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

.appveyor.yml

@@ -26,25 +26,24 @@ install:
 - cd ..
 
 # Install hypre
-- ps: Start-FileDownload 'https://github.com/hypre-space/hypre/archive/V2-10-0b.tar.gz'
-- 7z x V2-10-0b.tar.gz -so | 7z x -si -ttar > nul
-- cd hypre-2-10-0b
-- cmake -H. -Bbuild -DHYPRE_USING_FEI=OFF -DMPI_C_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DMPI_C_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include"
+- ps: Start-FileDownload 'https://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz'
+- 7z x hypre-2.10.0b.tar.gz -so | 7z x -si -ttar > nul
+- cd hypre-2.10.0b
+- cmake -Hsrc -Bbuild -DMPI_C_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DMPI_C_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include"
+# - cmake -Hsrc -Bbuild -DCMAKE_BUILD_TYPE=Release -DMPI_C_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DMPI_C_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include"
 - cmake --build build
 - cmake --build build --target install
 - cd ..
 
 # MFEM
 before_build:
-- cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_parallel -DMFEM_USE_MPI=TRUE -DMFEM_USE_METIS_5=TRUE -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DHYPRE_LIBRARIES=%cd%\hypre-2-10-0b\hypre\lib\HYPRE.lib -DHYPRE_INCLUDE_DIRS=%cd%\hypre-2-10-0b\hypre\include -DHYPRE_VERSION=21000 -DMETIS_LIBRARIES=%cd%\metis-5.1.0\build\libmetis\Debug\metis.lib -DMETIS_INCLUDE_DIRS=%cd%\metis-5.1.0\include
-- cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_serial -DMFEM_USE_MPI=FALSE
+- cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_parallel -DMFEM_USE_MPI=TRUE -DMFEM_USE_METIS_5=TRUE -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DHYPRE_LIBRARIES=%cd%\hypre-2.10.0b\src\hypre\lib\HYPRE.lib -DHYPRE_INCLUDE_DIRS=%cd%\hypre-2.10.0b\src\hypre\include -DHYPRE_VERSION=21000 -DMETIS_LIBRARIES=%cd%\metis-5.1.0\build\libmetis\Debug\metis.lib -DMETIS_INCLUDE_DIRS=%cd%\metis-5.1.0\include
+- cmake -H. -DCMAKE_INSTALL_PREFIX=install -Bbuild_serial -DMFEM_USE_MPI=FALSE -DMFEM_USE_METIS_5=TRUE -DMPI_CXX_LIBRARIES="C:\Program Files (x86)\Microsoft SDKs\MPI\Lib\x86\msmpi.lib" -DMPI_CXX_INCLUDE_PATH="C:\Program Files (x86)\Microsoft SDKs\MPI\Include" -DHYPRE_LIBRARIES=%cd%\hypre-2.10.0b\src\hypre\lib\HYPRE.lib -DHYPRE_INCLUDE_DIRS=%cd%\hypre-2.10.0b\src\hypre\include -DHYPRE_VERSION=21000 -DMETIS_LIBRARIES=%cd%\metis-5.1.0\build\libmetis\Debug\metis.lib -DMETIS_INCLUDE_DIRS=%cd%\metis-5.1.0\include
 
 build_script:
 - cmake --build build_parallel
 - cmake --build build_serial
-- cmake --build build_serial --target exec
 
 after_build:
 # - cmake --build build_parallel --target check
-- cmake --build build_serial --target RUN_TESTS
-
+- cmake --build build_serial --target check

.gitignore

@@ -9,7 +9,6 @@
 # Object and library files
 *.o
 /libmfem.*
-/miniapps/common/libmfem-common.*
 
 # CMake generated files
 CMakeCache.txt
@@ -46,15 +45,12 @@ examples/ex[1-9]
 examples/ex[1-9]p
 examples/ex1[04-9]
 examples/ex1[0-9]p
-examples/ex2[0-9]
-examples/ex2[0-9]p
 
 examples/refined.mesh
 examples/displaced.mesh
 examples/mesh.*
 examples/ex5.mesh
 examples/Example5*
-examples/PVExample*
 examples/Example9*
 examples/Example15*
 examples/Example16*
@@ -62,8 +58,6 @@ examples/sphere_refined.*
 examples/sol.*
 examples/sol_u.*
 examples/sol_p.*
-examples/sol_r.*
-examples/sol_i.*
 examples/ex9.mesh
 examples/ex9-mesh.*
 examples/ex9-init.*
@@ -82,13 +76,6 @@ examples/vortex-?-init.*
 examples/vortex-?-final.*
 examples/deformation.*
 examples/pressure.*
-examples/ex20.dat
-examples/ex20p_?????.dat
-examples/gnuplot_ex20.inp
-examples/gnuplot_ex20p.inp
-examples/ex21*.mesh
-examples/ex21*.sol
-examples/ex21p_*.*
 
 examples/sundials/ex9
 examples/sundials/ex1[06]
@@ -117,7 +104,6 @@ examples/petsc/sol.*
 examples/petsc/sol_p.*
 examples/petsc/sol_u.*
 examples/petsc/Example5*
-examples/petsc/ex9.mesh
 examples/petsc/ex9-mesh.*
 examples/petsc/ex9-init.*
 examples/petsc/ex9-final.*
@@ -129,11 +115,6 @@ examples/petsc/elastic_energy.*
 examples/pumi/ex1
 examples/pumi/ex[126]p
 
-examples/hiop/ex9.mesh
-examples/hiop/ex9-mesh.*
-examples/hiop/ex9-init.*
-examples/hiop/ex9-final.*
-
 examples/pumi/refined.mesh
 examples/pumi/sol.gf
 examples/pumi/mesh.*
@@ -152,20 +133,16 @@ miniapps/electromagnetics/Joule_*
 
 miniapps/meshing/mobius-strip
 miniapps/meshing/klein-bottle
-miniapps/meshing/toroid
 miniapps/meshing/mesh-explorer
 miniapps/meshing/shaper
-miniapps/meshing/extruder
 miniapps/meshing/mesh-optimizer
 miniapps/meshing/pmesh-optimizer
 
 miniapps/meshing/mobius-strip.mesh
 miniapps/meshing/klein-bottle.mesh
-miniapps/meshing/toroid-*.mesh
 miniapps/meshing/mesh-explorer.mesh
 miniapps/meshing/partitioning.txt
 miniapps/meshing/shaper.mesh
-miniapps/meshing/extruder.mesh
 miniapps/meshing/optimized*
 miniapps/meshing/perturbed*
 
@@ -179,8 +156,6 @@ miniapps/performance/sol.*
 miniapps/tools/display-basis
 miniapps/tools/load-dc
 miniapps/tools/convert-dc
-miniapps/tools/lor-transfer
-miniapps/tools/get-values
 
 miniapps/nurbs/ex1
 miniapps/nurbs/ex1p
@@ -190,14 +165,3 @@ miniapps/nurbs/mesh.*
 miniapps/nurbs/sol.*
 miniapps/nurbs/mode_*
 miniapps/nurbs/Example1*
-
-miniapps/gslib/field-diff
-miniapps/gslib/findpts
-miniapps/gslib/pfindpts
-
-# Unit test binary and outputs
-tests/unit/output_meshes
-tests/unit/unit_tests
-
-# VPATH builds
-build-*/*

.travis.yml

@@ -1,114 +1,28 @@
-language: cpp
-
 sudo: false
 
-stages:
-  - checks
-  - tests
-  - optional
+language: cpp
 
-jobs:
+matrix:
   include:
-
-    # ========================
-    #         Checks
-    # ========================
-    # - code-style
-    # - documentation
-    # - gitignore
-
-    - stage: checks
-      os: linux
-      name: "code-style"
-      addons:
-        apt:
-          packages:
-            - astyle=2.05.1-0ubuntu1
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - cd tests/scripts
-        - ./runtest code-style
-
-    - stage: checks
-      os: linux
-      name: "documentation"
-      addons:
-        apt:
-          packages:
-            - doxygen
-            - graphviz
-            - mpich
-            - libmpich-dev
-      env: MPI=YES
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - cd tests/scripts
-        - ./runtest documentation
-
-    - stage: checks
-      os: linux
-      name: "gitignore"
-      addons:
-        apt:
-          packages:
-            - mpich
-            - libmpich-dev
-      env: MPI=YES
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        - make config MFEM_USE_MPI=YES MFEM_MPI_NP=2
-        - make all -j3
-        - make test-noclean
-        - cd tests/scripts
-        - ./runtest gitignore
-
-    # ========================
-    #  Optional Checks/Tests
-    # ========================
-    # - branch-history
-
-    - stage: optional
-      name: "branch-history"
-      # need full git history for the binary/big files check
-      git:
-        depth: false
-      script:
-        - cd ${TRAVIS_BUILD_DIR}
-        # update master
-        - git fetch origin master:master
-        # checkout a branch (otherwise Travis works in detached head)
-        - git checkout -b travis_tests
-        - cd tests/scripts
-        - ./runtest branch-history
-
-    # ========================
-    #       Linux tests
-    # ========================
-    # - serial + debug
-    # - serial
-    # - parallel + debug
-    # - parallel
-
-    - stage: tests
-      os: linux
+    #
+    # Linux
+    #
+    - os: linux
       compiler: gcc
-      name: "Linux: Serial + Debug"
       env: DEBUG=YES
            MPI=NO
            CODECOV=NO
            MFEM_TEST_TARGET=check
-
+    #
     - os: linux
       compiler: gcc
-      name: "Linux: Serial"
       env: DEBUG=NO
            MPI=NO
            CODECOV=NO
            MFEM_TEST_TARGET=test
-
+    #
     - os: linux
       compiler: gcc
-      name: "Linux: Parallel + Debug"
       addons:
         apt:
           # sources:
@@ -135,10 +49,9 @@ jobs:
       before_cache:
         - cd $TRAVIS_BUILD_DIR/../metis-4.0;
           mv libmetis.a ..; rm -rf *; mv ../libmetis.a .
-
+    #
     - os: linux
       compiler: gcc
-      name: "Linux: Parallel"
       addons:
         apt:
           # sources:
@@ -165,37 +78,28 @@ jobs:
       before_cache:
         - cd $TRAVIS_BUILD_DIR/../metis-4.0;
           mv libmetis.a ..; rm -rf *; mv ../libmetis.a .
-
-    # ========================
-    #      Mac OS X tests
-    # ========================
-    # - serial + debug
-    # - serial
-    # - parallel + debug
-    # - parallel
-
+    #
+    # Mac OS X
+    #
     - os: osx
       # osx_image: xcode7.3
       compiler: clang
-      name: "Mac: Serial + Debug"
       env: DEBUG=YES
            MPI=NO
            CODECOV=NO
            MFEM_TEST_TARGET=check
-
+    #
     - os: osx
       # osx_image: xcode7.3
       compiler: clang
-      name: "Mac: Serial"
       env: DEBUG=NO
            MPI=NO
            CODECOV=NO
            MFEM_TEST_TARGET=test
-
+    #
     - os: osx
       # osx_image: xcode7.3
       compiler: clang
-      name: "Mac: Parallel + Debug"
       env: DEBUG=YES
            MPI=YES
            CODECOV=NO
@@ -211,11 +115,10 @@ jobs:
       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
-      name: "Mac: Parallel"
       env: DEBUG=NO
            MPI=YES
            CODECOV=YES
@@ -302,7 +205,6 @@ install:
         else
             echo "Reusing cached hypre-2.10.0b/";
         fi;
-        ln -s hypre-2.10.0b hypre;
      else
         echo "Serial build, not using hypre";
      fi

CHANGELOG

@@ -8,349 +8,17 @@
                                http://mfem.org
 
 
-Version 4.0.1 (development)
+Version 3.4.1 (development)
 ===========================
-
-Improved GPU support
---------------------
-- Added support for matrix-free diagonal smoothers on GPUs.
-
-- Added initial support for AMD GPUs based on HIP: a C++ runtime API and kernel
-  language that can run on both AMD and NVIDIA hardware. With this change and
-  the libCEED addition below, the current list of available backends is:
-  "ceed-cuda", "occa-cuda", "raja-cuda", "cuda", "hip", "occa-omp", "raja-omp",
-  "omp", "ceed-cpu", "occa-cpu", "raja-cpu", and "cpu".
-
-- Improved RAJA backend and multi-GPU MPI communications.
-
-libCEED support
----------------
-- Added support for libCEED, the portable library for high-order operator
-  evaluation developed by the Center for Efficient Exascale Discretizations in
-  the Exascale Computing Project, https://github.com/CEED/libCEED.
-
-- This initial integration includes Mass and Diffusion integrators. libCEED GPU
-  backends can be used without specific MFEM configuration, however it is highly
-  recommended to use the "cuda" build option to minimize memory transfers.
-
-- Both CPU and GPU modes are available as MFEM device backends (ceed-cpu and
-  ceed-cuda), using some of the best performing CPU and GPU backends from
-  libCEED, see the sample runs in examples 1 and 6.
-
-Meshing improvements
---------------------
-- Added support for non-conforming AMR on prisms and tetrahedra, including
-  coarsening and parallel load balancing. Anisotropic prism refinement is only
-  available in the serial version at the moment.
-
-- The TMOP mesh optimization algorithms were extended to support r-adaptivity.
-  Target matrices can now be constructed either via a given analytical function
-  (e.g. spatial dependence of size, aspect ratio, etc., for each element) or via
-  a (Par)GridFunction specified on the original mesh.
-
-- New method Mesh::GetHilbertElementOrdering for sorting mesh elements along the
-  Hilbert curve. The ordering can be used to improve caching and parallel
-  partitioning in non-conforming AMR.
-
-- Added support for creating refined versions of periodic meshes, making use of
-  the new L2ElementRestriction class. This class also allows for computing
-  geometric factors on periodic meshes using partial assembly.
-
-- The TMOP mesh optimization algorithms have been improved to support AMR meshes.
-
-- Improved element numbering after uniform mesh refinement.
-
-Discretization improvements
----------------------------
-- Added support for GSLIB-FindPoints, a general high-order interpolation utility
-  that can robustly evaluate a GridFunction in an arbitrary collection of points
-  in physical space. See INSTALL for details on building MFEM with GSLIB, and
-  miniapps/gslib for examples of how to use this feature.
-
-- Added support for complex-valued finite element operators and fields using a
-  2x2 block structured linear system to mimic complex arithmetic. New classes
-  include: ComplexGridFunction, SesquilinearForm, ComplexLinearForm, and their
-  parallel counterparts.
-
-- Two integrators related to Stokes problems, (Q grad u, v) and (Q div v, u),
-  where u and the components of v are in H1, were added/modified to support full
-  and partial assembly modes. See the new GradientIntegrator and the updated
-  VectorDivergenceIntegrator classes in fem/bilininteg.hpp, as well as the PA
-  kernels in fem/bilininteg_gradient.cpp and fem/bilininteg_divergence.cpp.
-
-- Diagonals of partially assembled operators can now be computed efficiently.
-  See the new methods AssembleDiagonal in BilinearForm, AssembleDiagonalPA in
-  BilinearFormIntegrator and the implementations in fem/bilininteg_*.cpp.
-
-- Added initial support for NonlinearForms to support the partial assembly mode.
-
-- Added a nonlinear vector valued convection integrator (Q u \cdot grad u, v)
-  where u_i and v_i are in H1. This form occurs e.g. in the Navier-Stokes
-  equations. The integrator supports the partial assembly mode for its
-  action. In full assembly mode we also provide the GetGradient method that
-  computes the linearized version of the integrator.
-
-- Added a new method, MixedBilinearForm::FormRectangularLinearSystem, that can
-  be used to impose boundary conditions on the non-square off-diagonal blocks of
-  a block operator (similar to FormLinearSystem in the square case).
-
-- Extended the support for partial assembly to vector mass and vector diffusion
-  bilinear integrators.
-
-Linear and nonlinear solvers
-----------------------------
-- Added a general interface for specifying and solving nonlinear constrained
-  optimization problems through the new classes OptimizationProblem and
-  OptimizationSolver, see linalg/solver.hpp
-
-- Added support for HiOp, a lightweight HPC solver for nonlinear optimization
-  problems see class HiOpNLPOptimizer and the example codes in examples/hiop.
-
-- Added support for Ginkgo, a high-performance linear algebra library for GPU
-  and manycore nodes, with a focus on sparse solution of linear systems. For
-  more details see linalg/ginkgo.hpp and the example code in examples/gingko.
-
-- Added Adams-Bashforth and Adams-Moulton time integrators.
-
-New and updated examples and miniapps
--------------------------------------
-- Added two new miniapps: Find Points (serial + parallel) and Field Diff in
-  miniapps/gslib that show how GSLIB-FindPoints can be used to interpolate a
-  (Par)GridFunction in an arbitrary number of physical space points in 2D and
-  3D. The GridFunction must be in H1 and in the same space as the mesh that is
-  used to find the points.
-
-- Added a new example, Example 22/22p, to demonstrate the use of the new
-  complex-valued finite element operators. The example defines and solves
-  a family of time-harmonic PDEs related to damped harmonic oscillators.
-
-- Updated Example 1/1p to use diagonal preconditioning in partial assembly mode.
-
-- The mesh-optimizer and pmesh-optimizer miniapps have been updated to
-  demonstrate the new r-adaptivity capabilities of TMOP.
-
-- New options to reorder and partition the mesh in the mesh-explorer miniapp.
-
-- The (p)mesh-optimizer miniapp has been updated to demonstrate mesh
-  optimization for an AMR mesh.
-
-- Added a modification of Example 1 in examples/ginkgo that demonstrates the use
-  of the Gingko interface to solve a linear system.
-
-- Added a modification of ex9 in examples/hiop that demonstrates the nonlinear
-  constrained optimization interface and the use of the SLBQP and HiOp solvers.
-
-Improved testing
-----------------
-- Added a new directory, tests/scripts, with several shell scripts that perform
-  simple checks on the code including: code styling, documentation formatting,
-  proper use of .gitignore, and preventing the accidental commit of large files.
-
-- It is recommended that developers run the above tests scripts (via the runtest
-  script) before pushing to GitHub. See the README file in tests/scripts.
-
-- The Travis CI settings have been updated to include an initial Checks stage
-  which currently runs the code-style, documentation and gitignore test scripts,
-  as well as a final stage for optional checks/tests which currently runs the
-  branch-history script.
-
-Miscellaneous
--------------
-- Upgraded the SUNDIALS interface to utilize version 5.0. This necessitated a
-  complete rework of the interface and requires changes at the application
-  level. Example usage of the new interface can be found in examples/sundials.
-
-- Added support for output in the ParaView XML format. See Examples 5/5p, 9/9p
-  and the new ParaViewDataCollection class.
-
-- Collected object files from the miniapps/common directory into a new library,
-  libmfem-common for the convenience of application developers. The new library
-  is now used in several miniapps in the electromagnetic and tools directories.
-
-- Added unit tests for time integrators.
-
-
-Version 4.0, released on May 24, 2019
-=====================================
-
-Unlike previous MFEM releases, this version requires a C++11 compiler.
-
-GPU support
------------
-- Added initial support for hardware devices, such as GPUs, and programming
-  models, such as CUDA, OCCA, RAJA and OpenMP.
-
-- The GPU/device support is based on MFEM's new backends and kernels working
-  seamlessly with a new lightweight device/host memory manager. The kernels can
-  be implemented either in OCCA, or as a simple wrapper around for-loops, which
-  can then be dispatched to RAJA and native backends. See the files forall.hpp
-  and mem_manager.hpp in the general/ directory for more details.
-
-- Several of the MFEM example codes (ex1, ex1p, ex6, and ex6p) can now take
-  advantage of GPU acceleration with the backend selectable at runtime. Many of
-  the linear algebra and finite element operations (e.g. partially assembled
-  bilinear forms) have been extended to take advantage of kernel acceleration by
-  simply replacing loops with the MFEM_FORALL() macro.
-
-- In addition to native CUDA kernels, the library currently supports OCCA, RAJA
-  and OpenMP kernels, which could be mixed and matched in different parts of the
-  same application. We plan on adding support for more programming models and
-  devices in the future, without the need for significant modifications in user
-  code. The list of current backends is: "occa-cuda", "raja-cuda", "cuda",
-  "occa-omp", "raja-omp", "omp", "occa-cpu", "raja-cpu", and "cpu".
-
-- GPU-related limitations:
-  * Hypre preconditioners are not yet available in GPU mode, and in particular
-    hypre must be built in CPU mode.
-  * Only constant coefficients are currently supported on GPUs.
-  * Optimized element assembly, and matrix-free bilinear forms are not
-    implemented yet. Element batching is currently ignored.
-  * In device mode, full assembly is performed on the host (but the matvec
-    action is performed on the device).
-  * Partial assembly kernels are not implemented yet for simplices.
-
-Discretization improvements
----------------------------
-- Partial assembled finite element operators are now available in the core
-  library, based on the new classes PABilinearFormExtension, ElementRestriction,
-  DofToQuad and GeometricFactors (associated with the classes BilinearForm,
-  FiniteElementSpace, FiniteElement and Mesh, respectively). The kernels for
-  partial assembled Setup/Assembly and Action/Mult are implemented in the
-  BilinearFormIntegrator methods AssemblePA and AddMultPA.
-
-- Added support for a general "low-order refined"-to-"high-order" transfer of
-  GridFunction data from a "low-order refined" (LOR) space defined on a refined
-  mesh to a "high-order" (HO) finite element space defined on a coarse mesh. See
-  the new classes InterpolationGridTransfer and L2ProjectionGridTransfer and the
-  new LOR Transfer miniapp: miniapps/tools/lor-transfer.cpp.
-
-- Added element flux, and flux energy computation in class ElasticityIntegrator,
-  allowing for the use of Zienkiewicz-Zhu type error estimators with the
-  integrator. For an illustration of this addition, see the new Example 21.
-
-- Added support for derefinement of vector (RT + ND) spaces.
-
-- Added a variety of coefficients which are sums or products of existing
-  coefficients as well as grid function coefficients which return the
-  divergence, gradient, or curl of their GridFunctions.
-
-Support for wedge elements and meshes with mixed element types
---------------------------------------------------------------
-- Added support for wedge-shaped mesh elements of arbitrary order (with Geometry
-  type PRISM) which have two triangular faces and three quadrilateral faces.
-  Several examples of such meshes can be found in the data/ directory.
-
-- Added support for mixed meshes containing triangles and quadrilaterals in 2D
-  or tetrahedra, wedges, and hexahedra in 3D. This includes support for uniform
-  refinement of such meshes. Several examples of such meshes can be found in the
-  data/ directory.
-
-- Added H1 and L2 finite elements of arbitrary order for Wedge elements.
-
-- Added support for reading and writing linear and quadratic meshes containing
-  wedge elements in VTK mesh format. Several examples of such meshes can be
-  found in the data/ directory.
-
-Other meshing improvements
---------------------------
-- Improved the uniform refinement of tetrahedral meshes (also part of the
-  uniform refinement of mixed 3D meshes). The previous refinement algorithm is
-  still available as an option in Mesh::UniformRefinement. Both can be used in
-  the updated Mesh Explorer miniapp.
-
-- The local tetrahedral mesh refinement algorithm in serial and in parallel now
-  follows precisely the paper:
-
-     D. Arnold, A. Mukherjee, and L. Pouly, "Locally Adapted Tetrahedral Meshes
-     Using Bisection", SIAM J. Sci. Comput. 22 (2000), 431–448.
-
-  This guarantees that the shape regularity of the elements will be preserved
-  under refinement.
-
-- The TMOP mesh optimization algorithms were extended to support user-defined
-  space-dependent limiting terms. Improved the TMOP objective functions by more
-  accurate normalization of the different terms.
-
-- Added support for parallel communication groups on non-conforming meshes.
-
-- Improved parallel partitioning of non-conforming meshes. If the coarse mesh
-  elements are ordered as a sequence of face-neighbors, the parallel partitions
-  are now guaranteed to be continuous. To that end, inline quadrilateral and
-  hexahedral meshes are now by default ordered along a space-filling curve.
-
-- A boundary in a NURBS mesh can now be connected with another boundary. Such a
-  periodic NURBS mesh is a simple way to impose periodic boundary conditions.
-
 - Added support for reading linear and quadratic 2D quadrilateral and triangular
   Cubit meshes.
 
-New and updated examples and miniapps
--------------------------------------
-- Added a new meshing miniapp, Toroid, which can produce a variety of torus
-  shaped meshes by twisting a stack of wedges or hexahedra.
-
-- Added a new meshing miniapp, Extruder, that demonstrates the capability to
-  produce 3D meshes by extruding 2D meshes.
-
-- Added a simple miniapp, LOR Transfer, for visualizing the actions of the
-  transfer operators between a high-order and a low-order refined spaces.
-
-- Added a new example, Example 20/20p, that solves a system of 1D ODEs derived
-  from a Hamiltonian. The example demonstrates the use of the variable order,
-  symplectic integration algorithm implemented in class SIAVSolver.
-
-- Added a new example, Example 21/21p, that illustrates the use of AMR to solve
-  a linear elasticity problem. This is an extension of Example 2/2p.
-
-New and improved solvers and preconditioners
---------------------------------------------
-- Added support for parallel ILU preconditioning via hypre's Euclid solver.
-
-- Added support for STRUMPACK v3 with a small API change in the class
-  STRUMPACKSolver, see "API changes" below.
-
-Miscellaneous
--------------
-- Added unit tests based on the Catch++ library in the test/ directory.
-
-- Renamed the option MFEM_USE_OPENMP to MFEM_USE_LEGACY_OPENMP. This legacy
-  option is deprecated and planned for removal in a future release. The original
-  option name, MFEM_USE_OPENMP, is now used to enable the new OpenMP backends in
-  the new kernels.
-
-- In SparseMatrix added the option to perform MultTranspose() by matvec with
-  computed and stored transpose matrix. This is required for deterministic
-  results when using devices such as CUDA and OpenMP.
-
-- Altered the way FGMRES counts its iterations so that it matches GMRES.
-
-- Various other simplifications, extensions, and bugfixes in the code.
-
-- Construct abstract parallel rectangular truedof-to-truedof operators via
-  Operator::FormDiscreteOperator().
-
-API changes
------------
-- In multiple places, use Geometry::Type instead of int, where appropriate.
-- In multiple places, use Element::Type instead of int, where appropriate.
-- The Mesh methods GetElementBaseGeometry and GetBdrElementBaseGeometry no
-  longer have a default value for their parameter, they only work with an
-  explicitly given index.
-- In class Mesh, added methods useful for queries regarding the types of
-  elements present in the mesh: HasGeometry, GetNumGeometries, GetGeometries,
-  and class Mesh::GeometryList.
-- The struct CoarseFineTransformations (returned by the Mesh method
-  GetRefinementTransforms) now stores the embedding matrices separately for each
-  Geometry::Type.
-- In class ParMesh, replaced the method GroupNFaces with two new methods:
-  GroupNTriangles and GroupNQuadrilaterals. Also, replaced GroupFace with two
-  methods: GroupTriangle and GroupQuadrilateral.
-- In class ParMesh, made the two RefineGroups methods protected.
-- Removed the virtual method Element::GetRefinementFlag, it is only used by the
-  derived class Tetrahedron.
-- Added new methods: Array::CopyTo, Tetrahedron::Init.
-- In class STRUMPACKSolver, the method SetMC64Job() was replaced by the new
-  methods: DisableMatching(), EnableMatching(), and EnableParallelMatching().
+- The tetrahedral mesh refinement algorithm in serial and in parallel now
+  follows precisely the paper:
+     D. Arnold, A. Mukherjee, and L. Pouly, "Locally Adapted Tetrahedral Meshes
+     Using Bisection", SIAM J. Sci. Comput., 22(2), 431–448.
+  This guarantees that the shape regularity of the elements will be preserved
+  under refinement.
 
 
 Version 3.4, released on May 29, 2018

CMakeLists.txt

@@ -13,11 +13,6 @@ cmake_minimum_required(VERSION 2.8.11)
 set(USER_CONFIG "${CMAKE_CURRENT_SOURCE_DIR}/config/user.cmake" CACHE PATH
   "Path to optional user configuration file.")
 
