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

@@ -1,167 +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/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/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/mesh-explorer
-miniapps/meshing/shaper
-miniapps/meshing/mesh-optimizer
-miniapps/meshing/pmesh-optimizer
-
-miniapps/meshing/mobius-strip.mesh
-miniapps/meshing/klein-bottle.mesh
-miniapps/meshing/mesh-explorer.mesh
-miniapps/meshing/partitioning.txt
-miniapps/meshing/shaper.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/nurbs/ex1
-miniapps/nurbs/ex1p
-miniapps/nurbs/ex11p
-miniapps/nurbs/refined.mesh
-miniapps/nurbs/mesh.*
-miniapps/nurbs/sol.*
-miniapps/nurbs/mode_*
-miniapps/nurbs/Example1*

.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

@@ -8,303 +8,16 @@
                                http://mfem.org
 
 
-Version 3.4.1 (development)
-===========================
-- Added support for reading linear and quadratic 2D quadrilateral and triangular
-  Cubit meshes.
-
-- The tetrahedral mesh refinement algorithm in serial and in parallel now
-  follows precisely the paper:
-     D. Arnold, A. Mukherjee, and L. Pouly, "Locally Adapted Tetrahedral Meshes
-     Using Bisection", SIAM J. Sci. Comput., 22(2), 431–448.
-  This guarantees that the shape regularity of the elements will be preserved
-  under refinement.
-
-
-Version 3.4, released on May 29, 2018
+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
@@ -460,7 +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

@@ -38,14 +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 ${PROJECT_BINARY_DIR})
@@ -53,65 +47,18 @@ if (${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
 #-------------------------------------------------------------------------------
@@ -123,23 +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")
@@ -148,19 +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
@@ -182,6 +129,7 @@ endif()
 if (MFEM_USE_SUITESPARSE)
   find_package(SuiteSparse REQUIRED
     UMFPACK KLU AMD BTF CHOLMOD COLAMD CAMD CCOLAMD config)
+  include_directories(${SuiteSparse_INCLUDE_DIRS})
 endif()
 
 # SUNDIALS
@@ -192,82 +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()
@@ -281,27 +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")
@@ -309,8 +228,6 @@ 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})
@@ -320,6 +237,7 @@ set(_USE_MATH_DEFINES ${WIN32})
 #-------------------------------------------------------------------------------
 
 # Headers and sources
+include(MfemCmakeUtilities)
 set(SOURCES "")
 set(HEADERS "")
 set(MFEM_SOURCE_DIRS general linalg mesh fem)
@@ -331,30 +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.
@@ -372,11 +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()
@@ -428,12 +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()
@@ -448,6 +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
@@ -467,15 +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}
@@ -488,11 +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)
@@ -502,15 +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})

CONTRIBUTING.md

@@ -1,538 +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
-  ```
-
-- 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.
-
-- 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`:
-    - [ ] Has a new optional library been added? (*Make sure the external library is licensed under LGPL, not GPL!*)
-    - [ ] Does `make` or `cmake` have a new target?
-    - [ ] Did the requirements or the installation process change? *(rare)*.
-- [ ] Update `.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.
-- [ ] (LLNL only) Clone the `tests` repository and run the following tests, see `mfem/tests/README.md`:
-   - [ ] `compilers`
-   - [ ] `memcheck`
-   - [ ] `unit-test`
-   - [ ] `documentation`
-- [ ] (LLNL only) After merging:
-   - [ ] Regenerate `README.html` files from companion documentation pull requests.
-   - [ ] Update 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

@@ -18,23 +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.
-
 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
 =========================
@@ -147,7 +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
@@ -159,8 +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
 
@@ -190,8 +181,6 @@ 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
@@ -202,14 +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)
@@ -218,21 +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 bahavior
-   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
@@ -257,16 +231,13 @@ 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
@@ -290,12 +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
@@ -307,9 +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.
 
@@ -336,13 +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
@@ -353,14 +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_BUILD_TAG = (any value)
    An optional tag to characterize the build. Exported to config/config.mk.
@@ -386,8 +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.
 
@@ -405,10 +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.
 
@@ -427,14 +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.
-  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).
@@ -448,7 +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:
@@ -465,16 +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.
-
 - 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.
@@ -485,11 +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
 ===================
@@ -521,12 +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.
 
@@ -534,30 +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.
 
@@ -565,11 +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.
@@ -577,8 +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
@@ -592,7 +485,6 @@ 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
@@ -602,12 +494,10 @@ 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 options are CMake specific:
 
@@ -646,14 +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:
 
@@ -669,15 +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.

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

@@ -1,182 +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()

config/cmake/MFEMConfig.cmake.in

@@ -12,42 +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_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
 
@@ -74,9 +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
 
@@ -95,14 +65,12 @@
 // 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@
 
@@ -113,11 +81,4 @@
 // Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
 #cmakedefine _USE_MATH_DEFINES
 
-// Version of HYPRE used for building MFEM.
-#cmakedefine MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@
-
-// Macro defined when PUMI is built with support for the Simmetrix SimModSuite
-// library.
-#cmakedefine MFEM_USE_SIMMETRIX
-
 #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
 #      ${Prefix}_INCLUDE_DIRS
@@ -255,14 +230,12 @@ function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
   mfem_find_component("${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 "")
 
@@ -301,22 +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
@@ -369,8 +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)
@@ -384,7 +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}")
@@ -394,139 +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)
@@ -543,6 +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
@@ -560,10 +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${I}}" STREQUAL "ADD_COMPONENT")
@@ -574,35 +434,22 @@ function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
       endif()
       math(EXPR I "${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)

config/config.hpp

@@ -30,13 +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

config/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.
-// #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)
-
-// 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
@@ -40,18 +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
 
@@ -69,7 +42,11 @@
 // #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@
 
@@ -85,9 +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
 
@@ -97,9 +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
 
@@ -109,20 +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
-
 // Windows specific options
 #ifdef _WIN32
 // Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
 #define _USE_MATH_DEFINES
 #endif
 
-// Version of HYPRE used for building MFEM.
-// #define MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@
-
-// Macro defined when PUMI is built with support for the Simmetrix SimModSuite
-// library.
-// #define MFEM_USE_SIMMETRIX
-
 #endif // MFEM_CONFIG_HEADER

config/config.mk.in

@@ -10,14 +10,9 @@
 # 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_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@
@@ -29,15 +24,12 @@ MFEM_USE_SUNDIALS    = @MFEM_USE_SUNDIALS@
 MFEM_USE_MESQUITE    = @MFEM_USE_MESQUITE@
 MFEM_USE_SUITESPARSE = @MFEM_USE_SUITESPARSE@
 MFEM_USE_SUPERLU     = @MFEM_USE_SUPERLU@
-MFEM_USE_STRUMPACK   = @MFEM_USE_STRUMPACK@
 MFEM_USE_GECKO       = @MFEM_USE_GECKO@
 MFEM_USE_GNUTLS      = @MFEM_USE_GNUTLS@
 MFEM_USE_NETCDF      = @MFEM_USE_NETCDF@
 MFEM_USE_PETSC       = @MFEM_USE_PETSC@
 MFEM_USE_MPFR        = @MFEM_USE_MPFR@
 MFEM_USE_SIDRE       = @MFEM_USE_SIDRE@
-MFEM_USE_CONDUIT     = @MFEM_USE_CONDUIT@
-MFEM_USE_PUMI        = @MFEM_USE_PUMI@
 
 # Compiler, compile options, and link options
 MFEM_CXX       = @MFEM_CXX@
@@ -45,25 +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@
 
 # Optional extra configuration
 @MFEM_CONFIG_EXTRA@

config/defaults.cmake

@@ -18,10 +18,8 @@ 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)
@@ -32,21 +30,17 @@ 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)
+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)
@@ -72,7 +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"
@@ -97,32 +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 "${MFEM_DIR}/../STRUMPACK-build" CACHE PATH
-    "Path to the STRUMPACK library.")
-# STRUMPACK may also depend on "OpenMP", depending on how it was compiled.
-set(STRUMPACK_REQUIRED_PACKAGES "MPI" "MPI_Fortran" "ParMETIS" "METIS"
-    "ScaLAPACK" "Scotch/ptscotch/ptscotcherr/scotch/scotcherr" CACHE STRING
-    "Additional packages required by STRUMPACK.")
-# If the MPI package does not find all required Fortran libraries:
-# set(STRUMPACK_REQUIRED_LIBRARIES "gfortran" "mpi_mpifh" CACHE STRING
-#     "Additional libraries required by STRUMPACK.")
-
-# The Scotch library, required by STRUMPACK
-set(Scotch_DIR "${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.")
@@ -134,20 +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

@@ -30,36 +30,15 @@ PREFIX = ./mfem
 # Install program
 INSTALL = /usr/bin/install
 
-STATIC = YES
-SHARED = NO
-
 ifneq ($(NOTMAC),)
    AR      = ar
    ARFLAGS = cruv
    RANLIB  = ranlib
-   PICFLAG = -fPIC
-   SO_EXT  = so
-   SO_VER  = so.$(MFEM_VERSION_STRING)
-   BUILD_SOFLAGS = -shared -Wl,-soname,libmfem.$(SO_VER)
-   BUILD_RPATH = -Wl,-rpath,$(BUILD_REAL_DIR)
-   INSTALL_SOFLAGS = $(BUILD_SOFLAGS)
-   INSTALL_RPATH = -Wl,-rpath,@MFEM_LIB_DIR@
 else
    # Silence "has no symbols" warnings on Mac OS X
    AR      = ar
    ARFLAGS = Scruv
    RANLIB  = ranlib -no_warning_for_no_symbols
-   PICFLAG = -fPIC
-   SO_EXT  = dylib
-   SO_VER  = $(MFEM_VERSION_STRING).dylib
-   MAKE_SOFLAGS = -Wl,-dylib,-install_name,$(1)/libmfem.$(SO_VER),\
-      -compatibility_version,$(MFEM_VERSION_STRING),\
-      -current_version,$(MFEM_VERSION_STRING),\
-      -undefined,dynamic_lookup
-   BUILD_SOFLAGS = $(subst $1 ,,$(call MAKE_SOFLAGS,$(BUILD_REAL_DIR)))
-   BUILD_RPATH = -Wl,-undefined,dynamic_lookup
-   INSTALL_SOFLAGS = $(subst $1 ,,$(call MAKE_SOFLAGS,$(MFEM_LIB_DIR)))
-   INSTALL_RPATH = -Wl,-undefined,dynamic_lookup
 endif
 
 # Set CXXFLAGS to overwrite the default selection of DEBUG_FLAGS/OPTIM_FLAGS
@@ -75,44 +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_MEMALLOC    = YES
-MFEM_TIMER_TYPE      = $(if $(NOTMAC),2,4)
+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_STRUMPACK   = NO
 MFEM_USE_GECKO       = NO
 MFEM_USE_GNUTLS      = NO
 MFEM_USE_NETCDF      = NO
 MFEM_USE_PETSC       = NO
 MFEM_USE_MPFR        = NO
 MFEM_USE_SIDRE       = NO
-MFEM_USE_CONDUIT     = NO
-MFEM_USE_PUMI        = NO
-
-# Compile and link options for zlib.
-ZLIB_DIR =
-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
 
 LIBUNWIND_OPT = -g
 LIBUNWIND_LIB = $(if $(NOTMAC),-lunwind -ldl,)
@@ -123,7 +89,7 @@ HYPRE_OPT = -I$(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 =
@@ -134,7 +100,7 @@ ifeq ($(MFEM_USE_SUPERLU)$(MFEM_USE_STRUMPACK),NONO)
