version of the
-   script 'glvis-keygen.sh' can be used to generate both types of keys.
    When MFEM_USE_GNUTLS is enabled, the additional build options, GNUTLS_*, are
    also used, see below.
 
@@ -365,13 +298,6 @@ MFEM_USE_SIDRE = YES/NO
    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
-   from Conduit Mesh Blueprint Descriptions (https://github.com/LLNL/conduit/)
-   and support for JSON and Binary I/O via Conduit Relay. This option requires
-   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_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
@@ -382,37 +308,6 @@ MFEM_USE_GZSTREAM = YES/NO
    able to properly read an input file if it is gzip compressed. In that case,
    the solution is to uncompress the file with an external tool (such as gunzip)
    before attempting to use it with MFEM.
-   When enabled, this option uses the ZLIB_* library options, see below.
-
-MFEM_USE_PUMI = YES/NO
-   Enable the usage of PUMI (https://scorec.rpi.edu/pumi/) in MFEM. The Parallel
-   Unstructured Mesh Infrastructure (PUMI) is an unstructured, distributed mesh
-   data management system that is capable of handling general non-manifold
-   models and effectively supports automated adaptive analysis. PUMI enables
-   support for parallel unstructured mesh modifications in MFEM.
-
-MFEM_USE_MM = YES/NO
-   Enables support for the MFEM's memory manager (MM), which is required to
-   support devices with different memory spaces.
-
-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). This option requires MFEM_USE_MM. 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_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 the RAJA CUDA backend, MFEM_USE_MM is required.
-
-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. When using the OCCA CUDA backend, MFEM_USE_MM is required.
 
 MFEM_BUILD_TAG = (any value)
    An optional tag to characterize the build. Exported to config/config.mk.
@@ -438,8 +333,8 @@ The specific libraries and their options are:
   URL: http://www.llnl.gov/CASC/hypre
   Options: HYPRE_OPT, HYPRE_LIB.
 
-- METIS, used when MFEM_USE_METIS = YES. If using METIS 5, set
-  MFEM_USE_METIS_5 = YES (default is to use METIS 4).
+- METIS, required for the parallel build, i.e. when MFEM_USE_MPI = 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.
 
@@ -449,8 +344,7 @@ 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
@@ -458,10 +352,7 @@ The specific libraries and their options are:
   Option: POSIX_CLOCKS_LIB (default = -lrt).
 
 - 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.
-  If MFEM_USE_MPI is enabled, we expect that SUNDIALS is built with support for
-  both MPI and hypre.
+  In parallel we expect that SUNDIALS is built with support for MPI and hypre.
   URL: http://computation.llnl.gov/projects/sundials/sundials-software
   Options: SUNDIALS_OPT, SUNDIALS_LIB.
 
@@ -480,15 +371,6 @@ The specific libraries and their options are:
   URL: http://crd-legacy.lbl.gov/~xiaoye/SuperLU
   Options: SUPERLU_OPT, SUPERLU_LIB.
 
-- 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.
-  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.
-
 - 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).
@@ -502,7 +384,7 @@ The specific libraries and their options are:
   URL: www.unidata.ucar.edu/software/netcdf
   Options: NETCDF_OPT, NETCDF_LIB.
 
-- PETSc (optional), used when MFEM_USE_PETSC = YES. Version 3.8 or higher of
+- 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
   libraries, e.g., hypre and SUNDIALS. Here's an example configuration, assuming
   PETSc has been cloned on the same level as mfem and hypre:
@@ -519,28 +401,6 @@ The specific libraries and their options are:
        https://support.hdfgroup.org/HDF5 (HDF5)
   Options: SIDRE_OPT, SIDRE_LIB.
 
-- 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.
-
-- PUMI, used when MFEM_USE_PUMI = YES.
-  URL: https://scorec.rpi.edu/pumi
-  Options: PUMI_OPT, PUMI_LIB.
-
-- CUDA, used when MFEM_USE_CUDA = YES.
-  URL: https://developer.nvidia.com/cuda-toolkit
-  Options: CUDA_CXX, CUDA_ARCH, CUDA_OPT, CUDA_LIB.
-
-- OCCA, used when MFEM_USE_OCCA = YES.
-  URL: https://libocca.org
-  Options: OCCA_DIR, OCCA_OPT, OCCA_LIB.
-
-- RAJA, used when MFEM_USE_RAJA = YES.
-  URL: https://github.com/LLNL/RAJA
-  Options: RAJA_DIR, RAJA_OPT, RAJA_LIB.
-
 - MPFR (optional), used when MFEM_USE_MPFR = YES.
   URL: http://mpfr.org, it depends on the GMP library: https://gmplib.org
   Options: MPFR_OPT, MPFR_LIB.
@@ -551,11 +411,6 @@ The specific libraries and their options are:
   URL: http://www.nongnu.org/libunwind
   Options: LIBUNWIND_OPT, LIBUNWIND_LIB.
 
-- 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
 ===================
@@ -587,12 +442,6 @@ Debug and optimization options are controlled through the CMake variable
 CMAKE_BUILD_TYPE which can be set to standard values like "Debug", and "Release"
 (default).
 
-To use a specific generator use the "-G <generator>" option of cmake:
-
-   cmake <mfem-source-dir> -G "Xcode"
-   cmake <mfem-source-dir> -G "Visual Studio 12 2013"
-   cmake <mfem-source-dir> -G "MinGW Makefiles"
-
 With CMake it is possible to build MFEM as a shared library using the standard
 CMake option -DBUILD_SHARED_LIBS=1.
 
@@ -600,30 +449,15 @@ Once configured, the library can be built simply with (assuming a UNIX type
 system, where the default is to generate "UNIX Makefiles")
 
    make -j 4
-or
-   cmake --build .
-or
-   cmake --build . --config Release  [Visual Studio, Xcode]
 
 The build can be quick-tested by running
 
    make check
-or
-   cmake --build . --target check
-or
-   cmake --build . --config Release --target check  [Visual Studio, Xcode]
 
 which will simply compile and run Example 1/1p. For more extensive tests that
 check the results from all the serial/parallel MFEM examples and miniapps use:
 
-   make exec -j 4
    make test
-or
-   cmake --build . --target exec
-   cmake --build . --target test
-or
-   cmake --build . --config Release --target exec  [Visual Studio, Xcode]
-   cmake --build . --config Release --target RUN_TESTS  [Visual Studio, Xcode]
 
 Note that running all the tests may take a while.
 
@@ -631,11 +465,6 @@ Installation prefix can be configured by setting the standard CMake variable
 CMAKE_INSTALL_PREFIX. To install the library, use
 
    make install
-or
-   cmake --build . --target install
-or
-   cmake --build . --config Release --target install  [Xcode]
-   cmake --build . --config Release --target INSTALL  [Visual Studio]
 
 The library will be installed in <PREFIX>/lib, the headers in <PREFIX>/include,
 and the configuration CMake files in <PREFIX>/lib/cmake/mfem.
@@ -643,8 +472,6 @@ and the configuration CMake files in <PREFIX>/lib/cmake/mfem.
 
 Configuration variables (CMake)
 ===============================
-See the configuration file config/defaults.cmake for the default settings.
-
 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
@@ -658,30 +485,19 @@ The following options are equivalent to the GNU make options with the same name:
 [see "MFEM library features/options (GNU make)" above]
 
 MFEM_USE_MPI
-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.
 MFEM_USE_MESQUITE
 MFEM_USE_SUITESPARSE
 MFEM_USE_SUPERLU
-MFEM_USE_STRUMPACK
 MFEM_USE_GNUTLS
 MFEM_USE_NETCDF
 MFEM_USE_MPFR
 MFEM_USE_GZSTREAM
-MFEM_USE_PUMI
-
-The following GNU make options are not supported with CMake yet:
-
-MFEM_USE_CUDA
-MFEM_USE_OCCA
-MFEM_USE_RAJA
-MFEM_USE_MM
 
 The following options are CMake specific:
 
@@ -720,14 +536,13 @@ The CMake build system adds auto-detection for the following packages/libraries:
  - METIS - The option MFEM_USE_METIS_5 is auto-detected.
  - MESQUITE
  - SuiteSparse
- - SuperLUDist, STRUMPACK
+ - SuperLUDist
  - ParMETIS
  - GNUTLS - Extends the built-in CMake support, to search GNUTLS_DIR as well.
  - NETCDF
  - MPFR
  - LIBUNWIND
  - POSIXCLOCKS
- - PUMI
 
 The following built-in CMake packages are also used:
 
@@ -743,15 +558,15 @@ Before using another build system (e.g. Visual Studio) it is necessary to create
 a proper configuration header file, config/config.hpp, using the template from
 config/config.hpp.in:
 
-   cp config/config.hpp.in config/_config.hpp
+   cp config/config.hpp.in config/config.hpp
 
-The file config/_config.hpp can then be edited to enable desired options.  The
+The file config/config.hpp can then be edited to enable desired options.  The
 MFEM library is simply a combination of all object files obtained by compiling
 the .cpp source files in the source directories: general, linalg, mesh, and fem.
 
 
-Specifying an MPI job launcher
-==============================
+Specifying a MPI job launcher
+=============================
 By default, MFEM will use 'mpirun -np #' to launch any of its parallel tests or
 miniapps, where # is the number of MPI tasks.  An alternate MPI launcher can be
 provided by setting the MFEM_MPIEXEC and MFEM_MPIEXEC_NP config variables.

LICENSE

@@ -1,5 +1,5 @@
-                  GNU LESSER GENERAL PUBLIC LICENSE
-                       Version 2.1, February 1999
+		  GNU LESSER GENERAL PUBLIC LICENSE
+		       Version 2.1, February 1999
 
  Copyright (C) 1991, 1999 Free Software Foundation, Inc.
  51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -10,7 +10,7 @@
  as the successor of the GNU Library Public License, version 2, hence
  the version number 2.1.]
 
-                            Preamble
+			    Preamble
 
   The licenses for most software are designed to take away your
 freedom to share and change it.  By contrast, the GNU General Public
@@ -112,7 +112,7 @@ modification follow.  Pay close attention to the difference between a
 former contains code derived from the library, whereas the latter must
 be combined with the library in order to run.
 
-                  GNU LESSER GENERAL PUBLIC LICENSE
+		  GNU LESSER GENERAL PUBLIC LICENSE
    TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
 
   0. This License Agreement applies to any software library or other
@@ -146,7 +146,7 @@ such a program is covered only if its contents constitute a work based
 on the Library (independent of the use of the Library in a tool for
 writing it).  Whether that is true depends on what the Library does
 and what the program that uses the Library does.
-
+  
   1. You may copy and distribute verbatim copies of the Library's
 complete source code as you receive it, in any medium, provided that
 you conspicuously and appropriately publish on each copy an
@@ -432,7 +432,7 @@ decision will be guided by the two goals of preserving the free status
 of all derivatives of our free software and of promoting the sharing
 and reuse of software generally.
 
-                            NO WARRANTY
+			    NO WARRANTY
 
   15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
 WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
@@ -455,7 +455,7 @@ FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
 SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
 DAMAGES.
 
-                     END OF TERMS AND CONDITIONS
+		     END OF TERMS AND CONDITIONS
 
            How to Apply These Terms to Your New Libraries
 
@@ -485,8 +485,7 @@ convey the exclusion of warranty; and each file should have at least the
 
     You should have received a copy of the GNU Lesser General Public
     License along with this library; if not, write to the Free Software
-    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301
-    USA
+    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 Also add information on how to contact you by electronic and paper mail.
 
@@ -495,10 +494,11 @@ school, if any, to sign a "copyright disclaimer" for the library, if
 necessary.  Here is a sample; alter the names:
 
   Yoyodyne, Inc., hereby disclaims all copyright interest in the
-  library `Frob' (a library for tweaking knobs) written by James Random
-  Hacker.
+  library `Frob' (a library for tweaking knobs) written by James Random Hacker.
 
   <signature of Ty Coon>, 1 April 1990
   Ty Coon, President of Vice
 
 That's all there is to it!
+
+

README

@@ -12,15 +12,11 @@ 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".
+For building instructions, see the file INSTALL, or type "make help". Copyright
+information and licensing restrictions can be found in the file COPYRIGHT.
 
-* 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.
-
-* Developers interested in contributing to the library, should read the
-  instructions and documentation in the CONTRIBUTING.md file.
+The best starting point for new users interested in MFEM's features is the
+interactive documentation in examples/README.html.
 
 Conceptually, MFEM can be viewed as a finite element toolbox that provides the
 building blocks for developing finite element algorithms in a manner similar to
@@ -60,8 +56,7 @@ 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.
 
-This project is released under the LGPL v2.1 license with static linking
-exception. See files COPYRIGHT and LICENSE file for full details.
+This project is released under the LGPL v2.1 license. See LICENSE file for full
+details.
 
 LLNL Release Number: LLNL-CODE-443211
-DOI: 10.11578/dc.20171025.1248

config/XSDKDefaults.cmake

@@ -1,254 +0,0 @@
-##################################################################################
-#
-#                    Set defaults for XSDK CMake projects
-#
-##################################################################################
-
-#
-# This module implements standard behavior for XSDK CMake projects.  The main
-# thing it does in XSDK mode (i.e. USE_XSDK_DEFAULTS=TRUE) is to print out
-# when the env vars CC, CXX, FC and compiler flags CFLAGS, CXXFLAGS, and
-# FFLAGS/FCFLAGS are used to select the compilers and compiler flags (raw
-# CMake does this silently) and to set BUILD_SHARED_LIBS=TRUE and
-# CMAKE_BUILD_TYPE=DEBUG by default.  It does not implement *all* of the
-# standard XSDK configuration parameters.  The parent CMake project must do
-# that.
-#
-# Note that when USE_XSDK_DEFAULTS=TRUE, then the Fortran flags will be read
-# from either of the env vars FFLAGS or FCFLAGS.  If both are set, but are the
-# same, then FFLAGS it used (which is the same as FCFLAGS).  However, if both
-# are set but are not equal, then a FATAL_ERROR is raised and CMake configure
-# processing is stopped.
-#
-# To be used in a parent project, this module must be included after
-#
-#   PROJECT(${PROJECT_NAME}  NONE)
-#
-# is called but before the compilers are defined and processed using:
-#
-#   ENABLE_LANGUAGE(<LANG>)
-#
-# For example, one would do:
-#
-#   PROJECT(${PROJECT_NAME}  NONE)
-#   ...
-#   SET(USE_XSDK_DEFAULTS_DEFAULT TRUE) # Set to false if desired
-#   INCLUDE("${CMAKE_CURRENT_SOURCE_DIR}/stdk/XSDKDefaults.cmake")
-#   ...
-#   ENABLE_LANGUAGE(C)
-#   ENABLE_LANGUAGE(C++)
-#   ENABLE_LANGUAGE(Fortran)
-#
-# The variable `USE_XSDK_DEFAULTS_DEFAULT` is used as the default for the
-# cache var `USE_XSDK_DEFAULTS`.  That way, a project can decide if it wants
-# XSDK defaults turned on or off by default and users can independently decide
-# if they want the CMake project to use standard XSDK behavior or raw CMake
-# behavior.
-#
-# By default, the XSDKDefaults.cmake module assumes that the project will need
-# C, C++, and Fortran.  If any language is not needed then, set
-# XSDK_ENABLE_C=OFF, XSDK_ENABLE_CXX=OFF, or XSDK_ENABLE_Fortran=OFF *before*
-# including this module.  Note, these variables are *not* cache vars because a
-# project either does or does not have C, C++ or Fortran source files, the
-# user has nothing to do with this so there is no need for cache vars.  The
-# parent CMake project just needs to tell XSDKDefault.cmake what languages is
-# needs or does not need.
-#
-# For example, if the parent CMake project only needs C, then it would do:
-#
-#   PROJECT(${PROJECT_NAME}  NONE)'
-#   ...
-#   SET(USE_XSDK_DEFAULTS_DEFAULT TRUE)
-#   SET(XSDK_ENABLE_CXX OFF)
-#   SET(XSDK_ENABLE_Fortran OFF)
-#   INCLUDE("${CMAKE_CURRENT_SOURCE_DIR}/stdk/XSDKDefaults.cmake")
-#   ...
-#   ENABLE_LANGAUGE(C)
-#
-# This module code will announce when it sets any variables.
-#
-
-#
-# Helper functions
-#
-
-IF (NOT COMMAND PRINT_VAR)
-  FUNCTION(PRINT_VAR  VAR_NAME)
-    MESSAGE("-- " "${VAR_NAME} = '${${VAR_NAME}}'")
-  ENDFUNCTION()
-ENDIF()
-
-IF (NOT COMMAND SET_DEFAULT)
-  MACRO(SET_DEFAULT VAR)
-    IF ("${${VAR}}" STREQUAL "")
-      SET(${VAR} ${ARGN})
-    ENDIF()
-  ENDMACRO()
-ENDIF()
-
-#
-# XSDKDefaults.cmake control variables
-#
-
-# USE_XSDK_DEFAULTS
-IF ("${USE_XSDK_DEFAULTS_DEFAULT}" STREQUAL "")
-  SET(USE_XSDK_DEFAULTS_DEFAULT  FALSE)
-ENDIF()
-SET(USE_XSDK_DEFAULTS  ${USE_XSDK_DEFAULTS_DEFAULT}  CACHE  BOOL
-  "Use XSDK defaults and behavior.")
-PRINT_VAR(USE_XSDK_DEFAULTS)
-
-SET_DEFAULT(XSDK_ENABLE_C  TRUE)
-SET_DEFAULT(XSDK_ENABLE_CXX  TRUE)
-SET_DEFAULT(XSDK_ENABLE_Fortran  TRUE)
-
-# Handle the compiler and flags for a language
-MACRO(XSDK_HANDLE_LANG_DEFAULTS  CMAKE_LANG_NAME  ENV_LANG_NAME
-  ENV_LANG_FLAGS_NAMES
-  )
-
-  # Announce using env var ${ENV_LANG_NAME}
-  IF (NOT "$ENV{${ENV_LANG_NAME}}" STREQUAL "" AND
-    "${CMAKE_${CMAKE_LANG_NAME}_COMPILER}" STREQUAL ""
-    )
-    MESSAGE("-- " "XSDK: Setting CMAKE_${CMAKE_LANG_NAME}_COMPILER from env var"
-      " ${ENV_LANG_NAME}='$ENV{${ENV_LANG_NAME}}'!")
-    SET(CMAKE_${CMAKE_LANG_NAME}_COMPILER "$ENV{${ENV_LANG_NAME}}" CACHE FILEPATH
-      "XSDK: Set by default from env var ${ENV_LANG_NAME}")
-  ENDIF()
-
-  # Announce using env var ${ENV_LANG_FLAGS_NAME}
-  FOREACH(ENV_LANG_FLAGS_NAME  ${ENV_LANG_FLAGS_NAMES})
-    IF (NOT "$ENV{${ENV_LANG_FLAGS_NAME}}" STREQUAL "" AND
-      "${CMAKE_${CMAKE_LANG_NAME}_FLAGS}" STREQUAL ""
-      )
-      MESSAGE("-- " "XSDK: Setting CMAKE_${CMAKE_LANG_NAME}_FLAGS from env var"
-        " ${ENV_LANG_FLAGS_NAME}='$ENV{${ENV_LANG_FLAGS_NAME}}'!")
-      SET(CMAKE_${CMAKE_LANG_NAME}_FLAGS "$ENV{${ENV_LANG_FLAGS_NAME}} " CACHE  STRING
-        "XSDK: Set by default from env var ${ENV_LANG_FLAGS_NAME}")
-      # NOTE: CMake adds the space after $ENV{${ENV_LANG_FLAGS_NAME}} so we
-      # duplicate that here!
-    ENDIF()
-  ENDFOREACH()
-
-ENDMACRO()
-
-
-#
-# Set XSDK Defaults
-#
-
-# Set default compilers and flags
-IF (USE_XSDK_DEFAULTS)
-
-  # Handle env vars for languages C, C++, and Fortran
-
-  IF (XSDK_ENABLE_C)
-    XSDK_HANDLE_LANG_DEFAULTS(C  CC  CFLAGS)
-  ENDIF()
-
-  IF (XSDK_ENABLE_CXX)
-    XSDK_HANDLE_LANG_DEFAULTS(CXX  CXX  CXXFLAGS)
-  ENDIF()
-
-  IF (XSDK_ENABLE_Fortran)
-    SET(ENV_FFLAGS "$ENV{FFLAGS}")
-    SET(ENV_FCFLAGS "$ENV{FCFLAGS}")
-    IF (
-      (NOT "${ENV_FFLAGS}" STREQUAL "") AND (NOT "${ENV_FCFLAGS}" STREQUAL "")
-      AND
-      ("${CMAKE_Fortran_FLAGS}" STREQUAL "")
-      )
-      IF (NOT "${ENV_FFLAGS}" STREQUAL "${ENV_FCFLAGS}")
-        MESSAGE(FATAL_ERROR "Error, env vars FFLAGS='${ENV_FFLAGS}' and"
-          " FCFLAGS='${ENV_FCFLAGS}' are both set in the env but are not equal!")
-      ENDIF()
-    ENDIF()
-    XSDK_HANDLE_LANG_DEFAULTS(Fortran  FC  "FFLAGS;FCFLAGS")
-  ENDIF()
-  
-  # Set XSDK defaults for other CMake variables
-  
-  IF ("${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()
-
-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_GZSTREAM)
-  SET(MFEM_USE_GZSTREAM ${TPL_ENABLE_GZSTREAM} CACHE BOOL "Enable gzstream 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_GECKO)
-  SET(MFEM_USE_GECKO ${TPL_ENABLE_GECKO} CACHE BOOL "Enable GECKO 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()

config/cmake/MFEMConfig.cmake.in

@@ -12,43 +12,31 @@
 include(${CMAKE_CURRENT_LIST_DIR}/MFEMConfigVersion.cmake)
 
 set(MFEM_VERSION ${PACKAGE_VERSION})
-set(MFEM_VERSION_INT @MFEM_VERSION@)
-set(MFEM_GIT_STRING "@MFEM_GIT_STRING@")
 
 set(MFEM_USE_MPI @MFEM_USE_MPI@)
-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_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@)
 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_GECKO @MFEM_USE_GECKO@)
 set(MFEM_USE_GNUTLS @MFEM_USE_GNUTLS@)
 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_CXX_COMPILER "@CMAKE_CXX_COMPILER@")
-set(MFEM_CXX_FLAGS "@CMAKE_CXX_FLAGS@")
 
 @PACKAGE_INIT@
 
 set(MFEM_INCLUDE_DIRS "@PACKAGE_INCLUDE_INSTALL_DIRS@")
 foreach (dir ${MFEM_INCLUDE_DIRS})
+  message("DIR = ${dir}")
+
   set_and_check(MFEM_INCLUDE_DIR "${dir}")
 endforeach (dir "${MFEM_INCLUDE_DIRS}")
 

config/cmake/config.hpp.in

@@ -12,27 +12,6 @@
 #ifndef MFEM_CONFIG_HEADER
 #define MFEM_CONFIG_HEADER
 
-// MFEM version: integer of the form: (major*100 + minor)*100 + patch.
-#cmakedefine MFEM_VERSION @MFEM_VERSION@
-
-// MFEM version string of the form "3.3" or "3.3.1".
-#cmakedefine MFEM_VERSION_STRING "@MFEM_VERSION_STRING@"
-
-// MFEM version type, see the MFEM_VERSION_TYPE_* constants below.
-#define MFEM_VERSION_TYPE ((MFEM_VERSION)%2)
-
-// MFEM version type constants.
-#define MFEM_VERSION_TYPE_RELEASE 0
-#define MFEM_VERSION_TYPE_DEVELOPMENT 1
-
-// Separate MFEM version numbers for major, minor, and patch.
-#define MFEM_VERSION_MAJOR ((MFEM_VERSION)/10000)
-#define MFEM_VERSION_MINOR (((MFEM_VERSION)/100)%100)
-#define MFEM_VERSION_PATCH ((MFEM_VERSION)%100)
-
-// Description of the git commit used to build MFEM.
-#cmakedefine MFEM_GIT_STRING "@MFEM_GIT_STRING@"
-
 // Build the parallel MFEM library.
 // Requires an MPI compiler, and the libraries HYPRE and METIS.
 #cmakedefine MFEM_USE_MPI
@@ -40,18 +19,12 @@
 // Enable debug checks in MFEM.
 #cmakedefine MFEM_DEBUG
 
-// Throw an exception on errors.
-#cmakedefine MFEM_USE_EXCEPTIONS
-
 // Enable gzstream in MFEM.
 #cmakedefine MFEM_USE_GZSTREAM
 
 // Enable backtraces for mfem_error through libunwind.
 #cmakedefine MFEM_USE_LIBUNWIND
 
-// Enable MFEM features that use the METIS library (parallel MFEM).
-#cmakedefine MFEM_USE_METIS
-
 // Enable this option if linking with METIS version 5 (parallel MFEM).
 #cmakedefine MFEM_USE_METIS_5
 
@@ -62,12 +35,9 @@
 // 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
 
@@ -77,9 +47,6 @@
 // Enable MFEM functionality based on the SuperLU_DIST library.
 #cmakedefine MFEM_USE_SUPERLU
 
-// Enable MFEM functionality based on the STRUMPACK library.
-#cmakedefine MFEM_USE_STRUMPACK
-
 // Internal MFEM option: enable group/batch allocation for some small objects.
 #cmakedefine MFEM_USE_MEMALLOC
 
@@ -98,25 +65,20 @@
 // Enable MFEM functionality based on the Sidre library
 #cmakedefine MFEM_USE_SIDRE
 
-// Enable MFEM functionality based on Conduit
-#cmakedefine MFEM_USE_CONDUIT
-
-// Enable MFEM functionality based on the PUMI library
-#cmakedefine MFEM_USE_PUMI
-
 // Which library functions to use in class StopWatch for measuring time.
-// For a list of the available options, see INSTALL.
+// The available options are:
+//   0 - use std::clock from <ctime>
+//   1 - use times from <sys/times.h>
+//   2 - use high-resolution POSIX clocks
+//   3 - use QueryPerformanceCounter from <windows.h>
 // If not defined, an option is selected automatically.
 #define MFEM_TIMER_TYPE @MFEM_TIMER_TYPE@
 
 // Enable MFEM functionality based on the SUNDIALS libraries.
 #cmakedefine MFEM_USE_SUNDIALS
 
-// Version of HYPRE used for building MFEM.
-#cmakedefine MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@
-
-// Macro defined when PUMI is built with support for the Simmetrix SimModSuite
-// library.
-#cmakedefine MFEM_USE_SIMMETRIX
+// Windows specific options
+// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
+#cmakedefine _USE_MATH_DEFINES
 
 #endif // MFEM_CONFIG_HEADER

config/cmake/modules/FindATK.cmake

@@ -10,14 +10,15 @@
 # Software Foundation) version 2.1 dated February 1999.
 
 # Defines the following variables:
-#   - AXOM_FOUND
-#   - AXOM_LIBRARIES
-#   - AXOM_INCLUDE_DIRS
+#   - ATK_FOUND
+#   - ATK_LIBRARIES
+#   - ATK_INCLUDE_DIRS
 
 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."
+mfem_find_package(ATK ATK ATK_DIR "include" "" "lib" ""
+  "Paths to headers required by ATK." "Libraries required by ATK."
   ADD_COMPONENT Sidre "include" sidre/sidre.hpp "lib" sidre
+  ADD_COMPONENT SPIO "include" spio/IOManager.hpp "lib" spio
   ADD_COMPONENT SLIC "include" slic/slic.hpp "lib" slic
-  ADD_COMPONENT axom_utils "include" axom_utils/Utilities.hpp "lib" axom_utils)
+  ADD_COMPONENT common "include" common/ATKMacros.hpp "lib" common)

config/cmake/modules/FindConduit.cmake

@@ -14,22 +14,9 @@
 #   - CONDUIT_LIBRARIES
 #   - CONDUIT_INCLUDE_DIRS
 
-# check to see if relay requires hdf5, if so make sure to set HDF5
-# as a required dep
-if(EXISTS ${CONDUIT_DIR}/include/conduit/conduit_relay_hdf5.hpp)
-  message(STATUS "Conduit Relay HDF5 Support is ENABLED")
-  # we only need  HDF5 if Conduit was built with HDF5 support
-  set(Conduit_REQUIRED_PACKAGES "HDF5" CACHE STRING
-      "Additional packages required by Conduit.")
-  else()
-    message(STATUS "Conduit Relay HDF5 Support is DISABLED")
-endif()
-
 include(MfemCmakeUtilities)
 mfem_find_package(Conduit CONDUIT CONDUIT_DIR
   "include;include/conduit" conduit.hpp "lib" conduit
   "Paths to headers required by Conduit." "Libraries required by Conduit."
   ADD_COMPONENT relay
-    "include;include/conduit" conduit_relay.hpp "lib" conduit_relay
-  ADD_COMPONENT blueprint
-      "include;include/conduit" conduit_blueprint.hpp "lib" conduit_blueprint)
+    "include;include/conduit" conduit_relay.hpp "lib" conduit_relay)

config/cmake/modules/FindHYPRE.cmake

@@ -13,23 +13,7 @@
 #   - HYPRE_FOUND
 #   - HYPRE_LIBRARIES
 #   - HYPRE_INCLUDE_DIRS
-#   - HYPRE_VERSION
 
 include(MfemCmakeUtilities)
 mfem_find_package(HYPRE HYPRE HYPRE_DIR "include" "HYPRE.h" "lib" "HYPRE"
   "Paths to headers required by HYPRE." "Libraries required by HYPRE.")
-
-if (HYPRE_FOUND AND (NOT HYPRE_VERSION))
-  try_run(HYPRE_VERSION_RUN_RESULT HYPRE_VERSION_COMPILE_RESULT
-          ${CMAKE_CURRENT_BINARY_DIR}/config
-          ${CMAKE_CURRENT_SOURCE_DIR}/config/get_hypre_version.cpp
-          CMAKE_FLAGS -DINCLUDE_DIRECTORIES:STRING=${HYPRE_INCLUDE_DIRS}
-          RUN_OUTPUT_VARIABLE HYPRE_VERSION_OUTPUT)
-  if ((HYPRE_VERSION_RUN_RESULT EQUAL 0) AND HYPRE_VERSION_OUTPUT)
-    string(STRIP "${HYPRE_VERSION_OUTPUT}" HYPRE_VERSION)
-    set(HYPRE_VERSION ${HYPRE_VERSION} CACHE STRING "HYPRE version." FORCE)
-    message(STATUS "Found HYPRE version ${HYPRE_VERSION}")
-  else()
-    message(FATAL_ERROR "Unable to determine HYPRE version.")
-  endif()
-endif()

config/cmake/modules/FindSTRUMPACK.cmake

@@ -1,36 +0,0 @@
-# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
-# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
-# See file COPYRIGHT for details.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability see http://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License (as published by the Free
-# Software Foundation) version 2.1 dated February 1999.
-
-# Sets the following variables:
-#   - STRUMPACK_FOUND
-#   - STRUMPACK_INCLUDE_DIRS
-#   - STRUMPACK_LIBRARIES
-
-include(MfemCmakeUtilities)
-mfem_find_package(STRUMPACK STRUMPACK STRUMPACK_DIR
-  "include" "StrumpackSparseSolverMPIDist.hpp"
-  "lib" "strumpack;strumpack_sparse" # add NAMES_PER_DIR?
-  "Paths to headers required by STRUMPACK."
-  "Libraries required by STRUMPACK."
-  CHECK_BUILD STRUMPACK_VERSION_OK TRUE
-"
-#include <StrumpackSparseSolverMPIDist.hpp>
-using namespace strumpack;
-int main(int argc, char *argv[])
-{
-   MPI_Init(&argc, &argv);
-   MPI_Comm comm = MPI_COMM_WORLD;
-   StrumpackSparseSolverMPIDist<double,int> solver(comm, argc, argv, false);
-   solver.options().set_from_command_line();
-   return 0;
-}
-"
-  )

config/cmake/modules/FindScotch.cmake

@@ -1,29 +0,0 @@
-# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
-# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
-# See file COPYRIGHT for details.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability see http://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License (as published by the Free
-# Software Foundation) version 2.1 dated February 1999.
-
-# Sets the following variables:
-#   - Scotch_FOUND
-#   - Scotch_INCLUDE_DIRS
-#   - Scotch_LIBRARIES
-
-include(MfemCmakeUtilities)
-mfem_find_package(Scotch Scotch Scotch_DIR "" "" "" ""
-  "Paths to headers required by Scotch."
-  "Libraries required by Scotch."
-  ADD_COMPONENT "scotch" "include" scotch.h "lib" scotch
-  ADD_COMPONENT "scotcherr" "" "" "lib" scotcherr
-  ADD_COMPONENT "scotcherrexit" "" "" "lib" scotcherrexit
-  ADD_COMPONENT "scotchmetis" "include" "metis.h" "lib" scotchmetis
-  ADD_COMPONENT "ptscotch" "include" ptscotch.h "lib" ptscotch
-  ADD_COMPONENT "ptscotcherr" "" "" "lib" ptscotcherr
-  ADD_COMPONENT "ptscotcherrexit" "" "" "lib" ptscotcherrexit
-  ADD_COMPONENT "ptscotchparmetis" "include" "parmetis.h" "lib" ptscotchparmetis
-  )

config/cmake/modules/MfemCmakeUtilities.cmake

@@ -9,30 +9,6 @@
 # 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.
-function(mfem_version_to_int VersionString VersionIntVar)
-  if ("${VersionString}" MATCHES "^([0-9]+)(.*)$")
-    set(Major "${CMAKE_MATCH_1}")
-    set(MinorPatchString "${CMAKE_MATCH_2}")
-  else()
-    set(Major 0)
-  endif()
-  if ("${MinorPatchString}" MATCHES "^\\.([0-9]+)(.*)$")
-    set(Minor "${CMAKE_MATCH_1}")
-    set(PatchString "${CMAKE_MATCH_2}")
-  else()
-    set(Minor 0)
-  endif()
-  if ("${PatchString}" MATCHES "^\\.([0-9]+)(.*)$")
-    set(Patch "${CMAKE_MATCH_1}")
-  else()
-    set(Patch 0)
-  endif()
-  math(EXPR VersionInt "(${Major}*100+${Minor})*100+${Patch}")
-  set(${VersionIntVar} ${VersionInt} PARENT_SCOPE)
-endfunction()
-
 # A handy function to add the current source directory to a local
 # filename. To be used for creating a list of sources.
 function(convert_filenames_to_full_paths NAMES)
@@ -74,8 +50,10 @@ function(add_mfem_examples EXE_SRCS)
 
     string(REPLACE ".cpp" "" EXE_NAME "${EXE_PREFIX}${SRC_FILENAME}")
     add_executable(${EXE_NAME} ${SRC_FILE})
-    add_dependencies(${MFEM_ALL_EXAMPLES_TARGET_NAME} ${EXE_NAME})
-    if (EXE_NEEDED_BY)
+    # If given a prefix, don't add the example to the list of examples to build.
+    if (NOT EXE_PREFIX)
+      add_dependencies(${MFEM_ALL_EXAMPLES_TARGET_NAME} ${EXE_NAME})
+    elseif (EXE_NEEDED_BY)
       add_dependencies(${EXE_NEEDED_BY} ${EXE_NAME})
     endif()
     add_dependencies(${EXE_NAME}
@@ -83,8 +61,7 @@ function(add_mfem_examples EXE_SRCS)
 
     target_link_libraries(${EXE_NAME} mfem)
     if (MFEM_USE_MPI)
-      # Not needed: (mfem already links with MPI_CXX_LIBRARIES)
-      # target_link_libraries(${EXE_NAME} ${MPI_CXX_LIBRARIES})
+      target_link_libraries(${EXE_NAME} ${MPI_CXX_LIBRARIES})
 
       # Language-specific include directories:
       if (MPI_CXX_INCLUDE_PATH)
@@ -155,7 +132,6 @@ function(add_mfem_miniapp MFEM_EXE_NAME)
 
   # Handle the MPI separately
   if (MFEM_USE_MPI)
-    # Add MPI_CXX_LIBRARIES, in case this target does not link with mfem.
     if(CMAKE_VERSION VERSION_GREATER 2.8.11)
       target_link_libraries(${MFEM_EXE_NAME} PRIVATE ${MPI_CXX_LIBRARIES})
     else()
@@ -183,26 +159,26 @@ function(mfem_find_component Prefix DirVar IncSuffixes Header LibSuffixes Lib
 
   if (Lib)
     if (${DirVar} OR EnvDirVar)
-      find_library(${Prefix}_LIBRARY ${Lib}
+      find_library(${Prefix}_LIBRARIES ${Lib}
         HINTS ${${DirVar}} ENV ${DirVar}
         PATH_SUFFIXES ${LibSuffixes}
         NO_DEFAULT_PATH
         DOC "${LibDoc}")
     endif()
-    find_library(${Prefix}_LIBRARY ${Lib}
+    find_library(${Prefix}_LIBRARIES ${Lib}
       PATH_SUFFIXES ${LibSuffixes}
       DOC "${LibDoc}")
   endif()
 
   if (Header)
     if (${DirVar} OR EnvDirVar)
-      find_path(${Prefix}_INCLUDE_DIR ${Header}
+      find_path(${Prefix}_INCLUDE_DIRS ${Header}
         HINTS ${${DirVar}} ENV ${DirVar}
         PATH_SUFFIXES ${IncSuffixes}
         NO_DEFAULT_PATH
         DOC "${IncDoc}")
     endif()
-    find_path(${Prefix}_INCLUDE_DIR ${Header}
+    find_path(${Prefix}_INCLUDE_DIRS ${Header}
       PATH_SUFFIXES ${IncSuffixes}
       DOC "${IncDoc}")
   endif()
@@ -214,9 +190,8 @@ endfunction(mfem_find_component)
 #   successful, optionally checks building (compile + link) one or more given
 #   code snippets. Additionally, a list of required/optional/alternative
 #   packages (given by ${Name}_REQUIRED_PACKAGES) are searched for and added to
-#   the ${Prefix}_INCLUDE_DIRS and ${Prefix}_LIBRARIES lists. The variable
-#   ${Name}_REQUIRED_LIBRARIES can be set to spcecify any additional libraries
-#   that are needed. This function defines the following CACHE variables:
+#   the ${Prefix}_INCLUDE_DIRS and ${Prefix}_LIBRARIES lists. The function
+#   defines the following CACHE variables:
 #
 #      ${Prefix}_FOUND
 #      ${Prefix}_INCLUDE_DIRS
@@ -229,15 +204,6 @@ 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()
@@ -264,14 +230,12 @@ function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
   mfem_find_component("${Prefix}" "${DirVar}" "${IncSuffixes}" "${Header}"
     "${LibSuffixes}" "${Lib}" "${IncDoc}" "${LibDoc}")
 
-  if (((NOT Lib) OR ${Prefix}_LIBRARY) AND
-      ((NOT Header) OR ${Prefix}_INCLUDE_DIR))
+  if (((NOT Lib) OR ${Prefix}_LIBRARIES) AND
+      ((NOT Header) OR ${Prefix}_INCLUDE_DIRS))
     set(Found TRUE)
   else()
     set(Found FALSE)
   endif()
-  set(${Prefix}_LIBRARIES ${${Prefix}_LIBRARY})
-  set(${Prefix}_INCLUDE_DIRS ${${Prefix}_INCLUDE_DIR})
 
   set(ReqVars "")
 
@@ -310,22 +274,25 @@ function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
           "${CompLibSuffixes}" "${CompLib}" "" "")
         if (CompRequired)
           if (CompLib)
-            list(APPEND ReqVars ${FullPrefix}_LIBRARY)
+            list(APPEND ReqVars ${FullPrefix}_LIBRARIES)
           endif()
           if (CompHeader)
-            list(APPEND ReqVars ${FullPrefix}_INCLUDE_DIR)
+            list(APPEND ReqVars ${FullPrefix}_INCLUDE_DIRS)
           endif()
         endif(CompRequired)
-        if (((NOT CompLib) OR ${FullPrefix}_LIBRARY) AND
-            ((NOT CompHeader) OR ${FullPrefix}_INCLUDE_DIR))
+        if (((NOT CompLib) OR ${FullPrefix}_LIBRARIES) AND
+            ((NOT CompHeader) OR ${FullPrefix}_INCLUDE_DIRS))
           # Component found
-          list(APPEND ${Prefix}_LIBRARIES ${${FullPrefix}_LIBRARY})
-          list(APPEND ${Prefix}_INCLUDE_DIRS ${${FullPrefix}_INCLUDE_DIR})
+          set(${FullPrefix}_FOUND TRUE CACHE BOOL
+              "${Name}/${CompPrefix} was found." FORCE)
+          list(APPEND ${Prefix}_LIBRARIES ${${FullPrefix}_LIBRARIES})
+          list(APPEND ${Prefix}_INCLUDE_DIRS ${${FullPrefix}_INCLUDE_DIRS})
           if (NOT ${Name}_FIND_QUIETLY)
+            # message(STATUS "${Name}: ${CompPrefix}: found")
             message(STATUS
-              "${Name}: ${CompPrefix}: ${${FullPrefix}_LIBRARY}")
+              "${Name}: ${CompPrefix}: ${${FullPrefix}_LIBRARIES}")
             # message(STATUS
-            #   "${Name}: ${CompPrefix}: ${${FullPrefix}_INCLUDE_DIR}")
+            #   "${Name}: ${CompPrefix}: ${${FullPrefix}_INCLUDE_DIRS}")
           endif()
         else()
           # Let FindPackageHandleStandardArgs() handle errors
@@ -378,8 +345,6 @@ function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
       if (NOT ${Name}_FIND_QUIETLY)
         message(STATUS "${Name}: trying alternative package: ${ReqPackM}")
       endif()
-      # Do not add ${Required} here, since that will prevent other potential
-      # alternative packages from being found.
       find_package(${ReqPack} ${Quiet} COMPONENTS ${PackComps})
       string(TOUPPER ${ReqPack} ReqPACK)
       if (${ReqPack}_FOUND)
@@ -393,7 +358,7 @@ function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
       endif()
     elseif (Alternative)
       set(Alternative FALSE)
-    elseif (Found)
+    else()
       if (NOT ${Name}_FIND_QUIETLY)
         if (Required)
           message(STATUS "${Name}: looking for required package: ${ReqPackM}")
@@ -403,139 +368,23 @@ function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
       endif()
       string(TOUPPER ${ReqPack} ReqPACK)
       if (NOT (${ReqPack}_FOUND OR ${ReqPACK}_FOUND))
-        if (NOT ${ReqPack}_TARGET_NAMES)
-          find_package(${ReqPack} ${Required} ${Quiet} COMPONENTS ${PackComps})
-        else()
-          foreach(_target ${ReqPack} ${${ReqPack}_TARGET_NAMES})
-            # Do not use ${Required} here:
-            find_package(${_target} NAMES ${_target} ${ReqPack} ${Quiet}
-              COMPONENTS ${PackComps})
-            string(TOUPPER ${_target} _TARGET)
-            if (${_target}_FOUND OR ${_TARGET}_FOUND)
-              set(${ReqPack}_FOUND TRUE)
-              break()
-            endif()
-          endforeach()
-          if (${Required} AND NOT ${ReqPack}_FOUND)
-            message(FATAL_ERROR " *** Required package ${ReqPack} not found."
-              "Checked target names: ${ReqPack} ${${ReqPack}_TARGET_NAMES}")
-          endif()
-        endif()
+        find_package(${ReqPack} ${Required} ${Quiet} COMPONENTS ${PackComps})
       endif()
-      if (Required AND NOT (${ReqPack}_FOUND OR ${ReqPACK}_FOUND))
-        message(FATAL_ERROR " --------- INTERNAL ERROR")
-      endif()
-      if ("${ReqPack}" STREQUAL "MPI" AND MPI_CXX_FOUND)
+      if ("${ReqPack}" STREQUAL "MPI")
         list(APPEND ${Prefix}_LIBRARIES ${MPI_CXX_LIBRARIES})
         list(APPEND ${Prefix}_INCLUDE_DIRS ${MPI_CXX_INCLUDE_PATH})
-      elseif (${ReqPack}_FOUND OR ${ReqPACK}_FOUND)
+      else()
         if (${ReqPack}_FOUND)
-          set(_Pack ${ReqPack})
-        else()
-          set(_Pack ${ReqPACK})
+          list(APPEND ${Prefix}_LIBRARIES ${${ReqPack}_LIBRARIES})
+          list(APPEND ${Prefix}_INCLUDE_DIRS ${${ReqPack}_INCLUDE_DIRS})
+        elseif (${ReqPACK}_FOUND)
+          list(APPEND ${Prefix}_LIBRARIES ${${ReqPACK}_LIBRARIES})
+          list(APPEND ${Prefix}_INCLUDE_DIRS ${${ReqPACK}_INCLUDE_DIRS})
         endif()
-        set(_Pack_LIBS)
-        set(_Pack_INCS)
-        # - ${_Pack}_CONFIG is defined by find_package() when a config file was
-        #   loaded
-        # - If ${ReqPack}_TARGET_NAMES is defined, use target mode
-        if (NOT ((DEFINED ${_Pack}_CONFIG) OR
-                 (DEFINED ${ReqPack}_TARGET_NAMES)))
-          # Defined variables expected:
-          # - ${ReqPack}_LIB_VARS, optional, default: ${_Pack}_LIBRARIES
-          # - ${ReqPack}_INCLUDE_VARS, optional, default: ${_Pack}_INCLUDE_DIRS
-          set(_lib_vars ${${ReqPack}_LIB_VARS})
-          if (NOT _lib_vars)
-            set(_lib_vars ${_Pack}_LIBRARIES)
-          endif()
-          foreach (_var ${_lib_vars})
-            if (${_var})
-              list(APPEND _Pack_LIBS ${${_var}})
-            endif()
-          endforeach()
-          # Includes
-          set(_inc_vars ${${ReqPack}_INCLUDE_VARS})
-          if (NOT _inc_vars)
-            set(_inc_vars ${_Pack}_INCLUDE_DIRS)
-          endif()
-          foreach (_include ${_inc_vars})
-            # message(STATUS "${Name}: ${ReqPack}: ${_include}")
-            if (${_include})
-              list(APPEND _Pack_INCS ${${_include}})
-            endif()
-          endforeach()
-        else()
-          # Target mode: check for a valid target:
-          # - an entry in the variable ${ReqPack}_TARGET_NAMES (optional)
-          # - ${_Pack}
-          # Other optional variables:
-          # - ${ReqPack}_IMPORT_CONFIG, default value: "RELEASE"
-          # - ${ReqPack}_TARGET_FORCE, default value: "FALSE"
-          set(TargetName)
-          foreach (_target ${${ReqPack}_TARGET_NAMES} ${_Pack})
-            if (TARGET ${_target})
-              set(TargetName ${_target})
-              break()
-            endif()
-          endforeach()
-          if ("${TargetName}" STREQUAL "")
-            message(FATAL_ERROR " *** ${ReqPack}: unknown target. "
-              "Please set ${ReqPack}_TARGET_NAMES.")
-          endif()
-          get_target_property(IsImported ${TargetName} IMPORTED)
-          if (IsImported)
-            set(ImportConfig ${${ReqPack}_IMPORT_CONFIG})
-            if (NOT ImportConfig)
-              set(ImportConfig RELEASE)
-            endif()
-            get_target_property(ImpConfigs ${TargetName} IMPORTED_CONFIGURATIONS)
-            list(FIND ImpConfigs ${ImportConfig} _Index)
-            if (_Index EQUAL -1)
-              message(FATAL_ERROR " *** ${ReqPack}: configuration "
-                "${ImportConfig} not found. Set ${ReqPack}_IMPORT_CONFIG "
-                "from the list: ${ImpConfigs}.")
-            endif()
-          endif()
-          # Set _Pack_LIBS
-          if (NOT IsImported OR ${ReqPack}_TARGET_FORCE)
-            # Set _Pack_LIBS to be the target itself
-            set(_Pack_LIBS ${TargetName})
-            if (NOT ${Name}_FIND_QUIETLY)
-              message(STATUS "Found ${ReqPack}: ${_Pack_LIBS} (target)")
-            endif()
-          else()
-            # Set _Pack_LIBS from the target properties for ImportConfig
-            foreach (_prop IMPORTED_LOCATION_${ImportConfig}
-                IMPORTED_LINK_INTERFACE_LIBRARIES_${ImportConfig})
-              get_target_property(_value ${TargetName} ${_prop})
-              if (_value)
-                list(APPEND _Pack_LIBS ${_value})
-              endif()
-            endforeach()
-            if (NOT ${Name}_FIND_QUIETLY)
-              message(STATUS
-                "Imported ${ReqPack}[${ImportConfig}]: ${_Pack_LIBS}")
-            endif()
-          endif()
-          # Set _Pack_INCS
-          foreach (_prop INCLUDE_DIRECTORIES)
-            get_target_property(_value ${TargetName} ${_prop})
-            if (_value)
-              list(APPEND _Pack_INCS ${_value})
-            endif()
-          endforeach()
-        endif()
-        # _Pack_LIBS and _Pack_INCS should be fully defined here
-        list(APPEND ${Prefix}_LIBRARIES ${_Pack_LIBS})
-        list(APPEND ${Prefix}_INCLUDE_DIRS ${_Pack_INCS})
       endif()
     endif()
   endforeach()
 
-  if (Found AND ${Name}_REQUIRED_LIBRARIES)
-    list(APPEND ${Prefix}_LIBRARIES ${${Name}_REQUIRED_LIBRARIES})
-  endif()
-
   if (NOT ("${${Prefix}_INCLUDE_DIRS}" STREQUAL ""))
     list(INSERT ReqVars 0 ${Prefix}_INCLUDE_DIRS)
     set(ReqHeaders 1)
@@ -552,6 +401,12 @@ function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
     if (ReqHeaders)
       list(REMOVE_DUPLICATES ${Prefix}_INCLUDE_DIRS)
     endif()
+    # Write the updated values to the cache.
+    set(${Prefix}_LIBRARIES ${${Prefix}_LIBRARIES} CACHE STRING
+        "${LibDoc}" FORCE)
+    set(${Prefix}_INCLUDE_DIRS ${${Prefix}_INCLUDE_DIRS} CACHE STRING
+        "${IncDoc}" FORCE)
+    set(${Prefix}_FOUND TRUE CACHE BOOL "${Name} was found." FORCE)
 
     # Check for optional "CHECK_BUILD" arguments.
     set(I 9) # 9 is the number of required arguments
@@ -569,10 +424,6 @@ function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
         set(CMAKE_REQUIRED_QUIET ${${Name}_FIND_QUIETLY})
         check_cxx_source_compiles("${TestSrc}" ${TestVar})
         if (TestReq)
-          if (NOT ${TestVar})
-            set(Found FALSE)
-            unset(${TestVar} CACHE)
-          endif()
           list(APPEND ReqVars ${TestVar})
         endif()
       elseif("${ARGV${I}}" STREQUAL "ADD_COMPONENT")
@@ -583,35 +434,22 @@ function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
       endif()
       math(EXPR I "${I}+1")
     endwhile()
+  else()
+    set(${Prefix}_FOUND FALSE CACHE BOOL "${Name} was not found." FORCE)
   endif()
   if ("_x_${ReqVars}" STREQUAL "_x_")
-    set(${Prefix}_FOUND ${Found})
     set(ReqVars ${Prefix}_FOUND)
   endif()
   # foreach(ReqVar ${ReqVars})
-  #   message(STATUS " *** ${ReqVar}=${${ReqVar}}")
-  #   get_property(IsCached CACHE ${ReqVar} PROPERTY "VALUE" SET)
-  #   if (IsCached)
-  #     get_property(CachedVal CACHE ${ReqVar} PROPERTY "VALUE")
-  #     message(STATUS " *** ${ReqVar}[cached]=${CachedVal}")
-  #   endif()
+  #   message(STATUS "${ReqVar}=${${ReqVar}}")
   # endforeach()
 
   include(FindPackageHandleStandardArgs)
   find_package_handle_standard_args(${Name}
     " *** ${Name} not found. Please set ${DirVar}." ${ReqVars})
 
-  string(TOUPPER ${Name} UName)
-  if (${UName}_FOUND)
-    # Write the ${Prefix}_* variables to the cache.
-    set(${Prefix}_LIBRARIES ${${Prefix}_LIBRARIES} CACHE STRING
-        "${LibDoc}" FORCE)
-    set(${Prefix}_INCLUDE_DIRS ${${Prefix}_INCLUDE_DIRS} CACHE STRING
-        "${IncDoc}" FORCE)
-    set(${Prefix}_FOUND TRUE CACHE BOOL "${Name} was found." FORCE)
-    if (ReqHeaders AND (NOT ${Name}_FIND_QUIETLY))
-      message(STATUS "${Prefix}_INCLUDE_DIRS=${${Prefix}_INCLUDE_DIRS}")
-    endif()
+  if (Found AND ReqLibs AND ReqHeaders AND (NOT ${Name}_FIND_QUIETLY))
+    message(STATUS "${Prefix}_INCLUDE_DIRS=${${Prefix}_INCLUDE_DIRS}")
   endif()
 
 endfunction(mfem_find_package)
@@ -694,162 +532,3 @@ 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_GZSTREAM 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_GECKO MFEM_USE_GNUTLS
-      MFEM_USE_NETCDF MFEM_USE_PETSC MFEM_USE_MPFR MFEM_USE_SIDRE
-      MFEM_USE_CONDUIT MFEM_USE_PUMI)
-  foreach(var ${CONFIG_MK_BOOL_VARS})
-    if (${var})
-      set(${var} YES)
-    else()
-      set(${var} NO)
-    endif()
-  endforeach()
-  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::.*")
-    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

@@ -15,9 +15,6 @@
 //
 // Otherwise, use the local file: _config.hpp.
 