-# Require C++11 and disable compiler-specific extensions
-set(CMAKE_CXX_STANDARD 11)
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_EXTENSIONS OFF)
-
 # Load user settings before the defaults - this way the defaults will not
 # overwrite the user set options. If the user has not set all options, we still
 # have the defaults.
@@ -50,7 +45,7 @@ project(mfem NONE)
 # Current version of MFEM, see also `makefile`.
 #   mfem_VERSION = (string)
 #   MFEM_VERSION = (int)   [automatically derived from mfem_VERSION]
-set(${PROJECT_NAME}_VERSION 4.0.1)
+set(${PROJECT_NAME}_VERSION 3.4.1)
 
 # Prohibit in-source build
 if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
@@ -86,13 +81,6 @@ include("${CMAKE_CURRENT_SOURCE_DIR}/config/XSDKDefaults.cmake")
 
 # Enable languages.
 enable_language(CXX)
-if (MFEM_USE_CUDA)
-   # MFEM_USE_CUDA requires CMake 3.8 or newer (for direct CUDA support)
-   cmake_minimum_required(VERSION 3.8 FATAL_ERROR)
-   enable_language(CUDA)
-   message(STATUS "Using CUDA architecture: ${CUDA_ARCH}")
-endif()
-
 if (XSDK_ENABLE_C)
    enable_language(C)
 endif()
@@ -164,15 +152,6 @@ if (MFEM_USE_METIS)
   find_package(METIS REQUIRED)
 endif()
 
-if (MFEM_USE_GINKGO)
-  find_package(Ginkgo REQUIRED)
-  if (Ginkgo_FOUND)
-    get_target_property(Ginkgo_INCLUDE_DIRS
-      Ginkgo::ginkgo INTERFACE_INCLUDE_DIRECTORIES)
-    set(Ginkgo_LIBRARIES Ginkgo::ginkgo)
-  endif()
-endif()
-
 # GZSTREAM -> zlib
 if (MFEM_USE_GZSTREAM)
   find_package(ZLIB REQUIRED)
@@ -191,11 +170,12 @@ if (MFEM_USE_LAPACK)
 endif()
 
 # OpenMP
-if (MFEM_USE_OPENMP OR MFEM_USE_LEGACY_OPENMP)
-  if (NOT MFEM_THREAD_SAFE AND MFEM_USE_LEGACY_OPENMP)
-    message(FATAL_ERROR " *** MFEM_USE_LEGACY_OPENMP requires MFEM_THREAD_SAFE=ON.")
+if (MFEM_USE_OPENMP)
+  if (MFEM_THREAD_SAFE)
+    find_package(OpenMP REQUIRED)
+  else()
+    message(FATAL_ERROR " *** MFEM_USE_OPENMP requires MFEM_THREAD_SAFE=ON.")
   endif()
-  find_package(OpenMP REQUIRED)
 endif()
 
 # SuiteSparse (before SUNDIALS which may depend on KLU)
@@ -257,17 +237,13 @@ if (MFEM_USE_MPFR)
   find_package(MPFR REQUIRED)
 endif()
 
-if (MFEM_USE_CEED)
-  find_package(libCEED REQUIRED)
-endif()
-
 if (MFEM_USE_CONDUIT)
     find_package(Conduit REQUIRED conduit relay blueprint )
 endif()
 
 # Axom/Sidre
 if (MFEM_USE_SIDRE)
-  find_package(Axom REQUIRED Axom)
+  find_package(Axom REQUIRED Sidre SLIC axom_utils)
 endif()
 
 # PUMI
@@ -286,37 +262,6 @@ if (MFEM_USE_PUMI)
   endif()
 endif()
 
-# HiOp optimizer
-if (MFEM_USE_HIOP)
-  find_package(HIOP REQUIRED)
-  # find_package updates HIOP_FOUND, HIOP_INCLUDE_DIRS, HIOP_LIBRARIES
-endif()
-
-# CUDA
-if (MFEM_USE_CUDA)
-   set(CMAKE_CUDA_STANDARD 11)
-   set(CMAKE_CUDA_STANDARD_REQUIRED ON)
-   set(CMAKE_CUDA_EXTENSIONS OFF)
-   set(CMAKE_CUDA_FLAGS "-arch=${CUDA_ARCH} --expt-extended-lambda"
-       CACHE STRING "CUDA flags set for MFEM" FORCE)
-   if (MFEM_USE_MPI)
-      set(CUDA_CCBIN_COMPILER ${MPI_CXX_COMPILER})
-   else()
-      set(CUDA_CCBIN_COMPILER ${CMAKE_CXX_COMPILER})
-   endif()
-   string(APPEND CMAKE_CUDA_FLAGS " -ccbin ${CUDA_CCBIN_COMPILER}")
-endif()
-
-# OCCA
-if (MFEM_USE_OCCA)
-   find_package(OCCA REQUIRED)
-endif()
-
-# RAJA
-if (MFEM_USE_RAJA)
-   find_package(RAJA REQUIRED)
-endif()
-
 # MFEM_TIMER_TYPE
 if (NOT DEFINED MFEM_TIMER_TYPE)
   if (APPLE)
@@ -341,8 +286,8 @@ endif()
 #    integers, the METIS header (with 32-bit indices, as used by mfem) needs to
 #    be before SuiteSparse.
 set(MFEM_TPLS MPI_CXX OPENMP BLAS LAPACK METIS HYPRE SuiteSparse SUNDIALS PETSC
-    MESQUITE SuperLUDist STRUMPACK AXOM CONDUIT GECKO Ginkgo GNUTLS NETCDF MPFR
-    PUMI HIOP POSIXCLOCKS MFEMBacktrace ZLIB OCCA CEED RAJA)
+    MESQUITE SuperLUDist STRUMPACK AXOM CONDUIT GECKO GNUTLS NETCDF MPFR PUMI
+    POSIXCLOCKS MFEMBacktrace ZLIB)
 # Add all *_FOUND libraries in the variable TPL_LIBRARIES.
 set(TPL_LIBRARIES "")
 set(TPL_INCLUDE_DIRS "")
@@ -367,6 +312,9 @@ message(STATUS "MFEM build type: CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
 message(STATUS "MFEM version: v${MFEM_VERSION_STRING}")
 message(STATUS "MFEM git string: ${MFEM_GIT_STRING}")
 
+# Windows specific
+set(_USE_MATH_DEFINES ${WIN32})
+
 #-------------------------------------------------------------------------------
 # Define and configure the MFEM library
 #-------------------------------------------------------------------------------
@@ -378,13 +326,6 @@ set(MFEM_SOURCE_DIRS general linalg mesh fem)
 foreach(DIR IN LISTS MFEM_SOURCE_DIRS)
   add_subdirectory(${DIR})
 endforeach()
-
-if (MFEM_USE_CUDA)
-   foreach(file IN LISTS SOURCES)
-      set_property(SOURCE ${file} PROPERTY LANGUAGE CUDA)
-   endforeach()
-endif()
-
 add_subdirectory(config)
 set(MASTER_HEADERS
   ${PROJECT_SOURCE_DIR}/mfem.hpp
@@ -395,11 +336,6 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON CACHE BOOL "")
 set(CMAKE_INSTALL_RPATH "${_lib_path}" CACHE PATH "")
 set(CMAKE_INSTALL_NAME_DIR "${_lib_path}" CACHE PATH "")
 
-set(MFEM_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR} CACHE PATH
-    "The MFEM source directory" FORCE)
-set(MFEM_INSTALL_DIR ${CMAKE_INSTALL_PREFIX} CACHE PATH
-    "The MFEM install directory" FORCE)
-
 # Declaring the library
 add_library(mfem ${SOURCES} ${HEADERS} ${MASTER_HEADERS})
 # message(STATUS "TPL_LIBRARIES = ${TPL_LIBRARIES}")
@@ -414,11 +350,11 @@ endif()
 set_target_properties(mfem PROPERTIES VERSION "${mfem_VERSION}")
 set_target_properties(mfem PROPERTIES SOVERSION "${mfem_VERSION}")
 
-# If building out-of-source, define MFEM_CONFIG_FILE to point to the config file
-# inside the build directory.
+# If building out-of-source, define MFEM_BUILD_DIR to point to the build
+# directory.
 if (NOT ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}"))
   target_compile_definitions(mfem PRIVATE
-    "MFEM_CONFIG_FILE=\"${PROJECT_BINARY_DIR}/config/_config.hpp\"")
+    "MFEM_BUILD_DIR=${PROJECT_BINARY_DIR}")
 endif()
 
 # Generate configuration file in the build directory: config/_config.hpp.
@@ -434,7 +370,7 @@ if (NOT ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}"))
       "Writing substitute header --> \"${Header}\"")
     file(WRITE "${PROJECT_BINARY_DIR}/${Header}"
 "// Auto-generated file.
-#define MFEM_CONFIG_FILE \"${PROJECT_BINARY_DIR}/config/_config.hpp\"
+#define MFEM_BUILD_DIR ${PROJECT_BINARY_DIR}
 #include \"${PROJECT_SOURCE_DIR}/${Header}\"
 ")
     # This version will be installed in the top include directory:
@@ -452,9 +388,6 @@ endif()
 # Enable testing if required
 if (MFEM_ENABLE_TESTING)
   enable_testing()
-  set(MFEM_ALL_TESTS_TARGET_NAME tests)
-  add_mfem_target(${MFEM_ALL_TESTS_TARGET_NAME} OFF)
-  add_subdirectory(tests EXCLUDE_FROM_ALL)
 endif()
 
 # Define a target that all examples and miniapps will depend on.
@@ -474,9 +407,7 @@ add_subdirectory(miniapps EXCLUDE_FROM_ALL)
 # Target to build all executables, i.e. everything.
 add_custom_target(exec)
 add_dependencies(exec
-  ${MFEM_ALL_EXAMPLES_TARGET_NAME}
-  ${MFEM_ALL_MINIAPPS_TARGET_NAME}
-  ${MFEM_ALL_TESTS_TARGET_NAME})
+  ${MFEM_ALL_EXAMPLES_TARGET_NAME} ${MFEM_ALL_MINIAPPS_TARGET_NAME})
 # Here, we want to "add_dependencies(test exec)". However, dependencies for
 # 'test' (and other built-in targets) can not be added with add_dependencies():
 #  - https://gitlab.kitware.com/cmake/cmake/issues/8438
@@ -497,12 +428,12 @@ endif()
 # Add 'check' target - quick test
 if (NOT MFEM_USE_MPI)
   add_custom_target(check
-    ${CMAKE_CTEST_COMMAND} -R \"^ex1_ser\" -C ${CMAKE_CFG_INTDIR}
+    ${CMAKE_CTEST_COMMAND} -R '^ex1_ser' -C ${CMAKE_CFG_INTDIR}
     USES_TERMINAL)
   add_dependencies(check ex1)
 else()
   add_custom_target(check
-    ${CMAKE_CTEST_COMMAND} -R \"^ex1p\" -C ${CMAKE_CFG_INTDIR}
+    ${CMAKE_CTEST_COMMAND} -R '^ex1p' -C ${CMAKE_CFG_INTDIR}
     USES_TERMINAL)
   add_dependencies(check ex1p)
 endif()
@@ -547,20 +478,6 @@ install(DIRECTORY ${MFEM_SOURCE_DIRS}
   DESTINATION ${INSTALL_INCLUDE_DIR}/mfem
   FILES_MATCHING PATTERN "*.hpp")
 
-# Install the okl files
-if (MFEM_USE_OCCA)
-  install(DIRECTORY ${MFEM_SOURCE_DIRS}
-    DESTINATION ${INSTALL_INCLUDE_DIR}/mfem
-    FILES_MATCHING PATTERN "*.okl")
-endif()
-
-# Install the libCEED files
-if (MFEM_USE_CEED)
-  install(DIRECTORY ${MFEM_SOURCE_DIRS}
-    DESTINATION ${INSTALL_INCLUDE_DIR}/mfem
-    FILES_MATCHING PATTERN "fem/libceed/*.h")
-endif()
-
 # Install ${HEADERS}
 # ---
 # foreach (HDR ${HEADERS})
@@ -626,10 +543,3 @@ install(FILES
 # Install the export set for use with the install-tree
 install(EXPORT ${PROJECT_NAME_UC}Targets
     DESTINATION ${INSTALL_CMAKE_DIR})
-
-#-------------------------------------------------------------------------------
-# Create 'config.mk' from 'config.mk.in' for the build and install locations and
-# define install rules for 'config.mk' and 'test.mk'
-#-------------------------------------------------------------------------------
-
-mfem_export_mk_files()