      METIS_LIB = -L$(METIS_DIR)/lib -lmetis
    endif
 else
-   # ParMETIS: currently needed by SuperLU or STRUMPACK. We assume that METIS 5
+   # ParMETIS currently needed only with SuperLU. We assume that METIS 5
    # (included with ParMETIS) is installed in the same location.
    METIS_DIR = @MFEM_DIR@/../parmetis-4.0.3
    METIS_OPT = -I$(METIS_DIR)/include
@@ -154,10 +120,10 @@ OPENMP_LIB =
 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 ($(MFEM_USE_MPI),YES)
    SUNDIALS_LIB += -lsundials_nvecparhyp -lsundials_nvecparallel
@@ -174,41 +140,14 @@ MESQUITE_LIB = -L$(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$(SUPERLU_DIR)/SRC -lsuperlu_dist
-
-# SCOTCH library configuration (required by STRUMPACK)
-SCOTCH_DIR = @MFEM_DIR@/../scotch_6.0.4
-SCOTCH_OPT = -I$(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
@@ -220,64 +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
+ifeq ($(MFEM_USE_MPI),YES)
+   SIDRE_LIB += -lspio -lcommon
+endif
 
 # 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

@@ -1,525 +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 "$0")"/.. && pwd)"
-mfem_build_dir=""
-build_log=""
-output_dir=""
-output_sfx=".out"
-# The group format is: '"group-name" "group-summary-title" "group-directory"
-# "group-source-patterns"'
-groups_serial=(
-'"examples"
-   "Examples:"
-   "examples"
-   "ex{,1}[0-9].cpp"'
-#   "ex1.cpp"'
-'"sundials"
-   "SUNDIALS examples:"
-   "examples/sundials"
-   "ex{9,10,16}.cpp"'
-'"performance"
-   "Performance miniapps:"
-   "miniapps/performance"
-   "ex1.cpp"'
-#   ""'
-'"meshing"
-   "Meshing miniapps:"
-   "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp mesh-optimizer.cpp"'
-)
-# Parallel groups
-groups_parallel=(
-'"examples"
-   "Examples:"
-   "examples"
-   "ex{,1}[0-9]p.cpp"'
-#   "ex1p.cpp"'
-'"sundials"
-   "SUNDIALS examples:"
-   "examples/sundials"
-   "ex{9,10,16}p.cpp"'
-'"petsc"
-   "PETSc examples:"
-   "examples/petsc"
-   "ex{,1}[0-9]p.cpp"'
-'"performance"
-   "Performance miniapps:"
-   "miniapps/performance"
-   "ex1p.cpp"'
-#   ""'
-'"meshing"
-   "Meshing miniapps:"
-   "miniapps/meshing"
-   "pmesh-optimizer.cpp"'
-'"electromagnetics"
-   "Electromagnetics miniapps:"
-   "miniapps/electromagnetics"
-   "joule.cpp"'
-#   "{volta,tesla,joule}.cpp"' # todo: multiline sample runs
-)
-# All groups serial + parallel runs mixed in the same group:
-groups_all=(
-'"examples"
-   "Examples:"
-   "examples"
-   "ex\"{,1}[0-9]\"{,p}.cpp"'
-'"sundials"
-   "SUNDIALS examples:"
-   "examples/sundials"
-   "ex\"{9,10,16}\"{,p}.cpp"'
-'"petsc"
-   "PETSc examples:"
-   "examples/petsc"
-   "ex{,1}[0-9]p.cpp"'
-'"performance"
-   "Performance miniapps:"
-   "miniapps/performance"
-   "ex1{,p}.cpp"'
-'"meshing"
-   "Meshing miniapps:"
-   "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp {,p}mesh-optimizer.cpp"'
-'"electromagnetics"
-   "Electromagnetics miniapps:"
-   "miniapps/electromagnetics"
-   "joule.cpp"'
-#   "{volta,tesla,joule}.cpp"' # todo: multiline sample runs
-)
-make_all="all"
-base_timeformat=$'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>
-      -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}]
-         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"
-      ;;
-   -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 -- $$($(1) -l $(SHELL) -c "$(2)" 2>&1; echo $$?); \
-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
@@ -60,20 +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) -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)
@@ -81,12 +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
-3 1 14 13
-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
-18 0 1
-19 1 10
-20 9 10
-21 0 9
-22 18 20
-23 0 18
-24 18 22
-25 21 22
-26 0 21
-27 20 22
-28 9 20
-29 9 21
-30 23 25
-31 25 28
-
-coarse_elements
-3
-3 0 3 2 1
-3 8 7 6 9
-3 17 4 5 18
-
-vertices
-32
-2
-0 0
-1 0
-2 0
-3 0
-4 0
-5 0
-6 0
-7 0
-8 0
-0 1
-1 1
-2 1
-3 1
-4 1
-5 1
-6 1
-7 1
-8 1
-0.5 0
-1 0.5
-0.5 1
-0 0.5
-0.5 0.5
-0.25 0
-0.5 0.25
-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/mixed-ele-meshes/annulus-trans-24.mesh

@@ -1,218 +0,0 @@
-MFEM mesh v1.0
-
-dimension
-2
-
-elements
-74
-2 3 0 1 2 3
-2 3 1 5 6 2
-2 3 5 8 9 6
-2 3 8 11 12 9
-2 3 11 14 15 12
-2 3 14 17 18 15
-2 3 17 20 21 18
-2 3 20 23 24 21
-2 3 23 26 27 24
-2 3 26 29 30 27
-2 3 29 32 33 30
-2 3 32 35 36 33
-2 3 35 38 39 36
-2 3 38 41 42 39
-2 3 41 44 45 42
-2 3 44 47 48 45
-2 3 47 50 51 48
-2 3 50 53 54 51
-2 3 53 56 57 54
-2 3 56 59 60 57
-2 3 59 62 63 60
-2 3 62 65 66 63
-2 3 65 68 69 66
-2 3 68 71 72 69
-2 3 71 74 75 72
-1 2 2 3 4
-1 2 6 2 7
-1 2 9 6 10
-1 2 12 9 13
-1 2 15 12 16
-1 2 18 15 19
-1 2 21 18 22
-1 2 24 21 25
-1 2 27 24 28
-1 2 30 27 31
-1 2 33 30 34
-1 2 36 33 37
-1 2 39 36 40
-1 2 42 39 43
-1 2 45 42 46
-1 2 48 45 49
-1 2 51 48 52
-1 2 54 51 55
-1 2 57 54 58
-1 2 60 57 61
-1 2 63 60 64
-1 2 66 63 67
-1 2 69 66 70
-1 2 72 69 73
-1 2 75 72 76
-1 2 2 4 7
-1 2 6 7 10
-1 2 9 10 13
-1 2 12 13 16
-1 2 15 16 19
-1 2 18 19 22
-1 2 21 22 25
-1 2 24 25 28
-1 2 27 28 31
-1 2 30 31 34
-1 2 33 34 37
-1 2 36 37 40
-1 2 39 40 43
-1 2 42 43 46
-1 2 45 46 49
-1 2 48 49 52
-1 2 51 52 55
-1 2 54 55 58
-1 2 57 58 61
-1 2 60 61 64
-1 2 63 64 67
-1 2 66 67 70
-1 2 69 70 73
-1 2 72 73 76
-
-boundary
-53
-1 1 0 1
-1 1 1 5
-1 1 5 8
-1 1 8 11
-1 1 11 14
-1 1 14 17
-1 1 17 20
-1 1 20 23
-1 1 23 26
-1 1 26 29
-1 1 29 32
-1 1 32 35
-1 1 35 38
-1 1 38 41
-1 1 41 44
-1 1 44 47
-1 1 47 50
-1 1 50 53
-1 1 53 56
-1 1 56 59
-1 1 59 62
-1 1 62 65
-1 1 65 68
-1 1 68 71
-1 1 71 74
-1 1 74 75
-1 1 75 76
-1 1 76 73
-1 1 73 70
-1 1 70 67
-1 1 67 64
-1 1 64 61
-1 1 61 58
-1 1 58 55
-1 1 55 52
-1 1 52 49
-1 1 49 46
-1 1 46 43
-1 1 43 40
-1 1 40 37
-1 1 37 34
-1 1 34 31
-1 1 31 28
-1 1 28 25
-1 1 25 22
-1 1 22 19
-1 1 19 16
-1 1 16 13
-1 1 13 10
-1 1 10 7
-1 1 7 4
-1 1 4 3
-1 1 3 0
-
-vertices
-77
-2
-3.9788735773 0.0
-3.84329674785 1.02980825986
-2.88247256089 0.772356194895
-2.98415518297 0.0
-1.97241688113 0.259673608685
-3.44580559639 1.98943678865
-2.58435419729 1.49207759149
-1.83799993026 0.761324498753
-2.81348848799 2.81348848799
-2.11011636599 2.11011636599
-1.57832632157 1.21109238238
-1.98943678865 3.44580559639
-1.49207759149 2.58435419729
-1.21109238238 1.57832632157
-1.02980825986 3.84329674785
-0.772356194895 2.88247256089
-0.761324498753 1.83799993026
-2.43635739532e-16 3.9788735773
-1.82726804649e-16 2.98415518297
-0.259673608685 1.97241688113
--1.02980825986 3.84329674785
--0.772356194895 2.88247256089
--0.259673608685 1.97241688113
--1.98943678865 3.44580559639
--1.49207759149 2.58435419729
--0.761324498753 1.83799993026
--2.81348848799 2.81348848799
--2.11011636599 2.11011636599
--1.21109238238 1.57832632157
--3.44580559639 1.98943678865
--2.58435419729 1.49207759149
--1.57832632157 1.21109238238
--3.84329674785 1.02980825986
--2.88247256089 0.772356194895
--1.83799993026 0.761324498753
--3.9788735773 4.87271479065e-16
--2.98415518297 3.65453609299e-16
--1.97241688113 0.259673608685
--3.84329674785 -1.02980825986
--2.88247256089 -0.772356194895
--1.97241688113 -0.259673608685
--3.44580559639 -1.98943678865
--2.58435419729 -1.49207759149
--1.83799993026 -0.761324498753
--2.81348848799 -2.81348848799
--2.11011636599 -2.11011636599
--1.57832632157 -1.21109238238
--1.98943678865 -3.44580559639
--1.49207759149 -2.58435419729
--1.21109238238 -1.57832632157
--1.02980825986 -3.84329674785
--0.772356194895 -2.88247256089
--0.761324498753 -1.83799993026
--7.30907218597e-16 -3.9788735773
--5.48180413948e-16 -2.98415518297
--0.259673608685 -1.97241688113
-1.02980825986 -3.84329674785
-0.772356194895 -2.88247256089
-0.259673608685 -1.97241688113
-1.98943678865 -3.44580559639
-1.49207759149 -2.58435419729
-0.761324498753 -1.83799993026
-2.81348848799 -2.81348848799
-2.11011636599 -2.11011636599
-1.21109238238 -1.57832632157
-3.44580559639 -1.98943678865
-2.58435419729 -1.49207759149
-1.57832632157 -1.21109238238
-3.84329674785 -1.02980825986
-2.88247256089 -0.772356194895
-1.83799993026 -0.761324498753
-3.9788735773 -9.7454295813e-16
-2.98415518297 -7.30907218597e-16
-1.97241688113 -0.259673608685
-3.84329674785 1.02980825986
-2.88247256089 0.772356194895
-1.97241688113 0.259673608685

data/mixed-ele-meshes/annulus-trans-6.mesh

@@ -1,74 +0,0 @@
-MFEM mesh v1.0
-
-dimension
-2
-
-elements
-20
-2 3 0 1 2 3
-2 3 1 5 6 2
-2 3 5 8 9 6
-2 3 8 11 12 9
-2 3 11 14 15 12
-2 3 14 17 18 15
-2 3 17 20 21 18
-1 2 2 3 4
-1 2 6 2 7
-1 2 9 6 10
-1 2 12 9 13
-1 2 15 12 16
-1 2 18 15 19
-1 2 21 18 22
-1 2 2 4 7
-1 2 6 7 10
-1 2 9 10 13
-1 2 12 13 16
-1 2 15 16 19
-1 2 18 19 22
-
-boundary
-17
-1 1 0 1
-1 1 1 5
-1 1 5 8
-1 1 8 11
-1 1 11 14
-1 1 14 17
-1 1 17 20
-1 1 20 21
-1 1 21 22
-1 1 22 19
-1 1 19 16
-1 1 16 13
-1 1 13 10
-1 1 10 7
-1 1 7 4
-1 1 4 3
-1 1 3 0
-
-vertices
-23
-2
-1.11408460164 0.0
-0.557042300822 0.964825566988
-0.417781725616 0.723619175241
-0.835563451232 0.0
-0.482412783494 0.278521150411
--0.557042300822 0.964825566988
--0.417781725616 0.723619175241
-3.41090035345e-17 0.557042300822
--1.11408460164 1.36436014138e-16
--0.835563451232 1.02327010604e-16
--0.482412783494 0.278521150411
--0.557042300822 -0.964825566988
--0.417781725616 -0.723619175241
--0.482412783494 -0.278521150411
-0.557042300822 -0.964825566988
-0.417781725616 -0.723619175241
--1.02327010604e-16 -0.557042300822
-1.11408460164 -2.72872028276e-16
-0.835563451232 -2.04654021207e-16
-0.482412783494 -0.278521150411
-0.557042300822 0.964825566988
-0.417781725616 0.723619175241
-0.482412783494 0.278521150411

data/mixed-ele-meshes/circInSquare.py

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

data/mixed-ele-meshes/comp_tri_quad_4_edges.mesh

@@ -1,264 +0,0 @@
-MFEM mesh v1.0
-
-dimension
-2
-
-elements
-128
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data/mixed-ele-meshes/spec-3-mixed-type.mesh

@@ -1,72 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-#
-
-dimension
-2
-
-elements
-17
-1 2 0 1 2
-1 2 0 2 3
-1 2 0 3 4
-2 3 0 4 5 6
-2 3 0 6 7 1
-1 2 7 8 1
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-1 2 2 10 11
-2 3 2 11 12 3
-1 2 3 12 13
-2 3 3 13 14 4
-1 2 4 14 15
-1 2 4 15 5
-1 2 5 16 6 
-1 2 6 16 17
-1 2 6 17 7
-
-boundary
-12
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-0.5 -1.866025

data/mixed-ele-meshes/spec-3-trans-and-ref.mesh

@@ -1,362 +0,0 @@
-MFEM mesh v1.0
-
-dimension
-2
-
-elements
-154
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-2 3 1 5 6 2
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-2 3 8 11 12 9
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--1.5 2.0
--0.5 2.0
-0.0 -0.125
-0.17678 -0.17678
-0.18954 -0.32357
-0.32357 -0.18954
-0.46194 -0.19134
-0.0 -0.375
-0.19134 -0.46194
-0.50569 -0.36729
-0.59418 -0.19384
-0.72444 -0.19411
-0.19384 -0.59418
-0.36729 -0.50569
-0.53033 -0.53033
-0.0 -0.625
-0.19411 -0.72444
-0.78835 -0.37964
-0.85299 -0.19501
-0.98079 -0.19509
-0.54563 -0.68405
-0.68405 -0.54563
-0.83147 -0.55557
-0.19501 -0.85299
-0.37964 -0.78835
-0.55557 -0.83147
-0.0 -0.875
-0.19509 -0.98079
-1.05851 -0.4599
-1.24928 -0.27462
-0.86872 -0.86872
-1.13007 -0.79668
-0.4599 -1.05851
-0.79668 -1.13007
-0.0 -1.125
-0.27462 -1.24928
-1.32748 -0.6142
-1.51779 -0.35426
-1.19194 -1.19194
-1.42864 -1.03762
-0.6142 -1.32748
-1.03762 -1.42864
-0.0 -1.375
-0.35426 -1.51779
-1.59649 -0.76852
-1.78629 -0.43396
-1.51516 -1.51516
-1.72721 -1.2785
-0.76852 -1.59649
-1.2785 -1.72721
-0.0 -1.625
-0.43396 -1.78629
-1.8655 -0.92284
-2.0 -0.5
-1.83839 -1.83839
-2.0 -1.5
-0.92284 -1.8655
-1.5 -2.0
-0.0 -1.875
-0.5 -2.0
--0.17678 -0.17678
--0.32357 -0.18954
--0.18954 -0.32357
--0.46194 -0.19134
--0.19134 -0.46194
--0.59418 -0.19384
--0.50569 -0.36729
--0.72444 -0.19411
--0.36729 -0.50569
--0.19384 -0.59418
--0.53033 -0.53033
--0.19411 -0.72444
--0.85299 -0.19501
--0.78835 -0.37964
--0.98079 -0.19509
--0.68405 -0.54563
--0.54563 -0.68405
--0.83147 -0.55557
--0.37964 -0.78835
--0.19501 -0.85299
--0.55557 -0.83147
--0.19509 -0.98079
--1.24928 -0.27462
--1.05851 -0.4599
--1.13007 -0.79668
--0.86872 -0.86872
--0.79668 -1.13007
--0.4599 -1.05851
--0.27462 -1.24928
--1.51779 -0.35426
--1.32748 -0.6142
--1.42864 -1.03762
--1.19194 -1.19194
--1.03762 -1.42864
--0.6142 -1.32748
--0.35426 -1.51779
--1.78629 -0.43396
--1.59649 -0.76852
--1.72721 -1.2785
--1.51516 -1.51516
--1.2785 -1.72721
--0.76852 -1.59649
--0.43396 -1.78629
--1.875 0.0
--2.0 -0.5
--1.8655 -0.92284
--2.0 -1.5
--1.83839 -1.83839
--1.5 -2.0
--0.92284 -1.8655
--0.5 -2.0
-1.0917 0.22992
-0.96356 0.66428
-0.66428 0.96356
-0.22992 1.0917
-1.35121 0.30709
-1.25968 0.90306
-0.90306 1.25968
-0.30709 1.35121
-1.61073 0.38425
-1.55581 1.14184
-1.14184 1.55581
-0.38425 1.61073
-1.87024 0.46142
-1.85194 1.38061
-1.38061 1.85194
-0.46142 1.87024
--1.0917 0.22992
--0.96356 0.66428
--0.66428 0.96356
--0.22992 1.0917
--1.35121 0.30709
--1.25968 0.90306
--0.90306 1.25968
--0.30709 1.35121
--1.61073 0.38425
--1.55581 1.14184
--1.14184 1.55581
--0.38425 1.61073
--1.87024 0.46142
--1.85194 1.38061
--1.38061 1.85194
--0.46142 1.87024
-1.0917 -0.22992
-0.96356 -0.66428
-0.66428 -0.96356
-0.22992 -1.0917
-1.35121 -0.30709
-1.25968 -0.90306
-0.90306 -1.25968
-0.30709 -1.35121
-1.61073 -0.38425
-1.55581 -1.14184
-1.14184 -1.55581
-0.38425 -1.61073
-1.87024 -0.46142
-1.85194 -1.38061
-1.38061 -1.85194
-0.46142 -1.87024
--1.0917 -0.22992
--0.96356 -0.66428
--0.66428 -0.96356
--0.22992 -1.0917
--1.35121 -0.30709
--1.25968 -0.90306
--0.90306 -1.25968
--0.30709 -1.35121
--1.61073 -0.38425
--1.55581 -1.14184
--1.14184 -1.55581
--0.38425 -1.61073
--1.87024 -0.46142
--1.85194 -1.38061
--1.38061 -1.85194
--0.46142 -1.87024

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
@@ -67,20 +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
  *
  * <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>
@@ -96,28 +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="shaper_8cpp_source.html">Shaper</a>: resolve material interfaces by mesh refinement
  * - <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="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

@@ -24,8 +24,6 @@ list(APPEND ALL_EXE_SRCS
   ex15.cpp
   ex16.cpp
   ex17.cpp
-  ex18.cpp
-  ex19.cpp
   )
 
 if (MFEM_USE_MPI)
@@ -47,13 +45,11 @@ if (MFEM_USE_MPI)
     ex15p.cpp
     ex16p.cpp
     ex17p.cpp
-    ex18p.cpp
-    ex19p.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)
@@ -63,6 +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")
@@ -70,7 +68,7 @@ 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()
@@ -82,17 +80,7 @@ foreach(SRC_FILE ${ALL_EXE_SRCS})
   endif()
 endforeach()
 
-# 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

@@ -80,8 +80,8 @@ int main(int argc, char *argv[])
    //    largest number that gives a final mesh with no more than 50,000
    //    elements.