-#ifndef MFEM_CONFIG_HPP
-#define MFEM_CONFIG_HPP
-
 #ifdef MFEM_BUILD_DIR
 #define MFEM_QUOTE(a) #a
 #define MFEM_MAKE_PATH(x,y) MFEM_QUOTE(x/y)
@@ -26,18 +23,6 @@
 #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
@@ -45,15 +30,7 @@
 #ifdef MFEM_USE_SUPERLU
 #error Building with SuperLU_DIST (MFEM_USE_SUPERLU=YES) requires MPI (MFEM_USE_MPI=YES)
 #endif
-#ifdef MFEM_USE_STRUMPACK
-#error Building with STRUMPACK (MFEM_USE_STRUMPACK=YES) requires MPI (MFEM_USE_MPI=YES)
-#endif
 #ifdef MFEM_USE_PETSC
 #error Building with PETSc (MFEM_USE_PETSC=YES) requires MPI (MFEM_USE_MPI=YES)
 #endif
-#ifdef MFEM_USE_PUMI
-#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

@@ -12,33 +12,6 @@
 #ifndef MFEM_CONFIG_HEADER
 #define MFEM_CONFIG_HEADER
 
-// MFEM version: integer of the form: (major*100 + minor)*100 + patch.
-// #define MFEM_VERSION @MFEM_VERSION@
-
-// MFEM version string of the form "3.3" or "3.3.1".
-// #define MFEM_VERSION_STRING "@MFEM_VERSION_STRING@"
-
-// MFEM version type, see the MFEM_VERSION_TYPE_* constants below.
-#define MFEM_VERSION_TYPE ((MFEM_VERSION)%2)
-
-// MFEM version type constants.
-#define MFEM_VERSION_TYPE_RELEASE 0
-#define MFEM_VERSION_TYPE_DEVELOPMENT 1
-
-// Separate MFEM version numbers for major, minor, and patch.
-#define MFEM_VERSION_MAJOR ((MFEM_VERSION)/10000)
-#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@"
-
 // Build the parallel MFEM library.
 // Requires an MPI compiler, and the libraries HYPRE and METIS.
 // #define MFEM_USE_MPI
@@ -46,18 +19,12 @@
 // Enable debug checks in MFEM.
 // #define MFEM_DEBUG
 
-// Throw an exception on errors.
-// #define MFEM_USE_EXCEPTIONS
-
 // Enable gzstream in MFEM.
 // #define MFEM_USE_GZSTREAM
 
 // Enable backtraces for mfem_error through libunwind.
 // #define MFEM_USE_LIBUNWIND
 
-// Enable MFEM features that use the METIS library (parallel MFEM).
-// #define MFEM_USE_METIS
-
 // Enable this option if linking with METIS version 5 (parallel MFEM).
 // #define MFEM_USE_METIS_5
 
@@ -68,17 +35,18 @@
 // 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
 
 // Which library functions to use in class StopWatch for measuring time.
-// For a list of the available options, see INSTALL.
+// The available options are:
+//   0 - use std::clock from <ctime>
+//   1 - use times from <sys/times.h>
+//   2 - use high-resolution POSIX clocks
+//   3 - use QueryPerformanceCounter from <windows.h>
 // If not defined, an option is selected automatically.
 // #define MFEM_TIMER_TYPE @MFEM_TIMER_TYPE@
 
@@ -94,9 +62,6 @@
 // Enable MFEM functionality based on the SuperLU library.
 // #define MFEM_USE_SUPERLU
 
-// Enable MFEM functionality based on the STRUMPACK library.
-// #define MFEM_USE_STRUMPACK
-
 // Enable functionality based on the Gecko library
 // #define MFEM_USE_GECKO
 
@@ -106,9 +71,6 @@
 // Enable Sidre support
 // #define MFEM_USE_SIDRE
 
-// Enable Conduit support
-// #define MFEM_USE_CONDUIT
-
 // Enable functionality based on the NetCDF library (reading CUBIT files)
 // #define MFEM_USE_NETCDF
 
@@ -118,27 +80,10 @@
 // Enable functionality based on the MPFR library.
 // #define MFEM_USE_MPFR
 
-// Enable MFEM functionality based on the PUMI library
-// #define MFEM_USE_PUMI
-
-// Build the GPU/CUDA-enabled version of the MFEM library.
-// Requires a CUDA compiler (nvcc).
-// #define MFEM_USE_CUDA
-
-// Enable functionality based on the RAJA library.
-// #define MFEM_USE_RAJA
-
-// Enable functionality based on the OCCA library.
-// #define MFEM_USE_OCCA
-
-// Enable MFEM's internal Memory Manager (needed e.g. for MFEM_USE_CUDA)
-// #define MFEM_USE_MM
-
-// Version of HYPRE used for building MFEM.
-// #define MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@
-
-// Macro defined when PUMI is built with support for the Simmetrix SimModSuite
-// library.
-// #define MFEM_USE_SIMMETRIX
+// Windows specific options
+#ifdef _WIN32
+// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
+#define _USE_MATH_DEFINES
+#endif
 
 #endif // MFEM_CONFIG_HEADER

config/config.mk.in

@@ -10,41 +10,26 @@
 # 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_GZSTREAM      = @MFEM_USE_GZSTREAM@
-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_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@
-MFEM_USE_CUDA          = @MFEM_USE_CUDA@
-MFEM_USE_RAJA          = @MFEM_USE_RAJA@
-MFEM_USE_OCCA          = @MFEM_USE_OCCA@
-MFEM_USE_MM            = @MFEM_USE_MM@
+MFEM_USE_MPI         = @MFEM_USE_MPI@
+MFEM_USE_METIS_5     = @MFEM_USE_METIS_5@
+MFEM_DEBUG           = @MFEM_DEBUG@
+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_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@
 
 # Compiler, compile options, and link options
 MFEM_CXX       = @MFEM_CXX@
@@ -52,28 +37,17 @@ MFEM_CPPFLAGS  = @MFEM_CPPFLAGS@
 MFEM_CXXFLAGS  = @MFEM_CXXFLAGS@
 MFEM_TPLFLAGS  = @MFEM_TPLFLAGS@
 MFEM_INCFLAGS  = @MFEM_INCFLAGS@
-MFEM_PICFLAG   = @MFEM_PICFLAG@
 MFEM_FLAGS     = @MFEM_FLAGS@
-MFEM_EXT_LIBS  = @MFEM_EXT_LIBS@
 MFEM_LIBS      = @MFEM_LIBS@
 MFEM_LIB_FILE  = @MFEM_LIB_FILE@
-MFEM_STATIC    = @MFEM_STATIC@
-MFEM_SHARED    = @MFEM_SHARED@
 MFEM_BUILD_TAG = @MFEM_BUILD_TAG@
 MFEM_PREFIX    = @MFEM_PREFIX@
 MFEM_INC_DIR   = @MFEM_INC_DIR@
 MFEM_LIB_DIR   = @MFEM_LIB_DIR@
 
-# Location of test.mk
-MFEM_TEST_MK = @MFEM_TEST_MK@
-
 # Command used to launch MPI jobs
 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

@@ -18,38 +18,29 @@ if (NOT CMAKE_BUILD_TYPE)
       "Build type: Debug, Release, RelWithDebInfo, or MinSizeRel." FORCE)
 endif()
 
-# MFEM options. Set to mimic the default "defaults.mk" file.
+# MFEM options. Set to mimic the default "default.mk" file.
 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_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_GECKO "Enable GECKO usage" OFF)
 option(MFEM_USE_GNUTLS "Enable GNUTLS 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)
-
-set(MFEM_MPI_NP 4 CACHE STRING "Number of processes used for MPI tests")
+option(MFEM_USE_SIDRE "Enable ATK/Sidre usage" OFF)
 
 # 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
-# need is the library, building all that stuff adds unnecessary overhead). Note
-# that the examples or miniapps can always be built using the targets 'examples'
-# or 'miniapps', respectively.
+# need is the library, building all that stuff adds unnecessary overhead). To
+# match "makefile" behavior, they are all enabled by default.
 option(MFEM_ENABLE_TESTING "Enable the ctest framework for testing" ON)
 option(MFEM_ENABLE_EXAMPLES "Build all of the examples" OFF)
 option(MFEM_ENABLE_MINIAPPS "Build all of the miniapps" OFF)
@@ -75,7 +66,7 @@ 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 "${MFEM_DIR}/../sundials-3.0.0" CACHE PATH
+set(SUNDIALS_DIR "${MFEM_DIR}/../sundials-2.7.0" 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"
@@ -100,34 +91,6 @@ set(SuperLUDist_DIR "${MFEM_DIR}/../SuperLU_DIST_5.1.0" CACHE PATH
 set(SuperLUDist_REQUIRED_PACKAGES "MPI" "BLAS" "ParMETIS" CACHE STRING
     "Additional packages required by SuperLU_DIST.")
 
-set(STRUMPACK_DIR "${MFEM_DIR}/../STRUMPACK-build" CACHE PATH
-    "Path to the STRUMPACK library.")
-# STRUMPACK may also depend on "OpenMP", depending on how it was compiled.
-# Starting with v2.2.0 of STRUMPACK, ParMETIS and Scotch are optional.
-set(STRUMPACK_REQUIRED_PACKAGES "MPI" "MPI_Fortran" "ParMETIS" "METIS"
-    "ScaLAPACK" "Scotch/ptscotch/ptscotcherr/scotch/scotcherr" CACHE STRING
-    "Additional packages required by STRUMPACK.")
-# If the MPI package does not find all required Fortran libraries:
-# set(STRUMPACK_REQUIRED_LIBRARIES "gfortran" "mpi_mpifh" CACHE STRING
-#     "Additional libraries required by STRUMPACK.")
-
-# The Scotch library, required by STRUMPACK <= v2.1.0, optional in STRUMPACK >=
-# v2.2.0.
-set(Scotch_DIR "${MFEM_DIR}/../scotch_6.0.4" CACHE PATH
-    "Path to the Scotch and PT-Scotch libraries.")
-set(Scotch_REQUIRED_PACKAGES "Threads" CACHE STRING
-    "Additional packages required by Scotch.")
-# Tell the "Threads" package/module to prefer pthreads.
-set(CMAKE_THREAD_PREFER_PTHREAD TRUE)
-set(Threads_LIB_VARS CMAKE_THREAD_LIBS_INIT)
-
-# The ScaLAPACK library, required by STRUMPACK
-set(ScaLAPACK_DIR "${MFEM_DIR}/../scalapack-2.0.2/lib/cmake/scalapack-2.0.2"
-    CACHE PATH "Path to the configuration file scalapack-config.cmake")
-set(ScaLAPACK_TARGET_NAMES scalapack)
-# set(ScaLAPACK_TARGET_FORCE)
-# set(ScaLAPACK_IMPORT_CONFIG DEBUG)
-
 set(GECKO_DIR "${MFEM_DIR}/../gecko" CACHE PATH "Path to the Gecko library.")
 
 set(GNUTLS_DIR "" CACHE PATH "Path to the GnuTLS library.")
@@ -139,20 +102,19 @@ set(NetCDF_REQUIRED_PACKAGES "" CACHE STRING
 
 set(PETSC_DIR "${MFEM_DIR}/../petsc" CACHE PATH
     "Path to the PETSc main directory.")
-set(PETSC_ARCH "arch-linux2-c-debug" CACHE STRING "PETSc build architecture.")
+set(PETSC_ARCH "arch-linux2-c-debug" CACHE PATH "PETSc build architecture.")
 
 set(MPFR_DIR "" CACHE PATH "Path to the MPFR library.")
 
 set(CONDUIT_DIR "${MFEM_DIR}/../conduit" CACHE PATH
     "Path to the Conduit library.")
+set(Conduit_REQUIRED_PACKAGES "HDF5" CACHE STRING
+    "Additional packages required by Conduit.")
 
-set(AXOM_DIR "${MFEM_DIR}/../axom" CACHE PATH "Path to the Axom library.")
+set(ATK_DIR "${MFEM_DIR}/../asctoolkit" CACHE PATH "Path to the ATK library.")
 # May need to add "Boost" as requirement.
-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(ATK_REQUIRED_PACKAGES "Conduit/relay" CACHE STRING
+    "Additional packages required by ATK.")
 
 set(BLAS_INCLUDE_DIRS "" CACHE STRING "Path to BLAS headers.")
 set(BLAS_LIBRARIES "" CACHE STRING "The BLAS library.")

config/defaults.mk

@@ -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
@@ -35,44 +30,15 @@ PREFIX = ./mfem
 # Install program
 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=$(CUDA_ARCH)
-# Prefixes for passing flags to the host compiler and linker when using CUDA_CXX
-CUDA_XCOMPILER = -Xcompiler=
-CUDA_XLINKER   = -Xlinker=
-
 ifneq ($(NOTMAC),)
    AR      = ar
    ARFLAGS = cruv
    RANLIB  = ranlib
-   PICFLAG = $(XCOMPILER)-fPIC
-   SO_EXT  = so
-   SO_VER  = so.$(MFEM_VERSION_STRING)
-   BUILD_SOFLAGS = -shared $(XLINKER)-soname,libmfem.$(SO_VER)
-   BUILD_RPATH = $(XLINKER)-rpath,$(BUILD_REAL_DIR)
-   INSTALL_SOFLAGS = $(BUILD_SOFLAGS)
-   INSTALL_RPATH = $(XLINKER)-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
-   SO_EXT  = dylib
-   SO_VER  = $(MFEM_VERSION_STRING).dylib
-   MAKE_SOFLAGS = $(XLINKER)-dylib,-install_name,$(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
-   INSTALL_SOFLAGS = $(subst $1 ,,$(call MAKE_SOFLAGS,$(MFEM_LIB_DIR)))
-   INSTALL_RPATH = $(XLINKER)-undefined,dynamic_lookup
 endif
 
 # Set CXXFLAGS to overwrite the default selection of DEBUG_FLAGS/OPTIM_FLAGS
@@ -88,49 +54,31 @@ endif
 # Command used to launch MPI jobs
 MFEM_MPIEXEC    = mpirun
 MFEM_MPIEXEC_NP = -np
-# Number of mpi tasks for parallel jobs
-MFEM_MPI_NP = 4
 
 # MFEM configuration options: YES/NO values, which are exported to config.mk and
 # 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_GZSTREAM      = 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_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
-MFEM_USE_CUDA          = NO
-MFEM_USE_RAJA          = NO
-MFEM_USE_OCCA          = NO
-MFEM_USE_MM            = NO
-
-# Compile and link options for zlib.
-ZLIB_DIR =
-ZLIB_OPT = $(if $(ZLIB_DIR),-I$(ZLIB_DIR)/include)
-ZLIB_LIB = $(if $(ZLIB_DIR),$(ZLIB_RPATH) -L$(ZLIB_DIR)/lib ,)-lz
-ZLIB_RPATH = -Wl,-rpath,$(ZLIB_DIR)/lib
+MFEM_USE_MPI         = NO
+MFEM_USE_METIS_5     = NO
+MFEM_DEBUG           = 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),2,0)
+MFEM_USE_SUNDIALS    = NO
+MFEM_USE_MESQUITE    = NO
+MFEM_USE_SUITESPARSE = NO
+MFEM_USE_SUPERLU     = 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
 
 LIBUNWIND_OPT = -g
 LIBUNWIND_LIB = $(if $(NOTMAC),-lunwind -ldl,)
@@ -141,7 +89,7 @@ HYPRE_OPT = -I$(HYPRE_DIR)/include
 HYPRE_LIB = -L$(HYPRE_DIR)/lib -lHYPRE
 
 # METIS library configuration
-ifeq ($(MFEM_USE_SUPERLU)$(MFEM_USE_STRUMPACK),NONO)
+ifeq ($(MFEM_USE_SUPERLU),NO)
    ifeq ($(MFEM_USE_METIS_5),NO)
      METIS_DIR = @MFEM_DIR@/../metis-4.0
      METIS_OPT =
@@ -152,10 +100,8 @@ ifeq ($(MFEM_USE_SUPERLU)$(MFEM_USE_STRUMPACK),NONO)
      METIS_LIB = -L$(METIS_DIR)/lib -lmetis
    endif
 else
-   # ParMETIS: currently needed by SuperLU or STRUMPACK. We assume that METIS 5
+   # ParMETIS currently needed only with SuperLU. We assume that METIS 5
    # (included with ParMETIS) is installed in the same location.
-   # Starting with STRUMPACK v2.2.0, ParMETIS is an optional dependency while
-   # METIS is still required.
    METIS_DIR = @MFEM_DIR@/../parmetis-4.0.3
    METIS_OPT = -I$(METIS_DIR)/include
    METIS_LIB = -L$(METIS_DIR)/lib -lparmetis -lmetis
@@ -167,17 +113,17 @@ 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-3.0.0
+SUNDIALS_DIR = @MFEM_DIR@/../sundials-2.7.0
 SUNDIALS_OPT = -I$(SUNDIALS_DIR)/include
 SUNDIALS_LIB = -Wl,-rpath,$(SUNDIALS_DIR)/lib -L$(SUNDIALS_DIR)/lib\
- -lsundials_arkode -lsundials_cvode -lsundials_nvecserial -lsundials_kinsol
+  -lsundials_arkode -lsundials_cvode -lsundials_nvecserial -lsundials_kinsol
 
 ifeq ($(MFEM_USE_MPI),YES)
    SUNDIALS_LIB += -lsundials_nvecparhyp -lsundials_nvecparallel
@@ -194,42 +140,14 @@ MESQUITE_LIB = -L$(MESQUITE_DIR)/lib -lmesquite
 LIB_RT = $(if $(NOTMAC),-lrt,)
 SUITESPARSE_DIR = @MFEM_DIR@/../SuiteSparse
 SUITESPARSE_OPT = -I$(SUITESPARSE_DIR)/include
-SUITESPARSE_LIB = -Wl,-rpath,$(SUITESPARSE_DIR)/lib -L$(SUITESPARSE_DIR)/lib\
- -lklu -lbtf -lumfpack -lcholmod -lcolamd -lamd -lcamd -lccolamd\
- -lsuitesparseconfig $(LIB_RT) $(METIS_LIB) $(LAPACK_LIB)
+SUITESPARSE_LIB = -L$(SUITESPARSE_DIR)/lib -lklu -lbtf -lumfpack -lcholmod\
+ -lcolamd -lamd -lcamd -lccolamd -lsuitesparseconfig $(LIB_RT) $(METIS_LIB)\
+ $(LAPACK_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)/SRC -L$(SUPERLU_DIR)/SRC -lsuperlu_dist
-
-# SCOTCH library configuration (required by STRUMPACK <= v2.1.0, optional in
-# STRUMPACK >= v2.2.0)
-SCOTCH_DIR = @MFEM_DIR@/../scotch_6.0.4
-SCOTCH_OPT = -I$(SCOTCH_DIR)/include
-SCOTCH_LIB = -L$(SCOTCH_DIR)/lib -lptscotch -lptscotcherr -lscotch -lscotcherr\
- -lpthread
-
-# SCALAPACK library configuration (required by STRUMPACK)
-SCALAPACK_DIR = @MFEM_DIR@/../scalapack-2.0.2
-SCALAPACK_OPT = -I$(SCALAPACK_DIR)/SRC
-SCALAPACK_LIB = -L$(SCALAPACK_DIR)/lib -lscalapack $(LAPACK_LIB)
-
-# MPI Fortran library, needed e.g. by STRUMPACK
-# MPICH:
-MPI_FORTRAN_LIB = -lmpifort
-# OpenMPI:
-# MPI_FORTRAN_LIB = -lmpi_mpifh
-# Additional Fortan library:
-# MPI_FORTRAN_LIB += -lgfortran
-
-# STRUMPACK library configuration
-STRUMPACK_DIR = @MFEM_DIR@/../STRUMPACK-build
-STRUMPACK_OPT = -I$(STRUMPACK_DIR)/include $(SCOTCH_OPT)
-# If STRUMPACK was build with OpenMP support, the following may be need:
-# STRUMPACK_OPT += $(OPENMP_OPT)
-STRUMPACK_LIB = -L$(STRUMPACK_DIR)/lib -lstrumpack $(MPI_FORTRAN_LIB)\
- $(SCOTCH_LIB) $(SCALAPACK_LIB)
+SUPERLU_LIB = -L$(SUPERLU_DIR)/SRC -lsuperlu_dist
 
 # Gecko library configuration
 GECKO_DIR = @MFEM_DIR@/../gecko
@@ -241,83 +159,43 @@ GNUTLS_OPT =
 GNUTLS_LIB = -lgnutls
 
 # NetCDF library configuration
-NETCDF_DIR = $(HOME)/local
-HDF5_DIR   = $(HOME)/local
-NETCDF_OPT = -I$(NETCDF_DIR)/include -I$(HDF5_DIR)/include $(ZLIB_OPT)
-NETCDF_LIB = -Wl,-rpath,$(NETCDF_DIR)/lib -L$(NETCDF_DIR)/lib\
- -Wl,-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib\
- -lnetcdf -lhdf5_hl -lhdf5 $(ZLIB_LIB)
+NETCDF_DIR  = $(HOME)/local
+HDF5_DIR    = $(HOME)/local
+ZLIB_DIR    = $(HOME)/local
+NETCDF_OPT  = -I$(NETCDF_DIR)/include
+NETCDF_LIB  = -L$(NETCDF_DIR)/lib -lnetcdf -L$(HDF5_DIR)/lib -lhdf5_hl -lhdf5\
+ -L$(ZLIB_DIR)/lib -lz
 
 # PETSc library configuration (version greater or equal to 3.8 or the dev branch)
-PETSC_ARCH := arch-linux2-c-debug
-PETSC_DIR  := $(MFEM_DIR)/../petsc/$(PETSC_ARCH)
-PETSC_VARS := $(PETSC_DIR)/lib/petsc/conf/petscvariables
-PETSC_FOUND := $(if $(wildcard $(PETSC_VARS)),YES,)
-PETSC_INC_VAR = PETSC_CC_INCLUDES
-PETSC_LIB_VAR = PETSC_EXTERNAL_LIB_BASIC
-ifeq ($(PETSC_FOUND),YES)
-   PETSC_OPT := $(shell sed -n "s/$(PETSC_INC_VAR) = *//p" $(PETSC_VARS))
-   PETSC_LIB := $(shell sed -n "s/$(PETSC_LIB_VAR) = *//p" $(PETSC_VARS))
-   PETSC_LIB := -Wl,-rpath,$(abspath $(PETSC_DIR))/lib\
-      -L$(abspath $(PETSC_DIR))/lib -lpetsc $(PETSC_LIB)
+ifeq ($(MFEM_USE_PETSC),YES)
+   PETSC_DIR := $(MFEM_DIR)/../petsc/arch-linux2-c-debug
+   PETSC_PC  := $(PETSC_DIR)/lib/pkgconfig/PETSc.pc
+   $(if $(wildcard $(PETSC_PC)),,$(error PETSc config not found - $(PETSC_PC)))
+   PETSC_OPT := $(shell sed -n "s/Cflags: *//p" $(PETSC_PC))
+   PETSC_LIB := $(shell sed -n "s/Libs.*: *//p" $(PETSC_PC))
+   PETSC_LIB := -Wl,-rpath -Wl,$(abspath $(PETSC_DIR))/lib $(PETSC_LIB)
 endif
 
 # MPFR library configuration
 MPFR_OPT =
 MPFR_LIB = -lmpfr
 
-# Conduit and required libraries configuration
-CONDUIT_DIR = @MFEM_DIR@/../conduit
-CONDUIT_OPT = -I$(CONDUIT_DIR)/include/conduit
-CONDUIT_LIB = \
-   -Wl,-rpath,$(CONDUIT_DIR)/lib -L$(CONDUIT_DIR)/lib \
-   -lconduit -lconduit_relay -lconduit_blueprint  -ldl
-
-# Check if Conduit was built with hdf5 support, by looking
-# for the relay hdf5 header
-CONDUIT_HDF5_HEADER=$(CONDUIT_DIR)/include/conduit/conduit_relay_hdf5.hpp
-ifneq (,$(wildcard $(CONDUIT_HDF5_HEADER)))
-   CONDUIT_OPT += -I$(HDF5_DIR)/include
-   CONDUIT_LIB += -Wl,-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib \
-                  -lhdf5 $(ZLIB_LIB)
-endif
-
 # Sidre and required libraries configuration
 # Be sure to check the HDF5_DIR (set above) is correct
-SIDRE_DIR = @MFEM_DIR@/../axom
+SIDRE_DIR = @MFEM_DIR@/../asctoolkit
+CONDUIT_DIR = @MFEM_DIR@/../conduit
 SIDRE_OPT = -I$(SIDRE_DIR)/include -I$(CONDUIT_DIR)/include/conduit\
  -I$(HDF5_DIR)/include
-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 \
-   -lsidre -lslic -laxom_utils -lconduit -lconduit_relay -lhdf5 $(ZLIB_LIB) -ldl
+SIDRE_LIB = -L$(SIDRE_DIR)/lib \
+            -L$(CONDUIT_DIR)/lib \
+            -Wl,-rpath -Wl,$(CONDUIT_DIR)/lib \
+            -L$(HDF5_DIR)/lib\
+            -Wl,-rpath -Wl,$(HDF5_DIR)/lib \
+            -lsidre -lslic -lcommon -lconduit -lconduit_relay -lhdf5 -lz -ldl
 
-# PUMI
-# Note that PUMI_DIR is needed -- it is used to check for gmi_sim.h
-PUMI_DIR = @MFEM_DIR@/../pumi-2.1.0
-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
-
-# CUDA library configuration. Since we compile and link with nvcc (when CUDA is
-# enabled) we only need to explicitly link with the CUDA driver, libcuda.*,
-# which is usually in a system path.
-CUDA_OPT =
-CUDA_LIB = $(if $(NOTMAC),,-L/usr/local/cuda/lib) -lcuda
-
-# OCCA library configuration
-OCCA_DIR ?= @MFEM_DIR@/../occa
-OCCA_OPT = -I$(OCCA_DIR)/include
-OCCA_LIB = $(XLINKER)-rpath,$(OCCA_DIR)/lib -L$(OCCA_DIR)/lib -locca
-
-# RAJA library configuration
-RAJA_DIR ?= @MFEM_DIR@/../raja
-RAJA_OPT = -I$(RAJA_DIR)/include
-ifdef CUB_DIR
-   RAJA_OPT += -I$(CUB_DIR)
+ifeq ($(MFEM_USE_MPI),YES)
+   SIDRE_LIB += -lspio -lcommon
 endif
-RAJA_LIB = $(XLINKER)-rpath,$(RAJA_DIR)/lib -L$(RAJA_DIR)/lib -lRAJA
 
 # If YES, enable some informational messages
 VERBOSE = NO

config/get_hypre_version.cpp

@@ -1,48 +0,0 @@
-// Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at
-// the Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights
-// reserved. See file COPYRIGHT for details.
-//
-// This file is part of the MFEM library. For more information and source code
-// availability see http://mfem.org.
-//
-// MFEM is free software; you can redistribute it and/or modify it under the
-// terms of the GNU Lesser General Public License (as published by the Free
-// Software Foundation) version 2.1 dated February 1999.
-
-#include "HYPRE_config.h"
-#include <cstdio>
-
-#ifdef HYPRE_RELEASE_VERSION
-#define HYPRE_VERSION_STRING HYPRE_RELEASE_VERSION
-#elif defined(HYPRE_PACKAGE_VERSION)
-#define HYPRE_VERSION_STRING HYPRE_PACKAGE_VERSION
-#endif
-
-// Macros to expand a macro as a string
-#define STR_EXPAND(s) #s
-#define STR(s) STR_EXPAND(s)
-
-// Convert the HYPRE_RELEASE_VERSION macro (string) to integer.
-// Examples: "2.10.0b" --> 21000, "2.11.2"  --> 21102
-int main()
-{
-#ifdef HYPRE_VERSION_STRING
-   const char *ptr = STR(HYPRE_VERSION_STRING);
-   if (*ptr == '"') { ptr++; }
-   int version = 0;
-   for (int i = 0; i < 3; i++, ptr++)
-   {
-      int pv = 0;
-      for (char d; d = *ptr, '0' <= d && d <= '9'; ptr++)
-      {
-         pv = 10*pv + (d - '0');
-         if (pv >= 100) { return 1; }
-      }
-      version = 100*version + pv;
-   }
-   printf("%i\n", version);
-   return 0;
-#else
-   return 2;
-#endif
-}

config/makefile

@@ -31,44 +31,17 @@ CONFIG_HPP = _config.hpp
 CONFIG_MK = config.mk
 
 .SUFFIXES:
-.PHONY: all get-hypre-version header config-mk
+.PHONY: all header config-mk
 
 all: header config-mk
 
-MPI = $(MFEM_USE_MPI:NO=)
-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)
-SMX_PATH = $(PUMI_DIR)/include/gmi_sim.h
-SMX_FILE = $(subst @MFEM_DIR@,$(if $(MFEM_DIR),$(MFEM_DIR),..),$(SMX_PATH))
-
-$(GHV): $(SRC)$(GHV).cpp
-	$(call mfem-info, Determining HYPRE version ...)
-	$(MFEM_CXX) ${GHV_FLAGS} $(SRC)$(GHV).cpp -o $(GHV)
-$(GHV).out: $(GHV)
-	./$(GHV) > $(GHV).out
-.INTERMEDIATE: $(GHV) $(GHV).out
-
-get-hypre-version: $(GHV).out
-	$(eval MFEM_HYPRE_VERSION:=$(shell cat $(GHV).out))
-	$(if $(MFEM_HYPRE_VERSION),$(eval export MFEM_HYPRE_VERSION)\
-	$(info HYPRE version: $(MFEM_HYPRE_VERSION)),\
-	$(error Unable to determine HYPRE version))
-
-check-smx:
-	$(call mfem-info, Checking for Simmetrix header [$(SMX_FILE)] ...)
-	$(eval MFEM_USE_SIMMETRIX:=$(if $(wildcard $(SMX_FILE)),YES,NO))
-	$(call mfem-info, MFEM_USE_SIMMETRIX = $(MFEM_USE_SIMMETRIX))
-	$(eval export MFEM_USE_SIMMETRIX)
-
-header: $(if $(MPI),get-hypre-version,) $(if $(SMX),check-smx)
+header:
 	$(call mfem-info, Writing $(CONFIG_HPP) ...)
 	@set -- && \
-	for def in $${MFEM_DEFINES} $(if $(MPI),MFEM_HYPRE_VERSION) $(SMX); do \
+	for def in $${MFEM_DEFINES}; do \
 	   eval var=\$$$$def && \
 	   if [ "NO" != "$${var}" ]; then \
-	      set -- "$$@" -e "s|// \(#define $${def} \)|\1|" && \
-	      set -- "$$@" -e "s|// \(#define $${def}\)$$|\1|" && \
+	      set -- "$$@" -e "s|// \(#define $${def}\)|\1|" && \
 	      set -- "$$@" -e "s#@$${def}@#$${var}#g"; \
 	   fi; \
 	done && \
@@ -89,4 +62,4 @@ config-mk:
 	sed "$$@" $(SRC)config.mk.in > $(CONFIG_MK)
 
 clean:
-	rm -f $(CONFIG_HPP) $(CONFIG_MK) sample-runs-build.log
+	rm -f $(CONFIG_HPP) $(CONFIG_MK)

config/sample-runs.sh

@@ -1,534 +0,0 @@
-#!/bin/bash
-
-# 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.
-
-make="${MAKE:-make}"
-mpiexec="${MPIEXEC:-mpirun}"
-mpiexec_np="${MPIEXEC_NP:--np}"
-run_prefix=""
-run_vg="valgrind --leak-check=full --show-reachable=yes --track-origins=yes"
-run_suffix="-no-vis"
-skip_gen_meshes="yes"
-cur_dir="${PWD}"
-mfem_dir="$(cd "$(dirname "$0")"/.. && pwd)"
-mfem_build_dir=""
-build_log=""
-output_dir=""
-output_sfx=".out"
-# The group format is: '"group-name" "group-summary-title" "group-directory"
-# "group-source-patterns"'
-groups_serial=(
-'"examples"
-   "Examples:"
-   "examples"
-   "ex{,1,2}[0-9].cpp"'
-#   "ex1.cpp"'
-'"sundials"
-   "SUNDIALS examples:"
-   "examples/sundials"
-   "ex{9,10,16}.cpp"'
-'"performance"
-   "Performance miniapps:"
-   "miniapps/performance"
-   "ex1.cpp"'
-#   ""'
-'"meshing"
-   "Meshing miniapps:"
-   "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
-    mesh-optimizer.cpp"'
-)
-# Parallel groups
-groups_parallel=(
-'"examples"
-   "Examples:"
-   "examples"
-   "ex{,1,2}[0-9]p.cpp"'
-#   "ex1p.cpp"'
-'"sundials"
-   "SUNDIALS examples:"
-   "examples/sundials"
-   "ex{9,10,16}p.cpp"'
-'"petsc"
-   "PETSc examples:"
-   "examples/petsc"
-   "ex{,1}[0-9]p.cpp"'
-'"performance"
-   "Performance miniapps:"
-   "miniapps/performance"
-   "ex1p.cpp"'
-#   ""'
-'"meshing"
-   "Meshing miniapps:"
-   "miniapps/meshing"
-   "pmesh-optimizer.cpp"'
-'"electromagnetics"
-   "Electromagnetics miniapps:"
-   "miniapps/electromagnetics"
-   "joule.cpp"'
-#   "{volta,tesla,joule}.cpp"' # todo: multiline sample runs
-)
-# All groups serial + parallel runs mixed in the same group:
-groups_all=(
-'"examples"
-   "Examples:"
-   "examples"
-   "ex\"{,1,2}[0-9]\"{,p}.cpp"'
-'"sundials"
-   "SUNDIALS examples:"
-   "examples/sundials"
-   "ex\"{9,10,16}\"{,p}.cpp"'
-'"petsc"
-   "PETSc examples:"
-   "examples/petsc"
-   "ex{,1}[0-9]p.cpp"'
-'"performance"
-   "Performance miniapps:"
-   "miniapps/performance"
-   "ex1{,p}.cpp"'
-'"meshing"
-   "Meshing miniapps:"
-   "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
-    {,p}mesh-optimizer.cpp"'
-'"electromagnetics"
-   "Electromagnetics miniapps:"
-   "miniapps/electromagnetics"
-   "joule.cpp"'
-#   "{volta,tesla,joule}.cpp"' # todo: multiline sample runs
-)
-make_all="all"
-base_timeformat=$'real: %3Rs  user: %3Us  sys: %3Ss  %%cpu: %P'
-# separator
-sep='----------------------------------------------------------------'
-
-# Command line parameters:
-opt_help="no"
-opt_show="no"
-mfem_config="MFEM_USE_MPI=NO MFEM_DEBUG=NO"
-groups=()
-group_name=""
-group_title=""
-valgrind="no"
-make_j="-j $(getconf _NPROCESSORS_ONLN)"
-color="no"
-built="no"
-timing="no"
-
-# Read the sample runs from the source "$1" and put them in the array variable
-# "runs".
-function extract_sample_runs()
-{
-   local old_IFS="${IFS}" sruns="" pruns=""
-   local src="$1"
-   if [ "${src}" == "" ]; then runs=(); return 1; fi
-   local app=${src%.cpp}
-   local vg_app="${app}"
-   if [ "${valgrind}" == "yes" ]; then vg_app="${run_vg} ${app}"; fi
-   # parallel sample runs are lines matching "^//.*  mpirun .* ${app}" with
-   # everything in front of "mpirun" removed:
-   pruns=`grep "^//.*  mpirun .* ${app}" "${src}" |
-          sed -e "s/.*  mpirun \(.*\) ${app}/${mpiexec} \1 ${app}/g" \
-              -e "s/ -np\(.*\) ${app}/ ${mpiexec_np}\1 ${vg_app}/g"`
-   # serial sample runs are lines that are not parallel sample runs and matching
-   # "^//.*  ${app}" with everything in front of "${app}" removed:
-   sruns=`grep -v "^//.*  mpirun .* ${app}" "${src}" |
-          grep "^//.*  ${app}" |
-          sed -e "s/.*  ${app}/${vg_app}/g"`
-   runs="${sruns}${pruns}"
-   if [ "$skip_gen_meshes" == "yes" ]; then
-      runs=`printf "%s" "$runs" | grep -v ".* -m .*\.gen"`
-   fi
-   IFS=$'\n'
-   runs=(${runs})
-   IFS="${old_IFS}"
-}
-
-# Echo usage information
-function help_message()
-{
-   cat <<EOF
-
-   $0 [options]
-
-   Options:
-      -h|-help    Print this usage information and exit
-      -p|-par     Build the parallel MFEM library + examples + miniapps.
-                  The default is to build the serial MFEM library + examples +
-                  miniapps. The build can be customized by setting the variable
-                  'mfem_config' or by building separately and using '-b'
-      -g <dir> <pattern>
-                  Specify explicitly a group (dir + file pattern) to run; This
-                  option can be used multiple times to define multiple groups
-      -v          Enable valgrind
-      -o <dir>    [${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
-      -t|-time    Measure and print execution time for each sample run
-      -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 varible; see below for valid variables
-       *          Any other parameter is treated as <mfem_dir>
-      <mfem_dir>  [${mfem_dir}] is the MFEM source directory
-
-   This script tests all the sample runs listed in the begining comments of
-   MFEM's serial or parallel example and miniapp codes. The list of sample runs
-   is auto-generated and can be viewed with the -s|-show option.
-
-   The following shell script variables can be set with <var>=<value>:
-      output_dir [${output_dir}]
-         Same as '-o': if not empty, save output to files in that directory
-      output_sfx [${output_sfx}]
-         Suffix to append to the output files
-      mfem_config [${mfem_config}]
-         Set MFEM configuration options
-      make [${make}], mpiexec [${mpiexec}], mpiexec_np [${mpiexec_np}]
-         Their values can also set using the respective uppercase environment
-         variable
-      mfem_build_dir [${mfem_build_dir}]
-         Same as '-d': set this variable to something different from <mfem_dir>
-         to use an out-of-source build
-
-   For other valid variables, see the script source.
-
-   The following environment variables, if non-empty, are used:
-      MAKE, MPIEXEC, MPIEXEC_NP
-
-   Example usage:
-       $0 -s                [ Show all configured sample runs ]
-       $0 -o baseline       [ Serial build; run and save all built sample runs ]
-       $0 -p -o baseline    [ Parallel build; run and save all sample runs ]
-       $0 -b -g examples ex8.cpp [ Use the existing build; run ex8 sample runs ]
-
-EOF
-}
-
-function show_runs()
-{
-   echo "${sep}"
-   for group_params in "${groups[@]}"; do
-      eval params=(${group_params})
-      name="${params[0]}"
-      title="${params[1]}"
-      group_dir="${mfem_dir}/${params[2]}"
-      pattern="${params[3]}"
-      printf "group name:    [%s]\n" "${name}"
-      printf "summary title: [%s]\n" "${title}"
-      printf "directory:     [%s]\n" "${group_dir}"
-      printf "pattern:       [%s]\n" "${pattern}"
-      cd "${cur_dir}"; cd "${group_dir}" || exit 1
-      eval sources=(${pattern})
-      eval sources=("${sources[@]}")
-      printf "sources:       (%s)\n" "${sources[*]}"
-      printf "sample runs:\n"
-      for src in "${sources[@]}"; do
-         extract_sample_runs "${src}"
-         for run in "${runs[@]}"; do
-            printf "   %s\n" "${run}"
-         done
-      done
-      echo "${sep}"
-   done
-}
-
-# Process command line parameters
-while [ $# -gt 0 ]; do
-
-case "$1" in
-   -h|-help)
-      opt_help="yes"
-      ;;
-   -p|-parallel)
-      mfem_config="MFEM_USE_MPI=YES MFEM_DEBUG=NO"
-      ;;
-   -g)
-      gbasename="$(basename "$2")"
-      gname="${group_name:-${gbasename}}"
-      gtitle="${group_title:-"Group <${gbasename}>:"}"
-      test_group="\"${gname}\" \"${gtitle}\" \"$2\" \"$3\""
-      groups=("${groups[@]}" "${test_group}")
-      shift 2
-      ;;
-   -v)
-      valgrind="yes"
-      ;;
-   -o)
-      shift
-      output_dir="$1"
-      ;;
-   -d)
-      shift
-      mfem_build_dir="$1"
-      ;;
-   -j)
-      shift
-      make_j="-j $1"
-      ;;
-   -c|-color)
-      color="yes"
-      ;;
-   -b|-built)
-      built="yes"
-      ;;
-   -t|-time)
-      timing="yes"
-      ;;
-   -s|-show)
-      opt_show="yes"
-      ;;
-   -n)
-      run_prefix="echo"
-      ;;
-   *=*)
-      eval $1
-      ;;
-   *)
-      mfem_dir="$1"
-      ;;
-esac
-
-shift
-done # while ...
-
-mfem_build_dir="${mfem_build_dir:-${mfem_dir}}"
-
-build_log="${build_log:-${mfem_build_dir}/config/sample-runs-build.log}"
-
-if [ 0 -eq ${#groups[*]} ]; then
-   groups=("${groups_all[@]}")
-   # These can be used as command line arguments:
-   #   'groups=("${groups_serial[@]}")'
-   #   'groups=("${groups_parallel[@]}")'
-fi
-
-if [ "${opt_help}" == "yes" ]; then
-   help_message
-   exit
-fi
-
-if [ "${opt_show}" == "yes" ]; then
-   show_runs
-   exit
-fi
-
-# Setup colors
-if [ -t 1 ] && [ -z "${output_dir}" ] || [ "${color}" == "yes" ]; then
-   red='\033[0;31m'
-   green='\033[0;32m'
-   yellow='\033[0;33m'
-   magenta='\033[0;35m'
-   cyan='\033[0;36m'
-   none='\033[0m'
-else
-   red=
-   green=
-   yellow=
-   magenta=
-   cyan=
-   none=
-fi
-
-# Run the given command, saving the rune time in the variable "timer".
-function timed_run()
-{
-   timer="$({ time "$@" 1>&3 2>&4; } 2>&1)"
-} 3>&1 4>&2
-
-# This function is used to execute the sample runs
-function go()
-{
-   local cmd=("$@")
-   local res=""
-   echo $sep
-   echo "<${group}>" "${cmd[@]}"
-   echo $sep
-   if [ "${timing}" == "yes" ]; then
-      timed_run "${cmd[@]}"
-   else
-      "${cmd[@]}"
-   fi
-   if [ "$?" -eq 0 ]; then
-      res="${green}  OK  ${none}"
-   else
-      res="${red}FAILED${none}"
-   fi
-   printf "[${res}] <${group}> ${cmd[*]}\n"
-   if [ "${timing}" == "yes" ]; then
-      printf "Run time: %s\n" "${timer}"
-      timer=(${timer})
-      timer="${timer[1]}"
-      printf -v line "[$res](%8s) ${cmd[*]}" "$timer"
-      summary=("${summary[@]}" "$line")
-   else
-      summary=("${summary[@]}" "[${res}] ${cmd[*]}")
-   fi
-   echo $sep
-}
-
-# This function is used to run a group of sample runs (in the same directory)
-function go_group()
-{
-   local res=""
-   if [ $# -eq 0 ]; then return 0; fi
-   local group_output_dir="" output_file="" output=""
-   if [ ! -z "$output_dir" ]; then
-      group_output_dir="${output_dir}/${group_dir}"
-      mkdir -p "${group_output_dir}" || exit 1
-   fi
-   for src in "$@"; do
-      cd "${mfem_dir}/${group_dir}" || exit 1
-      extract_sample_runs "${src}" || continue
-      [ "${#runs[@]}" -eq 0 ] && continue
-      cd "${mfem_build_dir}/${group_dir}" || exit 1
-      if [ ! -x "${src%.cpp}" ]; then
-         res="${magenta} SKIP ${none}"
-         echo $sep
-         printf "[${res}] <${group}> <${src}>\n"
-         echo $sep
-         summary=("${summary[@]}" "[${res}] <${src}>")
-         continue
-      fi
-      if [ ! -z "$output_dir" ]; then
-         output_file="${group_output_dir}/${src}${output_sfx}"
-         : > "${output_file}"
-         output=">> \"${output_file}\" 2>&1"
-      fi
-      for run in "${runs[@]}"; do
-         if [ "${run}" == "" ]; then continue; fi
-         eval go \${run_prefix} \${run} \${run_suffix} $output
-      done
-   done
-   ${make} clean-exec
-}
-
-# Make sure $mfem_dir exists and we can cd into it
-cd "$mfem_dir" || exit 1
-# Make sure $mfem_dir is an absolute path
-mfem_dir="$PWD"
-cd "${cur_dir}"
-if [ "${built}" == "no" ]; then
-   mkdir -p "${mfem_build_dir}" || exit 1
-fi
-# Make sure $mfem_build_dir exists and we can cd into it
-cd "${mfem_build_dir}" || exit 1
-# Make sure $mfem_build_dir is an absolute path
-mfem_build_dir="$PWD"
-# Setup 'output_dir'
-if [ ! -z "$output_dir" ]; then
-   cd "${cur_dir}"
-   mkdir -p "${output_dir}" && cd "${output_dir}" || exit 1
-   output_dir="$PWD"
-   echo "Sending output to files in: [${output_dir}]"
-   echo "Using suffix: [${output_sfx}]"
-fi
-
-TIMEFORMAT="${base_timeformat}"
-
-function set_echo_log()
-{
-   local dirname=`dirname "$1"`
-   cd "${cur_dir}"
-   mkdir -p "${dirname}" && cd "${dirname}" || exit 1
-   echo_log="$PWD"/`basename "$1"`
-}
-
-# Echo the given command line; then run it sending all output to $echo_log
-function echo_run()
-{
-   echo "   $@"
-   { echo "   $@"; echo "$sep";
-     "$@"
-     echo "$sep"; } >> "$echo_log" 2>&1
-}
-
-# Function that builds the mfem library, examples and miniapps
-function build_all()
-{
-   printf "Building MFEM with all examples and miniapps:\n"
-   set_echo_log "${build_log}"
-   echo "   ### build log: [$echo_log]"
-   { echo "$sep"; echo "   MFEM build log"; echo "$sep"; } > "$echo_log"
-   echo_run cd "${mfem_build_dir}"
-   if [ "${mfem_dir}" != "${mfem_build_dir}" ]; then
-      echo_run ${make} -f "${mfem_dir}"/makefile config
-   fi
-   # Don't use 'make distclean' as it will delete the default $build_log
-   echo_run ${make} clean || exit 1
-   echo_run ${make} config ${mfem_config} || exit 1
-   echo_run ${make} ${make_j} || exit 1
-   echo_run ${make} ${make_all} ${make_j} || exit 1
-}
-
-# Function that runs all sample runs, given by the array variable "groups".
-function all_go()
-{
-   for group_params in "${groups[@]}"; do
-      eval params=(${group_params})
-      group="${params[0]}"
-      group_dir="${params[2]}"
-      cd "${mfem_dir}/${group_dir}" || exit 1
-      eval sources=(${params[3]})
-      eval sources=("${sources[@]}")
-      summary=("${summary[@]}" "${params[1]}")
-      go_group "${sources[@]}"
-   done
-
-   printf "Summary:\n--------\n"
-   for line in "${summary[@]}"; do
-      printf "${line}\n"
-   done
-}
-
-function main()
-{
-   # Build all mfem examples and miniapps
-   if [ "${built}" == "no" ]; then
-      if [ "${timing}" == "yes" ]; then
-         timed_run build_all
-         printf "Build time: %s\n" "${timer}"
-      else
-         build_all
-      fi
-   fi
-
-   summary=()
-   PATH=.:$PATH
-
-   # Print the MFEM configuration info
-   cd "${mfem_build_dir}"
-   echo "$sep"
-   echo "MFEM configuration"
-   echo "$sep"
-   ${make} info
-   echo "$sep"
-
-   # Run all sample runs.
-   if [ "${timing}" == "yes" ]; then
-      timed_run all_go
-      printf "Total run time: %s\n" "${timer}"
-   else
-      all_go
-   fi
-   echo
-}
-
-output=""
-if [ ! -z "$output_dir" ]; then
-   output=">> \"${output_dir}/main${output_sfx}\" 2>&1"
-fi
-eval main $output

config/test.mk

@@ -10,49 +10,14 @@
 # Software Foundation) version 2.1 dated February 1999.
 