CONTRIBUTING.md

@@ -83,8 +83,6 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
   │   └── web
   │       └── examples
   ├── examples
-  │   ├── ginkgo
-  │   ├── hiop
   │   ├── petsc
   │   ├── pumi
   │   └── sundials
@@ -92,19 +90,13 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
   ├── general
   ├── linalg
   ├── mesh
-  ├── miniapps
-  │   ├── common
-  │   ├── electromagnetics
-  │   ├── gslib
-  │   ├── meshing
-  │   ├── nurbs
-  │   ├── performance
-  │   └── tools
-  └── tests
-      ├── unit
-      │   ├── ...
-      └── ...
-
+  └── miniapps
+      ├── common
+      ├── electromagnetics
+      ├── meshing
+      ├── nurbs
+      ├── performance
+      └── tools
   ```
 
 - The main directories are `fem/`, `mesh/` and `linalg/` containing the C++
@@ -145,16 +137,6 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
   + [`HypreParMatrix`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreParMatrix.html) and [`HypreParVector`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreParVector.html)
   + [`HypreSolver`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreSolver.html) and other [hypre classes](http://mfem.github.io/doxygen/html/hypre_8hpp.html)
 
-- GPU and multi-core CPU support is based on device kernels supporting different
-  backends (CUDA, OCCA, RAJA, OpenMP, etc.) and an internal lightweight
-  device/host memory manager.
-
-- The main device-relevant classes and sources are:
-  + [`Device`](http://mfem.github.io/doxygen/html/device_8hpp.html)
-  + [`MemoryManager`](http://mfem.github.io/doxygen/html/mem_manager_8hpp.html)
-  + the [`MFEM_FORALL`](http://mfem.github.io/doxygen/html/forall_8hpp.html) macro
-  + the [`cuda.hpp`](http://mfem.github.io/doxygen/html/cuda_8hpp.html) and [`occa.hpp`](http://mfem.github.io/doxygen/html/occa_8hpp.html) files
-
 - The `general/` directory contains C++ classes that serve as utilities for
   communication, error handling, arrays, (Boolean) tables, timing, etc.
 
@@ -169,9 +151,6 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
   in the simple example codes and more fully-featured mini applications in the
   `examples/` and `miniapps/` directories.
 
-- The `tests/` directory contains a unit test suite and will later contain more
-  tests that run example codes.
-
 - See also the [code overview](http://mfem.org/code-overview/) section on the
   MFEM website.
 
@@ -337,9 +316,9 @@ Before a PR can be merged, it should satisfy the following:
     - [ ] Is this a new feature users need to be aware of? New or updated example or miniapp?
     - [ ] Does it make sense to create a new section in the `CHANGELOG` to group with other related features?
 - [ ] Update `INSTALL`:
-    - [ ] Had a new optional library been added? (*Make sure the external library is licensed under LGPL, not GPL!*)
+    - [ ] 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)*
+    - [ ] 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.
@@ -353,7 +332,6 @@ Before a PR can be merged, it should satisfy the following:
       - [ ] Add the example code to the `ALL_EXE_SRCS` variable.
       - [ ] Make sure `THIS_TEST_OPTIONS` is set correctly for the new example.
    - [ ] List the new example in `doc/CodeDocumentation.dox`.
-   - [ ] If new examples directory (e.g.`examples/pumi`), list it in `doc/CodeDocumentation.conf.in`
    - [ ] Companion pull request for documentation in [mfem/web](https://github.com/mfem/web) repo:
       - [ ] Update or add example-specific documentation, see e.g. the `src/examples.md`.
       - [ ] Add the description, labels and screenshots in `src/examples.md` and `src/img`.
@@ -368,7 +346,6 @@ Before a PR can be merged, it should satisfy the following:
       - [ ] Add/update the `CMakeLists.txt` file in the new miniapp directory.
       - [ ] Consider adding a new test for the new miniapp.
    - [ ] List the new miniapp in `doc/CodeDocumentation.dox`
-   - [ ] If new miniapps directory (e.g.`miniapps/nurbs`), list it in `doc/CodeDocumentation.conf.in`
    - [ ] Companion pull request for documentation in [mfem/web](https://github.com/mfem/web) repo:
      - [ ] Update or add miniapp-specific documentation, see e.g. the `src/meshing.md` and `src/electromagnetics.md` files.
      - [ ] Add the description, labels and screenshots in `src/examples.md` and `src/img`.
@@ -381,10 +358,10 @@ Before a PR can be merged, it should satisfy the following:
    - [ ] If this is a major new feature, consider mentioning in the short summary inside `README` *(rare)*.
    - [ ] List major new classes in `doc/CodeDocumentation.dox` *(rare)*.
 - [ ] Update this checklist, if the new pull request affects it.
-- [ ] Run the unit tests and make sure they all pass `make unittest`.
 - [ ] (LLNL only) Clone the `tests` repository and run the following tests, see `mfem/tests/README.md`:
    - [ ] `compilers`
    - [ ] `memcheck`
+   - [ ] `unit-test`
    - [ ] `documentation`
 - [ ] (LLNL only) After merging:
    - [ ] Regenerate `README.html` files from companion documentation pull requests.
@@ -495,6 +472,7 @@ MFEM uses a `master`/`next`-branch workflow as described below:
   - `mfem:gh-next` -- Bleeding-edge development version, may be broken, use at
      your own risk.
 
+
 ## Automated Testing
 
 MFEM has several levels of automated testing running on GitHub, as well as on

INSTALL

@@ -13,41 +13,14 @@ of MFEM is a (modern) C++ compiler, such as g++. The parallel version of MFEM
 requires an MPI C++ compiler, as well as the following external libraries:
 
 - hypre (a library of high-performance preconditioners)
-  https://github.com/hypre-space/hypre
+  http://www.llnl.gov/CASC/hypre
 
 - METIS (a family of multilevel partitioning algorithms)
   http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
 
-The hypre dependency can be downloaded as a tarball from GitHub or from the
-project webpage https://www.llnl.gov/casc/hypre. For example, the 2.16.0 release
-of hypre is available at
-
-   https://github.com/hypre-space/hypre/archive/v2.16.0.tar.gz
-
 The METIS dependency can be disabled but that is not generally recommended, see
 the option MFEM_USE_METIS.
 
-MFEM also includes support for devices such as GPUs, and programming models such
-as CUDA, HIP, OCCA, OpenMP and RAJA.
-
-- Starting with version 4.0, MFEM requires a C++11 compiler
-
-- CUDA support requires an NVIDIA GPU and an installation of the CUDA Toolkit
-  https://developer.nvidia.com/cuda-toolkit
-
-- HIP support requires an AMD GPU and an installation of the ROCm software stack
-  https://rocm.github.io/ROCmInstall.html#installing-from-amd-rocm-repositories
-
-- OCCA support requires the OCCA library
-  https://libocca.org
-
-- OpenMP support requires a compiler implementing the OpenMP API
-  https://www.openmp.org
-
-- RAJA support requires installation of the RAJA performance portability layer
-  with (optionally) support for CUDA and OpenMP
-  https://github.com/LLNL/RAJA
-
 The library supports two build systems: one based on GNU make, and a second one
 based on CMake. Both build systems are described below. Some hints for building
 without GNU make or CMake can be found at the end of this file.
@@ -57,7 +30,7 @@ following package managers:
 
 - Spack, https://github.com/spack/spack
 - OpenHPC, http://openhpc.community
-- Homebrew/Science, https://github.com/Homebrew/homebrew-science (deprecated)
+- Homebrew/Science, https://github.com/Homebrew/homebrew-science
 
 We also recommend downloading and building the MFEM-based GLVis visualization
 tool which can be used to visualize the meshes and solution in MFEM's examples
@@ -69,19 +42,11 @@ Serial build:
    make serial -j 4
 
 Parallel build:
-   (download hypre and METIS 4 from above URLs)
+   (download hypre 2.10.0b and METIS 4 from above URLs)
    (build METIS 4 in ../metis-4.0 relative to mfem/)
-   (build hypre in ../hypre relative to mfem/)
+   (build hypre 2.10.0b in ../hypre-2.10.0b relative to mfem/)
    make parallel -j 4
 
-CUDA build:
-   make cuda -j 4
-   (build for a specific compute capability: 'make cuda -j 4 CUDA_ARCH=sm_30')
-
-HIP build:
-   make hip -j 4
-   (build for a specific AMD GPU chip: 'make hip -j 4 HIP_ARCH=gfx900')
-
 Example codes (serial/parallel, depending on the build):
    cd examples
    make -j 4
@@ -92,6 +57,7 @@ Build everything (library, examples and miniapps) with current configuration:
 Quick-check the build by running Example 1/1p (optional):
    make check
 
+
 Quick start with CMake
 ======================
 Serial build:
@@ -100,19 +66,13 @@ Serial build:
    make -j 4   (assuming "UNIX Makefiles" generator)
 
 Parallel build:
-   (download hypre and METIS 4 from above URLs)
+   (download hypre 2.10.0b and METIS 4 from above URLs)
    (build METIS 4 in ../metis-4.0 relative to mfem/)
-   (build hypre in ../hypre relative to mfem/)
+   (build hypre 2.10.0b in ../hypre-2.10.0b relative to mfem/)
    mkdir <mfem-build-dir> ; cd <mfem-build-dir>
    cmake <mfem-source-dir> -DMFEM_USE_MPI=YES
    make -j 4
 
-CUDA build:
-   (this build requires CMake 3.8 or newer)
-   mkdir <mfem-build-dir> ; cd <mfem-build-dir>
-   cmake <mfem-source-dir> -DMFEM_USE_CUDA=YES
-   make -j 4
-
 Example codes (serial/parallel, depending on the build):
    make examples -j 4
 
@@ -168,18 +128,10 @@ Note that re-configuration is only needed to change the currently configured
 options. Several shortcut targets combining (re-)configuration and compilation
 are also defined:
 
-   make serial    -> Builds serial optimized version of the library
-   make parallel  -> Builds parallel optimized version of the library
-   make debug     -> Builds serial debug version of the library
-   make pdebug    -> Builds parallel debug version of the library
-   make cuda      -> Builds serial cuda optimized version of the library
-   make pcuda     -> Builds parallel cuda optimized version of the library
-   make cudebug   -> Builds serial cuda debug version of the library
-   make pcudebug  -> Builds parallel cuda debug version of the library
-   make hip       -> Builds serial hip optimized version of the library
-   make phip      -> Builds parallel hip optimized version of the library
-   make hipdebug  -> Builds serial hip debug version of the library
-   make phipdebug -> Builds parallel hip debug version of the library
+   make serial   -> Builds serial optimized version of the library
+   make parallel -> Builds parallel optimized version of the library
+   make debug    -> Builds serial debug version of the library
+   make pdebug   -> Builds parallel debug version of the library
 
 Note that any of the above shortcuts accept configuration options, either at the
 command line or through a user configuration file.
@@ -241,9 +193,8 @@ Configuration options (GNU make)
 See the configuration file config/defaults.mk for the default settings.
 
 Compilers:
-   CXX      - C++ compiler, serial build
-   MPICXX   - MPI C++ compiler, parallel build
-   CUDA_CXX - The CUDA compiler, 'nvcc'
+   CXX    - C++ compiler, serial build
+   MPICXX - MPI C++ compiler, parallel build
 
 Compiler options:
    OPTIM_FLAGS - Options for optimized build
@@ -279,7 +230,7 @@ MFEM_DEBUG = YES/NO
    and consistency checks that may simplify bug-hunting.
 
 MFEM_USE_EXCEPTIONS = YES/NO
-   Enable the use of exceptions. In particular, modifies the default behavior
+   Enable the use of exceptions. In particular, modifies the default bahavior
    when errors are encountered: throw an exception, instead of aborting.
 
 MFEM_USE_LIBUNWIND = YES/NO
@@ -299,12 +250,8 @@ MFEM_THREAD_SAFE = YES/NO
    Use thread-safe implementation for some classes/methods. This comes at the
    cost of extra memory allocation and de-allocation.
 
-MFEM_USE_LEGACY_OPENMP = YES/NO
-   Enable (basic) experimental OpenMP support. Requires MFEM_THREAD_SAFE.
-   This option is deprecated.
-
 MFEM_USE_OPENMP = YES/NO
-   Enable the OpenMP backend.
+   Enable (basic) experimental OpenMP support. Requires MFEM_THREAD_SAFE.
 
 MFEM_USE_MEMALLOC = YES/NO
    Internal MFEM option: enable batch allocation for some small objects.
@@ -349,12 +296,6 @@ MFEM_USE_STRUMPACK = YES/NO
    classes. When enabled, this option uses the STRUMPACK_* library options, see
    below.
 
-MFEM_USE_GINKGO = YES/NO
-   Enable MFEM functionality based on the Ginkgo library, which provides
-   iterative linear solvers and preconditioners with OpenMP, CUDA backends, see
-   https://github.com/ginkgo-project/ginkgo. When enabled, the user can use
-   Ginkgo's solvers and preconditioners as shown in examples/ginkgo/.
-
 MFEM_USE_GNUTLS = YES/NO
    Enable secure socket support in class socketstream, using the auxiliary
    GnuTLS_* classes, based on the GnuTLS library. This option may be useful in
@@ -389,11 +330,11 @@ MFEM_USE_MPFR = YES/NO
    see below.
 
 MFEM_USE_SIDRE = YES/NO
-   Sidre is a component of LLNL's axom project, https://github.com/LLNL/axom,
-   that provides an HDF5-based file format for visualization or restart
-   capability following the Conduit (https://github.com/LLNL/conduit) mesh
-   blueprint specification. When enabled, this option requires installation of
-   HDF5 (see also MFEM_USE_NETCDF), Conduit and LLNL's axom project.
+   Sidre is a component of LLNL's axom project, http://goo.gl/cZyJdn, that
+   provides an HDF5-based file format for visualization or restart capability
+   following the Conduit (https://github.com/LLNL/conduit) mesh blueprint
+   specification. When enabled, this option requires installation of HDF5 (see
+   also MFEM_USE_NETCDF), Conduit and LLNL's axom project.
 
 MFEM_USE_CONDUIT = YES/NO
    Enables support for converting MFEM Mesh and Grid Function objects to and
@@ -421,48 +362,6 @@ MFEM_USE_PUMI = YES/NO
    models and effectively supports automated adaptive analysis. PUMI enables
    support for parallel unstructured mesh modifications in MFEM.
 
-MFEM_USE_HIOP = YES/NO
-  Enable the usage of HiOp (https://github.com/LLNL/hiop) in MFEM. HiOp is an
-  HPC solver for nonlinear optimization problems.
-
-MFEM_USE_CUDA = YES/NO
-   Enables support for CUDA devices in MFEM. CUDA is a parallel computing
-   platform and programming model for general computing on graphical processing
-   units (GPUs). The variable CUDA_ARCH is used to specify the CUDA compute
-   capability used during compilation (by default, CUDA_ARCH=sm_60). When
-   enabled, this option uses the CUDA_* build options, see below.
-
-MFEM_USE_HIP = YES/NO
-   Enables support for AMD devices in MFEM. HIP is a heterogeneous-compute
-   interface for portability developed by AMD that can target both AMD and
-   NVIDIA GPUs. The variable HIP_ARCH is used to specify the AMD GPU processor
-   used during compilation (by default, HIP_ARCH=gfx900).  When enabled, this
-   option uses the HIP_* build options, see below.
-
-MFEM_USE_RAJA = YES/NO
-   Enable support for the RAJA performance portability layer in MFEM. RAJA
-   provides a portable abstraction for loops, supporting different programming
-   model backends. When using RAJA built with CUDA support, CUDA support must be
-   also enabled in MFEM, i.e. MFEM_USE_CUDA=YES must be set.
-
-MFEM_USE_OCCA = YES/NO
-   Enables support for the OCCA library in MFEM. OCCA is an open-source library
-   which aims to make it easy to program different types of devices (e.g. CPU,
-   GPU, FPGA) by providing an unified API for interacting with JIT-compiled
-   backends. In order to use the OCCA CUDA backend, CUDA support must be enabled
-   in MFEM as well, i.e. MFEM_USE_CUDA=YES must be set.
-
-MFEM_USE_GSLIB = YES/NO
-   Enables MFEM functionality based on the GSLIB library, and specifically its
-   FindPoints component, which provides a robust algorithms to evaluate finite
-   element functions in a collection of points in physical space. When enabled,
-   the user can use the GSLIB-FindPoints methods as shown in miniapps/gslib.
-
-MFEM_USE_CEED = YES/NO
-   Enables support for the libCEED library in MFEM. libCEED is a portable
-   library for performant high-order operator evaluation developed by the Center
-   for Efficient Exascale Discretizations in the Exascale Computing Project.
-
 MFEM_BUILD_TAG = (any value)
    An optional tag to characterize the build. Exported to config/config.mk.
    Can be used to identify the MFEM build from other makefiles.
@@ -484,7 +383,7 @@ directory and use the string @MFEM_DIR@, e.g. HYPRE_OPT = -I@MFEM_DIR@/../hypre.
 The specific libraries and their options are:
 
 - HYPRE, required for the parallel build, i.e. when MFEM_USE_MPI = YES.
-  URL: https://github.com/hypre-space/hypre and https://www.llnl.gov/casc/hypre
+  URL: http://www.llnl.gov/CASC/hypre
   Options: HYPRE_OPT, HYPRE_LIB.
 
 - METIS, used when MFEM_USE_METIS = YES. If using METIS 5, set
@@ -498,8 +397,7 @@ The specific libraries and their options are:
        http://math-atlas.sourceforge.net (ATLAS)
   Options: LAPACK_OPT (currently not used/needed), LAPACK_LIB.
 
-- OpenMP (optional), usually part of compiler, used when either MFEM_USE_OPENMP
-  or MFEM_USE_LEGACY_OPENMP is set to YES.
+- OpenMP (optional), usually part of compiler, used when MFEM_USE_OPENMP = YES.
   Options: OPENMP_OPT, OPENMP_LIB.
 
 - High-resolution POSIX clocks: when using MFEM_TIMER_TYPE = 2, it may be
@@ -509,7 +407,6 @@ The specific libraries and their options are:
 - SUNDIALS (optional), used when MFEM_USE_SUNDIALS = YES.
   Beginning with MFEM v3.3, SUNDIALS v2.7.0 is supported.
   Beginning with MFEM v3.3.2, SUNDIALS v3.0.0 is also supported.
-  Beginning with MFEM v4.1, only SUNDIALS v5.0.0+ is supported.
   If MFEM_USE_MPI is enabled, we expect that SUNDIALS is built with support for
   both MPI and hypre.
   URL: http://computation.llnl.gov/projects/sundials/sundials-software
@@ -532,19 +429,12 @@ The specific libraries and their options are:
 
 - STRUMPACK (optional), used when MFEM_USE_STRUMPACK = YES. Note that STRUMPACK
   requires the PT-Scotch and Scalapack libraries as well as ParMETIS, which
-  includes METIS 5 in its distribution. Starting with STRUMPACK v2.2.0, ParMETIS
-  and PT-Scotch are optional dependencies.
+  includes METIS 5 in its distribution.
   The support for STRUMPACK was added in MFEM v3.3.2 and it requires STRUMPACK
   2.0.0 or later.
   URL: http://portal.nersc.gov/project/sparse/strumpack
   Options: STRUMPACK_OPT, STRUMPACK_LIB.
 
-- Ginkgo (optional), used when MFEM_USE_GINKGO = YES. Note that Ginkgo needs a
-  C++ compiler that supports the C++-11 standard. For additional requirements
-  and dependencies of specific modules see the Ginkgo webpage below.
-  URL: https://ginkgo-project.github.io
-  Options: GINKGO_OPT (Not used), GINKGO_LIB.
-
 - GnuTLS (optional), used when MFEM_USE_GNUTLS = YES. On most Linux systems,
   GnuTLS is available as a development package, e.g. gnutls-devel. On Mac OS X,
   one can get the library through the Homebrew package manager (http://brew.sh).
@@ -570,58 +460,21 @@ The specific libraries and their options are:
   Options: PETSC_OPT, PETSC_LIB.
 
 - Sidre (optional), part of LLNL's axom project, used when MFEM_USE_SIDRE = YES.
-  Starting with MFEM v4.1, Axom version 0.3.1 or later is required.
-  URL: https://github.com/LLNL/axom
+  URL: http://goo.gl/cZyJdn (axom, to be released)
        https://github.com/LLNL/conduit (Conduit)
        https://support.hdfgroup.org/HDF5 (HDF5)
   Options: SIDRE_OPT, SIDRE_LIB.
 
-- Conduit (optional), used when MFEM_USE_CONDUIT = YES. Conduit Mesh Blueprint
+- Conduit, used when MFEM_USE_CONDUIT = YES. Direct Conduit Mesh Blueprint
   support requires Conduit >= v0.3.1 and VisIt >= v2.13.1 to read the output.
   URL: https://github.com/LLNL/conduit (Conduit)
        https://support.hdfgroup.org/HDF5 (HDF5)
   Options: CONDUIT_OPT, CONDUIT_LIB.
 
-- PUMI (optional), used when MFEM_USE_PUMI = YES.
+- PUMI, used when MFEM_USE_PUMI = YES.
   URL: https://scorec.rpi.edu/pumi
   Options: PUMI_OPT, PUMI_LIB.
 
-- HiOp (optional), used when MFEM_USE_HIOP = YES.
-  URL: https://github.com/LLNL/hiop
-  Options: HIOP_OPT, HIOP_LIB.
-
-- GSLIB (optional), used when MFEM_USE_GSLIB = YES. The gslib library must be
-  built prior to the MFEM build, as follows: download gslib-1.0.5, untar it at
-  the same level as MFEM and create a symbolic link: "ln -s gslib-1.0.5 gslib".
-  Build gslib in parallel or in serial based on the desired MFEM build: "make
-  clean; make CC=mpicc" or "make clean; make CC=gcc MPI=0". Build MFEM with
-  MFEM_USE_GSLIB=YES.
-  URL: https://github.com/gslib/gslib/archive/v1.0.5.tar.gz
-  Options: GSLIB_OPT, GSLIB_LIB.
-
-- CUDA (optional), used when MFEM_USE_CUDA = YES.
-  URL: https://developer.nvidia.com/cuda-toolkit
-  Options: CUDA_CXX, CUDA_ARCH, CUDA_OPT, CUDA_LIB.
-
-- HIP (optional), used when MFEM_USE_HIP = YES.
-  URL: https://rocm.github.io/ROCmInstall.html
-  Options: HIP_CXX, HIP_ARCH, HIP_OPT, HIP_LIB.
-
-- OCCA (optional), used when MFEM_USE_OCCA = YES.
-  URL: https://libocca.org
-  Options: OCCA_DIR, OCCA_OPT, OCCA_LIB.
-
-- libCEED (optional), used when MFEM_USE_CEED = YES. Requires libCEED's master
-  branch, specifically, git-hash c00ee0d or later.
-  URL: https://github.com/CEED/libCEED
-       https://ceed.exascaleproject.org/libceed
-  Options: CEED_DIR, CEED_OPT, CEED_LIB.
-
-- RAJA (optional), used when MFEM_USE_RAJA = YES.
-  Beginning with MFEM v4.1, only RAJA v0.10.0+ is supported.
-  URL: https://github.com/LLNL/RAJA
-  Options: RAJA_DIR, RAJA_OPT, RAJA_LIB.
-
 - 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.
@@ -637,6 +490,7 @@ The specific libraries and their options are:
   URL: https://zlib.net
   Options: ZLIB_OPT, ZLIB_LIB.
 
+
 Building with CMake
 ===================
 The MFEM build system consists of two steps: configuration and compilation.
@@ -725,8 +579,6 @@ Configuration variables (CMake)
 ===============================
 See the configuration file config/defaults.cmake for the default settings.
 
-Note: the option MFEM_USE_CUDA requires CMake version 3.8 or newer!
-
 Non-standard CMake variables for compilers:
    CXX    - If set, overwrite the auto-detected C++ compiler, serial build
    MPICXX - If set, overwrite the auto-detected MPI C++ compiler, parallel build
@@ -744,7 +596,6 @@ MFEM_USE_METIS - Set to ${MFEM_USE_MPI}, can be overwritten.
 MFEM_USE_LIBUNWIND
 MFEM_USE_LAPACK
 MFEM_THREAD_SAFE
-MFEM_USE_LEGACY_OPENMP
 MFEM_USE_OPENMP
 MFEM_USE_MEMALLOC
 MFEM_TIMER_TYPE - Set automatically, can be overwritten.
@@ -752,18 +603,11 @@ MFEM_USE_MESQUITE
 MFEM_USE_SUITESPARSE
 MFEM_USE_SUPERLU
 MFEM_USE_STRUMPACK
-MFEM_USE_GINKGO
 MFEM_USE_GNUTLS
 MFEM_USE_NETCDF
 MFEM_USE_MPFR
 MFEM_USE_GZSTREAM
 MFEM_USE_PUMI
-MFEM_USE_HIOP
-MFEM_USE_CUDA
-MFEM_USE_OCCA
-MFEM_USE_CEED
-MFEM_USE_RAJA
-MFEM_USE_SIDRE
 
 The following options are CMake specific:
 
@@ -804,17 +648,12 @@ The CMake build system adds auto-detection for the following packages/libraries:
  - SuiteSparse
  - SuperLUDist, STRUMPACK
  - ParMETIS
- - Ginkgo
  - GNUTLS - Extends the built-in CMake support, to search GNUTLS_DIR as well.
  - NETCDF
  - MPFR
  - LIBUNWIND
  - POSIXCLOCKS
  - PUMI
- - HIOP
- - OCCA
- - RAJA
- - AXOM - Used when MFEM_USE_SIDRE is enabled
 
 The following built-in CMake packages are also used:
 

LICENSE

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

README

@@ -8,9 +8,9 @@
                                http://mfem.org
 
 MFEM is a modular parallel C++ library for finite element methods. Its goal is
-to enable high-performance scalable finite element discretization research and
-application development on a wide variety of platforms, ranging from laptops to
-supercomputers.
+to enable the research and development of scalable finite element discretization
+and solver algorithms through general finite element abstractions, accurate and
+flexible visualization, and tight integration with the hypre library.
 
 * For building instructions, see the file INSTALL, or type "make help".
 
@@ -39,24 +39,23 @@ conforming and non-conforming (AMR) adaptive refinement. Arbitrary element
 transformations, allowing for high-order mesh elements with curved boundaries,
 are also supported.
 
-When used as a "finite element to linear algebra translator", MFEM can take a
-problem described in terms of finite element-type objects, and produce the
-corresponding linear algebra vectors and fully or partially assembled operators,
-e.g. in the form of global sparse matrices or matrix-free operators. The library
-includes simple smoothers and Krylov solvers, such as PCG, MINRES and GMRES, as
-well as support for sequential sparse direct solvers from the SuiteSparse
+MFEM is commonly used as a "finite element to linear algebra translator", since
+it can take a problem described in terms of finite element-type objects, and
+produce the corresponding linear algebra vectors and sparse matrices. In order
+to facilitate this, MFEM uses compressed sparse row (CSR) sparse matrix storage
+and includes simple smoothers and Krylov solvers, such as PCG, MINRES and GMRES,
+as well as support for sequential sparse direct solvers from the SuiteSparse
 library. Nonlinear solvers (the Newton method), eigensolvers (LOBPCG), and
 several explicit and implicit Runge-Kutta time integrators are also available.
 
 MFEM supports MPI-based parallelism throughout the library, and can readily be
-used as a scalable unstructured finite element problem generator. As of version
-4.0, MFEM offers initial support for GPU acceleration, and programming models,
-such as CUDA, OCCA, RAJA and OpenMP. MFEM-based applications require minimal
-changes to switch from a serial to a high-performing MPI-parallel version of the
-code, where they can take advantage of the integrated linear solvers from the
-hypre library.  Comprehensive support for other external packages, e.g. PETSc
-and SUNDIALS is also included, giving access to many additional linear and
-nonlinear solvers, preconditioners, time integrators, etc.
+used as a scalable unstructured finite element problem generator. MFEM-based
+applications require minimal changes to transition from a serial to a
+high-performing parallel version of the code, where they can take advantage of
+the integrated scalable linear solvers from the hypre library. Comprehensive
+support for other external packages, e.g. PETSc and SUNDIALS is also included,
+giving access to many additional linear and nonlinear solvers, preconditioners,
+time integrators, etc.
 
 For examples of using MFEM, see the examples/ and miniapps/ directories, as well
 as the OpenGL visualization tool GLVis which is available at http://glvis.org.

config/XSDKDefaults.cmake

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

config/cmake/MFEMConfig.cmake.in

@@ -25,7 +25,6 @@ set(MFEM_USE_LIBUNWIND @MFEM_USE_LIBUNWIND@)
 set(MFEM_USE_LAPACK @MFEM_USE_LAPACK@)
 set(MFEM_THREAD_SAFE @MFEM_THREAD_SAFE@)
 set(MFEM_USE_OPENMP @MFEM_USE_OPENMP@)
-set(MFEM_USE_LEGACY_OPENMP @MFEM_USE_LEGACY_OPENMP@)
 set(MFEM_USE_MEMALLOC @MFEM_USE_MEMALLOC@)
 set(MFEM_TIMER_TYPE @MFEM_TIMER_TYPE@)
 set(MFEM_USE_SUNDIALS @MFEM_USE_SUNDIALS@)
@@ -34,7 +33,6 @@ 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_GINKGO @MFEM_USE_GINKGO@)