    {
-     int ref_levels = 0; 
-       //(int)floor(log(50000./mesh->GetNE())/log(2.)/dim);
+      int ref_levels =
+         (int)floor(log(50000./mesh->GetNE())/log(2.)/dim);
       for (int l = 0; l < ref_levels; l++)
       {
          mesh->UniformRefinement();

examples/ex10.cpp

@@ -9,7 +9,6 @@
 //    ex10 -m ../data/beam-tet.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
@@ -91,9 +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();
 };
@@ -133,12 +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() { }
@@ -222,14 +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;
    }
 
@@ -250,7 +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;
@@ -259,8 +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);
@@ -273,10 +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;
@@ -293,7 +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)
@@ -304,8 +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;
@@ -327,15 +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)
             {
@@ -348,7 +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);
@@ -449,7 +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)
 {
@@ -460,10 +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);
@@ -475,12 +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);
 
@@ -549,18 +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

@@ -9,7 +9,6 @@
 //    mpirun -np 4 ex10p -m ../data/beam-tet.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
@@ -58,7 +57,6 @@ class HyperelasticOperator : public TimeDependentOperator
 {
 protected:
    ParFiniteElementSpace &fespace;
-   Array<int> ess_tdof_list;
 
    ParBilinearForm M, S;
    ParNonlinearForm H;
@@ -93,10 +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();
 };
@@ -114,11 +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_);
@@ -138,12 +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() { }
@@ -244,7 +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;
@@ -254,7 +249,6 @@ int main(int argc, char *argv[])
          {
             cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
          }
-         delete mesh;
          MPI_Finalize();
          return 3;
    }
@@ -298,9 +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);
@@ -313,12 +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;
@@ -374,7 +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);
@@ -399,7 +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);
@@ -467,11 +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_,
@@ -488,7 +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
@@ -500,8 +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;
 }
 
@@ -526,11 +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);
@@ -543,14 +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);
@@ -587,7 +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);
@@ -617,12 +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;
@@ -632,7 +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

@@ -32,9 +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.
 
@@ -61,7 +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);
@@ -81,36 +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)
    {
@@ -203,20 +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;
@@ -226,42 +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->SetMC64Job(strumpack::MC64Job::NONE);
-         // strumpack->SetSymmetricPattern(true);
-         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);
@@ -352,7 +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

@@ -2,15 +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 -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 -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.
@@ -109,9 +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/ex16.cpp

@@ -157,14 +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
 //
@@ -173,14 +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/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

@@ -1,571 +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)
-{
-   const int dim = x.Size();
-   MFEM_ASSERT(dim == 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

@@ -1,537 +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
-//
-// 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

@@ -1,591 +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
-//
-// 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/ex2.cpp

@@ -84,9 +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/ex2p.cpp

@@ -107,9 +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/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/ex9.cpp

@@ -146,7 +146,6 @@ int main(int argc, char *argv[])
       case 6: ode_solver = new RK6Solver; break;
       default:
          cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
-         delete mesh;
          return 3;
    }
 

examples/ex9p.cpp

@@ -164,7 +164,6 @@ int main(int argc, char *argv[])
          {
             cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
          }
-         delete mesh;
          MPI_Finalize();
          return 3;
    }
@@ -271,8 +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
+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
-
+ 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: %
@@ -103,7 +76,7 @@ ex15p-test-par: ex15p
 $(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)
@@ -116,5 +89,3 @@ clean-exec:
 	@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.*

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
+  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() { }
@@ -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);
@@ -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/ex2p.cpp

@@ -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

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())
    {
@@ -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.

examples/petsc/ex6p.cpp

@@ -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);

examples/petsc/ex9p.cpp

@@ -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;

examples/petsc/makefile

@@ -14,9 +14,12 @@ MFEM_DIR ?= ../..
 MFEM_BUILD_DIR ?= ../..
 SRC = $(if $(MFEM_DIR:../..=),$(MFEM_DIR)/examples/petsc/,)
 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/petsc/,)
+# 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)
@@ -59,52 +62,40 @@ $(EXAMPLES):
 endif
 
 MFEM_TESTS = EXAMPLES
-include $(MFEM_TEST_MK)
+include $(TEST_MK)
 
 # Testing: Parallel runs
-RUN_MPI = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP) $(MFEM_MPI_NP)
+RUN_MPI = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP) 4
 TESTNAME = Parallel PETSc example
 %-test-par: %
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME))
 
 
 # Testing PETSc execution options.
-EX1_ARGS_W       := -m ../../data/amr-quad.mesh --usepetsc
-EX1_ARGS_P       := -m ../../data/amr-quad.mesh --usepetsc --petscopts rc_ex1p
-EX2_ARGS         := -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex2p
-EX3_ARGS         := -m ../../data/klein-bottle.mesh -o 2 -f 0.1 --usepetsc --petscopts rc_ex3p_bddc --nonoverlapping
-EX4_ARGS         := -m ../../data/klein-bottle.mesh -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping
-EX4_HYB_ARGS     := -m ../../data/klein-bottle.mesh -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping --hybridization
-EX5_BDDC_LB_ARGS := -m ../../data/star.mesh --usepetsc -o 0 --petscopts rc_ex5p_bddc --nonoverlapping --local-bdr
-EX5_BDDC_GB_ARGS := -m ../../data/star.mesh --usepetsc -o 0 --petscopts rc_ex5p_bddc --nonoverlapping
-EX5_FSPL_ARGS    := -m ../../data/beam-tet.mesh --usepetsc -o 0 --petscopts rc_ex5p_fieldsplit
-EX6_ARGS         := -m ../../data/amr-quad.mesh --usepetsc
-EX6_NONOVL_ARGS  := -m ../../data/amr-quad.mesh --usepetsc --nonoverlapping
-EX9_E_ARGS       := -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl -dt 0.1
-EX9_ES_ARGS      := -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl --no-step
-EX9_IS_ARGS      := -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_impl --implicit -tf 0.5
-EX10_ARGS        := -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex10p -tf 30 -s 3 -rs 2 -dt 3
+EX1_ARGS      := -m ../../data/amr-quad.mesh --usepetsc --petscopts rc_ex1p
+EX2_ARGS      := -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex2p
+EX3_ARGS      := -m ../../data/klein-bottle.mesh -o 2 -f 0.1 --usepetsc --petscopts rc_ex3p_bddc --nonoverlapping
+EX4_ARGS      := -m ../../data/klein-bottle.mesh -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping
+EX5_BDDC_ARGS := -m ../../data/star.mesh --usepetsc -o 0 --petscopts rc_ex5p_bddc --nonoverlapping
+EX5_FSPL_ARGS := -m ../../data/beam-tet.mesh --usepetsc -o 0 --petscopts rc_ex5p_fieldsplit
+EX6_ARGS      := -m ../../data/amr-quad.mesh --usepetsc
+EX9_ARGS      := -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl
+EX10_ARGS     := -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex10p -tf 30 -s 3 -rs 2 -dt 3
 ex1p-test-par: ex1p
-	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX1_ARGS_W))
-	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX1_ARGS_P))
+	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX1_ARGS))
 ex2p-test-par: ex2p
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX2_ARGS))
 ex3p-test-par: ex3p
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX3_ARGS))
 ex4p-test-par: ex4p
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX4_ARGS))
-	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX4_HYB_ARGS))
 ex5p-test-par: ex5p
-	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX5_BDDC_LB_ARGS))
-	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX5_BDDC_GB_ARGS))
+	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX5_BDDC_ARGS))
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX5_FSPL_ARGS))
 ex6p-test-par: ex6p
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX6_ARGS))
-	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX6_NONOVL_ARGS))
 ex9p-test-par: ex9p
-	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX9_E_ARGS))
-	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX9_ES_ARGS))
-	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX9_IS_ARGS))
+	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX9_ARGS))
 ex10p-test-par: ex10p
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX10_ARGS))
 
@@ -121,6 +112,6 @@ clean-build:
 	rm -rf *.dSYM *.TVD.*breakpoints
 
 clean-exec:
-	@rm -rf mesh.* sol.* sol_p.* sol_u.* Example5*
-	@rm -f ex9-mesh.* ex9-init.* ex9-final.* Example9*
-	@rm -f deformed.* velocity.* elastic_energy.*
+	@rm -rf sol_p.* sol_u.* Example5*
+	@rm -f ex9.mesh ex9-mesh.* ex9-init.* ex9-final.* Example9*
+	@rm -f mesh.* sol.* deformed.* velocity.* elastic_energy.*

examples/petsc/rc_ex3p

@@ -6,7 +6,4 @@
 # it needs PETSc configured with MUMPS
 
 -solver_pc_type cholesky
-# Petsc 3.9
--solver_pc_factor_mat_solver_type mumps
-# Older versions of PETSc
 -solver_pc_factor_mat_solver_package mumps

examples/petsc/rc_ex3p_bddc

@@ -16,10 +16,7 @@
 #-pc_bddc_adaptive_threshold 10
 
 # Customization of the local solvers
-# With PETSc versions older than 3.9
-# use "mat_solver_package" instead of "mat_solver_type"
-#
-#-pc_bddc_neumann_pc_factor_mat_solver_type mumps
-#-pc_bddc_dirichlet_pc_factor_mat_solver_type mumps
+#-pc_bddc_neumann_pc_factor_mat_solver_package mumps
+#-pc_bddc_dirichlet_pc_factor_mat_solver_package mumps
 #-pc_bddc_coarse_pc_type cholesky
-#-pc_bddc_coarse_pc_factor_mat_solver_type mumps
+#-pc_bddc_coarse_pc_factor_mat_solver_package mumps

examples/petsc/rc_ex4p

@@ -2,7 +2,4 @@
 # it needs PETSc configured with MUMPS
 
 -solver_pc_type cholesky
-# Petsc 3.9
--solver_pc_factor_mat_solver_type mumps
-# Older versions of PETSc
 -solver_pc_factor_mat_solver_package mumps

examples/petsc/rc_ex4p_bddc

@@ -13,10 +13,7 @@
 #-pc_bddc_adaptive_threshold 10
 
 # Customization of the local solvers
-# With PETSc versions older than 3.9
-# use "mat_solver_package" instead of "mat_solver_type"
-#
-#-pc_bddc_neumann_pc_factor_mat_solver_type mumps
-#-pc_bddc_dirichlet_pc_factor_mat_solver_type mumps
+#-pc_bddc_neumann_pc_factor_mat_solver_package mumps
+#-pc_bddc_dirichlet_pc_factor_mat_solver_package mumps
 #-pc_bddc_coarse_pc_type cholesky
-#-pc_bddc_coarse_pc_factor_mat_solver_type mumps
+#-pc_bddc_coarse_pc_factor_mat_solver_package mumps

examples/petsc/rc_ex5p_bddc

@@ -25,29 +25,15 @@
 # verbose output
 #-prec_pc_bddc_check_level 1
 
-# local solvers (default "petsc" solvers will fail)
-# needs PETSc compiled with support for MUMPS or SuiteSparse
-# use "umfpack" in place of "mumps" if you want to use
-# SuiteSparse solvers
-#
-# With PETSc versions older than 3.9
-# use "mat_solver_package" instead of "mat_solver_type"
-#
+# local solvers (needs PETSc compiled with support for SuiteSparse)
+# default solvers will fail
 -prec_pc_bddc_neumann_pc_type lu
--prec_pc_bddc_neumann_pc_factor_mat_solver_type mumps
--prec_pc_bddc_neumann_pc_factor_mat_solver_package mumps
+-prec_pc_bddc_neumann_pc_factor_mat_solver_package umfpack
 -prec_pc_bddc_dirichlet_pc_type lu
--prec_pc_bddc_dirichlet_pc_factor_mat_solver_type mumps
--prec_pc_bddc_dirichlet_pc_factor_mat_solver_package mumps
-
-#  MUMPS sometimes fails with a very annoying error
--mat_mumps_icntl_14 500
--prec_pc_bddc_dirichlet_mat_mumps_icntl_14 500
--prec_pc_bddc_neumann_mat_mumps_icntl_14 500
+-prec_pc_bddc_dirichlet_pc_factor_mat_solver_package umfpack
 
 # coarse solver (needs PETSc compiled with support for MUMPS)
 # default solver may fail
--prec_pc_bddc_coarse_pc_factor_mat_solver_type mumps
 -prec_pc_bddc_coarse_pc_factor_mat_solver_package mumps
 -prec_pc_bddc_coarse_pc_type cholesky
 

examples/pumi/CMakeLists.txt

@@ -1,72 +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.