 # Utilities for the "make test" and "make check" targets.
-
 # Colors used below:
 # green    '\033[0;32m'
 # red      '\033[0;31m'
-# yellow   '\033[0;33m'
 # no color '\033[0m'
 COLOR_PRINT = if [ -t 1 ]; then \
    printf $(1)$(2)'\033[0m'$(3); else printf $(2)$(3); fi
-PRINT_OK = $(call COLOR_PRINT,'\033[0;32m',OK,"  ($$1 $$2)\n")
-PRINT_FAILED = $(call COLOR_PRINT,'\033[0;31m',FAILED,"  ($$1 $$2)\n")
-PRINT_SKIP = $(call COLOR_PRINT,'\033[0;33m',SKIP,"\n")
-
-# Timing support
-define TIMECMD_detect
-timecmd=$$(which time 2> /dev/null);
-if [ -n "$$timecmd" ]; then
-   if $$timecmd --version > /dev/null 2>&1; then
-   echo "$$timecmd" GNU; else echo "$$timecmd" NOTGNU; fi;
-else timecmd=$$(command -v time);
-   if [ "$$timecmd" = time ]; then
-   echo "$$timecmd" BASH; else echo X NONE; fi;
-fi
-endef
-define TIMECMD.GNU
-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 -- "$$1"s "$$(($$7/1024))"kB "$${60}"
-endef
-define TIMECMD.BASH
-TIMEFORMAT=$$'%3Rs'; \
-set -- $$({ time $(2); } 2>&1; echo $$?); set -- "$$1" "" "$$2"
-endef
-define TIMECMD.NONE
-$(2); set -- "" "" "$$?"
-endef
-TIMECMD := $(shell $(TIMECMD_detect))
-TIMEFUN := TIMECMD.$(word 2,$(TIMECMD))
-TIMECMD := $(word 1,$(TIMECMD))
-# Sample use of the timing macro: (returns shell commands as text)
-# $(call $(TIMEFUN),$(TIMECMD),$(MY_SHELL_COMMANDS))
+PRINT_OK = $(call COLOR_PRINT,'\033[0;32m',OK,"\n")
+PRINT_FAILED = $(call COLOR_PRINT,'\033[0;31m',FAILED,"\n")
 
 ifneq (,$(filter test%,$(MAKECMDGOALS)))
    MAKEFLAGS += -k
@@ -60,21 +25,16 @@ 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); \
-   if [ "$$3" = 0 ]; \
-   then $(PRINT_OK); else $(PRINT_FAILED); cat $(1).stderr; fi; \
-   rm -f $(1).stderr; exit $$3
+   if ($(2) ./$(1) -no-vis $(4) > /dev/null); \
+   then $(PRINT_OK); else $(PRINT_FAILED); exit 1; fi
 
 # Test runs of the examples/miniapps - check exit code and if a file exists
 mfem-test-file = \
    printf "   $(3) [$(2) $(1) ... ]: "; \
-   $(call $(TIMEFUN),$(TIMECMD),$(2) ./$(1) -no-vis > $(1).stderr 2>&1); \
-   if [ "$$3" = 0 ] && [ -e $(4) ]; \
-   then $(PRINT_OK); else $(PRINT_FAILED); cat $(1).stderr; fi; \
-   rm -f $(1).stderr; exit $$3
+   if ($(2) ./$(1) -no-vis > /dev/null) && [ -e $(4) ]; \
+   then $(PRINT_OK); else $(PRINT_FAILED); exit 1; fi
 
-.PHONY: test test-par-YES test-par-NO test-ser test-par test-clean test-print
+.PHONY: test test-par-YES test-par-NO
 
 # What sets of tests to run in serial and parallel
 test-par-YES: $(PAR_$(MFEM_TESTS):=-test-par) $(SEQ_$(MFEM_TESTS):=-test-seq)
@@ -82,12 +42,3 @@ 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-clean: ; @rm -f *.stderr
-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)
-.PHONY: $(PAR_$(MFEM_TESTS)) $(SEQ_$(MFEM_TESTS))
-endif
-
-clean-exec: test-clean

data/beam-quad-amr.mesh

@@ -1,122 +0,0 @@
-MFEM mesh v1.1
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-#
-
-dimension
-2
-
-elements
-17
-1 3 0 23 30 26
-1 3 26 30 25 21
-1 3 30 24 22 25
-1 3 23 18 24 30
-1 3 18 1 19 22
-1 3 22 19 10 20
-1 3 31 27 20 28
-1 3 25 22 27 31
-1 3 21 25 31 29
-1 3 29 31 28 9
-1 3 1 2 11 10
-1 3 2 3 12 11
-1 3 3 4 13 12
-2 3 4 5 14 13
-2 3 5 6 15 14
-2 3 6 7 16 15
-2 3 7 8 17 16
-
-boundary
-25
-3 1 0 23
-1 1 26 0
-1 1 21 26
-3 1 23 18
-3 1 18 1
-3 1 10 20
-3 1 20 28
-1 1 29 21
-3 1 28 9
-1 1 9 29
-3 1 1 2
-3 1 11 10
-3 1 2 3
-3 1 12 11
-3 1 3 4
-3 1 13 12
-3 1 4 5
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-3 1 5 6
-3 1 15 14
-3 1 6 7
-3 1 16 15
-3 1 7 8
-2 1 8 17
-3 1 17 16
-
-vertex_parents
-14
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-24 18 22
-25 21 22
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-30 23 25
-31 25 28
-
-coarse_elements
-3
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-3 8 7 6 9
-3 17 4 5 18
-
-vertices
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-0 0
-1 0
-2 0
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-0.25 0
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-0.25 0.5
-0 0.25
-0.5 0.75
-0.25 1
-0 0.75
-0.25 0.25
-0.25 0.75

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
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-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
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-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
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-6 7 16 25 8 17 26
-CELL_TYPES 8
-13
-13
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-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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-15 3 15 14 23 24
-16 2 15 25 16
-16 2 25 15 24
-17 3 5 2 11 14
-18 3 3 0 9 12
-19 3 11 8 17 20
-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

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-1.0506786 -0.31289331 0.15076584
-0.81390971 -0.24238325 0.096279082

data/toroid-wedge.mesh

@@ -1,236 +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
-6
-1 6 0 1 2 3 4 5
-1 6 3 4 5 6 7 8
-1 6 6 7 8 9 10 11
-1 6 9 10 11 12 13 14
-1 6 12 13 14 15 16 17
-1 6 15 16 17 0 1 2
-
-boundary
-18
-1 3 0 1 4 3
-1 3 1 2 5 4
-1 3 2 0 3 5
-1 3 3 4 7 6
-1 3 4 5 8 7
-1 3 5 3 6 8
-1 3 6 7 10 9
-1 3 7 8 11 10
-1 3 8 6 9 11
-1 3 9 10 13 12
-1 3 10 11 14 13
-1 3 11 9 12 14
-1 3 12 13 16 15
-1 3 13 14 17 16
-1 3 14 12 15 17
-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
-
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-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
--0.6 1.0392305 -0.15491933
--0.51708204 0.89561236 -0.25066475
--0.38291796 0.66323336 -0.095745414
--0.51708204 0.89561236 0.25066475
--0.38291796 0.66323336 0.095745414
-0.21049196 0.88243173 0.38908379
--0.25356098 1.0629872 0.38908379
-0.32097654 1.3456091 -0.11416557
--0.29944203 1.2553313 -0.27491822
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--0.1430764 0.59980988 -0.11416557
--1.2341641 6.9922046e-16 -0.095745414
--0.96583592 -1.1684711e-15 -0.25066475
--0.8 4.5324311e-16 -0.15491933
--0.8 9.7971744e-17 0.15491933
--1.2341641 -3.9693744e-16 0.095745414
--0.96583592 -1.5973885e-15 0.25066475
--0.93742781 0.88699007 0.27491822
--1.3258199 0.3948307 0.11416557
--0.79379344 0.75108386 -0.38908379
--0.86945428 0.25892449 -0.38908379
--0.44791239 0.42381273 0.11416557
--0.67993886 0.20248658 0.27491822
--0.51708204 -0.89561236 -0.25066475
--0.38291796 -0.66323336 -0.095745414
--0.38291796 -0.66323336 0.095745414
--0.51708204 -0.89561236 0.25066475
--0.6 -1.0392305 -0.15491933
--0.6 -1.0392305 0.15491933
--1.3258199 -0.3948307 -0.11416557
--0.93742781 -0.88699007 -0.27491822
--0.67993886 -0.20248658 -0.27491822
--0.44791239 -0.42381273 -0.11416557
--0.86945428 -0.25892449 0.38908379
--0.79379344 -0.75108386 0.38908379
-0.4 -0.69282032 -0.15491933
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-0.48291796 -0.83643844 0.25066475
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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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-1 2.4196059e-15 -1.3788671e-16
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-0.76950592 0.22915975 0.15859651
-1.0583527 0.31517866 0.23048728
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-0.86954463 0.8227593 0.15859651
-1.1844891 0.35274221 0.091392579
-1.0997352 0.32750241 -0.20555815
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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
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--0.1862948 0.78099155 -0.15859651
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--0.17361359 0.72782894 0.024929133
--0.22302379 0.93496814 0.24998909
--1 -1.2098029e-15 1.3788671e-16
--0.89772824 0.84942651 0.091392579
--0.833493 0.78864741 -0.20555815
--1.1996835 0.35726714 -0.024929133
--0.99559063 0.29648804 -0.24998909
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--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
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--0.85845599 -0.25564918 -0.23048728
--0.80212907 -0.758971 -0.23048728
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--0.73231963 -0.21808563 -0.091392579
--0.8170735 -0.24332543 0.20555815
--0.54351156 -0.51426825 0.024929133
--0.69819427 -0.66062834 0.24998909
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--1.1996835 -0.35726714 0.024929133
--0.833493 -0.78864741 0.20555815
--0.89772824 -0.84942651 -0.091392579
-0.5 -0.8660254 -5.1344633e-17
--0.22302379 -0.93496814 -0.24998909
--0.17361359 -0.72782894 -0.024929133
-0.19781075 -0.82926913 -0.20555815
-0.17729212 -0.74325022 0.091392579
--0.1862948 -0.78099155 0.15859651
--0.25622363 -1.0741497 0.23048728
-0.20782931 -0.87126929 0.23048728
-0.27775814 -1.1644274 0.15859651
--0.28676082 -1.2021687 0.091392579
--0.26624219 -1.1161498 -0.20555815
-0.29043935 -1.21759 -0.024929133
-0.24102914 -1.0104508 -0.24998909
-0.55502751 -0.52516459 -0.091392579
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-0.92121806 -0.2743398 0.24998909
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-1.0997352 -0.32750241 0.20555815
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-0.95840435 0.28541392 -1.3795119e-16
-0.72637788 0.68729555 -1.1412456e-16
-0.23202647 0.97270947 -5.1760042e-17
--0.23202647 0.97270947 1.2226691e-17
--0.72637788 0.68729555 8.6191148e-17
--0.95840435 0.28541392 1.2635125e-16
--0.95840435 -0.28541392 1.3795119e-16
--0.72637788 -0.68729555 1.1412456e-16
--0.23202647 -0.97270947 5.1760042e-17
-0.23202647 -0.97270947 -1.2226691e-17
-0.72637788 -0.68729555 -8.6191148e-17
-0.95840435 -0.28541392 -1.2635125e-16

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         = v3.4.1
+PROJECT_NUMBER         = v3.3
 
 # 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
@@ -140,7 +140,7 @@ INLINE_INHERITED_MEMB  = NO
 # shortest path that makes the file name unique will be used
 # The default value is: YES.
 
-FULL_PATH_NAMES        = YES
+FULL_PATH_NAMES        = NO
 
 # The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
 # Stripping is only done if one of the specified strings matches the left-hand
@@ -152,7 +152,7 @@ FULL_PATH_NAMES        = YES
 # will be relative from the directory where doxygen is started.
 # This tag requires that the tag FULL_PATH_NAMES is set to YES.
 
-STRIP_FROM_PATH        = @MFEM_SOURCE_DIR@
+STRIP_FROM_PATH        =
 
 # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
 # path mentioned in the documentation of a class, which tells the reader which
@@ -767,12 +767,10 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/fem \
                          @MFEM_SOURCE_DIR@/examples \
                          @MFEM_SOURCE_DIR@/examples/petsc \
-                         @MFEM_SOURCE_DIR@/examples/pumi \
                          @MFEM_SOURCE_DIR@/examples/sundials \
                          @MFEM_SOURCE_DIR@/miniapps/common \
                          @MFEM_SOURCE_DIR@/miniapps/meshing \
                          @MFEM_SOURCE_DIR@/miniapps/tools \
-                         @MFEM_SOURCE_DIR@/miniapps/nurbs \
                          @MFEM_SOURCE_DIR@/miniapps/electromagnetics \
                          @MFEM_SOURCE_DIR@/miniapps/performance
 
@@ -810,8 +808,7 @@ RECURSIVE              = NO
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = @MFEM_SOURCE_DIR@/config/_config.hpp \
-                         @MFEM_SOURCE_DIR@/config/get_hypre_version.cpp
+EXCLUDE                =
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -1443,7 +1440,7 @@ FORMULA_TRANSPARENT    = YES
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = YES
+USE_MATHJAX            = NO
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:
@@ -1466,14 +1463,14 @@ MATHJAX_FORMAT         = HTML-CSS
 # The default value is: http://cdn.mathjax.org/mathjax/latest.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_RELPATH        = https://cdn.llnl.gov/mathjax/2.7.2
+MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example
 # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_EXTENSIONS     = TeX/AMSmath TeX/AMSsymbols
+MATHJAX_EXTENSIONS     =
 
 # The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
 # of code that will be used on startup of the MathJax code. See the MathJax site

doc/CodeDocumentation.dox

@@ -36,8 +36,8 @@ namespace mfem {
  * - HypreSolver and other \link hypre.hpp hypre classes\endlink
  *
  * <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
+ * - <a class="el" href="ex1_8cpp_source.html">Example 1</a>: nodal H1 FEM for the Laplace problem
+ * - <a class="el" href="ex1p_8cpp_source.html">Example 1p</a>: parallel nodal H1 FEM for the Laplace problem
  * - <a class="el" href="ex2_8cpp_source.html">Example 2</a>: vector FEM for linear elasticity
  * - <a class="el" href="ex2p_8cpp_source.html">Example 2p</a>: parallel vector FEM for linear elasticity
  * - <a class="el" href="ex3_8cpp_source.html">Example 3</a>: Nedelec H(curl) FEM for the definite Maxwell problem
@@ -56,7 +56,7 @@ namespace mfem {
  * - <a class="el" href="ex9p_8cpp_source.html">Example 9p</a>: parallel Discontinuous Galerkin (DG) time-dependent advection
  * - <a class="el" href="ex10_8cpp_source.html">Example 10</a>: time-dependent implicit nonlinear elasticity
  * - <a class="el" href="ex10p_8cpp_source.html">Example 10p</a>: parallel time-dependent implicit nonlinear elasticity
- * - <a class="el" href="examples_2ex11p_8cpp_source.html">Example 11p</a>: parallel Laplace eigensolver
+ * - <a class="el" href="ex11p_8cpp_source.html">Example 11p</a>: parallel Laplace eigensolver
  * - <a class="el" href="ex12p_8cpp_source.html">Example 12p</a>: parallel linear elasticity eigensolver
  * - <a class="el" href="ex13p_8cpp_source.html">Example 13p</a>: parallel Maxwell eigensolver
  * - <a class="el" href="ex14_8cpp_source.html">Example 14</a>: Discontinuous Galerkin (DG) for the Laplace problem
@@ -67,24 +67,14 @@ namespace mfem {
  * - <a class="el" href="ex16p_8cpp_source.html">Example 16p</a>: parallel time-dependent nonlinear heat equation
  * - <a class="el" href="ex17_8cpp_source.html">Example 17</a>: Discontinuous Galerkin (DG) for linear elasticity
  * - <a class="el" href="ex17p_8cpp_source.html">Example 17p</a>: parallel Discontinuous Galerkin (DG) for linear elasticity
- * - <a class="el" href="ex18_8cpp_source.html">Example 18</a>: Discontinuous Galerkin (DG) for the Euler equations
- * - <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="ex22_8cpp_source.html">Example 22</a>: adaptive mesh refinement for linear elasticity
- * - <a class="el" href="ex22p_8cpp_source.html">Example 22p</a>: parallel adaptive mesh refinement for linear elasticity
  *
  * <H4>SUNDIALS Examples</H4>
  * - Variants of Examples
  *   <a class="el" href="sundials_2ex9_8cpp_source.html">9</a>,
  *   <a class="el" href="sundials_2ex9p_8cpp_source.html">9p</a>,
  *   <a class="el" href="sundials_2ex10_8cpp_source.html">10</a>,
- *   <a class="el" href="sundials_2ex10p_8cpp_source.html">10p</a>,
- *   <a class="el" href="sundials_2ex16_8cpp_source.html">16</a>,
  *   and
- *   <a class="el" href="sundials_2ex16p_8cpp_source.html">16p</a>
+ *   <a class="el" class="el" href="sundials_2ex10p_8cpp_source.html">10p</a>
  *   demonstrating the use of MFEM's \link sundials.hpp SUNDIALS classes\endlink
  *
  * <H4>PETSc Examples</H4>
@@ -100,31 +90,14 @@ namespace mfem {
  *   <a class="el" href="petsc_2ex10p_8cpp_source.html">10p</a>
  *   demonstrating the use of MFEM's \link petsc.hpp PETSc classes\endlink
  *
- * <H4>PUMI Examples</H4>
- * - Variants of Examples
- *   <a class="el" href="examples_2pumi_2ex1_8cpp_source.html">1</a>,
- *   <a class="el" href="examples_2pumi_2ex1p_8cpp_source.html">1p</a>,
- *   <a class="el" href="pumi_2ex2_8cpp_source.html">2</a>,
- *   and
- *   <a class="el" href="pumi_2ex6p_8cpp_source.html">6p</a>
- *   demonstrating the use of MFEM's \link pumi.hpp PUMI 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
- * - <a class="el" href="maxwell_8cpp_source.html">Maxwell</a>: simple transient full-wave electromagnetics simulation code
  * - <a class="el" href="joule_8cpp_source.html">Joule</a>: transient magnetics and Joule heating miniapp
  * - <a class="el" href="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="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="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 diffirent 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="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

@@ -10,17 +10,17 @@
 # Software Foundation) version 2.1 dated February 1999.
 
 MFEM_DIR ?= ..
-DOXYGEN_CONF = CodeDocumentation.conf
+DOXYGEN_CONG = CodeDocumentation.conf
 
 # doxygen uses: graphviz, latex
-html: $(DOXYGEN_CONF)
-	doxygen $(DOXYGEN_CONF)
+html: $(DOXYGEN_CONG)
+	doxygen $(DOXYGEN_CONG)
 	rm -f CodeDocumentation.html
 	ln -s CodeDocumentation/html/index.html CodeDocumentation.html
 
 clean:
-	rm -rf $(DOXYGEN_CONF) CodeDocumentation CodeDocumentation.html *~
+	rm -rf $(DOXYGEN_CONG) CodeDocumentation CodeDocumentation.html *~
 
-$(DOXYGEN_CONF): $(MFEM_DIR)/doc/$(DOXYGEN_CONF).in
+$(DOXYGEN_CONG): $(MFEM_DIR)/doc/$(DOXYGEN_CONG).in
 	sed -e 's%@MFEM_SOURCE_DIR@%$(MFEM_DIR)%g' $(<) \
-	  > $(DOXYGEN_CONF)
+	  > $(DOXYGEN_CONG)

examples/CMakeLists.txt

@@ -24,11 +24,6 @@ list(APPEND ALL_EXE_SRCS
   ex15.cpp
   ex16.cpp
   ex17.cpp
-  ex18.cpp
-  ex19.cpp
-  ex20.cpp
-  ex21.cpp
-  ex22.cpp
   )
 
 if (MFEM_USE_MPI)
@@ -50,16 +45,11 @@ if (MFEM_USE_MPI)
     ex15p.cpp
     ex16p.cpp
     ex17p.cpp
-    ex18p.cpp
-    ex19p.cpp
-    ex20p.cpp
-    ex21p.cpp
-    ex22p.cpp
     )
 endif()
 
 # Include the source directory where mfem.hpp and mfem-performance.hpp are.
-include_directories(BEFORE ${PROJECT_BINARY_DIR})
+include_directories(${PROJECT_BINARY_DIR})
 
 # Add one executable per cpp file
 add_mfem_examples(ALL_EXE_SRCS)
@@ -69,6 +59,8 @@ foreach(SRC_FILE ${ALL_EXE_SRCS})
   get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
   string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
 
+  string(FIND ${TEST_NAME} "p" is_parallel_test)
+
   set(THIS_TEST_OPTIONS "-no-vis")
   if (${TEST_NAME} MATCHES "ex10p*")
     list(APPEND THIS_TEST_OPTIONS "-tf" "5")
@@ -76,38 +68,19 @@ foreach(SRC_FILE ${ALL_EXE_SRCS})
     list(APPEND THIS_TEST_OPTIONS "-e" "1")
   endif()
 
-  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+  if (is_parallel_test EQUAL -1)
     add_test(NAME ${TEST_NAME}_ser
       COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
   else()
     add_test(NAME ${TEST_NAME}_np=4
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4
       ${MPIEXEC_PREFLAGS}
       $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
       ${MPIEXEC_POSTFLAGS})
   endif()
 endforeach()
 
-# If STRUMPACK is enabled, add a test run that uses it.
-if (MFEM_USE_STRUMPACK)
-  add_test(NAME ex11p_strumpack_np=4
-    COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-    ${MPIEXEC_PREFLAGS}
-    $<TARGET_FILE:ex11p> "-no-vis" "--strumpack"
-    ${MPIEXEC_POSTFLAGS})
-endif()
-
-# Include the examples/sundials directory if SUNDIALS is enabled.
-if (MFEM_USE_SUNDIALS)
-  add_subdirectory(sundials)
-endif()
-
-# Include the examples/petsc directory if PETSc is enabled.
-if (MFEM_USE_PETSC)
-  add_subdirectory(petsc)
-endif()
-
-# Include the examples/pumi directory if PUMI is enabled
-if (MFEM_USE_PUMI)
-  add_subdirectory(pumi)
-endif()
+# Include the examples/sundials directory.
+add_subdirectory(sundials)
+# Include the examples/petsc directory.
+add_subdirectory(petsc)

examples/ex1.cpp

@@ -4,18 +4,13 @@
 //
 // Sample runs:  ex1 -m ../data/square-disc.mesh
 //               ex1 -m ../data/star.mesh
-//               ex1 -m ../data/star-mixed.mesh
 //               ex1 -m ../data/escher.mesh
 //               ex1 -m ../data/fichera.mesh
-//               ex1 -m ../data/fichera-mixed.mesh
-//               ex1 -m ../data/toroid-wedge.mesh
 //               ex1 -m ../data/square-disc-p2.vtk -o 2
 //               ex1 -m ../data/square-disc-p3.mesh -o 3
 //               ex1 -m ../data/square-disc-nurbs.mesh -o -1
-//               ex1 -m ../data/star-mixed-p2.mesh -o 2
 //               ex1 -m ../data/disc-nurbs.mesh -o -1
 //               ex1 -m ../data/pipe-nurbs.mesh -o -1
-//               ex1 -m ../data/fichera-mixed-p2.mesh -o 2
 //               ex1 -m ../data/star-surf.mesh
 //               ex1 -m ../data/square-disc-surf.mesh
 //               ex1 -m ../data/inline-segment.mesh
@@ -25,14 +20,6 @@
 //               ex1 -m ../data/mobius-strip.mesh
 //               ex1 -m ../data/mobius-strip.mesh -o -1 -sc
 //
-// Device sample runs:
-//             > ex1 -pa -d cuda
-//             > ex1 -pa -d raja-cuda
-//             > ex1 -pa -d occa-cuda
-//             > ex1 -pa -d raja-omp
-//             > ex1 -pa -d occa-omp
-//             > ex1 -m ../data/beam-hex.mesh -pa -d cuda
-//
 // Description:  This example code demonstrates the use of MFEM to define a
 //               simple finite element discretization of the Laplace problem
 //               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
@@ -61,9 +48,7 @@ int main(int argc, char *argv[])
    const char *mesh_file = "../data/star.mesh";
    int order = 1;
    bool static_cond = false;
-   bool pa = false;
-   const char *device = "cpu";
-   bool visualization = true;
+   bool visualization = 1;
 
    OptionsParser args(argc, argv);
    args.AddOption(&mesh_file, "-m", "--mesh",
@@ -73,10 +58,6 @@ int main(int argc, char *argv[])
                   " isoparametric space.");
    args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
                   "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -148,65 +129,48 @@ int main(int argc, char *argv[])
    b->AddDomainIntegrator(new DomainLFIntegrator(one));
    b->Assemble();
 
-   // 7. Set device config parameters from the command line options and switch
-   //    to working on the device.
-   Device::Configure(device);
-   Device::Print();
-   Device::Enable();
-
-   // 8. Define the solution vector x as a finite element grid function
+   // 7. Define the solution vector x as a finite element grid function
    //    corresponding to fespace. Initialize x with initial guess of zero,
    //    which satisfies the boundary conditions.
    GridFunction x(fespace);
    x = 0.0;
 
-   // 9. Set up the bilinear form a(.,.) on the finite element space
+   // 8. Set up the bilinear form a(.,.) on the finite element space
    //    corresponding to the Laplacian operator -Delta, by adding the Diffusion
    //    domain integrator.
    BilinearForm *a = new BilinearForm(fespace);
-   if (pa) { a->SetAssemblyLevel(AssemblyLevel::PARTIAL); }
    a->AddDomainIntegrator(new DiffusionIntegrator(one));
 
-   // 10. Assemble the bilinear form and the corresponding linear system,
-   //     applying any necessary transformations such as: eliminating boundary
-   //     conditions, applying conforming constraints for non-conforming AMR,
-   //     static condensation, etc.
+   // 9. Assemble the bilinear form and the corresponding linear system,
+   //    applying any necessary transformations such as: eliminating boundary
+   //    conditions, applying conforming constraints for non-conforming AMR,
+   //    static condensation, etc.
    if (static_cond) { a->EnableStaticCondensation(); }
    a->Assemble();
 
-   OperatorPtr A;
+   SparseMatrix A;
    Vector B, X;
    a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
 
-   cout << "Size of linear system: " << A->Height() << endl;
+   cout << "Size of linear system: " << A.Height() << endl;
 
-   // 11. Solve the linear system A X = B.
-   if (!pa)
-   {
 #ifndef MFEM_USE_SUITESPARSE
-      // Use a simple symmetric Gauss-Seidel preconditioner with PCG.
-      GSSmoother M((SparseMatrix&)(*A));
-      PCG(*A, M, B, X, 1, 200, 1e-12, 0.0);
+   // 10. Define a simple symmetric Gauss-Seidel preconditioner and use it to
+   //     solve the system A X = B with PCG.
+   GSSmoother M(A);
+   PCG(A, M, B, X, 1, 200, 1e-12, 0.0);
 #else
-      // If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
-      UMFPackSolver umf_solver;
-      umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-      umf_solver.SetOperator(*A);
-      umf_solver.Mult(B, X);
+   // 10. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
+   UMFPackSolver umf_solver;
+   umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
+   umf_solver.SetOperator(A);
+   umf_solver.Mult(B, X);
 #endif
-   }
-   else // No preconditioning for now in partial assembly mode.
-   {
-      CG(*A, B, X, 1, 2000, 1e-12, 0.0);
-   }
 
-   // 12. Recover the solution as a finite element grid function.
+   // 11. Recover the solution as a finite element grid function.
    a->RecoverFEMSolution(X, *b, x);
 
-   // 13. Switch back to the host.
-   Device::Disable();
-
-   // 14. Save the refined mesh and the solution. This output can be viewed later
+   // 12. Save the refined mesh and the solution. This output can be viewed later
    //     using GLVis: "glvis -m refined.mesh -g sol.gf".
    ofstream mesh_ofs("refined.mesh");
    mesh_ofs.precision(8);
@@ -215,7 +179,7 @@ int main(int argc, char *argv[])
    sol_ofs.precision(8);
    x.Save(sol_ofs);
 
-   // 15. Send the solution by socket to a GLVis server.
+   // 13. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       char vishost[] = "localhost";
@@ -225,7 +189,7 @@ int main(int argc, char *argv[])
       sol_sock << "solution\n" << *mesh << x << flush;
    }
 
-   // 16. Free the used memory.
+   // 14. Free the used memory.
    delete a;
    delete b;
    delete fespace;

examples/ex10.cpp

@@ -7,10 +7,8 @@
 //    ex10 -m ../data/beam-tri.mesh -s 3 -r 2 -o 2 -dt 3
 //    ex10 -m ../data/beam-hex.mesh -s 2 -r 1 -o 2 -dt 3
 //    ex10 -m ../data/beam-tet.mesh -s 2 -r 1 -o 2 -dt 3
-//    ex10 -m ../data/beam-wedge.mesh -s 2 -r 1 -o 2 -dt 3
 //    ex10 -m ../data/beam-quad.mesh -s 14 -r 2 -o 2 -dt 0.03 -vs 20
 //    ex10 -m ../data/beam-hex.mesh -s 14 -r 1 -o 2 -dt 0.05 -vs 20
-//    ex10 -m ../data/beam-quad-amr.mesh -s 3 -r 2 -o 2 -dt 3
 //
 // Description:  This examples solves a time dependent nonlinear elasticity
 //               problem of the form dv/dt = H(x) + S v, dx/dt = v, where H is a
@@ -92,9 +90,9 @@ public:
        This is the only requirement for high-order SDIRK implicit integration.*/
    virtual void ImplicitSolve(const double dt, const Vector &x, Vector &k);
 
-   double ElasticEnergy(const Vector &x) const;
-   double KineticEnergy(const Vector &v) const;
-   void GetElasticEnergyDensity(const GridFunction &x, GridFunction &w) const;
+   double ElasticEnergy(Vector &x) const;
+   double KineticEnergy(Vector &v) const;
+   void GetElasticEnergyDensity(GridFunction &x, GridFunction &w) const;
 
    virtual ~HyperelasticOperator();
 };
@@ -134,12 +132,12 @@ public:
 class ElasticEnergyCoefficient : public Coefficient
 {
 private:
-   HyperelasticModel  &model;
-   const GridFunction &x;
-   DenseMatrix         J;
+   HyperelasticModel &model;
+   GridFunction      &x;
+   DenseMatrix        J;
 
 public:
-   ElasticEnergyCoefficient(HyperelasticModel &m, const GridFunction &x_)
+   ElasticEnergyCoefficient(HyperelasticModel &m, GridFunction &x_)
       : model(m), x(x_) { }
    virtual double Eval(ElementTransformation &T, const IntegrationPoint &ip);
    virtual ~ElasticEnergyCoefficient() { }
@@ -223,14 +221,12 @@ int main(int argc, char *argv[])
       case 12: ode_solver = new RK2Solver(0.5); break; // midpoint method
       case 13: ode_solver = new RK3SSPSolver; break;
       case 14: ode_solver = new RK4Solver; break;
-      case 15: ode_solver = new GeneralizedAlphaSolver(0.5); break;
       // Implicit A-stable methods (not L-stable)
       case 22: ode_solver = new ImplicitMidpointSolver; break;
       case 23: ode_solver = new SDIRK23Solver; break;
       case 24: ode_solver = new SDIRK34Solver; break;
       default:
          cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
-         delete mesh;
          return 3;
    }
 
@@ -251,7 +247,7 @@ int main(int argc, char *argv[])
    H1_FECollection fe_coll(order, dim);
    FiniteElementSpace fespace(mesh, &fe_coll, dim);
 
-   int fe_size = fespace.GetTrueVSize();
+   int fe_size = fespace.GetVSize();
    cout << "Number of velocity/deformation unknowns: " << fe_size << endl;
    Array<int> fe_offset(3);
    fe_offset[0] = 0;
@@ -260,8 +256,8 @@ int main(int argc, char *argv[])
 
    BlockVector vx(fe_offset);
    GridFunction v, x;
-   v.MakeTRef(&fespace, vx.GetBlock(0), 0);
-   x.MakeTRef(&fespace, vx.GetBlock(1), 0);
+   v.MakeRef(&fespace, vx.GetBlock(0), 0);
+   x.MakeRef(&fespace, vx.GetBlock(1), 0);
 
    GridFunction x_ref(&fespace);
    mesh->GetNodes(x_ref);
@@ -274,10 +270,8 @@ int main(int argc, char *argv[])
    //    a beam-like mesh (see description above).
    VectorFunctionCoefficient velo(dim, InitialVelocity);
    v.ProjectCoefficient(velo);
-   v.SetTrueVector();
    VectorFunctionCoefficient deform(dim, InitialDeformation);
    x.ProjectCoefficient(deform);
-   x.SetTrueVector();
 
    Array<int> ess_bdr(fespace.GetMesh()->bdr_attributes.Max());
    ess_bdr = 0;
@@ -294,7 +288,6 @@ int main(int argc, char *argv[])
       int  visport   = 19916;
       vis_v.open(vishost, visport);
       vis_v.precision(8);
-      v.SetFromTrueVector(); x.SetFromTrueVector();
       visualize(vis_v, mesh, &x, &v, "Velocity", true);
       vis_w.open(vishost, visport);
       if (vis_w)
@@ -305,8 +298,8 @@ int main(int argc, char *argv[])
       }
    }
 
-   double ee0 = oper.ElasticEnergy(x.GetTrueVector());
-   double ke0 = oper.KineticEnergy(v.GetTrueVector());
+   double ee0 = oper.ElasticEnergy(x);
+   double ke0 = oper.KineticEnergy(v);
    cout << "initial elastic energy (EE) = " << ee0 << endl;
    cout << "initial kinetic energy (KE) = " << ke0 << endl;
    cout << "initial   total energy (TE) = " << (ee0 + ke0) << endl;
@@ -328,15 +321,14 @@ int main(int argc, char *argv[])
 
       if (last_step || (ti % vis_steps) == 0)
       {
-         double ee = oper.ElasticEnergy(x.GetTrueVector());
-         double ke = oper.KineticEnergy(v.GetTrueVector());
+         double ee = oper.ElasticEnergy(x);
+         double ke = oper.KineticEnergy(v);
 
          cout << "step " << ti << ", t = " << t << ", EE = " << ee << ", KE = "
               << ke << ", ΔTE = " << (ee+ke)-(ee0+ke0) << endl;
 
          if (visualization)
          {
-            v.SetFromTrueVector(); x.SetFromTrueVector();
             visualize(vis_v, mesh, &x, &v);
             if (vis_w)
             {
@@ -349,7 +341,6 @@ int main(int argc, char *argv[])
 
    // 9. Save the displaced mesh, the velocity and elastic energy.
    {
-      v.SetFromTrueVector(); x.SetFromTrueVector();
       GridFunction *nodes = &x;
       int owns_nodes = 0;
       mesh->SwapNodes(nodes, owns_nodes);
@@ -450,7 +441,7 @@ ReducedSystemOperator::~ReducedSystemOperator()
 HyperelasticOperator::HyperelasticOperator(FiniteElementSpace &f,
                                            Array<int> &ess_bdr, double visc,
                                            double mu, double K)
-   : TimeDependentOperator(2*f.GetTrueVSize(), 0.0), fespace(f),
+   : TimeDependentOperator(2*f.GetVSize(), 0.0), fespace(f),
      M(&fespace), S(&fespace), H(&fespace),
      viscosity(visc), z(height/2)
 {
@@ -461,10 +452,8 @@ HyperelasticOperator::HyperelasticOperator(FiniteElementSpace &f,
    ConstantCoefficient rho0(ref_density);
    M.AddDomainIntegrator(new VectorMassIntegrator(rho0));
    M.Assemble(skip_zero_entries);
-   Array<int> ess_tdof_list;
-   fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   SparseMatrix tmp;
-   M.FormSystemMatrix(ess_tdof_list, tmp);
+   M.EliminateEssentialBC(ess_bdr);
+   M.Finalize(skip_zero_entries);
 
    M_solver.iterative_mode = false;
    M_solver.SetRelTol(rel_tol);
@@ -476,12 +465,13 @@ HyperelasticOperator::HyperelasticOperator(FiniteElementSpace &f,
 
    model = new NeoHookeanModel(mu, K);
    H.AddDomainIntegrator(new HyperelasticNLFIntegrator(model));
-   H.SetEssentialTrueDofs(ess_tdof_list);
+   H.SetEssentialBC(ess_bdr);
 
    ConstantCoefficient visc_coeff(viscosity);
    S.AddDomainIntegrator(new VectorDiffusionIntegrator(visc_coeff));
    S.Assemble(skip_zero_entries);
-   S.FormSystemMatrix(ess_tdof_list, tmp);
+   S.EliminateEssentialBC(ess_bdr);
+   S.Finalize(skip_zero_entries);
 
    reduced_oper = new ReducedSystemOperator(&M, &S, &H);
 
@@ -550,18 +540,18 @@ void HyperelasticOperator::ImplicitSolve(const double dt,
    add(v, dt, dv_dt, dx_dt);
 }
 
-double HyperelasticOperator::ElasticEnergy(const Vector &x) const
+double HyperelasticOperator::ElasticEnergy(Vector &x) const
 {
    return H.GetEnergy(x);
 }
 
-double HyperelasticOperator::KineticEnergy(const Vector &v) const
+double HyperelasticOperator::KineticEnergy(Vector &v) const
 {
    return 0.5*M.InnerProduct(v, v);
 }
 
 void HyperelasticOperator::GetElasticEnergyDensity(
-   const GridFunction &x, GridFunction &w) const
+   GridFunction &x, GridFunction &w) const
 {
    ElasticEnergyCoefficient w_coeff(*model, x);
    w.ProjectCoefficient(w_coeff);

examples/ex10p.cpp

@@ -7,10 +7,8 @@
 //    mpirun -np 4 ex10p -m ../data/beam-tri.mesh -s 3 -rs 2 -dt 3
 //    mpirun -np 4 ex10p -m ../data/beam-hex.mesh -s 2 -rs 1 -dt 3
 //    mpirun -np 4 ex10p -m ../data/beam-tet.mesh -s 2 -rs 1 -dt 3
-//    mpirun -np 4 ex10p -m ../data/beam-wedge.mesh -s 2 -rs 1 -dt 3
 //    mpirun -np 4 ex10p -m ../data/beam-quad.mesh -s 14 -rs 2 -dt 0.03 -vs 20
 //    mpirun -np 4 ex10p -m ../data/beam-hex.mesh -s 14 -rs 1 -dt 0.05 -vs 20
-//    mpirun -np 4 ex10p -m ../data/beam-quad-amr.mesh -s 3 -rs 2 -dt 3
 //
 // Description:  This examples solves a time dependent nonlinear elasticity
 //               problem of the form dv/dt = H(x) + S v, dx/dt = v, where H is a
@@ -59,7 +57,6 @@ class HyperelasticOperator : public TimeDependentOperator
 {
 protected:
    ParFiniteElementSpace &fespace;
-   Array<int> ess_tdof_list;
 
    ParBilinearForm M, S;
    ParNonlinearForm H;
@@ -94,10 +91,9 @@ public:
        This is the only requirement for high-order SDIRK implicit integration.*/
    virtual void ImplicitSolve(const double dt, const Vector &x, Vector &k);
 
-   double ElasticEnergy(const ParGridFunction &x) const;
-   double KineticEnergy(const ParGridFunction &v) const;
-   void GetElasticEnergyDensity(const ParGridFunction &x,
-                                ParGridFunction &w) const;
+   double ElasticEnergy(ParGridFunction &x) const;
+   double KineticEnergy(ParGridFunction &v) const;
+   void GetElasticEnergyDensity(ParGridFunction &x, ParGridFunction &w) const;
 
    virtual ~HyperelasticOperator();
 };
@@ -115,11 +111,10 @@ private:
    double dt;
    const Vector *v, *x;
    mutable Vector w, z;
-   const Array<int> &ess_tdof_list;
 
 public:
    ReducedSystemOperator(ParBilinearForm *M_, ParBilinearForm *S_,
-                         ParNonlinearForm *H_, const Array<int> &ess_tdof_list);
+                         ParNonlinearForm *H_);
 
    /// Set current dt, v, x values - needed to compute action and Jacobian.
    void SetParameters(double dt_, const Vector *v_, const Vector *x_);
@@ -139,12 +134,12 @@ public:
 class ElasticEnergyCoefficient : public Coefficient
 {
 private:
-   HyperelasticModel     &model;
-   const ParGridFunction &x;
-   DenseMatrix            J;
+   HyperelasticModel &model;
+   ParGridFunction   &x;
+   DenseMatrix        J;
 
 public:
-   ElasticEnergyCoefficient(HyperelasticModel &m, const ParGridFunction &x_)
+   ElasticEnergyCoefficient(HyperelasticModel &m, ParGridFunction &x_)
       : model(m), x(x_) { }
    virtual double Eval(ElementTransformation &T, const IntegrationPoint &ip);
    virtual ~ElasticEnergyCoefficient() { }
@@ -245,7 +240,6 @@ int main(int argc, char *argv[])
       case 12: ode_solver = new RK2Solver(0.5); break; // midpoint method
       case 13: ode_solver = new RK3SSPSolver; break;
       case 14: ode_solver = new RK4Solver; break;
-      case 15: ode_solver = new GeneralizedAlphaSolver(0.5); break;
       // Implicit A-stable methods (not L-stable)
       case 22: ode_solver = new ImplicitMidpointSolver; break;
       case 23: ode_solver = new SDIRK23Solver; break;
@@ -255,7 +249,6 @@ int main(int argc, char *argv[])
          {
             cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
          }
-         delete mesh;
          MPI_Finalize();
          return 3;
    }
@@ -299,9 +292,7 @@ int main(int argc, char *argv[])
    true_offset[2] = 2*true_size;
 
    BlockVector vx(true_offset);
-   ParGridFunction v_gf, x_gf;
-   v_gf.MakeTRef(&fespace, vx, true_offset[0]);
-   x_gf.MakeTRef(&fespace, vx, true_offset[1]);
+   ParGridFunction v_gf(&fespace), x_gf(&fespace);
 
    ParGridFunction x_ref(&fespace);
    pmesh->GetNodes(x_ref);
@@ -314,12 +305,11 @@ int main(int argc, char *argv[])
    //    boundary conditions on a beam-like mesh (see description above).
    VectorFunctionCoefficient velo(dim, InitialVelocity);
    v_gf.ProjectCoefficient(velo);
-   v_gf.SetTrueVector();
    VectorFunctionCoefficient deform(dim, InitialDeformation);
    x_gf.ProjectCoefficient(deform);
-   x_gf.SetTrueVector();
 
-   v_gf.SetFromTrueVector(); x_gf.SetFromTrueVector();
+   v_gf.GetTrueDofs(vx.GetBlock(0));
+   x_gf.GetTrueDofs(vx.GetBlock(1));
 
    Array<int> ess_bdr(fespace.GetMesh()->bdr_attributes.Max());
    ess_bdr = 0;
@@ -375,7 +365,8 @@ int main(int argc, char *argv[])
 
       if (last_step || (ti % vis_steps) == 0)
       {
-         v_gf.SetFromTrueVector(); x_gf.SetFromTrueVector();
+         v_gf.Distribute(vx.GetBlock(0));
+         x_gf.Distribute(vx.GetBlock(1));
 
          double ee = oper.ElasticEnergy(x_gf);
          double ke = oper.KineticEnergy(v_gf);
@@ -400,7 +391,6 @@ int main(int argc, char *argv[])
 
    // 11. Save the displaced mesh, the velocity and elastic energy.
    {
-      v_gf.SetFromTrueVector(); x_gf.SetFromTrueVector();
       GridFunction *nodes = &x_gf;
       int owns_nodes = 0;
       pmesh->SwapNodes(nodes, owns_nodes);
@@ -468,11 +458,9 @@ void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
 
 
 ReducedSystemOperator::ReducedSystemOperator(
-   ParBilinearForm *M_, ParBilinearForm *S_, ParNonlinearForm *H_,
-   const Array<int> &ess_tdof_list_)
+   ParBilinearForm *M_, ParBilinearForm *S_, ParNonlinearForm *H_)
    : Operator(M_->ParFESpace()->TrueVSize()), M(M_), S(S_), H(H_),
-     Jacobian(NULL), dt(0.0), v(NULL), x(NULL), w(height), z(height),
-     ess_tdof_list(ess_tdof_list_)
+     Jacobian(NULL), dt(0.0), v(NULL), x(NULL), w(height), z(height)
 { }
 
 void ReducedSystemOperator::SetParameters(double dt_, const Vector *v_,
@@ -489,7 +477,6 @@ void ReducedSystemOperator::Mult(const Vector &k, Vector &y) const
    H->Mult(z, y);
    M->TrueAddMult(k, y);
    S->TrueAddMult(w, y);
-   y.SetSubVector(ess_tdof_list, 0.0);
 }
 
 Operator &ReducedSystemOperator::GetGradient(const Vector &k) const
@@ -501,8 +488,6 @@ Operator &ReducedSystemOperator::GetGradient(const Vector &k) const
    localJ->Add(dt*dt, H->GetLocalGradient(z));
    Jacobian = M->ParallelAssemble(localJ);
    delete localJ;
-   HypreParMatrix *Je = Jacobian->EliminateRowsCols(ess_tdof_list);
-   delete Je;
    return *Jacobian;
 }
 
@@ -527,11 +512,9 @@ HyperelasticOperator::HyperelasticOperator(ParFiniteElementSpace &f,
    ConstantCoefficient rho0(ref_density);
    M.AddDomainIntegrator(new VectorMassIntegrator(rho0));
    M.Assemble(skip_zero_entries);
+   M.EliminateEssentialBC(ess_bdr);
    M.Finalize(skip_zero_entries);
    Mmat = M.ParallelAssemble();
-   fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   HypreParMatrix *Me = Mmat->EliminateRowsCols(ess_tdof_list);
-   delete Me;
 
    M_solver.iterative_mode = false;
    M_solver.SetRelTol(rel_tol);
@@ -544,14 +527,15 @@ HyperelasticOperator::HyperelasticOperator(ParFiniteElementSpace &f,
 
    model = new NeoHookeanModel(mu, K);
    H.AddDomainIntegrator(new HyperelasticNLFIntegrator(model));
-   H.SetEssentialTrueDofs(ess_tdof_list);
+   H.SetEssentialBC(ess_bdr);
 
    ConstantCoefficient visc_coeff(viscosity);
    S.AddDomainIntegrator(new VectorDiffusionIntegrator(visc_coeff));
    S.Assemble(skip_zero_entries);
+   S.EliminateEssentialBC(ess_bdr);
    S.Finalize(skip_zero_entries);
 
-   reduced_oper = new ReducedSystemOperator(&M, &S, &H, ess_tdof_list);
+   reduced_oper = new ReducedSystemOperator(&M, &S, &H);
 
    HypreSmoother *J_hypreSmoother = new HypreSmoother;
    J_hypreSmoother->SetType(HypreSmoother::l1Jacobi);
@@ -588,7 +572,6 @@ void HyperelasticOperator::Mult(const Vector &vx, Vector &dvx_dt) const
    if (viscosity != 0.0)
    {
       S.TrueAddMult(v, z);
-      z.SetSubVector(ess_tdof_list, 0.0);
    }
    z.Neg(); // z = -z
    M_solver.Mult(z, dv_dt);
@@ -618,12 +601,12 @@ void HyperelasticOperator::ImplicitSolve(const double dt,
    add(v, dt, dv_dt, dx_dt);
 }
 
-double HyperelasticOperator::ElasticEnergy(const ParGridFunction &x) const
+double HyperelasticOperator::ElasticEnergy(ParGridFunction &x) const
 {
    return H.GetEnergy(x);
 }
 
-double HyperelasticOperator::KineticEnergy(const ParGridFunction &v) const
+double HyperelasticOperator::KineticEnergy(ParGridFunction &v) const
 {
    double loc_energy = 0.5*M.InnerProduct(v, v);
    double energy;
@@ -633,7 +616,7 @@ double HyperelasticOperator::KineticEnergy(const ParGridFunction &v) const
 }
 
 void HyperelasticOperator::GetElasticEnergyDensity(
-   const ParGridFunction &x, ParGridFunction &w) const
+   ParGridFunction &x, ParGridFunction &w) const
 {
    ElasticEnergyCoefficient w_coeff(*model, x);
    w.ProjectCoefficient(w_coeff);

examples/ex11p.cpp

@@ -4,11 +4,8 @@
 //
 // Sample runs:  mpirun -np 4 ex11p -m ../data/square-disc.mesh
 //               mpirun -np 4 ex11p -m ../data/star.mesh
-//               mpirun -np 4 ex11p -m ../data/star-mixed.mesh
 //               mpirun -np 4 ex11p -m ../data/escher.mesh
 //               mpirun -np 4 ex11p -m ../data/fichera.mesh
-//               mpirun -np 4 ex11p -m ../data/fichera-mixed.mesh
-//               mpirun -np 4 ex11p -m ../data/toroid-wedge.mesh -o 2
 //               mpirun -np 4 ex11p -m ../data/square-disc-p2.vtk -o 2
 //               mpirun -np 4 ex11p -m ../data/square-disc-p3.mesh -o 3
 //               mpirun -np 4 ex11p -m ../data/square-disc-nurbs.mesh -o -1
@@ -18,11 +15,6 @@
 //               mpirun -np 4 ex11p -m ../data/star-surf.mesh
 //               mpirun -np 4 ex11p -m ../data/square-disc-surf.mesh
 //               mpirun -np 4 ex11p -m ../data/inline-segment.mesh
-//               mpirun -np 4 ex11p -m ../data/inline-quad.mesh
-//               mpirun -np 4 ex11p -m ../data/inline-tri.mesh
-//               mpirun -np 4 ex11p -m ../data/inline-hex.mesh
-//               mpirun -np 4 ex11p -m ../data/inline-tet.mesh
-//               mpirun -np 4 ex11p -m ../data/inline-wedge.mesh -s 83
 //               mpirun -np 4 ex11p -m ../data/amr-quad.mesh
 //               mpirun -np 4 ex11p -m ../data/amr-hex.mesh
 //               mpirun -np 4 ex11p -m ../data/mobius-strip.mesh -n 8
@@ -40,9 +32,9 @@
 //
 //               The example highlights the use of the LOBPCG eigenvalue solver
 //               together with the BoomerAMG preconditioner in HYPRE, as well as
-//               optionally the SuperLU or STRUMPACK parallel direct solvers.
-//               Reusing a single GLVis visualization window for multiple
-//               eigenfunctions is also illustrated.
+//               optionally the SuperLU parallel direct solver. Reusing a single
+//               GLVis visualization window for multiple eigenfunctions is also
+//               illustrated.
 //
 //               We recommend viewing Example 1 before viewing this example.
 