 set(MFEM_USE_GNUTLS @MFEM_USE_GNUTLS@)
 set(MFEM_USE_NETCDF @MFEM_USE_NETCDF@)
 set(MFEM_USE_PETSC @MFEM_USE_PETSC@)
@@ -42,10 +40,6 @@ set(MFEM_USE_MPFR @MFEM_USE_MPFR@)
 set(MFEM_USE_SIDRE @MFEM_USE_SIDRE@)
 set(MFEM_USE_CONDUIT @MFEM_USE_CONDUIT@)
 set(MFEM_USE_PUMI @MFEM_USE_PUMI@)
-set(MFEM_USE_CUDA @MFEM_USE_CUDA@)
-set(MFEM_USE_OCCA @MFEM_USE_OCCA@)
-set(MFEM_USE_RAJA @MFEM_USE_RAJA@)
-set(MFEM_USE_CEED @MFEM_USE_CEED@)
 
 set(MFEM_CXX_COMPILER "@CMAKE_CXX_COMPILER@")
 set(MFEM_CXX_FLAGS "@CMAKE_CXX_FLAGS@")

config/cmake/config.hpp.in

@@ -30,12 +30,6 @@
 #define MFEM_VERSION_MINOR (((MFEM_VERSION)/100)%100)
 #define MFEM_VERSION_PATCH ((MFEM_VERSION)%100)
 
-// MFEM source directory.
-#define MFEM_SOURCE_DIR "@MFEM_SOURCE_DIR@"
-
-// MFEM install directory.
-#define MFEM_INSTALL_DIR "@MFEM_INSTALL_DIR@"
-
 // Description of the git commit used to build MFEM.
 #cmakedefine MFEM_GIT_STRING "@MFEM_GIT_STRING@"
 
@@ -68,12 +62,9 @@
 // allocation and de-allocation.
 #cmakedefine MFEM_THREAD_SAFE
 
-// Enable the OpenMP backend.
+// Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
 #cmakedefine MFEM_USE_OPENMP
 
-// [Deprecated] Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
-#cmakedefine MFEM_USE_LEGACY_OPENMP
-
 // Enable MFEM functionality based on the Mesquite library.
 #cmakedefine MFEM_USE_MESQUITE
 
@@ -92,9 +83,6 @@
 // Enable functionality based on the Gecko library
 #cmakedefine MFEM_USE_GECKO
 
-// Enable functionality based on the Ginkgo library
-#cmakedefine MFEM_USE_GINKGO
-
 // Enable MFEM functionality based on the GnuTLS library
 #cmakedefine MFEM_USE_GNUTLS
 
@@ -113,22 +101,6 @@
 // Enable MFEM functionality based on the PUMI library
 #cmakedefine MFEM_USE_PUMI
 
-// Enable MFEM functionality based on the HiOp library
-#cmakedefine MFEM_USE_HIOP
-
-// Build the GPU/CUDA-enabled version of the MFEM library.
-// Requires a CUDA compiler (nvcc).
-#cmakedefine MFEM_USE_CUDA
-
-// Enable MFEM functionality based on the RAJA library
-#cmakedefine MFEM_USE_RAJA
-
-// Enable MFEM functionality based on the OCCA library
-#cmakedefine MFEM_USE_OCCA
-
-// Enable MFEM functionality based on the libCEED library
-#cmakedefine MFEM_USE_CEED
-
 // Which library functions to use in class StopWatch for measuring time.
 // For a list of the available options, see INSTALL.
 // If not defined, an option is selected automatically.
@@ -137,6 +109,10 @@
 // Enable MFEM functionality based on the SUNDIALS libraries.
 #cmakedefine MFEM_USE_SUNDIALS
 
+// Windows specific options
+// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
+#cmakedefine _USE_MATH_DEFINES
+
 // Version of HYPRE used for building MFEM.
 #cmakedefine MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@
 

config/cmake/modules/FindAxom.cmake

@@ -18,4 +18,6 @@ include(MfemCmakeUtilities)
 # Note: components are enabled based on the find_package() parameters.
 mfem_find_package(Axom AXOM AXOM_DIR "include" "" "lib" ""
   "Paths to headers required by Axom." "Libraries required by Axom."
-  ADD_COMPONENT Axom "include" axom/config.hpp "lib" axom)
+  ADD_COMPONENT Sidre "include" sidre/sidre.hpp "lib" sidre
+  ADD_COMPONENT SLIC "include" slic/slic.hpp "lib" slic
+  ADD_COMPONENT axom_utils "include" axom_utils/Utilities.hpp "lib" axom_utils)

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

config/cmake/modules/FindOCCA.cmake

@@ -1,19 +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.
-
-# Defines the following variables:
-#   - OCCA_FOUND
-#   - OCCA_LIBRARIES
-#   - OCCA_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(OCCA OCCA OCCA_DIR "include" "occa.hpp" "lib" "occa"
-  "Paths to headers required by OCCA." "Libraries required by OCCA.")

config/cmake/modules/FindRAJA.cmake

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

config/cmake/modules/FindlibCEED.cmake

@@ -1,19 +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.
-
-# Defines the following variables:
-#   - CEED_FOUND
-#   - CEED_LIBRARIES
-#   - CEED_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(libCEED CEED CEED_DIR "include" ceed.h "lib" ceed
-  "Paths to headers required by libCEED." "Libraries required by libCEED.")

config/cmake/modules/MfemCmakeUtilities.cmake

@@ -229,17 +229,6 @@ endfunction(mfem_find_component)
 function(mfem_find_package Name Prefix DirVar IncSuffixes Header LibSuffixes
          Lib IncDoc LibDoc)
 
-  # If we have the TPL_ versions of _INCLUDE_DIRS and _LIBRARIES then set the
-  # standard ${Prefix} versions
-  if (TPL_${Prefix}_INCLUDE_DIRS)
-    set(${Prefix}_INCLUDE_DIRS ${TPL_${Prefix}_INCLUDE_DIRS} CACHE STRING
-      "TPL_${Prefix}_INCLUDE_DIRS was found." FORCE)
-  endif()
-  if (TPL_${Prefix}_LIBRARIES)
-    set(${Prefix}_LIBRARIES ${TPL_${Prefix}_LIBRARIES} CACHE STRING
-      "TPL_${Prefix}_LIBRARIES was found." FORCE)
-  endif()
-
   # Quick return
   if (${Prefix}_FOUND)
     return()
@@ -696,163 +685,3 @@ function(mfem_find_library Name Prefix Lib LibDoc CheckVar CheckSrc)
   endif()
 
 endfunction(mfem_find_library)
-
-
-#
-#   Function that creates 'config.mk' from 'config.mk.in' for the both the
-#   build- and the install-locations and define install rules for 'config.mk'
-#   and 'test.mk'.
-#
-function(mfem_export_mk_files)
-
-  # Define a few auxiliary variables (not written to 'config.mk')
-  string(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE)
-  # CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG -> '-Wl,-rpath,'
-  set(shared_link_flag ${CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG})
-  if (NOT shared_link_flag)
-    set(shared_link_flag "-Wl,-rpath,")
-  endif()
-
-  # Convert Boolean vars to YES/NO without writting the values to cache
-  set(CONFIG_MK_BOOL_VARS MFEM_USE_MPI MFEM_USE_METIS MFEM_USE_METIS_5
-      MFEM_DEBUG MFEM_USE_EXCEPTIONS MFEM_USE_GZSTREAM MFEM_USE_LIBUNWIND
-      MFEM_USE_LAPACK MFEM_THREAD_SAFE MFEM_USE_OPENMP MFEM_USE_LEGACY_OPENMP
-      MFEM_USE_MEMALLOC MFEM_USE_SUNDIALS MFEM_USE_MESQUITE MFEM_USE_SUITESPARSE
-      MFEM_USE_SUPERLU MFEM_USE_STRUMPACK MFEM_USE_GECKO MFEM_USE_GNUTLS
-      MFEM_USE_NETCDF MFEM_USE_PETSC MFEM_USE_MPFR MFEM_USE_SIDRE
-      MFEM_USE_CONDUIT MFEM_USE_PUMI MFEM_USE_CUDA MFEM_USE_OCCA MFEM_USE_RAJA)
-  foreach(var ${CONFIG_MK_BOOL_VARS})
-    if (${var})
-      set(${var} YES)
-    else()
-      set(${var} NO)
-    endif()
-  endforeach()
-  # TODO: Add support for MFEM_USE_CUDA=YES
-  set(MFEM_CXX ${CMAKE_CXX_COMPILER})
-  set(MFEM_CPPFLAGS "")
-  string(STRIP "${CMAKE_CXX_FLAGS_${BUILD_TYPE}} ${CMAKE_CXX_FLAGS}"
-         MFEM_CXXFLAGS)
-  set(MFEM_TPLFLAGS "")
-  foreach(dir ${MFEM_TPL_INCLUDE_DIRS})
-    set(MFEM_TPLFLAGS "${MFEM_TPLFLAGS} -I${dir}")
-  endforeach()
-  # TODO: MFEM_TPLFLAGS: add other TPL flags, in addition to the -I flags.
-  set(MFEM_INCFLAGS "-I\$(MFEM_INC_DIR) \$(MFEM_TPLFLAGS)")
-  set(MFEM_PICFLAG "")
-  if (BUILD_SHARED_LIBS)
-    set(MFEM_PICFLAG "${CMAKE_SHARED_LIBRARY_CXX_FLAGS}")
-  endif()
-  set(MFEM_FLAGS "\$(MFEM_CPPFLAGS) \$(MFEM_CXXFLAGS) \$(MFEM_INCFLAGS)")
-  # TPL link flags: set below
-  set(MFEM_EXT_LIBS "")
-  if (BUILD_SHARED_LIBS)
-    set(MFEM_LIBS "${shared_link_flag}\$(MFEM_LIB_DIR) -L\$(MFEM_LIB_DIR)")
-    set(MFEM_LIBS "${MFEM_LIBS} -lmfem \$(MFEM_EXT_LIBS)")
-    if (APPLE)
-      set(SO_VER ".${mfem_VERSION}${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    else()
-      set(SO_VER "${CMAKE_SHARED_LIBRARY_SUFFIX}.${mfem_VERSION}")
-    endif()
-    set(MFEM_LIB_FILE "\$(MFEM_LIB_DIR)/libmfem${SO_VER}")
-    set(MFEM_SHARED YES)
-    set(MFEM_STATIC NO)
-  else()
-    set(MFEM_LIBS "-L\$(MFEM_LIB_DIR) -lmfem \$(MFEM_EXT_LIBS)")
-    set(MFEM_LIB_FILE "\$(MFEM_LIB_DIR)/libmfem.a")
-    set(MFEM_SHARED NO)
-    set(MFEM_STATIC YES)
-  endif()
-  set(MFEM_BUILD_TAG "${CMAKE_SYSTEM}")
-  set(MFEM_PREFIX "${CMAKE_INSTALL_PREFIX}")
-  # For the next 4 variable, these are the values for the build-tree version of
-  # 'config.mk'
-  set(MFEM_INC_DIR "${PROJECT_BINARY_DIR}")
-  set(MFEM_LIB_DIR "${PROJECT_BINARY_DIR}")
-  set(MFEM_TEST_MK "${PROJECT_SOURCE_DIR}/config/test.mk")
-  set(MFEM_CONFIG_EXTRA "MFEM_BUILD_DIR ?= ${PROJECT_BINARY_DIR}")
-  set(MFEM_MPIEXEC ${MPIEXEC})
-  if (NOT MFEM_MPIEXEC)
-    set(MFEM_MPIEXEC "mpirun")
-  endif()
-  set(MFEM_MPIEXEC_NP ${MPIEXEC_NUMPROC_FLAG})
-  if (NOT MFEM_MPIEXEC_NP)
-    set(MFEM_MPIEXEC_NP "-np")
-  endif()
-  # MFEM_MPI_NP is already set
-  # Define the variable 'MFEM_EXT_LIBS': handle PUMI libs
-  if ("${MFEM_USE_PUMI}" STREQUAL "YES")
-    message(STATUS "simmodsuite_dir = '${SIMMODSUITE_DIR}'")
-    get_target_property(liblist ${PUMI_LIBRARIES} INTERFACE_LINK_LIBRARIES)
-    set(pumi_dep_libs "${liblist}")
-    foreach(pumilib ${liblist})
-      get_target_property(libdeps ${pumilib} INTERFACE_LINK_LIBRARIES)
-      if (NOT "${libdeps}" MATCHES "libdeps-NOTFOUND")
-        list(APPEND pumi_dep_libs ${libdeps})
-      endif()
-    endforeach()
-    list(REMOVE_DUPLICATES pumi_dep_libs)
-    foreach(pumilib ${pumi_dep_libs})
-      unset(lib CACHE)
-      string(REGEX REPLACE "^SCOREC::" "" libname ${pumilib})
-      string(FIND "${pumilib}" ".a" staticlib)
-      string(FIND "${pumilib}" ".so" sharedlib)
-      find_library(lib ${libname} PATHS ${PUMI_DIR}/lib NO_DEFUALT_PATH)
-      if (NOT "${sharedlib}" MATCHES "-1" OR
-          NOT "${staticlib}" MATCHES "-1"   )
-        set(MFEM_EXT_LIBS "${pumilib} ${MFEM_EXT_LIBS}")
-      elseif (NOT "${lib}" MATCHES "lib-NOTFOUND")
-        set(MFEM_EXT_LIBS "${lib} ${MFEM_EXT_LIBS}")
-      elseif ("${lib}" MATCHES "lib-NOTFOUND" AND
-              NOT "${libname}" MATCHES "can" AND
-              NOT "${libname}" MATCHES "pthread")
-        message(FATAL_ERROR "SCOREC lib ${libname} not found")
-      endif()
-    endforeach()
-  endif()
-  # Define the variable 'MFEM_EXT_LIBS': handle other (not PUMI) libs
-  foreach(lib ${TPL_LIBRARIES})
-    get_filename_component(suffix ${lib} EXT)
-    # handle interfaces (e.g., SCOREC::apf)
-    if ("${lib}" MATCHES "SCOREC::.*" OR "${lib}" MATCHES "Ginkgo::.*")
-    elseif (NOT "${lib}" MATCHES "SCOREC::.*" AND "${lib}" MATCHES ".*::.*")
-      message(FATAL_ERROR "***** interface lib found ... exiting *****")
-      # handle static and shared libs
-    elseif ("${suffix}" STREQUAL "${CMAKE_SHARED_LIBRARY_SUFFIX}")
-      get_filename_component(dir ${lib} DIRECTORY)
-      get_filename_component(fullLibName ${lib} NAME_WE)
-      string(REGEX REPLACE "^lib" "" libname ${fullLibName})
-      set(MFEM_EXT_LIBS
-          "${MFEM_EXT_LIBS} ${shared_link_flag}${dir} -L${dir} -l${libname}")
-    else()
-      set(MFEM_EXT_LIBS "${MFEM_EXT_LIBS} ${lib}")
-    endif()
-  endforeach()
-
-  # Create the build-tree version of 'config.mk'
-  configure_file(
-    "${PROJECT_SOURCE_DIR}/config/config.mk.in"
-    "${PROJECT_BINARY_DIR}/config/config.mk")
-  # Copy 'test.mk' from the source-tree to the build-tree
-  configure_file(
-    "${PROJECT_SOURCE_DIR}/config/test.mk"
-    "${PROJECT_BINARY_DIR}/config/test.mk" COPYONLY)
-
-  # Update variables for the install-tree version of 'config.mk'
-  set(MFEM_INC_DIR "${CMAKE_INSTALL_PREFIX}/include")
-  set(MFEM_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib")
-  set(MFEM_TEST_MK "${CMAKE_INSTALL_PREFIX}/share/mfem/test.mk")
-  set(MFEM_CONFIG_EXTRA "")
-
-  # Create the install-tree version of 'config.mk'
-  configure_file(
-    "${PROJECT_SOURCE_DIR}/config/config.mk.in"
-    "${PROJECT_BINARY_DIR}/config/config-install.mk")
-
-  # Install rules for 'config.mk' and 'test.mk'
-  install(FILES ${PROJECT_SOURCE_DIR}/config/test.mk
-    DESTINATION ${CMAKE_INSTALL_PREFIX}/share/mfem/)
-  install(FILES ${PROJECT_BINARY_DIR}/config/config-install.mk
-    DESTINATION ${CMAKE_INSTALL_PREFIX}/share/mfem/ RENAME config.mk)
-
-endfunction()

config/config.hpp

@@ -10,31 +10,19 @@
 // Software Foundation) version 2.1 dated February 1999.
 
 
-// Support out-of-source builds: if MFEM_CONFIG_FILE is defined, include it.
+// Support out-of-source builds: if MFEM_BUILD_DIR is defined, load the config
+// file MFEM_BUILD_DIR/config/_config.hpp.
 //
 // Otherwise, use the local file: _config.hpp.
 
-#ifndef MFEM_CONFIG_HPP
-#define MFEM_CONFIG_HPP
-
-#ifdef MFEM_CONFIG_FILE
-#include MFEM_CONFIG_FILE
+#ifdef MFEM_BUILD_DIR
+#define MFEM_QUOTE(a) #a
+#define MFEM_MAKE_PATH(x,y) MFEM_QUOTE(x/y)
+#include MFEM_MAKE_PATH(MFEM_BUILD_DIR,config/_config.hpp)
 #else
 #include "_config.hpp"
 #endif
 
-// Common configuration macros
-
-#if (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 7)) || defined(__clang__)
-#define MFEM_HAVE_GCC_PRAGMA_DIAGNOSTIC
-#endif
-
-// Windows specific options
-#ifdef _WIN32
-// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
-#define _USE_MATH_DEFINES
-#endif
-
 // Check dependencies:
 
 // Options that require MPI
@@ -52,5 +40,3 @@
 #error Building with PUMI (MFEM_USE_PUMI=YES) requires MPI (MFEM_USE_MPI=YES)
 #endif
 #endif // MFEM_USE_MPI not defined
-
-#endif // MFEM_CONFIG_HPP

config/config.hpp.in

@@ -30,12 +30,6 @@
 #define MFEM_VERSION_MINOR (((MFEM_VERSION)/100)%100)
 #define MFEM_VERSION_PATCH ((MFEM_VERSION)%100)
 
-// The absolute path of the MFEM source prefix
-// #define MFEM_SOURCE_DIR "@MFEM_SOURCE_DIR@"
-
-// The absolute path of the MFEM installation prefix
-// #define MFEM_INSTALL_DIR "@MFEM_INSTALL_DIR@"
-
 // Description of the git commit used to build MFEM.
 // #define MFEM_GIT_STRING "@MFEM_GIT_STRING@"
 
@@ -68,12 +62,9 @@
 // allocation and de-allocation.
 // #define MFEM_THREAD_SAFE
 
-// Enable the OpenMP backend.
+// Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
 // #define MFEM_USE_OPENMP
 
-// [Deprecated] Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
-// #define MFEM_USE_LEGACY_OPENMP
-
 // Internal MFEM option: enable group/batch allocation for some small objects.
 // #define MFEM_USE_MEMALLOC
 
@@ -100,9 +91,6 @@
 // Enable functionality based on the Gecko library
 // #define MFEM_USE_GECKO
 
-// Enable MFEM features based on the Ginkgo library
-// #define MFEM_USE_GINKGO
-
 // Enable secure socket streams based on the GNUTLS library
 // #define MFEM_USE_GNUTLS
 
@@ -124,28 +112,11 @@
 // Enable MFEM functionality based on the PUMI library
 // #define MFEM_USE_PUMI
 
-// Enable MFEM functionality based on the HIOP library.
-// #define MFEM_USE_HIOP
-
-// Enable MFEM functionality based on the GSLIB library
-// #define MFEM_USE_GSLIB
-
-// Build the NVIDIA GPU/CUDA-enabled version of the MFEM library.
-// Requires a CUDA compiler (nvcc).
-// #define MFEM_USE_CUDA
-
-// Build the AMD GPU/HIP-enabled version of the MFEM library.
-// Requires a HIP compiler (hipcc).
-// #define MFEM_USE_HIP
-
-// Enable functionality based on the RAJA library.
-// #define MFEM_USE_RAJA
-
-// Enable functionality based on the OCCA library.
-// #define MFEM_USE_OCCA
-
-// Enable functionality based on the libCEED library.
-// #define MFEM_USE_CEED
+// Windows specific options
+#ifdef _WIN32
+// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
+#define _USE_MATH_DEFINES
+#endif
 
 // Version of HYPRE used for building MFEM.
 // #define MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@

config/config.mk.in

@@ -10,45 +10,34 @@
 # Software Foundation) version 2.1 dated February 1999.
 
 # Variables corresponding to defines in config.hpp (YES, NO, or value)
-MFEM_VERSION           = @MFEM_VERSION@
-MFEM_VERSION_STRING    = @MFEM_VERSION_STRING@
-MFEM_SOURCE_DIR        = @MFEM_SOURCE_DIR@
-MFEM_INSTALL_DIR       = @MFEM_INSTALL_DIR@
-MFEM_GIT_STRING        = @MFEM_GIT_STRING@
-MFEM_USE_MPI           = @MFEM_USE_MPI@
-MFEM_USE_METIS         = @MFEM_USE_METIS@
-MFEM_USE_METIS_5       = @MFEM_USE_METIS_5@
-MFEM_DEBUG             = @MFEM_DEBUG@
-MFEM_USE_EXCEPTIONS    = @MFEM_USE_EXCEPTIONS@
-MFEM_USE_GZSTREAM      = @MFEM_USE_GZSTREAM@
-MFEM_USE_LIBUNWIND     = @MFEM_USE_LIBUNWIND@
-MFEM_USE_LAPACK        = @MFEM_USE_LAPACK@
-MFEM_THREAD_SAFE       = @MFEM_THREAD_SAFE@
-MFEM_USE_LEGACY_OPENMP = @MFEM_USE_LEGACY_OPENMP@
-MFEM_USE_OPENMP        = @MFEM_USE_OPENMP@
-MFEM_USE_MEMALLOC      = @MFEM_USE_MEMALLOC@
-MFEM_TIMER_TYPE        = @MFEM_TIMER_TYPE@
-MFEM_USE_SUNDIALS      = @MFEM_USE_SUNDIALS@
-MFEM_USE_MESQUITE      = @MFEM_USE_MESQUITE@
-MFEM_USE_SUITESPARSE   = @MFEM_USE_SUITESPARSE@
-MFEM_USE_SUPERLU       = @MFEM_USE_SUPERLU@
-MFEM_USE_STRUMPACK     = @MFEM_USE_STRUMPACK@
-MFEM_USE_GECKO         = @MFEM_USE_GECKO@
-MFEM_USE_GINKGO        = @MFEM_USE_GINKGO@
-MFEM_USE_GNUTLS        = @MFEM_USE_GNUTLS@
-MFEM_USE_NETCDF        = @MFEM_USE_NETCDF@
-MFEM_USE_PETSC         = @MFEM_USE_PETSC@
-MFEM_USE_MPFR          = @MFEM_USE_MPFR@
-MFEM_USE_SIDRE         = @MFEM_USE_SIDRE@
-MFEM_USE_CONDUIT       = @MFEM_USE_CONDUIT@
-MFEM_USE_PUMI          = @MFEM_USE_PUMI@
-MFEM_USE_HIOP          = @MFEM_USE_HIOP@
-MFEM_USE_GSLIB         = @MFEM_USE_GSLIB@
-MFEM_USE_CUDA          = @MFEM_USE_CUDA@
-MFEM_USE_HIP           = @MFEM_USE_HIP@
-MFEM_USE_RAJA          = @MFEM_USE_RAJA@
-MFEM_USE_OCCA          = @MFEM_USE_OCCA@
-MFEM_USE_CEED          = @MFEM_USE_CEED@
+MFEM_VERSION         = @MFEM_VERSION@
+MFEM_VERSION_STRING  = @MFEM_VERSION_STRING@
+MFEM_GIT_STRING      = @MFEM_GIT_STRING@
+MFEM_USE_MPI         = @MFEM_USE_MPI@
+MFEM_USE_METIS       = @MFEM_USE_METIS@
+MFEM_USE_METIS_5     = @MFEM_USE_METIS_5@
+MFEM_DEBUG           = @MFEM_DEBUG@
+MFEM_USE_EXCEPTIONS  = @MFEM_USE_EXCEPTIONS@
+MFEM_USE_GZSTREAM    = @MFEM_USE_GZSTREAM@
+MFEM_USE_LIBUNWIND   = @MFEM_USE_LIBUNWIND@
+MFEM_USE_LAPACK      = @MFEM_USE_LAPACK@
+MFEM_THREAD_SAFE     = @MFEM_THREAD_SAFE@
+MFEM_USE_OPENMP      = @MFEM_USE_OPENMP@
+MFEM_USE_MEMALLOC    = @MFEM_USE_MEMALLOC@
+MFEM_TIMER_TYPE      = @MFEM_TIMER_TYPE@
+MFEM_USE_SUNDIALS    = @MFEM_USE_SUNDIALS@
+MFEM_USE_MESQUITE    = @MFEM_USE_MESQUITE@
+MFEM_USE_SUITESPARSE = @MFEM_USE_SUITESPARSE@
+MFEM_USE_SUPERLU     = @MFEM_USE_SUPERLU@
+MFEM_USE_STRUMPACK   = @MFEM_USE_STRUMPACK@
+MFEM_USE_GECKO       = @MFEM_USE_GECKO@
+MFEM_USE_GNUTLS      = @MFEM_USE_GNUTLS@
+MFEM_USE_NETCDF      = @MFEM_USE_NETCDF@
+MFEM_USE_PETSC       = @MFEM_USE_PETSC@
+MFEM_USE_MPFR        = @MFEM_USE_MPFR@
+MFEM_USE_SIDRE       = @MFEM_USE_SIDRE@
+MFEM_USE_CONDUIT     = @MFEM_USE_CONDUIT@
+MFEM_USE_PUMI        = @MFEM_USE_PUMI@
 
 # Compiler, compile options, and link options
 MFEM_CXX       = @MFEM_CXX@
@@ -76,8 +65,5 @@ MFEM_MPIEXEC    = @MFEM_MPIEXEC@
 MFEM_MPIEXEC_NP = @MFEM_MPIEXEC_NP@
 MFEM_MPI_NP     = @MFEM_MPI_NP@
 
-# The NVCC compiler cannot link with -x=cu
-MFEM_LINK_FLAGS := $(filter-out -x=cu, $(MFEM_FLAGS))
-
 # Optional extra configuration
 @MFEM_CONFIG_EXTRA@

config/defaults.cmake

@@ -26,8 +26,7 @@ option(MFEM_USE_GZSTREAM "Enable gzstream for compressed data streams." OFF)
 option(MFEM_USE_LIBUNWIND "Enable backtrace for errors." OFF)
 option(MFEM_USE_LAPACK "Enable LAPACK usage" OFF)
 option(MFEM_THREAD_SAFE "Enable thread safety" OFF)
-option(MFEM_USE_OPENMP "Enable the OpenMP backend" OFF)
-option(MFEM_USE_LEGACY_OPENMP "Enable legacy OpenMP usage" OFF)
+option(MFEM_USE_OPENMP "Enable OpenMP usage" OFF)
 option(MFEM_USE_MEMALLOC "Enable the internal MEMALLOC option." ON)
 option(MFEM_USE_SUNDIALS "Enable SUNDIALS usage" OFF)
 option(MFEM_USE_MESQUITE "Enable MESQUITE usage" OFF)
@@ -35,7 +34,6 @@ 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_GINKGO "Enable Ginkgo 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)
@@ -43,15 +41,6 @@ option(MFEM_USE_MPFR "Enable MPFR usage." OFF)
 option(MFEM_USE_SIDRE "Enable Axom/Sidre usage" OFF)
 option(MFEM_USE_CONDUIT "Enable Conduit usage" OFF)
 option(MFEM_USE_PUMI "Enable PUMI" OFF)
-option(MFEM_USE_HIOP "Enable HiOp" OFF)
-option(MFEM_USE_CUDA "Enable CUDA" OFF)
-option(MFEM_USE_OCCA "Enable OCCA" OFF)
-option(MFEM_USE_RAJA "Enable RAJA" OFF)
-option(MFEM_USE_CEED "Enable CEED" OFF)
-option(MFEM_USE_ADEPT "Enable AD using ADEPT"   OFF)
-option(MFEM_USE_CODIPACK "Enable AD using CoDiPack" OFF)
-
-set(MFEM_MPI_NP 4 CACHE STRING "Number of processes used for MPI tests")
 
 # Allow a user to disable testing, examples, and/or miniapps at CONFIGURE TIME
 # if they don't want/need them (e.g. if MFEM is "just a dependency" and all they
@@ -67,16 +56,13 @@ option(MFEM_ENABLE_MINIAPPS "Build all of the miniapps" OFF)
 # set(CXX g++)
 # set(MPICXX mpicxx)
 
-# Set the target CUDA architecture
-set(CUDA_ARCH "sm_60" CACHE STRING "Target CUDA architecture.")
-
 set(MFEM_DIR ${CMAKE_CURRENT_SOURCE_DIR})
 
 # The *_DIR paths below will be the first place searched for the corresponding
 # headers and library. If these fail, then standard cmake search is performed.
 # Note: if the variables are already in the cache, they are not overwritten.
 
-set(HYPRE_DIR "${MFEM_DIR}/../hypre/src/hypre" CACHE PATH
+set(HYPRE_DIR "${MFEM_DIR}/../hypre-2.10.0b/src/hypre" CACHE PATH
     "Path to the hypre library.")
 # If hypre was compiled to depend on BLAS and LAPACK:
 # set(HYPRE_REQUIRED_PACKAGES "BLAS" "LAPACK" CACHE STRING
@@ -86,7 +72,7 @@ set(METIS_DIR "${MFEM_DIR}/../metis-4.0" CACHE PATH "Path to the METIS library."
 
 set(LIBUNWIND_DIR "" CACHE PATH "Path to Libunwind.")
 
-set(SUNDIALS_DIR "${MFEM_DIR}/../sundials-5.0.0/instdir" CACHE PATH
+set(SUNDIALS_DIR "${MFEM_DIR}/../sundials-3.0.0" CACHE PATH
     "Path to the SUNDIALS library.")
 # The following may be necessary, if SUNDIALS was built with KLU:
 # set(SUNDIALS_REQUIRED_PACKAGES "SuiteSparse/KLU/AMD/BTF/COLAMD/config"
@@ -114,7 +100,6 @@ set(SuperLUDist_REQUIRED_PACKAGES "MPI" "BLAS" "ParMETIS" CACHE STRING
 set(STRUMPACK_DIR "${MFEM_DIR}/../STRUMPACK-build" CACHE PATH
     "Path to the STRUMPACK library.")
 # STRUMPACK may also depend on "OpenMP", depending on how it was compiled.
-# Starting with v2.2.0 of STRUMPACK, ParMETIS and Scotch are optional.
 set(STRUMPACK_REQUIRED_PACKAGES "MPI" "MPI_Fortran" "ParMETIS" "METIS"
     "ScaLAPACK" "Scotch/ptscotch/ptscotcherr/scotch/scotcherr" CACHE STRING
     "Additional packages required by STRUMPACK.")
@@ -122,8 +107,7 @@ set(STRUMPACK_REQUIRED_PACKAGES "MPI" "MPI_Fortran" "ParMETIS" "METIS"
 # set(STRUMPACK_REQUIRED_LIBRARIES "gfortran" "mpi_mpifh" CACHE STRING
 #     "Additional libraries required by STRUMPACK.")
 
-# The Scotch library, required by STRUMPACK <= v2.1.0, optional in STRUMPACK >=
-# v2.2.0.
+# The Scotch library, required by STRUMPACK
 set(Scotch_DIR "${MFEM_DIR}/../scotch_6.0.4" CACHE PATH
     "Path to the Scotch and PT-Scotch libraries.")
 set(Scotch_REQUIRED_PACKAGES "Threads" CACHE STRING
@@ -141,8 +125,6 @@ set(ScaLAPACK_TARGET_NAMES scalapack)
 
 set(GECKO_DIR "${MFEM_DIR}/../gecko" CACHE PATH "Path to the Gecko library.")
 
-set(Ginkgo_DIR "${MFEM_DIR}/../ginkgo" CACHE PATH "Path to the Ginkgo library.")
-
 set(GNUTLS_DIR "" CACHE PATH "Path to the GnuTLS library.")
 
 set(NETCDF_DIR "" CACHE PATH "Path to the NetCDF library.")
@@ -161,33 +143,17 @@ set(CONDUIT_DIR "${MFEM_DIR}/../conduit" CACHE PATH
 
 set(AXOM_DIR "${MFEM_DIR}/../axom" CACHE PATH "Path to the Axom library.")
 # May need to add "Boost" as requirement.
-set(Axom_REQUIRED_PACKAGES "Conduit/relay/blueprint" CACHE STRING
+set(Axom_REQUIRED_PACKAGES "Conduit/relay" CACHE STRING
     "Additional packages required by Axom.")
 
 set(PUMI_DIR "${MFEM_DIR}/../pumi-2.1.0" CACHE STRING
     "Directory where PUMI is installed")
 
-set(HIOP_DIR "${MFEM_DIR}/../hiop/install" CACHE STRING
-    "Directory where HiOp is installed")
-set(HIOP_REQUIRED_PACKAGES "BLAS" "LAPACK" CACHE STRING
-    "Packages that HiOp depends on.")
-
-set(OCCA_DIR "${MFEM_DIR}/../occa" CACHE PATH "Path to OCCA")
-set(RAJA_DIR "${MFEM_DIR}/../raja" CACHE PATH "Path to RAJA")
-set(CEED_DIR "${MFEM_DIR}/../libCEED" CACHE PATH "Path to libCEED")
-
 set(BLAS_INCLUDE_DIRS "" CACHE STRING "Path to BLAS headers.")
 set(BLAS_LIBRARIES "" CACHE STRING "The BLAS library.")
 set(LAPACK_INCLUDE_DIRS "" CACHE STRING "Path to LAPACK headers.")
 set(LAPACK_LIBRARIES "" CACHE STRING "The LAPACK library.")
 
-set(ADEPT_INCLUDE_DIRS "${MFEM_DIR}/../adept-1.1op/include" CACHE STRING "Path to ADEPT headers.")
-set(ADEPT_LIBRARIES    "-L${MFEM_DIR}/../adept-1.1op/lib -ladept" CACHE STRING "The ADEPT library.")
-
-set(CODIPACK_INCLUDE_DIRS "${MFEM_DIR}/../CoDiPack/include" CACHE STRING "Path to CoDiPack headers.")
-
-
-
 # Some useful variables:
 set(CMAKE_SKIP_PREPROCESSED_SOURCE_RULES ON) # Skip *.i rules
 set(CMAKE_SKIP_ASSEMBLY_SOURCE_RULES  ON)    # Skip *.s rules

config/defaults.mk

@@ -21,13 +21,8 @@ NOTMAC := $(subst Darwin,,$(shell uname -s))
 CXX = g++
 MPICXX = mpicxx
 
-BASE_FLAGS  = -std=c++11
-OPTIM_FLAGS = -O3 $(BASE_FLAGS)
-DEBUG_FLAGS = -g $(XCOMPILER)-Wall $(BASE_FLAGS)
-
-# Prefixes for passing flags to the compiler and linker when using CXX or MPICXX
-CXX_XCOMPILER =
-CXX_XLINKER   = -Wl,
+OPTIM_FLAGS = -O3
+DEBUG_FLAGS = -g -Wall
 
 # Destination location of make install
 # PREFIX = $(HOME)/mfem
@@ -38,49 +33,33 @@ INSTALL = /usr/bin/install
 STATIC = YES
 SHARED = NO
 
-# CUDA configuration options
-CUDA_CXX = nvcc
-CUDA_ARCH = sm_60
-CUDA_FLAGS = -x=cu --expt-extended-lambda -arch=$(CUDA_ARCH)
-# Prefixes for passing flags to the host compiler and linker when using CUDA_CXX
-CUDA_XCOMPILER = -Xcompiler=
-CUDA_XLINKER   = -Xlinker=
-
-# HIP configuration options
-HIP_CXX = hipcc
-# The HIP_ARCH option specifies the AMD GPU processor, similar to CUDA_ARCH. For
-# example: gfx600 (tahiti), gfx700 (kaveri), gfx701 (hawaii), gfx801 (carrizo),
-# gfx900, gfx1010, etc.
-HIP_ARCH = gfx900
-HIP_FLAGS = --amdgpu-target=$(HIP_ARCH)
-
 ifneq ($(NOTMAC),)
    AR      = ar
    ARFLAGS = cruv
    RANLIB  = ranlib
-   PICFLAG = $(XCOMPILER)-fPIC
+   PICFLAG = -fPIC
    SO_EXT  = so
    SO_VER  = so.$(MFEM_VERSION_STRING)
-   BUILD_SOFLAGS = -shared $(XLINKER)-soname,libmfem.$(SO_VER)
-   BUILD_RPATH = $(XLINKER)-rpath,$(BUILD_REAL_DIR)
+   BUILD_SOFLAGS = -shared -Wl,-soname,libmfem.$(SO_VER)
+   BUILD_RPATH = -Wl,-rpath,$(BUILD_REAL_DIR)
    INSTALL_SOFLAGS = $(BUILD_SOFLAGS)
-   INSTALL_RPATH = $(XLINKER)-rpath,@MFEM_LIB_DIR@
+   INSTALL_RPATH = -Wl,-rpath,@MFEM_LIB_DIR@
 else
    # Silence "has no symbols" warnings on Mac OS X
    AR      = ar
    ARFLAGS = Scruv
    RANLIB  = ranlib -no_warning_for_no_symbols
-   PICFLAG = $(XCOMPILER)-fPIC
+   PICFLAG = -fPIC
    SO_EXT  = dylib
    SO_VER  = $(MFEM_VERSION_STRING).dylib
-   MAKE_SOFLAGS = $(XLINKER)-dylib,-install_name,$(1)/libmfem.$(SO_VER),\
+   MAKE_SOFLAGS = -Wl,-dylib,-install_name,$(1)/libmfem.$(SO_VER),\
       -compatibility_version,$(MFEM_VERSION_STRING),\
       -current_version,$(MFEM_VERSION_STRING),\
       -undefined,dynamic_lookup
    BUILD_SOFLAGS = $(subst $1 ,,$(call MAKE_SOFLAGS,$(BUILD_REAL_DIR)))
-   BUILD_RPATH = $(XLINKER)-undefined,dynamic_lookup
+   BUILD_RPATH = -Wl,-undefined,dynamic_lookup
    INSTALL_SOFLAGS = $(subst $1 ,,$(call MAKE_SOFLAGS,$(MFEM_LIB_DIR)))
-   INSTALL_RPATH = $(XLINKER)-undefined,dynamic_lookup
+   INSTALL_RPATH = -Wl,-undefined,dynamic_lookup
 endif
 
 # Set CXXFLAGS to overwrite the default selection of DEBUG_FLAGS/OPTIM_FLAGS
@@ -103,40 +82,31 @@ MFEM_MPI_NP = 4
 # config.hpp. The values below are the defaults for generating the actual values
 # in config.mk and config.hpp.
 
-MFEM_USE_MPI           = NO