-
-set(PUMI_EXAMPLES_SRCS)
-# All PUMI examples require MPI
-if (MFEM_USE_MPI)
-  list(APPEND PUMI_EXAMPLES_SRCS
-    ex1.cpp
-    ex1p.cpp
-    ex2.cpp
-    ex6p.cpp
-    )
-endif()
-
-# Include the source directory where mfem.hpp and mfem-performance.hpp are.
-include_directories(BEFORE ${PROJECT_BINARY_DIR})
-
-# Add "test_pumi" target, see below.
-add_custom_target(test_pumi
-  ${CMAKE_CTEST_COMMAND} -R pumi USES_TERMINAL)
-
-# Add one executable per cpp file, adding "pumi_" as prefix. Sets
-# "test_pumi" as a target that depends on the given examples.
-set(PFX pumi_)
-add_mfem_examples(PUMI_EXAMPLES_SRCS ${PFX} "" test_pumi)
-
-# Testing.
-# The PUMI tests can be run separately using the target "test_pumi"
-# which builds the examples and runs:
-#   ctest -R pumi
-
-# Command line options for the tests.
-# TODO...
-
-# Set the number of processors for the parallel examples.
-set(EX1_TEST_NP 1)
-set(EX1P_TEST_NP 8)
-set(EX2_TEST_NP 1)
-set(EX6P_TEST_NP 8)
-
-# Add the tests: one test per source file.
-foreach(SRC_FILE ${PUMI_EXAMPLES_SRCS})
-  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
-  set(TEST_NAME ${PFX}${TEST_NAME})
-
-  set(THIS_TEST_OPTIONS "-no-vis")
-  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
-  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
-
-  # All PUMI examples require MPI
-  if (FALSE)
-    add_test(NAME ${TEST_NAME}_ser
-      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-  else()
-    set(TEST_NP ${${UP_TEST_NAME}_TEST_NP})
-    add_test(NAME ${TEST_NAME}_np=${TEST_NP}
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${TEST_NP}
-      ${MPIEXEC_PREFLAGS}
-      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-      ${MPIEXEC_POSTFLAGS})
-  endif()
-endforeach()

examples/pumi/README

@@ -1,18 +0,0 @@
-                    Finite Element Discretization Library
-                                   __
-                       _ __ ___   / _|  ___  _ __ ___
-                      | '_ ` _ \ | |_  / _ \| '_ ` _ \
-                      | | | | | ||  _||  __/| | | | | |
-                      |_| |_| |_||_|   \___||_| |_| |_|
-
-                               http://mfem.org
-
-This directory contains modifications of the example codes that illustrate the
-use of MFEM features based on the Parallel Unstructured Mesh Infrastructure,
-PUMI, from https://scorec.rpi.edu/pumi.
-
-To build these examples, make sure that MFEM is configured with the option
-"MFEM_USE_PUMI = YES", see the top-level INSTALL file for details.
-
-We recommend comparing the original example codes with the corresponding files
-in the current directory.

examples/pumi/ex1.cpp

@@ -1,262 +0,0 @@
-//                                MFEM Example 1
-//                              PUMI Modification
-//
-// Compile with: make ex1
-//
-// Sample runs:
-//    ex1 -m ../../data/pumi/serial/Kova.smb -p ../../data/pumi/geom/Kova.dmg
-//
-// Note:         Example models + meshes for the PUMI examples can be downloaded
-//               from github.com/mfem/data/pumi. After downloading we recommend
-//               creating a symbolic link to the above directory in ../../data.
-//
-// Description:  This example code demonstrates the use of MFEM to define a
-//               simple finite element discretization of the Laplace problem
-//               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
-//               Specifically, we discretize using a FE space of the specified
-//               order, or if order < 1 using an isoparametric/isogeometric
-//               space (i.e. quadratic for quadratic curvilinear mesh, NURBS for
-//               NURBS mesh, etc.)
-//
-//               The example highlights the use of mesh refinement, finite
-//               element grid functions, as well as linear and bilinear forms
-//               corresponding to the left-hand side and right-hand side of the
-//               discrete linear system. We also cover the explicit elimination
-//               of essential boundary conditions, static condensation, and the
-//               optional connection to the GLVis tool for visualization.
-//
-//               This PUMI modification demonstrates how PUMI's API can be used
-//               to load a PUMI mesh classified on a geometric model and then
-//               convert it to the MFEM mesh format. The inputs are a Parasolid
-//               model, "*.xmt_txt" and a SCOREC mesh "*.smb". The option "-o"
-//               is used for the Finite Element order and "-go" is used for the
-//               geometry order. Note that they can be used independently, i.e.
-//               "-o 8 -go 3" solves for 8th order FE on a third order geometry.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-#ifdef MFEM_USE_SIMMETRIX
-#include <SimUtil.h>
-#include <gmi_sim.h>
-#endif
-#include <apfMDS.h>
-#include <gmi_null.h>
-#include <PCU.h>
-#include <apfConvert.h>
-#include <gmi_mesh.h>
-#include <crv.h>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI (required by PUMI).
-   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/pumi/serial/Kova.smb";
-#ifdef MFEM_USE_SIMMETRIX
-   const char *model_file = "../../data/pumi/geom/Kova.x_t";
-#else
-   const char *model_file = "../../data/pumi/geom/Kova.dmg";
-#endif
-   int order = 1;
-   bool static_cond = false;
-   bool visualization = 1;
-   int geom_order = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree) or -1 for"
-                  " isoparametric space.");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&model_file, "-p", "--parasolid",
-                  "Parasolid model to use.");
-   args.AddOption(&geom_order, "-go", "--geometry_order",
-                  "Geometric order of the model");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 3. Read the SCOREC Mesh.
-   PCU_Comm_Init();
-#ifdef MFEM_USE_SIMMETRIX
-   Sim_readLicenseFile(0);
-   gmi_sim_start();
-   gmi_register_sim();
-#endif
-   gmi_register_mesh();
-
-   apf::Mesh2* pumi_mesh;
-   pumi_mesh = apf::loadMdsMesh(model_file, mesh_file);
-
-   // 4. Increase the geometry order if necessary.
-   if (geom_order > 1)
-   {
-      crv::BezierCurver bc(pumi_mesh, geom_order, 2);
-      bc.run();
-   }
-
-   pumi_mesh->verify();
-
-   // 5. Create the MFEM mesh object from the PUMI mesh. We can handle
-   //    triangular and tetrahedral meshes. Other inputs are the same as the
-   //    MFEM default constructor.
-   Mesh *mesh = new PumiMesh(pumi_mesh, 1, 1);
-   int dim = mesh->Dimension();
-
-   // 6. Refine the mesh to increase the resolution. In this example we do
-   //    'ref_levels' of uniform refinement. We choose 'ref_levels' to be the
-   //    largest number that gives a final mesh with no more than 50,000
-   //    elements.
-   {
-      int ref_levels =
-         (int)floor(log(50000./mesh->GetNE())/log(2.)/dim);
-      for (int l = 0; l < ref_levels; l++)
-      {
-         mesh->UniformRefinement();
-      }
-   }
-
-   // 7. Define a finite element space on the mesh. Here we use continuous
-   //    Lagrange finite elements of the specified order. If order < 1, we
-   //    instead use an isoparametric/isogeometric space.
-   FiniteElementCollection *fec;
-   if (order > 0)
-   {
-      fec = new H1_FECollection(order, dim);
-   }
-   else if (mesh->GetNodes())
-   {
-      fec = mesh->GetNodes()->OwnFEC();
-      cout << "Using isoparametric FEs: " << fec->Name() << endl;
-   }
-   else
-   {
-      fec = new H1_FECollection(order = 1, dim);
-   }
-   FiniteElementSpace *fespace = new FiniteElementSpace(mesh, fec);
-   cout << "Number of finite element unknowns: "
-        << fespace->GetTrueVSize() << endl;
-
-   // 8. Determine the list of true (i.e. conforming) essential boundary dofs.
-   //    In this example, the boundary conditions are defined by marking all
-   //    the boundary attributes from the mesh as essential (Dirichlet) and
-   //    converting them to a list of true dofs.
-   Array<int> ess_tdof_list;
-   if (mesh->bdr_attributes.Size())
-   {
-      Array<int> ess_bdr(mesh->bdr_attributes.Max());
-      ess_bdr = 1;
-      fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   // 9. Set up the linear form b(.) which corresponds to the right-hand side of
-   //    the FEM linear system, which in this case is (1,phi_i) where phi_i are
-   //    the basis functions in the finite element fespace.
-   LinearForm *b = new LinearForm(fespace);
-   ConstantCoefficient one(1.0);
-   b->AddDomainIntegrator(new DomainLFIntegrator(one));
-   b->Assemble();
-
-   // 10. 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;
-
-   // 11. Set up the bilinear form a(.,.) on the finite element space
-   //     corresponding to the Laplacian operator -Delta, by adding the
-   //     Diffusion domain integrator.
-   BilinearForm *a = new BilinearForm(fespace);
-   a->AddDomainIntegrator(new DiffusionIntegrator(one));
-
-   // 12. Assemble the bilinear form and the corresponding linear system,
-   //     applying any necessary transformations such as: eliminating boundary
-   //     conditions, applying conforming constraints for non-conforming AMR,
-   //     static condensation, etc.
-   if (static_cond) { a->EnableStaticCondensation(); }
-   a->Assemble();
-
-   SparseMatrix A;
-   Vector B, X;
-   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
-
-   cout << "Size of linear system: " << A.Height() << endl;
-
-#ifndef MFEM_USE_SUITESPARSE
-   // 13. 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
-   // 13. 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
-
-   // 14. Recover the solution as a finite element grid function.
-   a->RecoverFEMSolution(X, *b, x);
-
-   // 15. Save the refined mesh and the solution. This output can be viewed later
-   //     using GLVis: "glvis -m refined.mesh -g sol.gf".
-   ofstream mesh_ofs("refined.mesh");
-   mesh_ofs.precision(8);
-   mesh->Print(mesh_ofs);
-   ofstream sol_ofs("sol.gf");
-   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.precision(8);
-      sol_sock << "solution\n" << *mesh << x << flush;
-   }
-
-   // 17. Free the used memory.
-   delete a;
-   delete b;
-   delete fespace;
-   if (order > 0) { delete fec; }
-   delete mesh;
-
-   pumi_mesh->destroyNative();
-   apf::destroyMesh(pumi_mesh);
-   PCU_Comm_Free();
-#ifdef MFEM_USE_SIMMETRIX
-   gmi_sim_stop();
-   Sim_unregisterAllKeys();
-#endif
-
-   MPI_Finalize();
-   return 0;
-}

examples/pumi/ex1p.cpp

@@ -1,292 +0,0 @@
-//                       MFEM Example 1 - Parallel Version
-//                              PUMI Modification
-//
-// Compile with: make ex1p
-//
-// Sample runs:
-//    mpirun -np 8 ex1p -m ../../data/pumi/parallel/Kova/Kova100k_8.smb
-//                      -p ../../data/pumi/geom/Kova.dmg -o 1 -go 2
-//
-// Note:         Example models + meshes for the PUMI examples can be downloaded
-//               from github.com/mfem/data/pumi. After downloading we recommend
-//               creating a symbolic link to the above directory in ../../data.
-//
-// Description:  This example code demonstrates the use of MFEM to define a
-//               simple finite element discretization of the Laplace problem
-//               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
-//               Specifically, we discretize using a FE space of the specified
-//               order, or if order < 1 using an isoparametric/isogeometric
-//               space (i.e. quadratic for quadratic curvilinear mesh, NURBS for
-//               NURBS mesh, etc.)
-//
-//               The example highlights the use of mesh refinement, finite
-//               element grid functions, as well as linear and bilinear forms
-//               corresponding to the left-hand side and right-hand side of the
-//               discrete linear system. We also cover the explicit elimination
-//               of essential boundary conditions, static condensation, and the
-//               optional connection to the GLVis tool for visualization.
-//
-//               This PUMI modification demonstrates how PUMI's API can be used
-//               to load a parallel PUMI mesh classified on a geometric model
-//               and then generate the corresponding parallel MFEM mesh. The
-//               example also performs a "uniform" refinement, similar to the
-//               MFEM examples, for coarse meshes. However, the refinement is
-//               performed using the PUMI API.  The inputs are a Parasolid
-//               model, "*.xmt_txt" and SCOREC parallel meshes "*.smb". The
-//               option "-o" is used for the Finite Element order and "-go" for
-//               the geometry order. Note that they can be used independently:
-//               "-o 8 -go 3" solves for 8th order FE on third order geometry.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-#ifdef MFEM_USE_SIMMETRIX
-#include <SimUtil.h>
-#include <gmi_sim.h>
-#endif
-#include <apfMDS.h>
-#include <gmi_null.h>
-#include <PCU.h>
-#include <apfConvert.h>
-#include <gmi_mesh.h>
-#include <crv.h>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "../../data/pumi/parallel/Kova/Kova100k_8.smb";
-#ifdef MFEM_USE_SIMMETRIX
-   const char *model_file = "../../data/pumi/geom/Kova.x_t";
-#else
-   const char *model_file = "../../data/pumi/geom/Kova.dmg";
-#endif
-   int order = 1;
-   bool static_cond = false;
-   bool visualization = 1;
-   int geom_order = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree) or -1 for"
-                  " isoparametric space.");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&model_file, "-p", "--parasolid",
-                  "Parasolid model to use.");
-   args.AddOption(&geom_order, "-go", "--geometry_order",
-                  "Geometric order of the model");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 3. Read the SCOREC Mesh
-   PCU_Comm_Init();
-#ifdef MFEM_USE_SIMMETRIX
-   Sim_readLicenseFile(0);
-   gmi_sim_start();
-   gmi_register_sim();
-#endif
-   gmi_register_mesh();
-
-   apf::Mesh2* pumi_mesh;
-   pumi_mesh = apf::loadMdsMesh(model_file, mesh_file);
-
-   // 4. Increase the geometry order and refine the mesh if necessary. Parallel
-   //    uniform refinement is performed if the total number of elements is less
-   //    than 10,000.