@@ -69,7 +61,6 @@ int main(int argc, char *argv[])
    int nev = 5;
    int seed = 75;
    bool slu_solver  = false;
-   bool sp_solver = false;
    bool visualization = 1;
 
    OptionsParser args(argc, argv);
@@ -89,36 +80,19 @@ int main(int argc, char *argv[])
 #ifdef MFEM_USE_SUPERLU
    args.AddOption(&slu_solver, "-slu", "--superlu", "-no-slu",
                   "--no-superlu", "Use the SuperLU Solver.");
-#endif
-#ifdef MFEM_USE_STRUMPACK
-   args.AddOption(&sp_solver, "-sp", "--strumpack", "-no-sp",
-                  "--no-strumpack", "Use the STRUMPACK Solver.");
 #endif
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
    args.Parse();
-   if (slu_solver && sp_solver)
+   if (!args.Good())
    {
       if (myid == 0)
-         cout << "WARNING: Both SuperLU and STRUMPACK have been selected,"
-              << " please choose either one." << endl
-              << "         Defaulting to SuperLU." << endl;
-      sp_solver = false;
-   }
-   // The command line options are also passed to the STRUMPACK
-   // solver. So do not exit if some options are not recognized.
-   if (!sp_solver)
-   {
-      if (!args.Good())
       {
-         if (myid == 0)
-         {
-            args.PrintUsage(cout);
-         }
-         MPI_Finalize();
-         return 1;
+         args.PrintUsage(cout);
       }
+      MPI_Finalize();
+      return 1;
    }
    if (myid == 0)
    {
@@ -211,20 +185,12 @@ int main(int argc, char *argv[])
    HypreParMatrix *A = a->ParallelAssemble();
    HypreParMatrix *M = m->ParallelAssemble();
 
-#if defined(MFEM_USE_SUPERLU) || defined(MFEM_USE_STRUMPACK)
-   Operator * Arow = NULL;
 #ifdef MFEM_USE_SUPERLU
+   Operator * Arow = NULL;
    if (slu_solver)
    {
       Arow = new SuperLURowLocMatrix(*A);
    }
-#endif
-#ifdef MFEM_USE_STRUMPACK
-   if (sp_solver)
-   {
-      Arow = new STRUMPACKRowLocMatrix(*A);
-   }
-#endif
 #endif
 
    delete a;
@@ -234,41 +200,23 @@ int main(int argc, char *argv[])
    //    preconditioner for A to be used within the solver. Set the matrices
    //    which define the generalized eigenproblem A x = lambda M x.
    Solver * precond = NULL;
-   if (!slu_solver && !sp_solver)
+   if (!slu_solver)
    {
       HypreBoomerAMG * amg = new HypreBoomerAMG(*A);
       amg->SetPrintLevel(0);
       precond = amg;
    }
+#ifdef MFEM_USE_SUPERLU
    else
    {
-#ifdef MFEM_USE_SUPERLU
-      if (slu_solver)
-      {
-         SuperLUSolver * superlu = new SuperLUSolver(MPI_COMM_WORLD);
-         superlu->SetPrintStatistics(false);
-         superlu->SetSymmetricPattern(true);
-         superlu->SetColumnPermutation(superlu::PARMETIS);
-         superlu->SetOperator(*Arow);
-         precond = superlu;
-      }
-#endif
-#ifdef MFEM_USE_STRUMPACK
-      if (sp_solver)
-      {
-         STRUMPACKSolver * strumpack = new STRUMPACKSolver(argc, argv, MPI_COMM_WORLD);
-         strumpack->SetPrintFactorStatistics(true);
-         strumpack->SetPrintSolveStatistics(false);
-         strumpack->SetKrylovSolver(strumpack::KrylovSolver::DIRECT);
-         strumpack->SetReorderingStrategy(strumpack::ReorderingStrategy::METIS);
-         strumpack->DisableMatching();
-         strumpack->SetOperator(*Arow);
-         strumpack->SetFromCommandLine();
-         precond = strumpack;
-      }
-#endif
+      SuperLUSolver * superlu = new SuperLUSolver(MPI_COMM_WORLD);
+      superlu->SetPrintStatistics(false);
+      superlu->SetSymmetricPattern(true);
+      superlu->SetColumnPermutation(superlu::PARMETIS);
+      superlu->SetOperator(*Arow);
+      precond = superlu;
    }
-
+#endif
 
    HypreLOBPCG * lobpcg = new HypreLOBPCG(MPI_COMM_WORLD);
    lobpcg->SetNumModes(nev);
@@ -359,7 +307,7 @@ int main(int argc, char *argv[])
    delete precond;
    delete M;
    delete A;
-#if defined(MFEM_USE_SUPERLU) || defined(MFEM_USE_STRUMPACK)
+#ifdef MFEM_USE_SUPERLU
    delete Arow;
 #endif
 

examples/ex12p.cpp

@@ -2,16 +2,14 @@
 //
 // Compile with: make ex12p
 //
-// Sample runs:
-//    mpirun -np 4 ex12p -m ../data/beam-tri.mesh
-//    mpirun -np 4 ex12p -m ../data/beam-quad.mesh
-//    mpirun -np 4 ex12p -m ../data/beam-tet.mesh -s 79 -n 10 -o 2 -elast
-//    mpirun -np 4 ex12p -m ../data/beam-hex.mesh -s 3876
-//    mpirun -np 4 ex12p -m ../data/beam-wedge.mesh -s 79
-//    mpirun -np 4 ex12p -m ../data/beam-tri.mesh -s 3876 -o 2 -sys
-//    mpirun -np 4 ex12p -m ../data/beam-quad.mesh -s 4526 -n 6 -o 3 -elast
-//    mpirun -np 4 ex12p -m ../data/beam-quad-nurbs.mesh
-//    mpirun -np 4 ex12p -m ../data/beam-hex-nurbs.mesh
+// Sample runs:  mpirun -np 4 ex12p -m ../data/beam-tri.mesh
+//               mpirun -np 4 ex12p -m ../data/beam-quad.mesh
+//               mpirun -np 4 ex12p -m ../data/beam-tet.mesh -n 10 -o 2 -elast
+//               mpirun -np 4 ex12p -m ../data/beam-hex.mesh -s 3876
+//               mpirun -np 4 ex12p -m ../data/beam-tri.mesh -o 2 -sys
+//               mpirun -np 4 ex12p -m ../data/beam-quad.mesh -n 6 -o 3 -elast
+//               mpirun -np 4 ex12p -m ../data/beam-quad-nurbs.mesh
+//               mpirun -np 4 ex12p -m ../data/beam-hex-nurbs.mesh
 //
 // Description:  This example code solves the linear elasticity eigenvalue
 //               problem for a multi-material cantilever beam.
@@ -110,9 +108,9 @@ int main(int argc, char *argv[])
 
    // 4. Select the order of the finite element discretization space. For NURBS
    //    meshes, we increase the order by degree elevation.
-   if (mesh->NURBSext)
+   if (mesh->NURBSext && order > mesh->NURBSext->GetOrder())
    {
-      mesh->DegreeElevate(order, order);
+      mesh->DegreeElevate(order - mesh->NURBSext->GetOrder());
    }
 
    // 5. Refine the serial mesh on all processors to increase the resolution. In

examples/ex13p.cpp

@@ -110,7 +110,6 @@ int main(int argc, char *argv[])
    {
       pmesh->UniformRefinement();
    }
-   pmesh->ReorientTetMesh();
 
    // 6. Define a parallel finite element space on the parallel mesh. Here we
    //    use the Nedelec finite elements of the specified order.

examples/ex14.cpp

@@ -4,10 +4,8 @@
 //
 // Sample runs:  ex14 -m ../data/inline-quad.mesh -o 0
 //               ex14 -m ../data/star.mesh -r 4 -o 2
-//               ex14 -m ../data/star-mixed.mesh -r 4 -o 2
 //               ex14 -m ../data/escher.mesh -s 1
 //               ex14 -m ../data/fichera.mesh -s 1 -k 1
-//               ex14 -m ../data/fichera-mixed.mesh -s 1 -k 1
 //               ex14 -m ../data/square-disc-p2.vtk -r 3 -o 2
 //               ex14 -m ../data/square-disc-p3.mesh -r 2 -o 3
 //               ex14 -m ../data/square-disc-nurbs.mesh -o 1

examples/ex14p.cpp

@@ -4,10 +4,8 @@
 //
 // Sample runs:  mpirun -np 4 ex14p -m ../data/inline-quad.mesh -o 0
 //               mpirun -np 4 ex14p -m ../data/star.mesh -o 2
-//               mpirun -np 4 ex14p -m ../data/star-mixed.mesh -o 2
 //               mpirun -np 4 ex14p -m ../data/escher.mesh -s 1
 //               mpirun -np 4 ex14p -m ../data/fichera.mesh -s 1 -k 1
-//               mpirun -np 4 ex14p -m ../data/fichera-mixed.mesh -s 1 -k 1
 //               mpirun -np 4 ex14p -m ../data/square-disc-p2.vtk -o 2
 //               mpirun -np 4 ex14p -m ../data/square-disc-p3.mesh -o 3
 //               mpirun -np 4 ex14p -m ../data/square-disc-nurbs.mesh -o 1

examples/ex15.cpp

@@ -135,8 +135,6 @@ int main(int argc, char *argv[])
    {
       mesh.UniformRefinement();
    }
-   // Make sure tet-only meshes are marked for local refinement.
-   mesh.Finalize(true);
 
    // 4. All boundary attributes will be used for essential (Dirichlet) BC.
    MFEM_VERIFY(mesh.bdr_attributes.Size() > 0,

examples/ex15p.cpp

@@ -151,8 +151,6 @@ int main(int argc, char *argv[])
    {
       mesh->UniformRefinement();
    }
-   // Make sure tet-only meshes are marked for local refinement.
-   mesh->Finalize(true);
 
    // 5. Define a parallel mesh by partitioning the serial mesh.  Once the
    //    parallel mesh is defined, the serial mesh can be deleted.

examples/ex16.cpp

@@ -10,7 +10,6 @@
 //               ex16 -s 3 -a 0.5 -k 0.5 -o 4
 //               ex16 -s 14 -dt 1.0e-4 -tf 4.0e-2 -vs 40
 //               ex16 -m ../data/fichera-q2.mesh
-//               ex16 -m ../data/fichera-mixed.mesh
 //               ex16 -m ../data/escher.mesh
 //               ex16 -m ../data/beam-tet.mesh -tf 10 -dt 0.1
 //               ex16 -m ../data/amr-quad.mesh -o 4 -r 0
@@ -158,14 +157,12 @@ int main(int argc, char *argv[])
       case 12: ode_solver = new RK2Solver(0.5); break; // midpoint method
       case 13: ode_solver = new RK3SSPSolver; break;
       case 14: ode_solver = new RK4Solver; break;
-      case 15: ode_solver = new GeneralizedAlphaSolver(0.5); break;
       // Implicit A-stable methods (not L-stable)
       case 22: ode_solver = new ImplicitMidpointSolver; break;
       case 23: ode_solver = new SDIRK23Solver; break;
       case 24: ode_solver = new SDIRK34Solver; break;
       default:
          cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
-         delete mesh;
          return 3;
    }
 

examples/ex16p.cpp

@@ -1,4 +1,4 @@
-//                       MFEM Example 16 - Parallel Version
+//                                MFEM Example 16 - Parallel Version
 //
 // Compile with: make ex16p
 //
@@ -10,7 +10,6 @@
 //               mpirun -np 8 ex16p -s 3 -a 0.5 -k 0.5 -o 4
 //               mpirun -np 4 ex16p -s 14 -dt 1.0e-4 -tf 4.0e-2 -vs 40
 //               mpirun -np 16 ex16p -m ../data/fichera-q2.mesh
-//               mpirun -np 16 ex16p -m ../data/fichera-mixed.mesh
 //               mpirun -np 16 ex16p -m ../data/escher-p2.mesh
 //               mpirun -np 8 ex16p -m ../data/beam-tet.mesh -tf 10 -dt 0.1
 //               mpirun -np 4 ex16p -m ../data/amr-quad.mesh -o 4 -rs 0 -rp 0
@@ -174,14 +173,12 @@ int main(int argc, char *argv[])
       case 12: ode_solver = new RK2Solver(0.5); break; // midpoint method
       case 13: ode_solver = new RK3SSPSolver; break;
       case 14: ode_solver = new RK4Solver; break;
-      case 15: ode_solver = new GeneralizedAlphaSolver(0.5); break;
       // Implicit A-stable methods (not L-stable)
       case 22: ode_solver = new ImplicitMidpointSolver; break;
       case 23: ode_solver = new SDIRK23Solver; break;
       case 24: ode_solver = new SDIRK34Solver; break;
       default:
          cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
-         delete mesh;
          return 3;
    }
 

examples/ex17.cpp

@@ -8,7 +8,6 @@
 //       ex17 -m ../data/beam-quad.mesh
 //       ex17 -m ../data/beam-tet.mesh
 //       ex17 -m ../data/beam-hex.mesh
-//       ex17 -m ../data/beam-wedge.mesh
 //       ex17 -m ../data/beam-quad.mesh -r 2 -o 3
 //       ex17 -m ../data/beam-quad.mesh -r 2 -o 2 -a 1 -k 1
 //       ex17 -m ../data/beam-hex.mesh -r 2 -o 2

examples/ex17p.cpp

@@ -8,7 +8,6 @@
 //       mpirun -np 4 ex17p -m ../data/beam-quad.mesh
 //       mpirun -np 4 ex17p -m ../data/beam-tet.mesh
 //       mpirun -np 4 ex17p -m ../data/beam-hex.mesh
-//       mpirun -np 4 ex17p -m ../data/beam-wedge.mesh
 //       mpirun -np 4 ex17p -m ../data/beam-quad.mesh -rs 2 -rp 2 -o 3 -elast
 //       mpirun -np 4 ex17p -m ../data/beam-quad.mesh -rs 2 -rp 3 -o 2 -a 1 -k 1
 //       mpirun -np 4 ex17p -m ../data/beam-hex.mesh -rs 2 -rp 1 -o 2

examples/ex18.cpp

@@ -1,309 +0,0 @@
-//                                MFEM Example 18
-//
-// Compile with: make ex18
-//
-// Sample runs:
-//
-//       ex18 -p 1 -r 2 -o 1 -s 3
-//       ex18 -p 1 -r 1 -o 3 -s 4
-//       ex18 -p 1 -r 0 -o 5 -s 6
-//       ex18 -p 2 -r 1 -o 1 -s 3
-//       ex18 -p 2 -r 0 -o 3 -s 3
-//
-// Description:  This example code solves the compressible Euler system of
-//               equations, a model nonlinear hyperbolic PDE, with a
-//               discontinuous Galerkin (DG) formulation.
-//
-//               Specifically, it solves for an exact solution of the equations
-//               whereby a vortex is transported by a uniform flow. Since all
-//               boundaries are periodic here, the method's accuracy can be
-//               assessed by measuring the difference between the solution and
-//               the initial condition at a later time when the vortex returns
-//               to its initial location.
-//
-//               Note that as the order of the spatial discretization increases,
-//               the timestep must become smaller. This example currently uses a
-//               simple estimate derived by Cockburn and Shu for the 1D RKDG
-//               method. An additional factor can be tuned by passing the --cfl
-//               (or -c shorter) flag.
-//
-//               The example demonstrates user-defined bilinear and nonlinear
-//               form integrators for systems of equations that are defined with
-//               block vectors, and how these are used with an operator for
-//               explicit time integrators. In this case the system also
-//               involves an external approximate Riemann solver for the DG
-//               interface flux. It also demonstrates how to use GLVis for
-//               in-situ visualization of vector grid functions.
-//
-//               We recommend viewing examples 9, 14 and 17 before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <sstream>
-#include <iostream>
-
-// Classes FE_Evolution, RiemannSolver, DomainIntegrator and FaceIntegrator
-// shared between the serial and parallel version of the example.
-#include "ex18.hpp"
-
-// Choice for the problem setup. See InitialCondition in ex18.hpp.
-int problem;
-
-// Equation constant parameters.
-const int num_equation = 4;
-const double specific_heat_ratio = 1.4;
-const double gas_constant = 1.0;
-
-// Maximum characteristic speed (updated by integrators)
-double max_char_speed;
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   problem = 1;
-   const char *mesh_file = "../data/periodic-square.mesh";
-   int ref_levels = 1;
-   int order = 3;
-   int ode_solver_type = 4;
-   double t_final = 2.0;
-   double dt = -0.01;
-   double cfl = 0.3;
-   bool visualization = true;
-   int vis_steps = 50;
-
-   int precision = 8;
-   cout.precision(precision);
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&problem, "-p", "--problem",
-                  "Problem setup to use. See options in velocity_function().");
-   args.AddOption(&ref_levels, "-r", "--refine",
-                  "Number of times to refine the mesh uniformly.");
-   args.AddOption(&order, "-o", "--order",
-                  "Order (degree) of the finite elements.");
-   args.AddOption(&ode_solver_type, "-s", "--ode-solver",
-                  "ODE solver: 1 - Forward Euler,\n\t"
-                  "            2 - RK2 SSP, 3 - RK3 SSP, 4 - RK4, 6 - RK6.");
-   args.AddOption(&t_final, "-tf", "--t-final",
-                  "Final time; start time is 0.");
-   args.AddOption(&dt, "-dt", "--time-step",
-                  "Time step. Positive number skips CFL timestep calculation.");
-   args.AddOption(&cfl, "-c", "--cfl-number",
-                  "CFL number for timestep calculation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&vis_steps, "-vs", "--visualization-steps",
-                  "Visualize every n-th timestep.");
-
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   // 2. Read the mesh from the given mesh file. This example requires a 2D
-   //    periodic mesh, such as ../data/periodic-square.mesh.
-   Mesh mesh(mesh_file, 1, 1);
-   const int dim = mesh.Dimension();
-
-   MFEM_ASSERT(dim == 2, "Need a two-dimensional mesh for the problem definition");
-
-   // 3. Define the ODE solver used for time integration. Several explicit
-   //    Runge-Kutta methods are available.
-   ODESolver *ode_solver = NULL;
-   switch (ode_solver_type)
-   {
-      case 1: ode_solver = new ForwardEulerSolver; break;
-      case 2: ode_solver = new RK2Solver(1.0); break;
-      case 3: ode_solver = new RK3SSPSolver; break;
-      case 4: ode_solver = new RK4Solver; break;
-      case 6: ode_solver = new RK6Solver; break;
-      default:
-         cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
-         return 3;
-   }
-
-   // 4. Refine the mesh to increase the resolution. In this example we do
-   //    'ref_levels' of uniform refinement, where 'ref_levels' is a
-   //    command-line parameter.
-   for (int lev = 0; lev < ref_levels; lev++)
-   {
-      mesh.UniformRefinement();
-   }
-
-   // 5. Define the discontinuous DG finite element space of the given
-   //    polynomial order on the refined mesh.
-   DG_FECollection fec(order, dim);
-   // Finite element space for a scalar (thermodynamic quantity)
-   FiniteElementSpace fes(&mesh, &fec);
-   // Finite element space for a mesh-dim vector quantity (momentum)
-   FiniteElementSpace dfes(&mesh, &fec, dim, Ordering::byNODES);
-   // Finite element space for all variables together (total thermodynamic state)
-   FiniteElementSpace vfes(&mesh, &fec, num_equation, Ordering::byNODES);
-
-   // This example depends on this ordering of the space.
-   MFEM_ASSERT(fes.GetOrdering() == Ordering::byNODES, "");
-
-   cout << "Number of unknowns: " << vfes.GetVSize() << endl;
-
-   // 6. Define the initial conditions, save the corresponding mesh and grid
-   //    functions to a file. This can be opened with GLVis with the -gc option.
-
-   // The solution u has components {density, x-momentum, y-momentum, energy}.
-   // These are stored contiguously in the BlockVector u_block.
-   Array<int> offsets(num_equation + 1);
-   for (int k = 0; k <= num_equation; k++) { offsets[k] = k * vfes.GetNDofs(); }
-   BlockVector u_block(offsets);
-
-   // Momentum grid function on dfes for visualization.
-   GridFunction mom(&dfes, u_block.GetData() + offsets[1]);
-
-   // Initialize the state.
-   VectorFunctionCoefficient u0(num_equation, InitialCondition);
-   GridFunction sol(&vfes, u_block.GetData());
-   sol.ProjectCoefficient(u0);
-
-   // Output the initial solution.
-   {
-      ofstream mesh_ofs("vortex.mesh");
-      mesh_ofs.precision(precision);
-      mesh_ofs << mesh;
-
-      for (int k = 0; k < num_equation; k++)
-      {
-         GridFunction uk(&fes, u_block.GetBlock(k));
-         ostringstream sol_name;
-         sol_name << "vortex-" << k << "-init.gf";
-         ofstream sol_ofs(sol_name.str().c_str());
-         sol_ofs.precision(precision);
-         sol_ofs << uk;
-      }
-   }
-
-   // 7. Set up the nonlinear form corresponding to the DG discretization of the
-   //    flux divergence, and assemble the corresponding mass matrix.
-   MixedBilinearForm Aflux(&dfes, &fes);
-   Aflux.AddDomainIntegrator(new DomainIntegrator(dim));
-   Aflux.Assemble();
-
-   NonlinearForm A(&vfes);
-   RiemannSolver rsolver;
-   A.AddInteriorFaceIntegrator(new FaceIntegrator(rsolver, dim));
-
-   // 8. Define the time-dependent evolution operator describing the ODE
-   //    right-hand side, and perform time-integration (looping over the time
-   //    iterations, ti, with a time-step dt).
-   FE_Evolution euler(vfes, A, Aflux.SpMat());
-
-   // Visualize the density
-   socketstream sout;
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-
-      sout.open(vishost, visport);
-      if (!sout)
-      {
-         cout << "Unable to connect to GLVis server at "
-              << vishost << ':' << visport << endl;
-         visualization = false;
-         cout << "GLVis visualization disabled.\n";
-      }
-      else
-      {
-         sout.precision(precision);
-         sout << "solution\n" << mesh << mom;
-         sout << "pause\n";
-         sout << flush;
-         cout << "GLVis visualization paused."
-              << " Press space (in the GLVis window) to resume it.\n";
-      }
-   }
-
-   // Determine the minimum element size.
-   double hmin = 0.0;
-   if (cfl > 0)
-   {
-      hmin = mesh.GetElementSize(0, 1);
-      for (int i = 1; i < mesh.GetNE(); i++)
-      {
-         hmin = min(mesh.GetElementSize(i, 1), hmin);
-      }
-   }
-
-   // Start the timer.
-   tic_toc.Clear();
-   tic_toc.Start();
-
-   double t = 0.0;
-   euler.SetTime(t);
-   ode_solver->Init(euler);
-
-   if (cfl > 0)
-   {
-      // Find a safe dt, using a temporary vector. Calling Mult() computes the
-      // maximum char speed at all quadrature points on all faces.
-      Vector z(A.Width());
-      max_char_speed = 0.;
-      A.Mult(sol, z);
-      dt = cfl * hmin / max_char_speed / (2*order+1);
-   }
-
-   // Integrate in time.
-   bool done = false;
-   for (int ti = 0; !done; )
-   {
-      double dt_real = min(dt, t_final - t);
-
-      ode_solver->Step(sol, t, dt_real);
-      if (cfl > 0)
-      {
-         dt = cfl * hmin / max_char_speed / (2*order+1);
-      }
-      ti++;
-
-      done = (t >= t_final - 1e-8*dt);
-      if (done || ti % vis_steps == 0)
-      {
-         cout << "time step: " << ti << ", time: " << t << endl;
-         if (visualization)
-         {
-            sout << "solution\n" << mesh << mom << flush;
-         }
-      }
-   }
-
-   tic_toc.Stop();
-   cout << " done, " << tic_toc.RealTime() << "s." << endl;
-
-   // 9. Save the final solution. This output can be viewed later using GLVis:
-   //    "glvis -m vortex.mesh -g vortex-1-final.gf".
-   for (int k = 0; k < num_equation; k++)
-   {
-      GridFunction uk(&fes, u_block.GetBlock(k));
-      ostringstream sol_name;
-      sol_name << "vortex-" << k << "-final.gf";
-      ofstream sol_ofs(sol_name.str().c_str());
-      sol_ofs.precision(precision);
-      sol_ofs << uk;
-   }
-
-   // 10. Compute the L2 solution error summed for all components.
-   if (t_final == 2.0)
-   {
-      const double error = sol.ComputeLpError(2, u0);
-      cout << "Solution error: " << error << endl;
-   }
-
-   // Free the used memory.
-   delete ode_solver;
-
-   return 0;
-}

examples/ex18.hpp

@@ -1,570 +0,0 @@
-//                  MFEM Example 18 - Serial/Parallel Shared Code
-
-#include "mfem.hpp"
-
-using namespace std;
-using namespace mfem;
-
-// Problem definition
-extern int problem;
-
-// Maximum characteristic speed (updated by integrators)
-extern double max_char_speed;
-
-extern const int num_equation;
-extern const double specific_heat_ratio;
-extern const double gas_constant;
-
-// Time-dependent operator for the right-hand side of the ODE representing the
-// DG weak form.
-class FE_Evolution : public TimeDependentOperator
-{
-private:
-   const int dim;
-
-   FiniteElementSpace &vfes;
-   Operator &A;
-   SparseMatrix &Aflux;
-   DenseTensor Me_inv;
-
-   mutable Vector state;
-   mutable DenseMatrix f;
-   mutable DenseTensor flux;
-   mutable Vector z;
-
-   void GetFlux(const DenseMatrix &state, DenseTensor &flux) const;
-
-public:
-   FE_Evolution(FiniteElementSpace &_vfes,
-                Operator &_A, SparseMatrix &_Aflux);
-
-   virtual void Mult(const Vector &x, Vector &y) const;
-
-   virtual ~FE_Evolution() { }
-};
-
-// Implements a simple Rusanov flux
-class RiemannSolver
-{
-private:
-   Vector flux1;
-   Vector flux2;
-
-public:
-   RiemannSolver();
-   double Eval(const Vector &state1, const Vector &state2,
-               const Vector &nor, Vector &flux);
-};
-
-
-// Constant (in time) mixed bilinear form multiplying the flux grid function.
-// The form is (vec(v), grad(w)) where the trial space = vector L2 space (mesh
-// dim) and test space = scalar L2 space.
-class DomainIntegrator : public BilinearFormIntegrator
-{
-private:
-   Vector shape;
-   DenseMatrix flux;
-   DenseMatrix dshapedr;
-   DenseMatrix dshapedx;
-
-public:
-   DomainIntegrator(const int dim);
-
-   virtual void AssembleElementMatrix2(const FiniteElement &trial_fe,
-                                       const FiniteElement &test_fe,
-                                       ElementTransformation &Tr,
-                                       DenseMatrix &elmat);
-};
-
-// Interior face term: <F.n(u),[w]>
-class FaceIntegrator : public NonlinearFormIntegrator
-{
-private:
-   RiemannSolver rsolver;
-   Vector shape1;
-   Vector shape2;
-   Vector funval1;
-   Vector funval2;
-   Vector nor;
-   Vector fluxN;
-   IntegrationPoint eip1;
-   IntegrationPoint eip2;
-
-public:
-   FaceIntegrator(RiemannSolver &rsolver_, const int dim);
-
-   virtual void AssembleFaceVector(const FiniteElement &el1,
-                                   const FiniteElement &el2,
-                                   FaceElementTransformations &Tr,
-                                   const Vector &elfun, Vector &elvect);
-};
-
-// Implementation of class FE_Evolution
-FE_Evolution::FE_Evolution(FiniteElementSpace &_vfes,
-                           Operator &_A, SparseMatrix &_Aflux)
-   : TimeDependentOperator(_A.Height()),
-     dim(_vfes.GetFE(0)->GetDim()),
-     vfes(_vfes),
-     A(_A),
-     Aflux(_Aflux),
-     Me_inv(vfes.GetFE(0)->GetDof(), vfes.GetFE(0)->GetDof(), vfes.GetNE()),
-     state(num_equation),
-     f(num_equation, dim),
-     flux(vfes.GetNDofs(), dim, num_equation),
-     z(A.Height())
-{
-   // Standard local assembly and inversion for energy mass matrices.
-   const int dof = vfes.GetFE(0)->GetDof();
-   DenseMatrix Me(dof);
-   DenseMatrixInverse inv(&Me);
-   MassIntegrator mi;
-   for (int i = 0; i < vfes.GetNE(); i++)
-   {
-      mi.AssembleElementMatrix(*vfes.GetFE(i), *vfes.GetElementTransformation(i), Me);
-      inv.Factor();
-      inv.GetInverseMatrix(Me_inv(i));
-   }
-}
-
-void FE_Evolution::Mult(const Vector &x, Vector &y) const
-{
-   // 0. Reset wavespeed computation before operator application.
-   max_char_speed = 0.;
-
-   // 1. Create the vector z with the face terms -<F.n(u), [w]>.
-   A.Mult(x, z);
-
-   // 2. Add the element terms.
-   // i.  computing the flux approximately as a grid function by interpolating
-   //     at the solution nodes.
-   // ii. multiplying this grid function by a (constant) mixed bilinear form for
-   //     each of the num_equation, computing (F(u), grad(w)) for each equation.
-
-   DenseMatrix xmat(x.GetData(), vfes.GetNDofs(), num_equation);
-   GetFlux(xmat, flux);
-
-   for (int k = 0; k < num_equation; k++)
-   {
-      Vector fk(flux(k).GetData(), dim * vfes.GetNDofs());
-      Vector zk(z.GetData() + k * vfes.GetNDofs(), vfes.GetNDofs());
-      Aflux.AddMult(fk, zk);
-   }
-
-   // 3. Multiply element-wise by the inverse mass matrices.
-   Vector zval;
-   Array<int> vdofs;
-   const int dof = vfes.GetFE(0)->GetDof();
-   DenseMatrix zmat, ymat(dof, num_equation);
-
-   for (int i = 0; i < vfes.GetNE(); i++)
-   {
-      // Return the vdofs ordered byNODES
-      vfes.GetElementVDofs(i, vdofs);
-      z.GetSubVector(vdofs, zval);
-      zmat.UseExternalData(zval.GetData(), dof, num_equation);
-      mfem::Mult(Me_inv(i), zmat, ymat);
-      y.SetSubVector(vdofs, ymat.GetData());
-   }
-}
-
-// Physicality check (at end)
-bool StateIsPhysical(const Vector &state, const int dim);
-
-// Pressure (EOS) computation
-inline double ComputePressure(const Vector &state, int dim)
-{
-   const double den = state(0);
-   const Vector den_vel(state.GetData() + 1, dim);
-   const double den_energy = state(1 + dim);
-
-   double den_vel2 = 0;
-   for (int d = 0; d < dim; d++) { den_vel2 += den_vel(d) * den_vel(d); }
-   den_vel2 /= den;
-
-   return (specific_heat_ratio - 1.0) * (den_energy - 0.5 * den_vel2);
-}
-
-// Compute the vector flux F(u)
-void ComputeFlux(const Vector &state, int dim, DenseMatrix &flux)
-{
-   const double den = state(0);
-   const Vector den_vel(state.GetData() + 1, dim);
-   const double den_energy = state(1 + dim);
-
-   MFEM_ASSERT(StateIsPhysical(state, dim), "");
-
-   const double pres = ComputePressure(state, dim);
-
-   for (int d = 0; d < dim; d++)
-   {
-      flux(0, d) = den_vel(d);
-      for (int i = 0; i < dim; i++)
-      {
-         flux(1+i, d) = den_vel(i) * den_vel(d) / den;
-      }
-      flux(1+d, d) += pres;
-   }
-
-   const double H = (den_energy + pres) / den;
-   for (int d = 0; d < dim; d++)
-   {
-      flux(1+dim, d) = den_vel(d) * H;
-   }
-}
-
-// Compute the scalar F(u).n
-void ComputeFluxDotN(const Vector &state, const Vector &nor,
-                     Vector &fluxN)
-{
-   // NOTE: nor in general is not a unit normal
-   const int dim = nor.Size();
-   const double den = state(0);
-   const Vector den_vel(state.GetData() + 1, dim);
-   const double den_energy = state(1 + dim);
-
-   MFEM_ASSERT(StateIsPhysical(state, dim), "");
-
-   const double pres = ComputePressure(state, dim);
-
-   double den_velN = 0;
-   for (int d = 0; d < dim; d++) { den_velN += den_vel(d) * nor(d); }
-
-   fluxN(0) = den_velN;
-   for (int d = 0; d < dim; d++)
-   {
-      fluxN(1+d) = den_velN * den_vel(d) / den + pres * nor(d);
-   }
-
-   const double H = (den_energy + pres) / den;
-   fluxN(1 + dim) = den_velN * H;
-}
-
-// Compute the maximum characteristic speed.
-inline double ComputeMaxCharSpeed(const Vector &state, const int dim)
-{
-   const double den = state(0);
-   const Vector den_vel(state.GetData() + 1, dim);
-
-   double den_vel2 = 0;
-   for (int d = 0; d < dim; d++) { den_vel2 += den_vel(d) * den_vel(d); }
-   den_vel2 /= den;
-
-   const double pres = ComputePressure(state, dim);
-   const double sound = sqrt(specific_heat_ratio * pres / den);
-   const double vel = sqrt(den_vel2 / den);
-
-   return vel + sound;
-}
-
-// Compute the flux at solution nodes.
-void FE_Evolution::GetFlux(const DenseMatrix &x, DenseTensor &flux) const
-{
-   const int dof = flux.SizeI();
-   const int dim = flux.SizeJ();
-
-   for (int i = 0; i < dof; i++)
-   {
-      for (int k = 0; k < num_equation; k++) { state(k) = x(i, k); }
-      ComputeFlux(state, dim, f);
-
-      for (int d = 0; d < dim; d++)
-      {
-         for (int k = 0; k < num_equation; k++)
-         {
-            flux(i, d, k) = f(k, d);
-         }
-      }
-
-      // Update max char speed
-      const double mcs = ComputeMaxCharSpeed(state, dim);
-      if (mcs > max_char_speed) { max_char_speed = mcs; }
-   }
-}
-
-// Implementation of class RiemannSolver
-RiemannSolver::RiemannSolver() :
-   flux1(num_equation),
-   flux2(num_equation) { }
-
-double RiemannSolver::Eval(const Vector &state1, const Vector &state2,
-                           const Vector &nor, Vector &flux)
-{
-   // NOTE: nor in general is not a unit normal
-   const int dim = nor.Size();
-
-   MFEM_ASSERT(StateIsPhysical(state1, dim), "");
-   MFEM_ASSERT(StateIsPhysical(state2, dim), "");
-
-   const double maxE1 = ComputeMaxCharSpeed(state1, dim);
-   const double maxE2 = ComputeMaxCharSpeed(state2, dim);
-
-   const double maxE = max(maxE1, maxE2);
-
-   ComputeFluxDotN(state1, nor, flux1);
-   ComputeFluxDotN(state2, nor, flux2);
-
-   double normag = 0;
-   for (int i = 0; i < dim; i++)
-   {
-      normag += nor(i) * nor(i);
-   }
-   normag = sqrt(normag);
-
-   for (int i = 0; i < num_equation; i++)
-   {
-      flux(i) = 0.5 * (flux1(i) + flux2(i))
-                - 0.5 * maxE * (state2(i) - state1(i)) * normag;
-   }
-
-   return maxE;
-}
-
-// Implementation of class DomainIntegrator
-DomainIntegrator::DomainIntegrator(const int dim) : flux(num_equation, dim) { }
-
-void DomainIntegrator::AssembleElementMatrix2(const FiniteElement &trial_fe,
-                                              const FiniteElement &test_fe,
-                                              ElementTransformation &Tr,
-                                              DenseMatrix &elmat)
-{
-   // Assemble the form (vec(v), grad(w))
-
-   // Trial space = vector L2 space (mesh dim)
-   // Test space  = scalar L2 space
-
-   const int dof_trial = trial_fe.GetDof();
-   const int dof_test = test_fe.GetDof();
-   const int dim = trial_fe.GetDim();
-
-   shape.SetSize(dof_trial);
-   dshapedr.SetSize(dof_test, dim);
-   dshapedx.SetSize(dof_test, dim);
-
-   elmat.SetSize(dof_test, dof_trial * dim);
-   elmat = 0.0;
-
-   const int maxorder = max(trial_fe.GetOrder(), test_fe.GetOrder());
-   const int intorder = 2 * maxorder;
-   const IntegrationRule *ir = &IntRules.Get(trial_fe.GetGeomType(), intorder);
-
-   for (int i = 0; i < ir->GetNPoints(); i++)
-   {
-      const IntegrationPoint &ip = ir->IntPoint(i);
-
-      // Calculate the shape functions
-      trial_fe.CalcShape(ip, shape);
-      shape *= ip.weight;
-
-      // Compute the physical gradients of the test functions
-      Tr.SetIntPoint(&ip);
-      test_fe.CalcDShape(ip, dshapedr);
-      Mult(dshapedr, Tr.AdjugateJacobian(), dshapedx);
-
-      for (int d = 0; d < dim; d++)
-      {
-         for (int j = 0; j < dof_test; j++)
-         {
-            for (int k = 0; k < dof_trial; k++)
-            {
-               elmat(j, k + d * dof_trial) += shape(k) * dshapedx(j, d);
-            }
-         }
-      }
-   }
-}
-
-// Implementation of class FaceIntegrator
-FaceIntegrator::FaceIntegrator(RiemannSolver &rsolver_, const int dim) :
-   rsolver(rsolver_),
-   funval1(num_equation),
-   funval2(num_equation),
-   nor(dim),
-   fluxN(num_equation) { }
-
-void FaceIntegrator::AssembleFaceVector(const FiniteElement &el1,
-                                        const FiniteElement &el2,
-                                        FaceElementTransformations &Tr,
-                                        const Vector &elfun, Vector &elvect)
-{
-   // Compute the term <F.n(u),[w]> on the interior faces.
-   const int dof1 = el1.GetDof();
-   const int dof2 = el2.GetDof();
-
-   shape1.SetSize(dof1);
-   shape2.SetSize(dof2);
-
-   elvect.SetSize((dof1 + dof2) * num_equation);
-   elvect = 0.0;
-
-   DenseMatrix elfun1_mat(elfun.GetData(), dof1, num_equation);
-   DenseMatrix elfun2_mat(elfun.GetData() + dof1 * num_equation, dof2,
-                          num_equation);
-
-   DenseMatrix elvect1_mat(elvect.GetData(), dof1, num_equation);
-   DenseMatrix elvect2_mat(elvect.GetData() + dof1 * num_equation, dof2,
-                           num_equation);
-
-   // Integration order calculation from DGTraceIntegrator
-   int intorder;
-   if (Tr.Elem2No >= 0)
-      intorder = (min(Tr.Elem1->OrderW(), Tr.Elem2->OrderW()) +
-                  2*max(el1.GetOrder(), el2.GetOrder()));
-   else
-   {
-      intorder = Tr.Elem1->OrderW() + 2*el1.GetOrder();
-   }
-   if (el1.Space() == FunctionSpace::Pk)
-   {
-      intorder++;
-   }
-   const IntegrationRule *ir = &IntRules.Get(Tr.FaceGeom, intorder);
-
-   for (int i = 0; i < ir->GetNPoints(); i++)
-   {
-      const IntegrationPoint &ip = ir->IntPoint(i);
-
-      Tr.Loc1.Transform(ip, eip1);
-      Tr.Loc2.Transform(ip, eip2);
-
-      // Calculate basis functions on both elements at the face
-      el1.CalcShape(eip1, shape1);
-      el2.CalcShape(eip2, shape2);
-
-      // Interpolate elfun at the point
-      elfun1_mat.MultTranspose(shape1, funval1);
-      elfun2_mat.MultTranspose(shape2, funval2);
-
-      Tr.Face->SetIntPoint(&ip);
-
-      // Get the normal vector and the flux on the face
-      CalcOrtho(Tr.Face->Jacobian(), nor);
-      const double mcs = rsolver.Eval(funval1, funval2, nor, fluxN);
-
-      // Update max char speed
-      if (mcs > max_char_speed) { max_char_speed = mcs; }
-
-      fluxN *= ip.weight;
-      for (int k = 0; k < num_equation; k++)
-      {
-         for (int s = 0; s < dof1; s++)
-         {
-            elvect1_mat(s, k) -= fluxN(k) * shape1(s);
-         }
-         for (int s = 0; s < dof2; s++)
-         {
-            elvect2_mat(s, k) += fluxN(k) * shape2(s);
-         }
-      }
-   }
-}
-
-// Check that the state is physical - enabled in debug mode
-bool StateIsPhysical(const Vector &state, const int dim)
-{
-   const double den = state(0);
-   const Vector den_vel(state.GetData() + 1, dim);
-   const double den_energy = state(1 + dim);
-
-   if (den < 0)
-   {
-      cout << "Negative density: ";
-      for (int i = 0; i < state.Size(); i++)
-      {
-         cout << state(i) << " ";
-      }
-      cout << endl;
-      return false;
-   }
-   if (den_energy <= 0)
-   {
-      cout << "Negative energy: ";
-      for (int i = 0; i < state.Size(); i++)
-      {
-         cout << state(i) << " ";
-      }
-      cout << endl;
-      return false;
-   }
-
-   double den_vel2 = 0;
-   for (int i = 0; i < dim; i++) { den_vel2 += den_vel(i) * den_vel(i); }
-   den_vel2 /= den;
-
-   const double pres = (specific_heat_ratio - 1.0) * (den_energy - 0.5 * den_vel2);
-
-   if (pres <= 0)
-   {
-      cout << "Negative pressure: " << pres << ", state: ";
-      for (int i = 0; i < state.Size(); i++)
-      {
-         cout << state(i) << " ";
-      }
-      cout << endl;
-      return false;
-   }
-   return true;
-}
-
-// Initial condition
-void InitialCondition(const Vector &x, Vector &y)
-{
-   MFEM_ASSERT(x.Size() == 2, "");
-
-   double radius = 0, Minf = 0, beta = 0;
-   if (problem == 1)
-   {
-      // "Fast vortex"
-      radius = 0.2;
-      Minf = 0.5;
-      beta = 1. / 5.;
-   }
-   else if (problem == 2)
-   {
-      // "Slow vortex"
-      radius = 0.2;
-      Minf = 0.05;
-      beta = 1. / 50.;
-   }
-   else
-   {
-      mfem_error("Cannot recognize problem."
-                 "Options are: 1 - fast vortex, 2 - slow vortex");
-   }
-
-   const double xc = 0.0, yc = 0.0;
-
-   // Nice units
-   const double vel_inf = 1.;
-   const double den_inf = 1.;
-
-   // Derive remainder of background state from this and Minf
-   const double pres_inf = (den_inf / specific_heat_ratio) * (vel_inf / Minf) *
-                           (vel_inf / Minf);
-   const double temp_inf = pres_inf / (den_inf * gas_constant);
-
-   double r2rad = 0.0;
-   r2rad += (x(0) - xc) * (x(0) - xc);
-   r2rad += (x(1) - yc) * (x(1) - yc);
-   r2rad /= (radius * radius);
-
-   const double shrinv1 = 1.0 / (specific_heat_ratio - 1.);
-
-   const double velX = vel_inf * (1 - beta * (x(1) - yc) / radius * exp(
-                                     -0.5 * r2rad));
-   const double velY = vel_inf * beta * (x(0) - xc) / radius * exp(-0.5 * r2rad);
-   const double vel2 = velX * velX + velY * velY;
-
-   const double specific_heat = gas_constant * specific_heat_ratio * shrinv1;
-   const double temp = temp_inf - 0.5 * (vel_inf * beta) *
-                       (vel_inf * beta) / specific_heat * exp(-r2rad);
-
-   const double den = den_inf * pow(temp/temp_inf, shrinv1);
-   const double pres = den * gas_constant * temp;
-   const double energy = shrinv1 * pres / den + 0.5 * vel2;
-
-   y(0) = den;
-   y(1) = den * velX;
-   y(2) = den * velY;
-   y(3) = den * energy;
-}

examples/ex18p.cpp

@@ -1,364 +0,0 @@
-//                         MFEM Example 18 - Parallel Version
-//
-// Compile with: make ex18
-//
-// Sample runs:
-//
-//       mpirun -np 4 ex18p -p 1 -rs 2 -rp 1 -o 1 -s 3
-//       mpirun -np 4 ex18p -p 1 -rs 1 -rp 1 -o 3 -s 4
-//       mpirun -np 4 ex18p -p 1 -rs 1 -rp 1 -o 5 -s 6
-//       mpirun -np 4 ex18p -p 2 -rs 1 -rp 1 -o 1 -s 3
-//       mpirun -np 4 ex18p -p 2 -rs 1 -rp 1 -o 3 -s 3
-//
-// Description:  This example code solves the compressible Euler system of
-//               equations, a model nonlinear hyperbolic PDE, with a
-//               discontinuous Galerkin (DG) formulation.
-//
-//               Specifically, it solves for an exact solution of the equations
-//               whereby a vortex is transported by a uniform flow. Since all
-//               boundaries are periodic here, the method's accuracy can be
-//               assessed by measuring the difference between the solution and
-//               the initial condition at a later time when the vortex returns
-//               to its initial location.
-//
-//               Note that as the order of the spatial discretization increases,
-//               the timestep must become smaller. This example currently uses a
-//               simple estimate derived by Cockburn and Shu for the 1D RKDG
-//               method. An additional factor can be tuned by passing the --cfl
-//               (or -c shorter) flag.
-//
-//               The example demonstrates user-defined bilinear and nonlinear
-//               form integrators for systems of equations that are defined with
-//               block vectors, and how these are used with an operator for
-//               explicit time integrators. In this case the system also
-//               involves an external approximate Riemann solver for the DG
-//               interface flux. It also demonstrates how to use GLVis for
-//               in-situ visualization of vector grid functions.
-//
-//               We recommend viewing examples 9, 14 and 17 before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <sstream>
-#include <iostream>
-
-// Classes FE_Evolution, RiemannSolver, DomainIntegrator and FaceIntegrator
-// shared between the serial and parallel version of the example.
-#include "ex18.hpp"
-
-// Choice for the problem setup. See InitialCondition in ex18.hpp.
-int problem;
-
-// Equation constant parameters.
-const int num_equation = 4;
-const double specific_heat_ratio = 1.4;
-const double gas_constant = 1.0;
-
-// Maximum characteristic speed (updated by integrators)
-double max_char_speed;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   MPI_Session mpi(argc, argv);
-
-   // 2. Parse command-line options.
-   problem = 1;
-   const char *mesh_file = "../data/periodic-square.mesh";
-   int ser_ref_levels = 0;
-   int par_ref_levels = 1;
-   int order = 3;
-   int ode_solver_type = 4;
-   double t_final = 2.0;
-   double dt = -0.01;
-   double cfl = 0.3;
-   bool visualization = true;
-   int vis_steps = 50;
-
-   int precision = 8;
-   cout.precision(precision);
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&problem, "-p", "--problem",
-                  "Problem setup to use. See options in velocity_function().");
-   args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
-                  "Number of times to refine the mesh uniformly before parallel"
-                  " partitioning, -1 for auto.");
-   args.AddOption(&par_ref_levels, "-rp", "--refine-parallel",
-                  "Number of times to refine the mesh uniformly after parallel"
-                  " partitioning.");
-   args.AddOption(&order, "-o", "--order",
-                  "Order (degree) of the finite elements.");
-   args.AddOption(&ode_solver_type, "-s", "--ode-solver",
-                  "ODE solver: 1 - Forward Euler,\n\t"
-                  "            2 - RK2 SSP, 3 - RK3 SSP, 4 - RK4, 6 - RK6.");
-   args.AddOption(&t_final, "-tf", "--t-final",
-                  "Final time; start time is 0.");
-   args.AddOption(&dt, "-dt", "--time-step",
-                  "Time step. Positive number skips CFL timestep calculation.");
-   args.AddOption(&cfl, "-c", "--cfl-number",
-                  "CFL number for timestep calculation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&vis_steps, "-vs", "--visualization-steps",
-                  "Visualize every n-th timestep.");
-
-   args.Parse();
-   if (!args.Good())
-   {
-      if (mpi.Root()) { args.PrintUsage(cout); }
-      return 1;
-   }
-   if (mpi.Root()) { args.PrintOptions(cout); }
-
-   // 3. Read the mesh from the given mesh file. This example requires a 2D
-   //    periodic mesh, such as ../data/periodic-square.mesh.
-   Mesh mesh(mesh_file, 1, 1);
-   const int dim = mesh.Dimension();
-
-   MFEM_ASSERT(dim == 2, "Need a two-dimensional mesh for the problem definition");
-
-   // 4. Define the ODE solver used for time integration. Several explicit
-   //    Runge-Kutta methods are available.
-   ODESolver *ode_solver = NULL;
-   switch (ode_solver_type)
-   {
-      case 1: ode_solver = new ForwardEulerSolver; break;
-      case 2: ode_solver = new RK2Solver(1.0); break;
-      case 3: ode_solver = new RK3SSPSolver; break;
-      case 4: ode_solver = new RK4Solver; break;
-      case 6: ode_solver = new RK6Solver; break;
-      default:
-         if (mpi.Root())
-         {
-            cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
-         }
-         return 3;
-   }
-
-   // 5. Refine the mesh in serial to increase the resolution. In this example
-   //    we do 'ser_ref_levels' of uniform refinement, where 'ser_ref_levels' is
-   //    a command-line parameter.
-   for (int lev = 0; lev < ser_ref_levels; lev++)
-   {
-      mesh.UniformRefinement();
-   }
-
-   // 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
-   //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
-   ParMesh pmesh(MPI_COMM_WORLD, mesh);
-   mesh.Clear();
-   for (int lev = 0; lev < par_ref_levels; lev++)
-   {
-      pmesh.UniformRefinement();
-   }
-
-   // 7. Define the discontinuous DG finite element space of the given
-   //    polynomial order on the refined mesh.
-   DG_FECollection fec(order, dim);
-   // Finite element space for a scalar (thermodynamic quantity)
-   ParFiniteElementSpace fes(&pmesh, &fec);
-   // Finite element space for a mesh-dim vector quantity (momentum)
-   ParFiniteElementSpace dfes(&pmesh, &fec, dim, Ordering::byNODES);
-   // Finite element space for all variables together (total thermodynamic state)
-   ParFiniteElementSpace vfes(&pmesh, &fec, num_equation, Ordering::byNODES);
-
-   // This example depends on this ordering of the space.
-   MFEM_ASSERT(fes.GetOrdering() == Ordering::byNODES, "");
-
-   HYPRE_Int glob_size = vfes.GlobalTrueVSize();
-   if (mpi.Root()) { cout << "Number of unknowns: " << glob_size << endl; }
-
-   // 8. Define the initial conditions, save the corresponding mesh and grid
-   //    functions to a file. This can be opened with GLVis with the -gc option.
-
-   // The solution u has components {density, x-momentum, y-momentum, energy}.
-   // These are stored contiguously in the BlockVector u_block.
-   Array<int> offsets(num_equation + 1);
-   for (int k = 0; k <= num_equation; k++) { offsets[k] = k * vfes.GetNDofs(); }
-   BlockVector u_block(offsets);
-
-   // Momentum grid function on dfes for visualization.
-   ParGridFunction mom(&dfes, u_block.GetData() + offsets[1]);
-
-   // Initialize the state.
-   VectorFunctionCoefficient u0(num_equation, InitialCondition);
-   ParGridFunction sol(&vfes, u_block.GetData());
-   sol.ProjectCoefficient(u0);
-
-   // Output the initial solution.
-   {
-      ostringstream mesh_name;
-      mesh_name << "vortex-mesh." << setfill('0') << setw(6) << mpi.WorldRank();
-      ofstream mesh_ofs(mesh_name.str().c_str());
-      mesh_ofs.precision(precision);
-      mesh_ofs << pmesh;
-
-      for (int k = 0; k < num_equation; k++)
-      {
-         ParGridFunction uk(&fes, u_block.GetBlock(k));
-         ostringstream sol_name;
-         sol_name << "vortex-" << k << "-init."
-                  << setfill('0') << setw(6) << mpi.WorldRank();
-         ofstream sol_ofs(sol_name.str().c_str());
-         sol_ofs.precision(precision);
-         sol_ofs << uk;
-      }
-   }
-
-   // 9. Set up the nonlinear form corresponding to the DG discretization of the
-   //    flux divergence, and assemble the corresponding mass matrix.
-   MixedBilinearForm Aflux(&dfes, &fes);
-   Aflux.AddDomainIntegrator(new DomainIntegrator(dim));
-   Aflux.Assemble();
-
-   ParNonlinearForm A(&vfes);
-   RiemannSolver rsolver;
-   A.AddInteriorFaceIntegrator(new FaceIntegrator(rsolver, dim));
-
-   // 10. Define the time-dependent evolution operator describing the ODE
-   //     right-hand side, and perform time-integration (looping over the time
-   //     iterations, ti, with a time-step dt).
-   FE_Evolution euler(vfes, A, Aflux.SpMat());
-
-   // Visualize the density
-   socketstream sout;
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-
-      MPI_Barrier(pmesh.GetComm());
-      sout.open(vishost, visport);
-      if (!sout)
-      {
-         if (mpi.Root())
-         {
-            cout << "Unable to connect to GLVis server at "
-                 << vishost << ':' << visport << endl;
-         }
-         visualization = false;
-         if (mpi.Root()) { cout << "GLVis visualization disabled.\n"; }
-      }
-      else
-      {
-         sout << "parallel " << mpi.WorldSize() << " " << mpi.WorldRank() << "\n";
-         sout.precision(precision);
-         sout << "solution\n" << pmesh << mom;
-         sout << "pause\n";
-         sout << flush;
-         if (mpi.Root())
-         {
-            cout << "GLVis visualization paused."
-                 << " Press space (in the GLVis window) to resume it.\n";
-         }
-      }
-   }
-
-   // Determine the minimum element size.
-   double hmin;
-   if (cfl > 0)
-   {
-      double my_hmin = pmesh.GetElementSize(0, 1);
-      for (int i = 1; i < pmesh.GetNE(); i++)
-      {
-         my_hmin = min(pmesh.GetElementSize(i, 1), my_hmin);
-      }
-      // Reduce to find the global minimum element size
-      MPI_Allreduce(&my_hmin, &hmin, 1, MPI_DOUBLE, MPI_MIN, pmesh.GetComm());
-   }
-
-   // Start the timer.
-   tic_toc.Clear();
-   tic_toc.Start();
-
-   double t = 0.0;
-   euler.SetTime(t);
-   ode_solver->Init(euler);
-
-   if (cfl > 0)
-   {
-      // Find a safe dt, using a temporary vector. Calling Mult() computes the
-      // maximum char speed at all quadrature points on all faces.
-      max_char_speed = 0.;
-      Vector z(sol.Size());
-      A.Mult(sol, z);
-      // Reduce to find the global maximum wave speed
-      {
-         double all_max_char_speed;
-         MPI_Allreduce(&max_char_speed, &all_max_char_speed,
-                       1, MPI_DOUBLE, MPI_MAX, pmesh.GetComm());
-         max_char_speed = all_max_char_speed;
-      }
-      dt = cfl * hmin / max_char_speed / (2*order+1);
-   }
-
-   // Integrate in time.
-   bool done = false;
-   for (int ti = 0; !done; )
-   {
-      double dt_real = min(dt, t_final - t);
-
-      ode_solver->Step(sol, t, dt_real);
-      if (cfl > 0)
-      {
-         // Reduce to find the global maximum wave speed
-         {
-            double all_max_char_speed;
-            MPI_Allreduce(&max_char_speed, &all_max_char_speed,
-                          1, MPI_DOUBLE, MPI_MAX, pmesh.GetComm());
-            max_char_speed = all_max_char_speed;
-         }
-         dt = cfl * hmin / max_char_speed / (2*order+1);
-      }
-      ti++;
-
-      done = (t >= t_final - 1e-8*dt);
-      if (done || ti % vis_steps == 0)
-      {
-         if (mpi.Root())
-         {
-            cout << "time step: " << ti << ", time: " << t << endl;
-         }
-         if (visualization)
-         {
-            MPI_Barrier(pmesh.GetComm());
-            sout << "parallel " << mpi.WorldSize() << " " << mpi.WorldRank() << "\n";
-            sout << "solution\n" << pmesh << mom << flush;
-         }
-      }
-   }
-
-   tic_toc.Stop();
-   if (mpi.Root()) { cout << " done, " << tic_toc.RealTime() << "s." << endl; }
-
-   // 11. Save the final solution. This output can be viewed later using GLVis:
-   //     "glvis -np 4 -m vortex-mesh -g vortex-1-final".
-   for (int k = 0; k < num_equation; k++)
-   {
-      ParGridFunction uk(&fes, u_block.GetBlock(k));
-      ostringstream sol_name;
-      sol_name << "vortex-" << k << "-final."
-               << setfill('0') << setw(6) << mpi.WorldRank();
-      ofstream sol_ofs(sol_name.str().c_str());
-      sol_ofs.precision(precision);
-      sol_ofs << uk;
-   }
-
-   // 12. Compute the L2 solution error summed for all components.
-   if (t_final == 2.0)
-   {
-      const double error = sol.ComputeLpError(2, u0);
-      if (mpi.Root()) { cout << "Solution error: " << error << endl; }
-   }
-
-   // Free the used memory.
-   delete ode_solver;
-
-   return 0;
-}