-MFEM_USE_METIS         = $(MFEM_USE_MPI)
-MFEM_USE_METIS_5       = NO
-MFEM_DEBUG             = NO
-MFEM_USE_EXCEPTIONS    = NO
-MFEM_USE_GZSTREAM      = NO
-MFEM_USE_LIBUNWIND     = NO
-MFEM_USE_LAPACK        = NO
-MFEM_THREAD_SAFE       = NO
-MFEM_USE_OPENMP        = NO
-MFEM_USE_LEGACY_OPENMP = NO
-MFEM_USE_MEMALLOC      = YES
-MFEM_TIMER_TYPE        = $(if $(NOTMAC),2,4)
-MFEM_USE_SUNDIALS      = NO
-MFEM_USE_MESQUITE      = NO
-MFEM_USE_SUITESPARSE   = NO
-MFEM_USE_SUPERLU       = NO
-MFEM_USE_STRUMPACK     = NO
-MFEM_USE_GECKO         = NO
-MFEM_USE_GINKGO        = NO
-MFEM_USE_GNUTLS        = NO
-MFEM_USE_NETCDF        = NO
-MFEM_USE_PETSC         = NO
-MFEM_USE_MPFR          = NO
-MFEM_USE_SIDRE         = NO
-MFEM_USE_CONDUIT       = NO
-MFEM_USE_PUMI          = NO
-MFEM_USE_HIOP          = NO
-MFEM_USE_GSLIB         = NO
-MFEM_USE_CUDA          = NO
-MFEM_USE_HIP           = NO
-MFEM_USE_RAJA          = NO
-MFEM_USE_OCCA          = NO
-MFEM_USE_CEED          = NO
+MFEM_USE_MPI         = NO
+MFEM_USE_METIS       = $(MFEM_USE_MPI)
+MFEM_USE_METIS_5     = NO
+MFEM_DEBUG           = NO
+MFEM_USE_EXCEPTIONS  = NO
+MFEM_USE_GZSTREAM    = NO
+MFEM_USE_LIBUNWIND   = NO
+MFEM_USE_LAPACK      = NO
+MFEM_THREAD_SAFE     = NO
+MFEM_USE_OPENMP      = NO
+MFEM_USE_MEMALLOC    = YES
+MFEM_TIMER_TYPE      = $(if $(NOTMAC),2,4)
+MFEM_USE_SUNDIALS    = NO
+MFEM_USE_MESQUITE    = NO
+MFEM_USE_SUITESPARSE = NO
+MFEM_USE_SUPERLU     = NO
+MFEM_USE_STRUMPACK   = NO
+MFEM_USE_GECKO       = NO
+MFEM_USE_GNUTLS      = NO
+MFEM_USE_NETCDF      = NO
+MFEM_USE_PETSC       = NO
+MFEM_USE_MPFR        = NO
+MFEM_USE_SIDRE       = NO
+MFEM_USE_CONDUIT     = NO
+MFEM_USE_PUMI        = NO
 
 # Compile and link options for zlib.
 ZLIB_DIR =
@@ -148,7 +118,7 @@ LIBUNWIND_OPT = -g
 LIBUNWIND_LIB = $(if $(NOTMAC),-lunwind -ldl,)
 
 # HYPRE library configuration (needed to build the parallel version)
-HYPRE_DIR = @MFEM_DIR@/../hypre/src/hypre
+HYPRE_DIR = @MFEM_DIR@/../hypre-2.10.0b/src/hypre
 HYPRE_OPT = -I$(HYPRE_DIR)/include
 HYPRE_LIB = -L$(HYPRE_DIR)/lib -lHYPRE
 
@@ -166,8 +136,6 @@ ifeq ($(MFEM_USE_SUPERLU)$(MFEM_USE_STRUMPACK),NONO)
 else
    # ParMETIS: currently needed by SuperLU or STRUMPACK. We assume that METIS 5
    # (included with ParMETIS) is installed in the same location.
-   # Starting with STRUMPACK v2.2.0, ParMETIS is an optional dependency while
-   # METIS is still required.
    METIS_DIR = @MFEM_DIR@/../parmetis-4.0.3
    METIS_OPT = -I$(METIS_DIR)/include
    METIS_LIB = -L$(METIS_DIR)/lib -lparmetis -lmetis
@@ -179,16 +147,16 @@ LAPACK_OPT =
 LAPACK_LIB = $(if $(NOTMAC),-llapack -lblas,-framework Accelerate)
 
 # OpenMP configuration
-OPENMP_OPT = $(XCOMPILER)-fopenmp
+OPENMP_OPT = -fopenmp
 OPENMP_LIB =
 
 # Used when MFEM_TIMER_TYPE = 2
 POSIX_CLOCKS_LIB = -lrt
 
 # SUNDIALS library configuration
-SUNDIALS_DIR = @MFEM_DIR@/../sundials-5.0.0/instdir
+SUNDIALS_DIR = @MFEM_DIR@/../sundials-3.0.0
 SUNDIALS_OPT = -I$(SUNDIALS_DIR)/include
-SUNDIALS_LIB = -Wl,-rpath,$(SUNDIALS_DIR)/lib64 -L$(SUNDIALS_DIR)/lib64\
+SUNDIALS_LIB = -Wl,-rpath,$(SUNDIALS_DIR)/lib -L$(SUNDIALS_DIR)/lib\
  -lsundials_arkode -lsundials_cvode -lsundials_nvecserial -lsundials_kinsol
 
 ifeq ($(MFEM_USE_MPI),YES)
@@ -213,10 +181,9 @@ SUITESPARSE_LIB = -Wl,-rpath,$(SUITESPARSE_DIR)/lib -L$(SUITESPARSE_DIR)/lib\
 # SuperLU library configuration
 SUPERLU_DIR = @MFEM_DIR@/../SuperLU_DIST_5.1.0
 SUPERLU_OPT = -I$(SUPERLU_DIR)/SRC
-SUPERLU_LIB = -Wl,-rpath,$(SUPERLU_DIR)/lib -L$(SUPERLU_DIR)/lib -lsuperlu_dist_5.1.0
+SUPERLU_LIB = -Wl,-rpath,$(SUPERLU_DIR)/SRC -L$(SUPERLU_DIR)/SRC -lsuperlu_dist
 
-# SCOTCH library configuration (required by STRUMPACK <= v2.1.0, optional in
-# STRUMPACK >= v2.2.0)
+# SCOTCH library configuration (required by STRUMPACK)
 SCOTCH_DIR = @MFEM_DIR@/../scotch_6.0.4
 SCOTCH_OPT = -I$(SCOTCH_DIR)/include
 SCOTCH_LIB = -L$(SCOTCH_DIR)/lib -lptscotch -lptscotcherr -lscotch -lscotcherr\
@@ -248,11 +215,6 @@ GECKO_DIR = @MFEM_DIR@/../gecko
 GECKO_OPT = -I$(GECKO_DIR)/inc
 GECKO_LIB = -L$(GECKO_DIR)/lib -lgecko
 
-# Ginkgo library configuration (currently not needed)
-GINKGO_DIR = @MFEM_DIR@/../ginkgo/install
-GINKGO_OPT = -isystem $(GINKGO_DIR)/include
-GINKGO_LIB = $(XLINKER)-rpath,$(GINKGO_DIR)/lib -L$(GINKGO_DIR)/lib -lginkgo -lginkgo_omp -lginkgo_cuda -lginkgo_reference
-
 # GnuTLS library configuration
 GNUTLS_OPT =
 GNUTLS_LIB = -lgnutls
@@ -308,7 +270,7 @@ SIDRE_LIB = \
    -Wl,-rpath,$(SIDRE_DIR)/lib -L$(SIDRE_DIR)/lib \
    -Wl,-rpath,$(CONDUIT_DIR)/lib -L$(CONDUIT_DIR)/lib \
    -Wl,-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib \
-   -laxom -lconduit -lconduit_relay -lconduit_blueprint -lhdf5 $(ZLIB_LIB) -ldl
+   -lsidre -lslic -laxom_utils -lconduit -lconduit_relay -lhdf5 $(ZLIB_LIB) -ldl
 
 # PUMI
 # Note that PUMI_DIR is needed -- it is used to check for gmi_sim.h
@@ -317,42 +279,6 @@ PUMI_OPT = -I$(PUMI_DIR)/include
 PUMI_LIB = -L$(PUMI_DIR)/lib -lpumi -lcrv -lma -lmds -lapf -lpcu -lgmi -lparma\
    -llion -lmth -lapf_zoltan -lspr
 
-# HIOP
-HIOP_DIR = @MFEM_DIR@/../hiop/install
-HIOP_OPT = -I$(HIOP_DIR)/include
-HIOP_LIB = -L$(HIOP_DIR)/lib -lhiop $(LAPACK_LIB)
-
-# GSLIB library
-GSLIB_DIR = @MFEM_DIR@/../gslib/build
-GSLIB_OPT = -I$(GSLIB_DIR)/include
-GSLIB_LIB = -L$(GSLIB_DIR)/lib -lgs
-
-# CUDA library configuration (currently not needed)
-CUDA_OPT =
-CUDA_LIB =
-
-# HIP library configuration (currently not needed)
-HIP_OPT =
-HIP_LIB =
-
-# OCCA library configuration
-OCCA_DIR = @MFEM_DIR@/../occa
-OCCA_OPT = -I$(OCCA_DIR)/include
-OCCA_LIB = $(XLINKER)-rpath,$(OCCA_DIR)/lib -L$(OCCA_DIR)/lib -locca
-
-# libCEED library configuration
-CEED_DIR ?= @MFEM_DIR@/../libCEED
-CEED_OPT = -I$(CEED_DIR)/include
-CEED_LIB = $(XLINKER)-rpath,$(CEED_DIR)/lib -L$(CEED_DIR)/lib -lceed
-
-# RAJA library configuration
-RAJA_DIR = @MFEM_DIR@/../raja
-RAJA_OPT = -I$(RAJA_DIR)/include
-ifdef CUB_DIR
-   RAJA_OPT += -I$(CUB_DIR)
-endif
-RAJA_LIB = $(XLINKER)-rpath,$(RAJA_DIR)/lib -L$(RAJA_DIR)/lib -lRAJA
-
 # If YES, enable some informational messages
 VERBOSE = NO
 

config/makefile

@@ -36,7 +36,6 @@ CONFIG_MK = config.mk
 all: header config-mk
 
 MPI = $(MFEM_USE_MPI:NO=)
-GHV_CXX ?= $(MFEM_CXX)
 GHV = get_hypre_version
 GHV_FLAGS = $(subst @MFEM_DIR@,$(if $(MFEM_DIR),$(MFEM_DIR),..),$(HYPRE_OPT))
 SMX = $(if $(MFEM_USE_PUMI:NO=),MFEM_USE_SIMMETRIX)
@@ -45,7 +44,7 @@ SMX_FILE = $(subst @MFEM_DIR@,$(if $(MFEM_DIR),$(MFEM_DIR),..),$(SMX_PATH))
 
 $(GHV): $(SRC)$(GHV).cpp
 	$(call mfem-info, Determining HYPRE version ...)
-	$(GHV_CXX) ${GHV_FLAGS} $(SRC)$(GHV).cpp -o $(GHV)
+	$(MFEM_CXX) ${GHV_FLAGS} $(SRC)$(GHV).cpp -o $(GHV)
 $(GHV).out: $(GHV)
 	./$(GHV) > $(GHV).out
 .INTERMEDIATE: $(GHV) $(GHV).out

config/sample-runs.sh

@@ -18,8 +18,6 @@ run_prefix=""
 run_vg="valgrind --leak-check=full --show-reachable=yes --track-origins=yes"
 run_suffix="-no-vis"
 skip_gen_meshes="yes"
-# filter-out device runs ("no") or non-device runs ("yes"):
-device_runs="no"
 cur_dir="${PWD}"
 mfem_dir="$(cd "$(dirname "$0")"/.. && pwd)"
 mfem_build_dir=""
@@ -32,7 +30,7 @@ groups_serial=(
 '"examples"
    "Examples:"
    "examples"
-   "ex{,1,2}[0-9].cpp"'
+   "ex{,1}[0-9].cpp"'
 #   "ex1.cpp"'
 '"sundials"
    "SUNDIALS examples:"
@@ -46,15 +44,14 @@ groups_serial=(
 '"meshing"
    "Meshing miniapps:"
    "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
-    mesh-optimizer.cpp"'
+   "mobius-strip.cpp klein-bottle.cpp mesh-optimizer.cpp"'
 )
 # Parallel groups
 groups_parallel=(
 '"examples"
    "Examples:"
    "examples"
-   "ex{,1,2}[0-9]p.cpp"'
+   "ex{,1}[0-9]p.cpp"'
 #   "ex1p.cpp"'
 '"sundials"
    "SUNDIALS examples:"
@@ -84,7 +81,7 @@ groups_all=(
 '"examples"
    "Examples:"
    "examples"
-   "ex\"{,1,2}[0-9]\"{,p}.cpp"'
+   "ex\"{,1}[0-9]\"{,p}.cpp"'
 '"sundials"
    "SUNDIALS examples:"
    "examples/sundials"
@@ -100,8 +97,7 @@ groups_all=(
 '"meshing"
    "Meshing miniapps:"
    "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
-    {,p}mesh-optimizer.cpp"'
+   "mobius-strip.cpp klein-bottle.cpp {,p}mesh-optimizer.cpp"'
 '"electromagnetics"
    "Electromagnetics miniapps:"
    "miniapps/electromagnetics"
@@ -150,20 +146,6 @@ function extract_sample_runs()
    if [ "$skip_gen_meshes" == "yes" ]; then
       runs=`printf "%s" "$runs" | grep -v ".* -m .*\.gen"`
    fi
-   if [ "$device_runs" == "yes" ]; then
-      runs=`printf "%s" "$runs" | grep ".* -d .*"`
-      if [ "$have_occa" == "no" ]; then
-         runs=`printf "%s" "$runs" | grep -v ".* -d occa-.*"`
-      fi
-      if [ "$have_raja" == "no" ]; then
-         runs=`printf "%s" "$runs" | grep -v ".* -d raja-.*"`
-      fi
-      if [ "$have_ceed" == "no" ]; then
-         runs=`printf "%s" "$runs" | grep -v ".* -d ceed-.*"`
-      fi
-   else
-      runs=`printf "%s" "$runs" | grep -v ".* -d .*"`
-   fi
    IFS=$'\n'
    runs=(${runs})
    IFS="${old_IFS}"
@@ -185,15 +167,9 @@ function help_message()
       -g <dir> <pattern>
                   Specify explicitly a group (dir + file pattern) to run; This
                   option can be used multiple times to define multiple groups
-      -dev        configure only sample runs using devices.
-                  To test with a parallel build, the parallel (-p|-par) option
-                  should be set first on the command line.
       -v          Enable valgrind
       -o <dir>    [${output_dir:-"<empty>: output goes to stdout"}]
                   If not empty, save output to files inside <dir>
-      -d <dir>    [${mfem_build_dir}]
-                  If <dir> is different from <mfem_dir> then use an
-                  out-of-source build in <dir>
       -j <np>     [${make_j}] Specify the number of jobs to use for building
       -c|-color   Always use colors for the status messages: OK, FAILED, etc
       -b|-built   Do NOT rebuild the library and the executables
@@ -220,8 +196,8 @@ function help_message()
          Their values can also set using the respective uppercase environment
          variable
       mfem_build_dir [${mfem_build_dir}]
-         Same as '-d': set this variable to something different from <mfem_dir>
-         to use an out-of-source build
+         Set this variable to something different from <mfem_dir> to use an
+         out-of-source build
 
    For other valid variables, see the script source.
 
@@ -272,7 +248,7 @@ case "$1" in
    -h|-help)
       opt_help="yes"
       ;;
-   -p|-par)
+   -p|-parallel)
       mfem_config="MFEM_USE_MPI=YES MFEM_DEBUG=NO"
       ;;
    -g)
@@ -283,11 +259,6 @@ case "$1" in
       groups=("${groups[@]}" "${test_group}")
       shift 2
       ;;
-   -dev)
-       device_runs="yes"
-       mfem_config+=" MFEM_USE_CUDA=YES MFEM_USE_OPENMP=YES"
-       # OCCA, RAJA, libCEED are enabled below, if available
-      ;;
    -v)
       valgrind="yes"
       ;;
@@ -295,10 +266,6 @@ case "$1" in
       shift
       output_dir="$1"
       ;;
-   -d)
-      shift
-      mfem_build_dir="$1"
-      ;;
    -j)
       shift
       make_j="-j $1"
@@ -318,10 +285,6 @@ case "$1" in
    -n)
       run_prefix="echo"
       ;;
-   -*)
-      echo "unknown option: '$1'"
-      exit 1
-      ;;
    *=*)
       eval $1
       ;;
@@ -467,30 +430,6 @@ fi
 
 TIMEFORMAT="${base_timeformat}"
 
-# Setup optional libraries when not using externally built MFEM:
-if [ "${built}" == "no" ]; then
-   have_occa="no"
-   have_raja="no"
-   have_ceed="no"
-   if [ "${device_runs}" == "yes" ]; then
-      if [ -n "${CUDA_ARCH}" ]; then
-         mfem_config+=" CUDA_ARCH=${CUDA_ARCH}"
-      fi
-      if [ -d "${mfem_dir}/../occa" ]; then
-         mfem_config+=" MFEM_USE_OCCA=YES"
-         have_occa="yes"
-      fi
-      if [ -d "${mfem_dir}/../raja" ]; then
-         mfem_config+=" MFEM_USE_RAJA=YES"
-         have_raja="yes"
-      fi
-      if [ -d "${mfem_dir}/../libCEED" ]; then
-         mfem_config+=" MFEM_USE_CEED=YES"
-         have_ceed="yes"
-      fi
-   fi
-fi
-
 function set_echo_log()
 {
    local dirname=`dirname "$1"`

config/tconfig.hpp

@@ -43,14 +43,15 @@
 #define MFEM_ALIGN_SIZE(size,type) \
    MFEM_ROUNDUP(size,(MFEM_SIMD_SIZE)/sizeof(type))
 
-#ifdef MFEM_COUNT_FLOPS
 namespace mfem
 {
 namespace internal
 {
-extern long long flop_count;
+long long flop_count;
 }
 }
+
+#ifdef MFEM_COUNT_FLOPS
 #define MFEM_FLOPS_RESET() (mfem::internal::flop_count = 0)
 #define MFEM_FLOPS_ADD(cnt) (mfem::internal::flop_count += (cnt))
 #define MFEM_FLOPS_GET() (mfem::internal::flop_count)

config/test.mk

@@ -38,7 +38,7 @@ export TIME='%es %MkB %x'; \
 set -- $$($(1) $(SHELL) -c "$(2)" 2>&1); while [ "$$#" -gt 3 ]; do shift; done
 endef
 define TIMECMD.NOTGNU
-set -- $$($(1) -l $(SHELL) -c "{ $(2); } > /dev/null 2>&1" 2>&1; echo $$?); \
+set -- $$($(1) -l $(SHELL) -c "$(2)" 2>&1; echo $$?); \
 set -- "$$1"s "$$(($$7/1024))"kB "$${60}"
 endef
 define TIMECMD.BASH
@@ -60,8 +60,7 @@ endif
 # Test runs of the examples/miniapps with parameters - check exit code
 mfem-test = \
    printf "   $(3) [$(2) $(1) ... ]: "; \
-   $(call $(TIMEFUN),$(TIMECMD),$(2) ./$(1) $(if $(5),,-no-vis )$(4) \
-     > $(1).stderr 2>&1); \
+   $(call $(TIMEFUN),$(TIMECMD),$(2) ./$(1) -no-vis $(4) > $(1).stderr 2>&1); \
    if [ "$$3" = 0 ]; \
    then $(PRINT_OK); else $(PRINT_FAILED); cat $(1).stderr; fi; \
    rm -f $(1).stderr; exit $$3
@@ -82,7 +81,6 @@ test-par-NO:  $(SEQ_$(MFEM_TESTS):=-test-seq)
 test-ser:     test-par-NO
 test-par:     test-par-YES
 test:         all test-par-$(MFEM_USE_MPI) clean-exec
-test-noclean: all test-par-$(MFEM_USE_MPI)
 test-clean: ; @rm -f *.stderr
 test-print: mfem-test=printf "   $(3) [$(2) ./$(1) -no-vis $(if $(4),$(4) )]\n"
 test-print: mfem-test-file=printf "   $(3) [$(2) ./$(1) -no-vis ]\n"

data/beam-wedge.mesh

@@ -1,87 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-#
-
-dimension
-3
-
-elements
-8
-1 6  0  9 18  1 10 19
-1 6  1 10 19  2 11 20
-1 6  2 11 20  3 12 21
-1 6  3 12 21  4 13 22
-2 6  4 13 22  5 14 23
-2 6  5 14 23  6 15 24
-2 6  6 15 24  7 16 25
-2 6  7 16 25  8 17 26
-
-boundary
-26
-1 2  0 18  9
-2 2  8 17 26
-3 3  0  9 10  1
-3 3  1 10 11  2
-3 3  2 11 12  3
-3 3  3 12 13  4
-3 3  4 13 14  5
-3 3  5 14 15  6
-3 3  6 15 16  7
-3 3  7 16 17  8
-3 3 18  0  1 19
-3 3 19  1  2 20
-3 3 20  2  3 21
-3 3 21  3  4 22
-3 3 22  4  5 23
-3 3 23  5  6 24
-3 3 24  6  7 25
-3 3 25  7  8 26
-3 3  9 18 19 10
-3 3 10 19 20 11
-3 3 11 20 21 12
-3 3 12 21 22 13
-3 3 13 22 23 14
-3 3 14 23 24 15
-3 3 15 24 25 16
-3 3 16 25 26 17
-
-vertices
-27
-3
-0 0 0
-1 0 0
-2 0 0
-3 0 0
-4 0 0
-5 0 0
-6 0 0
-7 0 0
-8 0 0
-0 1 0
-1 1 0
-2 1 0
-3 1 0
-4 1 0
-5 1 0
-6 1 0
-7 1 0
-8 1 0
-0 0.5 1
-1 0.5 1
-2 0.5 1
-3 0.5 1
-4 0.5 1
-5 0.5 1
-6 0.5 1
-7 0.5 1
-8 0.5 1

data/beam-wedge.vtk

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

data/fichera-mixed-p2.mesh

@@ -1,192 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-#
-
-dimension
-3
-
-elements
-14
-1 4 13 15 21 25
-1 4 15 13 21 12
-1 4 21 13 25 22
-1 4 15 21 25 24
-1 4 13 15 25 16
-1 5 0 1 4 3 9 10 13 12
-1 5 8 9 12 11 17 18 21 20
-1 5 2 3 6 5 11 12 15 14
-1 6 3 4 6 12 13 15
-1 6 4 7 6 13 16 15
-1 6 12 13 21 9 10 18
-1 6 13 22 21 10 19 18
-1 6 11 14 20 12 15 21
-1 6 15 21 24 14 20 23
-
-boundary
-30
-1 3 5 6 3 2
-2 2 6 4 3
-2 2 4 6 7
-3 3 3 4 1 0
-4 3 11 12 9 8
-5 3 2 3 12 11
-6 3 0 1 10 9
-7 2 10 18 9
-7 2 18 10 19
-8 3 8 9 18 17
-9 3 1 4 13 10
-10 3 4 7 16 13
-11 2 25 13 16
-11 2 13 25 22
-12 3 10 13 22 19
-13 3 7 6 15 16
-14 3 6 5 14 15
-15 3 15 14 23 24
-16 2 15 25 16
-16 2 25 15 24
-17 3 5 2 11 14
-18 3 3 0 9 12
-19 3 11 8 17 20
-20 2 20 14 11
-20 2 14 20 23
-21 3 17 18 21 20
-22 3 18 19 22 21
-23 2 25 21 22
-23 2 21 25 24
-24 3 20 21 24 23
-
-vertices
-26
-
-nodes
-FiniteElementSpace
-FiniteElementCollection: H1_3D_P2
-VDim: 3
-Ordering: 1
-
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data/fichera-mixed-p2.vtk

@@ -1,168 +0,0 @@
-# vtk DataFile Version 3.0
-Generated by MFEM
-ASCII
-DATASET UNSTRUCTURED_GRID
-POINTS 116 double
-0.028213666146621 -1.0129124616273 -1.0197422793601
-0.99151103207842 -0.97408353323117 -1.0219424221199
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data/fichera.mesh

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

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data/mixed-ele-meshes/circInSquare.py

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+#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

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

@@ -0,0 +1,72 @@
+MFEM mesh v1.0
+
+#
+# MFEM Geometry Types (see mesh/geom.hpp):
+#
+# POINT       = 0
+# SEGMENT     = 1
+# TRIANGLE    = 2
+# SQUARE      = 3
+# TETRAHEDRON = 4
+# CUBE        = 5
+#
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data/mixed-ele-meshes/spec-3-trans-and-ref.mesh

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

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--0.833493 -0.78864741 0.20555815
--0.89772824 -0.84942651 -0.091392579
-0.5 -0.8660254 -5.1344633e-17
--0.22302379 -0.93496814 -0.24998909
--0.17361359 -0.72782894 -0.024929133
-0.19781075 -0.82926913 -0.20555815
-0.17729212 -0.74325022 0.091392579
--0.1862948 -0.78099155 0.15859651
--0.25622363 -1.0741497 0.23048728
-0.20782931 -0.87126929 0.23048728
-0.27775814 -1.1644274 0.15859651
--0.28676082 -1.2021687 0.091392579
--0.26624219 -1.1161498 -0.20555815
-0.29043935 -1.21759 -0.024929133
-0.24102914 -1.0104508 -0.24998909
-0.55502751 -0.52516459 -0.091392579
-0.61926276 -0.5859437 0.20555815
-0.71712515 -0.2135607 0.024929133
-0.92121806 -0.2743398 0.24998909
-0.75456149 -0.71396276 0.24998909
-0.9092442 -0.86032286 0.024929133
-1.0997352 -0.32750241 0.20555815
-1.1844891 -0.35274221 -0.091392579
-0.86954463 -0.8227593 -0.15859651
-0.65062668 -0.6156201 -0.23048728
-1.0583527 -0.31517866 -0.23048728
-0.76950592 -0.22915975 -0.15859651
-0.95840435 0.28541392 -1.3795119e-16
-0.72637788 0.68729555 -1.1412456e-16
-0.23202647 0.97270947 -5.1760042e-17
--0.23202647 0.97270947 1.2226691e-17
--0.72637788 0.68729555 8.6191148e-17
--0.95840435 0.28541392 1.2635125e-16
--0.95840435 -0.28541392 1.3795119e-16
--0.72637788 -0.68729555 1.1412456e-16
--0.23202647 -0.97270947 5.1760042e-17
-0.23202647 -0.97270947 -1.2226691e-17
-0.72637788 -0.68729555 -8.6191148e-17
-0.95840435 -0.28541392 -1.2635125e-16

doc/CodeDocumentation.conf.in

@@ -38,7 +38,7 @@ PROJECT_NAME           = "MFEM"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v4.0.1
+PROJECT_NUMBER         = v3.4.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -768,13 +768,11 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/examples \
                          @MFEM_SOURCE_DIR@/examples/petsc \
                          @MFEM_SOURCE_DIR@/examples/pumi \
-                         @MFEM_SOURCE_DIR@/examples/hiop \
                          @MFEM_SOURCE_DIR@/examples/sundials \
                          @MFEM_SOURCE_DIR@/miniapps/common \
                          @MFEM_SOURCE_DIR@/miniapps/meshing \
                          @MFEM_SOURCE_DIR@/miniapps/tools \
                          @MFEM_SOURCE_DIR@/miniapps/nurbs \
-                         @MFEM_SOURCE_DIR@/miniapps/gslib \
                          @MFEM_SOURCE_DIR@/miniapps/electromagnetics \
                          @MFEM_SOURCE_DIR@/miniapps/performance
 

doc/CodeDocumentation.dox

@@ -35,12 +35,6 @@ namespace mfem {
  * - HypreParMatrix and HypreParVector
  * - HypreSolver and other \link hypre.hpp hypre classes\endlink
  *
- * <H3>Main GPU classes</H3>
- * - Device
- * - Memory
- * - MemoryManager
- * - MFEM_FORALL macro in forall.hpp
- *
  * <H3>Example codes</H3>
  * - <a class="el" href="examples_2ex1_8cpp_source.html">Example 1</a>: nodal H1 FEM for the Laplace problem
  * - <a class="el" href="examples_2ex1p_8cpp_source.html">Example 1p</a>: parallel nodal H1 FEM for the Laplace problem
@@ -77,12 +71,6 @@ namespace mfem {
  * - <a class="el" href="ex18p_8cpp_source.html">Example 18p</a>: parallel Discontinuous Galerkin (DG) for the Euler equations
  * - <a class="el" href="ex19_8cpp_source.html">Example 19</a>: incompressible nonlinear elasticity
  * - <a class="el" href="ex19p_8cpp_source.html">Example 19p</a>: parallel incompressible nonlinear elasticity
- * - <a class="el" href="ex20_8cpp_source.html">Example 20</a>: symplectic ODE integration
- * - <a class="el" href="ex20p_8cpp_source.html">Example 20p</a>: parallel symplectic ODE integration
- * - <a class="el" href="ex21_8cpp_source.html">Example 21</a>: adaptive mesh refinement for linear elasticity
- * - <a class="el" href="ex21p_8cpp_source.html">Example 21p</a>: parallel adaptive mesh refinement for linear elasticity
- * - <a class="el" href="ex22_8cpp_source.html">Example 22</a>: complex-valued linear systems for damped harmonic oscillators
- * - <a class="el" href="ex22p_8cpp_source.html">Example 22p</a>: parallel complex-valued linear systems for damped harmonic oscillators
  *
  * <H4>SUNDIALS Examples</H4>
  * - Variants of Examples
@@ -117,12 +105,6 @@ namespace mfem {
  *   <a class="el" href="pumi_2ex6p_8cpp_source.html">6p</a>
  *   demonstrating the use of MFEM's \link pumi.hpp PUMI classes\endlink
  *
- * <H4>HiOp Examples</H4>
- * - Variants of Examples
- *   <a class="el" href="hiop_2ex9_8cpp_source.html">9</a> and
- *   <a class="el" href="hiop_2ex9p_8cpp_source.html">9p</a>,
- *   demonstrating the use of MFEM's \link hiop.hpp HiOp classes\endlink
- *
  * <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
@@ -130,18 +112,12 @@ namespace mfem {
  * - <a class="el" href="joule_8cpp_source.html">Joule</a>: transient magnetics and Joule heating miniapp
  * - <a class="el" href="mobius-strip_8cpp_source.html">Mobius Strip</a>: generate various Mobius strip-like meshes
  * - <a class="el" href="klein-bottle_8cpp_source.html">Klein Bottle</a>: generate three types of Klein bottle surfaces
- * - <a class="el" href="toroid_8cpp_source.html">Toroid</a>: generate simple toroidal meshes
  * - <a class="el" href="shaper_8cpp_source.html">Shaper</a>: resolve material interfaces by mesh refinement
- * - <a class="el" href="extruder_8cpp_source.html">Extruder</a>: extrude a low-dimensional mesh into a higher dimension
  * - <a class="el" href="mesh-explorer_8cpp_source.html">Mesh Explorer</a>: visualize and manipulate meshes
  * - <a class="el" href="mesh-optimizer_8cpp_source.html">Mesh Optimizer</a>: optimize high-order meshes, <a class="el" href="mesh-optimizer_8cpp_source.html">serial</a> and <a class="el" href="pmesh-optimizer_8cpp_source.html">parallel</a> versions
  * - <a class="el" href="display-basis_8cpp_source.html">Display Basis</a>: visualize finite element basis functions
- * - <a class="el" href="get-values_8cpp_source.html">Get Values</a>: extract field values via DataCollection classes
  * - <a class="el" href="load-dc_8cpp_source.html">Load DC</a>: visualize fields saved via DataCollection classes
- * - <a class="el" href="convert-dc_8cpp_source.html">Convert DC</a>: convert between different DataCollection formats
- * - <a class="el" href="lor-transfer_8cpp_source.html">LOR Transfer</a>: map functions between high-order and low-order refined spaces
- * - <a class="el" href="findpts_8cpp_source.html">Find Points</a>: evaluate grid function in physical space, <a class="el" href="findpts_8cpp_source.html">serial</a> and <a class="el" href="pfindpts_8cpp_source.html">parallel</a> versions
- * - <a class="el" href="field-diff_8cpp_source.html">Field Diff</a>: compare grid functions on different meshes
+ * - <a class="el" href="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
  *

examples/CMakeLists.txt

@@ -26,9 +26,6 @@ list(APPEND ALL_EXE_SRCS
   ex17.cpp
   ex18.cpp
   ex19.cpp
-  ex20.cpp
-  ex21.cpp
-  ex22.cpp
   )
 
 if (MFEM_USE_MPI)
@@ -52,9 +49,6 @@ if (MFEM_USE_MPI)
     ex17p.cpp
     ex18p.cpp
     ex19p.cpp
-    ex20p.cpp
-    ex21p.cpp
-    ex22p.cpp
     )
 endif()
 
@@ -81,32 +75,18 @@ foreach(SRC_FILE ${ALL_EXE_SRCS})
       COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
   else()
     add_test(NAME ${TEST_NAME}_np=4
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4
       ${MPIEXEC_PREFLAGS}
       $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
       ${MPIEXEC_POSTFLAGS})
   endif()
 endforeach()
 
-# If STRUMPACK is enabled, add a test run that uses it.
-if (MFEM_USE_STRUMPACK)
-  add_test(NAME ex11p_strumpack_np=4
-    COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-    ${MPIEXEC_PREFLAGS}
-    $<TARGET_FILE:ex11p> "-no-vis" "--strumpack"
-    ${MPIEXEC_POSTFLAGS})
-endif()
-
 # Include the examples/sundials directory if SUNDIALS is enabled.
 if (MFEM_USE_SUNDIALS)
   add_subdirectory(sundials)
 endif()
 
-# Include the examples/sundials directory if SUNDIALS is enabled.
-if (MFEM_USE_GINKGO)
-  add_subdirectory(ginkgo)
-endif()
-
 # Include the examples/petsc directory if PETSc is enabled.
 if (MFEM_USE_PETSC)
   add_subdirectory(petsc)
@@ -116,11 +96,3 @@ endif()
 if (MFEM_USE_PUMI)
   add_subdirectory(pumi)
 endif()
-
-if (MFEM_USE_HIOP)
-  add_subdirectory(hiop)
-endif()
-
-if (MFEM_USE_ADEPT)
-  add_subdirectory(ad)
-endif()

examples/ex1.cpp

@@ -4,18 +4,13 @@
 //
 // Sample runs:  ex1 -m ../data/square-disc.mesh
 //               ex1 -m ../data/star.mesh
-//               ex1 -m ../data/star-mixed.mesh
 //               ex1 -m ../data/escher.mesh
 //               ex1 -m ../data/fichera.mesh
-//               ex1 -m ../data/fichera-mixed.mesh
-//               ex1 -m ../data/toroid-wedge.mesh
 //               ex1 -m ../data/square-disc-p2.vtk -o 2
 //               ex1 -m ../data/square-disc-p3.mesh -o 3
 //               ex1 -m ../data/square-disc-nurbs.mesh -o -1
-//               ex1 -m ../data/star-mixed-p2.mesh -o 2
 //               ex1 -m ../data/disc-nurbs.mesh -o -1
 //               ex1 -m ../data/pipe-nurbs.mesh -o -1
-//               ex1 -m ../data/fichera-mixed-p2.mesh -o 2
 //               ex1 -m ../data/star-surf.mesh
 //               ex1 -m ../data/square-disc-surf.mesh
 //               ex1 -m ../data/inline-segment.mesh
@@ -25,16 +20,6 @@
 //               ex1 -m ../data/mobius-strip.mesh
 //               ex1 -m ../data/mobius-strip.mesh -o -1 -sc
 //
-// Device sample runs:
-//               ex1 -pa -d cuda
-//               ex1 -pa -d raja-cuda
-//               ex1 -pa -d occa-cuda
-//               ex1 -pa -d raja-omp
-//               ex1 -pa -d occa-omp
-//               ex1 -pa -d ceed-cpu
-//               ex1 -pa -d ceed-cuda
-//               ex1 -m ../data/beam-hex.mesh -pa -d cuda
-//
 // Description:  This example code demonstrates the use of MFEM to define a
 //               simple finite element discretization of the Laplace problem
 //               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
@@ -63,9 +48,7 @@ int main(int argc, char *argv[])
    const char *mesh_file = "../data/star.mesh";
    int order = 1;
    bool static_cond = false;
-   bool pa = false;
-   const char *device_config = "cpu";
-   bool visualization = true;
+   bool visualization = 1;
 
    OptionsParser args(argc, argv);
    args.AddOption(&mesh_file, "-m", "--mesh",
@@ -75,10 +58,6 @@ int main(int argc, char *argv[])