-   int dim = pumi_mesh->getDimension();
-   int nEle = pumi_mesh->count(dim);
-   int ref_levels = (int)floor(log(10000./nEle)/log(2.)/dim);
-
-   if (geom_order > 1)
-   {
-      crv::BezierCurver bc(pumi_mesh, geom_order, 2);
-      bc.run();
-   }
-
-   // Perform Uniform refinement
-   if (ref_levels > 1)
-   {
-      ma::Input* uniInput = ma::configureUniformRefine(pumi_mesh, ref_levels);
-
-      if (geom_order > 1)
-      {
-         crv::adapt(uniInput);
-      }
-      else
-      {
-         ma::adapt(uniInput);
-      }
-   }
-
-   pumi_mesh->verify();
-
-   // 5. Create the parallel MFEM mesh object from the parallel PUMI mesh.
-   //    We can handle triangular and tetrahedral meshes. Note that the
-   //    mesh resolution is performed on the PUMI mesh.
-   ParMesh *pmesh = new ParPumiMesh(MPI_COMM_WORLD, pumi_mesh);
-
-   // 6. Define a parallel finite element space on the parallel mesh. Here we
-   //    use continuous Lagrange finite elements of the specified order. If
-   //    order < 1, we instead use an isoparametric/isogeometric space.
-   FiniteElementCollection *fec;
-   if (order > 0)
-   {
-      fec = new H1_FECollection(order, dim);
-   }
-   else if (pmesh->GetNodes())
-   {
-      fec = pmesh->GetNodes()->OwnFEC();
-      if (myid == 0)
-      {
-         cout << "Using isoparametric FEs: " << fec->Name() << endl;
-      }
-   }
-   else
-   {
-      fec = new H1_FECollection(order = 1, dim);
-   }
-   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
-   HYPRE_Int size = fespace->GlobalTrueVSize();
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 7. Determine the list of true (i.e. parallel conforming) essential
-   //    boundary dofs. In this example, the boundary conditions are defined
-   //    by marking all the boundary attributes from the mesh as essential
-   //    (Dirichlet) and converting them to a list of true dofs.
-   Array<int> ess_tdof_list;
-   if (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
-   //    (1,phi_i) where phi_i are the basis functions in fespace.
-   ParLinearForm *b = new ParLinearForm(fespace);
-   ConstantCoefficient one(1.0);
-   b->AddDomainIntegrator(new DomainLFIntegrator(one));
-   b->Assemble();
-
-   // 9. Define the solution vector x as a parallel finite element grid function
-   //    corresponding to fespace. Initialize x with initial guess of zero,
-   //    which satisfies the boundary conditions.
-   ParGridFunction x(fespace);
-   x = 0.0;
-
-   // 10. Set up the parallel bilinear form a(.,.) on the finite element space
-   //     corresponding to the Laplacian operator -Delta, by adding the Diffusion
-   //     domain integrator.
-   ParBilinearForm *a = new ParBilinearForm(fespace);
-   a->AddDomainIntegrator(new DiffusionIntegrator(one));
-
-   // 11. Assemble the parallel bilinear form and the corresponding linear
-   //     system, applying any necessary transformations such as: parallel
-   //     assembly, eliminating boundary conditions, applying conforming
-   //     constraints for non-conforming AMR, static condensation, etc.
-   if (static_cond) { a->EnableStaticCondensation(); }
-   a->Assemble();
-
-   HypreParMatrix A;
-   Vector B, X;
-   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
-
-   if (myid == 0)
-   {
-      cout << "Size of linear system: " << A.GetGlobalNumRows() << endl;
-   }
-
-   // 12. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
-   //     preconditioner from hypre.
-   HypreSolver *amg = new HypreBoomerAMG(A);
-   HyprePCG *pcg = new HyprePCG(A);
-   pcg->SetTol(1e-12);
-   pcg->SetMaxIter(200);
-   pcg->SetPrintLevel(2);
-   pcg->SetPreconditioner(*amg);
-   pcg->Mult(B, X);
-
-   // 13. Recover the parallel grid function corresponding to X. This is the
-   //     local finite element solution on each processor.
-   a->RecoverFEMSolution(X, *b, x);
-
-   // 14. Save the refined mesh and the solution in parallel. This output can
-   //     be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
-   {
-      ostringstream mesh_name, sol_name;
-      mesh_name << "mesh." << setfill('0') << setw(6) << myid;
-      sol_name << "sol." << setfill('0') << setw(6) << myid;
-
-      ofstream mesh_ofs(mesh_name.str().c_str());
-      mesh_ofs.precision(8);
-      pmesh->Print(mesh_ofs);
-
-      ofstream sol_ofs(sol_name.str().c_str());
-      sol_ofs.precision(8);
-      x.Save(sol_ofs);
-   }
-
-   // 15. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << *pmesh << x << flush;
-   }
-
-   // 16. Free the used memory.
-   delete pcg;
-   delete amg;
-   delete a;
-   delete b;
-   delete fespace;
-   if (order > 0) { delete fec; }
-   delete pmesh;
-
-   pumi_mesh->destroyNative();
-   apf::destroyMesh(pumi_mesh);
-   PCU_Comm_Free();
-
-#ifdef MFEM_USE_SIMMETRIX
-   gmi_sim_stop();
-   Sim_unregisterAllKeys();
-#endif
-
-   MPI_Finalize();
-
-   return 0;
-}

examples/pumi/ex2.cpp

@@ -1,413 +0,0 @@
-//                                MFEM Example 2
-//                              PUMI Modification
-//
-// Compile with: make ex2
-//
-// Sample runs:
-//    ex2 -m ../../data/pumi/serial/pillbox.smb -p ../../data/pumi/geom/pillbox.dmg
-//        -bf ../../data/pumi/serial/boundary.mesh
-//
-// Note:         Example models + meshes for the PUMI examples can be downloaded
-//               from github.com/mfem/data/pumi. After downloading we recommend
-//               creating a symbolic link to the above directory in ../../data.
-//
-// Description:  This example code solves a simple linear elasticity problem
-//               describing a multi-material cantilever beam.
-//
-//               Specifically, we approximate the weak form of -div(sigma(u))=0
-//               where sigma(u)=lambda*div(u)*I+mu*(grad*u+u*grad) is the stress
-//               tensor corresponding to displacement field u, and lambda and mu
-//               are the material Lame constants. The boundary conditions are
-//               u=0 on the fixed part of the boundary with attribute 1, and
-//               sigma(u).n=f on the remainder with f being a constant pull down
-//               vector on boundary elements with attribute 2, and zero
-//               otherwise. The geometry of the domain is assumed to be as
-//               follows:
-//                                        boundary
-//                                       attribute 2
-//                                       (push down)
-//                                            ||
-//                                            \/
-//                                       +----------+
-//                                       |          |
-//                                       |          |
-//                             +---------| material |----------+
-//                boundary --->| material|    2     | material |<--- boundary
-//                attribute 1  |    1    |          |    3     |     attribute 1
-//                 (fixed)     +---------+----------+----------+     (fixed)
-//
-//               The example demonstrates the use of high-order and NURBS vector
-//               finite element spaces with the linear elasticity bilinear form,
-//               meshes with curved elements, and the definition of piece-wise
-//               constant and vector coefficient objects. Static condensation is
-//               also illustrated.
-//
-//               We recommend viewing Example 1 before viewing this example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-#include "../../general/text.hpp"
-
-#ifdef MFEM_USE_SIMMETRIX
-#include <SimUtil.h>
-#include <gmi_sim.h>
-#endif
-#include <apfMDS.h>
-#include <gmi_null.h>
-#include <PCU.h>
-#include <apfConvert.h>
-#include <gmi_mesh.h>
-#include <crv.h>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI (required by PUMI).
-   int num_proc, myId;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_proc);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myId);
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "../../data/pumi/serial/pillbox.smb";
-   const char *boundary_file = "../../data/pumi/serial/boundary.mesh";
-#ifdef MFEM_USE_SIMMETRIX
-   const char *model_file = "../../data/pumi/geom/pillbox.smd";
-#else
-   const char *model_file = "../../data/pumi/geom/pillbox.dmg";
-#endif
-   int order = 1;
-   bool static_cond = false;
-   bool visualization = 1;
-   int geom_order = 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(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&model_file, "-p", "--parasolid",
-                  "Parasolid model to use.");
-   args.AddOption(&geom_order, "-go", "--geometry_order",
-                  "Geometric order of the model");
-   args.AddOption(&boundary_file, "-bf", "--txt",
-                  "txt file containing boundary tags");
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   // 3. Read the SCOREC Mesh.
-   PCU_Comm_Init();
-#ifdef MFEM_USE_SIMMETRIX
-   Sim_readLicenseFile(0);
-   gmi_sim_start();
-   gmi_register_sim();
-#endif
-   gmi_register_mesh();
-
-   apf::Mesh2* pumi_mesh;
-   pumi_mesh = apf::loadMdsMesh(model_file, mesh_file);
-
-   // 4. Increase the geometry order if necessary.
-   if (geom_order > 1)
-   {
-      crv::BezierCurver bc(pumi_mesh, geom_order, 0);
-      bc.run();
-   }
-   pumi_mesh->verify();
-
-   // Read boundary
-   string bdr_tags;
-   named_ifgzstream input_bdr(boundary_file);
-   input_bdr >> ws;
-   getline(input_bdr, bdr_tags);
-   filter_dos(bdr_tags);
-   cout << " the boundary tag is : " << bdr_tags << endl;
-   Array<int> Dirichlet;
-   int numOfent;
-   if (bdr_tags == "Dirichlet")
-   {
-      input_bdr >> numOfent;
-      cout << " num of Dirichlet bdr conditions : " << numOfent << endl;
-      Dirichlet.SetSize(numOfent);
-      for (int kk = 0; kk < numOfent; kk++)
-      {
-         input_bdr >> Dirichlet[kk];
-      }
-   }
-   Dirichlet.Print();
-
-   Array<int> load_bdr;
-   skip_comment_lines(input_bdr, '#');
-   input_bdr >> bdr_tags;
-   filter_dos(bdr_tags);
-   cout << " the boundary tag is : " << bdr_tags << endl;
-   if (bdr_tags == "Load")
-   {
-      input_bdr >> numOfent;
-      load_bdr.SetSize(numOfent);
-      cout << " num of load bdr conditions : " << numOfent << endl;
-      for (int kk = 0; kk < numOfent; kk++)
-      {
-         input_bdr >> load_bdr[kk];
-      }
-   }
-   load_bdr.Print();
-
-   // 5. Create the MFEM mesh object from the PUMI mesh. We can handle triangular
-   //    and tetrahedral meshes. Other inputs are the same as MFEM default
-   //    constructor.
-   Mesh *mesh = new PumiMesh(pumi_mesh, 1, 1);
-   int dim = mesh->Dimension();
-
-   //  Boundary conditions hack.
-   apf::MeshIterator* itr = pumi_mesh->begin(dim-1);
-   apf::MeshEntity* ent ;
-   int bdr_cnt = 0;
-   while ((ent = pumi_mesh->iterate(itr)))
-   {
-      apf::ModelEntity *me = pumi_mesh->toModel(ent);
-      if (pumi_mesh->getModelType(me) == (dim-1))
-      {
-         // Everywhere 3 as initial
-         (mesh->GetBdrElement(bdr_cnt))->SetAttribute(3);
-         int tag = pumi_mesh->getModelTag(me);
-         if (Dirichlet.Find(tag) != -1)
-         {
-            // Dirichlet attr -> 1
-            (mesh->GetBdrElement(bdr_cnt))->SetAttribute(1);
-         }
-         else if (load_bdr.Find(tag) != -1)
-         {
-            // Load attr -> 2
-            (mesh->GetBdrElement(bdr_cnt))->SetAttribute(2);
-         }
-         bdr_cnt++;
-      }
-   }
-   pumi_mesh->end(itr);
-
-   // Assign attributes for elements.
-   double ppt[3];
-   Vector cent(ppt, dim);
-   for (int el = 0; el < mesh->GetNE(); el++)
-   {
-      (mesh->GetElementTransformation(el))->
-      Transform(Geometries.GetCenter(mesh->GetElementBaseGeometry(el)),cent);
-      if (cent(0) <= -0.05)
-      {
-         mesh->SetAttribute(el , 1);
-      }
-      else if (cent(0) >= 0.05)
-      {
-         mesh->SetAttribute(el , 2);
-      }
-      else
-      {
-         mesh->SetAttribute(el , 3);
-      }
-   }
-   mesh->SetAttributes();
-   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;
-   }
-
-   // 6. Refine the mesh to increase the resolution. In this example we do
-   //    'ref_levels' of uniform refinement. We choose 'ref_levels' to be the
-   //    largest number that gives a final mesh with no more than 5,000
-   //    elements.
-   {
-      int ref_levels =
-         (int)floor(log(5000./mesh->GetNE())/log(2.)/dim);
-      for (int l = 0; l < ref_levels; l++)
-      {
-         mesh->UniformRefinement();
-      }
-   }
-
-   // 7. Define a finite element space on the mesh. Here we use vector finite
-   //    elements, i.e. dim copies of a scalar finite element space. The vector
-   //    dimension is specified by the last argument of the FiniteElementSpace
-   //    constructor. For NURBS meshes, we use the (degree elevated) NURBS space
-   //    associated with the mesh nodes.
-   FiniteElementCollection *fec;
-   FiniteElementSpace *fespace;
-   if (mesh->NURBSext)
-   {
-      fec = NULL;
-      fespace = mesh->GetNodes()->FESpace();
-   }
-   else
-   {
-      fec = new H1_FECollection(order, dim);
-      fespace = new FiniteElementSpace(mesh, fec, dim);
-   }
-   cout << "Number of finite element unknowns: " << fespace->GetTrueVSize()
-        << endl << "Assembling: " << flush;
-
-   // 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.
-   Array<int> ess_tdof_list, ess_bdr(mesh->bdr_attributes.Max());
-   ess_bdr = 0;
-   ess_bdr[0] = 1;
-   fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-
-   // 9. 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.
-   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) = -3.0e-2;
-      f.Set(dim-1, new PWConstCoefficient(pull_force));
-      f.Set(dim-2, new PWConstCoefficient(pull_force));
-   }
-
-   LinearForm *b = new LinearForm(fespace);
-   b->AddBoundaryIntegrator(new VectorBoundaryLFIntegrator(f));
-   cout << "r.h.s. ... " << flush;
-   b->Assemble();
-
-   // 10. 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;
-
-   // 11. 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)*10;
-   lambda(1) = lambda(1)*100;
-   PWConstCoefficient lambda_func(lambda);
-   Vector mu(mesh->attributes.Max());
-   mu = 1.0;
-   mu(0) = mu(1)*10;
-   mu(1) = mu(1)*100;
-   PWConstCoefficient mu_func(mu);
-
-   BilinearForm *a = new BilinearForm(fespace);
-   a->AddDomainIntegrator(new ElasticityIntegrator(lambda_func,mu_func));
-
-   // 12. 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.