examples/ex19.cpp

@@ -1,538 +0,0 @@
-//                                MFEM Example 19
-//
-// Compile with: make ex19
-//
-// Sample runs:
-//    ex19 -m ../data/beam-quad.mesh
-//    ex19 -m ../data/beam-tri.mesh
-//    ex19 -m ../data/beam-hex.mesh
-//    ex19 -m ../data/beam-tet.mesh
-//    ex19 -m ../data/beam-wedge.mesh
-//
-// Description:  This examples solves a quasi-static incompressible nonlinear
-//               elasticity problem of the form 0 = H(x), where H is an
-//               incompressible hyperelastic model and x is a block state vector
-//               containing displacement and pressure variables. The geometry of
-//               the domain is assumed to be as follows:
-//
-//                                 +---------------------+
-//                    boundary --->|                     |<--- boundary
-//                    attribute 1  |                     |     attribute 2
-//                    (fixed)      +---------------------+     (fixed, nonzero)
-//
-//               The example demonstrates the use of block nonlinear operators
-//               (the class RubberOperator defining H(x)) as well as a nonlinear
-//               Newton solver for the quasi-static problem. Each Newton step
-//               requires the inversion of a Jacobian matrix, which is done
-//               through a (preconditioned) inner solver. The specialized block
-//               preconditioner is implemented as a user-defined solver.
-//
-//               We recommend viewing examples 2, 5, and 10 before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <memory>
-#include <iostream>
-#include <fstream>
-
-using namespace std;
-using namespace mfem;
-
-// Custom block preconditioner for the Jacobian of the incompressible nonlinear
-// elasticity operator. It has the form
-//
-// P^-1 = [ K^-1 0 ][ I -B^T ][ I  0           ]
-//        [ 0    I ][ 0  I   ][ 0 -\gamma S^-1 ]
-//
-// where the original Jacobian has the form
-//
-// J = [ K B^T ]
-//     [ B 0   ]
-//
-// and K^-1 is an approximation of the inverse of the displacement part of the
-// Jacobian and S^-1 is an approximation of the inverse of the Schur
-// complement S = B K^-1 B^T. The Schur complement is approximated using
-// a mass matrix of the pressure variables.
-class JacobianPreconditioner : public Solver
-{
-protected:
-   // Finite element spaces for setting up preconditioner blocks
-   Array<FiniteElementSpace *> spaces;
-
-   // Offsets for extracting block vector segments
-   Array<int> &block_offsets;
-
-   // Jacobian for block access
-   BlockOperator *jacobian;
-
-   // Scaling factor for the pressure mass matrix in the block preconditioner
-   double gamma;
-
-   // Objects for the block preconditioner application
-   SparseMatrix *pressure_mass;
-   Solver *mass_pcg;
-   Solver *mass_prec;
-   Solver *stiff_pcg;
-   Solver *stiff_prec;
-
-public:
-   JacobianPreconditioner(Array<FiniteElementSpace *> &fes,
-                          SparseMatrix &mass, Array<int> &offsets);
-
-   virtual void Mult(const Vector &k, Vector &y) const;
-   virtual void SetOperator(const Operator &op);
-
-   virtual ~JacobianPreconditioner();
-};
-
-// After spatial discretization, the rubber model can be written as:
-//     0 = H(x)
-// where x is the block vector representing the deformation and pressure and
-// H(x) is the nonlinear incompressible neo-Hookean operator.
-class RubberOperator : public Operator
-{
-protected:
-   // Finite element spaces
-   Array<FiniteElementSpace *> spaces;
-
-   // Block nonlinear form
-   BlockNonlinearForm *Hform;
-
-   // Pressure mass matrix for the preconditioner
-   SparseMatrix *pressure_mass;
-
-   // Newton solver for the hyperelastic operator
-   NewtonSolver newton_solver;
-
-   // Solver for the Jacobian solve in the Newton method
-   Solver *j_solver;
-
-   // Preconditioner for the Jacobian
-   Solver *j_prec;
-
-   // Shear modulus coefficient
-   Coefficient &mu;
-
-   // Block offsets for variable access
-   Array<int> &block_offsets;
-
-public:
-   RubberOperator(Array<FiniteElementSpace *> &fes, Array<Array<int> *>&ess_bdr,
-                  Array<int> &block_trueOffsets, double rel_tol, double abs_tol,
-                  int iter, Coefficient &mu);
-
-   // Required to use the native newton solver
-   virtual Operator &GetGradient(const Vector &xp) const;
-   virtual void Mult(const Vector &k, Vector &y) const;
-
-   // Driver for the newton solver
-   void Solve(Vector &xp) const;
-
-   virtual ~RubberOperator();
-};
-
-// Visualization driver
-void visualize(ostream &out, Mesh *mesh, GridFunction *deformed_nodes,
-               GridFunction *field, const char *field_name = NULL,
-               bool init_vis = false);
-
-// Configuration definition functions
-void ReferenceConfiguration(const Vector &x, Vector &y);
-void InitialDeformation(const Vector &x, Vector &y);
-
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options
-   const char *mesh_file = "../data/beam-hex.mesh";
-   int ref_levels = 0;
-   int order = 2;
-   bool visualization = true;
-   double newton_rel_tol = 1e-4;
-   double newton_abs_tol = 1e-6;
-   int newton_iter = 500;
-   double mu = 1.0;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&ref_levels, "-r", "--refine",
-                  "Number of times to refine the mesh uniformly.");
-   args.AddOption(&order, "-o", "--order",
-                  "Order (degree) of the finite elements.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&newton_rel_tol, "-rel", "--relative-tolerance",
-                  "Relative tolerance for the Newton solve.");
-   args.AddOption(&newton_abs_tol, "-abs", "--absolute-tolerance",
-                  "Absolute tolerance for the Newton solve.");
-   args.AddOption(&newton_iter, "-it", "--newton-iterations",
-                  "Maximum iterations for the Newton solve.");
-   args.AddOption(&mu, "-mu", "--shear-modulus",
-                  "Shear modulus for the neo-Hookean material.");
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   // 2. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral and hexahedral meshes with the same code.
-   Mesh *mesh = new Mesh(mesh_file, 1, 1);
-   int dim = mesh->Dimension();
-
-   // 3. Refine the mesh to increase the resolution. In this example we do
-   //    'ref_levels' of uniform refinement, where 'ref_levels' is a
-   //    command-line parameter.
-   for (int lev = 0; lev < ref_levels; lev++)
-   {
-      mesh->UniformRefinement();
-   }
-
-   // 4. Define the shear modulus for the incompressible Neo-Hookean material
-   ConstantCoefficient c_mu(mu);
-
-   // 5. Define the finite element spaces for displacement and pressure
-   //    (Taylor-Hood elements). By default, the displacement (u/x) is a second
-   //    order vector field, while the pressure (p) is a linear scalar function.
-   H1_FECollection quad_coll(order, dim);
-   H1_FECollection lin_coll(order-1, dim);
-
-   FiniteElementSpace R_space(mesh, &quad_coll, dim, Ordering::byVDIM);
-   FiniteElementSpace W_space(mesh, &lin_coll);
-
-   Array<FiniteElementSpace *> spaces(2);
-   spaces[0] = &R_space;
-   spaces[1] = &W_space;
-
-   int R_size = R_space.GetVSize();
-   int W_size = W_space.GetVSize();
-
-   // 6. Define the Dirichlet conditions (set to boundary attribute 1 and 2)
-   Array<Array<int> *> ess_bdr(2);
-
-   Array<int> ess_bdr_u(R_space.GetMesh()->bdr_attributes.Max());
-   Array<int> ess_bdr_p(W_space.GetMesh()->bdr_attributes.Max());
-
-   ess_bdr_p = 0;
-   ess_bdr_u = 0;
-   ess_bdr_u[0] = 1;
-   ess_bdr_u[1] = 1;
-
-   ess_bdr[0] = &ess_bdr_u;
-   ess_bdr[1] = &ess_bdr_p;
-
-   // 7. Print the mesh statistics
-   std::cout << "***********************************************************\n";
-   std::cout << "dim(u) = " << R_size << "\n";
-   std::cout << "dim(p) = " << W_size << "\n";
-   std::cout << "dim(u+p) = " << R_size + W_size << "\n";
-   std::cout << "***********************************************************\n";
-
-   // 8. Define the block structure of the solution vector (u then p)
-   Array<int> block_offsets(3);
-   block_offsets[0] = 0;
-   block_offsets[1] = R_space.GetVSize();
-   block_offsets[2] = W_space.GetVSize();
-   block_offsets.PartialSum();
-
-   BlockVector xp(block_offsets);
-
-   // 9. Define grid functions for the current configuration, reference
-   //    configuration, final deformation, and pressure
-   GridFunction x_gf(&R_space);
-   GridFunction x_ref(&R_space);
-   GridFunction x_def(&R_space);
-   GridFunction p_gf(&W_space);
-
-   x_gf.MakeRef(&R_space, xp.GetBlock(0), 0);
-   p_gf.MakeRef(&W_space, xp.GetBlock(1), 0);
-
-   VectorFunctionCoefficient deform(dim, InitialDeformation);
-   VectorFunctionCoefficient refconfig(dim, ReferenceConfiguration);
-
-   x_gf.ProjectCoefficient(deform);
-   x_ref.ProjectCoefficient(refconfig);
-   p_gf = 0.0;
-
-   // 10. Initialize the incompressible neo-Hookean operator
-   RubberOperator oper(spaces, ess_bdr, block_offsets,
-                       newton_rel_tol, newton_abs_tol, newton_iter, c_mu);
-
-   // 11. Solve the Newton system
-   oper.Solve(xp);
-
-   // 12. Compute the final deformation
-   subtract(x_gf, x_ref, x_def);
-
-   // 13. Visualize the results if requested
-   socketstream vis_u, vis_p;
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      vis_u.open(vishost, visport);
-      vis_u.precision(8);
-      visualize(vis_u, mesh, &x_gf, &x_def, "Deformation", true);
-      vis_p.open(vishost, visport);
-      vis_p.precision(8);
-      visualize(vis_p, mesh, &x_gf, &p_gf, "Pressure", true);
-   }
-
-   // 14. Save the displaced mesh, the final deformation, and the pressure
-   {
-      GridFunction *nodes = &x_gf;
-      int owns_nodes = 0;
-      mesh->SwapNodes(nodes, owns_nodes);
-
-      ofstream mesh_ofs("deformed.mesh");
-      mesh_ofs.precision(8);
-      mesh->Print(mesh_ofs);
-
-      ofstream pressure_ofs("pressure.sol");
-      pressure_ofs.precision(8);
-      p_gf.Save(pressure_ofs);
-
-      ofstream deformation_ofs("deformation.sol");
-      deformation_ofs.precision(8);
-      x_def.Save(deformation_ofs);
-   }
-
-   // 15. Free the used memory
-   delete mesh;
-
-   return 0;
-}
-
-
-JacobianPreconditioner::JacobianPreconditioner(Array<FiniteElementSpace *> &fes,
-                                               SparseMatrix &mass,
-                                               Array<int> &offsets)
-   : Solver(offsets[2]), block_offsets(offsets), pressure_mass(&mass)
-{
-   fes.Copy(spaces);
-
-   gamma = 0.00001;
-
-   // The mass matrix and preconditioner do not change every Newton cycle, so we
-   // only need to define them once
-   GSSmoother *mass_prec_gs = new GSSmoother(*pressure_mass);
-
-   mass_prec = mass_prec_gs;
-
-   CGSolver *mass_pcg_iter = new CGSolver();
-   mass_pcg_iter->SetRelTol(1e-12);
-   mass_pcg_iter->SetAbsTol(1e-12);
-   mass_pcg_iter->SetMaxIter(200);
-   mass_pcg_iter->SetPrintLevel(0);
-   mass_pcg_iter->SetPreconditioner(*mass_prec);
-   mass_pcg_iter->SetOperator(*pressure_mass);
-   mass_pcg_iter->iterative_mode = false;
-
-   mass_pcg = mass_pcg_iter;
-
-   // The stiffness matrix does change every Newton cycle, so we will define it
-   // during SetOperator
-   stiff_pcg = NULL;
-   stiff_prec = NULL;
-}
-
-void JacobianPreconditioner::Mult(const Vector &k, Vector &y) const
-{
-   // Extract the blocks from the input and output vectors
-   Vector disp_in(k.GetData() + block_offsets[0],
-                  block_offsets[1]-block_offsets[0]);
-   Vector pres_in(k.GetData() + block_offsets[1],
-                  block_offsets[2]-block_offsets[1]);
-
-   Vector disp_out(y.GetData() + block_offsets[0],
-                   block_offsets[1]-block_offsets[0]);
-   Vector pres_out(y.GetData() + block_offsets[1],
-                   block_offsets[2]-block_offsets[1]);
-
-   Vector temp(block_offsets[1]-block_offsets[0]);
-   Vector temp2(block_offsets[1]-block_offsets[0]);
-
-   // Perform the block elimination for the preconditioner
-   mass_pcg->Mult(pres_in, pres_out);
-   pres_out *= -gamma;
-
-   jacobian->GetBlock(0,1).Mult(pres_out, temp);
-   subtract(disp_in, temp, temp2);
-
-   stiff_pcg->Mult(temp2, disp_out);
-}
-
-void JacobianPreconditioner::SetOperator(const Operator &op)
-{
-   jacobian = (BlockOperator *) &op;
-
-   // Initialize the stiffness preconditioner and solver
-   if (stiff_prec == NULL)
-   {
-      GSSmoother *stiff_prec_gs = new GSSmoother();
-
-      stiff_prec = stiff_prec_gs;
-
-      GMRESSolver *stiff_pcg_iter = new GMRESSolver();
-      stiff_pcg_iter->SetRelTol(1e-8);
-      stiff_pcg_iter->SetAbsTol(1e-8);
-      stiff_pcg_iter->SetMaxIter(200);
-      stiff_pcg_iter->SetPrintLevel(0);
-      stiff_pcg_iter->SetPreconditioner(*stiff_prec);
-      stiff_pcg_iter->iterative_mode = false;
-
-      stiff_pcg = stiff_pcg_iter;
-   }
-
-   // At each Newton cycle, compute the new stiffness preconditioner by updating
-   // the iterative solver which, in turn, updates its preconditioner
-   stiff_pcg->SetOperator(jacobian->GetBlock(0,0));
-}
-
-JacobianPreconditioner::~JacobianPreconditioner()
-{
-   delete mass_pcg;
-   delete mass_prec;
-   delete stiff_prec;
-   delete stiff_pcg;
-}
-
-
-RubberOperator::RubberOperator(Array<FiniteElementSpace *> &fes,
-                               Array<Array<int> *> &ess_bdr,
-                               Array<int> &offsets,
-                               double rel_tol,
-                               double abs_tol,
-                               int iter,
-                               Coefficient &c_mu)
-   : Operator(fes[0]->GetVSize() + fes[1]->GetVSize()),
-     newton_solver(), mu(c_mu), block_offsets(offsets)
-{
-   Array<Vector *> rhs(2);
-   rhs = NULL; // Set all entries in the array
-
-   fes.Copy(spaces);
-
-   // Define the block nonlinear form
-   Hform = new BlockNonlinearForm(spaces);
-
-   // Add the incompressible neo-Hookean integrator
-   Hform->AddDomainIntegrator(new IncompressibleNeoHookeanIntegrator(mu));
-
-   // Set the essential boundary conditions
-   Hform->SetEssentialBC(ess_bdr, rhs);
-
-   // Compute the pressure mass stiffness matrix
-   BilinearForm *a = new BilinearForm(spaces[1]);
-   ConstantCoefficient one(1.0);
-   a->AddDomainIntegrator(new MassIntegrator(one));
-   a->Assemble();
-   a->Finalize();
-   pressure_mass = a->LoseMat();
-   delete a;
-
-   // Initialize the Jacobian preconditioner
-   JacobianPreconditioner *jac_prec =
-      new JacobianPreconditioner(fes, *pressure_mass, block_offsets);
-   j_prec = jac_prec;
-
-   // Set up the Jacobian solver
-   GMRESSolver *j_gmres = new GMRESSolver();
-   j_gmres->iterative_mode = false;
-   j_gmres->SetRelTol(1e-12);
-   j_gmres->SetAbsTol(1e-12);
-   j_gmres->SetMaxIter(300);
-   j_gmres->SetPrintLevel(0);
-   j_gmres->SetPreconditioner(*j_prec);
-   j_solver = j_gmres;
-
-   // Set the newton solve parameters
-   newton_solver.iterative_mode = true;
-   newton_solver.SetSolver(*j_solver);
-   newton_solver.SetOperator(*this);
-   newton_solver.SetPrintLevel(1);
-   newton_solver.SetRelTol(rel_tol);
-   newton_solver.SetAbsTol(abs_tol);
-   newton_solver.SetMaxIter(iter);
-}
-
-// Solve the Newton system
-void RubberOperator::Solve(Vector &xp) const
-{
-   Vector zero;
-   newton_solver.Mult(zero, xp);
-   MFEM_VERIFY(newton_solver.GetConverged(),
-               "Newton Solver did not converge.");
-}
-
-// compute: y = H(x,p)
-void RubberOperator::Mult(const Vector &k, Vector &y) const
-{
-   Hform->Mult(k, y);
-}
-
-// Compute the Jacobian from the nonlinear form
-Operator &RubberOperator::GetGradient(const Vector &xp) const
-{
-   return Hform->GetGradient(xp);
-}
-
-RubberOperator::~RubberOperator()
-{
-   delete Hform;
-   delete pressure_mass;
-   delete j_solver;
-   delete j_prec;
-}
-
-
-// Inline visualization
-void visualize(ostream &out, Mesh *mesh, GridFunction *deformed_nodes,
-               GridFunction *field, const char *field_name, bool init_vis)
-{
-   if (!out)
-   {
-      return;
-   }
-
-   GridFunction *nodes = deformed_nodes;
-   int owns_nodes = 0;
-
-   mesh->SwapNodes(nodes, owns_nodes);
-
-   out << "solution\n" << *mesh << *field;
-
-   mesh->SwapNodes(nodes, owns_nodes);
-
-   if (init_vis)
-   {
-      out << "window_size 800 800\n";
-      out << "window_title '" << field_name << "'\n";
-      if (mesh->SpaceDimension() == 2)
-      {
-         out << "view 0 0\n"; // view from top
-         out << "keys jlA\n"; // turn off perspective and light, +anti-aliasing
-      }
-      out << "keys cmA\n";        // show colorbar and mesh, +anti-aliasing
-      out << "autoscale value\n"; // update value-range; keep mesh-extents fixed
-   }
-   out << flush;
-}
-
-void ReferenceConfiguration(const Vector &x, Vector &y)
-{
-   // Set the reference, stress free, configuration
-   y = x;
-}
-
-void InitialDeformation(const Vector &x, Vector &y)
-{
-   // Set the initial configuration. Having this different from the reference
-   // configuration can help convergence
-   y = x;
-   y[1] = x[1] + 0.25*x[0];
-}

examples/ex19p.cpp

@@ -1,592 +0,0 @@
-//                       MFEM Example 19 - Parallel Version
-//
-// Compile with: make ex19p
-//
-// Sample runs:
-//    mpirun -np 2 ex19p -m ../data/beam-quad.mesh
-//    mpirun -np 2 ex19p -m ../data/beam-tri.mesh
-//    mpirun -np 2 ex19p -m ../data/beam-hex.mesh
-//    mpirun -np 2 ex19p -m ../data/beam-tet.mesh
-//    mpirun -np 2 ex19p -m ../data/beam-wedge.mesh
-//
-// Description:  This examples solves a quasi-static incompressible nonlinear
-//               elasticity problem of the form 0 = H(x), where H is an
-//               incompressible hyperelastic model and x is a block state vector
-//               containing displacement and pressure variables. The geometry of
-//               the domain is assumed to be as follows:
-//
-//                                 +---------------------+
-//                    boundary --->|                     |<--- boundary
-//                    attribute 1  |                     |     attribute 2
-//                    (fixed)      +---------------------+     (fixed, nonzero)
-//
-//               The example demonstrates the use of block nonlinear operators
-//               (the class RubberOperator defining H(x)) as well as a nonlinear
-//               Newton solver for the quasi-static problem. Each Newton step
-//               requires the inversion of a Jacobian matrix, which is done
-//               through a (preconditioned) inner solver. The specialized block
-//               preconditioner is implemented as a user-defined solver.
-//
-//               We recommend viewing examples 2, 5, and 10 before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <memory>
-#include <iostream>
-#include <fstream>
-
-using namespace std;
-using namespace mfem;
-
-// Custom block preconditioner for the Jacobian of the incompressible nonlinear
-// elasticity operator. It has the form
-//
-// P^-1 = [ K^-1 0 ][ I -B^T ][ I  0           ]
-//        [ 0    I ][ 0  I   ][ 0 -\gamma S^-1 ]
-//
-// where the original Jacobian has the form
-//
-// J = [ K B^T ]
-//     [ B 0   ]
-//
-// and K^-1 is an approximation of the inverse of the displacement part of the
-// Jacobian and S^-1 is an approximation of the inverse of the Schur
-// complement S = B K^-1 B^T. The Schur complement is approximated using
-// a mass matrix of the pressure variables.
-class JacobianPreconditioner : public Solver
-{
-protected:
-   // Finite element spaces for setting up preconditioner blocks
-   Array<ParFiniteElementSpace *> spaces;
-
-   // Offsets for extracting block vector segments
-   Array<int> &block_trueOffsets;
-
-   // Jacobian for block access
-   BlockOperator *jacobian;
-
-   // Scaling factor for the pressure mass matrix in the block preconditioner
-   double gamma;
-
-   // Objects for the block preconditioner application
-   Operator *pressure_mass;
-   Solver *mass_pcg;
-   Solver *mass_prec;
-   Solver *stiff_pcg;
-   Solver *stiff_prec;
-
-public:
-   JacobianPreconditioner(Array<ParFiniteElementSpace *> &fes,
-                          Operator &mass, Array<int> &offsets);
-
-   virtual void Mult(const Vector &k, Vector &y) const;
-   virtual void SetOperator(const Operator &op);
-
-   virtual ~JacobianPreconditioner();
-};
-
-// After spatial discretization, the rubber model can be written as:
-//     0 = H(x)
-// where x is the block vector representing the deformation and pressure and
-// H(x) is the nonlinear incompressible neo-Hookean operator.
-class RubberOperator : public Operator
-{
-protected:
-   // Finite element spaces
-   Array<ParFiniteElementSpace *> spaces;
-
-   // Block nonlinear form
-   ParBlockNonlinearForm *Hform;
-
-   // Pressure mass matrix for the preconditioner
-   Operator *pressure_mass;
-
-   // Newton solver for the hyperelastic operator
-   NewtonSolver newton_solver;
-
-   // Solver for the Jacobian solve in the Newton method
-   Solver *j_solver;
-
-   // Preconditioner for the Jacobian
-   Solver *j_prec;
-
-   // Shear modulus coefficient
-   Coefficient &mu;
-
-   // Block offsets for variable access
-   Array<int> &block_trueOffsets;
-
-public:
-   RubberOperator(Array<ParFiniteElementSpace *> &fes, Array<Array<int> *>&ess_bdr,
-                  Array<int> &block_trueOffsets, double rel_tol, double abs_tol,
-                  int iter, Coefficient &mu);
-
-   // Required to use the native newton solver
-   virtual Operator &GetGradient(const Vector &xp) const;
-   virtual void Mult(const Vector &k, Vector &y) const;
-
-   // Driver for the newton solver
-   void Solve(Vector &xp) const;
-
-   virtual ~RubberOperator();
-};
-
-// Visualization driver
-void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
-               ParGridFunction *field, const char *field_name = NULL,
-               bool init_vis = false);
-
-// Configuration definition functions
-void ReferenceConfiguration(const Vector &x, Vector &y);
-void InitialDeformation(const Vector &x, Vector &y);
-
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 2. Parse command-line options
-   const char *mesh_file = "../data/beam-hex.mesh";
-   int ser_ref_levels = 0;
-   int par_ref_levels = 0;
-   int order = 2;
-   bool visualization = true;
-   double newton_rel_tol = 1e-4;
-   double newton_abs_tol = 1e-6;
-   int newton_iter = 500;
-   double mu = 1.0;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
-                  "Number of times to refine the mesh uniformly in serial.");
-   args.AddOption(&par_ref_levels, "-rp", "--refine-parallel",
-                  "Number of times to refine the mesh uniformly in parallel.");
-   args.AddOption(&order, "-o", "--order",
-                  "Order (degree) of the finite elements.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&newton_rel_tol, "-rel", "--relative-tolerance",
-                  "Relative tolerance for the Newton solve.");
-   args.AddOption(&newton_abs_tol, "-abs", "--absolute-tolerance",
-                  "Absolute tolerance for the Newton solve.");
-   args.AddOption(&newton_iter, "-it", "--newton-iterations",
-                  "Maximum iterations for the Newton solve.");
-   args.AddOption(&mu, "-mu", "--shear-modulus",
-                  "Shear modulus for the neo-Hookean material.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
-   //    can handle triangular, quadrilateral, tetrahedral and hexahedral meshes
-   //    with the same code.
-   Mesh *mesh = new Mesh(mesh_file, 1, 1);
-   int dim = mesh->Dimension();
-
-   // 4. Refine the mesh in serial to increase the resolution. In this example
-   //    we do 'ser_ref_levels' of uniform refinement, where 'ser_ref_levels' is
-   //    a command-line parameter.
-   for (int lev = 0; lev < ser_ref_levels; lev++)
-   {
-      mesh->UniformRefinement();
-   }
-
-   // 5. Define a parallel mesh by a partitioning of the serial mesh. Refine
-   //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
-   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
-   delete mesh;
-   for (int lev = 0; lev < par_ref_levels; lev++)
-   {
-      pmesh->UniformRefinement();
-   }
-
-   // 6. Define the shear modulus for the incompressible Neo-Hookean material
-   ConstantCoefficient c_mu(mu);
-
-   // 7. Define the finite element spaces for displacement and pressure
-   //    (Taylor-Hood elements). By default, the displacement (u/x) is a second
-   //    order vector field, while the pressure (p) is a linear scalar function.
-   H1_FECollection quad_coll(order, dim);
-   H1_FECollection lin_coll(order-1, dim);
-
-   ParFiniteElementSpace R_space(pmesh, &quad_coll, dim, Ordering::byVDIM);
-   ParFiniteElementSpace W_space(pmesh, &lin_coll);
-
-   Array<ParFiniteElementSpace *> spaces(2);
-   spaces[0] = &R_space;
-   spaces[1] = &W_space;
-
-   HYPRE_Int glob_R_size = R_space.GlobalTrueVSize();
-   HYPRE_Int glob_W_size = W_space.GlobalTrueVSize();
-
-   // 8. Define the Dirichlet conditions (set to boundary attribute 1 and 2)
-   Array<Array<int> *> ess_bdr(2);
-
-   Array<int> ess_bdr_u(R_space.GetMesh()->bdr_attributes.Max());
-   Array<int> ess_bdr_p(W_space.GetMesh()->bdr_attributes.Max());
-
-   ess_bdr_p = 0;
-   ess_bdr_u = 0;
-   ess_bdr_u[0] = 1;
-   ess_bdr_u[1] = 1;
-
-   ess_bdr[0] = &ess_bdr_u;
-   ess_bdr[1] = &ess_bdr_p;
-
-   // 9. Print the mesh statistics
-   if (myid == 0)
-   {
-      std::cout << "***********************************************************\n";
-      std::cout << "dim(u) = " << glob_R_size << "\n";
-      std::cout << "dim(p) = " << glob_W_size << "\n";
-      std::cout << "dim(u+p) = " << glob_R_size + glob_W_size << "\n";
-      std::cout << "***********************************************************\n";
-   }
-
-   // 10. Define the block structure of the solution vector (u then p)
-   Array<int> block_trueOffsets(3);
-   block_trueOffsets[0] = 0;
-   block_trueOffsets[1] = R_space.TrueVSize();
-   block_trueOffsets[2] = W_space.TrueVSize();
-   block_trueOffsets.PartialSum();
-
-   BlockVector xp(block_trueOffsets);
-
-   // 11. Define grid functions for the current configuration, reference
-   //     configuration, final deformation, and pressure
-   ParGridFunction x_gf(&R_space);
-   ParGridFunction x_ref(&R_space);
-   ParGridFunction x_def(&R_space);
-   ParGridFunction p_gf(&W_space);
-
-   VectorFunctionCoefficient deform(dim, InitialDeformation);
-   VectorFunctionCoefficient refconfig(dim, ReferenceConfiguration);
-
-   x_gf.ProjectCoefficient(deform);
-   x_ref.ProjectCoefficient(refconfig);
-   p_gf = 0.0;
-
-   // 12. Set up the block solution vectors
-   x_gf.GetTrueDofs(xp.GetBlock(0));
-   p_gf.GetTrueDofs(xp.GetBlock(1));
-
-   // 13. Initialize the incompressible neo-Hookean operator
-   RubberOperator oper(spaces, ess_bdr, block_trueOffsets,
-                       newton_rel_tol, newton_abs_tol, newton_iter, c_mu);
-
-   // 14. Solve the Newton system
-   oper.Solve(xp);
-
-   // 15. Distribute the shared degrees of freedom
-   x_gf.Distribute(xp.GetBlock(0));
-   p_gf.Distribute(xp.GetBlock(1));
-
-   // 16. Compute the final deformation
-   subtract(x_gf, x_ref, x_def);
-
-   // 17. Visualize the results if requested
-   socketstream vis_u, vis_p;
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      vis_u.open(vishost, visport);
-      vis_u.precision(8);
-      visualize(vis_u, pmesh, &x_gf, &x_def, "Deformation", true);
-      // Make sure all ranks have sent their 'u' solution before initiating
-      // another set of GLVis connections (one from each rank):
-      MPI_Barrier(pmesh->GetComm());
-      vis_p.open(vishost, visport);
-      vis_p.precision(8);
-      visualize(vis_p, pmesh, &x_gf, &p_gf, "Pressure", true);
-   }
-
-   // 18. Save the displaced mesh, the final deformation, and the pressure
-   {
-      GridFunction *nodes = &x_gf;
-      int owns_nodes = 0;
-      pmesh->SwapNodes(nodes, owns_nodes);
-
-      ostringstream mesh_name, pressure_name, deformation_name;
-      mesh_name << "mesh." << setfill('0') << setw(6) << myid;
-      pressure_name << "pressure." << setfill('0') << setw(6) << myid;
-      deformation_name << "deformation." << setfill('0') << setw(6) << myid;
-
-      ofstream mesh_ofs(mesh_name.str().c_str());
-      mesh_ofs.precision(8);
-      pmesh->Print(mesh_ofs);
-
-      ofstream pressure_ofs(pressure_name.str().c_str());
-      pressure_ofs.precision(8);
-      p_gf.Save(pressure_ofs);
-
-      ofstream deformation_ofs(deformation_name.str().c_str());
-      deformation_ofs.precision(8);
-      x_def.Save(deformation_ofs);
-   }
-
-   // 19. Free the used memory
-   delete pmesh;
-
-   MPI_Finalize();
-
-   return 0;
-}
-
-
-JacobianPreconditioner::JacobianPreconditioner(Array<ParFiniteElementSpace *>
-                                               &fes,
-                                               Operator &mass,
-                                               Array<int> &offsets)
-   : Solver(offsets[2]), block_trueOffsets(offsets), pressure_mass(&mass)
-{
-   fes.Copy(spaces);
-
-   gamma = 0.00001;
-
-   // The mass matrix and preconditioner do not change every Newton cycle, so
-   // we only need to define them once
-   HypreBoomerAMG *mass_prec_amg = new HypreBoomerAMG();
-   mass_prec_amg->SetPrintLevel(0);
-
-   mass_prec = mass_prec_amg;
-
-   CGSolver *mass_pcg_iter = new CGSolver(spaces[0]->GetComm());
-   mass_pcg_iter->SetRelTol(1e-12);
-   mass_pcg_iter->SetAbsTol(1e-12);
-   mass_pcg_iter->SetMaxIter(200);
-   mass_pcg_iter->SetPrintLevel(0);
-   mass_pcg_iter->SetPreconditioner(*mass_prec);
-   mass_pcg_iter->SetOperator(*pressure_mass);
-   mass_pcg_iter->iterative_mode = false;
-
-   mass_pcg = mass_pcg_iter;
-
-   // The stiffness matrix does change every Newton cycle, so we will define it
-   // during SetOperator
-   stiff_pcg = NULL;
-   stiff_prec = NULL;
-}
-
-void JacobianPreconditioner::Mult(const Vector &k, Vector &y) const
-{
-   // Extract the blocks from the input and output vectors
-   Vector disp_in(k.GetData() + block_trueOffsets[0],
-                  block_trueOffsets[1]-block_trueOffsets[0]);
-   Vector pres_in(k.GetData() + block_trueOffsets[1],
-                  block_trueOffsets[2]-block_trueOffsets[1]);
-
-   Vector disp_out(y.GetData() + block_trueOffsets[0],
-                   block_trueOffsets[1]-block_trueOffsets[0]);
-   Vector pres_out(y.GetData() + block_trueOffsets[1],
-                   block_trueOffsets[2]-block_trueOffsets[1]);
-
-   Vector temp(block_trueOffsets[1]-block_trueOffsets[0]);
-   Vector temp2(block_trueOffsets[1]-block_trueOffsets[0]);
-
-   // Perform the block elimination for the preconditioner
-   mass_pcg->Mult(pres_in, pres_out);
-   pres_out *= -gamma;
-
-   jacobian->GetBlock(0,1).Mult(pres_out, temp);
-   subtract(disp_in, temp, temp2);
-
-   stiff_pcg->Mult(temp2, disp_out);
-}
-
-void JacobianPreconditioner::SetOperator(const Operator &op)
-{
-   jacobian = (BlockOperator *) &op;
-
-   // Initialize the stiffness preconditioner and solver
-   if (stiff_prec == NULL)
-   {
-      HypreBoomerAMG *stiff_prec_amg = new HypreBoomerAMG();
-      stiff_prec_amg->SetPrintLevel(0);
-      stiff_prec_amg->SetElasticityOptions(spaces[0]);
-
-      stiff_prec = stiff_prec_amg;
-
-      GMRESSolver *stiff_pcg_iter = new GMRESSolver(spaces[0]->GetComm());
-      stiff_pcg_iter->SetRelTol(1e-8);
-      stiff_pcg_iter->SetAbsTol(1e-8);
-      stiff_pcg_iter->SetMaxIter(200);
-      stiff_pcg_iter->SetPrintLevel(0);
-      stiff_pcg_iter->SetPreconditioner(*stiff_prec);
-      stiff_pcg_iter->iterative_mode = false;
-
-      stiff_pcg = stiff_pcg_iter;
-   }
-
-   // At each Newton cycle, compute the new stiffness AMG preconditioner by
-   // updating the iterative solver which, in turn, updates its preconditioner
-   stiff_pcg->SetOperator(jacobian->GetBlock(0,0));
-}
-
-JacobianPreconditioner::~JacobianPreconditioner()
-{
-   delete mass_pcg;
-   delete mass_prec;
-   delete stiff_prec;
-   delete stiff_pcg;
-}
-
-
-RubberOperator::RubberOperator(Array<ParFiniteElementSpace *> &fes,
-                               Array<Array<int> *> &ess_bdr,
-                               Array<int> &trueOffsets,
-                               double rel_tol,
-                               double abs_tol,
-                               int iter,
-                               Coefficient &c_mu)
-   : Operator(fes[0]->TrueVSize() + fes[1]->TrueVSize()),
-     newton_solver(fes[0]->GetComm()), mu(c_mu), block_trueOffsets(trueOffsets)
-{
-   Array<Vector *> rhs(2);
-   rhs = NULL; // Set all entries in the array
-
-   fes.Copy(spaces);
-
-   // Define the block nonlinear form
-   Hform = new ParBlockNonlinearForm(spaces);
-
-   // Add the incompressible neo-Hookean integrator
-   Hform->AddDomainIntegrator(new IncompressibleNeoHookeanIntegrator(mu));
-
-   // Set the essential boundary conditions
-   Hform->SetEssentialBC(ess_bdr, rhs);
-
-   // Compute the pressure mass stiffness matrix
-   ParBilinearForm *a = new ParBilinearForm(spaces[1]);
-   ConstantCoefficient one(1.0);
-   OperatorHandle mass(Operator::Hypre_ParCSR);
-   a->AddDomainIntegrator(new MassIntegrator(one));
-   a->Assemble();
-   a->Finalize();
-   a->ParallelAssemble(mass);
-   delete a;
-
-   mass.SetOperatorOwner(false);
-   pressure_mass = mass.Ptr();
-
-   // Initialize the Jacobian preconditioner
-   JacobianPreconditioner *jac_prec =
-      new JacobianPreconditioner(fes, *pressure_mass, block_trueOffsets);
-   j_prec = jac_prec;
-
-   // Set up the Jacobian solver
-   GMRESSolver *j_gmres = new GMRESSolver(spaces[0]->GetComm());
-   j_gmres->iterative_mode = false;
-   j_gmres->SetRelTol(1e-12);
-   j_gmres->SetAbsTol(1e-12);
-   j_gmres->SetMaxIter(300);
-   j_gmres->SetPrintLevel(0);
-   j_gmres->SetPreconditioner(*j_prec);
-   j_solver = j_gmres;
-
-   // Set the newton solve parameters
-   newton_solver.iterative_mode = true;
-   newton_solver.SetSolver(*j_solver);
-   newton_solver.SetOperator(*this);
-   newton_solver.SetPrintLevel(1);
-   newton_solver.SetRelTol(rel_tol);
-   newton_solver.SetAbsTol(abs_tol);
-   newton_solver.SetMaxIter(iter);
-}
-
-// Solve the Newton system
-void RubberOperator::Solve(Vector &xp) const
-{
-   Vector zero;
-   newton_solver.Mult(zero, xp);
-   MFEM_VERIFY(newton_solver.GetConverged(),
-               "Newton Solver did not converge.");
-}
-
-// compute: y = H(x,p)
-void RubberOperator::Mult(const Vector &k, Vector &y) const
-{
-   Hform->Mult(k, y);
-}
-
-// Compute the Jacobian from the nonlinear form
-Operator &RubberOperator::GetGradient(const Vector &xp) const
-{
-   return Hform->GetGradient(xp);
-}
-
-RubberOperator::~RubberOperator()
-{
-   delete Hform;
-   delete pressure_mass;
-   delete j_solver;
-   delete j_prec;
-}
-
-
-// Inline visualization
-void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
-               ParGridFunction *field, const char *field_name, bool init_vis)
-{
-   if (!out)
-   {
-      return;
-   }
-
-   GridFunction *nodes = deformed_nodes;
-   int owns_nodes = 0;
-
-   mesh->SwapNodes(nodes, owns_nodes);
-
-   out << "parallel " << mesh->GetNRanks() << " " << mesh->GetMyRank() << "\n";
-   out << "solution\n" << *mesh << *field;
-
-   mesh->SwapNodes(nodes, owns_nodes);
-
-   if (init_vis)
-   {
-      out << "window_size 800 800\n";
-      out << "window_title '" << field_name << "'\n";
-      if (mesh->SpaceDimension() == 2)
-      {
-         out << "view 0 0\n"; // view from top
-         out << "keys jlA\n"; // turn off perspective and light, +anti-aliasing
-      }
-      out << "keys cmA\n";        // show colorbar and mesh, +anti-aliasing
-      out << "autoscale value\n"; // update value-range; keep mesh-extents fixed
-   }
-   out << flush;
-}
-
-void ReferenceConfiguration(const Vector &x, Vector &y)
-{
-   // Set the reference, stress free, configuration
-   y = x;
-}
-
-void InitialDeformation(const Vector &x, Vector &y)
-{
-   // Set the initial configuration. Having this different from the reference
-   // configuration can help convergence
-   y = x;
-   y[1] = x[1] + 0.25*x[0];
-}

examples/ex1p.cpp

@@ -4,19 +4,14 @@
 //
 // Sample runs:  mpirun -np 4 ex1p -m ../data/square-disc.mesh
 //               mpirun -np 4 ex1p -m ../data/star.mesh
-//               mpirun -np 4 ex1p -m ../data/star-mixed.mesh
 //               mpirun -np 4 ex1p -m ../data/escher.mesh
 //               mpirun -np 4 ex1p -m ../data/fichera.mesh
-//               mpirun -np 4 ex1p -m ../data/fichera-mixed.mesh
-//               mpirun -np 4 ex1p -m ../data/toroid-wedge.mesh
 //               mpirun -np 4 ex1p -m ../data/square-disc-p2.vtk -o 2
 //               mpirun -np 4 ex1p -m ../data/square-disc-p3.mesh -o 3
 //               mpirun -np 4 ex1p -m ../data/square-disc-nurbs.mesh -o -1
-//               mpirun -np 4 ex1p -m ../data/star-mixed-p2.mesh -o 2
 //               mpirun -np 4 ex1p -m ../data/disc-nurbs.mesh -o -1
 //               mpirun -np 4 ex1p -m ../data/pipe-nurbs.mesh -o -1
 //               mpirun -np 4 ex1p -m ../data/ball-nurbs.mesh -o 2
-//               mpirun -np 4 ex1p -m ../data/fichera-mixed-p2.mesh -o 2
 //               mpirun -np 4 ex1p -m ../data/star-surf.mesh
 //               mpirun -np 4 ex1p -m ../data/square-disc-surf.mesh
 //               mpirun -np 4 ex1p -m ../data/inline-segment.mesh
@@ -25,11 +20,6 @@
 //               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh
 //               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh -o -1 -sc
 //
-// Device sample runs:
-//             > mpirun -np 4 ex1p -pa -d cuda
-//             > mpirun -np 4 ex1p -pa -d occa-cuda
-//             > mpirun -np 4 ex1p -pa -d raja-omp
-//
 // Description:  This example code demonstrates the use of MFEM to define a
 //               simple finite element discretization of the Laplace problem
 //               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
@@ -64,9 +54,7 @@ int main(int argc, char *argv[])
    const char *mesh_file = "../data/star.mesh";
    int order = 1;
    bool static_cond = false;
-   bool pa = false;
-   const char *device = "cpu";
-   bool visualization = true;
+   bool visualization = 1;
 
    OptionsParser args(argc, argv);
    args.AddOption(&mesh_file, "-m", "--mesh",
@@ -76,10 +64,6 @@ int main(int argc, char *argv[])
                   " isoparametric space.");
    args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
                   "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -177,58 +161,49 @@ int main(int argc, char *argv[])
    b->AddDomainIntegrator(new DomainLFIntegrator(one));
    b->Assemble();
 
-   // 9. Set device config parameters from the command line options and switch
-   //    to working on the device.
-   Device::Configure(device);
-   if (myid == 0) { Device::Print(); }
-   Device::Enable();
-
-   // 10. Define the solution vector x as a parallel finite element grid function
-   //     corresponding to fespace. Initialize x with initial guess of zero,
-   //     which satisfies the boundary conditions.
+   // 9. Define the solution vector x as a parallel finite element grid function
+   //    corresponding to fespace. Initialize x with initial guess of zero,
+   //    which satisfies the boundary conditions.
    ParGridFunction x(fespace);
    x = 0.0;
 
-   // 11. Set up the parallel bilinear form a(.,.) on the finite element space
+   // 10. Set up the parallel bilinear form a(.,.) on the finite element space
    //     corresponding to the Laplacian operator -Delta, by adding the Diffusion
    //     domain integrator.
    ParBilinearForm *a = new ParBilinearForm(fespace);
-   if (pa) { a->SetAssemblyLevel(AssemblyLevel::PARTIAL); }
    a->AddDomainIntegrator(new DiffusionIntegrator(one));
 
-   // 12. Assemble the parallel bilinear form and the corresponding linear
+   // 11. Assemble the parallel bilinear form and the corresponding linear
    //     system, applying any necessary transformations such as: parallel
    //     assembly, eliminating boundary conditions, applying conforming
    //     constraints for non-conforming AMR, static condensation, etc.
    if (static_cond) { a->EnableStaticCondensation(); }
    a->Assemble();
 
-   OperatorPtr A;
+   HypreParMatrix A;
    Vector B, X;
    a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
 
-   // 13. Solve the linear system A X = B.
-   //     * With full assembly, use the BoomerAMG preconditioner from hypre.
-   //     * With partial assembly, use no preconditioner, for now.
-   Solver *prec = NULL;
-   if (!pa) { prec = new HypreBoomerAMG; }
-   CGSolver cg(MPI_COMM_WORLD);
-   cg.SetRelTol(1e-12);
-   cg.SetMaxIter(2000);
-   cg.SetPrintLevel(1);
-   if (prec) { cg.SetPreconditioner(*prec); }
-   cg.SetOperator(*A);
-   cg.Mult(B, X);
-   delete prec;
+   if (myid == 0)
+   {
+      cout << "Size of linear system: " << A.GetGlobalNumRows() << endl;
+   }
 
-   // 14. Recover the parallel grid function corresponding to X. This is the
+   // 12. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
+   //     preconditioner from hypre.
+   HypreSolver *amg = new HypreBoomerAMG(A);
+   HyprePCG *pcg = new HyprePCG(A);
+   pcg->SetTol(1e-12);
+   pcg->SetMaxIter(200);
+   pcg->SetPrintLevel(2);
+   pcg->SetPreconditioner(*amg);
+   pcg->Mult(B, X);
+
+   // 13. Recover the parallel grid function corresponding to X. This is the
    //     local finite element solution on each processor.
    a->RecoverFEMSolution(X, *b, x);
 
-   // 15. Switch back to the host.
-   Device::Disable();
-
-   // 16. Save the refined mesh and the solution in parallel. This output can
+   // 14. Save the refined mesh and the solution in parallel. This output can
    //     be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
    {
       ostringstream mesh_name, sol_name;
@@ -244,7 +219,7 @@ int main(int argc, char *argv[])
       x.Save(sol_ofs);
    }
 
-   // 17. Send the solution by socket to a GLVis server.
+   // 15. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       char vishost[] = "localhost";
@@ -255,7 +230,9 @@ int main(int argc, char *argv[])
       sol_sock << "solution\n" << *pmesh << x << flush;
    }
 