                   " isoparametric space.");
    args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
                   "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device_config, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -90,31 +69,26 @@ int main(int argc, char *argv[])
    }
    args.PrintOptions(cout);
 
-   // 2. Enable hardware devices such as GPUs, and programming models such as
-   //    CUDA, OCCA, RAJA and OpenMP based on command line options.
-   Device device(device_config);
-   device.Print();
-
-   // 3. Read the mesh from the given mesh file. We can handle triangular,
+   // 2. Read the mesh from the given mesh file. We can handle triangular,
    //    quadrilateral, tetrahedral, hexahedral, surface and volume meshes with
    //    the same code.
    Mesh *mesh = new Mesh(mesh_file, 1, 1);
    int dim = mesh->Dimension();
 
-   // 4. Refine the mesh to increase the resolution. In this example we do
+   // 3. Refine the mesh to increase the resolution. In this example we do
    //    'ref_levels' of uniform refinement. We choose 'ref_levels' to be the
    //    largest number that gives a final mesh with no more than 50,000
    //    elements.
    {
-      int ref_levels =
-         (int)floor(log(50000./mesh->GetNE())/log(2.)/dim);
+     int ref_levels = 0; 
+       //(int)floor(log(50000./mesh->GetNE())/log(2.)/dim);
       for (int l = 0; l < ref_levels; l++)
       {
          mesh->UniformRefinement();
       }
    }
 
-   // 5. Define a finite element space on the mesh. Here we use continuous
+   // 4. Define a finite element space on the mesh. Here we use continuous
    //    Lagrange finite elements of the specified order. If order < 1, we
    //    instead use an isoparametric/isogeometric space.
    FiniteElementCollection *fec;
@@ -135,7 +109,7 @@ int main(int argc, char *argv[])
    cout << "Number of finite element unknowns: "
         << fespace->GetTrueVSize() << endl;
 
-   // 6. Determine the list of true (i.e. conforming) essential boundary dofs.
+   // 5. Determine the list of true (i.e. conforming) essential boundary dofs.
    //    In this example, the boundary conditions are defined by marking all
    //    the boundary attributes from the mesh as essential (Dirichlet) and
    //    converting them to a list of true dofs.
@@ -147,7 +121,7 @@ int main(int argc, char *argv[])
       fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
    }
 
-   // 7. Set up the linear form b(.) which corresponds to the right-hand side of
+   // 6. Set up the linear form b(.) which corresponds to the right-hand side of
    //    the FEM linear system, which in this case is (1,phi_i) where phi_i are
    //    the basis functions in the finite element fespace.
    LinearForm *b = new LinearForm(fespace);
@@ -155,57 +129,48 @@ int main(int argc, char *argv[])
    b->AddDomainIntegrator(new DomainLFIntegrator(one));
    b->Assemble();
 
-   // 8. Define the solution vector x as a finite element grid function
+   // 7. Define the solution vector x as a finite element grid function
    //    corresponding to fespace. Initialize x with initial guess of zero,
    //    which satisfies the boundary conditions.
    GridFunction x(fespace);
    x = 0.0;
 
-   // 9. Set up the bilinear form a(.,.) on the finite element space
+   // 8. Set up the bilinear form a(.,.) on the finite element space
    //    corresponding to the Laplacian operator -Delta, by adding the Diffusion
    //    domain integrator.
    BilinearForm *a = new BilinearForm(fespace);
-   if (pa) { a->SetAssemblyLevel(AssemblyLevel::PARTIAL); }
    a->AddDomainIntegrator(new DiffusionIntegrator(one));
 
-   // 10. Assemble the bilinear form and the corresponding linear system,
-   //     applying any necessary transformations such as: eliminating boundary
-   //     conditions, applying conforming constraints for non-conforming AMR,
-   //     static condensation, etc.
+   // 9. Assemble the bilinear form and the corresponding linear system,
+   //    applying any necessary transformations such as: eliminating boundary
+   //    conditions, applying conforming constraints for non-conforming AMR,
+   //    static condensation, etc.
    if (static_cond) { a->EnableStaticCondensation(); }
    a->Assemble();
 
-   OperatorPtr A;
+   SparseMatrix A;
    Vector B, X;
    a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
 
-   cout << "Size of linear system: " << A->Height() << endl;
+   cout << "Size of linear system: " << A.Height() << endl;
 
-   // 11. Solve the linear system A X = B.
-   if (!pa)
-   {
 #ifndef MFEM_USE_SUITESPARSE
-      // Use a simple symmetric Gauss-Seidel preconditioner with PCG.
-      GSSmoother M((SparseMatrix&)(*A));
-      PCG(*A, M, B, X, 1, 200, 1e-12, 0.0);
+   // 10. Define a simple symmetric Gauss-Seidel preconditioner and use it to
+   //     solve the system A X = B with PCG.
+   GSSmoother M(A);
+   PCG(A, M, B, X, 1, 200, 1e-12, 0.0);
 #else
-      // If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
-      UMFPackSolver umf_solver;
-      umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-      umf_solver.SetOperator(*A);
-      umf_solver.Mult(B, X);
+   // 10. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
+   UMFPackSolver umf_solver;
+   umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
+   umf_solver.SetOperator(A);
+   umf_solver.Mult(B, X);
 #endif
-   }
-   else // Jacobi preconditioning in partial assembly mode
-   {
-      OperatorJacobiSmoother M(*a, ess_tdof_list);
-      PCG(*A, M, B, X, 1, 400, 1e-12, 0.0);
-   }
 
-   // 12. Recover the solution as a finite element grid function.
+   // 11. Recover the solution as a finite element grid function.
    a->RecoverFEMSolution(X, *b, x);
 
-   // 13. Save the refined mesh and the solution. This output can be viewed later
+   // 12. Save the refined mesh and the solution. This output can be viewed later
    //     using GLVis: "glvis -m refined.mesh -g sol.gf".
    ofstream mesh_ofs("refined.mesh");
    mesh_ofs.precision(8);
@@ -214,7 +179,7 @@ int main(int argc, char *argv[])
    sol_ofs.precision(8);
    x.Save(sol_ofs);
 
-   // 14. Send the solution by socket to a GLVis server.
+   // 13. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       char vishost[] = "localhost";
@@ -224,7 +189,7 @@ int main(int argc, char *argv[])
       sol_sock << "solution\n" << *mesh << x << flush;
    }
 
-   // 15. Free the used memory.
+   // 14. Free the used memory.
    delete a;
    delete b;
    delete fespace;

examples/ex10.cpp

@@ -7,7 +7,6 @@
 //    ex10 -m ../data/beam-tri.mesh -s 3 -r 2 -o 2 -dt 3
 //    ex10 -m ../data/beam-hex.mesh -s 2 -r 1 -o 2 -dt 3
 //    ex10 -m ../data/beam-tet.mesh -s 2 -r 1 -o 2 -dt 3
-//    ex10 -m ../data/beam-wedge.mesh -s 2 -r 1 -o 2 -dt 3
 //    ex10 -m ../data/beam-quad.mesh -s 14 -r 2 -o 2 -dt 0.03 -vs 20
 //    ex10 -m ../data/beam-hex.mesh -s 14 -r 1 -o 2 -dt 0.05 -vs 20
 //    ex10 -m ../data/beam-quad-amr.mesh -s 3 -r 2 -o 2 -dt 3

examples/ex10p.cpp

@@ -7,7 +7,6 @@
 //    mpirun -np 4 ex10p -m ../data/beam-tri.mesh -s 3 -rs 2 -dt 3
 //    mpirun -np 4 ex10p -m ../data/beam-hex.mesh -s 2 -rs 1 -dt 3
 //    mpirun -np 4 ex10p -m ../data/beam-tet.mesh -s 2 -rs 1 -dt 3
-//    mpirun -np 4 ex10p -m ../data/beam-wedge.mesh -s 2 -rs 1 -dt 3
 //    mpirun -np 4 ex10p -m ../data/beam-quad.mesh -s 14 -rs 2 -dt 0.03 -vs 20
 //    mpirun -np 4 ex10p -m ../data/beam-hex.mesh -s 14 -rs 1 -dt 0.05 -vs 20
 //    mpirun -np 4 ex10p -m ../data/beam-quad-amr.mesh -s 3 -rs 2 -dt 3

examples/ex11p.cpp

@@ -4,11 +4,8 @@
 //
 // Sample runs:  mpirun -np 4 ex11p -m ../data/square-disc.mesh
 //               mpirun -np 4 ex11p -m ../data/star.mesh
-//               mpirun -np 4 ex11p -m ../data/star-mixed.mesh
 //               mpirun -np 4 ex11p -m ../data/escher.mesh
 //               mpirun -np 4 ex11p -m ../data/fichera.mesh
-//               mpirun -np 4 ex11p -m ../data/fichera-mixed.mesh
-//               mpirun -np 4 ex11p -m ../data/toroid-wedge.mesh -o 2
 //               mpirun -np 4 ex11p -m ../data/square-disc-p2.vtk -o 2
 //               mpirun -np 4 ex11p -m ../data/square-disc-p3.mesh -o 3
 //               mpirun -np 4 ex11p -m ../data/square-disc-nurbs.mesh -o -1
@@ -18,11 +15,6 @@
 //               mpirun -np 4 ex11p -m ../data/star-surf.mesh
 //               mpirun -np 4 ex11p -m ../data/square-disc-surf.mesh
 //               mpirun -np 4 ex11p -m ../data/inline-segment.mesh
-//               mpirun -np 4 ex11p -m ../data/inline-quad.mesh
-//               mpirun -np 4 ex11p -m ../data/inline-tri.mesh
-//               mpirun -np 4 ex11p -m ../data/inline-hex.mesh
-//               mpirun -np 4 ex11p -m ../data/inline-tet.mesh
-//               mpirun -np 4 ex11p -m ../data/inline-wedge.mesh -s 83
 //               mpirun -np 4 ex11p -m ../data/amr-quad.mesh
 //               mpirun -np 4 ex11p -m ../data/amr-hex.mesh
 //               mpirun -np 4 ex11p -m ../data/mobius-strip.mesh -n 8
@@ -261,7 +253,8 @@ int main(int argc, char *argv[])
          strumpack->SetPrintSolveStatistics(false);
          strumpack->SetKrylovSolver(strumpack::KrylovSolver::DIRECT);
          strumpack->SetReorderingStrategy(strumpack::ReorderingStrategy::METIS);
-         strumpack->DisableMatching();
+         strumpack->SetMC64Job(strumpack::MC64Job::NONE);
+         // strumpack->SetSymmetricPattern(true);
          strumpack->SetOperator(*Arow);
          strumpack->SetFromCommandLine();
          precond = strumpack;

examples/ex12p.cpp

@@ -5,11 +5,10 @@
 // Sample runs:
 //    mpirun -np 4 ex12p -m ../data/beam-tri.mesh
 //    mpirun -np 4 ex12p -m ../data/beam-quad.mesh
-//    mpirun -np 4 ex12p -m ../data/beam-tet.mesh -s 462 -n 10 -o 2 -elast
-//    mpirun -np 4 ex12p -m ../data/beam-hex.mesh -s 3878
-//    mpirun -np 4 ex12p -m ../data/beam-wedge.mesh -s 81
-//    mpirun -np 4 ex12p -m ../data/beam-tri.mesh -s 3877 -o 2 -sys
-//    mpirun -np 4 ex12p -m ../data/beam-quad.mesh -s 4544 -n 6 -o 3 -elast
+//    mpirun -np 4 ex12p -m ../data/beam-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
 //
@@ -57,7 +56,7 @@ int main(int argc, char *argv[])
    const char *mesh_file = "../data/beam-tri.mesh";
    int order = 1;
    int nev = 5;
-   int seed = 66;
+   int seed = 75;
    bool visualization = 1;
    bool amg_elast = 0;
 

examples/ex13p.cpp

@@ -3,7 +3,7 @@
 // Compile with: make ex13p
 //
 // Sample runs:  mpirun -np 4 ex13p -m ../data/star.mesh
-//               mpirun -np 4 ex13p -m ../data/square-disc.mesh -o 2 -n 4
+//               mpirun -np 4 ex13p -m ../data/square-disc.mesh -o 2
 //               mpirun -np 4 ex13p -m ../data/beam-tet.mesh
 //               mpirun -np 4 ex13p -m ../data/beam-hex.mesh
 //               mpirun -np 4 ex13p -m ../data/escher.mesh

examples/ex14.cpp

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

examples/ex14p.cpp

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

examples/ex15.cpp

@@ -16,6 +16,9 @@
 //               ex15 -m ../data/ball-nurbs.mesh -tf 0.3
 //               ex15 -m ../data/mobius-strip.mesh
 //               ex15 -m ../data/amr-quad.mesh
+//
+//               Conforming meshes (no derefinement):
+//
 //               ex15 -m ../data/square-disc.mesh
 //               ex15 -m ../data/escher.mesh -r 2 -tf 0.3
 //
@@ -127,13 +130,11 @@ int main(int argc, char *argv[])
       if (ref_levels > 0) { ref_levels--; }
       mesh.SetCurvature(2);
    }
-   mesh.EnsureNCMesh(true);
+   mesh.EnsureNCMesh();
    for (int l = 0; l < ref_levels; l++)
    {
       mesh.UniformRefinement();
    }
-   // Make sure tet-only meshes are marked for local refinement.
-   mesh.Finalize(true);
 
    // 4. All boundary attributes will be used for essential (Dirichlet) BC.
    MFEM_VERIFY(mesh.bdr_attributes.Size() > 0,

examples/ex15p.cpp

@@ -16,6 +16,9 @@
 //               mpirun -np 4 ex15p -m ../data/ball-nurbs.mesh -tf 0.5
 //               mpirun -np 4 ex15p -m ../data/mobius-strip.mesh
 //               mpirun -np 4 ex15p -m ../data/amr-quad.mesh
+//
+//               Conforming meshes (no load balancing and derefinement):
+//
 //               mpirun -np 4 ex15p -m ../data/square-disc.mesh
 //               mpirun -np 4 ex15p -m ../data/escher.mesh -r 2 -tf 0.3
 //
@@ -143,13 +146,11 @@ int main(int argc, char *argv[])
       if (ref_levels > 0) { ref_levels--; }
       mesh->SetCurvature(2);
    }
-   mesh->EnsureNCMesh(true);
+   mesh->EnsureNCMesh();
    for (int l = 0; l < ref_levels; l++)
    {
       mesh->UniformRefinement();
    }
-   // Make sure tet-only meshes are marked for local refinement.
-   mesh->Finalize(true);
 
    // 5. Define a parallel mesh by partitioning the serial mesh.  Once the
    //    parallel mesh is defined, the serial mesh can be deleted.

examples/ex16.cpp

@@ -10,7 +10,6 @@
 //               ex16 -s 3 -a 0.5 -k 0.5 -o 4
 //               ex16 -s 14 -dt 1.0e-4 -tf 4.0e-2 -vs 40
 //               ex16 -m ../data/fichera-q2.mesh
-//               ex16 -m ../data/fichera-mixed.mesh
 //               ex16 -m ../data/escher.mesh
 //               ex16 -m ../data/beam-tet.mesh -tf 10 -dt 0.1
 //               ex16 -m ../data/amr-quad.mesh -o 4 -r 0

examples/ex16p.cpp

@@ -10,7 +10,6 @@
 //               mpirun -np 8 ex16p -s 3 -a 0.5 -k 0.5 -o 4
 //               mpirun -np 4 ex16p -s 14 -dt 1.0e-4 -tf 4.0e-2 -vs 40
 //               mpirun -np 16 ex16p -m ../data/fichera-q2.mesh
-//               mpirun -np 16 ex16p -m ../data/fichera-mixed.mesh
 //               mpirun -np 16 ex16p -m ../data/escher-p2.mesh
 //               mpirun -np 8 ex16p -m ../data/beam-tet.mesh -tf 10 -dt 0.1
 //               mpirun -np 4 ex16p -m ../data/amr-quad.mesh -o 4 -rs 0 -rp 0

examples/ex17.cpp

@@ -8,7 +8,6 @@
 //       ex17 -m ../data/beam-quad.mesh
 //       ex17 -m ../data/beam-tet.mesh
 //       ex17 -m ../data/beam-hex.mesh
-//       ex17 -m ../data/beam-wedge.mesh
 //       ex17 -m ../data/beam-quad.mesh -r 2 -o 3
 //       ex17 -m ../data/beam-quad.mesh -r 2 -o 2 -a 1 -k 1
 //       ex17 -m ../data/beam-hex.mesh -r 2 -o 2
@@ -252,7 +251,7 @@ int main(int argc, char *argv[])
    }
    else
    {
-      GMRES(A, M, B, X, 3, 5000, 100, rtol*rtol, 0.0);
+      GMRES(A, M, B, X, 3, 5000, 50, rtol*rtol, 0.0);
    }
 #else
    // 11. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.

examples/ex17p.cpp

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

examples/ex18.hpp

@@ -509,7 +509,8 @@ bool StateIsPhysical(const Vector &state, const int dim)
 // Initial condition
 void InitialCondition(const Vector &x, Vector &y)
 {
-   MFEM_ASSERT(x.Size() == 2, "");
+   const int dim = x.Size();
+   MFEM_ASSERT(dim == 2, "");
 
    double radius = 0, Minf = 0, beta = 0;
    if (problem == 1)

examples/ex19.cpp

@@ -7,7 +7,6 @@
 //    ex19 -m ../data/beam-tri.mesh
 //    ex19 -m ../data/beam-hex.mesh
 //    ex19 -m ../data/beam-tet.mesh
-//    ex19 -m ../data/beam-wedge.mesh
 //
 // Description:  This examples solves a quasi-static incompressible nonlinear
 //               elasticity problem of the form 0 = H(x), where H is an
@@ -144,7 +143,7 @@ void InitialDeformation(const Vector &x, Vector &y);
 int main(int argc, char *argv[])
 {
    // 1. Parse command-line options
-   const char *mesh_file = "../data/beam-tet.mesh";
+   const char *mesh_file = "../data/beam-hex.mesh";
    int ref_levels = 0;
    int order = 2;
    bool visualization = true;

examples/ex19p.cpp

@@ -7,7 +7,6 @@
 //    mpirun -np 2 ex19p -m ../data/beam-tri.mesh
 //    mpirun -np 2 ex19p -m ../data/beam-hex.mesh
 //    mpirun -np 2 ex19p -m ../data/beam-tet.mesh
-//    mpirun -np 2 ex19p -m ../data/beam-wedge.mesh
 //
 // Description:  This examples solves a quasi-static incompressible nonlinear
 //               elasticity problem of the form 0 = H(x), where H is an
@@ -150,7 +149,7 @@ int main(int argc, char *argv[])
    MPI_Comm_rank(MPI_COMM_WORLD, &myid);
 
    // 2. Parse command-line options
-   const char *mesh_file = "../data/beam-tet.mesh";
+   const char *mesh_file = "../data/beam-hex.mesh";
    int ser_ref_levels = 0;
    int par_ref_levels = 0;
    int order = 2;

examples/ex1p.cpp

@@ -4,19 +4,14 @@
 //
 // Sample runs:  mpirun -np 4 ex1p -m ../data/square-disc.mesh
 //               mpirun -np 4 ex1p -m ../data/star.mesh
-//               mpirun -np 4 ex1p -m ../data/star-mixed.mesh
 //               mpirun -np 4 ex1p -m ../data/escher.mesh
 //               mpirun -np 4 ex1p -m ../data/fichera.mesh
-//               mpirun -np 4 ex1p -m ../data/fichera-mixed.mesh
-//               mpirun -np 4 ex1p -m ../data/toroid-wedge.mesh
 //               mpirun -np 4 ex1p -m ../data/square-disc-p2.vtk -o 2
 //               mpirun -np 4 ex1p -m ../data/square-disc-p3.mesh -o 3
 //               mpirun -np 4 ex1p -m ../data/square-disc-nurbs.mesh -o -1
-//               mpirun -np 4 ex1p -m ../data/star-mixed-p2.mesh -o 2
 //               mpirun -np 4 ex1p -m ../data/disc-nurbs.mesh -o -1
 //               mpirun -np 4 ex1p -m ../data/pipe-nurbs.mesh -o -1
 //               mpirun -np 4 ex1p -m ../data/ball-nurbs.mesh -o 2
-//               mpirun -np 4 ex1p -m ../data/fichera-mixed-p2.mesh -o 2
 //               mpirun -np 4 ex1p -m ../data/star-surf.mesh
 //               mpirun -np 4 ex1p -m ../data/square-disc-surf.mesh
 //               mpirun -np 4 ex1p -m ../data/inline-segment.mesh
@@ -25,13 +20,6 @@
 //               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh
 //               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh -o -1 -sc
 //
-// Device sample runs:
-//               mpirun -np 4 ex1p -pa -d cuda
-//               mpirun -np 4 ex1p -pa -d occa-cuda
-//               mpirun -np 4 ex1p -pa -d raja-omp
-//               mpirun -np 4 ex1p -pa -d ceed-cpu
-//               mpirun -np 4 ex1p -pa -d ceed-cuda
-//
 // Description:  This example code demonstrates the use of MFEM to define a
 //               simple finite element discretization of the Laplace problem
 //               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
@@ -66,9 +54,7 @@ int main(int argc, char *argv[])
    const char *mesh_file = "../data/star.mesh";
    int order = 1;
    bool static_cond = false;
-   bool pa = false;
-   const char *device_config = "cpu";
-   bool visualization = true;
+   bool visualization = 1;
 
    OptionsParser args(argc, argv);
    args.AddOption(&mesh_file, "-m", "--mesh",
@@ -78,10 +64,6 @@ int main(int argc, char *argv[])
                   " isoparametric space.");
    args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
                   "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device_config, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -100,18 +82,13 @@ int main(int argc, char *argv[])
       args.PrintOptions(cout);
    }
 
-   // 3. Enable hardware devices such as GPUs, and programming models such as
-   //    CUDA, OCCA, RAJA and OpenMP based on command line options.
-   Device device(device_config);
-   if (myid == 0) { device.Print(); }
-
-   // 4. Read the (serial) mesh from the given mesh file on all processors.  We
+   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
    //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
    //    and volume meshes with the same code.
    Mesh *mesh = new Mesh(mesh_file, 1, 1);
    int dim = mesh->Dimension();
 
-   // 5. Refine the serial mesh on all processors to increase the resolution. In
+   // 4. Refine the serial mesh on all processors to increase the resolution. In
    //    this example we do 'ref_levels' of uniform refinement. We choose
    //    'ref_levels' to be the largest number that gives a final mesh with no
    //    more than 10,000 elements.
@@ -124,7 +101,7 @@ int main(int argc, char *argv[])
       }
    }
 
-   // 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
+   // 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);
@@ -137,7 +114,7 @@ int main(int argc, char *argv[])
       }
    }
 
-   // 7. Define a parallel finite element space on the parallel mesh. Here we
+   // 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;
@@ -164,7 +141,7 @@ int main(int argc, char *argv[])
       cout << "Number of finite element unknowns: " << size << endl;
    }
 
-   // 8. Determine the list of true (i.e. parallel conforming) essential
+   // 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.
@@ -176,7 +153,7 @@ int main(int argc, char *argv[])
       fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
    }
 
-   // 9. Set up the parallel linear form b(.) which corresponds to the
+   // 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);
@@ -184,56 +161,49 @@ int main(int argc, char *argv[])
    b->AddDomainIntegrator(new DomainLFIntegrator(one));
    b->Assemble();
 
-   // 10. Define the solution vector x as a parallel finite element grid function
-   //     corresponding to fespace. Initialize x with initial guess of zero,
-   //     which satisfies the boundary conditions.
+   // 9. Define the solution vector x as a parallel finite element grid function
+   //    corresponding to fespace. Initialize x with initial guess of zero,
+   //    which satisfies the boundary conditions.
    ParGridFunction x(fespace);
    x = 0.0;
 
-   // 11. Set up the parallel bilinear form a(.,.) on the finite element space
+   // 10. Set up the parallel bilinear form a(.,.) on the finite element space
    //     corresponding to the Laplacian operator -Delta, by adding the Diffusion
    //     domain integrator.
    ParBilinearForm *a = new ParBilinearForm(fespace);
-   if (pa) { a->SetAssemblyLevel(AssemblyLevel::PARTIAL); }
    a->AddDomainIntegrator(new DiffusionIntegrator(one));
 
-   // 12. Assemble the parallel bilinear form and the corresponding linear
+   // 11. Assemble the parallel bilinear form and the corresponding linear
    //     system, applying any necessary transformations such as: parallel
    //     assembly, eliminating boundary conditions, applying conforming
    //     constraints for non-conforming AMR, static condensation, etc.
    if (static_cond) { a->EnableStaticCondensation(); }
    a->Assemble();
 
-   OperatorPtr A;
+   HypreParMatrix A;
    Vector B, X;
    a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
 
-   // 13. Solve the linear system A X = B.
-   //     * With full assembly, use the BoomerAMG preconditioner from hypre.
-   //     * With partial assembly, use Jacobi smoothing, for now.
-   Solver *prec = NULL;
-   if (pa)
+   if (myid == 0)
    {
-      prec = new OperatorJacobiSmoother(*a, ess_tdof_list);
+      cout << "Size of linear system: " << A.GetGlobalNumRows() << endl;
    }
-   else
-   {
-      prec = new HypreBoomerAMG;
-   }
-   CGSolver cg(MPI_COMM_WORLD);
-   cg.SetRelTol(1e-12);
-   cg.SetMaxIter(2000);
-   cg.SetPrintLevel(1);
-   if (prec) { cg.SetPreconditioner(*prec); }
-   cg.SetOperator(*A);
-   cg.Mult(B, X);
-   delete prec;
 
-   // 14. Recover the parallel grid function corresponding to X. This is the
+   // 12. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
+   //     preconditioner from hypre.
+   HypreSolver *amg = new HypreBoomerAMG(A);
+   HyprePCG *pcg = new HyprePCG(A);
+   pcg->SetTol(1e-12);
+   pcg->SetMaxIter(200);
+   pcg->SetPrintLevel(2);
+   pcg->SetPreconditioner(*amg);
+   pcg->Mult(B, X);
+
+   // 13. Recover the parallel grid function corresponding to X. This is the
    //     local finite element solution on each processor.
    a->RecoverFEMSolution(X, *b, x);
 
-   // 15. Save the refined mesh and the solution in parallel. This output can
+   // 14. Save the refined mesh and the solution in parallel. This output can
    //     be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
    {
       ostringstream mesh_name, sol_name;
@@ -249,7 +219,7 @@ int main(int argc, char *argv[])
       x.Save(sol_ofs);
    }
 
-   // 16. Send the solution by socket to a GLVis server.
+   // 15. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       char vishost[] = "localhost";
@@ -260,7 +230,9 @@ int main(int argc, char *argv[])
       sol_sock << "solution\n" << *pmesh << x << flush;
    }
 
-   // 17. Free the used memory.
+   // 16. Free the used memory.
+   delete pcg;
+   delete amg;
    delete a;
    delete b;
    delete fespace;

examples/ex2.cpp

@@ -6,7 +6,6 @@
 //               ex2 -m ../data/beam-quad.mesh
 //               ex2 -m ../data/beam-tet.mesh
 //               ex2 -m ../data/beam-hex.mesh
-//               ex2 -m ../data/beam-wedge.mesh
 //               ex2 -m ../data/beam-quad.mesh -o 3 -sc
 //               ex2 -m ../data/beam-quad-nurbs.mesh
 //               ex2 -m ../data/beam-hex-nurbs.mesh

examples/ex20.cpp

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

examples/ex20p.cpp

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

examples/ex21.cpp

@@ -1,310 +0,0 @@
-//                                MFEM Example 21
-//
-// Compile with: make ex21
-//
-// Sample runs:  ex21
-//               ex21 -o 3
-//               ex21 -m ../data/beam-quad.mesh
-//               ex21 -m ../data/beam-quad.mesh -o 3
-//               ex21 -m ../data/beam-quad.mesh -o 3 -f 1
-//               ex21 -m ../data/beam-tet.mesh
-//               ex21 -m ../data/beam-tet.mesh -o 2
-//               ex21 -m ../data/beam-hex.mesh
-//               ex21 -m ../data/beam-hex.mesh -o 2
-//
-// Description:  This is a version of Example 2 with a simple adaptive mesh
-//               refinement loop. The problem being solved is again the linear
-//               elasticity describing a multi-material cantilever beam.
-//               The problem is solved on a sequence of meshes which
-//               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
-//               to a simple ZZ error estimator.
-//
-//               The example demonstrates MFEM's capability to work with both
-//               conforming and nonconforming refinements, in 2D and 3D, on
-//               linear and curved meshes. Interpolation of functions from
-//               coarse to fine meshes, as well as persistent GLVis
-//               visualization are also illustrated.
-//
-//               We recommend viewing Examples 2 and 6 before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/beam-tri.mesh";
-   int order = 1;
-   bool static_cond = false;
-   int flux_averaging = 0;
-   bool visualization = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&flux_averaging, "-f", "--flux-averaging",
-                  "Flux averaging: 0 - global, 1 - by mesh attribute.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   // 2. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral, and hexahedral meshes with the same code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
-   MFEM_VERIFY(mesh.SpaceDimension() == dim, "invalid mesh");
-
-   if (mesh.attributes.Max() < 2 || mesh.bdr_attributes.Max() < 2)
-   {
-      cerr << "\nInput mesh should have at least two materials and "
-           << "two boundary attributes! (See schematic in ex2.cpp)\n"
-           << endl;
-      return 3;
-   }
-
-   // 3. Since a NURBS mesh can currently only be refined uniformly, we need to