-   cout << "matrix ... " << flush;
-   if (static_cond) { a->EnableStaticCondensation(); }
-   a->Assemble();
-
-   SparseMatrix A;
-   Vector B, X;
-   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
-   cout << "done." << endl;
-
-   cout << "Size of linear system: " << A.Height() << endl;
-
-#ifndef MFEM_USE_SUITESPARSE
-   // 13. Define a simple symmetric Gauss-Seidel preconditioner and use it to
-   //     solve the system Ax=b with PCG.
-   GSSmoother M(A);
-   PCG(A, M, B, X, 1, 500, 1e-8, 0.0);
-#else
-   // 13. 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
-
-   // 14. Recover the solution as a finite element grid function.
-   a->RecoverFEMSolution(X, *b, x);
-
-   // 15. For non-NURBS meshes, make the mesh curved based on the finite element
-   //     space. This means that we define the mesh elements through a fespace
-   //     based transformation of the reference element. This allows us to save
-   //     the displaced mesh as a curved mesh when using high-order finite
-   //     element displacement field. We assume that the initial mesh (read from
-   //     the file) is not higher order curved mesh compared to the chosen FE
-   //     space.
-   if (!mesh->NURBSext)
-   {
-      mesh->SetNodalFESpace(fespace);
-   }
-
-   // 16. Save the displaced mesh and the inverted solution (which gives the
-   //     backward displacements to the original grid). This output can be
-   //     viewed later using GLVis: "glvis -m displaced.mesh -g sol.gf".
-   {
-      GridFunction *nodes = mesh->GetNodes();
-      *nodes += x;
-      x *= -1;
-      ofstream mesh_ofs("displaced.mesh");
-      mesh_ofs.precision(8);
-      mesh->Print(mesh_ofs);
-      ofstream sol_ofs("sol.gf");
-      sol_ofs.precision(8);
-      x.Save(sol_ofs);
-   }
-
-   // 17. Send the above data by socket to a GLVis server. Use the "n" and "b"
-   //     keys in GLVis to visualize the displacements.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << *mesh << x << flush;
-   }
-
-   // 18. Free the used memory.
-   delete a;
-   delete b;
-   if (fec)
-   {
-      delete fespace;
-      delete fec;
-   }
-   delete mesh;
-
-   pumi_mesh->destroyNative();
-   apf::destroyMesh(pumi_mesh);
-   PCU_Comm_Free();
-#ifdef MFEM_USE_SIMMETRIX
-   gmi_sim_stop();
-   Sim_unregisterAllKeys();
-#endif
-
-   MPI_Finalize();
-
-   return 0;
-}

examples/pumi/ex6p.cpp

@@ -1,387 +0,0 @@
-//                       MFEM Example 6 - Parallel Version
-//                              PUMI Modification
-//
-// Compile with: make ex1p
-//
-// Sample runs:  mpirun -np 8 ex6p
-//
-// 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 adapted in a conforming (tetrahedrons) manner according
-//               to a simple SPR ZZ error estimator.
-//
-//               This PUMI variation also performs a "uniform" refinement,
-//               similar to MFEM examples, for coarse meshes. However, the
-//               refinement is performed using the PUMI API. A new option "-ar"
-//               is added to modify the "adapt_ratio" which is the fraction of
-//               allowable error that scales the output size field of the error
-//               estimator.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-#ifdef MFEM_USE_SIMMETRIX
-#include <SimUtil.h>
-#include <gmi_sim.h>
-#endif
-#include <apfMDS.h>
-#include <gmi_null.h>
-#include <PCU.h>
-#include <spr.h>
-#include <apfConvert.h>
-#include <gmi_mesh.h>
-#include <crv.h>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "../../data/pumi/parallel/Kova/Kova100k_8.smb";
-#ifdef MFEM_USE_SIMMETRIX
-   const char *model_file = "../../data/pumi/geom/Kova.x_t";
-   const char *smd_file = NULL;
-#else
-   const char *model_file = "../../data/pumi/geom/Kova.dmg";
-#endif
-   int order = 1;
-   bool static_cond = false;
-   bool visualization = 1;
-   int geom_order = 1;
-   double adapt_ratio = 0.05;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree) or -1 for"
-                  " isoparametric space.");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&model_file, "-p", "--model",
-                  "parasolid or .dmg model to use.");
-#ifdef MFEM_USE_SIMMETRIX
-   args.AddOption(&smd_file, "-sm", "--smd_model",
-                  "smd model file to use.");
-#endif
-   args.AddOption(&geom_order, "-go", "--geometry_order",
-                  "Geometric order of the model");
-   args.AddOption(&adapt_ratio, "-ar", "--adapt_ratio",
-                  "adaptation factor used in MeshAdapt");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 3. Read the SCOREC Mesh.
-   PCU_Comm_Init();
-#ifdef MFEM_USE_SIMMETRIX
-   Sim_readLicenseFile(0);
-   gmi_sim_start();
-   gmi_register_sim();
-#endif
-   gmi_register_mesh();
-
-   apf::Mesh2* pumi_mesh;
-#ifdef MFEM_USE_SIMMETRIX
-   if (smd_file)
-   {
-      gmi_model *mixed_model = gmi_sim_load(model_file, smd_file);
-      pumi_mesh = apf::loadMdsMesh(mixed_model, mesh_file);
-   }
-   else
-#endif
-   {
-      pumi_mesh = apf::loadMdsMesh(model_file, mesh_file);
-   }
-
-   // 4. Increase the geometry order and refine the mesh if necessary.  Parallel
-   //    uniform refinement is performed if the total number of elements is less
-   //    than 100,000.
-   int dim = pumi_mesh->getDimension();
-   int nEle = pumi_mesh->count(dim);
-   int ref_levels = (int)floor(log(100000./nEle)/log(2.)/dim);
-
-   if (geom_order > 1)
-   {
-      crv::BezierCurver bc(pumi_mesh, geom_order, 2);
-      bc.run();
-   }
-
-   // Perform Uniform refinement
-   if (myid == 1)
-   {
-      std::cout << " ref level : " <<     ref_levels << std::endl;
-   }
-
-   if (ref_levels > 1)
-   {
-      ma::Input* uniInput = ma::configureUniformRefine(pumi_mesh, ref_levels);
-
-      if ( geom_order > 1)
-      {
-         crv::adapt(uniInput);
-      }
-      else
-      {
-         ma::adapt(uniInput);
-      }
-   }
-
-   pumi_mesh->verify();
-
-   // 5. Create the parallel MFEM mesh object from the parallel PUMI mesh.  We
-   //    can handle triangular and tetrahedral meshes. Note that the mesh
-   //    resolution is performed on the PUMI mesh.
-   ParMesh *pmesh = new ParPumiMesh(MPI_COMM_WORLD, pumi_mesh);
-
-   // 6. Define a parallel finite element space on the parallel mesh. Here we
-   //    use continuous Lagrange finite elements of the specified order. If
-   //    order < 1, we instead use an isoparametric/isogeometric space.
-   FiniteElementCollection *fec;
-   if (order > 0)
-   {
-      fec = new H1_FECollection(order, dim);
-   }
-   else if (pmesh->GetNodes())
-   {
-      fec = pmesh->GetNodes()->OwnFEC();
-      if (myid == 1)
-      {
-         cout << "Using isoparametric FEs: " << fec->Name() << endl;
-      }
-   }
-   else
-   {
-      fec = new H1_FECollection(order = 1, dim);
-   }
-   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
-   HYPRE_Int size = fespace->GlobalTrueVSize();
-   if (myid == 1)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 7. Set up the parallel linear form b(.) which corresponds to the
-   //    right-hand side of the FEM linear system, which in this case is
-   //    (1,phi_i) where phi_i are the basis functions in fespace.
-   ParLinearForm *b = new ParLinearForm(fespace);
-   ConstantCoefficient one(1.0);
-   b->AddDomainIntegrator(new DomainLFIntegrator(one));
-
-   // 8. 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;
-
-   // 9. Connect to GLVis.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-
-   socketstream sout;
-   if (visualization)
-   {
-      sout.open(vishost, visport);
-      if (!sout)
-      {
-         if (myid == 0)
-         {
-            cout << "Unable to connect to GLVis server at "
-                 << vishost << ':' << visport << endl;
-            cout << "GLVis visualization disabled.\n";
-         }
-         visualization = false;
-      }
-
-      sout.precision(8);
-   }
-
-   // 10. Set up the parallel bilinear form a(.,.) on the finite element space
-   //     corresponding to the Laplacian operator -Delta, by adding the
-   //     Diffusion domain integrator.
-   ParBilinearForm *a = new ParBilinearForm(fespace);
-   a->AddDomainIntegrator(new DiffusionIntegrator(one));
-
-   // 11. Assemble the parallel bilinear form and the corresponding linear
-   //     system, applying any necessary transformations such as: parallel
-   //     assembly, eliminating boundary conditions, applying conforming
-   //     constraints for non-conforming AMR, static condensation, etc.
-   if (static_cond) { a->EnableStaticCondensation(); }
-
-   // 12. The main AMR loop. In each iteration we solve the problem on the
-   //     current mesh, visualize the solution, and adapt the mesh.
-   apf::Field* Tmag_field = 0;
-   apf::Field* temp_field = 0;
-   apf::Field* ipfield = 0;
-   apf::Field* sizefield = 0;
-   int max_iter = 3;
-
-   for (int Itr = 0; Itr < max_iter; Itr++)
-   {
-      HYPRE_Int global_dofs = fespace->GlobalTrueVSize();
-      if (myid == 1)
-      {
-         cout << "\nAMR iteration " << Itr << endl;
-         cout << "Number of unknowns: " << global_dofs << endl;
-      }
-
-      // Assemble.
-      a->Assemble();
-      b->Assemble();
-
-      // Essential boundary condition.
-      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);
-      }
-
-      // Form linear system.
-      HypreParMatrix A;
-      Vector B, X;
-      const int copy_interior = 1;
-      a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B, copy_interior);
-
-      // 13. 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);
-
-      // 14. Recover the parallel grid function corresponding to X. This is the
-      //     local finite element solution on each processor.
-      a->RecoverFEMSolution(X, *b, x);
-
-      // 15. Save in parallel the displaced mesh and the inverted solution (which
-      //     gives the backward displacements to the original grid). 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 above data by socket to a GLVis server.  Use the "n" and "b"
-      //     keys in GLVis to visualize the displacements.
-      if (visualization)
-      {
-         sout << "parallel " << num_procs << " " << myid << "\n";
-         sout << "solution\n" << *pmesh << x << flush;
-      }
-
-      // 17. Field transfer. Scalar solution field and magnitude field for error
-      //     estimation are created the PUMI mesh.
-      if (order > geom_order)
-      {
-         Tmag_field = apf::createField(pumi_mesh, "field_mag",
-                                       apf::SCALAR, apf::getLagrange(order));
-         temp_field = apf::createField(pumi_mesh, "T_field",
-                                       apf::SCALAR, apf::getLagrange(order));
-      }
-      else
-      {
-         Tmag_field = apf::createFieldOn(pumi_mesh, "field_mag",apf::SCALAR);
-         temp_field = apf::createFieldOn(pumi_mesh, "T_field", apf::SCALAR);
-      }
-
-      ParPumiMesh* pPPmesh = dynamic_cast<ParPumiMesh*>(pmesh);
-      pPPmesh->FieldMFEMtoPUMI(pumi_mesh, &x, temp_field, Tmag_field);
-
-      ipfield= spr::getGradIPField(Tmag_field, "MFEM_gradip", 2);
-      sizefield = spr::getSPRSizeField(ipfield, adapt_ratio);
-
-      apf::destroyField(Tmag_field);
-      apf::destroyField(ipfield);
-      apf::destroyNumbering(pumi_mesh->findNumbering("LocalVertexNumbering"));
-
-      // 18. Perform MesAdapt.
-      ma::Input* erinput = ma::configure(pumi_mesh, sizefield);
-      erinput->shouldFixShape = true;
-      erinput->maximumIterations = 2;
-      if ( geom_order > 1)
-      {
-         crv::adapt(erinput);
-      }
-      else
-      {
-         ma::adapt(erinput);
-      }
-
-      ParMesh* Adapmesh = new ParPumiMesh(MPI_COMM_WORLD, pumi_mesh);
-      pPPmesh->UpdateMesh(Adapmesh);
-      delete Adapmesh;
-
-      // 19. Update the FiniteElementSpace, GridFunction, and bilinear form.
-      fespace->Update();
-      x.Update();
-      x = 0.0;
-
-      pPPmesh->FieldPUMItoMFEM(pumi_mesh, temp_field, &x);
-      a->Update();
-      b->Update();
-
-      // Destroy fields.
-      apf::destroyField(temp_field);
-      apf::destroyField(sizefield);
-   }
-
-   // 20. Free the used memory.
-   delete a;
-   delete b;
-   delete fespace;
-   if (order > 0) { delete fec; }
-   delete pmesh;
-
-   pumi_mesh->destroyNative();
-   apf::destroyMesh(pumi_mesh);
-   PCU_Comm_Free();
-
-#ifdef MFEM_USE_SIMMETRIX
-   gmi_sim_stop();
-   Sim_unregisterAllKeys();
-#endif
-
-   MPI_Finalize();
-
-   return 0;
-}

examples/pumi/makefile

@@ -1,94 +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.
-
-# Use the MFEM build directory
-MFEM_DIR ?= ../..
-MFEM_BUILD_DIR ?= ../..
-SRC = $(if $(MFEM_DIR:../..=),$(MFEM_DIR)/examples/pumi/,)
-CONFIG_MK = $(MFEM_BUILD_DIR)/config/config.mk
-# Use the MFEM install directory
-# MFEM_INSTALL_DIR = ../../mfem
-# CONFIG_MK = $(MFEM_INSTALL_DIR)/share/mfem/config.mk
-
-MFEM_LIB_FILE = mfem_is_not_built
--include $(CONFIG_MK)
-
-# All PUMI examples require MPI
-SEQ_EXAMPLES =
-PAR_EXAMPLES = ex1 ex1p ex2 ex6p
-ifeq ($(MFEM_USE_MPI),NO)
-   EXAMPLES = $(SEQ_EXAMPLES)
-else
-   EXAMPLES = $(PAR_EXAMPLES) $(SEQ_EXAMPLES)
-endif
-
-.SUFFIXES:
-.SUFFIXES: .o .cpp .mk
-.PHONY: all clean clean-build clean-exec
-
-# Remove built-in rule
-%: %.cpp
-
-# Replace the default implicit rule for *.cpp files
-%: $(SRC)%.cpp $(MFEM_LIB_FILE) $(CONFIG_MK)
-	$(MFEM_CXX) $(MFEM_FLAGS) $< -o $@ $(MFEM_LIBS)
-
-all: $(EXAMPLES)
-
-ifeq ($(MFEM_USE_PUMI),NO)
-$(EXAMPLES):
-	$(error MFEM is not configured with PUMI)
-endif
-
-MFEM_TESTS = EXAMPLES
-include $(MFEM_TEST_MK)
-
-ifneq (,$(filter test%,$(MAKECMDGOALS)))
-   ifeq (,$(wildcard ../../data/pumi))
-      $(info PUMI data directory not found. The PUMI tests will be SKIPPED.)