-   // 18. Free the used memory.
+   // 16. Free the used memory.
+   delete pcg;
+   delete amg;
    delete a;
    delete b;
    delete fespace;

examples/ex2.cpp

@@ -6,7 +6,6 @@
 //               ex2 -m ../data/beam-quad.mesh
 //               ex2 -m ../data/beam-tet.mesh
 //               ex2 -m ../data/beam-hex.mesh
-//               ex2 -m ../data/beam-wedge.mesh
 //               ex2 -m ../data/beam-quad.mesh -o 3 -sc
 //               ex2 -m ../data/beam-quad-nurbs.mesh
 //               ex2 -m ../data/beam-hex-nurbs.mesh
@@ -85,9 +84,9 @@ int main(int argc, char *argv[])
 
    // 3. Select the order of the finite element discretization space. For NURBS
    //    meshes, we increase the order by degree elevation.
-   if (mesh->NURBSext)
+   if (mesh->NURBSext && order > mesh->NURBSext->GetOrder())
    {
-      mesh->DegreeElevate(order, order);
+      mesh->DegreeElevate(order - mesh->NURBSext->GetOrder());
    }
 
    // 4. Refine the mesh to increase the resolution. In this example we do

examples/ex20.cpp

@@ -1,298 +0,0 @@
-//                                MFEM Example 20
-//
-// Compile with: make ex20
-//
-// Sample runs:  ex20
-//
-// Description: This example demonstrates the use of the variable order,
-//              symplectic ODE integration algorithm.  Symplectic integration
-//              algorithms are designed to conserve energy when integrating, in
-//              time, systems of ODEs which are derived from Hamiltonian
-//              systems.
-//
-//              Hamiltonian systems define the energy of a system as a function
-//              of time (t), a set of generalized coordinates (q), and their
-//              corresponding generalized momenta (p).
-//
-//                 H(q,p,t) = T(p) + V(q,t)
-//
-//              Hamilton's equations then specify how q and p evolve in time:
-//
-//                 dq/dt =  dH/dp
-//                 dp/dt = -dH/dq
-//
-//              To use the symplectic integration classes we need to define an
-//              mfem::Operator P which evaluates the action of dH/dp, and an
-//              mfem::TimeDependentOperator F which computes -dH/dq.
-//
-//              This example offers five simple 1D Hamiltonians:
-//              0) Simple Harmonic Oscillator (mass on a spring)
-//                 H = ( p^2 / m + q^2 / k ) / 2
-//              1) Pendulum
-//                 H = ( p^2 / m - k ( 1 - cos(q) ) ) / 2
-//              2) Gaussian Potential Well
-//                 H = ( p^2 / m ) / 2 - k exp(-q^2 / 2)
-//              3) Quartic Potential
-//                 H = ( p^2 / m + k ( 1 + q^2 ) q^2 ) / 2
-//              4) Negative Quartic Potential
-//                 H = ( p^2 / m + k ( 1 - q^2 /8 ) q^2 ) / 2
-//
-//              In all cases these Hamiltonians are shifted by constant values
-//              so that the energy will remain positive. The mean and standard
-//              deviation of the computed energies at each time step are
-//              displayed upon completion.
-//
-//              We then use GLVis to visualize the results in a non-standard way
-//              by defining the axes to be q, p, and t rather than x, y, and z.
-//              In this space we build a ribbon-like mesh with nodes at (0,0,t)
-//              and (q,p,t). Finally we plot the energy as a function of time
-//              as a scalar field on this ribbon-like mesh.
-//
-//              For a more traditional plot of the results, including q, p, and
-//              H, can be obtained by selecting the "-gp" option. This creates
-//              a data file and input deck for the GnuPlot application (not
-//              included with MFEM). To visualize these results on most Linux
-//              systems type the command "gnuplot gnuplot_ex20.inp". The data
-//              file, named "ex20.dat", should be simple enough to display with
-//              other plotting programs as well.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-// Constants used in the Hamiltonian
-static int prob_ = 0;
-static double m_ = 1.0;
-static double k_ = 1.0;
-
-// Hamiltonian functional, see below for implementation
-double hamiltonian(double q, double p, double t);
-
-class GradT : public Operator
-{
-public:
-   GradT() : Operator(1) {}
-   void Mult(const Vector &x, Vector &y) const { y.Set(1.0/m_, x); }
-};
-
-class NegGradV : public TimeDependentOperator
-{
-public:
-   NegGradV() : TimeDependentOperator(1) {}
-   void Mult(const Vector &x, Vector &y) const;
-};
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   int order  = 1;
-   int nsteps = 100;
-   double dt  = 0.1;
-   bool visualization = true;
-   bool gnuplot = false;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&order, "-o", "--order",
-                  "Time integration order.");
-   args.AddOption(&prob_, "-p", "--problem-type",
-                  "Problem Type:\n"
-                  "\t  0 - Simple Harmonic Oscillator\n"
-                  "\t  1 - Pendulum\n"
-                  "\t  2 - Gaussian Potential Well\n"
-                  "\t  3 - Quartic Potential\n"
-                  "\t  4 - Negative Quartic Potential");
-   args.AddOption(&nsteps, "-n", "--number-of-steps",
-                  "Number of time steps.");
-   args.AddOption(&dt, "-dt", "--time-step",
-                  "Time step size.");
-   args.AddOption(&m_, "-m", "--mass",
-                  "Mass.");
-   args.AddOption(&k_, "-k", "--spring-const",
-                  "Spring constant.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&gnuplot, "-gp", "--gnuplot", "-no-gp", "--no-gnuplot",
-                  "Enable or disable GnuPlot visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   // 2. Create and Initialize the Symplectic Integration Solver
-   SIAVSolver siaSolver(order);
-   GradT    P;
-   NegGradV F;
-   siaSolver.Init(P,F);
-
-   // 3. Set the initial conditions
-   double t = 0.0;
-   Vector q(1), p(1);
-   Vector e(nsteps+1);
-   q(0) = 0.0;
-   p(0) = 1.0;
-
-   // 4. Prepare GnuPlot output file if needed
-   ofstream ofs;
-   if (gnuplot)
-   {
-      ofs.open("ex20.dat");
-      ofs << t << "\t" << q(0) << "\t" << p(0) << endl;
-   }
-
-   // 5. Create a Mesh for visualization in phase space
-   int nverts = (visualization) ? 2*(nsteps+1) : 0;
-   int nelems = (visualization) ? nsteps : 0;
-   Mesh mesh(2, nverts, nelems, 0, 3);
-
-   int    v[4];
-   Vector x0(3); x0 = 0.0;
-   Vector x1(3); x1 = 0.0;
-
-   // 6. Perform time-stepping
-   double e_mean = 0.0;
-
-   for (int i = 0; i < nsteps; i++)
-   {
-      // 6a. Record initial state
-      if (i == 0)
-      {
-         e[0] = hamiltonian(q(0),p(0),t);
-         e_mean += e[0];
-
-         if (visualization)
-         {
-            x1[0] = q(0);
-            x1[1] = p(0);
-            x1[2] = 0.0;
-            mesh.AddVertex(x0);
-            mesh.AddVertex(x1);
-         }
-      }
-
-      // 6b. Advance the state of the system
-      siaSolver.Step(q,p,t,dt);
-      e[i+1] = hamiltonian(q(0),p(0),t);
-      e_mean += e[i+1];
-
-      // 6c. Record the state of the system
-      if (gnuplot)
-      {
-         ofs << t << "\t" << q(0) << "\t" << p(0) << "\t" << e[i+1] << endl;
-      }
-
-      // 6d. Add results to GLVis visualization
-      if (visualization)
-      {
-         x0[2] = t;
-         x1[0] = q(0);
-         x1[1] = p(0);
-         x1[2] = t;
-         mesh.AddVertex(x0);
-         mesh.AddVertex(x1);
-         v[0] = 2*i;
-         v[1] = 2*(i+1);
-         v[2] = 2*(i+1)+1;
-         v[3] = 2*i+1;
-         mesh.AddQuad(v);
-      }
-   }
-
-   // 7. Compute and display mean and standard deviation of the energy
-   e_mean /= (nsteps + 1);
-   double e_var = 0.0;
-   for (int i=0; i<=nsteps; i++)
-   {
-      e_var += pow(e[i] - e_mean, 2);
-   }
-   e_var /= (nsteps + 1);
-   double e_sd = sqrt(e_var);
-   cout << endl << "Mean and standard deviation of the energy" << endl;
-   cout << e_mean << "\t" << e_sd << endl;
-
-   // 8. Finalize the GnuPlot output
-   if (gnuplot)
-   {
-      ofs.close();
-
-      ofs.open("gnuplot_ex20.inp");
-      ofs << "plot 'ex20.dat' using 1:2 w l t 'q', "
-          << "'ex20.dat' using 1:3 w l t 'p', "
-          << "'ex20.dat' using 1:4 w l t 'H'" << endl;
-      ofs.close();
-   }
-
-   // 9. Finalize the GLVis output
-   if (visualization)
-   {
-      H1_FECollection fec(order = 1, 2);
-      FiniteElementSpace fespace(&mesh, &fec);
-      GridFunction energy(&fespace);
-      energy = 0.0;
-      for (int i = 0; i <= nsteps; i++)
-      {
-         energy[2*i+0] = e[i];
-         energy[2*i+1] = e[i];
-      }
-
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sock(vishost, visport);
-      sock.precision(8);
-      sock << "solution\n" << mesh << energy
-           << "window_title 'Energy in Phase Space'\n"
-           << "keys\n maac\n" << "axis_labels 'q' 'p' 't'\n"<< flush;
-   }
-}
-
-double hamiltonian(double q, double p, double t)
-{
-   double h = 1.0 - 0.5 / m_ + 0.5 * p * p / m_;
-   switch (prob_)
-   {
-      case 1:
-         h += k_ * (1.0 - cos(q));
-         break;
-      case 2:
-         h += k_ * (1.0 - exp(-0.5 * q * q));
-         break;
-      case 3:
-         h += 0.5 * k_ * (1.0 + q * q) * q * q;
-         break;
-      case 4:
-         h += 0.5 * k_ * (1.0 - 0.125 * q * q) * q * q;
-         break;
-      default:
-         h += 0.5 * k_ * q * q;
-         break;
-   }
-   return h;
-}
-
-void NegGradV::Mult(const Vector &x, Vector &y) const
-{
-   switch (prob_)
-   {
-      case 1:
-         y(0) = - k_* sin(x(0));
-         break;
-      case 2:
-         y(0) = - k_ * x(0) * exp(-0.5 * x(0) * x(0));
-         break;
-      case 3:
-         y(0) = - k_ * (1.0 + 2.0 * x(0) * x(0)) * x(0);
-         break;
-      case 4:
-         y(0) = - k_ * (1.0 - 0.25 * x(0) * x(0)) * x(0);
-         break;
-      default:
-         y(0) = - k_ * x(0);
-         break;
-   };
-}

examples/ex20p.cpp

@@ -1,364 +0,0 @@
-//                       MFEM Example 20 - Parallel Version
-//
-// Compile with: make ex20p
-//
-// Sample runs:  mpirun -np 4 ex20p
-//
-// Description: This example demonstrates the use of the variable order,
-//              symplectic ODE integration algorithm.  Symplectic integration
-//              algorithms are designed to conserve energy when integrating, in
-//              time, systems of ODEs which are derived from Hamiltonian
-//              systems.
-//
-//              Hamiltonian systems define the energy of a system as a function
-//              of time (t), a set of generalized coordinates (q), and their
-//              corresponding generalized momenta (p).
-//
-//                 H(q,p,t) = T(p) + V(q,t)
-//
-//              Hamilton's equations then specify how q and p evolve in time:
-//
-//                 dq/dt =  dH/dp
-//                 dp/dt = -dH/dq
-//
-//              To use the symplectic integration classes we need to define an
-//              mfem::Operator P which evaluates the action of dH/dp, and an
-//              mfem::TimeDependentOperator F which computes -dH/dq.
-//
-//              This example offers five simple 1D Hamiltonians:
-//              0) Simple Harmonic Oscillator (mass on a spring)
-//                 H = ( p^2 / m + q^2 / k ) / 2
-//              1) Pendulum
-//                 H = ( p^2 / m - k ( 1 - cos(q) ) ) / 2
-//              2) Gaussian Potential Well
-//                 H = ( p^2 / m ) / 2 - k exp(-q^2 / 2)
-//              3) Quartic Potential
-//                 H = ( p^2 / m + k ( 1 + q^2 ) q^2 ) / 2
-//              4) Negative Quartic Potential
-//                 H = ( p^2 / m + k ( 1 - q^2 /8 ) q^2 ) / 2
-//
-//              In all cases these Hamiltonians are shifted by constant values
-//              so that the energy will remain positive. The mean and standard
-//              deviation of the computed energies at each time step are
-//              displayed upon completion. When run in parallel the same
-//              Hamiltonian system is evolved on each processor but starting
-//              from different initial conditions.
-//
-//              We then use GLVis to visualize the results in a non-standard way
-//              by defining the axes to be q, p, and t rather than x, y, and z.
-//              In this space we build a ribbon-like mesh on each processor with
-//              nodes at (0,0,t) and (q,p,t).  When these ribbons are bonded
-//              together on the t-axis they resemble a Rotini pasta.  Finally we
-//              plot the energy as a function of time as a scalar field on this
-//              Rotini-like mesh.
-//
-//              For a more traditional plot of the results, including q, p, and
-//              H from each processor, can be obtained by selecting the "-gp"
-//              option. This creates a collection of data files and an input
-//              deck for the GnuPlot application (not included with MFEM). To
-//              visualize these results on most linux systems type the command
-//              "gnuplot gnuplot_ex20p.inp". The data files, named
-//              "ex20p_?????.dat", should be simple enough to display with other
-//              plotting programs as well.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-// Constants used in the Hamiltonian
-static int prob_ = 0;
-static double m_ = 1.0;
-static double k_ = 1.0;
-
-// Hamiltonian functional, see below for implementation
-double hamiltonian(double q, double p, double t);
-
-class GradT : public Operator
-{
-public:
-   GradT() : Operator(1) {}
-   void Mult(const Vector &x, Vector &y) const { y.Set(1.0/m_, x); }
-};
-
-class NegGradV : public TimeDependentOperator
-{
-public:
-   NegGradV() : TimeDependentOperator(1) {}
-   void Mult(const Vector &x, Vector &y) const;
-};
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Comm comm = MPI_COMM_WORLD;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(comm, &num_procs);
-   MPI_Comm_rank(comm, &myid);
-
-   // 2. Parse command-line options.
-   int order  = 1;
-   int nsteps = 100;
-   double dt  = 0.1;
-   bool visualization = true;
-   bool gnuplot = false;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&order, "-o", "--order",
-                  "Time integration order.");
-   args.AddOption(&prob_, "-p", "--problem-type",
-                  "Problem Type:\n"
-                  "\t  0 - Simple Harmonic Oscillator\n"
-                  "\t  1 - Pendulum\n"
-                  "\t  2 - Gaussian Potential Well\n"
-                  "\t  3 - Quartic Potential\n"
-                  "\t  4 - Negative Quartic Potential");
-   args.AddOption(&nsteps, "-n", "--number-of-steps",
-                  "Number of time steps.");
-   args.AddOption(&dt, "-dt", "--time-step",
-                  "Time step size.");
-   args.AddOption(&m_, "-m", "--mass",
-                  "Mass.");
-   args.AddOption(&k_, "-k", "--spring-const",
-                  "Spring constant.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&gnuplot, "-gp", "--gnuplot", "-no-gp", "--no-gnuplot",
-                  "Enable or disable GnuPlot visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 3. Create and Initialize the Symplectic Integration Solver
-   SIAVSolver siaSolver(order);
-   GradT    P;
-   NegGradV F;
-   siaSolver.Init(P,F);
-
-   // 4. Set the initial conditions
-   double t = 0.0;
-   Vector q(1), p(1);
-   Vector e(nsteps+1);
-   q(0) = sin(2.0*M_PI*(double)myid/num_procs);
-   p(0) = cos(2.0*M_PI*(double)myid/num_procs);
-
-   // 5. Prepare GnuPlot output file if needed
-   ostringstream oss;
-   ofstream ofs;
-   if (gnuplot)
-   {
-      oss << "ex20p_" << setfill('0') << setw(5) << myid << ".dat";
-      ofs.open(oss.str().c_str());
-      ofs << t << "\t" << q(0) << "\t" << p(0) << endl;
-   }
-
-   // 6. Create a Mesh for visualization in phase space
-   int nverts = (visualization) ? (num_procs+1)*(nsteps+1) : 0;
-   int nelems = (visualization) ? (nsteps * num_procs) : 0;
-   Mesh mesh(2, nverts, nelems, 0, 3);
-
-   int   *part = (visualization) ? (new int[nelems]) : NULL;
-   int    v[4];
-   Vector x0(3); x0 = 0.0;
-   Vector x1(3); x1 = 0.0;
-
-   // 7. Perform time-stepping
-   double e_mean = 0.0;
-
-   for (int i = 0; i < nsteps; i++)
-   {
-      // 7a. Record initial state
-      if (i == 0)
-      {
-         e[0] = hamiltonian(q(0),p(0),t);
-         e_mean += e[0];
-
-         if (visualization)
-         {
-            mesh.AddVertex(x0);
-            for (int j = 0; j < num_procs; j++)
-            {
-               x1[0] = q(0);
-               x1[1] = p(0);
-               x1[2] = 0.0;
-               mesh.AddVertex(x1);
-            }
-         }
-      }
-
-      // 7b. Advance the state of the system
-      siaSolver.Step(q,p,t,dt);
-      e[i+1] = hamiltonian(q(0),p(0),t);
-      e_mean += e[i+1];
-
-      // 7c. Record the state of the system
-      if (gnuplot)
-      {
-         ofs << t << "\t" << q(0) << "\t" << p(0) << "\t" << e[i+1] << endl;
-      }
-
-      // 7d. Add results to GLVis visualization
-      if (visualization)
-      {
-         x0[2] = t;
-         mesh.AddVertex(x0);
-         for (int j = 0; j < num_procs; j++)
-         {
-            x1[0] = q(0);
-            x1[1] = p(0);
-            x1[2] = t;
-            mesh.AddVertex(x1);
-            v[0] = (num_procs + 1) * i;
-            v[1] = (num_procs + 1) * (i + 1);
-            v[2] = (num_procs + 1) * (i + 1) + j + 1;
-            v[3] = (num_procs + 1) * i + j + 1;
-            mesh.AddQuad(v);
-            part[num_procs * i + j] = j;
-         }
-      }
-   }
-
-   // 8. Compute and display mean and standard deviation of the energy
-   e_mean /= (nsteps + 1);
-   double e_var = 0.0;
-   for (int i = 0; i <= nsteps; i++)
-   {
-      e_var += pow(e[i] - e_mean, 2);
-   }
-   e_var /= (nsteps + 1);
-   double e_sd = sqrt(e_var);
-
-   if (myid == 0)
-   {
-      cout << endl << "Mean and standard deviation of the energy" << endl;
-   }
-   for (int i = 0; i < num_procs; i++)
-   {
-      if (myid == i)
-      {
-         cout << myid << ": " << e_mean << "\t" << e_sd << endl;
-      }
-      MPI_Barrier(comm);
-   }
-
-   // 9. Finalize the GnuPlot output
-   if (gnuplot)
-   {
-      ofs.close();
-      if (myid == 0)
-      {
-         ofs.open("gnuplot_ex20p.inp");
-         for (int i = 0; i < num_procs; i++)
-         {
-            ostringstream ossi;
-            ossi << "ex20p_" << setfill('0') << setw(5) << i << ".dat";
-            if (i == 0)
-            {
-               ofs << "plot";
-            }
-            ofs << " '" << ossi.str() << "' using 1:2 w l t 'q" << i << "',"
-                << " '" << ossi.str() << "' using 1:3 w l t 'p" << i << "',"
-                << " '" << ossi.str() << "' using 1:4 w l t 'H" << i << "'";
-            if (i < num_procs-1)
-            {
-               ofs << ",";
-            }
-            else
-            {
-               ofs << ";" << endl;
-            }
-         }
-         ofs.close();
-      }
-   }
-
-   // 10. Finalize the GLVis output
-   if (visualization)
-   {
-      mesh.FinalizeQuadMesh(1);
-      ParMesh pmesh(comm, mesh, part);
-      delete [] part;
-
-      H1_FECollection fec(order = 1, 2);
-      ParFiniteElementSpace fespace(&pmesh, &fec);
-      ParGridFunction energy(&fespace);
-      energy = 0.0;
-      for (int i = 0; i <= nsteps; i++)
-      {
-         energy[2*i+0] = e[i];
-         energy[2*i+1] = e[i];
-      }
-
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sock(vishost, visport);
-      sock.precision(8);
-      sock << "parallel " << num_procs << " " << myid << "\n"
-           << "solution\n" << pmesh << energy
-           << "window_title 'Energy in Phase Space'\n"
-           << "keys\n maac\n" << "axis_labels 'q' 'p' 't'\n"<< flush;
-   }
-
-   MPI_Finalize();
-}
-
-double hamiltonian(double q, double p, double t)
-{
-   double h = 1.0 - 0.5 / m_ + 0.5 * p * p / m_;
-   switch (prob_)
-   {
-      case 1:
-         h += k_ * (1.0 - cos(q));
-         break;
-      case 2:
-         h += k_ * (1.0 - exp(-0.5 * q * q));
-         break;
-      case 3:
-         h += 0.5 * k_ * (1.0 + q * q) * q * q;
-         break;
-      case 4:
-         h += 0.5 * k_ * (1.0 - 0.125 * q * q) * q * q;
-         break;
-      default:
-         h += 0.5 * k_ * q * q;
-         break;
-   }
-   return h;
-}
-
-void NegGradV::Mult(const Vector &x, Vector &y) const
-{
-   switch (prob_)
-   {
-      case 1:
-         y(0) = - k_* sin(x(0));
-         break;
-      case 2:
-         y(0) = - k_ * x(0) * exp(-0.5 * x(0) * x(0));
-         break;
-      case 3:
-         y(0) = - k_ * (1.0 + 2.0 * x(0) * x(0)) * x(0);
-         break;
-      case 4:
-         y(0) = - k_ * (1.0 - 0.25 * x(0) * x(0)) * x(0);
-         break;
-      default:
-         y(0) = - k_ * x(0);
-         break;
-   };
-}

examples/ex21.cpp

@@ -1,477 +0,0 @@
-//                               MFEM Example 21
-//
-// Compile with: make ex21
-//
-// Sample runs:  ex21 -m ../data/inline-segment.mesh -o 3
-//               ex21 -m ../data/inline-tri.mesh -o 3
-//               ex21 -m ../data/inline-quad.mesh -o 3
-//               ex21 -m ../data/inline-quad.mesh -o 3 -p 1
-//               ex21 -m ../data/inline-quad.mesh -o 3 -p 2
-//               ex21 -m ../data/inline-tet.mesh -o 2
-//               ex21 -m ../data/inline-hex.mesh -o 2
-//               ex21 -m ../data/inline-hex.mesh -o 2 -p 1
-//               ex21 -m ../data/inline-hex.mesh -o 2 -p 2
-//               ex21 -m ../data/star.mesh -o 2 -sigma 10.0
-//
-// Description:  This example code demonstrates the use of MFEM to define and
-//               solve simple complex-valued linear systems.  We implement three
-//               variants of a damped harmonic oscillator:
-//
-//               1) A scalar H1 field
-//                  -Div(a Grad u) - omega^2 b u + i omega c u = 0
-//
-//               2) A vector H(Curl) field
-//                  Curl(a Curl u) - omega^2 b u + i omega c u = 0
-//
-//               3) A vector H(Div) field
-//                  -Grad(a Div u) - omega^2 b u + i omega c u = 0
-//
-//               In each case the field is driven by a forced oscillation, with
-//               angular frequency omega, imposed at the boundary or a portion
-//               of the boundary.
-//
-//               In electromagnetics the coefficients are typically named the
-//               permeability, mu = 1/a, permittivity, epsilon = b, and
-//               conductivity, sigma = c.  The user can specify these constants
-//               using either set of names.
-//
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-static double mu_ = 1.0;
-static double epsilon_ = 1.0;
-static double sigma_ = 20.0;
-static double omega_ = 10.0;
-
-double u0_real_exact(const Vector &);
-double u0_imag_exact(const Vector &);
-
-void u1_real_exact(const Vector &, Vector &);
-void u1_imag_exact(const Vector &, Vector &);
-
-void u2_real_exact(const Vector &, Vector &);
-void u2_imag_exact(const Vector &, Vector &);
-
-bool check_for_inline_mesh(const char * mesh_file);
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/inline-quad.mesh";
-   int ref_levels = 0;
-   int order = 1;
-   int prob = 0;
-   double freq = -1.0;
-   double a_coef = 0.0;
-   bool visualization = 1;
-   bool herm_conv = true;
-   bool exact_sol = true;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&ref_levels, "-r", "--refine",
-                  "Number of times to refine the mesh uniformly.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&prob, "-p", "--problem-type",
-                  "Choose from 0: H_1, 1: H(Curl), or 2: H(Div) "
-                  "damped harmonic oscillator.");
-   args.AddOption(&a_coef, "-a", "--stiffness-coef",
-                  "Stiffness coefficient (spring constant or 1/mu).");
-   args.AddOption(&epsilon_, "-b", "--mass-coef",
-                  "Mass coefficient (or epsilon).");
-   args.AddOption(&sigma_, "-c", "--damping-coef",
-                  "Damping coefficient (or sigma).");
-   args.AddOption(&mu_, "-mu", "--permeability",
-                  "Permeability of free space (or 1/(spring constant)).");
-   args.AddOption(&epsilon_, "-eps", "--permittivity",
-                  "Permittivity of free space (or mass constant).");
-   args.AddOption(&sigma_, "-sigma", "--conductivity",
-                  "Conductivity (or damping constant).");
-   args.AddOption(&freq, "-f", "--frequency",
-                  "Frequency (in Hz).");
-   args.AddOption(&herm_conv, "-herm", "--hermitian", "-no-herm",
-                  "--no-hermitian", "Use convention for Hermitian operators.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   if ( a_coef != 0.0 )
-   {
-      mu_ = 1.0 / a_coef;
-   }
-   if ( freq > 0.0 )
-   {
-      omega_ = 2.0 * M_PI * freq;
-   }
-
-   exact_sol = check_for_inline_mesh(mesh_file);
-   if (exact_sol)
-   {
-      cout << "Identified an 'inline' mesh" << endl;
-   }
-
-   ComplexOperator::Convention conv =
-      herm_conv ? ComplexOperator::HERMITIAN : ComplexOperator::BLOCK_SYMMETRIC;
-
-   // 2. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral, hexahedral, surface and volume meshes
-   //    with the same code.
-   Mesh *mesh = new Mesh(mesh_file, 1, 1);
-   int dim = mesh->Dimension();
-
-   // 3. Refine the mesh to increase resolution. In this example we do
-   //    'ref_levels' of uniform refinement where the user specifies
-   //    the number of levels with the '-r' option.
-   for (int l = 0; l < ref_levels; l++)
-   {
-      mesh->UniformRefinement();
-   }
-
-   // 4. Define a finite element space on the mesh. Here we use continuous
-   //    Lagrange, Nedelec, or Raviart-Thomas finite elements of the specified
-   //    order.
-   if (dim == 1 && prob != 0 )
-   {
-      cout << "Switching to problem type 0, H1 basis functions, "
-           << "for 1 dimensional mesh." << endl;
-      prob = 0;
-   }
-
-   FiniteElementCollection *fec;
-   switch (prob)
-   {
-      case 0:  fec = new H1_FECollection(order, dim);      break;
-      case 1:  fec = new ND_FECollection(order, dim);      break;
-      case 2:  fec = new RT_FECollection(order - 1, dim);  break;
-   }
-   FiniteElementSpace *fespace = new FiniteElementSpace(mesh, fec);
-   cout << "Number of finite element unknowns: " << fespace->GetTrueVSize()
-        << endl;
-
-   // 5. Determine the list of true (i.e. conforming) essential boundary dofs.
-   //    In this example, the boundary conditions are defined based on the type
-   //    of mesh and the problem type.
-   Array<int> ess_tdof_list;
-   Array<int> ess_bdr;
-   if (mesh->bdr_attributes.Size())
-   {
-      ess_bdr.SetSize(mesh->bdr_attributes.Max());
-      ess_bdr = 1;
-      if (exact_sol)
-      {
-         switch (prob)
-         {
-            case 0:   ess_bdr = 0; ess_bdr[0] = 1;  break;
-            default:  ess_bdr = 1; ess_bdr[2] = 0;  break;
-         }
-      }
-      fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   // 6. Set up the linear form b(.) which corresponds to the
-   //    right-hand side of the FEM linear system.
-   ComplexLinearForm b(fespace, conv);
-   b.Vector::operator=(0.0);
-
-   // 7. Define the solution vector u as a finite element grid function
-   //    corresponding to fespace. Initialize u with initial guess of 1+0i
-   //    or the exact solution if it is known.
-   ComplexGridFunction u(fespace);
-   ComplexGridFunction * u_exact = NULL;
-   if (exact_sol) { u_exact = new ComplexGridFunction(fespace); }
-
-   FunctionCoefficient u0_r(u0_real_exact);
-   FunctionCoefficient u0_i(u0_imag_exact);
-   VectorFunctionCoefficient u1_r(dim, u1_real_exact);
-   VectorFunctionCoefficient u1_i(dim, u1_imag_exact);
-   VectorFunctionCoefficient u2_r(dim, u2_real_exact);
-   VectorFunctionCoefficient u2_i(dim, u2_imag_exact);
-
-   ConstantCoefficient zeroCoef(0.0);
-   ConstantCoefficient oneCoef(1.0);
-
-   Vector zeroVec(dim); zeroVec = 0.0;
-   Vector  oneVec(dim);  oneVec = 0.0; oneVec[(prob==2)?(dim-1):0] = 1.0;
-   VectorConstantCoefficient zeroVecCoef(zeroVec);
-   VectorConstantCoefficient oneVecCoef(oneVec);
-
-   switch (prob)
-   {
-      case 0:
-         u.ProjectBdrCoefficient(oneCoef, zeroCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u0_r, u0_i); }
-         break;
-      case 1:
-         u.ProjectBdrCoefficientTangent(oneVecCoef, zeroVecCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u1_r, u1_i); }
-         break;
-      case 2:
-         u.ProjectBdrCoefficientNormal(oneVecCoef, zeroVecCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u2_r, u2_i); }
-         break;
-   }
-
-   if (visualization && exact_sol)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *mesh << u_exact->real()
-                 << "window_title 'Exact Real Part'" << flush;
-      sol_sock_i << "solution\n" << *mesh << u_exact->imag()
-                 << "window_title 'Exact Imaginary Part'" << flush;
-   }
-
-   // 8. Set up the sesquilinear form a(.,.) on the finite element
-   //    space corresponding to the damped harmonic oscillator operator
-   //    of the appropriate type:
-   //
-   //    0) A scalar H1 field
-   //       -Div(a Grad) - omega^2 b + i omega c
-   //
-   //    1) A vector H(Curl) field
-   //       Curl(a Curl) - omega^2 b + i omega c
-   //
-   //    2) A vector H(Div) field
-   //       -Grad(a Div) - omega^2 b + i omega c
-   //
-   ConstantCoefficient stiffnessCoef(1.0/mu_);
-   ConstantCoefficient massCoef(-omega_ * omega_ * epsilon_);
-   ConstantCoefficient lossCoef(omega_ * sigma_);
-   ConstantCoefficient negMassCoef(omega_ * omega_ * epsilon_);
-
-   SesquilinearForm *a = new SesquilinearForm(fespace, conv);
-   switch (prob)
-   {
-      case 0:
-         a->AddDomainIntegrator(new DiffusionIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new MassIntegrator(massCoef),
-                                new MassIntegrator(lossCoef));
-         break;
-      case 1:
-         a->AddDomainIntegrator(new CurlCurlIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef),
-                                new VectorFEMassIntegrator(lossCoef));
-         break;
-      case 2:
-         a->AddDomainIntegrator(new DivDivIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef),
-                                new VectorFEMassIntegrator(lossCoef));
-         break;
-   }
-
-   // 9. Assemble the bilinear form and the corresponding linear
-   //    system, applying any necessary transformations such as:
-   //    assembly, eliminating boundary conditions, applying conforming
-   //    constraints for non-conforming AMR, etc.
-   a->Assemble();
-
-   OperatorHandle A;
-   Vector B, U;
-
-   a->FormLinearSystem(ess_tdof_list, u, b, A, U, B);
-   u = 0.0;
-   U = 0.0;
-
-   {
-      ComplexSparseMatrix * Asp =
-         dynamic_cast<ComplexSparseMatrix*>(A.Ptr());
-
-      cout << "Size of linear system: "
-           << 2 * Asp->real().Width() << endl << endl;
-   }
-
-   // 10. Define and apply a GMRES solver for AU=B.
-   {
-      GMRESSolver gmres;
-      gmres.SetOperator(*A.Ptr());
-      gmres.SetRelTol(1e-12);
-      gmres.SetMaxIter(1000);
-      gmres.SetPrintLevel(1);
-      gmres.Mult(B, U);
-   }
-
-   // 11. Recover the solution as a finite element grid function and
-   //     compute the errors if the exact solution is known.
-   a->RecoverFEMSolution(U, b, u);
-
-   if (exact_sol)
-   {
-      double err_r = -1.0;
-      double err_i = -1.0;
-
-      switch (prob)
-      {
-         case 0:
-            err_r = u.real().ComputeL2Error(u0_r);
-            err_i = u.imag().ComputeL2Error(u0_i);
-            break;
-         case 1:
-            err_r = u.real().ComputeL2Error(u1_r);
-            err_i = u.imag().ComputeL2Error(u1_i);
-            break;
-         case 2:
-            err_r = u.real().ComputeL2Error(u2_r);
-            err_i = u.imag().ComputeL2Error(u2_i);
-            break;
-      }
-
-      cout << endl;
-      cout << "|| Re (u_h - u) ||_{L^2} = " << err_r << endl;
-      cout << "|| Im (u_h - u) ||_{L^2} = " << err_i << endl;
-      cout << endl;
-   }
-
-   // 12. Save the refined mesh and the solution. This output can be
-   //     viewed later using GLVis: "glvis -m mesh -g sol".
-   {
-      ofstream mesh_ofs("refined.mesh");
-      mesh_ofs.precision(8);
-      mesh->Print(mesh_ofs);
-
-      ofstream sol_r_ofs("sol_r.gf");
-      ofstream sol_i_ofs("sol_i.gf");
-      sol_r_ofs.precision(8);
-      sol_i_ofs.precision(8);
-      u.real().Save(sol_r_ofs);
-      u.imag().Save(sol_i_ofs);
-   }
-
-   // 13. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *mesh << u.real()
-                 << "window_title 'Comp Real Part'" << flush;
-      sol_sock_i << "solution\n" << *mesh << u.imag()
-                 << "window_title 'Comp Imaginary Part'" << flush;
-   }
-   if (visualization && exact_sol)
-   {
-      *u_exact -= u;
-
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *mesh << u_exact->real()
-                 << "window_title 'Exact-Comp Real Part'" << flush;
-      sol_sock_i << "solution\n" << *mesh << u_exact->imag()
-                 << "window_title 'Exact-Comp Imaginary Part'" << flush;
-   }
-   if (visualization)
-   {
-      GridFunction u_t(fespace);
-      u_t = u.real();
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << *mesh << u_t
-               << "window_title 'Harmonic Solution (t = 0.0 T)'"
-               << "pause\n" << flush;
-
-      cout << "GLVis visualization paused."
-           << " Press space (in the GLVis window) to resume it.\n";
-      int num_frames = 32;
-      int i = 0;
-      while (sol_sock)
-      {
-         double t = (double)(i % num_frames) / num_frames;
-         ostringstream oss;
-         oss << "Harmonic Solution (t = " << t << " T)";
-
-         add(cos( 2.0 * M_PI * t), u.real(),
-             sin(-2.0 * M_PI * t), u.imag(), u_t);
-         sol_sock << "solution\n" << *mesh << u_t
-                  << "window_title '" << oss.str() << "'" << flush;
-         i++;
-      }
-   }
-
-   // 14. Free the used memory.
-   delete a;
-   delete u_exact;
-   delete fespace;
-   delete fec;
-   delete mesh;
-
-   return 0;
-}
-
-bool check_for_inline_mesh(const char * mesh_file)
-{
-   string file(mesh_file);
-   size_t p0 = file.find_last_of("/");
-   string s0 = file.substr((p0==string::npos)?0:(p0+1),7);
-   return s0 == "inline-";
-}
-
-complex<double> u0_exact(const Vector &x)
-{
-   int dim = x.Size();
-   complex<double> i(0.0, 1.0);
-   complex<double> alpha = (epsilon_ * omega_ - i * sigma_);
-   complex<double> kappa = std::sqrt(mu_ * omega_* alpha);
-   return std::exp(-i * kappa * x[dim - 1]);
-}
-
-double u0_real_exact(const Vector &x)
-{
-   return u0_exact(x).real();
-}
-
-double u0_imag_exact(const Vector &x)
-{
-   return u0_exact(x).imag();
-}
-
-void u1_real_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[0] = u0_real_exact(x);
-}
-
-void u1_imag_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[0] = u0_imag_exact(x);
-}
-
-void u2_real_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[dim-1] = u0_real_exact(x);
-}
-
-void u2_imag_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[dim-1] = u0_imag_exact(x);
-}

examples/ex21p.cpp

@@ -1,658 +0,0 @@
-//                       MFEM Example 21 - Parallel Version
-//
-// Compile with: make ex21p
-//
-// Sample runs:  mpirun -np 4 ex21p -m ../data/inline-segment.mesh -o 3
-//               mpirun -np 4 ex21p -m ../data/inline-tri.mesh -o 3
-//               mpirun -np 4 ex21p -m ../data/inline-quad.mesh -o 3
-//               mpirun -np 4 ex21p -m ../data/inline-quad.mesh -o 3 -p 1
-//               mpirun -np 4 ex21p -m ../data/inline-quad.mesh -o 3 -p 2
-//               mpirun -np 4 ex21p -m ../data/inline-tet.mesh -o 2
-//               mpirun -np 4 ex21p -m ../data/inline-hex.mesh -o 2
-//               mpirun -np 4 ex21p -m ../data/inline-hex.mesh -o 2 -p 1
-//               mpirun -np 4 ex21p -m ../data/inline-hex.mesh -o 2 -p 2
-//               mpirun -np 4 ex21p -m ../data/star.mesh -o 2 -sigma 10.0
-//
-// Description:  This example code demonstrates the use of MFEM to define and
-//               solve simple complex-valued linear systems.  We implement three
-//               variants of a damped harmonic oscillator:
-//
-//               1) A scalar H1 field
-//                  -Div(a Grad u) - omega^2 b u + i omega c u = 0
-//
-//               2) A vector H(Curl) field
-//                  Curl(a Curl u) - omega^2 b u + i omega c u = 0
-//
-//               3) A vector H(Div) field
-//                  -Grad(a Div u) - omega^2 b u + i omega c u = 0
-//
-//               In each case the field is driven by a forced oscillation, with
-//               angular frequency omega, imposed at the boundary or a portion
-//               of the boundary.
-//
-//               In electromagnetics the coefficients are typically named the
-//               permeability, mu = 1/a, permittivity, epsilon = b, and
-//               conductivity, sigma = c.  The user can specify these constants
-//               using either set of names.
-//
-//#define MFEM_STRUMPACK_SRC
-
-#include <fstream>
-#include <iostream>
-#include "mfem.hpp"
-
-using namespace std;
-using namespace mfem;
-
-static double mu_ = 1.0;
-static double epsilon_ = 1.0;
-static double sigma_ = 20.0;
-static double omega_ = 10.0;
-
-double u0_real_exact(const Vector &);
-double u0_imag_exact(const Vector &);
-
-void u1_real_exact(const Vector &, Vector &);
-void u1_imag_exact(const Vector &, Vector &);
-
-void u2_real_exact(const Vector &, Vector &);
-void u2_imag_exact(const Vector &, Vector &);
-
-bool check_for_inline_mesh(const char * mesh_file);
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm comm = MPI_COMM_WORLD;
-   MPI_Comm_size(comm, &num_procs);
-   MPI_Comm_rank(comm, &myid);
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "../data/inline-quad.mesh";
-   int ser_ref_levels = 1;
-   int par_ref_levels = 1;
-   int order = 1;
-   int prob = 0;
-   double freq = -1.0;
-   double a_coef = 0.0;
-   bool visualization = 1;
-   bool herm_conv = true;
-   bool exact_sol = true;
-#ifdef MFEM_USE_STRUMPACK
-   bool strumpack = false;
-#endif
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
-                  "Number of times to refine the mesh uniformly in serial.");
-   args.AddOption(&par_ref_levels, "-rp", "--refine-parallel",
-                  "Number of times to refine the mesh uniformly in parallel.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&prob, "-p", "--problem-type",
-                  "Choose from 0: H_1, 1: H(Curl), or 2: H(Div) "
-                  "damped harmonic oscillator.");
-   args.AddOption(&a_coef, "-a", "--stiffness-coef",
-                  "Stiffness coefficient (spring constant or 1/mu).");
-   args.AddOption(&epsilon_, "-b", "--mass-coef",
-                  "Mass coefficient (or epsilon).");
-   args.AddOption(&sigma_, "-c", "--damping-coef",
-                  "Damping coefficient (or sigma).");
-   args.AddOption(&mu_, "-mu", "--permeability",
-                  "Permeability of free space (or 1/(spring constant)).");
-   args.AddOption(&epsilon_, "-eps", "--permittivity",
-                  "Permittivity of free space (or mass constant).");
-   args.AddOption(&sigma_, "-sigma", "--conductivity",
-                  "Conductivity (or damping constant).");
-   args.AddOption(&freq, "-f", "--frequency",
-                  "Frequency (in Hz).");
-#ifdef MFEM_USE_STRUMPACK
-   args.AddOption(&strumpack, "-strumpack", "--strumpack-solver",
-                  "-no-strumpack", "--no-strumpack-solver",
-                  "Use STRUMPACK's double complex linear solver.");
-#endif
-   args.AddOption(&herm_conv, "-herm", "--hermitian", "-no-herm",
-                  "--no-hermitian", "Use convention for Hermitian operators.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   if ( a_coef != 0.0 )
-   {
-      mu_ = 1.0 / a_coef;
-   }
-   if ( freq > 0.0 )
-   {
-      omega_ = 2.0 * M_PI * freq;
-   }
-
-   exact_sol = check_for_inline_mesh(mesh_file);
-   if (myid == 0 && exact_sol)
-   {
-      cout << "Identified an 'inline' mesh" << endl;
-   }
-
-   ComplexOperator::Convention conv =
-      herm_conv ? ComplexOperator::HERMITIAN : ComplexOperator::BLOCK_SYMMETRIC;
-
-   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
-   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
-   //    and volume meshes with the same code.
-   Mesh *mesh = new Mesh(mesh_file, 1, 1);
-   int dim = mesh->Dimension();
-
-   // 4. Refine the serial mesh on all processors to increase the resolution.
-   for (int l = 0; l < ser_ref_levels; l++)
-   {
-      mesh->UniformRefinement();
-   }
-
-   // 5. Define a parallel mesh by a partitioning of the serial mesh. Refine
-   //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
-   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
-   delete mesh;
-   for (int l = 0; l < par_ref_levels; l++)
-   {
-      pmesh->UniformRefinement();
-   }
-
-   // 6. Define a parallel finite element space on the parallel
-   //    mesh. Here we use continuous Lagrange, Nedelec, or
-   //    Raviart-Thomas finite elements of the specified order.
-   if (dim == 1 && prob != 0 )
-   {
-      if (myid == 0)
-      {
-         cout << "Switching to problem type 0, H1 basis functions, "
-              << "for 1 dimensional mesh." << endl;
-      }
-      prob = 0;
-   }
-
-   FiniteElementCollection *fec;
-   switch (prob)
-   {
-      case 0:  fec = new H1_FECollection(order, dim);      break;
-      case 1:  fec = new ND_FECollection(order, dim);      break;
-      case 2:  fec = new RT_FECollection(order - 1, dim);  break;
-   }
-   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
-   HYPRE_Int size = fespace->GlobalTrueVSize();
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 7. Determine the list of true (i.e. parallel conforming) essential
-   //    boundary dofs. In this example, the boundary conditions are defined
-   //    based on the type of mesh and the problem type.
-   Array<int> ess_tdof_list;
-   Array<int> ess_bdr;
-   if (pmesh->bdr_attributes.Size())
-   {
-      ess_bdr.SetSize(pmesh->bdr_attributes.Max());
-      ess_bdr = 1;
-      if (exact_sol)
-      {
-         switch (prob)
-         {
-            case 0:   ess_bdr = 0; ess_bdr[0] = 1;  break;
-            default:  ess_bdr = 1; ess_bdr[2] = 0;  break;
-         }
-      }
-      fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   // 8. Set up the parallel linear form b(.) which corresponds to the
-   //    right-hand side of the FEM linear system.
-   ParComplexLinearForm b(fespace, conv);
-   b.Vector::operator=(0.0);
-
-   // 9. Define the solution vector u as a parallel finite element
-   //    grid function corresponding to fespace. Initialize u with
-   //    initial guess of 1+0i or the exact solution if it is known.
-   ParComplexGridFunction u(fespace);
-   ParComplexGridFunction * u_exact = NULL;
-   if (exact_sol) { u_exact = new ParComplexGridFunction(fespace); }
-
-   FunctionCoefficient u0_r(u0_real_exact);
-   FunctionCoefficient u0_i(u0_imag_exact);
-   VectorFunctionCoefficient u1_r(dim, u1_real_exact);
-   VectorFunctionCoefficient u1_i(dim, u1_imag_exact);
-   VectorFunctionCoefficient u2_r(dim, u2_real_exact);
-   VectorFunctionCoefficient u2_i(dim, u2_imag_exact);
-
-   ConstantCoefficient zeroCoef(0.0);
-   ConstantCoefficient oneCoef(1.0);
-
-   Vector zeroVec(dim); zeroVec = 0.0;
-   Vector  oneVec(dim);  oneVec = 0.0; oneVec[(prob==2)?(dim-1):0] = 1.0;
-   VectorConstantCoefficient zeroVecCoef(zeroVec);
-   VectorConstantCoefficient oneVecCoef(oneVec);
-
-   switch (prob)
-   {
-      case 0:
-         u.ProjectBdrCoefficient(oneCoef, zeroCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u0_r, u0_i); }
-         break;
-      case 1:
-         u.ProjectBdrCoefficientTangent(oneVecCoef, zeroVecCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u1_r, u1_i); }
-         break;
-      case 2:
-         u.ProjectBdrCoefficientNormal(oneVecCoef, zeroVecCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u2_r, u2_i); }
-         break;
-   }
-
-   if (visualization && exact_sol)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *pmesh << u_exact->real()
-                 << "window_title 'Exact Real Part'" << flush;
-      sol_sock_i << "solution\n" << *pmesh << u_exact->imag()
-                 << "window_title 'Exact Imaginary Part'" << flush;
-   }
-
-   // 10. Set up the parallel sesquilinear form a(.,.) on the finite element
-   //     space corresponding to the damped harmonic oscillator operator
-   //     of the appropriate type:
-   //
-   //     0) A scalar H1 field
-   //        -Div(a Grad) - omega^2 b + i omega c
-   //
-   //     1) A vector H(Curl) field
-   //        Curl(a Curl) - omega^2 b + i omega c
-   //
-   //     2) A vector H(Div) field
-   //        -Grad(a Div) - omega^2 b + i omega c
-   //
-   ConstantCoefficient stiffnessCoef(1.0/mu_);
-   ConstantCoefficient massCoef(-omega_ * omega_ * epsilon_);
-   ConstantCoefficient lossCoef(omega_ * sigma_);
-   ConstantCoefficient negMassCoef(omega_ * omega_ * epsilon_);
-
-   ParSesquilinearForm *a = new ParSesquilinearForm(fespace, conv);
-   switch (prob)
-   {
-      case 0:
-         a->AddDomainIntegrator(new DiffusionIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new MassIntegrator(massCoef),
-                                new MassIntegrator(lossCoef));
-         break;
-      case 1:
-         a->AddDomainIntegrator(new CurlCurlIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef),
-                                new VectorFEMassIntegrator(lossCoef));
-         break;
-      case 2:
-         a->AddDomainIntegrator(new DivDivIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef),
-                                new VectorFEMassIntegrator(lossCoef));
-         break;
-   }
-
-   // 10a. Set up the parallel bilinear form for the preconditioner
-   //      corresponding to the appropriate operator if the STRUMPACK solver
-   //      has not been selected.
-   //
-   //      0) A scalar H1 field
-   //         -Div(a Grad) - omega^2 b + omega c
-   //
-   //      1) A vector H(Curl) field
-   //         Curl(a Curl) + omega^2 b + omega c
-   //
-   //      2) A vector H(Div) field
-   //         -Grad(a Div) - omega^2 b + omega c
-   //
-   ParBilinearForm *pcOp = NULL;
-#ifdef MFEM_USE_STRUMPACK
-   if (!strumpack)
-#endif
-   {
-      pcOp = new ParBilinearForm(fespace);
-      switch (prob)
-      {
-         case 0:
-            pcOp->AddDomainIntegrator(new DiffusionIntegrator(stiffnessCoef));
-            pcOp->AddDomainIntegrator(new MassIntegrator(massCoef));
-            pcOp->AddDomainIntegrator(new MassIntegrator(lossCoef));
-            break;
-         case 1:
-            pcOp->AddDomainIntegrator(new CurlCurlIntegrator(stiffnessCoef));
-            pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(negMassCoef));
-            pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(lossCoef));
-            break;
-         case 2:
-            pcOp->AddDomainIntegrator(new DivDivIntegrator(stiffnessCoef));
-            pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef));
-            pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(lossCoef));
-            break;
-      }
-   }
-
-   // 11. Assemble the parallel bilinear form and the corresponding linear
-   //     system, applying any necessary transformations such as: parallel
-   //     assembly, eliminating boundary conditions, applying conforming
-   //     constraints for non-conforming AMR, etc.
-   a->Assemble();
-   if (pcOp) { pcOp->Assemble(); }
-
-   OperatorHandle A;
-   Vector B, U;
-
-   a->FormLinearSystem(ess_tdof_list, u, b, A, U, B);
-   u = 0.0;
-   U = 0.0;
-
-   OperatorHandle PCOp;
-   if (pcOp) { pcOp->FormSystemMatrix(ess_tdof_list, PCOp); }
-
-   if (myid == 0)
-   {
-      ComplexHypreParMatrix * Ahyp =
-         dynamic_cast<ComplexHypreParMatrix*>(A.Ptr());
-
-      cout << "Size of linear system: "
-           << 2 * Ahyp->real().GetGlobalNumRows() << endl << endl;
-   }
-
-   // 12. Define and apply a parallel FGMRES solver for AU=B with a
-   //     block diagonal preconditioner based on the appropriate multigrid
-   //     preconditioner from hypre or simply use STRUMPACK.
-#ifdef MFEM_USE_STRUMPACK
-   if (!strumpack)
-#endif
-   {
-      Array<HYPRE_Int> blockTrueOffsets;
-      blockTrueOffsets.SetSize(3);
-      blockTrueOffsets[0] = 0;
-      blockTrueOffsets[1] = PCOp.Ptr()->Height();
-      blockTrueOffsets[2] = PCOp.Ptr()->Height();
-      blockTrueOffsets.PartialSum();
-
-      BlockDiagonalPreconditioner BDP(blockTrueOffsets);
-
-      Operator * pc_r = NULL;
-      Operator * pc_i = NULL;
-
-      switch (prob)
-      {
-         case 0:
-            pc_r =
-               new HypreBoomerAMG(dynamic_cast<HypreParMatrix&>(*PCOp.Ptr()));
-            pc_i = new ScaledOperator(pc_r,
-                                      (conv == ComplexOperator::HERMITIAN) ?
-                                      1.0:-1.0);
-            break;
-         case 1:
-            pc_r = new HypreAMS(dynamic_cast<HypreParMatrix&>(*PCOp.Ptr()),
-                                fespace);
-            pc_i = new ScaledOperator(pc_r,
-                                      (conv == ComplexOperator::HERMITIAN) ?
-                                      1.0:-1.0);
-            break;
-         case 2:
-            if (dim == 2 )
-            {
-               pc_r = new HypreAMS(dynamic_cast<HypreParMatrix&>(*PCOp.Ptr()),
-                                   fespace);
-            }
-            else
-            {
-               pc_r = new HypreADS(dynamic_cast<HypreParMatrix&>(*PCOp.Ptr()),
-                                   fespace);
-            }
-            pc_i = new ScaledOperator(pc_r,
-                                      (conv == ComplexOperator::HERMITIAN) ?
-                                      1.0:-1.0);
-            break;
-      }
-      BDP.SetDiagonalBlock(0, pc_r);
-      BDP.SetDiagonalBlock(1, pc_i);
-      BDP.owns_blocks = 0;
-
-      FGMRESSolver fgmres(MPI_COMM_WORLD);
-      fgmres.SetPreconditioner(BDP);
-      fgmres.SetOperator(*A.Ptr());
-      fgmres.SetRelTol(1e-12);
-      fgmres.SetMaxIter(1000);
-      fgmres.SetPrintLevel(1);
-      fgmres.Mult(B, U);
-   }
-#ifdef MFEM_USE_STRUMPACK
-   else
-   {
-      ComplexHypreParMatrix * Ahyp =
-         dynamic_cast<ComplexHypreParMatrix*>(A.Ptr());
-
-      STRUMPACKRowLocCmplxMatrix A_strmp(Ahyp->real(), Ahyp->imag());
-
-      STRUMPACKCmplxSolver strmp(argc, argv, comm);
-
-      strmp.SetPrintFactorStatistics(true);
-      strmp.SetPrintSolveStatistics(true);
-      // strmp.SetKrylovSolver(strumpack::KrylovSolver::AUTO); // core dump
-      strmp.SetKrylovSolver(strumpack::KrylovSolver::DIRECT); // core dump
-      // strmp.SetKrylovSolver(strumpack::KrylovSolver::REFINE); // core dump
-      // strmp.SetKrylovSolver(strumpack::KrylovSolver::PREC_GMRES); // index out of range asserts from strumpack::DenseMatrix
-      // strmp.SetKrylovSolver(strumpack::KrylovSolver::GMRES); // WORKS
-      strmp.SetReorderingStrategy(strumpack::ReorderingStrategy::METIS);
-      strmp.SetOperator(A_strmp);
-      strmp.SetFromCommandLine();
-      strmp.Mult(B, U);
-   }
-#endif
-
-   // 13. Recover the parallel grid function corresponding to U. This is the
-   //     local finite element solution on each processor.
-   a->RecoverFEMSolution(U, b, u);
-
-   if (exact_sol)
-   {
-      double err_r = -1.0;
-      double err_i = -1.0;
-
-      switch (prob)
-      {
-         case 0:
-            err_r = u.real().ComputeL2Error(u0_r);
-            err_i = u.imag().ComputeL2Error(u0_i);
-            break;
-         case 1:
-            err_r = u.real().ComputeL2Error(u1_r);
-            err_i = u.imag().ComputeL2Error(u1_i);
-            break;
-         case 2:
-            err_r = u.real().ComputeL2Error(u2_r);
-            err_i = u.imag().ComputeL2Error(u2_i);
-            break;
-      }
-
-      if ( myid == 0 )
-      {
-         cout << endl;
-         cout << "|| Re (u_h - u) ||_{L^2} = " << err_r << endl;
-         cout << "|| Im (u_h - u) ||_{L^2} = " << err_i << endl;
-         cout << endl;
-      }
-   }
-
-   // 14. Save the refined mesh and the solution in parallel. This output can be
-   //     viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
-   {
-      ostringstream mesh_name, sol_r_name, sol_i_name;
-      mesh_name << "mesh." << setfill('0') << setw(6) << myid;
-      sol_r_name << "sol_r." << setfill('0') << setw(6) << myid;
-      sol_i_name << "sol_i." << setfill('0') << setw(6) << myid;
-
-      ofstream mesh_ofs(mesh_name.str().c_str());
-      mesh_ofs.precision(8);
-      pmesh->Print(mesh_ofs);
-
-      ofstream sol_r_ofs(sol_r_name.str().c_str());
-      ofstream sol_i_ofs(sol_i_name.str().c_str());
-      sol_r_ofs.precision(8);
-      sol_i_ofs.precision(8);
-      u.real().Save(sol_r_ofs);
-      u.imag().Save(sol_i_ofs);
-   }
-
-   // 15. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *pmesh << u.real()
-                 << "window_title 'Comp Real Part'" << flush;
-      sol_sock_i << "solution\n" << *pmesh << u.imag()
-                 << "window_title 'Comp Imaginary Part'" << flush;
-   }
-   if (visualization && exact_sol)
-   {
-      *u_exact -= u;
-
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *pmesh << u_exact->real()
-                 << "window_title 'Exact-Comp Real Part'" << flush;
-      sol_sock_i << "solution\n" << *pmesh << u_exact->imag()
-                 << "window_title 'Exact-Comp Imaginary Part'" << flush;
-   }
-   if (visualization)
-   {
-      ParGridFunction u_t(fespace);
-      u_t = u.real();
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << *pmesh << u_t
-               << "window_title 'Harmonic Solution (t = 0.0 T)'"
-               << "pause\n" << flush;
-      if (myid == 0)
-         cout << "GLVis visualization paused."
-              << " Press space (in the GLVis window) to resume it.\n";
-      int num_frames = 32;
-      int i = 0;
-      while (sol_sock)
-      {
-         double t = (double)(i % num_frames) / num_frames;
-         ostringstream oss;
-         oss << "Harmonic Solution (t = " << t << " T)";
-
-         add(cos( 2.0 * M_PI * t), u.real(),
-             sin(-2.0 * M_PI * t), u.imag(), u_t);
-         sol_sock << "parallel " << num_procs << " " << myid << "\n";
-         sol_sock << "solution\n" << *pmesh << u_t
-                  << "window_title '" << oss.str() << "'" << flush;
-         i++;
-      }
-   }
-
-   // 16. Free the used memory.
-   delete a;
-   delete u_exact;
-   delete pcOp;
-   delete fespace;
-   delete fec;
-   delete pmesh;
-
-   MPI_Finalize();
-
-   return 0;
-}
-
-bool check_for_inline_mesh(const char * mesh_file)
-{
-   string file(mesh_file);
-   size_t p0 = file.find_last_of("/");
-   string s0 = file.substr((p0==string::npos)?0:(p0+1),7);
-   return s0 == "inline-";
-}
-
-complex<double> u0_exact(const Vector &x)
-{
-   int dim = x.Size();
-   complex<double> i(0.0, 1.0);
-   complex<double> alpha = (epsilon_ * omega_ - i * sigma_);
-   complex<double> kappa = std::sqrt(mu_ * omega_* alpha);
-   return std::exp(-i * kappa * x[dim - 1]);
-}
-
-double u0_real_exact(const Vector &x)
-{
-   return u0_exact(x).real();
-}
-
-double u0_imag_exact(const Vector &x)
-{
-   return u0_exact(x).imag();
-}
-
-void u1_real_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[0] = u0_real_exact(x);
-}
-
-void u1_imag_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[0] = u0_imag_exact(x);
-}
-
-void u2_real_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[dim-1] = u0_real_exact(x);
-}
-
-void u2_imag_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[dim-1] = u0_imag_exact(x);
-}