-   //    convert it to a piecewise-polynomial curved mesh. First we refine the
-   //    NURBS mesh a bit more and then project the curvature to quadratic Nodes.
-   if (mesh.NURBSext)
-   {
-      for (int i = 0; i < 2; i++)
-      {
-         mesh.UniformRefinement();
-      }
-      mesh.SetCurvature(2);
-   }
-
-   // 4. Define a finite element space on the mesh. The polynomial order is
-   //    one (linear) by default, but this can be changed on the command line.
-   H1_FECollection fec(order, dim);
-   FiniteElementSpace fespace(&mesh, &fec, dim);
-
-   // 5. As in Example 2, we set up the linear form b(.) which corresponds to
-   //    the right-hand side of the FEM linear system. In this case, b_i equals
-   //    the boundary integral of f*phi_i where f represents a "pull down"
-   //    force on the Neumann part of the boundary and phi_i are the basis
-   //    functions in the finite element fespace. The force is defined by the
-   //    VectorArrayCoefficient object f, which is a vector of Coefficient
-   //    objects. The fact that f is non-zero on boundary attribute 2 is
-   //    indicated by the use of piece-wise constants coefficient for its last
-   //    component. We don't assemble the discrete problem yet, this will be
-   //    done in the main loop.
-   VectorArrayCoefficient f(dim);
-   for (int i = 0; i < dim-1; i++)
-   {
-      f.Set(i, new ConstantCoefficient(0.0));
-   }
-   {
-      Vector pull_force(mesh.bdr_attributes.Max());
-      pull_force = 0.0;
-      pull_force(1) = -1.0e-2;
-      f.Set(dim-1, new PWConstCoefficient(pull_force));
-   }
-
-   LinearForm b(&fespace);
-   b.AddDomainIntegrator(new VectorBoundaryLFIntegrator(f));
-
-   // 6. Set up the bilinear form a(.,.) on the finite element space
-   //    corresponding to the linear elasticity integrator with piece-wise
-   //    constants coefficient lambda and mu.
-   Vector lambda(mesh.attributes.Max());
-   lambda = 1.0;
-   lambda(0) = lambda(1)*50;
-   PWConstCoefficient lambda_func(lambda);
-   Vector mu(mesh.attributes.Max());
-   mu = 1.0;
-   mu(0) = mu(1)*50;
-   PWConstCoefficient mu_func(mu);
-
-   BilinearForm a(&fespace);
-   BilinearFormIntegrator *integ =
-      new ElasticityIntegrator(lambda_func,mu_func);
-   a.AddDomainIntegrator(integ);
-   if (static_cond) { a.EnableStaticCondensation(); }
-
-   // 7. The solution vector x and the associated finite element grid function
-   //    will be maintained over the AMR iterations. We initialize it to zero.
-   Vector zero_vec(dim);
-   zero_vec = 0.0;
-   VectorConstantCoefficient zero_vec_coeff(zero_vec);
-   GridFunction x(&fespace);
-   x = 0.0;
-
-   // 8. Determine the list of true (i.e. conforming) essential boundary dofs.
-   //    In this example, the boundary conditions are defined by marking only
-   //    boundary attribute 1 from the mesh as essential and converting it to a
-   //    list of true dofs.  The conversion to true dofs will be done in the
-   //    main loop.
-   Array<int> ess_bdr(mesh.bdr_attributes.Max());
-   ess_bdr = 0;
-   ess_bdr[0] = 1;
-
-   // 9. Connect to GLVis.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock;
-   if (visualization)
-   {
-      sol_sock.open(vishost, visport);
-      sol_sock.precision(8);
-   }
-
-   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
-   //     that uses the ComputeElementFlux method of the ElasticityIntegrator to
-   //     recover a smoothed flux (stress) that is subtracted from the element
-   //     flux to get an error indicator. We need to supply the space for the
-   //     smoothed flux: an (H1)^tdim (i.e., vector-valued) space is used here.
-   //     Here, tdim represents the number of components for a symmetric (dim x
-   //     dim) tensor.
-   const int tdim = dim*(dim+1)/2;
-   FiniteElementSpace flux_fespace(&mesh, &fec, tdim);
-   ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace);
-   estimator.SetFluxAveraging(flux_averaging);
-
-   // 11. A refiner selects and refines elements based on a refinement strategy.
-   //     The strategy here is to refine elements with errors larger than a
-   //     fraction of the maximum element error. Other strategies are possible.
-   //     The refiner will call the given error estimator.
-   ThresholdRefiner refiner(estimator);
-   refiner.SetTotalErrorFraction(0.7);
-
-   // 12. The main AMR loop. In each iteration we solve the problem on the
-   //     current mesh, visualize the solution, and refine the mesh.
-   const int max_dofs = 50000;
-   const int max_amr_itr = 20;
-   for (int it = 0; it <= max_amr_itr; it++)
-   {
-      int cdofs = fespace.GetTrueVSize();
-      cout << "\nAMR iteration " << it << endl;
-      cout << "Number of unknowns: " << cdofs << endl;
-
-      // 13. Assemble the stiffness matrix and the right-hand side.
-      a.Assemble();
-      b.Assemble();
-
-      // 14. Set Dirichlet boundary values in the GridFunction x.
-      //     Determine the list of Dirichlet true DOFs in the linear system.
-      Array<int> ess_tdof_list;
-      x.ProjectBdrCoefficient(zero_vec_coeff, ess_bdr);
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-
-      // 15. Create the linear system: eliminate boundary conditions, constrain
-      //     hanging nodes and possibly apply other transformations. The system
-      //     will be solved for true (unconstrained) DOFs only.
-      SparseMatrix A;
-      Vector B, X;
-      const int copy_interior = 1;
-      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
-
-#ifndef MFEM_USE_SUITESPARSE
-      // 16. Define a simple symmetric Gauss-Seidel preconditioner and use it to
-      //     solve the linear system with PCG.
-      GSSmoother M(A);
-      PCG(A, M, B, X, 3, 2000, 1e-12, 0.0);
-#else
-      // 16. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the
-      //     the linear system.
-      UMFPackSolver umf_solver;
-      umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-      umf_solver.SetOperator(A);
-      umf_solver.Mult(B, X);
-#endif
-
-      // 17. After solving the linear system, reconstruct the solution as a
-      //     finite element GridFunction. Constrained nodes are interpolated
-      //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
-      a.RecoverFEMSolution(X, b, x);
-
-      // 18. Send solution by socket to the GLVis server.
-      if (visualization && sol_sock.good())
-      {
-         GridFunction nodes(&fespace), *nodes_p = &nodes;
-         mesh.GetNodes(nodes);
-         nodes += x;
-         int own_nodes = 0;
-         mesh.SwapNodes(nodes_p, own_nodes);
-         x.Neg(); // visualize the backward displacement
-         sol_sock << "solution\n" << mesh << x << flush;
-         x.Neg();
-         mesh.SwapNodes(nodes_p, own_nodes);
-         if (it == 0)
-         {
-            sol_sock << "keys '" << ((dim == 2) ? "Rjl" : "") << "m'" << endl;
-         }
-         sol_sock << "window_title 'AMR iteration: " << it << "'\n"
-                  << "pause" << endl;
-         cout << "Visualization paused. "
-              "Press <space> in the GLVis window to continue." << endl;
-      }
-
-      if (cdofs > max_dofs)
-      {
-         cout << "Reached the maximum number of dofs. Stop." << endl;
-         break;
-      }
-
-      // 19. Call the refiner to modify the mesh. The refiner calls the error
-      //     estimator to obtain element errors, then it selects elements to be
-      //     refined and finally it modifies the mesh. The Stop() method can be
-      //     used to determine if a stopping criterion was met.
-      refiner.Apply(mesh);
-      if (refiner.Stop())
-      {
-         cout << "Stopping criterion satisfied. Stop." << endl;
-         break;
-      }
-
-      // 20. Update the space to reflect the new state of the mesh. Also,
-      //     interpolate the solution x so that it lies in the new space but
-      //     represents the same function. This saves solver iterations later
-      //     since we'll have a good initial guess of x in the next step.
-      //     Internally, FiniteElementSpace::Update() calculates an
-      //     interpolation matrix which is then used by GridFunction::Update().
-      fespace.Update();
-      x.Update();
-
-      // 21. Inform also the bilinear and linear forms that the space has
-      //     changed.
-      a.Update();
-      b.Update();
-   }
-
-   {
-      ofstream mesh_ref_out("ex21_reference.mesh");
-      mesh_ref_out.precision(16);
-      mesh.Print(mesh_ref_out);
-
-      ofstream mesh_out("ex21_deformed.mesh");
-      mesh_out.precision(16);
-      GridFunction nodes(&fespace), *nodes_p = &nodes;
-      mesh.GetNodes(nodes);
-      nodes += x;
-      int own_nodes = 0;
-      mesh.SwapNodes(nodes_p, own_nodes);
-      mesh.Print(mesh_out);
-      mesh.SwapNodes(nodes_p, own_nodes);
-
-      ofstream x_out("ex21_displacement.sol");
-      x_out.precision(16);
-      x.Save(x_out);
-   }
-
-   return 0;
-}

examples/ex21p.cpp

@@ -1,366 +0,0 @@
-//                                MFEM Example 21
-//
-// Compile with: make ex21p
-//
-// Sample runs:  mpirun -np 4 ex21p
-//               mpirun -np 4 ex21p -o 3
-//               mpirun -np 4 ex21p -m ../data/beam-quad.mesh
-//               mpirun -np 4 ex21p -m ../data/beam-quad.mesh -o 3
-//               mpirun -np 4 ex21p -m ../data/beam-tet.mesh
-//               mpirun -np 4 ex21p -m ../data/beam-tet.mesh -o 2
-//               mpirun -np 4 ex21p -m ../data/beam-hex.mesh
-//               mpirun -np 4 ex21p -m ../data/beam-hex.mesh -o 2
-//
-// Description:  This is a version of Example 2p with a simple adaptive mesh
-//               refinement loop. The problem being solved is again the linear
-//               elasticity describing a multi-material cantilever beam.
-//               The problem is solved on a sequence of meshes which
-//               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
-//               to a simple ZZ error estimator.
-//
-//               The example demonstrates MFEM's capability to work with both
-//               conforming and nonconforming refinements, in 2D and 3D, on
-//               linear and curved meshes. Interpolation of functions from
-//               coarse to fine meshes, as well as persistent GLVis
-//               visualization are also illustrated.
-//
-//               We recommend viewing Examples 2p and 6p before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 0. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/beam-tri.mesh";
-   int serial_ref_levels = 0;
-   int order = 1;
-   bool static_cond = false;
-   bool visualization = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&serial_ref_levels, "-rs", "--refine-serial",
-                  "Number of uniform serial refinements (before parallel"
-                  " partitioning)");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 2. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral, and hexahedral meshes with the same code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
-   MFEM_VERIFY(mesh.SpaceDimension() == dim, "invalid mesh");
-
-   if (mesh.attributes.Max() < 2 || mesh.bdr_attributes.Max() < 2)
-   {
-      cerr << "\nInput mesh should have at least two materials and "
-           << "two boundary attributes! (See schematic in ex2.cpp)\n"
-           << endl;
-      MPI_Finalize();
-      return 3;
-   }
-
-   // 3. Refine the mesh before parallel partitioning. Since a NURBS mesh can
-   //    currently only be refined uniformly, we need to convert it to a
-   //    piecewise-polynomial curved mesh. First we refine the NURBS mesh a bit
-   //    more and then project the curvature to quadratic Nodes.
-   if (mesh.NURBSext && serial_ref_levels == 0)
-   {
-      serial_ref_levels = 2;
-   }
-   for (int i = 0; i < serial_ref_levels; i++)
-   {
-      mesh.UniformRefinement();
-   }
-   if (mesh.NURBSext)
-   {
-      mesh.SetCurvature(2);
-   }
-   mesh.EnsureNCMesh();
-
-   ParMesh pmesh(MPI_COMM_WORLD, mesh);
-   mesh.Clear();
-
-   // 4. Define a finite element space on the mesh. The polynomial order is
-   //    one (linear) by default, but this can be changed on the command line.
-   H1_FECollection fec(order, dim);
-   ParFiniteElementSpace fespace(&pmesh, &fec, dim);
-
-   // 5. As in Example 2, we set up the linear form b(.) which corresponds to
-   //    the right-hand side of the FEM linear system. In this case, b_i equals
-   //    the boundary integral of f*phi_i where f represents a "pull down"
-   //    force on the Neumann part of the boundary and phi_i are the basis
-   //    functions in the finite element fespace. The force is defined by the
-   //    VectorArrayCoefficient object f, which is a vector of Coefficient
-   //    objects. The fact that f is non-zero on boundary attribute 2 is
-   //    indicated by the use of piece-wise constants coefficient for its last
-   //    component. We don't assemble the discrete problem yet, this will be
-   //    done in the main loop.
-   VectorArrayCoefficient f(dim);
-   for (int i = 0; i < dim-1; i++)
-   {
-      f.Set(i, new ConstantCoefficient(0.0));
-   }
-   {
-      Vector pull_force(pmesh.bdr_attributes.Max());
-      pull_force = 0.0;
-      pull_force(1) = -1.0e-2;
-      f.Set(dim-1, new PWConstCoefficient(pull_force));
-   }
-
-   ParLinearForm b(&fespace);
-   b.AddDomainIntegrator(new VectorBoundaryLFIntegrator(f));
-
-   // 6. Set up the bilinear form a(.,.) on the finite element space
-   //    corresponding to the linear elasticity integrator with piece-wise
-   //    constants coefficient lambda and mu.
-   Vector lambda(pmesh.attributes.Max());
-   lambda = 1.0;
-   lambda(0) = lambda(1)*50;
-   PWConstCoefficient lambda_func(lambda);
-   Vector mu(pmesh.attributes.Max());
-   mu = 1.0;
-   mu(0) = mu(1)*50;
-   PWConstCoefficient mu_func(mu);
-
-   ParBilinearForm a(&fespace);
-   BilinearFormIntegrator *integ =
-      new ElasticityIntegrator(lambda_func,mu_func);
-   a.AddDomainIntegrator(integ);
-   if (static_cond) { a.EnableStaticCondensation(); }
-
-   // 7. The solution vector x and the associated finite element grid function
-   //    will be maintained over the AMR iterations. We initialize it to zero.
-   Vector zero_vec(dim);
-   zero_vec = 0.0;
-   VectorConstantCoefficient zero_vec_coeff(zero_vec);
-   ParGridFunction x(&fespace);
-   x = 0.0;
-
-   // 8. Determine the list of true (i.e. conforming) essential boundary dofs.
-   //    In this example, the boundary conditions are defined by marking only
-   //    boundary attribute 1 from the mesh as essential and converting it to a
-   //    list of true dofs.  The conversion to true dofs will be done in the
-   //    main loop.
-   Array<int> ess_bdr(pmesh.bdr_attributes.Max());
-   ess_bdr = 0;
-   ess_bdr[0] = 1;
-
-   // 9. GLVis visualization.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock;
-
-   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
-   //     that uses the ComputeElementFlux method of the ElasticityIntegrator to
-   //     recover a smoothed flux (stress) that is subtracted from the element
-   //     flux to get an error indicator. We need to supply the space for the
-   //     smoothed flux: an (H1)^tdim (i.e., vector-valued) space is used here.
-   //     Here, tdim represents the number of components for a symmetric (dim x
-   //     dim) tensor.
-   const int tdim = dim*(dim+1)/2;
-   L2_FECollection flux_fec(order, dim);
-   ParFiniteElementSpace flux_fespace(&pmesh, &flux_fec, tdim);
-   ParFiniteElementSpace smooth_flux_fespace(&pmesh, &fec, tdim);
-   L2ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace,
-                                       smooth_flux_fespace);
-
-   // 11. A refiner selects and refines elements based on a refinement strategy.
-   //     The strategy here is to refine elements with errors larger than a
-   //     fraction of the maximum element error. Other strategies are possible.
-   //     The refiner will call the given error estimator.
-   ThresholdRefiner refiner(estimator);
-   refiner.SetTotalErrorFraction(0.7);
-
-   // 12. The main AMR loop. In each iteration we solve the problem on the
-   //     current mesh, visualize the solution, and refine the mesh.
-   const int max_dofs = 50000;
-   const int max_amr_itr = 20;
-   for (int it = 0; it <= max_amr_itr; it++)
-   {
-      HYPRE_Int global_dofs = fespace.GlobalTrueVSize();
-      if (myid == 0)
-      {
-         cout << "\nAMR iteration " << it << endl;
-         cout << "Number of unknowns: " << global_dofs << endl;
-      }
-
-      // 13. Assemble the stiffness matrix and the right-hand side.
-      a.Assemble();
-      b.Assemble();
-
-      // 14. Set Dirichlet boundary values in the GridFunction x.
-      //     Determine the list of Dirichlet true DOFs in the linear system.
-      Array<int> ess_tdof_list;
-      x.ProjectBdrCoefficient(zero_vec_coeff, ess_bdr);
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-
-      // 15. Create the linear system: eliminate boundary conditions, constrain
-      //     hanging nodes and possibly apply other transformations. The system
-      //     will be solved for true (unconstrained) DOFs only.
-
-      HypreParMatrix A;
-      Vector B, X;
-      const int copy_interior = 1;
-      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
-
-      // 16. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
-      //     preconditioner from hypre.
-      HypreBoomerAMG amg;
-      amg.SetPrintLevel(0);
-      // amg.SetSystemsOptions(dim); // optional
-      CGSolver pcg(A.GetComm());
-      pcg.SetPreconditioner(amg);
-      pcg.SetOperator(A);
-      pcg.SetRelTol(1e-6);
-      pcg.SetMaxIter(500);
-      pcg.SetPrintLevel(3); // print the first and the last iterations only
-      pcg.Mult(B, X);
-
-      // 17. After solving the linear system, reconstruct the solution as a
-      //     finite element GridFunction. Constrained nodes are interpolated
-      //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
-      a.RecoverFEMSolution(X, b, x);
-
-      // 18. Send solution by socket to the GLVis server.
-      if (visualization && it == 0)
-      {
-         sol_sock.open(vishost, visport);
-         sol_sock.precision(8);
-      }
-      if (visualization && sol_sock.good())
-      {
-         GridFunction nodes(&fespace), *nodes_p = &nodes;
-         pmesh.GetNodes(nodes);
-         nodes += x;
-         int own_nodes = 0;
-         pmesh.SwapNodes(nodes_p, own_nodes);
-         x.Neg(); // visualize the backward displacement
-         sol_sock << "parallel " << num_procs << ' ' << myid << '\n';
-         sol_sock << "solution\n" << pmesh << x << flush;
-         x.Neg();
-         pmesh.SwapNodes(nodes_p, own_nodes);
-         if (it == 0)
-         {
-            sol_sock << "keys '" << ((dim == 2) ? "Rjl" : "") << "m'" << endl;
-         }
-         sol_sock << "window_title 'AMR iteration: " << it << "'\n"
-                  << "pause" << endl;
-         if (myid == 0)
-         {
-            cout << "Visualization paused. "
-                 "Press <space> in the GLVis window to continue." << endl;
-         }
-      }
-
-      if (global_dofs > max_dofs)
-      {
-         if (myid == 0)
-         {
-            cout << "Reached the maximum number of dofs. Stop." << endl;
-         }
-         break;
-      }
-
-      // 19. Call the refiner to modify the mesh. The refiner calls the error
-      //     estimator to obtain element errors, then it selects elements to be
-      //     refined and finally it modifies the mesh. The Stop() method can be
-      //     used to determine if a stopping criterion was met.
-      refiner.Apply(pmesh);
-      if (refiner.Stop())
-      {
-         if (myid == 0)
-         {
-            cout << "Stopping criterion satisfied. Stop." << endl;
-         }
-         break;
-      }
-
-      // 20. Update the space to reflect the new state of the mesh. Also,
-      //     interpolate the solution x so that it lies in the new space but
-      //     represents the same function. This saves solver iterations later
-      //     since we'll have a good initial guess of x in the next step.
-      //     Internally, FiniteElementSpace::Update() calculates an
-      //     interpolation matrix which is then used by GridFunction::Update().
-      fespace.Update();
-      x.Update();
-
-      // 21. Load balance the mesh, and update the space and solution. Currently
-      //     available only for nonconforming meshes.
-      if (pmesh.Nonconforming())
-      {
-         pmesh.Rebalance();
-
-         // Update the space and the GridFunction. This time the update matrix
-         // redistributes the GridFunction among the processors.
-         fespace.Update();
-         x.Update();
-      }
-
-      // 21. Inform also the bilinear and linear forms that the space has
-      //     changed.
-      a.Update();
-      b.Update();
-   }
-
-   {
-      ostringstream mref_name, mesh_name, sol_name;
-      mref_name << "ex21p_reference_mesh." << setfill('0') << setw(6) << myid;
-      mesh_name << "ex21p_deformed_mesh." << setfill('0') << setw(6) << myid;
-      sol_name << "ex21p_displacement." << setfill('0') << setw(6) << myid;
-
-      ofstream mesh_ref_out(mref_name.str().c_str());
-      mesh_ref_out.precision(16);
-      pmesh.Print(mesh_ref_out);
-
-      ofstream mesh_out(mesh_name.str().c_str());
-      mesh_out.precision(16);
-      GridFunction nodes(&fespace), *nodes_p = &nodes;
-      pmesh.GetNodes(nodes);
-      nodes += x;
-      int own_nodes = 0;
-      pmesh.SwapNodes(nodes_p, own_nodes);
-      pmesh.Print(mesh_out);
-      pmesh.SwapNodes(nodes_p, own_nodes);
-
-      ofstream x_out(sol_name.str().c_str());
-      x_out.precision(16);
-      x.Save(x_out);
-   }
-
-   MPI_Finalize();
-   return 0;
-}

examples/ex22.cpp

@@ -1,561 +0,0 @@
-//                               MFEM Example 22
-//
-// Compile with: make ex22
-//
-// Sample runs:  ex22 -m ../data/inline-segment.mesh -o 3
-//               ex22 -m ../data/inline-tri.mesh -o 3
-//               ex22 -m ../data/inline-quad.mesh -o 3
-//               ex22 -m ../data/inline-quad.mesh -o 3 -p 1
-//               ex22 -m ../data/inline-quad.mesh -o 3 -p 2
-//               ex22 -m ../data/inline-tet.mesh -o 2
-//               ex22 -m ../data/inline-hex.mesh -o 2
-//               ex22 -m ../data/inline-hex.mesh -o 2 -p 1
-//               ex22 -m ../data/inline-hex.mesh -o 2 -p 2
-//               ex22 -m ../data/star.mesh -r 1 -o 2 -sigma 10.0
-//
-// Description:  This example code demonstrates the use of MFEM to define and
-//               solve simple complex-valued linear systems. It implements three
-//               variants of a damped harmonic oscillator:
-//
-//               1) A scalar H1 field
-//                  -Div(a Grad u) - omega^2 b u + i omega c u = 0
-//
-//               2) A vector H(Curl) field
-//                  Curl(a Curl u) - omega^2 b u + i omega c u = 0
-//
-//               3) A vector H(Div) field
-//                  -Grad(a Div u) - omega^2 b u + i omega c u = 0
-//
-//               In each case the field is driven by a forced oscillation, with
-//               angular frequency omega, imposed at the boundary or a portion
-//               of the boundary.
-//
-//               In electromagnetics, the coefficients are typically named the
-//               permeability, mu = 1/a, permittivity, epsilon = b, and
-//               conductivity, sigma = c. The user can specify these constants
-//               using either set of names.
-//
-//               The example also demonstrates how to display a time-varying
-//               solution as a sequence of fields sent to a single GLVis socket.
-//
-//               We recommend viewing examples 1, 3 and 4 before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-static double mu_ = 1.0;
-static double epsilon_ = 1.0;
-static double sigma_ = 20.0;
-static double omega_ = 10.0;
-
-double u0_real_exact(const Vector &);
-double u0_imag_exact(const Vector &);
-
-void u1_real_exact(const Vector &, Vector &);
-void u1_imag_exact(const Vector &, Vector &);
-
-void u2_real_exact(const Vector &, Vector &);
-void u2_imag_exact(const Vector &, Vector &);
-
-bool check_for_inline_mesh(const char * mesh_file);
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/inline-quad.mesh";
-   int ref_levels = 0;
-   int order = 1;
-   int prob = 0;
-   double freq = -1.0;
-   double a_coef = 0.0;
-   bool visualization = 1;
-   bool herm_conv = true;
-   bool exact_sol = true;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&ref_levels, "-r", "--refine",
-                  "Number of times to refine the mesh uniformly.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&prob, "-p", "--problem-type",
-                  "Choose between 0: H_1, 1: H(Curl), or 2: H(Div) "
-                  "damped harmonic oscillator.");
-   args.AddOption(&a_coef, "-a", "--stiffness-coef",
-                  "Stiffness coefficient (spring constant or 1/mu).");
-   args.AddOption(&epsilon_, "-b", "--mass-coef",
-                  "Mass coefficient (or epsilon).");
-   args.AddOption(&sigma_, "-c", "--damping-coef",
-                  "Damping coefficient (or sigma).");
-   args.AddOption(&mu_, "-mu", "--permeability",
-                  "Permeability of free space (or 1/(spring constant)).");
-   args.AddOption(&epsilon_, "-eps", "--permittivity",
-                  "Permittivity of free space (or mass constant).");
-   args.AddOption(&sigma_, "-sigma", "--conductivity",
-                  "Conductivity (or damping constant).");
-   args.AddOption(&freq, "-f", "--frequency",
-                  "Frequency (in Hz).");
-   args.AddOption(&herm_conv, "-herm", "--hermitian", "-no-herm",
-                  "--no-hermitian", "Use convention for Hermitian operators.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   MFEM_VERIFY(prob >= 0 && prob <=2,
-               "Unrecognized problem type: " << prob);
-
-   if ( a_coef != 0.0 )
-   {
-      mu_ = 1.0 / a_coef;
-   }
-   if ( freq > 0.0 )
-   {
-      omega_ = 2.0 * M_PI * freq;
-   }
-
-   exact_sol = check_for_inline_mesh(mesh_file);
-   if (exact_sol)
-   {
-      cout << "Identified a mesh with known exact solution" << endl;
-   }
-
-   ComplexOperator::Convention conv =
-      herm_conv ? ComplexOperator::HERMITIAN : ComplexOperator::BLOCK_SYMMETRIC;
-
-   // 2. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral, hexahedral, surface and volume meshes
-   //    with the same code.
-   Mesh *mesh = new Mesh(mesh_file, 1, 1);
-   int dim = mesh->Dimension();
-
-   // 3. Refine the mesh to increase resolution. In this example we do
-   //    'ref_levels' of uniform refinement where the user specifies
-   //    the number of levels with the '-r' option.
-   for (int l = 0; l < ref_levels; l++)
-   {
-      mesh->UniformRefinement();
-   }
-
-   // 4. Define a finite element space on the mesh. Here we use continuous
-   //    Lagrange, Nedelec, or Raviart-Thomas finite elements of the specified
-   //    order.