-      mfem-test = printf "   $(3) [$(2) $(1) ... ]: "; $(PRINT_SKIP)
-   endif
-endif
-
-# Testing: Parallel vs. serial runs
-RUN_MPI_NP = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP)
-RUN_MPI = $(RUN_MPI_NP) $(MFEM_MPI_NP)
-SERIAL_NAME := Serial PUMI example
-PARALLEL_NAME := Parallel PUMI example
-%-test-par: %
-	@$(call mfem-test,$<, $(RUN_MPI), $(PARALLEL_NAME))
-%-test-seq: %
-	@$(call mfem-test,$<,, $(SERIAL_NAME))
-
-# Testing: Example-specific execution options:
-ex1-test-par: ex1
-	@$(call mfem-test,$<, $(RUN_MPI_NP) 1, $(PARALLEL_NAME))
-ex1p-test-par: ex1p
-	@$(call mfem-test,$<, $(RUN_MPI_NP) 8, $(PARALLEL_NAME))
-ex2-test-par: ex2
-	@$(call mfem-test,$<, $(RUN_MPI_NP) 1, $(PARALLEL_NAME))
-ex6p-test-par: ex6p
-	@$(call mfem-test,$<, $(RUN_MPI_NP) 8, $(PARALLEL_NAME))
-
-# Testing: "test" target and mfem-test* variables are defined in config/test.mk
-
-# Generate an error message if the MFEM library is not built and exit
-$(MFEM_LIB_FILE):
-	$(error The MFEM library is not built)
-
-clean: clean-build clean-exec
-
-clean-build:
-	rm -f *.o *~ $(SEQ_EXAMPLES) $(PAR_EXAMPLES)
-	rm -rf *.dSYM *.TVD.*breakpoints
-
-clean-exec:
-	@rm -f refined.mesh sol.gf mesh.* sol.* displaced.mesh

examples/sundials/CMakeLists.txt

@@ -13,23 +13,21 @@ set(SUNDIALS_EXAMPLES_SRCS)
 list(APPEND SUNDIALS_EXAMPLES_SRCS
   ex9.cpp
   ex10.cpp
-  ex16.cpp
   )
 
 if (MFEM_USE_MPI)
   list(APPEND SUNDIALS_EXAMPLES_SRCS
     ex9p.cpp
     ex10p.cpp
-    ex16p.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 "test_sundials" target, see below.
 add_custom_target(test_sundials
-  ${CMAKE_CTEST_COMMAND} -R sundials USES_TERMINAL)
+  ${CMAKE_CTEST_COMMAND} -R sundials -C SUNDIALS USES_TERMINAL)
 
 # Add one executable per cpp file, adding "sundials_" as prefix. Sets
 # "test_sundials" as a target that depends on the given examples.
@@ -37,9 +35,10 @@ set(PFX sundials_)
 add_mfem_examples(SUNDIALS_EXAMPLES_SRCS ${PFX} "" test_sundials)
 
 # Testing.
-# The SUNDIALS tests can be run separately using the target "test_sundials"
-# which builds the examples and runs:
-#   ctest -R sundials
+# We do not want these tests to be run by default, so we add them to their own
+# configuration - SUNDIALS. To run the tests defined here use the
+# "test_sundials" target which builds the examples and runs:
+#   ctest -C SUNDIALS -R sundials
 
 # Command line options for the tests.
 # Example 9: test explicit CVODE time stepping
@@ -50,7 +49,6 @@ set(EX9P_TEST_OPTS ${EX9_COMMON_OPTS} -rp 1 -dt 0.0009 -vs 50)
 set(EX10_COMMON_OPTS -m ../../data/beam-quad.mesh -o 2 -s 5 -dt 0.15 -vs 10)
 set(EX10_TEST_OPTS ${EX10_COMMON_OPTS}  -r  2)
 set(EX10P_TEST_OPTS ${EX10_COMMON_OPTS} -rp 1)
-# Example 16: use the default options
 
 # Add the tests: one test per source file.
 foreach(SRC_FILE ${SUNDIALS_EXAMPLES_SRCS})
@@ -65,12 +63,14 @@ foreach(SRC_FILE ${SUNDIALS_EXAMPLES_SRCS})
 
   if (NOT (${TEST_NAME} MATCHES ".*p$"))
     add_test(NAME ${TEST_NAME}_ser
-      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS}
+      CONFIGURATIONS SUNDIALS)
   else()
     add_test(NAME ${TEST_NAME}_np=4
       COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4
       ${MPIEXEC_PREFLAGS}
       $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-      ${MPIEXEC_POSTFLAGS})
+      ${MPIEXEC_POSTFLAGS}
+      CONFIGURATIONS SUNDIALS)
   endif()
 endforeach()

examples/sundials/ex10.cpp

@@ -13,7 +13,6 @@
 //    ex10 -m ../../data/beam-quad.mesh -r 2 -o 2 -s 15 -dt 5e-3 -vs 60
 //    ex10 -m ../../data/beam-tri.mesh  -r 2 -o 2 -s 16 -dt 0.01 -vs 30
 //    ex10 -m ../../data/beam-hex.mesh  -r 1 -o 2 -s 15 -dt 0.01 -vs 30
-//    ex10 -m ../../data/beam-quad-amr.mesh -r 2 -o 2 -s 5 -dt 0.15 -vs 10
 //
 // 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
@@ -116,9 +115,9 @@ public:
        method of SundialsJacSolver. */
    void InitSundialsJacSolver(SundialsJacSolver &sjsolv);
 
-   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();
 };
@@ -205,12 +204,12 @@ 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() { }
@@ -349,7 +348,6 @@ int main(int argc, char *argv[])
       case 24: ode_solver = new SDIRK34Solver; break;
       default:
          cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
-         delete mesh;
          return 3;
    }
 
@@ -379,7 +377,7 @@ 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;
@@ -388,8 +386,8 @@ 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);
@@ -402,10 +400,8 @@ 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;
@@ -422,7 +418,6 @@ 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)
@@ -433,8 +428,8 @@ 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;
@@ -456,8 +451,8 @@ 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;
@@ -467,7 +462,6 @@ int main(int argc, char *argv[])
 
          if (visualization)
          {
-            v.SetFromTrueVector(); x.SetFromTrueVector();
             visualize(vis_v, mesh, &x, &v);
             if (vis_w)
             {
@@ -480,7 +474,6 @@ 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);
@@ -651,7 +644,7 @@ HyperelasticOperator::HyperelasticOperator(FiniteElementSpace &f,
                                            Array<int> &ess_bdr, double visc,
                                            double mu, double K,
                                            NonlinearSolverType nls_type)
-   : 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)
 {
@@ -662,10 +655,8 @@ 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);
@@ -677,12 +668,13 @@ 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);
 
@@ -773,18 +765,18 @@ void HyperelasticOperator::InitSundialsJacSolver(SundialsJacSolver &sjsolv)
    sjsolv.SetOperators(M, S, H, *J_solver);
 }
 
-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/sundials/ex10p.cpp

@@ -13,7 +13,6 @@
 //    mpirun -np 4 ex10p -m ../../data/beam-quad.mesh -rp 1 -o 2 -s 15 -dt 3e-3 -vs 120
 //    mpirun -np 4 ex10p -m ../../data/beam-tri.mesh  -rp 1 -o 2 -s 16 -dt 5e-3 -vs 60
 //    mpirun -np 4 ex10p -m ../../data/beam-hex.mesh  -rp 0 -o 2 -s 15 -dt 5e-3 -vs 60
-//    mpirun -np 4 ex10p -m ../../data/beam-quad-amr.mesh -rp 1 -o 2 -s 5 -dt 0.15 -vs 10
 //
 // 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
@@ -69,7 +68,6 @@ class HyperelasticOperator : public TimeDependentOperator
 {
 protected:
    ParFiniteElementSpace &fespace;
-   Array<int> ess_tdof_list;
 
    ParBilinearForm M, S;
    ParNonlinearForm H;
@@ -118,10 +116,9 @@ public:
        method of SundialsJacSolver. */
    void InitSundialsJacSolver(SundialsJacSolver &sjsolv);
 
-   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();
 };
@@ -139,11 +136,10 @@ 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_);
@@ -177,7 +173,6 @@ private:
    const SparseMatrix *local_grad_H;
    HypreParMatrix *Jacobian;
    Solver *J_solver;
-   const Array<int> *ess_tdof_list;
 
 public:
    SundialsJacSolver()
@@ -185,11 +180,9 @@ public:
 
    /// Connect the solver to the objects created inside HyperelasticOperator.
    void SetOperators(ParBilinearForm &M_, ParBilinearForm &S_,
-                     ParNonlinearForm &H_, Solver &solver,
-                     const Array<int> &ess_tdof_list_)
+                     ParNonlinearForm &H_, Solver &solver)
    {
       M = &M_; S = &S_; H = &H_; J_solver = &solver;
-      ess_tdof_list = &ess_tdof_list_;
    }
 
    /** Linear solve applicable to the SUNDIALS format.
@@ -214,12 +207,12 @@ 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() { }
@@ -377,7 +370,6 @@ int main(int argc, char *argv[])
          {
             cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
          }
-         delete mesh;
          MPI_Finalize();
          return 3;
    }
@@ -391,8 +383,6 @@ int main(int argc, char *argv[])
       {
          cout << "Unknown type of nonlinear solver: " << nls << endl;
       }
-      delete ode_solver;
-      delete mesh;
       MPI_Finalize();
       return 4;
    }
@@ -436,9 +426,7 @@ 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);
@@ -451,12 +439,11 @@ 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;
@@ -512,7 +499,8 @@ 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);
@@ -540,7 +528,6 @@ 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);
@@ -609,11 +596,9 @@ 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_,
@@ -630,7 +615,6 @@ 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
@@ -642,8 +626,6 @@ 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;
 }
 
@@ -685,8 +667,6 @@ int SundialsJacSolver::SetupSystem(void *sundials_mem, int conv_fail,
    localJ->Add(dt*dt, *local_grad_H);
    Jacobian = M->ParallelAssemble(localJ);
    delete localJ;
-   HypreParMatrix *Je = Jacobian->EliminateRowsCols(*ess_tdof_list);
-   delete Je;
 
    J_solver->SetOperator(*Jacobian);
 
@@ -706,8 +686,6 @@ int SundialsJacSolver::SolveSystem(void *sundials_mem, Vector &b,
    Vector rhs(sc);
    double dt = GetTimeStep(sundials_mem);
 
-   // We can assume that b_v and b_x have zeros at essential tdofs.
-
    // rhs = M b_v - dt*grad(H) b_x
    ParGridFunction lb_x(fes), lrhs(fes);
    lb_x.Distribute(b_x);
@@ -715,7 +693,6 @@ int SundialsJacSolver::SolveSystem(void *sundials_mem, Vector &b,
    lrhs.ParallelAssemble(rhs);
    rhs *= -dt;
    M->TrueAddMult(b_v, rhs);
-   rhs.SetSubVector(*ess_tdof_list, 0.0);
 
    J_solver->iterative_mode = false;
    J_solver->Mult(rhs, b_v);
@@ -747,11 +724,9 @@ 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);
@@ -764,14 +739,15 @@ 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);
@@ -820,7 +796,6 @@ 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);
@@ -860,15 +835,15 @@ void HyperelasticOperator::ImplicitSolve(const double dt,
 
 void HyperelasticOperator::InitSundialsJacSolver(SundialsJacSolver &sjsolv)
 {
-   sjsolv.SetOperators(M, S, H, *J_solver, ess_tdof_list);
+   sjsolv.SetOperators(M, S, H, *J_solver);
 }
 
-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;
@@ -878,7 +853,7 @@ 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/sundials/ex16.cpp

@@ -1,524 +0,0 @@
-//                                MFEM Example 16
-//                             SUNDIALS Modification
-//
-// Compile with: make ex16
-//
-// Sample runs:  ex16
-//               ex16 -m ../../data/inline-tri.mesh
-//               ex16 -m ../../data/disc-nurbs.mesh -tf 2
-//               ex16 -s 12 -a 0.0 -k 1.0
-//               ex16 -s 1 -a 1.0 -k 0.0 -dt 1e-4 -tf 5e-2 -vs 25
-//               ex16 -s 2 -a 0.5 -k 0.5 -o 4 -dt 1e-4 -tf 2e-2 -vs 25
-//               ex16 -s 3 -dt 1.0e-4 -tf 4.0e-2 -vs 40
-//               ex16 -m ../../data/fichera-q2.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
-//               ex16 -m ../../data/amr-hex.mesh -o 2 -r 0
-//
-// Description:  This example solves a time dependent nonlinear heat equation
-//               problem of the form du/dt = C(u), with a non-linear diffusion
-//               operator C(u) = \nabla \cdot (\kappa + \alpha u) \nabla u.
-//
-//               The example demonstrates the use of nonlinear operators (the
-//               class ConductionOperator defining C(u)), as well as their
-//               implicit time integration. Note that implementing the method
-//               ConductionOperator::ImplicitSolve is the only requirement for
-//               high-order implicit (SDIRK) time integration. By default, this
-//               example uses the SUNDIALS ODE solvers from CVODE and ARKODE.
-//
-//               We recommend viewing examples 2, 9 and 10 before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-/** After spatial discretization, the conduction model can be written as:
- *
- *     du/dt = M^{-1}(-Ku)
- *
- *  where u is the vector representing the temperature, M is the mass matrix,
- *  and K is the diffusion operator with diffusivity depending on u:
- *  (\kappa + \alpha u).
- *
- *  Class ConductionOperator represents the right-hand side of the above ODE.
- */
-class ConductionOperator : public TimeDependentOperator
-{
-protected:
-   FiniteElementSpace &fespace;
-   Array<int> ess_tdof_list; // this list remains empty for pure Neumann b.c.
-
-   BilinearForm *M;
-   BilinearForm *K;
-
-   SparseMatrix Mmat, Kmat;
-   SparseMatrix *T; // T = M + dt K
-   double current_dt;
-
-   CGSolver M_solver; // Krylov solver for inverting the mass matrix M
-   DSmoother M_prec;  // Preconditioner for the mass matrix M
-
-   CGSolver T_solver; // Implicit solver for T = M + dt K
-   DSmoother T_prec;  // Preconditioner for the implicit solver
-
-   double alpha, kappa;
-
-   mutable Vector z; // auxiliary vector
-
-public:
-   ConductionOperator(FiniteElementSpace &f, double alpha, double kappa,
-                      const Vector &u);
-
-   virtual void Mult(const Vector &u, Vector &du_dt) const;
-   /** Solve the Backward-Euler equation: k = f(u + dt*k, t), for the unknown k.