examples/ex22.cpp

@@ -1,310 +0,0 @@
-//                                MFEM Example 22
-//
-// Compile with: make ex22
-//
-// Sample runs:  ex22
-//               ex22 -o 3
-//               ex22 -m ../data/beam-quad.mesh
-//               ex22 -m ../data/beam-quad.mesh -o 3
-//               ex22 -m ../data/beam-quad.mesh -o 3 -f 1
-//               ex22 -m ../data/beam-tet.mesh
-//               ex22 -m ../data/beam-tet.mesh -o 2
-//               ex22 -m ../data/beam-hex.mesh
-//               ex22 -m ../data/beam-hex.mesh -o 2
-//
-// Description:  This is a version of Example 2 with a simple adaptive mesh
-//               refinement loop. The problem being solved is again the linear
-//               elasticity describing a multi-material cantilever beam.
-//               The problem is solved on a sequence of meshes which
-//               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
-//               to a simple ZZ error estimator.
-//
-//               The example demonstrates MFEM's capability to work with both
-//               conforming and nonconforming refinements, in 2D and 3D, on
-//               linear and curved meshes. Interpolation of functions from
-//               coarse to fine meshes, as well as persistent GLVis
-//               visualization are also illustrated.
-//
-//               We recommend viewing Examples 2 and 6 before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/beam-tri.mesh";
-   int order = 1;
-   bool static_cond = false;
-   int flux_averaging = 0;
-   bool visualization = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&flux_averaging, "-f", "--flux-averaging",
-                  "Flux averaging: 0 - global, 1 - by mesh attribute.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   // 2. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral, and hexahedral meshes with the same code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
-   MFEM_VERIFY(mesh.SpaceDimension() == dim, "invalid mesh");
-
-   if (mesh.attributes.Max() < 2 || mesh.bdr_attributes.Max() < 2)
-   {
-      cerr << "\nInput mesh should have at least two materials and "
-           << "two boundary attributes! (See schematic in ex2.cpp)\n"
-           << endl;
-      return 3;
-   }
-
-   // 3. Since a NURBS mesh can currently only be refined uniformly, we need to
-   //    convert it to a piecewise-polynomial curved mesh. First we refine the
-   //    NURBS mesh a bit more and then project the curvature to quadratic Nodes.
-   if (mesh.NURBSext)
-   {
-      for (int i = 0; i < 2; i++)
-      {
-         mesh.UniformRefinement();
-      }
-      mesh.SetCurvature(2);
-   }
-
-   // 4. Define a finite element space on the mesh. The polynomial order is
-   //    one (linear) by default, but this can be changed on the command line.
-   H1_FECollection fec(order, dim);
-   FiniteElementSpace fespace(&mesh, &fec, dim);
-
-   // 5. As in Example 2, we set up the linear form b(.) which corresponds to
-   //    the right-hand side of the FEM linear system. In this case, b_i equals
-   //    the boundary integral of f*phi_i where f represents a "pull down"
-   //    force on the Neumann part of the boundary and phi_i are the basis
-   //    functions in the finite element fespace. The force is defined by the
-   //    VectorArrayCoefficient object f, which is a vector of Coefficient
-   //    objects. The fact that f is non-zero on boundary attribute 2 is
-   //    indicated by the use of piece-wise constants coefficient for its last
-   //    component. We don't assemble the discrete problem yet, this will be
-   //    done in the main loop.
-   VectorArrayCoefficient f(dim);
-   for (int i = 0; i < dim-1; i++)
-   {
-      f.Set(i, new ConstantCoefficient(0.0));
-   }
-   {
-      Vector pull_force(mesh.bdr_attributes.Max());
-      pull_force = 0.0;
-      pull_force(1) = -1.0e-2;
-      f.Set(dim-1, new PWConstCoefficient(pull_force));
-   }
-
-   LinearForm b(&fespace);
-   b.AddDomainIntegrator(new VectorBoundaryLFIntegrator(f));
-
-   // 6. Set up the bilinear form a(.,.) on the finite element space
-   //    corresponding to the linear elasticity integrator with piece-wise
-   //    constants coefficient lambda and mu.
-   Vector lambda(mesh.attributes.Max());
-   lambda = 1.0;
-   lambda(0) = lambda(1)*50;
-   PWConstCoefficient lambda_func(lambda);
-   Vector mu(mesh.attributes.Max());
-   mu = 1.0;
-   mu(0) = mu(1)*50;
-   PWConstCoefficient mu_func(mu);
-
-   BilinearForm a(&fespace);
-   BilinearFormIntegrator *integ =
-      new ElasticityIntegrator(lambda_func,mu_func);
-   a.AddDomainIntegrator(integ);
-   if (static_cond) { a.EnableStaticCondensation(); }
-
-   // 7. The solution vector x and the associated finite element grid function
-   //    will be maintained over the AMR iterations. We initialize it to zero.
-   Vector zero_vec(dim);
-   zero_vec = 0.0;
-   VectorConstantCoefficient zero_vec_coeff(zero_vec);
-   GridFunction x(&fespace);
-   x = 0.0;
-
-   // 8. Determine the list of true (i.e. conforming) essential boundary dofs.
-   //    In this example, the boundary conditions are defined by marking only
-   //    boundary attribute 1 from the mesh as essential and converting it to a
-   //    list of true dofs.  The conversion to true dofs will be done in the
-   //    main loop.
-   Array<int> ess_bdr(mesh.bdr_attributes.Max());
-   ess_bdr = 0;
-   ess_bdr[0] = 1;
-
-   // 9. Connect to GLVis.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock;
-   if (visualization)
-   {
-      sol_sock.open(vishost, visport);
-      sol_sock.precision(8);
-   }
-
-   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
-   //     that uses the ComputeElementFlux method of the ElasticityIntegrator to
-   //     recover a smoothed flux (stress) that is subtracted from the element
-   //     flux to get an error indicator. We need to supply the space for the
-   //     smoothed flux: an (H1)^tdim (i.e., vector-valued) space is used here.
-   //     Here, tdim represents the number of components for a symmetric (dim x
-   //     dim) tensor.
-   const int tdim = dim*(dim+1)/2;
-   FiniteElementSpace flux_fespace(&mesh, &fec, tdim);
-   ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace);
-   estimator.SetFluxAveraging(flux_averaging);
-
-   // 11. A refiner selects and refines elements based on a refinement strategy.
-   //     The strategy here is to refine elements with errors larger than a
-   //     fraction of the maximum element error. Other strategies are possible.
-   //     The refiner will call the given error estimator.
-   ThresholdRefiner refiner(estimator);
-   refiner.SetTotalErrorFraction(0.7);
-
-   // 12. The main AMR loop. In each iteration we solve the problem on the
-   //     current mesh, visualize the solution, and refine the mesh.
-   const int max_dofs = 50000;
-   const int max_amr_itr = 20;
-   for (int it = 0; it <= max_amr_itr; it++)
-   {
-      int cdofs = fespace.GetTrueVSize();
-      cout << "\nAMR iteration " << it << endl;
-      cout << "Number of unknowns: " << cdofs << endl;
-
-      // 13. Assemble the stiffness matrix and the right-hand side.
-      a.Assemble();
-      b.Assemble();
-
-      // 14. Set Dirichlet boundary values in the GridFunction x.
-      //     Determine the list of Dirichlet true DOFs in the linear system.
-      Array<int> ess_tdof_list;
-      x.ProjectBdrCoefficient(zero_vec_coeff, ess_bdr);
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-
-      // 15. Create the linear system: eliminate boundary conditions, constrain
-      //     hanging nodes and possibly apply other transformations. The system
-      //     will be solved for true (unconstrained) DOFs only.
-      SparseMatrix A;
-      Vector B, X;
-      const int copy_interior = 1;
-      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
-
-#ifndef MFEM_USE_SUITESPARSE
-      // 16. Define a simple symmetric Gauss-Seidel preconditioner and use it to
-      //     solve the linear system with PCG.
-      GSSmoother M(A);
-      PCG(A, M, B, X, 3, 2000, 1e-12, 0.0);
-#else
-      // 16. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the
-      //     the linear system.
-      UMFPackSolver umf_solver;
-      umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-      umf_solver.SetOperator(A);
-      umf_solver.Mult(B, X);
-#endif
-
-      // 17. After solving the linear system, reconstruct the solution as a
-      //     finite element GridFunction. Constrained nodes are interpolated
-      //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
-      a.RecoverFEMSolution(X, b, x);
-
-      // 18. Send solution by socket to the GLVis server.
-      if (visualization && sol_sock.good())
-      {
-         GridFunction nodes(&fespace), *nodes_p = &nodes;
-         mesh.GetNodes(nodes);
-         nodes += x;
-         int own_nodes = 0;
-         mesh.SwapNodes(nodes_p, own_nodes);
-         x.Neg(); // visualize the backward displacement
-         sol_sock << "solution\n" << mesh << x << flush;
-         x.Neg();
-         mesh.SwapNodes(nodes_p, own_nodes);
-         if (it == 0)
-         {
-            sol_sock << "keys '" << ((dim == 2) ? "Rjl" : "") << "m'" << endl;
-         }
-         sol_sock << "window_title 'AMR iteration: " << it << "'\n"
-                  << "pause" << endl;
-         cout << "Visualization paused. "
-              "Press <space> in the GLVis window to continue." << endl;
-      }
-
-      if (cdofs > max_dofs)
-      {
-         cout << "Reached the maximum number of dofs. Stop." << endl;
-         break;
-      }
-
-      // 19. Call the refiner to modify the mesh. The refiner calls the error
-      //     estimator to obtain element errors, then it selects elements to be
-      //     refined and finally it modifies the mesh. The Stop() method can be
-      //     used to determine if a stopping criterion was met.
-      refiner.Apply(mesh);
-      if (refiner.Stop())
-      {
-         cout << "Stopping criterion satisfied. Stop." << endl;
-         break;
-      }
-
-      // 20. Update the space to reflect the new state of the mesh. Also,
-      //     interpolate the solution x so that it lies in the new space but
-      //     represents the same function. This saves solver iterations later
-      //     since we'll have a good initial guess of x in the next step.
-      //     Internally, FiniteElementSpace::Update() calculates an
-      //     interpolation matrix which is then used by GridFunction::Update().
-      fespace.Update();
-      x.Update();
-
-      // 21. Inform also the bilinear and linear forms that the space has
-      //     changed.
-      a.Update();
-      b.Update();
-   }
-
-   {
-      ofstream mesh_ref_out("ex22_reference.mesh");
-      mesh_ref_out.precision(16);
-      mesh.Print(mesh_ref_out);
-
-      ofstream mesh_out("ex22_deformed.mesh");
-      mesh_out.precision(16);
-      GridFunction nodes(&fespace), *nodes_p = &nodes;
-      mesh.GetNodes(nodes);
-      nodes += x;
-      int own_nodes = 0;
-      mesh.SwapNodes(nodes_p, own_nodes);
-      mesh.Print(mesh_out);
-      mesh.SwapNodes(nodes_p, own_nodes);
-
-      ofstream x_out("ex22_displacement.sol");
-      x_out.precision(16);
-      x.Save(x_out);
-   }
-
-   return 0;
-}

examples/ex22p.cpp

@@ -1,366 +0,0 @@
-//                                MFEM Example 22
-//
-// Compile with: make ex22p
-//
-// Sample runs:  mpirun -np 4 ex22p
-//               mpirun -np 4 ex22p -o 3
-//               mpirun -np 4 ex22p -m ../data/beam-quad.mesh
-//               mpirun -np 4 ex22p -m ../data/beam-quad.mesh -o 3
-//               mpirun -np 4 ex22p -m ../data/beam-tet.mesh
-//               mpirun -np 4 ex22p -m ../data/beam-tet.mesh -o 2
-//               mpirun -np 4 ex22p -m ../data/beam-hex.mesh
-//               mpirun -np 4 ex22p -m ../data/beam-hex.mesh -o 2
-//
-// Description:  This is a version of Example 2p with a simple adaptive mesh
-//               refinement loop. The problem being solved is again the linear
-//               elasticity describing a multi-material cantilever beam.
-//               The problem is solved on a sequence of meshes which
-//               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
-//               to a simple ZZ error estimator.
-//
-//               The example demonstrates MFEM's capability to work with both
-//               conforming and nonconforming refinements, in 2D and 3D, on
-//               linear and curved meshes. Interpolation of functions from
-//               coarse to fine meshes, as well as persistent GLVis
-//               visualization are also illustrated.
-//
-//               We recommend viewing Examples 2p and 6p before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 0. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/beam-tri.mesh";
-   int serial_ref_levels = 0;
-   int order = 1;
-   bool static_cond = false;
-   bool visualization = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&serial_ref_levels, "-rs", "--refine-serial",
-                  "Number of uniform serial refinements (before parallel"
-                  " partitioning)");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 2. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral, and hexahedral meshes with the same code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
-   MFEM_VERIFY(mesh.SpaceDimension() == dim, "invalid mesh");
-
-   if (mesh.attributes.Max() < 2 || mesh.bdr_attributes.Max() < 2)
-   {
-      cerr << "\nInput mesh should have at least two materials and "
-           << "two boundary attributes! (See schematic in ex2.cpp)\n"
-           << endl;
-      MPI_Finalize();
-      return 3;
-   }
-
-   // 3. Refine the mesh before parallel partitioning. Since a NURBS mesh can
-   //    currently only be refined uniformly, we need to convert it to a
-   //    piecewise-polynomial curved mesh. First we refine the NURBS mesh a bit
-   //    more and then project the curvature to quadratic Nodes.
-   if (mesh.NURBSext && serial_ref_levels == 0)
-   {
-      serial_ref_levels = 2;
-   }
-   for (int i = 0; i < serial_ref_levels; i++)
-   {
-      mesh.UniformRefinement();
-   }
-   if (mesh.NURBSext)
-   {
-      mesh.SetCurvature(2);
-   }
-   mesh.EnsureNCMesh();
-
-   ParMesh pmesh(MPI_COMM_WORLD, mesh);
-   mesh.Clear();
-
-   // 4. Define a finite element space on the mesh. The polynomial order is
-   //    one (linear) by default, but this can be changed on the command line.
-   H1_FECollection fec(order, dim);
-   ParFiniteElementSpace fespace(&pmesh, &fec, dim);
-
-   // 5. As in Example 2, we set up the linear form b(.) which corresponds to
-   //    the right-hand side of the FEM linear system. In this case, b_i equals
-   //    the boundary integral of f*phi_i where f represents a "pull down"
-   //    force on the Neumann part of the boundary and phi_i are the basis
-   //    functions in the finite element fespace. The force is defined by the
-   //    VectorArrayCoefficient object f, which is a vector of Coefficient
-   //    objects. The fact that f is non-zero on boundary attribute 2 is
-   //    indicated by the use of piece-wise constants coefficient for its last
-   //    component. We don't assemble the discrete problem yet, this will be
-   //    done in the main loop.
-   VectorArrayCoefficient f(dim);
-   for (int i = 0; i < dim-1; i++)
-   {
-      f.Set(i, new ConstantCoefficient(0.0));
-   }
-   {
-      Vector pull_force(pmesh.bdr_attributes.Max());
-      pull_force = 0.0;
-      pull_force(1) = -1.0e-2;
-      f.Set(dim-1, new PWConstCoefficient(pull_force));
-   }
-
-   ParLinearForm b(&fespace);
-   b.AddDomainIntegrator(new VectorBoundaryLFIntegrator(f));
-
-   // 6. Set up the bilinear form a(.,.) on the finite element space
-   //    corresponding to the linear elasticity integrator with piece-wise
-   //    constants coefficient lambda and mu.
-   Vector lambda(pmesh.attributes.Max());
-   lambda = 1.0;
-   lambda(0) = lambda(1)*50;
-   PWConstCoefficient lambda_func(lambda);
-   Vector mu(pmesh.attributes.Max());
-   mu = 1.0;
-   mu(0) = mu(1)*50;
-   PWConstCoefficient mu_func(mu);
-
-   ParBilinearForm a(&fespace);
-   BilinearFormIntegrator *integ =
-      new ElasticityIntegrator(lambda_func,mu_func);
-   a.AddDomainIntegrator(integ);
-   if (static_cond) { a.EnableStaticCondensation(); }
-
-   // 7. The solution vector x and the associated finite element grid function
-   //    will be maintained over the AMR iterations. We initialize it to zero.
-   Vector zero_vec(dim);
-   zero_vec = 0.0;
-   VectorConstantCoefficient zero_vec_coeff(zero_vec);
-   ParGridFunction x(&fespace);
-   x = 0.0;
-
-   // 8. Determine the list of true (i.e. conforming) essential boundary dofs.
-   //    In this example, the boundary conditions are defined by marking only
-   //    boundary attribute 1 from the mesh as essential and converting it to a
-   //    list of true dofs.  The conversion to true dofs will be done in the
-   //    main loop.
-   Array<int> ess_bdr(pmesh.bdr_attributes.Max());
-   ess_bdr = 0;
-   ess_bdr[0] = 1;
-
-   // 9. GLVis visualization.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock;
-
-   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
-   //     that uses the ComputeElementFlux method of the ElasticityIntegrator to
-   //     recover a smoothed flux (stress) that is subtracted from the element
-   //     flux to get an error indicator. We need to supply the space for the
-   //     smoothed flux: an (H1)^tdim (i.e., vector-valued) space is used here.
-   //     Here, tdim represents the number of components for a symmetric (dim x
-   //     dim) tensor.
-   const int tdim = dim*(dim+1)/2;
-   L2_FECollection flux_fec(order, dim);
-   ParFiniteElementSpace flux_fespace(&pmesh, &flux_fec, tdim);
-   ParFiniteElementSpace smooth_flux_fespace(&pmesh, &fec, tdim);
-   L2ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace,
-                                       smooth_flux_fespace);
-
-   // 11. A refiner selects and refines elements based on a refinement strategy.
-   //     The strategy here is to refine elements with errors larger than a
-   //     fraction of the maximum element error. Other strategies are possible.
-   //     The refiner will call the given error estimator.
-   ThresholdRefiner refiner(estimator);
-   refiner.SetTotalErrorFraction(0.7);
-
-   // 12. The main AMR loop. In each iteration we solve the problem on the
-   //     current mesh, visualize the solution, and refine the mesh.
-   const int max_dofs = 50000;
-   const int max_amr_itr = 20;
-   for (int it = 0; it <= max_amr_itr; it++)
-   {
-      HYPRE_Int global_dofs = fespace.GlobalTrueVSize();
-      if (myid == 0)
-      {
-         cout << "\nAMR iteration " << it << endl;
-         cout << "Number of unknowns: " << global_dofs << endl;
-      }
-
-      // 13. Assemble the stiffness matrix and the right-hand side.
-      a.Assemble();
-      b.Assemble();
-
-      // 14. Set Dirichlet boundary values in the GridFunction x.
-      //     Determine the list of Dirichlet true DOFs in the linear system.
-      Array<int> ess_tdof_list;
-      x.ProjectBdrCoefficient(zero_vec_coeff, ess_bdr);
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-
-      // 15. Create the linear system: eliminate boundary conditions, constrain
-      //     hanging nodes and possibly apply other transformations. The system
-      //     will be solved for true (unconstrained) DOFs only.
-
-      HypreParMatrix A;
-      Vector B, X;
-      const int copy_interior = 1;
-      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
-
-      // 16. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
-      //     preconditioner from hypre.
-      HypreBoomerAMG amg;
-      amg.SetPrintLevel(0);
-      // amg.SetSystemsOptions(dim); // optional
-      CGSolver pcg(A.GetComm());
-      pcg.SetPreconditioner(amg);
-      pcg.SetOperator(A);
-      pcg.SetRelTol(1e-6);
-      pcg.SetMaxIter(500);
-      pcg.SetPrintLevel(3); // print the first and the last iterations only
-      pcg.Mult(B, X);
-
-      // 17. After solving the linear system, reconstruct the solution as a
-      //     finite element GridFunction. Constrained nodes are interpolated
-      //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
-      a.RecoverFEMSolution(X, b, x);
-
-      // 18. Send solution by socket to the GLVis server.
-      if (visualization && it == 0)
-      {
-         sol_sock.open(vishost, visport);
-         sol_sock.precision(8);
-      }
-      if (visualization && sol_sock.good())
-      {
-         GridFunction nodes(&fespace), *nodes_p = &nodes;
-         pmesh.GetNodes(nodes);
-         nodes += x;
-         int own_nodes = 0;
-         pmesh.SwapNodes(nodes_p, own_nodes);
-         x.Neg(); // visualize the backward displacement
-         sol_sock << "parallel " << num_procs << ' ' << myid << '\n';
-         sol_sock << "solution\n" << pmesh << x << flush;
-         x.Neg();
-         pmesh.SwapNodes(nodes_p, own_nodes);
-         if (it == 0)
-         {
-            sol_sock << "keys '" << ((dim == 2) ? "Rjl" : "") << "m'" << endl;
-         }
-         sol_sock << "window_title 'AMR iteration: " << it << "'\n"
-                  << "pause" << endl;
-         if (myid == 0)
-         {
-            cout << "Visualization paused. "
-                 "Press <space> in the GLVis window to continue." << endl;
-         }
-      }
-
-      if (global_dofs > max_dofs)
-      {
-         if (myid == 0)
-         {
-            cout << "Reached the maximum number of dofs. Stop." << endl;
-         }
-         break;
-      }
-
-      // 19. Call the refiner to modify the mesh. The refiner calls the error
-      //     estimator to obtain element errors, then it selects elements to be
-      //     refined and finally it modifies the mesh. The Stop() method can be
-      //     used to determine if a stopping criterion was met.
-      refiner.Apply(pmesh);
-      if (refiner.Stop())
-      {
-         if (myid == 0)
-         {
-            cout << "Stopping criterion satisfied. Stop." << endl;
-         }
-         break;
-      }
-
-      // 20. Update the space to reflect the new state of the mesh. Also,
-      //     interpolate the solution x so that it lies in the new space but
-      //     represents the same function. This saves solver iterations later
-      //     since we'll have a good initial guess of x in the next step.
-      //     Internally, FiniteElementSpace::Update() calculates an
-      //     interpolation matrix which is then used by GridFunction::Update().
-      fespace.Update();
-      x.Update();
-
-      // 21. Load balance the mesh, and update the space and solution. Currently
-      //     available only for nonconforming meshes.
-      if (pmesh.Nonconforming())
-      {
-         pmesh.Rebalance();
-
-         // Update the space and the GridFunction. This time the update matrix
-         // redistributes the GridFunction among the processors.
-         fespace.Update();
-         x.Update();
-      }
-
-      // 22. Inform also the bilinear and linear forms that the space has
-      //     changed.
-      a.Update();
-      b.Update();
-   }
-
-   {
-      ostringstream mref_name, mesh_name, sol_name;
-      mref_name << "ex22p_reference_mesh." << setfill('0') << setw(6) << myid;
-      mesh_name << "ex22p_deformed_mesh." << setfill('0') << setw(6) << myid;
-      sol_name << "ex22p_displacement." << setfill('0') << setw(6) << myid;
-
-      ofstream mesh_ref_out(mref_name.str().c_str());
-      mesh_ref_out.precision(16);
-      pmesh.Print(mesh_ref_out);
-
-      ofstream mesh_out(mesh_name.str().c_str());
-      mesh_out.precision(16);
-      GridFunction nodes(&fespace), *nodes_p = &nodes;
-      pmesh.GetNodes(nodes);
-      nodes += x;
-      int own_nodes = 0;
-      pmesh.SwapNodes(nodes_p, own_nodes);
-      pmesh.Print(mesh_out);
-      pmesh.SwapNodes(nodes_p, own_nodes);
-
-      ofstream x_out(sol_name.str().c_str());
-      x_out.precision(16);
-      x.Save(x_out);
-   }
-
-   MPI_Finalize();
-   return 0;
-}

examples/ex2p.cpp

@@ -6,7 +6,6 @@
 //               mpirun -np 4 ex2p -m ../data/beam-quad.mesh
 //               mpirun -np 4 ex2p -m ../data/beam-tet.mesh
 //               mpirun -np 4 ex2p -m ../data/beam-hex.mesh
-//               mpirun -np 4 ex2p -m ../data/beam-wedge.mesh
 //               mpirun -np 4 ex2p -m ../data/beam-tri.mesh -o 2 -sys
 //               mpirun -np 4 ex2p -m ../data/beam-quad.mesh -o 3 -elast
 //               mpirun -np 4 ex2p -m ../data/beam-quad.mesh -o 3 -sc
@@ -108,9 +107,9 @@ int main(int argc, char *argv[])
 
    // 4. Select the order of the finite element discretization space. For NURBS
    //    meshes, we increase the order by degree elevation.
-   if (mesh->NURBSext)
+   if (mesh->NURBSext && order > mesh->NURBSext->GetOrder())
    {
-      mesh->DegreeElevate(order, order);
+      mesh->DegreeElevate(order - mesh->NURBSext->GetOrder());
    }
 
    // 5. Refine the serial mesh on all processors to increase the resolution. In

examples/ex3.cpp

@@ -7,7 +7,6 @@
 //               ex3 -m ../data/beam-tet.mesh
 //               ex3 -m ../data/beam-hex.mesh
 //               ex3 -m ../data/escher.mesh
-//               ex3 -m ../data/escher.mesh -o 2
 //               ex3 -m ../data/fichera.mesh
 //               ex3 -m ../data/fichera-q2.vtk
 //               ex3 -m ../data/fichera-q3.mesh

examples/ex3p.cpp

@@ -7,7 +7,6 @@
 //               mpirun -np 4 ex3p -m ../data/beam-tet.mesh
 //               mpirun -np 4 ex3p -m ../data/beam-hex.mesh
 //               mpirun -np 4 ex3p -m ../data/escher.mesh
-//               mpirun -np 4 ex3p -m ../data/escher.mesh -o 2
 //               mpirun -np 4 ex3p -m ../data/fichera.mesh
 //               mpirun -np 4 ex3p -m ../data/fichera-q2.vtk
 //               mpirun -np 4 ex3p -m ../data/fichera-q3.mesh

examples/ex3p_sp.cpp

@@ -1,334 +0,0 @@
-//                       MFEM Example 3 - Parallel Version
-//
-// Compile with: make ex3p
-//
-// Sample runs:  mpirun -np 4 ex3p -m ../data/star.mesh
-//               mpirun -np 4 ex3p -m ../data/square-disc.mesh -o 2
-//               mpirun -np 4 ex3p -m ../data/beam-tet.mesh
-//               mpirun -np 4 ex3p -m ../data/beam-hex.mesh
-//               mpirun -np 4 ex3p -m ../data/escher.mesh
-//               mpirun -np 4 ex3p -m ../data/escher.mesh -o 2
-//               mpirun -np 4 ex3p -m ../data/fichera.mesh
-//               mpirun -np 4 ex3p -m ../data/fichera-q2.vtk
-//               mpirun -np 4 ex3p -m ../data/fichera-q3.mesh
-//               mpirun -np 4 ex3p -m ../data/square-disc-nurbs.mesh
-//               mpirun -np 4 ex3p -m ../data/beam-hex-nurbs.mesh
-//               mpirun -np 4 ex3p -m ../data/amr-quad.mesh -o 2
-//               mpirun -np 4 ex3p -m ../data/amr-hex.mesh
-//               mpirun -np 4 ex3p -m ../data/star-surf.mesh -o 2
-//               mpirun -np 4 ex3p -m ../data/mobius-strip.mesh -o 2 -f 0.1
-//               mpirun -np 4 ex3p -m ../data/klein-bottle.mesh -o 2 -f 0.1
-//
-// Description:  This example code solves a simple electromagnetic diffusion
-//               problem corresponding to the second order definite Maxwell
-//               equation curl curl E + E = f with boundary condition
-//               E x n = <given tangential field>. Here, we use a given exact
-//               solution E and compute the corresponding r.h.s. f.
-//               We discretize with Nedelec finite elements in 2D or 3D.
-//
-//               The example demonstrates the use of H(curl) finite element
-//               spaces with the curl-curl and the (vector finite element) mass
-//               bilinear form, as well as the computation of discretization
-//               error when the exact solution is known. Static condensation is
-//               also illustrated.
-//
-//               We recommend viewing examples 1-2 before viewing this example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-// Exact solution, E, and r.h.s., f. See below for implementation.
-void E_exact(const Vector &, Vector &);
-void f_exact(const Vector &, Vector &);
-double freq = 1.0, kappa;
-int dim;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "../data/beam-tet.mesh";
-   int order = 1;
-   bool static_cond = false;
-   bool visualization = 1;
-#ifdef MFEM_USE_STRUMPACK
-   bool use_strumpack = false;
-#endif
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&freq, "-f", "--frequency", "Set the frequency for the exact"
-                  " solution.");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-#ifdef MFEM_USE_STRUMPACK
-   args.AddOption(&use_strumpack, "-strumpack", "--strumpack-solver",
-                  "-no-strumpack", "--no-strumpack-solver",
-                  "Use STRUMPACK's double complex linear solver.");
-#endif
-
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-   kappa = freq * M_PI;
-
-   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
-   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
-   //    and volume meshes with the same code.
-   Mesh *mesh = new Mesh(mesh_file, 1, 1);
-   dim = mesh->Dimension();
-   int sdim = mesh->SpaceDimension();
-
-   // 4. Refine the serial mesh on all processors to increase the resolution. In
-   //    this example we do 'ref_levels' of uniform refinement. We choose
-   //    'ref_levels' to be the largest number that gives a final mesh with no
-   //    more than 1,000 elements.
-   {
-      int ref_levels =
-         (int)floor(log(100000./mesh->GetNE())/log(2.)/dim);
-      for (int l = 0; l < ref_levels; l++)
-      {
-         mesh->UniformRefinement();
-      }
-   }
-
-   // 5. Define a parallel mesh by a partitioning of the serial mesh. Refine
-   //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted. Tetrahedral
-   //    meshes need to be reoriented before we can define high-order Nedelec
-   //    spaces on them.
-   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
-   delete mesh;
-   {
-      int par_ref_levels = 2;
-      for (int l = 0; l < par_ref_levels; l++)
-      {
-         pmesh->UniformRefinement();
-      }
-   }
-   pmesh->ReorientTetMesh();
-
-   // 6. Define a parallel finite element space on the parallel mesh. Here we
-   //    use the Nedelec finite elements of the specified order.
-   FiniteElementCollection *fec = new ND_FECollection(order, dim);
-   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
-   HYPRE_Int size = fespace->GlobalTrueVSize();
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 7. Determine the list of true (i.e. parallel conforming) essential
-   //    boundary dofs. In this example, the boundary conditions are defined
-   //    by marking all the boundary attributes from the mesh as essential
-   //    (Dirichlet) and converting them to a list of true dofs.
-   Array<int> ess_tdof_list;
-   if (pmesh->bdr_attributes.Size())
-   {
-      Array<int> ess_bdr(pmesh->bdr_attributes.Max());
-      ess_bdr = 1;
-      fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   // 8. Set up the parallel linear form b(.) which corresponds to the
-   //    right-hand side of the FEM linear system, which in this case is
-   //    (f,phi_i) where f is given by the function f_exact and phi_i are the
-   //    basis functions in the finite element fespace.
-   VectorFunctionCoefficient f(sdim, f_exact);
-   ParLinearForm *b = new ParLinearForm(fespace);
-   b->AddDomainIntegrator(new VectorFEDomainLFIntegrator(f));
-   b->Assemble();
-
-   // 9. Define the solution vector x as a parallel finite element grid function
-   //    corresponding to fespace. Initialize x by projecting the exact
-   //    solution. Note that only values from the boundary edges will be used
-   //    when eliminating the non-homogeneous boundary condition to modify the
-   //    r.h.s. vector b.
-   ParGridFunction x(fespace);
-   VectorFunctionCoefficient E(sdim, E_exact);
-   x.ProjectCoefficient(E);
-
-   // 10. Set up the parallel bilinear form corresponding to the EM diffusion
-   //     operator curl muinv curl + sigma I, by adding the curl-curl and the
-   //     mass domain integrators.
-   Coefficient *muinv = new ConstantCoefficient(1.0);
-   Coefficient *sigma = new ConstantCoefficient(-1.0);
-   ParBilinearForm *a = new ParBilinearForm(fespace);
-   a->AddDomainIntegrator(new CurlCurlIntegrator(*muinv));
-   a->AddDomainIntegrator(new VectorFEMassIntegrator(*sigma));
-
-   // 11. Assemble the parallel bilinear form and the corresponding linear
-   //     system, applying any necessary transformations such as: parallel
-   //     assembly, eliminating boundary conditions, applying conforming
-   //     constraints for non-conforming AMR, static condensation, etc.
-   if (static_cond) { a->EnableStaticCondensation(); }
-   a->Assemble();
-
-   HypreParMatrix A;
-   Vector B, X;
-   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
-
-   if (myid == 0)
-   {
-      cout << "Size of linear system: " << A.GetGlobalNumRows() << endl;
-   }
-
-   StopWatch chrono;
-   chrono.Clear();
-   chrono.Start();
-
-#ifdef MFEM_USE_STRUMPACK
-   if (use_strumpack)
-   {
-      Operator * Arow = new STRUMPACKRowLocMatrix(A);
-
-      STRUMPACKSolver * strumpack = new STRUMPACKSolver(argc, argv, MPI_COMM_WORLD);
-      strumpack->SetPrintFactorStatistics(true);
-      strumpack->SetPrintSolveStatistics(false);
-      strumpack->SetKrylovSolver(strumpack::KrylovSolver::DIRECT);
-      strumpack->SetReorderingStrategy(strumpack::ReorderingStrategy::METIS);
-      // strumpack->SetMC64Job(strumpack::MC64Job::NONE);
-      // strumpack->SetSymmetricPattern(true);
-      strumpack->SetOperator(*Arow);
-      strumpack->SetFromCommandLine();
-      //Solver * precond = strumpack;
-
-      strumpack->Mult(B, X);
-
-      delete strumpack;
-      delete Arow;
-   }
-   else
-#endif
-   {
-      // 12. Define and apply a parallel PCG solver for AX=B with the AMS
-      //     preconditioner from hypre.
-      ParFiniteElementSpace *prec_fespace =
-         (a->StaticCondensationIsEnabled() ? a->SCParFESpace() : fespace);
-      HypreSolver *ams = new HypreAMS(A, prec_fespace);
-      HyprePCG *pcg = new HyprePCG(A);
-      pcg->SetTol(1e-12);
-      pcg->SetMaxIter(500);
-      pcg->SetPrintLevel(2);
-      pcg->SetPreconditioner(*ams);
-      pcg->Mult(B, X);
-
-      delete pcg;
-      delete ams;
-   }
-
-   chrono.Stop();
-   cout << "Solver time " << chrono.RealTime() << endl;
-
-   // 13. Recover the parallel grid function corresponding to X. This is the
-   //     local finite element solution on each processor.
-   a->RecoverFEMSolution(X, *b, x);
-
-   // 14. Compute and print the L^2 norm of the error.
-   {
-      double err = x.ComputeL2Error(E);
-      if (myid == 0)
-      {
-         cout << "\n|| E_h - E ||_{L^2} = " << err << '\n' << endl;
-      }
-   }
-
-   // 15. Save the refined mesh and the solution in parallel. This output can
-   //     be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
-   {
-      ostringstream mesh_name, sol_name;
-      mesh_name << "mesh." << setfill('0') << setw(6) << myid;
-      sol_name << "sol." << setfill('0') << setw(6) << myid;
-
-      ofstream mesh_ofs(mesh_name.str().c_str());
-      mesh_ofs.precision(8);
-      pmesh->Print(mesh_ofs);
-
-      ofstream sol_ofs(sol_name.str().c_str());
-      sol_ofs.precision(8);
-      x.Save(sol_ofs);
-   }
-
-   // 16. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << *pmesh << x << flush;
-   }
-
-   // 17. Free the used memory.
-   delete a;
-   delete sigma;
-   delete muinv;
-   delete b;
-   delete fespace;
-   delete fec;
-   delete pmesh;
-
-   MPI_Finalize();
-
-   return 0;
-}
-
-
-void E_exact(const Vector &x, Vector &E)
-{
-   if (dim == 3)
-   {
-      E(0) = sin(kappa * x(1));
-      E(1) = sin(kappa * x(2));
-      E(2) = sin(kappa * x(0));
-   }
-   else
-   {
-      E(0) = sin(kappa * x(1));
-      E(1) = sin(kappa * x(0));
-      if (x.Size() == 3) { E(2) = 0.0; }
-   }
-}
-
-void f_exact(const Vector &x, Vector &f)
-{
-   if (dim == 3)
-   {
-      f(0) = (1. + kappa * kappa) * sin(kappa * x(1));
-      f(1) = (1. + kappa * kappa) * sin(kappa * x(2));
-      f(2) = (1. + kappa * kappa) * sin(kappa * x(0));
-   }
-   else
-   {
-      f(0) = (1. + kappa * kappa) * sin(kappa * x(1));
-      f(1) = (1. + kappa * kappa) * sin(kappa * x(0));
-      if (x.Size() == 3) { f(2) = 0.0; }
-   }
-}

examples/ex5p.cpp

@@ -53,7 +53,6 @@ int main(int argc, char *argv[])
    // 2. Parse command-line options.
    const char *mesh_file = "../data/star.mesh";
    int order = 1;
-   bool par_format = false;
    bool visualization = 1;
 
    OptionsParser args(argc, argv);
@@ -61,9 +60,6 @@ int main(int argc, char *argv[])
                   "Mesh file to use.");
    args.AddOption(&order, "-o", "--order",
                   "Finite element order (polynomial degree).");
-   args.AddOption(&par_format, "-pf", "--parallel-format", "-sf",
-                  "--serial-format",
-                  "Format to use when saving the results for VisIt.");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -321,9 +317,6 @@ int main(int argc, char *argv[])
    VisItDataCollection visit_dc("Example5-Parallel", pmesh);
    visit_dc.RegisterField("velocity", u);
    visit_dc.RegisterField("pressure", p);
-   visit_dc.SetFormat(!par_format ?
-                      DataCollection::SERIAL_FORMAT :
-                      DataCollection::PARALLEL_FORMAT);
    visit_dc.Save();
 
    // 16. Send the solution by socket to a GLVis server.

examples/ex6.cpp

@@ -15,17 +15,12 @@
 //               ex6 -m ../data/square-disc-surf.mesh -o 2
 //               ex6 -m ../data/amr-quad.mesh
 //
-// Device sample runs:
-//             > ex6 -pa -d cuda
-//             > ex6 -pa -d occa-cuda
-//             > ex6 -pa -d raja-omp
-//
 // Description:  This is a version of Example 1 with a simple adaptive mesh
 //               refinement loop. The problem being solved is again the Laplace
 //               equation -Delta u = 1 with homogeneous Dirichlet boundary
 //               conditions. The problem is solved on a sequence of meshes which
 //               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
+//               or non-conforming (quadrilateral, hexahedrons) manner according
 //               to a simple ZZ error estimator.
 //
 //               The example demonstrates MFEM's capability to work with both
@@ -48,19 +43,13 @@ int main(int argc, char *argv[])
    // 1. Parse command-line options.
    const char *mesh_file = "../data/star.mesh";
    int order = 1;
-   bool pa = false;
-   const char *device = "cpu";
-   bool visualization = true;
+   bool visualization = 1;
 
    OptionsParser args(argc, argv);
    args.AddOption(&mesh_file, "-m", "--mesh",
                   "Mesh file to use.");
    args.AddOption(&order, "-o", "--order",
                   "Finite element order (polynomial degree).");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -96,15 +85,10 @@ int main(int argc, char *argv[])
    H1_FECollection fec(order, dim);
    FiniteElementSpace fespace(&mesh, &fec);
 
-   // 5. Set device config parameters from the command line options.
-   Device::Configure(device);
-   Device::Print();
-
-   // 6. As in Example 1, we set up bilinear and linear forms corresponding to
+   // 5. As in Example 1, we set up bilinear and linear forms corresponding to
    //    the Laplace problem -\Delta u = 1. We don't assemble the discrete
    //    problem yet, this will be done in the main loop.
    BilinearForm a(&fespace);
-   if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
    LinearForm b(&fespace);
 
    ConstantCoefficient one(1.0);
@@ -114,18 +98,18 @@ int main(int argc, char *argv[])
    a.AddDomainIntegrator(integ);
    b.AddDomainIntegrator(new DomainLFIntegrator(one));
 
-   // 7. The solution vector x and the associated finite element grid function
+   // 6. The solution vector x and the associated finite element grid function
    //    will be maintained over the AMR iterations. We initialize it to zero.
    GridFunction x(&fespace);
    x = 0.0;
 
-   // 8. All boundary attributes will be used for essential (Dirichlet) BC.
+   // 7. All boundary attributes will be used for essential (Dirichlet) BC.
    MFEM_VERIFY(mesh.bdr_attributes.Size() > 0,
                "Boundary attributes required in the mesh.");
    Array<int> ess_bdr(mesh.bdr_attributes.Max());
    ess_bdr = 1;
 
-   // 9. Connect to GLVis.
+   // 8. Connect to GLVis.
    char vishost[] = "localhost";
    int  visport   = 19916;
    socketstream sol_sock;
@@ -134,23 +118,23 @@ int main(int argc, char *argv[])
       sol_sock.open(vishost, visport);
    }
 
-   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
-   //     that uses the ComputeElementFlux method of the DiffusionIntegrator to
-   //     recover a smoothed flux (gradient) that is subtracted from the element
-   //     flux to get an error indicator. We need to supply the space for the
-   //     smoothed flux: an (H1)^sdim (i.e., vector-valued) space is used here.
+   // 9. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
+   //    that uses the ComputeElementFlux method of the DiffusionIntegrator to
+   //    recover a smoothed flux (gradient) that is subtracted from the element
+   //    flux to get an error indicator. We need to supply the space for the
+   //    smoothed flux: an (H1)^sdim (i.e., vector-valued) space is used here.
    FiniteElementSpace flux_fespace(&mesh, &fec, sdim);
    ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace);
    estimator.SetAnisotropic();
 
-   // 11. A refiner selects and refines elements based on a refinement strategy.
+   // 10. A refiner selects and refines elements based on a refinement strategy.
    //     The strategy here is to refine elements with errors larger than a
    //     fraction of the maximum element error. Other strategies are possible.
    //     The refiner will call the given error estimator.
    ThresholdRefiner refiner(estimator);
    refiner.SetTotalErrorFraction(0.7);
 
-   // 12. The main AMR loop. In each iteration we solve the problem on the
+   // 11. The main AMR loop. In each iteration we solve the problem on the
    //     current mesh, visualize the solution, and refine the mesh.
    const int max_dofs = 50000;
    for (int it = 0; ; it++)
@@ -159,55 +143,44 @@ int main(int argc, char *argv[])
       cout << "\nAMR iteration " << it << endl;
       cout << "Number of unknowns: " << cdofs << endl;
 