-       This is the only requirement for high-order SDIRK implicit integration.*/
-   virtual void ImplicitSolve(const double dt, const Vector &u, Vector &k);
-
-   /** Solve the system (M + dt K) y = M b. The result y replaces the input b.
-       This method is used by the implicit SUNDIALS solvers. */
-   void SundialsSolve(const double dt, Vector &b);
-
-   /// Update the diffusion BilinearForm K using the given true-dof vector `u`.
-   void SetParameters(const Vector &u);
-
-   virtual ~ConductionOperator();
-};
-
-/// Custom Jacobian system solver for the SUNDIALS time integrators.
-/** For the ODE system represented by ConductionOperator
-
-        M du/dt = -K(u),
-
-    this class facilitates the solution of linear systems of the form
-
-        (M + γK) y = M b,
-
-    for given b, u (not used), and γ = GetTimeStep(). */
-class SundialsJacSolver : public SundialsODELinearSolver
-{
-private:
-   ConductionOperator *oper;
-
-public:
-   SundialsJacSolver() : oper(NULL) { }
-
-   int InitSystem(void *sundials_mem);
-   int SetupSystem(void *sundials_mem, int conv_fail,
-                   const Vector &y_pred, const Vector &f_pred, int &jac_cur,
-                   Vector &v_temp1, Vector &v_temp2, Vector &v_temp3);
-   int SolveSystem(void *sundials_mem, Vector &b, const Vector &weight,
-                   const Vector &y_cur, const Vector &f_cur);
-   int FreeSystem(void *sundials_mem);
-};
-
-double InitialTemperature(const Vector &x);
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   const char *mesh_file = "../../data/star.mesh";
-   int ref_levels = 2;
-   int order = 2;
-   int ode_solver_type = 11; // 11 = CVODE implicit
-   double t_final = 0.5;
-   double dt = 1.0e-2;
-   double alpha = 1.0e-2;
-   double kappa = 0.5;
-   bool visualization = true;
-   bool visit = false;
-   int vis_steps = 5;
-
-   // Relative and absolute tolerances for CVODE and ARKODE.
-   const double reltol = 1e-4, abstol = 1e-4;
-
-   int precision = 8;
-   cout.precision(precision);
-
-   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(&ode_solver_type, "-s", "--ode-solver",
-                  "ODE solver:\n"
-                  "\t 1/11 - CVODE (explicit/implicit),\n"
-                  "\t 2/12 - ARKODE (default explicit/implicit),\n"
-                  "\t 3 - ARKODE (Fehlberg-6-4-5)\n"
-                  "\t 4 - Forward Euler, 5 - RK2, 6 - RK3 SSP, 7 - RK4,\n"
-                  "\t 8 - Backward Euler, 9 - SDIRK23, 10 - SDIRK33.");
-   args.AddOption(&t_final, "-tf", "--t-final",
-                  "Final time; start time is 0.");
-   args.AddOption(&dt, "-dt", "--time-step",
-                  "Time step.");
-   args.AddOption(&alpha, "-a", "--alpha",
-                  "Alpha coefficient.");
-   args.AddOption(&kappa, "-k", "--kappa",
-                  "Kappa coefficient offset.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&visit, "-visit", "--visit-datafiles", "-no-visit",
-                  "--no-visit-datafiles",
-                  "Save data files for VisIt (visit.llnl.gov) 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. 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. Define the ODE solver used for time integration. Several
-   // SUNDIALS solvers are available, as well as included both
-   // explicit and implicit MFEM ODE solvers.
-   ODESolver *ode_solver = NULL;
-   CVODESolver *cvode = NULL;
-   ARKODESolver *arkode = NULL;
-   SundialsJacSolver sun_solver; // Used by the implicit SUNDIALS ode solvers.
-   switch (ode_solver_type)
-   {
-      // SUNDIALS solvers
-      case 1:
-         cvode = new CVODESolver(CV_ADAMS, CV_FUNCTIONAL);
-         cvode->SetSStolerances(reltol, abstol);
-         cvode->SetMaxStep(dt);
-         ode_solver = cvode; break;
-      case 11:
-         cvode = new CVODESolver(CV_BDF, CV_NEWTON);
-         cvode->SetLinearSolver(sun_solver);
-         cvode->SetSStolerances(reltol, abstol);
-         cvode->SetMaxStep(dt);
-         ode_solver = cvode; break;
-      case 2:
-      case 3:
-         arkode = new ARKODESolver(ARKODESolver::EXPLICIT);
-         arkode->SetSStolerances(reltol, abstol);
-         arkode->SetMaxStep(dt);
-         if (ode_solver_type == 3) { arkode->SetERKTableNum(FEHLBERG_13_7_8); }
-         ode_solver = arkode; break;
-      case 12:
-         arkode = new ARKODESolver(ARKODESolver::IMPLICIT);
-         arkode->SetLinearSolver(sun_solver);
-         arkode->SetSStolerances(reltol, abstol);
-         arkode->SetMaxStep(dt);
-         ode_solver = arkode; break;
-      // Other MFEM explicit methods
-      case 4: ode_solver = new ForwardEulerSolver; break;
-      case 5: ode_solver = new RK2Solver(0.5); break; // midpoint method
-      case 6: ode_solver = new RK3SSPSolver; break;
-      case 7: ode_solver = new RK4Solver; break;
-      // MFEM implicit L-stable methods
-      case 8:  ode_solver = new BackwardEulerSolver; break;
-      case 9:  ode_solver = new SDIRK23Solver(2); break;
-      case 10: ode_solver = new SDIRK33Solver; break;
-      default:
-         cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
-         delete mesh;
-         return 3;
-   }
-
-   // Since we want to update the diffusion coefficient after every time step,
-   // we need to use the "one-step" mode of the SUNDIALS solvers.
-   if (cvode) { cvode->SetStepMode(CV_ONE_STEP); }
-   if (arkode) { arkode->SetStepMode(ARK_ONE_STEP); }
-
-   // 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 vector finite element space representing the current and the
-   //    initial temperature, u_ref.
-   H1_FECollection fe_coll(order, dim);
-   FiniteElementSpace fespace(mesh, &fe_coll);
-
-   int fe_size = fespace.GetTrueVSize();
-   cout << "Number of temperature unknowns: " << fe_size << endl;
-
-   GridFunction u_gf(&fespace);
-
-   // 6. Set the initial conditions for u. All boundaries are considered
-   //    natural.
-   FunctionCoefficient u_0(InitialTemperature);
-   u_gf.ProjectCoefficient(u_0);
-   Vector u;
-   u_gf.GetTrueDofs(u);
-
-   // 7. Initialize the conduction operator and the visualization.
-   ConductionOperator oper(fespace, alpha, kappa, u);
-
-   u_gf.SetFromTrueDofs(u);
-   {
-      ofstream omesh("ex16.mesh");
-      omesh.precision(precision);
-      mesh->Print(omesh);
-      ofstream osol("ex16-init.gf");
-      osol.precision(precision);
-      u_gf.Save(osol);
-   }
-
-   VisItDataCollection visit_dc("Example16", mesh);
-   visit_dc.RegisterField("temperature", &u_gf);
-   if (visit)
-   {
-      visit_dc.SetCycle(0);
-      visit_dc.SetTime(0.0);
-      visit_dc.Save();
-   }
-
-   socketstream sout;
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      sout.open(vishost, visport);
-      if (!sout)
-      {
-         cout << "Unable to connect to GLVis server at "
-              << vishost << ':' << visport << endl;
-         visualization = false;
-         cout << "GLVis visualization disabled.\n";
-      }
-      else
-      {
-         sout.precision(precision);
-         sout << "solution\n" << *mesh << u_gf;
-         sout << "pause\n";
-         sout << flush;
-         cout << "GLVis visualization paused."
-              << " Press space (in the GLVis window) to resume it.\n";
-      }
-   }
-
-   // 8. Perform time-integration (looping over the time iterations, ti, with a
-   //    time-step dt).
-   cout << "Integrating the ODE ..." << endl;
-   tic_toc.Clear();
-   tic_toc.Start();
-   ode_solver->Init(oper);
-   double t = 0.0;
-
-   bool last_step = false;
-   for (int ti = 1; !last_step; ti++)
-   {
-      double dt_real = min(dt, t_final - t);
-
-      // Note that since we are using the "one-step" mode of the SUNDIALS
-      // solvers, they will, generally, step over the final time and will not
-      // explicitly perform the interpolation to t_final as they do in the
-      // "normal" step mode.
-
-      ode_solver->Step(u, t, dt_real);
-
-      last_step = (t >= t_final - 1e-8*dt);
-
-      if (last_step || (ti % vis_steps) == 0)
-      {
-         cout << "step " << ti << ", t = " << t << endl;
-         if (cvode) { cvode->PrintInfo(); }
-         if (arkode) { arkode->PrintInfo(); }
-
-         u_gf.SetFromTrueDofs(u);
-         if (visualization)
-         {
-            sout << "solution\n" << *mesh << u_gf << flush;
-         }
-
-         if (visit)
-         {
-            visit_dc.SetCycle(ti);
-            visit_dc.SetTime(t);
-            visit_dc.Save();
-         }
-      }
-      oper.SetParameters(u);
-   }
-   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 ex16.mesh -g ex16-final.gf".
-   {
-      ofstream osol("ex16-final.gf");
-      osol.precision(precision);
-      u_gf.Save(osol);
-   }
-
-   // 10. Free the used memory.
-   delete ode_solver;
-   delete mesh;
-
-   return 0;
-}
-
-ConductionOperator::ConductionOperator(FiniteElementSpace &f, double al,
-                                       double kap, const Vector &u)
-   : TimeDependentOperator(f.GetTrueVSize(), 0.0), fespace(f), M(NULL), K(NULL),
-     T(NULL), current_dt(0.0), z(height)
-{
-   const double rel_tol = 1e-8;
-
-   M = new BilinearForm(&fespace);
-   M->AddDomainIntegrator(new MassIntegrator());
-   M->Assemble();
-   M->FormSystemMatrix(ess_tdof_list, Mmat);
-
-   M_solver.iterative_mode = false;
-   M_solver.SetRelTol(rel_tol);
-   M_solver.SetAbsTol(0.0);
-   M_solver.SetMaxIter(50);
-   M_solver.SetPrintLevel(0);
-   M_solver.SetPreconditioner(M_prec);
-   M_solver.SetOperator(Mmat);
-
-   alpha = al;
-   kappa = kap;
-
-   T_solver.iterative_mode = false;
-   T_solver.SetRelTol(rel_tol);
-   T_solver.SetAbsTol(0.0);
-   T_solver.SetMaxIter(100);
-   T_solver.SetPrintLevel(0);
-   T_solver.SetPreconditioner(T_prec);
-
-   SetParameters(u);
-}
-
-void ConductionOperator::Mult(const Vector &u, Vector &du_dt) const
-{
-   // Compute:
-   //    du_dt = M^{-1}*-K(u)
-   // for du_dt
-   Kmat.Mult(u, z);
-   z.Neg(); // z = -z
-   M_solver.Mult(z, du_dt);
-}
-
-void ConductionOperator::ImplicitSolve(const double dt,
-                                       const Vector &u, Vector &du_dt)
-{
-   // Solve the equation:
-   //    du_dt = M^{-1}*[-K(u + dt*du_dt)]
-   // for du_dt
-   if (!T)
-   {
-      T = Add(1.0, Mmat, dt, Kmat);
-      current_dt = dt;
-      T_solver.SetOperator(*T);
-   }
-   MFEM_VERIFY(dt == current_dt, ""); // SDIRK methods use the same dt
-   Kmat.Mult(u, z);
-   z.Neg();
-   T_solver.Mult(z, du_dt);
-}
-
-void ConductionOperator::SundialsSolve(const double dt, Vector &b)
-{
-   // Solve the system (M + dt K) y = M b. The result y replaces the input b.
-   if (!T || dt != current_dt)
-   {
-      delete T;
-      T = Add(1.0, Mmat, dt, Kmat);
-      current_dt = dt;
-      T_solver.SetOperator(*T);
-   }
-   Mmat.Mult(b, z);
-   T_solver.Mult(z, b);
-}
-
-void ConductionOperator::SetParameters(const Vector &u)
-{
-   GridFunction u_alpha_gf(&fespace);
-   u_alpha_gf.SetFromTrueDofs(u);
-   for (int i = 0; i < u_alpha_gf.Size(); i++)
-   {
-      u_alpha_gf(i) = kappa + alpha*u_alpha_gf(i);
-   }
-
-   delete K;
-   K = new BilinearForm(&fespace);
-
-   GridFunctionCoefficient u_coeff(&u_alpha_gf);
-
-   K->AddDomainIntegrator(new DiffusionIntegrator(u_coeff));
-   K->Assemble();
-   K->FormSystemMatrix(ess_tdof_list, Kmat);
-   delete T;
-   T = NULL; // re-compute T on the next ImplicitSolve or SundialsSolve
-}
-
-ConductionOperator::~ConductionOperator()
-{
-   delete T;
-   delete M;
-   delete K;
-}
-
-
-int SundialsJacSolver::InitSystem(void *sundials_mem)
-{
-   TimeDependentOperator *td_oper = GetTimeDependentOperator(sundials_mem);
-
-   // During development, we use dynamic_cast<> to ensure the setup is correct:
-   oper = dynamic_cast<ConductionOperator*>(td_oper);
-   MFEM_VERIFY(oper, "operator is not ConductionOperator");
-
-   // When the implementation is finalized, we can switch to static_cast<>:
-   // oper = static_cast<ConductionOperator*>(td_oper);
-
-   return 0;
-}
-
-int SundialsJacSolver::SetupSystem(void *sundials_mem, int conv_fail,
-                                   const Vector &y_pred, const Vector &f_pred,
-                                   int &jac_cur, Vector &v_temp1,
-                                   Vector &v_temp2, Vector &v_temp3)
-{
-   jac_cur = 1;
-
-   return 0;
-}
-
-int SundialsJacSolver::SolveSystem(void *sundials_mem, Vector &b,
-                                   const Vector &weight, const Vector &y_cur,
-                                   const Vector &f_cur)
-{
-   oper->SundialsSolve(GetTimeStep(sundials_mem), b);
-
-   return 0;
-}
-
-int SundialsJacSolver::FreeSystem(void *sundials_mem)
-{
-   return 0;
-}
-
-
-double InitialTemperature(const Vector &x)
-{
-   if (x.Norml2() < 0.5)
-   {
-      return 2.0;
-   }
-   else
-   {
-      return 1.0;
-   }
-}