-      // 13. Assemble the right-hand side.
+      // 12. Assemble the stiffness matrix and the right-hand side.
+      a.Assemble();
       b.Assemble();
 
-      // 14. Set Dirichlet boundary values in the GridFunction x.
+      // 13. Set Dirichlet boundary values in the GridFunction x.
       //     Determine the list of Dirichlet true DOFs in the linear system.
       Array<int> ess_tdof_list;
       x.ProjectBdrCoefficient(zero, ess_bdr);
       fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
 
-      // 15. Switch to the device and assemble the stiffness matrix.
-      Device::Enable();
-      a.Assemble();
-
-      // 16. Create the linear system: eliminate boundary conditions, constrain
+      // 14. Create the linear system: eliminate boundary conditions, constrain
       //     hanging nodes and possibly apply other transformations. The system
       //     will be solved for true (unconstrained) DOFs only.
-      OperatorPtr A;
+      SparseMatrix A;
       Vector B, X;
-
       const int copy_interior = 1;
       a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
 
-      // 17. Solve the linear system A X = B.
-      if (!pa)
-      {
 #ifndef MFEM_USE_SUITESPARSE
-         // Use a simple symmetric Gauss-Seidel preconditioner with PCG.
-         GSSmoother M((SparseMatrix&)(*A));
-         PCG(*A, M, B, X, 3, 200, 1e-12, 0.0);
+      // 15. Define a simple symmetric Gauss-Seidel preconditioner and use it to
+      //     solve the linear system with PCG.
+      GSSmoother M(A);
+      PCG(A, M, B, X, 3, 200, 1e-12, 0.0);
 #else
-         // If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
-         UMFPackSolver umf_solver;
-         umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-         umf_solver.SetOperator(*A);
-         umf_solver.Mult(B, X);
+      // 15. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the
+      //     the linear system.
+      UMFPackSolver umf_solver;
+      umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
+      umf_solver.SetOperator(A);
+      umf_solver.Mult(B, X);
 #endif
-      }
-      else // No preconditioning for now in partial assembly mode.
-      {
-         CG(*A, B, X, 3, 2000, 1e-12, 0.0);
-      }
 
-      // 18. After solving the linear system, reconstruct the solution as a
+      // 16. After solving the linear system, reconstruct the solution as a
       //     finite element GridFunction. Constrained nodes are interpolated
       //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
-      Device::Disable();
       a.RecoverFEMSolution(X, b, x);
 
-      // 19. Send solution by socket to the GLVis server.
+      // 17. Send solution by socket to the GLVis server.
       if (visualization && sol_sock.good())
       {
          sol_sock.precision(8);
@@ -220,7 +193,7 @@ int main(int argc, char *argv[])
          break;
       }
 
-      // 20. Call the refiner to modify the mesh. The refiner calls the error
+      // 18. Call the refiner to modify the mesh. The refiner calls the error
       //     estimator to obtain element errors, then it selects elements to be
       //     refined and finally it modifies the mesh. The Stop() method can be
       //     used to determine if a stopping criterion was met.
@@ -231,7 +204,7 @@ int main(int argc, char *argv[])
          break;
       }
 
-      // 21. Update the space to reflect the new state of the mesh. Also,
+      // 19. Update the space to reflect the new state of the mesh. Also,
       //     interpolate the solution x so that it lies in the new space but
       //     represents the same function. This saves solver iterations later
       //     since we'll have a good initial guess of x in the next step.
@@ -240,7 +213,7 @@ int main(int argc, char *argv[])
       fespace.Update();
       x.Update();
 
-      // 22. Inform also the bilinear and linear forms that the space has
+      // 20. Inform also the bilinear and linear forms that the space has
       //     changed.
       a.Update();
       b.Update();

examples/ex6p.cpp

@@ -15,17 +15,12 @@
 //               mpirun -np 4 ex6p -m ../data/square-disc-surf.mesh -o 2
 //               mpirun -np 4 ex6p -m ../data/amr-quad.mesh
 //
-// Device sample runs:
-//             > mpirun -np 4 ex6p -pa -d cuda
-//             > mpirun -np 4 ex6p -pa -d occa-cuda
-//             > mpirun -np 4 ex6p -pa -d raja-omp
-//
 // Description:  This is a version of Example 1 with a simple adaptive mesh
 //               refinement loop. The problem being solved is again the Laplace
 //               equation -Delta u = 1 with homogeneous Dirichlet boundary
 //               conditions. The problem is solved on a sequence of meshes which
 //               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
+//               or non-conforming (quadrilateral, hexahedrons) manner according
 //               to a simple ZZ error estimator.
 //
 //               The example demonstrates MFEM's capability to work with both
@@ -54,8 +49,6 @@ int main(int argc, char *argv[])
    // 2. Parse command-line options.
    const char *mesh_file = "../data/star.mesh";
    int order = 1;
-   bool pa = false;
-   const char *device = "cpu";
    bool visualization = true;
 
    OptionsParser args(argc, argv);
@@ -63,10 +56,6 @@ int main(int argc, char *argv[])
                   "Mesh file to use.");
    args.AddOption(&order, "-o", "--order",
                   "Finite element order (polynomial degree).");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -117,15 +106,10 @@ int main(int argc, char *argv[])
    H1_FECollection fec(order, dim);
    ParFiniteElementSpace fespace(&pmesh, &fec);
 
-   // 7. Set device config parameters from the command line options.
-   Device::Configure(device);
-   if (myid == 0) { Device::Print(); }
-
-   // 8. As in Example 1p, we set up bilinear and linear forms corresponding to
+   // 7. As in Example 1p, we set up bilinear and linear forms corresponding to
    //    the Laplace problem -\Delta u = 1. We don't assemble the discrete
    //    problem yet, this will be done in the main loop.
    ParBilinearForm a(&fespace);
-   if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
    ParLinearForm b(&fespace);
 
    ConstantCoefficient one(1.0);
@@ -134,12 +118,12 @@ int main(int argc, char *argv[])
    a.AddDomainIntegrator(integ);
    b.AddDomainIntegrator(new DomainLFIntegrator(one));
 
-   // 9. The solution vector x and the associated finite element grid function
+   // 8. The solution vector x and the associated finite element grid function
    //    will be maintained over the AMR iterations. We initialize it to zero.
    ParGridFunction x(&fespace);
    x = 0;
 
-   // 10. Connect to GLVis.
+   // 9. Connect to GLVis.
    char vishost[] = "localhost";
    int  visport   = 19916;
 
@@ -161,7 +145,7 @@ int main(int argc, char *argv[])
       sout.precision(8);
    }
 
-   // 11. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
+   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
    //     with L2 projection in the smoothing step to better handle hanging
    //     nodes and parallel partitioning. We need to supply a space for the
    //     discontinuous flux (L2) and a space for the smoothed flux (H(div) is
@@ -175,14 +159,14 @@ int main(int argc, char *argv[])
    // ParFiniteElementSpace smooth_flux_fes(&pmesh, &smooth_flux_fec, dim);
    L2ZienkiewiczZhuEstimator estimator(*integ, x, flux_fes, smooth_flux_fes);
 
-   // 12. A refiner selects and refines elements based on a refinement strategy.
+   // 11. A refiner selects and refines elements based on a refinement strategy.
    //     The strategy here is to refine elements with errors larger than a
    //     fraction of the maximum element error. Other strategies are possible.
    //     The refiner will call the given error estimator.
    ThresholdRefiner refiner(estimator);
    refiner.SetTotalErrorFraction(0.7);
 
-   // 13. The main AMR loop. In each iteration we solve the problem on the
+   // 12. The main AMR loop. In each iteration we solve the problem on the
    //     current mesh, visualize the solution, and refine the mesh.
    const int max_dofs = 100000;
    for (int it = 0; ; it++)
@@ -194,48 +178,41 @@ int main(int argc, char *argv[])
          cout << "Number of unknowns: " << global_dofs << endl;
       }
 
-      // 14. Assemble the right-hand side and determine the list of true
-      //     (i.e. parallel conforming) essential boundary dofs.
-      Array<int> ess_tdof_list;
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
+      // 13. Assemble the stiffness matrix and the right-hand side. Note that
+      //     MFEM doesn't care at this point that the mesh is nonconforming
+      //     and parallel. The FE space is considered 'cut' along hanging
+      //     edges/faces, and also across processor boundaries.
+      a.Assemble();
       b.Assemble();
 
-      // 15. Switch to the device and assemble the stiffness matrix. Note that
-      //     MFEM doesn't care at this point that the mesh is nonconforming and
-      //     parallel.  The FE space is considered 'cut' along hanging
-      //     edges/faces, and also across processor boundaries.
-      Device::Enable();
-      a.Assemble();
-
-      // 16. Create the parallel linear system: eliminate boundary conditions.
+      // 14. Create the parallel linear system: eliminate boundary conditions,
+      //     constrain hanging nodes and nodes across processor boundaries.
       //     The system will be solved for true (unconstrained/unique) DOFs only.
-      OperatorPtr A;
-      Vector B, X;
+      Array<int> ess_tdof_list;
+      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
 
+      HypreParMatrix A;
+      Vector B, X;
       const int copy_interior = 1;
       a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
 
-      // 17. Solve the linear system A X = B.
-      //     * With full assembly, use the BoomerAMG preconditioner from hypre.
-      //     * With partial assembly, use no preconditioner, for now.
-      HypreBoomerAMG *amg = NULL;
-      if (!pa) { amg = new HypreBoomerAMG; amg->SetPrintLevel(0); }
-      CGSolver cg(MPI_COMM_WORLD);
-      cg.SetRelTol(1e-6);
-      cg.SetMaxIter(2000);
-      cg.SetPrintLevel(3); // print the first and the last iterations only
-      if (amg) { cg.SetPreconditioner(*amg); }
-      cg.SetOperator(*A);
-      cg.Mult(B, X);
-      delete amg;
+      // 15. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
+      //     preconditioner from hypre.
+      HypreBoomerAMG amg;
+      amg.SetPrintLevel(0);
+      CGSolver pcg(A.GetComm());
+      pcg.SetPreconditioner(amg);
+      pcg.SetOperator(A);
+      pcg.SetRelTol(1e-6);
+      pcg.SetMaxIter(200);
+      pcg.SetPrintLevel(3); // print the first and the last iterations only
+      pcg.Mult(B, X);
 
-      // 18. Switch back to the host and extract the parallel grid function
-      //     corresponding to the finite element approximation X. This is the
-      //     local solution on each processor.
-      Device::Disable();
+      // 16. Extract the parallel grid function corresponding to the finite element
+      //     approximation X. This is the local solution on each processor.
       a.RecoverFEMSolution(X, b, x);
 
-      // 19. Send the solution by socket to a GLVis server.
+      // 17. Send the solution by socket to a GLVis server.
       if (visualization)
       {
          sout << "parallel " << num_procs << " " << myid << "\n";
@@ -251,7 +228,7 @@ int main(int argc, char *argv[])
          break;
       }
 
-      // 20. Call the refiner to modify the mesh. The refiner calls the error
+      // 18. Call the refiner to modify the mesh. The refiner calls the error
       //     estimator to obtain element errors, then it selects elements to be
       //     refined and finally it modifies the mesh. The Stop() method can be
       //     used to determine if a stopping criterion was met.
@@ -265,7 +242,7 @@ int main(int argc, char *argv[])
          break;
       }
 
-      // 21. Update the finite element space (recalculate the number of DOFs,
+      // 19. Update the finite element space (recalculate the number of DOFs,
       //     etc.) and create a grid function update matrix. Apply the matrix
       //     to any GridFunctions over the space. In this case, the update
       //     matrix is an interpolation matrix so the updated GridFunction will
@@ -273,7 +250,7 @@ int main(int argc, char *argv[])
       fespace.Update();
       x.Update();
 
-      // 22. Load balance the mesh, and update the space and solution. Currently
+      // 20. Load balance the mesh, and update the space and solution. Currently
       //     available only for nonconforming meshes.
       if (pmesh.Nonconforming())
       {
@@ -285,7 +262,7 @@ int main(int argc, char *argv[])
          x.Update();
       }
 
-      // 23. Inform also the bilinear and linear forms that the space has
+      // 21. Inform also the bilinear and linear forms that the space has
       //     changed.
       a.Update();
       b.Update();

examples/ex8.cpp

@@ -4,10 +4,8 @@
 //
 // Sample runs:  ex8 -m ../data/square-disc.mesh
 //               ex8 -m ../data/star.mesh
-//               ex8 -m ../data/star-mixed.mesh
 //               ex8 -m ../data/escher.mesh
 //               ex8 -m ../data/fichera.mesh
-//               ex8 -m ../data/fichera-mixed.mesh
 //               ex8 -m ../data/square-disc-p2.vtk
 //               ex8 -m ../data/square-disc-p3.mesh
 //               ex8 -m ../data/star-surf.mesh -o 2

examples/ex8p.cpp

@@ -4,10 +4,8 @@
 //
 // Sample runs:  mpirun -np 4 ex8p -m ../data/square-disc.mesh
 //               mpirun -np 4 ex8p -m ../data/star.mesh
-//               mpirun -np 4 ex8p -m ../data/star-mixed.mesh
 //               mpirun -np 4 ex8p -m ../data/escher.mesh
 //               mpirun -np 4 ex8p -m ../data/fichera.mesh
-//               mpirun -np 4 ex8p -m ../data/fichera-mixed.mesh
 //               mpirun -np 4 ex8p -m ../data/square-disc-p2.vtk
 //               mpirun -np 4 ex8p -m ../data/square-disc-p3.mesh
 //               mpirun -np 4 ex8p -m ../data/star-surf.mesh -o 2
@@ -125,13 +123,9 @@ int main(int argc, char *argv[])
       test_order++;
    }
    if (test_order < trial_order)
-   {
       if (myid == 0)
-      {
          cerr << "Warning, test space not enriched enough to handle primal"
               << " trial space\n";
-      }
-   }
 
    FiniteElementCollection *x0_fec, *xhat_fec, *test_fec;
 

examples/ex9.cpp

@@ -10,7 +10,6 @@
 //    ex9 -m ../data/periodic-hexagon.mesh -p 1 -r 2 -dt 0.005 -tf 9
 //    ex9 -m ../data/amr-quad.mesh -p 1 -r 2 -dt 0.002 -tf 9
 //    ex9 -m ../data/star-q3.mesh -p 1 -r 2 -dt 0.005 -tf 9
-//    ex9 -m ../data/star-mixed.mesh -p 1 -r 2 -dt 0.005 -tf 9
 //    ex9 -m ../data/disc-nurbs.mesh -p 1 -r 3 -dt 0.005 -tf 9
 //    ex9 -m ../data/disc-nurbs.mesh -p 2 -r 3 -dt 0.005 -tf 9
 //    ex9 -m ../data/periodic-square.mesh -p 3 -r 4 -dt 0.0025 -tf 9 -vs 20
@@ -132,8 +131,8 @@ int main(int argc, char *argv[])
 
    // 2. Read the mesh from the given mesh file. We can handle geometrically
    //    periodic meshes in this code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
+   Mesh *mesh = new Mesh(mesh_file, 1, 1);
+   int dim = mesh->Dimension();
 
    // 3. Define the ODE solver used for time integration. Several explicit
    //    Runge-Kutta methods are available.
@@ -156,18 +155,18 @@ int main(int argc, char *argv[])
    //    a (piecewise-polynomial) high-order mesh.
    for (int lev = 0; lev < ref_levels; lev++)
    {
-      mesh.UniformRefinement();
+      mesh->UniformRefinement();
    }
-   if (mesh.NURBSext)
+   if (mesh->NURBSext)
    {
-      mesh.SetCurvature(max(order, 1));
+      mesh->SetCurvature(max(order, 1));
    }
-   mesh.GetBoundingBox(bb_min, bb_max, max(order, 1));
+   mesh->GetBoundingBox(bb_min, bb_max, max(order, 1));
 
    // 5. Define the discontinuous DG finite element space of the given
    //    polynomial order on the refined mesh.
    DG_FECollection fec(order, dim);
-   FiniteElementSpace fes(&mesh, &fec);
+   FiniteElementSpace fes(mesh, &fec);
 
    cout << "Number of unknowns: " << fes.GetVSize() << endl;
 
@@ -207,7 +206,7 @@ int main(int argc, char *argv[])
    {
       ofstream omesh("ex9.mesh");
       omesh.precision(precision);
-      mesh.Print(omesh);
+      mesh->Print(omesh);
       ofstream osol("ex9-init.gf");
       osol.precision(precision);
       u.Save(osol);
@@ -221,14 +220,14 @@ int main(int argc, char *argv[])
       if (binary)
       {
 #ifdef MFEM_USE_SIDRE
-         dc = new SidreDataCollection("Example9", &mesh);
+         dc = new SidreDataCollection("Example9", mesh);
 #else
          MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
 #endif
       }
       else
       {
-         dc = new VisItDataCollection("Example9", &mesh);
+         dc = new VisItDataCollection("Example9", mesh);
          dc->SetPrecision(precision);
       }
       dc->RegisterField("solution", &u);
@@ -253,7 +252,7 @@ int main(int argc, char *argv[])
       else
       {
          sout.precision(precision);
-         sout << "solution\n" << mesh << u;
+         sout << "solution\n" << *mesh << u;
          sout << "pause\n";
          sout << flush;
          cout << "GLVis visualization paused."
@@ -285,7 +284,7 @@ int main(int argc, char *argv[])
 
          if (visualization)
          {
-            sout << "solution\n" << mesh << u << flush;
+            sout << "solution\n" << *mesh << u << flush;
          }
 
          if (visit)

examples/ex9p.cpp

@@ -10,7 +10,6 @@
 //    mpirun -np 4 ex9p -m ../data/periodic-hexagon.mesh -p 1 -dt 0.005 -tf 9
 //    mpirun -np 4 ex9p -m ../data/amr-quad.mesh -p 1 -rp 1 -dt 0.002 -tf 9
 //    mpirun -np 4 ex9p -m ../data/star-q3.mesh -p 1 -rp 1 -dt 0.004 -tf 9
-//    mpirun -np 4 ex9p -m ../data/star-mixed.mesh -p 1 -rp 1 -dt 0.004 -tf 9
 //    mpirun -np 4 ex9p -m ../data/disc-nurbs.mesh -p 1 -rp 1 -dt 0.005 -tf 9
 //    mpirun -np 4 ex9p -m ../data/disc-nurbs.mesh -p 2 -rp 1 -dt 0.005 -tf 9
 //    mpirun -np 4 ex9p -m ../data/periodic-square.mesh -p 3 -rp 2 -dt 0.0025 -tf 9 -vs 20
@@ -165,7 +164,6 @@ int main(int argc, char *argv[])
          {
             cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
          }
-         delete mesh;
          MPI_Finalize();
          return 3;
    }
@@ -272,8 +270,6 @@ int main(int argc, char *argv[])
       {
          dc = new VisItDataCollection("Example9-Parallel", pmesh);
          dc->SetPrecision(precision);
-         // To save the mesh using MFEM's parallel mesh format:
-         // dc->SetFormat(DataCollection::PARALLEL_FORMAT);
       }
       dc->RegisterField("solution", u);
       dc->SetCycle(0);

examples/makefile

@@ -14,37 +14,24 @@ MFEM_DIR ?= ..
 MFEM_BUILD_DIR ?= ..
 SRC = $(if $(MFEM_DIR:..=),$(MFEM_DIR)/examples/,)
 CONFIG_MK = $(MFEM_BUILD_DIR)/config/config.mk
+TEST_MK = $(MFEM_DIR)/config/test.mk
 # Use the MFEM install directory
-# MFEM_INSTALL_DIR = ../mfem
-# CONFIG_MK = $(MFEM_INSTALL_DIR)/share/mfem/config.mk
+# SRC = $(if $(MFEM_DIR),$(MFEM_DIR)/examples/,)
+# MFEM_DIR = ../mfem
+# CONFIG_MK = $(MFEM_DIR)/config.mk
+# TEST_MK = $(MFEM_DIR)/test.mk
 
 MFEM_LIB_FILE = mfem_is_not_built
 -include $(CONFIG_MK)
 
-SEQ_EXAMPLES = ex1 ex2 ex3 ex4 ex5 ex6 ex7 ex8 ex9 ex10 ex14 ex15 ex16 ex17\
-  ex18 ex19 ex20 ex21 ex22
+SEQ_EXAMPLES = ex1 ex2 ex3 ex4 ex5 ex6 ex7 ex8 ex9 ex10 ex14 ex15 ex16 ex17
 PAR_EXAMPLES = ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex8p ex9p ex10p ex11p ex12p\
- ex13p ex14p ex15p ex16p ex17p ex18p ex19p ex20p ex21p ex22p
-
+ ex13p ex14p ex15p ex16p ex17p
 ifeq ($(MFEM_USE_MPI),NO)
    EXAMPLES = $(SEQ_EXAMPLES)
 else
    EXAMPLES = $(PAR_EXAMPLES) $(SEQ_EXAMPLES)
 endif
-SUBDIRS =
-ifeq ($(MFEM_USE_SUNDIALS),YES)
-   SUBDIRS += sundials
-endif
-ifeq ($(MFEM_USE_PETSC),YES)
-   SUBDIRS += petsc
-endif
-ifeq ($(MFEM_USE_PUMI),YES)
-   SUBDIRS += pumi
-endif
-SUBDIRS_ALL = $(addsuffix /all,$(SUBDIRS))
-SUBDIRS_TEST = $(addsuffix /test,$(SUBDIRS))
-SUBDIRS_CLEAN = $(addsuffix /clean,$(SUBDIRS))
-SUBDIRS_TPRINT = $(addsuffix /test-print,$(SUBDIRS))
 
 .SUFFIXES:
 .SUFFIXES: .o .cpp .mk
@@ -57,27 +44,13 @@ SUBDIRS_TPRINT = $(addsuffix /test-print,$(SUBDIRS))
 %: $(SRC)%.cpp $(MFEM_LIB_FILE) $(CONFIG_MK)
 	$(MFEM_CXX) $(MFEM_FLAGS) $< -o $@ $(MFEM_LIBS)
 
-all: $(EXAMPLES) $(SUBDIRS_ALL)
-
-.PHONY: $(SUBDIRS_ALL) $(SUBDIRS_TEST) $(SUBDIRS_CLEAN) $(SUBDIRS_TPRINT)
-$(SUBDIRS_ALL) $(SUBDIRS_TEST) $(SUBDIRS_CLEAN):
-	$(MAKE) -C $(@D) $(@F)
-$(SUBDIRS_TPRINT):
-	@$(MAKE) -C $(@D) $(@F)
-
-# Additional dependencies
-ex18: $(SRC)ex18.hpp
-ifeq ($(MFEM_USE_MPI),YES)
-ex18p: $(SRC)ex18.hpp
-endif
+all: $(EXAMPLES)
 
 MFEM_TESTS = EXAMPLES
-include $(MFEM_TEST_MK)
-test: $(SUBDIRS_TEST)
-test-print: $(SUBDIRS_TPRINT)
+include $(TEST_MK)
 
 # Testing: Parallel vs. serial runs
-RUN_MPI = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP) $(MFEM_MPI_NP)
+RUN_MPI = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP) 4
 %-test-par: %
 	@$(call mfem-test,$<, $(RUN_MPI), Parallel example)
 %-test-seq: %
@@ -96,12 +69,6 @@ ex15-test-seq: ex15
 	@$(call mfem-test,$<,, Serial example,-e 1)
 ex15p-test-par: ex15p
 	@$(call mfem-test,$<, $(RUN_MPI), Parallel example,-e 1)
-# Testing: optional tests
-ifeq ($(MFEM_USE_STRUMPACK),YES)
-ex11p-test-strumpack: ex11p
-	@$(call mfem-test,$<, $(RUN_MPI), STRUMPACK example,--strumpack)
-test-par-YES: ex11p-test-strumpack
-endif
 
 # Testing: "test" target and mfem-test* variables are defined in config/test.mk
 
@@ -109,7 +76,7 @@ endif
 $(MFEM_LIB_FILE):
 	$(error The MFEM library is not built)
 
-clean: clean-build clean-exec $(SUBDIRS_CLEAN)
+clean: clean-build clean-exec
 
 clean-build:
 	rm -f *.o *~ $(SEQ_EXAMPLES) $(PAR_EXAMPLES)
@@ -118,11 +85,7 @@ clean-build:
 clean-exec:
 	@rm -f refined.mesh displaced.mesh mesh.* ex5.mesh
 	@rm -rf Example5* Example9* Example15* Example16*
-	@rm -f sphere_refined.* sol.* sol_u.* sol_p.* sol_r.* sol_i.*
+	@rm -f sphere_refined.* sol.* sol_u.* sol_p.*
 	@rm -f ex9.mesh ex9-mesh.* ex9-init.* ex9-final.*
 	@rm -f deformed.* velocity.* elastic_energy.* mode_*
 	@rm -f ex16.mesh ex16-mesh.* ex16-init.* ex16-final.*
-	@rm -f vortex-mesh.* vortex.mesh vortex-?-init.* vortex-?-final.*
-	@rm -f deformation.* pressure.*
-	@rm -f ex20.dat ex20p_?????.dat gnuplot_ex20.inp gnuplot_ex20p.inp
-	@rm -f ex22*.mesh ex22*.sol ex22p_*.*

examples/petsc/CMakeLists.txt

@@ -35,7 +35,7 @@ if (MFEM_USE_MPI)
 endif()
 
 # Include the source directory where mfem.hpp and mfem-performance.hpp are.
-include_directories(BEFORE ${PROJECT_BINARY_DIR})
+include_directories(${PROJECT_BINARY_DIR})
 
 # Add targets to copy rc_* files from the source directory
 foreach(RC_FILE ${PETSC_RC_FILES})
@@ -49,7 +49,7 @@ add_custom_target(copy_petsc_rc_files DEPENDS ${PETSC_RC_FILES}
 
 # Add "test_petsc" target, see below.
 add_custom_target(test_petsc
-  ${CMAKE_CTEST_COMMAND} -R petsc USES_TERMINAL)
+  ${CMAKE_CTEST_COMMAND} -R petsc -C PETSC USES_TERMINAL)
 
 # Add one executable per cpp file, adding "petsc_" as prefix. Sets
 # "copy_petsc_rc_files" as a prerequisite for the given examples. Also, sets
@@ -58,47 +58,50 @@ set(PFX petsc_)
 add_mfem_examples(PETSC_EXAMPLES_SRCS ${PFX} copy_petsc_rc_files test_petsc)
 
 # Testing.
-# The PETSc tests can be run separately using the target "test_petsc" which
-# builds the examples and runs:
-#   ctest -R petsc
+# We do not want these tests to be run by default, so we add them to their own
+# configuration - PETSC. To run the tests defined here use the "test_petsc"
+# target which builds the examples and runs:
+#   ctest -C PETSC -R petsc
 
 # Command line options for the tests.
-set(EX1_ARGS_W       -m ../../data/amr-quad.mesh --usepetsc)
-set(EX1_ARGS_P       -m ../../data/amr-quad.mesh --usepetsc --petscopts rc_ex1p)
-set(EX2_ARGS         -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex2p)
-set(EX3_ARGS         -m ../../data/klein-bottle.mesh -o 2 -f 0.1 --usepetsc --petscopts rc_ex3p_bddc --nonoverlapping)
-set(EX4_ARGS         -m ../../data/klein-bottle.mesh -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping)
-set(EX4_HYB_ARGS     -m ../../data/klein-bottle.mesh -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping --hybridization)
-set(EX5_BDDC_LB_ARGS -m ../../data/star.mesh --usepetsc -o 0 --petscopts rc_ex5p_bddc --nonoverlapping --local-bdr)
-set(EX5_BDDC_GB_ARGS -m ../../data/star.mesh --usepetsc -o 0 --petscopts rc_ex5p_bddc --nonoverlapping)
-set(EX5_FSPL_ARGS    -m ../../data/beam-tet.mesh --usepetsc -o 0 --petscopts rc_ex5p_fieldsplit)
-set(EX6_ARGS         -m ../../data/amr-quad.mesh --usepetsc)
-set(EX6_NONOVL_ARGS  -m ../../data/amr-quad.mesh --usepetsc --nonoverlapping)
-set(EX9_E_ARGS       -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl -dt 0.1)
-set(EX9_ES_ARGS      -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl --no-step)
-set(EX9_IS_ARGS      -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_impl --implicit -tf 0.5)
-set(EX10_ARGS        -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex10p -tf 30 -s 3 -rs 2 -dt 3)
+set(EX1P_ARGS -m ../../data/amr-quad.mesh --usepetsc --petscopts rc_ex1p)
+set(EX2P_ARGS -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex2p)
+set(EX3P_ARGS -m ../../data/klein-bottle.mesh
+    -o 2 -f 0.1 --usepetsc --petscopts rc_ex3p_bddc --nonoverlapping)
+set(EX4P_ARGS -m ../../data/klein-bottle.mesh
+    -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping)
+set(EX5_BDDC_ARGS -m ../../data/star.mesh
+    --usepetsc --petscopts rc_ex5p_bddc --nonoverlapping)
+set(EX5_FSPL_ARGS -m ../../data/beam-tet.mesh
+    --usepetsc --petscopts rc_ex5p_fieldsplit)
+set(EX5P_ARGS ${EX5_FSPL_ARGS})
+set(EX6P_ARGS -m ../../data/amr-quad.mesh --usepetsc)
+set(EX9P_ARGS -m ../../data/periodic-hexagon.mesh
+    --usepetsc --petscopts rc_ex9p_expl)
+set(EX10P_ARGS -m ../../data/beam-quad.mesh
+    -tf 30 -s 3 -rs 2 -dt 3 --usepetsc --petscopts rc_ex10p)
 
-# Add the tests: one test per command-line-variable.
-foreach(TEST_OPTIONS_VAR
-        EX1_ARGS_W EX1_ARGS_P EX2_ARGS EX3_ARGS EX4_ARGS EX4_HYB_ARGS
-        EX5_BDDC_LB_ARGS EX5_BDDC_GB_ARGS EX5_FSPL_ARGS EX6_ARGS EX6_NONOVL_ARGS
-        EX9_E_ARGS EX9_ES_ARGS EX9_IS_ARGS EX10_ARGS)
-  string(REGEX REPLACE "^(.+)_ARGS" "\\1" TEST_NAME_UC ${TEST_OPTIONS_VAR})
-  string(REGEX REPLACE "^([^_]+)" "\\1P" TEST_NAME_UC ${TEST_NAME_UC})
-  string(TOLOWER ${TEST_NAME_UC} TEST_NAME_FULL)
-  string(REGEX REPLACE "^([^_]+).*" "\\1" TEST_NAME ${TEST_NAME_FULL})
-  set(TEST_NAME_FULL ${PFX}${TEST_NAME_FULL})
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${PETSC_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
   set(TEST_NAME ${PFX}${TEST_NAME})
-  set(TEST_OPTIONS "-no-vis" ${${TEST_OPTIONS_VAR}})
-  # message(STATUS "${TEST_NAME_FULL} --> ${TEST_NAME} ${TEST_OPTIONS}")
 
-  # All PETSC tests are parallel.
-  if (MFEM_USE_MPI)
-    add_test(NAME ${TEST_NAME_FULL}_np=4
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_ARGS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS}
+      CONFIGURATIONS PETSC)
+  else()
+    add_test(NAME ${TEST_NAME}_np=4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4
       ${MPIEXEC_PREFLAGS}
-      $<TARGET_FILE:${TEST_NAME}> ${TEST_OPTIONS}
-      ${MPIEXEC_POSTFLAGS})
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS}
+      CONFIGURATIONS PETSC)
   endif()
 endforeach()

examples/petsc/ex10p.cpp

@@ -5,7 +5,6 @@
 //
 // Sample runs:
 //    mpirun -np 4 ex10p -m ../../data/beam-quad.mesh --petscopts rc_ex10p -s 3 -rs 2 -dt 3
-//    mpirun -np 4 ex10p -m ../../data/beam-quad-amr.mesh --petscopts rc_ex10p -s 3 -rs 2 -dt 3
 //
 // Description:  This examples solves a time dependent nonlinear elasticity
 //               problem of the form dv/dt = H(x) + S v, dx/dt = v, where H is a
@@ -61,7 +60,6 @@ class HyperelasticOperator : public TimeDependentOperator
 {
 protected:
    ParFiniteElementSpace &fespace;
-   Array<int> ess_tdof_list;
 
    ParBilinearForm M, S;
    ParNonlinearForm H;
@@ -99,10 +97,9 @@ public:
        This is the only requirement for high-order SDIRK implicit integration.*/
    virtual void ImplicitSolve(const double dt, const Vector &x, Vector &k);
 
-   double ElasticEnergy(const ParGridFunction &x) const;
-   double KineticEnergy(const ParGridFunction &v) const;
-   void GetElasticEnergyDensity(const ParGridFunction &x,
-                                ParGridFunction &w) const;
+   double ElasticEnergy(ParGridFunction &x) const;
+   double KineticEnergy(ParGridFunction &v) const;
+   void GetElasticEnergyDensity(ParGridFunction &x, ParGridFunction &w) const;
 
    virtual ~HyperelasticOperator();
 };
@@ -116,15 +113,14 @@ class ReducedSystemOperator : public Operator
 private:
    ParBilinearForm *M, *S;
    ParNonlinearForm *H;
-   mutable HypreParMatrix *Jacobian;
+   mutable Operator *Jacobian;
    double dt;
    const Vector *v, *x;
    mutable Vector w, z;
-   const Array<int> &ess_tdof_list;
 
 public:
    ReducedSystemOperator(ParBilinearForm *M_, ParBilinearForm *S_,
-                         ParNonlinearForm *H_, const Array<int> &ess_tdof_list);
+                         ParNonlinearForm *H_);
 
    /// Set current dt, v, x values - needed to compute action and Jacobian.
    void SetParameters(double dt_, const Vector *v_, const Vector *x_);
@@ -144,12 +140,12 @@ public:
 class ElasticEnergyCoefficient : public Coefficient
 {
 private:
-   HyperelasticModel     &model;
-   const ParGridFunction &x;
-   DenseMatrix            J;
+   HyperelasticModel &model;
+   ParGridFunction   &x;
+   DenseMatrix        J;
 
 public:
-   ElasticEnergyCoefficient(HyperelasticModel &m, const ParGridFunction &x_)
+   ElasticEnergyCoefficient(HyperelasticModel &m, ParGridFunction &x_)
       : model(m), x(x_) { }
    virtual double Eval(ElementTransformation &T, const IntegrationPoint &ip);
    virtual ~ElasticEnergyCoefficient() { }
@@ -239,7 +235,7 @@ int main(int argc, char *argv[])
    // 2b. We initialize PETSc
    if (use_petsc)
    {
-      MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL);
+      PetscInitialize(NULL,NULL,petscrc_file,NULL);
    }
 
    // 3. Read the serial mesh from the given mesh file on all processors. We can
@@ -315,9 +311,7 @@ int main(int argc, char *argv[])
    true_offset[2] = 2*true_size;
 
    BlockVector vx(true_offset);
-   ParGridFunction v_gf, x_gf;
-   v_gf.MakeTRef(&fespace, vx, true_offset[0]);
-   x_gf.MakeTRef(&fespace, vx, true_offset[1]);
+   ParGridFunction v_gf(&fespace), x_gf(&fespace);
 
    ParGridFunction x_ref(&fespace);
    pmesh->GetNodes(x_ref);
@@ -330,12 +324,11 @@ int main(int argc, char *argv[])
    //    boundary conditions on a beam-like mesh (see description above).
    VectorFunctionCoefficient velo(dim, InitialVelocity);
    v_gf.ProjectCoefficient(velo);
-   v_gf.SetTrueVector();
    VectorFunctionCoefficient deform(dim, InitialDeformation);
    x_gf.ProjectCoefficient(deform);
-   x_gf.SetTrueVector();
 
-   v_gf.SetFromTrueVector(); x_gf.SetFromTrueVector();
+   v_gf.GetTrueDofs(vx.GetBlock(0));
+   x_gf.GetTrueDofs(vx.GetBlock(1));
 
    Array<int> ess_bdr(fespace.GetMesh()->bdr_attributes.Max());
    ess_bdr = 0;
@@ -392,7 +385,8 @@ int main(int argc, char *argv[])
 
       if (last_step || (ti % vis_steps) == 0)
       {
-         v_gf.SetFromTrueVector(); x_gf.SetFromTrueVector();
+         v_gf.Distribute(vx.GetBlock(0));
+         x_gf.Distribute(vx.GetBlock(1));
 
          double ee = oper->ElasticEnergy(x_gf);
          double ke = oper->KineticEnergy(v_gf);
@@ -417,7 +411,6 @@ int main(int argc, char *argv[])
 
    // 11. Save the displaced mesh, the velocity and elastic energy.
    {
-      v_gf.SetFromTrueVector(); x_gf.SetFromTrueVector();
       GridFunction *nodes = &x_gf;
       int owns_nodes = 0;
       pmesh->SwapNodes(nodes, owns_nodes);
@@ -446,7 +439,7 @@ int main(int argc, char *argv[])
    delete oper;
 
    // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }
 
    MPI_Finalize();
 
@@ -489,11 +482,9 @@ void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
 
 
 ReducedSystemOperator::ReducedSystemOperator(
-   ParBilinearForm *M_, ParBilinearForm *S_, ParNonlinearForm *H_,
-   const Array<int> &ess_tdof_list_)
+   ParBilinearForm *M_, ParBilinearForm *S_, ParNonlinearForm *H_)
    : Operator(M_->ParFESpace()->TrueVSize()), M(M_), S(S_), H(H_),
-     Jacobian(NULL), dt(0.0), v(NULL), x(NULL), w(height), z(height),
-     ess_tdof_list(ess_tdof_list_)
+     Jacobian(NULL), dt(0.0), v(NULL), x(NULL), w(height), z(height)
 { }
 
 void ReducedSystemOperator::SetParameters(double dt_, const Vector *v_,
@@ -510,7 +501,6 @@ void ReducedSystemOperator::Mult(const Vector &k, Vector &y) const
    H->Mult(z, y);
    M->TrueAddMult(k, y);
    S->TrueAddMult(w, y);
-   y.SetSubVector(ess_tdof_list, 0.0);
 }
 
 Operator &ReducedSystemOperator::GetGradient(const Vector &k) const
@@ -524,8 +514,6 @@ Operator &ReducedSystemOperator::GetGradient(const Vector &k) const
    // PETSc's AIJ on the fly
    Jacobian = M->ParallelAssemble(localJ);
    delete localJ;
-   HypreParMatrix *Je = Jacobian->EliminateRowsCols(ess_tdof_list);
-   delete Je;
    return *Jacobian;
 }
 
@@ -550,11 +538,9 @@ HyperelasticOperator::HyperelasticOperator(ParFiniteElementSpace &f,
    ConstantCoefficient rho0(ref_density);
    M.AddDomainIntegrator(new VectorMassIntegrator(rho0));
    M.Assemble(skip_zero_entries);
+   M.EliminateEssentialBC(ess_bdr);
    M.Finalize(skip_zero_entries);
    Mmat = M.ParallelAssemble();
-   fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   HypreParMatrix *Me = Mmat->EliminateRowsCols(ess_tdof_list);
-   delete Me;
 
    M_solver.iterative_mode = false;
    M_solver.SetRelTol(rel_tol);
@@ -567,14 +553,15 @@ HyperelasticOperator::HyperelasticOperator(ParFiniteElementSpace &f,
 
    model = new NeoHookeanModel(mu, K);
    H.AddDomainIntegrator(new HyperelasticNLFIntegrator(model));
-   H.SetEssentialTrueDofs(ess_tdof_list);
+   H.SetEssentialBC(ess_bdr);
 
    ConstantCoefficient visc_coeff(viscosity);
    S.AddDomainIntegrator(new VectorDiffusionIntegrator(visc_coeff));
    S.Assemble(skip_zero_entries);
+   S.EliminateEssentialBC(ess_bdr);
    S.Finalize(skip_zero_entries);
 
-   reduced_oper = new ReducedSystemOperator(&M, &S, &H, ess_tdof_list);
+   reduced_oper = new ReducedSystemOperator(&M, &S, &H);
    if (!use_petsc)
    {
       HypreSmoother *J_hypreSmoother = new HypreSmoother;
@@ -626,7 +613,6 @@ void HyperelasticOperator::Mult(const Vector &vx, Vector &dvx_dt) const
    if (viscosity != 0.0)
    {
       S.TrueAddMult(v, z);
-      z.SetSubVector(ess_tdof_list, 0.0);
    }
    z.Neg(); // z = -z
    M_solver.Mult(z, dv_dt);
@@ -666,12 +652,12 @@ void HyperelasticOperator::ImplicitSolve(const double dt,
    add(v, dt, dv_dt, dx_dt);
 }
 
-double HyperelasticOperator::ElasticEnergy(const ParGridFunction &x) const
+double HyperelasticOperator::ElasticEnergy(ParGridFunction &x) const
 {
    return H.GetEnergy(x);
 }
 
-double HyperelasticOperator::KineticEnergy(const ParGridFunction &v) const
+double HyperelasticOperator::KineticEnergy(ParGridFunction &v) const
 {
    double loc_energy = 0.5*M.InnerProduct(v, v);
    double energy;
@@ -681,7 +667,7 @@ double HyperelasticOperator::KineticEnergy(const ParGridFunction &v) const
 }
 
 void HyperelasticOperator::GetElasticEnergyDensity(
-   const ParGridFunction &x, ParGridFunction &w) const
+   ParGridFunction &x, ParGridFunction &w) const
 {
    ElasticEnergyCoefficient w_coeff(*model, x);
    w.ProjectCoefficient(w_coeff);

examples/petsc/ex1p.cpp

@@ -123,7 +123,7 @@ int main(int argc, char *argv[])
    }
 
    // 2b. We initialize PETSc
-   MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL);
+   PetscInitialize(NULL,NULL,petscrc_file,NULL);
 
    // 3. Read the (serial) mesh from the given mesh file on all processors.  We
    //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
@@ -266,6 +266,7 @@ int main(int argc, char *argv[])
       if (visualization && petscmonitor)
       {
          pcg->SetMonitor(&mymon);
+         pcg->SetPrintLevel(4);
          pcg->iterative_mode = true;
          X.Randomize();
       }
@@ -313,7 +314,7 @@ int main(int argc, char *argv[])
    delete pmesh;
 
    // We finalize PETSc
-   MFEMFinalizePetsc();
+   PetscFinalize();
 
    MPI_Finalize();
 

examples/petsc/ex2p.cpp

@@ -101,7 +101,7 @@ int main(int argc, char *argv[])
    }
 
    // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
 
    // 3. Read the (serial) mesh from the given mesh file on all processors.  We
    //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
@@ -121,9 +121,9 @@ int main(int argc, char *argv[])
 
    // 4. Select the order of the finite element discretization space. For NURBS
    //    meshes, we increase the order by degree elevation.
-   if (mesh->NURBSext)
+   if (mesh->NURBSext && order > mesh->NURBSext->GetOrder())
    {
-      mesh->DegreeElevate(order, order);
+      mesh->DegreeElevate(order - mesh->NURBSext->GetOrder());
    }
 
    // 5. Refine the serial mesh on all processors to increase the resolution. In
@@ -359,7 +359,7 @@ int main(int argc, char *argv[])
    delete pmesh;
 
    // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }
 
    MPI_Finalize();
 

examples/petsc/ex3p.cpp

@@ -96,7 +96,7 @@ int main(int argc, char *argv[])
       args.PrintOptions(cout);
    }
    // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
    kappa = freq * M_PI;
 
    // 3. Read the (serial) mesh from the given mesh file on all processors.  We
@@ -309,7 +309,7 @@ int main(int argc, char *argv[])
    delete pmesh;
 
    // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }
 
    MPI_Finalize();
 

examples/petsc/ex4p.cpp

@@ -97,7 +97,7 @@ int main(int argc, char *argv[])
       args.PrintOptions(cout);
    }
    // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
    kappa = freq * M_PI;
 
    // 3. Read the (serial) mesh from the given mesh file on all processors.  We
@@ -330,7 +330,7 @@ int main(int argc, char *argv[])
    delete pmesh;
 
    // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }
 
    MPI_Finalize();
 

examples/petsc/ex5p.cpp

@@ -60,11 +60,9 @@ int main(int argc, char *argv[])
    // 2. Parse command-line options.
    const char *mesh_file = "../../data/star.mesh";
    int order = 1;
-   bool par_format = false;
    bool visualization = 1;
    bool use_petsc = true;
    bool use_nonoverlapping = false;
-   bool local_bdr_spec = false;
    const char *petscrc_file = "";
 
    OptionsParser args(argc, argv);
@@ -72,9 +70,6 @@ int main(int argc, char *argv[])
                   "Mesh file to use.");
    args.AddOption(&order, "-o", "--order",
                   "Finite element order (polynomial degree).");
-   args.AddOption(&par_format, "-pf", "--parallel-format", "-sf",
-                  "--serial-format",
-                  "Format to use when saving the results for VisIt.");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -87,9 +82,6 @@ int main(int argc, char *argv[])
                   "-no-nonoverlapping", "--no-nonoverlapping",
                   "Use or not the block diagonal PETSc's matrix format "
                   "for non-overlapping domain decomposition.");
-   args.AddOption(&local_bdr_spec, "-local-bdr", "--local-bdr", "-no-local-bdr",
-                  "--no-local-bdr",
-                  "Specify boundary dofs in local (Vdofs) ordering.");
    args.Parse();
    if (!args.Good())
    {
@@ -105,7 +97,7 @@ int main(int argc, char *argv[])
       args.PrintOptions(cout);
    }
    // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
 
    // 3. Read the (serial) mesh from the given mesh file on all processors.  We
    //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
@@ -218,7 +210,7 @@ int main(int argc, char *argv[])
    PetscParMatrix *pM = NULL, *pB = NULL, *pBT = NULL;
    HypreParMatrix *M = NULL, *B = NULL, *BT = NULL;
    Operator::Type tid =
-      !use_petsc ? Operator::Hypre_ParCSR :
+      !use_petsc ? Operator::HYPRE_PARCSR :
       (use_nonoverlapping ? Operator::PETSC_MATIS : Operator::PETSC_MATAIJ);
    OperatorHandle Mh(tid), Bh(tid);
 
@@ -310,38 +302,33 @@ int main(int argc, char *argv[])
    {
       if (use_nonoverlapping)
       {
-         PetscBDDCSolverParams opts;
-
          // For saddle point problems, we need to provide BDDC the list of
          // boundary dofs either essential or natural.
          // Since R_space is the only space that may have boundary dofs and it
          // is ordered first then W_space, we don't need any local offset when
          // specifying the dofs.
          Array<int> bdr_tdof_list;
+         bool local = false;
          if (pmesh->bdr_attributes.Size())
          {
             Array<int> bdr(pmesh->bdr_attributes.Max());
             bdr = 1;
 
-            if (!local_bdr_spec)
-            {
-               // Essential dofs in global ordering
-               R_space->GetEssentialTrueDofs(bdr, bdr_tdof_list);
-            }
-            else
-            {
-               // Alternatively, you can also provide the list of dofs in local
-               // ordering
-               R_space->GetEssentialVDofs(bdr, bdr_tdof_list);
-               bdr_tdof_list.SetSize(R_space->GetVSize()+W_space->GetVSize(),0);
-            }
-            opts.SetNatBdrDofs(&bdr_tdof_list,local_bdr_spec);
+            R_space->GetEssentialTrueDofs(bdr, bdr_tdof_list);
+            local = false;
+            // Alternatively, you can also provide the list of dofs in local
+            // ordering:
+            // R_space->GetEssentialVDofs(bdr, bdr_tdof_list);
+            // bdr_tdof_list.SetSize(R_space->GetVSize()+W_space->GetVSize(),0);
+            // local = true;
          }
          else
          {
-            MFEM_WARNING("Missing boundary dofs. This may cause solver failures.");
+            MFEM_ABORT("Need to know the boundary dofs");
          }
 
+         PetscBDDCSolverParams opts;
+         opts.SetNatBdrDofs(&bdr_tdof_list,local);
          // See also command line options rc_ex5p_bddc
          pdarcyPr = new PetscBDDCSolver(MPI_COMM_WORLD,*darcyOp,opts,"prec_");
       }
@@ -491,9 +478,6 @@ int main(int argc, char *argv[])
    VisItDataCollection visit_dc("Example5-Parallel", pmesh);
    visit_dc.RegisterField("velocity", u);
    visit_dc.RegisterField("pressure", p);
-   visit_dc.SetFormat(!par_format ?
-                      DataCollection::SERIAL_FORMAT :
-                      DataCollection::PARALLEL_FORMAT);
    visit_dc.Save();
 
    // 16. Send the solution by socket to a GLVis server.
@@ -544,7 +528,7 @@ int main(int argc, char *argv[])
    delete pmesh;
 
    // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }
 
    MPI_Finalize();
 

examples/petsc/ex6p.cpp

@@ -12,7 +12,7 @@
 //               equation -Delta u = 1 with homogeneous Dirichlet boundary
 //               conditions. The problem is solved on a sequence of meshes which
 //               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
+//               or non-conforming (quadrilateral, hexahedrons) manner according
 //               to a simple ZZ error estimator.
 //
 //               The example demonstrates MFEM's capability to work with both
@@ -88,7 +88,7 @@ int main(int argc, char *argv[])
       args.PrintOptions(cout);
    }
    // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
 
    // 3. Read the (serial) mesh from the given mesh file on all processors.  We
    //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
@@ -224,7 +224,7 @@ int main(int argc, char *argv[])
 
       a.Assemble();
       b.Assemble();
-      a.SetOperatorType(Operator::Hypre_ParCSR);
+      a.SetOperatorType(Operator::HYPRE_PARCSR);
       HypreParMatrix A;
       Vector B, X;
       MPI_Barrier(MPI_COMM_WORLD);
@@ -315,7 +315,7 @@ int main(int argc, char *argv[])
    }
 
    // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }
 
    MPI_Finalize();
    return 0;

examples/petsc/ex9p.cpp

@@ -248,7 +248,7 @@ int main(int argc, char *argv[])
    {
       // When using PETSc, we just create the ODE solver. We use command line
       // customization to select a specific solver.
-      MFEMInitializePetsc(NULL, NULL, petscrc_file, NULL);
+      PetscInitialize(NULL, NULL, petscrc_file, NULL);
       ode_solver = pode_solver = new PetscODESolver(MPI_COMM_WORLD);
    }
 
@@ -403,14 +403,7 @@ int main(int argc, char *argv[])
 
    double t = 0.0;
    adv->SetTime(t);
-   if (use_petsc)
-   {
-      pode_solver->Init(*adv,PetscODESolver::ODE_SOLVER_LINEAR);
-   }
-   else
-   {
-      ode_solver->Init(*adv);
-   }
+   ode_solver->Init(*adv);
 
    // Explicitly perform time-integration (looping over the time iterations, ti,
    // with a time-step dt), or use the Run method of the ODE solver class.
@@ -431,6 +424,7 @@ int main(int argc, char *argv[])
             {
                cout << "time step: " << ti << ", time: " << t << endl;
             }
+
             // 11. Extract the parallel grid function corresponding to the finite
             //     element approximation U (the local solution on each processor).
             *u = *U;
@@ -481,7 +475,7 @@ int main(int argc, char *argv[])
    delete pmon;
 
    // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }
 
    MPI_Finalize();
    return 0;