-   if (dim == 1 && prob != 0 )
-   {
-      cout << "Switching to problem type 0, H1 basis functions, "
-           << "for 1 dimensional mesh." << endl;
-      prob = 0;
-   }
-
-   FiniteElementCollection *fec = NULL;
-   switch (prob)
-   {
-      case 0:  fec = new H1_FECollection(order, dim);      break;
-      case 1:  fec = new ND_FECollection(order, dim);      break;
-      case 2:  fec = new RT_FECollection(order - 1, dim);  break;
-      default: break; // This should be unreachable
-   }
-   FiniteElementSpace *fespace = new FiniteElementSpace(mesh, fec);
-   cout << "Number of finite element unknowns: " << fespace->GetTrueVSize()
-        << endl;
-
-   // 5. Determine the list of true (i.e. conforming) essential boundary dofs.
-   //    In this example, the boundary conditions are defined based on the type
-   //    of mesh and the problem type.
-   Array<int> ess_tdof_list;
-   Array<int> ess_bdr;
-   if (mesh->bdr_attributes.Size())
-   {
-      ess_bdr.SetSize(mesh->bdr_attributes.Max());
-      ess_bdr = 1;
-      if (exact_sol)
-      {
-         switch (prob)
-         {
-            case 0:   ess_bdr = 0; ess_bdr[0] = 1;  break;
-            default:  ess_bdr = 1; ess_bdr[2] = 0;  break;
-         }
-      }
-      fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   // 6. Set up the linear form b(.) which corresponds to the right-hand side of
-   //    the FEM linear system.
-   ComplexLinearForm b(fespace, conv);
-   b.Vector::operator=(0.0);
-
-   // 7. Define the solution vector u as a complex finite element grid function
-   //    corresponding to fespace. Initialize u with initial guess of 1+0i or
-   //    the exact solution if it is known.
-   ComplexGridFunction u(fespace);
-   ComplexGridFunction * u_exact = NULL;
-   if (exact_sol) { u_exact = new ComplexGridFunction(fespace); }
-
-   FunctionCoefficient u0_r(u0_real_exact);
-   FunctionCoefficient u0_i(u0_imag_exact);
-   VectorFunctionCoefficient u1_r(dim, u1_real_exact);
-   VectorFunctionCoefficient u1_i(dim, u1_imag_exact);
-   VectorFunctionCoefficient u2_r(dim, u2_real_exact);
-   VectorFunctionCoefficient u2_i(dim, u2_imag_exact);
-
-   ConstantCoefficient zeroCoef(0.0);
-   ConstantCoefficient oneCoef(1.0);
-
-   Vector zeroVec(dim); zeroVec = 0.0;
-   Vector  oneVec(dim);  oneVec = 0.0; oneVec[(prob==2)?(dim-1):0] = 1.0;
-   VectorConstantCoefficient zeroVecCoef(zeroVec);
-   VectorConstantCoefficient oneVecCoef(oneVec);
-
-   u = 0.0;
-   switch (prob)
-   {
-      case 0:
-         u.ProjectBdrCoefficient(oneCoef, zeroCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u0_r, u0_i); }
-         break;
-      case 1:
-         u.ProjectBdrCoefficientTangent(oneVecCoef, zeroVecCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u1_r, u1_i); }
-         break;
-      case 2:
-         u.ProjectBdrCoefficientNormal(oneVecCoef, zeroVecCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u2_r, u2_i); }
-         break;
-      default: break; // This should be unreachable
-   }
-
-   if (visualization && exact_sol)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *mesh << u_exact->real()
-                 << "window_title 'Exact: Real Part'" << flush;
-      sol_sock_i << "solution\n" << *mesh << u_exact->imag()
-                 << "window_title 'Exact: Imaginary Part'" << flush;
-   }
-
-   // 8. Set up the sesquilinear form a(.,.) on the finite element space
-   //    corresponding to the damped harmonic oscillator operator of the
-   //    appropriate type:
-   //
-   //    0) A scalar H1 field
-   //       -Div(a Grad) - omega^2 b + i omega c
-   //
-   //    1) A vector H(Curl) field
-   //       Curl(a Curl) - omega^2 b + i omega c
-   //
-   //    2) A vector H(Div) field
-   //       -Grad(a Div) - omega^2 b + i omega c
-   //
-   ConstantCoefficient stiffnessCoef(1.0/mu_);
-   ConstantCoefficient massCoef(-omega_ * omega_ * epsilon_);
-   ConstantCoefficient lossCoef(omega_ * sigma_);
-   ConstantCoefficient negMassCoef(omega_ * omega_ * epsilon_);
-
-   SesquilinearForm *a = new SesquilinearForm(fespace, conv);
-   switch (prob)
-   {
-      case 0:
-         a->AddDomainIntegrator(new DiffusionIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new MassIntegrator(massCoef),
-                                new MassIntegrator(lossCoef));
-         break;
-      case 1:
-         a->AddDomainIntegrator(new CurlCurlIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef),
-                                new VectorFEMassIntegrator(lossCoef));
-         break;
-      case 2:
-         a->AddDomainIntegrator(new DivDivIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef),
-                                new VectorFEMassIntegrator(lossCoef));
-         break;
-      default: break; // This should be unreachable
-   }
-
-   // 8a. Set up the bilinear form for the preconditioner corresponding to the
-   //     appropriate operator
-   //
-   //      0) A scalar H1 field
-   //         -Div(a Grad) - omega^2 b + omega c
-   //
-   //      1) A vector H(Curl) field
-   //         Curl(a Curl) + omega^2 b + omega c
-   //
-   //      2) A vector H(Div) field
-   //         -Grad(a Div) - omega^2 b + omega c
-   //
-   BilinearForm *pcOp = new BilinearForm(fespace);
-   switch (prob)
-   {
-      case 0:
-         pcOp->AddDomainIntegrator(new DiffusionIntegrator(stiffnessCoef));
-         pcOp->AddDomainIntegrator(new MassIntegrator(massCoef));
-         pcOp->AddDomainIntegrator(new MassIntegrator(lossCoef));
-         break;
-      case 1:
-         pcOp->AddDomainIntegrator(new CurlCurlIntegrator(stiffnessCoef));
-         pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(negMassCoef));
-         pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(lossCoef));
-         break;
-      case 2:
-         pcOp->AddDomainIntegrator(new DivDivIntegrator(stiffnessCoef));
-         pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef));
-         pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(lossCoef));
-         break;
-      default: break; // This should be unreachable
-   }
-
-   // 9. Assemble the form and the corresponding linear system, applying any
-   //    necessary transformations such as: assembly, eliminating boundary
-   //    conditions, conforming constraints for non-conforming AMR, etc.
-   a->Assemble();
-   pcOp->Assemble();
-
-   OperatorHandle A;
-   Vector B, U;
-
-   a->FormLinearSystem(ess_tdof_list, u, b, A, U, B);
-   u = 0.0;
-   U = 0.0;
-
-   OperatorHandle PCOp;
-   pcOp->FormSystemMatrix(ess_tdof_list, PCOp);
-
-   {
-      ComplexSparseMatrix * Asp =
-         dynamic_cast<ComplexSparseMatrix*>(A.Ptr());
-
-      cout << "Size of linear system: "
-           << 2 * Asp->real().Width() << endl << endl;
-   }
-
-   // 10. Define and apply a GMRES solver for AU=B with a block diagonal
-   //     preconditioner based on the appropriate sparse smoother.
-   {
-      Array<int> blockOffsets;
-      blockOffsets.SetSize(3);
-      blockOffsets[0] = 0;
-      blockOffsets[1] = PCOp.Ptr()->Height();
-      blockOffsets[2] = PCOp.Ptr()->Height();
-      blockOffsets.PartialSum();
-
-      BlockDiagonalPreconditioner BDP(blockOffsets);
-
-      Operator * pc_r = NULL;
-      Operator * pc_i = NULL;
-
-      switch (prob)
-      {
-         case 0: // fallthrough to case 2
-         case 2:
-            pc_r = new DSmoother(*PCOp.As<SparseMatrix>());
-            break;
-         case 1:
-            pc_r = new GSSmoother(*PCOp.As<SparseMatrix>());
-            break;
-         default: break; // This should be unreachable
-      }
-      pc_i = new ScaledOperator(pc_r,
-                                (conv == ComplexOperator::HERMITIAN) ?
-                                1.0:-1.0);
-
-      BDP.SetDiagonalBlock(0, pc_r);
-      BDP.SetDiagonalBlock(1, pc_i);
-      BDP.owns_blocks = 1;
-
-      GMRESSolver gmres;
-      gmres.SetPreconditioner(BDP);
-      gmres.SetOperator(*A.Ptr());
-      gmres.SetRelTol(1e-12);
-      gmres.SetMaxIter(1000);
-      gmres.SetPrintLevel(1);
-      gmres.Mult(B, U);
-   }
-
-   // 11. Recover the solution as a finite element grid function and compute the
-   //     errors if the exact solution is known.
-   a->RecoverFEMSolution(U, b, u);
-
-   if (exact_sol)
-   {
-      double err_r = -1.0;
-      double err_i = -1.0;
-
-      switch (prob)
-      {
-         case 0:
-            err_r = u.real().ComputeL2Error(u0_r);
-            err_i = u.imag().ComputeL2Error(u0_i);
-            break;
-         case 1:
-            err_r = u.real().ComputeL2Error(u1_r);
-            err_i = u.imag().ComputeL2Error(u1_i);
-            break;
-         case 2:
-            err_r = u.real().ComputeL2Error(u2_r);
-            err_i = u.imag().ComputeL2Error(u2_i);
-            break;
-         default: break; // This should be unreachable
-      }
-
-      cout << endl;
-      cout << "|| Re (u_h - u) ||_{L^2} = " << err_r << endl;
-      cout << "|| Im (u_h - u) ||_{L^2} = " << err_i << endl;
-      cout << endl;
-   }
-
-   // 12. Save the refined mesh and the solution. This output can be viewed
-   //     later using GLVis: "glvis -m mesh -g sol".
-   {
-      ofstream mesh_ofs("refined.mesh");
-      mesh_ofs.precision(8);
-      mesh->Print(mesh_ofs);
-
-      ofstream sol_r_ofs("sol_r.gf");
-      ofstream sol_i_ofs("sol_i.gf");
-      sol_r_ofs.precision(8);
-      sol_i_ofs.precision(8);
-      u.real().Save(sol_r_ofs);
-      u.imag().Save(sol_i_ofs);
-   }
-
-   // 13. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *mesh << u.real()
-                 << "window_title 'Solution: Real Part'" << flush;
-      sol_sock_i << "solution\n" << *mesh << u.imag()
-                 << "window_title 'Solution: Imaginary Part'" << flush;
-   }
-   if (visualization && exact_sol)
-   {
-      *u_exact -= u;
-
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *mesh << u_exact->real()
-                 << "window_title 'Error: Real Part'" << flush;
-      sol_sock_i << "solution\n" << *mesh << u_exact->imag()
-                 << "window_title 'Error: Imaginary Part'" << flush;
-   }
-   if (visualization)
-   {
-      GridFunction u_t(fespace);
-      u_t = u.real();
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << *mesh << u_t
-               << "window_title 'Harmonic Solution (t = 0.0 T)'"
-               << "pause\n" << flush;
-
-      cout << "GLVis visualization paused."
-           << " Press space (in the GLVis window) to resume it.\n";
-      int num_frames = 32;
-      int i = 0;
-      while (sol_sock)
-      {
-         double t = (double)(i % num_frames) / num_frames;
-         ostringstream oss;
-         oss << "Harmonic Solution (t = " << t << " T)";
-
-         add(cos( 2.0 * M_PI * t), u.real(),
-             sin(-2.0 * M_PI * t), u.imag(), u_t);
-         sol_sock << "solution\n" << *mesh << u_t
-                  << "window_title '" << oss.str() << "'" << flush;
-         i++;
-      }
-   }
-
-   // 14. Free the used memory.
-   delete a;
-   delete u_exact;
-   delete pcOp;
-   delete fespace;
-   delete fec;
-   delete mesh;
-
-   return 0;
-}
-
-bool check_for_inline_mesh(const char * mesh_file)
-{
-   string file(mesh_file);
-   size_t p0 = file.find_last_of("/");
-   string s0 = file.substr((p0==string::npos)?0:(p0+1),7);
-   return s0 == "inline-";
-}
-
-complex<double> u0_exact(const Vector &x)
-{
-   int dim = x.Size();
-   complex<double> i(0.0, 1.0);
-   complex<double> alpha = (epsilon_ * omega_ - i * sigma_);
-   complex<double> kappa = std::sqrt(mu_ * omega_* alpha);
-   return std::exp(-i * kappa * x[dim - 1]);
-}
-
-double u0_real_exact(const Vector &x)
-{
-   return u0_exact(x).real();
-}
-
-double u0_imag_exact(const Vector &x)
-{
-   return u0_exact(x).imag();
-}
-
-void u1_real_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[0] = u0_real_exact(x);
-}
-
-void u1_imag_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[0] = u0_imag_exact(x);
-}
-
-void u2_real_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[dim-1] = u0_real_exact(x);
-}
-
-void u2_imag_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[dim-1] = u0_imag_exact(x);
-}

examples/ex22p.cpp

@@ -1,622 +0,0 @@
-//                       MFEM Example 22 - Parallel Version
-//
-// Compile with: make ex22p
-//
-// Sample runs:  mpirun -np 4 ex22p -m ../data/inline-segment.mesh -o 3
-//               mpirun -np 4 ex22p -m ../data/inline-tri.mesh -o 3
-//               mpirun -np 4 ex22p -m ../data/inline-quad.mesh -o 3
-//               mpirun -np 4 ex22p -m ../data/inline-quad.mesh -o 3 -p 1
-//               mpirun -np 4 ex22p -m ../data/inline-quad.mesh -o 3 -p 2
-//               mpirun -np 4 ex22p -m ../data/inline-tet.mesh -o 2
-//               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 2
-//               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 2 -p 1
-//               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 2 -p 2
-//               mpirun -np 4 ex22p -m ../data/star.mesh -o 2 -sigma 10.0
-//
-// Description:  This example code demonstrates the use of MFEM to define and
-//               solve simple complex-valued linear systems. It implements three
-//               variants of a damped harmonic oscillator:
-//
-//               1) A scalar H1 field
-//                  -Div(a Grad u) - omega^2 b u + i omega c u = 0
-//
-//               2) A vector H(Curl) field
-//                  Curl(a Curl u) - omega^2 b u + i omega c u = 0
-//
-//               3) A vector H(Div) field
-//                  -Grad(a Div u) - omega^2 b u + i omega c u = 0
-//
-//               In each case the field is driven by a forced oscillation, with
-//               angular frequency omega, imposed at the boundary or a portion
-//               of the boundary.
-//
-//               In electromagnetics the coefficients are typically named the
-//               permeability, mu = 1/a, permittivity, epsilon = b, and
-//               conductivity, sigma = c. The user can specify these constants
-//               using either set of names.
-//
-//               The example also demonstrates how to display a time-varying
-//               solution as a sequence of fields sent to a single GLVis socket.
-//
-//               We recommend viewing examples 1, 3 and 4 before viewing this
-//               example.
-
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-static double mu_ = 1.0;
-static double epsilon_ = 1.0;
-static double sigma_ = 20.0;
-static double omega_ = 10.0;
-
-double u0_real_exact(const Vector &);
-double u0_imag_exact(const Vector &);
-
-void u1_real_exact(const Vector &, Vector &);
-void u1_imag_exact(const Vector &, Vector &);
-
-void u2_real_exact(const Vector &, Vector &);
-void u2_imag_exact(const Vector &, Vector &);
-
-bool check_for_inline_mesh(const char * mesh_file);
-
-int main(int argc, char *argv[])
-{
-   // 1. 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/inline-quad.mesh";
-   int ser_ref_levels = 1;
-   int par_ref_levels = 1;
-   int order = 1;
-   int prob = 0;
-   double freq = -1.0;
-   double a_coef = 0.0;
-   bool visualization = 1;
-   bool herm_conv = true;
-   bool exact_sol = true;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
-                  "Number of times to refine the mesh uniformly in serial.");
-   args.AddOption(&par_ref_levels, "-rp", "--refine-parallel",
-                  "Number of times to refine the mesh uniformly in parallel.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&prob, "-p", "--problem-type",
-                  "Choose between 0: H_1, 1: H(Curl), or 2: H(Div) "
-                  "damped harmonic oscillator.");
-   args.AddOption(&a_coef, "-a", "--stiffness-coef",
-                  "Stiffness coefficient (spring constant or 1/mu).");
-   args.AddOption(&epsilon_, "-b", "--mass-coef",
-                  "Mass coefficient (or epsilon).");
-   args.AddOption(&sigma_, "-c", "--damping-coef",
-                  "Damping coefficient (or sigma).");
-   args.AddOption(&mu_, "-mu", "--permeability",
-                  "Permeability of free space (or 1/(spring constant)).");
-   args.AddOption(&epsilon_, "-eps", "--permittivity",
-                  "Permittivity of free space (or mass constant).");
-   args.AddOption(&sigma_, "-sigma", "--conductivity",
-                  "Conductivity (or damping constant).");
-   args.AddOption(&freq, "-f", "--frequency",
-                  "Frequency (in Hz).");
-   args.AddOption(&herm_conv, "-herm", "--hermitian", "-no-herm",
-                  "--no-hermitian", "Use convention for Hermitian operators.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   MFEM_VERIFY(prob >= 0 && prob <=2,
-               "Unrecognized problem type: " << prob);
-
-   if ( a_coef != 0.0 )
-   {
-      mu_ = 1.0 / a_coef;
-   }
-   if ( freq > 0.0 )
-   {
-      omega_ = 2.0 * M_PI * freq;
-   }
-
-   exact_sol = check_for_inline_mesh(mesh_file);
-   if (myid == 0 && exact_sol)
-   {
-      cout << "Identified a mesh with known exact solution" << endl;
-   }
-
-   ComplexOperator::Convention conv =
-      herm_conv ? ComplexOperator::HERMITIAN : ComplexOperator::BLOCK_SYMMETRIC;
-
-   // 3. Read the (serial) mesh from the given mesh file on all processors. We
-   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
-   //    and volume meshes with the same code.
-   Mesh *mesh = new Mesh(mesh_file, 1, 1);
-   int dim = mesh->Dimension();
-
-   // 4. Refine the serial mesh on all processors to increase the resolution.
-   for (int l = 0; l < ser_ref_levels; l++)
-   {
-      mesh->UniformRefinement();
-   }
-
-   // 5. Define a parallel mesh by a partitioning of the serial mesh. Refine
-   //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
-   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
-   delete mesh;
-   for (int l = 0; l < par_ref_levels; l++)
-   {
-      pmesh->UniformRefinement();
-   }
-
-   // 6. Define a parallel finite element space on the parallel mesh. Here we
-   //    use continuous Lagrange, Nedelec, or Raviart-Thomas finite elements of
-   //    the specified order.
-   if (dim == 1 && prob != 0 )
-   {
-      if (myid == 0)
-      {
-         cout << "Switching to problem type 0, H1 basis functions, "
-              << "for 1 dimensional mesh." << endl;
-      }
-      prob = 0;
-   }
-
-   FiniteElementCollection *fec = NULL;
-   switch (prob)
-   {
-      case 0:  fec = new H1_FECollection(order, dim);      break;
-      case 1:  fec = new ND_FECollection(order, dim);      break;
-      case 2:  fec = new RT_FECollection(order - 1, dim);  break;
-      default: break; // This should be unreachable
-   }
-   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
-   HYPRE_Int size = fespace->GlobalTrueVSize();
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 7. Determine the list of true (i.e. parallel conforming) essential
-   //    boundary dofs. In this example, the boundary conditions are defined
-   //    based on the type of mesh and the problem type.
-   Array<int> ess_tdof_list;
-   Array<int> ess_bdr;
-   if (pmesh->bdr_attributes.Size())
-   {
-      ess_bdr.SetSize(pmesh->bdr_attributes.Max());
-      ess_bdr = 1;
-      if (exact_sol)
-      {
-         switch (prob)
-         {
-            case 0:   ess_bdr = 0; ess_bdr[0] = 1;  break;
-            default:  ess_bdr = 1; ess_bdr[2] = 0;  break;
-         }
-      }
-      fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   // 8. Set up the parallel linear form b(.) which corresponds to the
-   //    right-hand side of the FEM linear system.
-   ParComplexLinearForm b(fespace, conv);
-   b.Vector::operator=(0.0);
-
-   // 9. Define the solution vector u as a parallel complex finite element grid
-   //    function corresponding to fespace. Initialize u with initial guess of
-   //    1+0i or the exact solution if it is known.
-   ParComplexGridFunction u(fespace);
-   ParComplexGridFunction * u_exact = NULL;
-   if (exact_sol) { u_exact = new ParComplexGridFunction(fespace); }
-
-   FunctionCoefficient u0_r(u0_real_exact);
-   FunctionCoefficient u0_i(u0_imag_exact);
-   VectorFunctionCoefficient u1_r(dim, u1_real_exact);
-   VectorFunctionCoefficient u1_i(dim, u1_imag_exact);
-   VectorFunctionCoefficient u2_r(dim, u2_real_exact);
-   VectorFunctionCoefficient u2_i(dim, u2_imag_exact);
-
-   ConstantCoefficient zeroCoef(0.0);
-   ConstantCoefficient oneCoef(1.0);
-
-   Vector zeroVec(dim); zeroVec = 0.0;
-   Vector  oneVec(dim);  oneVec = 0.0; oneVec[(prob==2)?(dim-1):0] = 1.0;
-   VectorConstantCoefficient zeroVecCoef(zeroVec);
-   VectorConstantCoefficient oneVecCoef(oneVec);
-
-   u = 0.0;
-   switch (prob)
-   {
-      case 0:
-         u.ProjectBdrCoefficient(oneCoef, zeroCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u0_r, u0_i); }
-         break;
-      case 1:
-         u.ProjectBdrCoefficientTangent(oneVecCoef, zeroVecCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u1_r, u1_i); }
-         break;
-      case 2:
-         u.ProjectBdrCoefficientNormal(oneVecCoef, zeroVecCoef, ess_bdr);
-         if (exact_sol) { u_exact->ProjectCoefficient(u2_r, u2_i); }
-         break;
-      default: break; // This should be unreachable
-   }
-
-   if (visualization && exact_sol)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *pmesh << u_exact->real()
-                 << "window_title 'Exact: Real Part'" << flush;
-      sol_sock_i << "solution\n" << *pmesh << u_exact->imag()
-                 << "window_title 'Exact: Imaginary Part'" << flush;
-   }
-
-   // 10. Set up the parallel sesquilinear form a(.,.) on the finite element
-   //     space corresponding to the damped harmonic oscillator operator of the
-   //     appropriate type:
-   //
-   //     0) A scalar H1 field
-   //        -Div(a Grad) - omega^2 b + i omega c
-   //
-   //     1) A vector H(Curl) field
-   //        Curl(a Curl) - omega^2 b + i omega c
-   //
-   //     2) A vector H(Div) field
-   //        -Grad(a Div) - omega^2 b + i omega c
-   //
-   ConstantCoefficient stiffnessCoef(1.0/mu_);
-   ConstantCoefficient massCoef(-omega_ * omega_ * epsilon_);
-   ConstantCoefficient lossCoef(omega_ * sigma_);
-   ConstantCoefficient negMassCoef(omega_ * omega_ * epsilon_);
-
-   ParSesquilinearForm *a = new ParSesquilinearForm(fespace, conv);
-   switch (prob)
-   {
-      case 0:
-         a->AddDomainIntegrator(new DiffusionIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new MassIntegrator(massCoef),
-                                new MassIntegrator(lossCoef));
-         break;
-      case 1:
-         a->AddDomainIntegrator(new CurlCurlIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef),
-                                new VectorFEMassIntegrator(lossCoef));
-         break;
-      case 2:
-         a->AddDomainIntegrator(new DivDivIntegrator(stiffnessCoef),
-                                NULL);
-         a->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef),
-                                new VectorFEMassIntegrator(lossCoef));
-         break;
-      default: break; // This should be unreachable
-   }
-
-   // 10a. Set up the parallel bilinear form for the preconditioner
-   //      corresponding to the appropriate operator
-   //
-   //      0) A scalar H1 field
-   //         -Div(a Grad) - omega^2 b + omega c
-   //
-   //      1) A vector H(Curl) field
-   //         Curl(a Curl) + omega^2 b + omega c
-   //
-   //      2) A vector H(Div) field
-   //         -Grad(a Div) - omega^2 b + omega c
-   //
-   ParBilinearForm *pcOp = new ParBilinearForm(fespace);
-   switch (prob)
-   {
-      case 0:
-         pcOp->AddDomainIntegrator(new DiffusionIntegrator(stiffnessCoef));
-         pcOp->AddDomainIntegrator(new MassIntegrator(massCoef));
-         pcOp->AddDomainIntegrator(new MassIntegrator(lossCoef));
-         break;
-      case 1:
-         pcOp->AddDomainIntegrator(new CurlCurlIntegrator(stiffnessCoef));
-         pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(negMassCoef));
-         pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(lossCoef));
-         break;
-      case 2:
-         pcOp->AddDomainIntegrator(new DivDivIntegrator(stiffnessCoef));
-         pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(massCoef));
-         pcOp->AddDomainIntegrator(new VectorFEMassIntegrator(lossCoef));
-         break;
-      default: break; // This should be unreachable
-   }
-
-   // 11. Assemble the parallel bilinear form and the corresponding linear
-   //     system, applying any necessary transformations such as: parallel
-   //     assembly, eliminating boundary conditions, applying conforming
-   //     constraints for non-conforming AMR, etc.
-   a->Assemble();
-   pcOp->Assemble();
-
-   OperatorHandle A;
-   Vector B, U;
-
-   a->FormLinearSystem(ess_tdof_list, u, b, A, U, B);
-   u = 0.0;
-   U = 0.0;
-
-   OperatorHandle PCOp;
-   pcOp->FormSystemMatrix(ess_tdof_list, PCOp);
-
-   if (myid == 0)
-   {
-      ComplexHypreParMatrix * Ahyp =
-         dynamic_cast<ComplexHypreParMatrix*>(A.Ptr());
-
-      cout << "Size of linear system: "
-           << 2 * Ahyp->real().GetGlobalNumRows() << endl << endl;
-   }
-
-   // 12. Define and apply a parallel FGMRES solver for AU=B with a block
-   //     diagonal preconditioner based on the appropriate multigrid
-   //     preconditioner from hypre.
-   {
-      Array<HYPRE_Int> blockTrueOffsets;
-      blockTrueOffsets.SetSize(3);
-      blockTrueOffsets[0] = 0;
-      blockTrueOffsets[1] = PCOp.Ptr()->Height();
-      blockTrueOffsets[2] = PCOp.Ptr()->Height();
-      blockTrueOffsets.PartialSum();
-
-      BlockDiagonalPreconditioner BDP(blockTrueOffsets);
-
-      Operator * pc_r = NULL;
-      Operator * pc_i = NULL;
-
-      switch (prob)
-      {
-         case 0:
-            pc_r = new HypreBoomerAMG(*PCOp.As<HypreParMatrix>());
-            break;
-         case 1:
-            pc_r = new HypreAMS(*PCOp.As<HypreParMatrix>(), fespace);
-            break;
-         case 2:
-            if (dim == 2 )
-            {
-               pc_r = new HypreAMS(*PCOp.As<HypreParMatrix>(), fespace);
-            }
-            else
-            {
-               pc_r = new HypreADS(*PCOp.As<HypreParMatrix>(), fespace);
-            }
-            break;
-         default: break; // This should be unreachable
-      }
-      pc_i = new ScaledOperator(pc_r,
-                                (conv == ComplexOperator::HERMITIAN) ?
-                                1.0:-1.0);
-
-      BDP.SetDiagonalBlock(0, pc_r);
-      BDP.SetDiagonalBlock(1, pc_i);
-      BDP.owns_blocks = 1;
-
-      FGMRESSolver fgmres(MPI_COMM_WORLD);
-      fgmres.SetPreconditioner(BDP);
-      fgmres.SetOperator(*A.Ptr());
-      fgmres.SetRelTol(1e-12);
-      fgmres.SetMaxIter(1000);
-      fgmres.SetPrintLevel(1);
-      fgmres.Mult(B, U);
-   }
-
-   // 13. Recover the parallel grid function corresponding to U. This is the
-   //     local finite element solution on each processor.
-   a->RecoverFEMSolution(U, b, u);
-
-   if (exact_sol)
-   {
-      double err_r = -1.0;
-      double err_i = -1.0;
-
-      switch (prob)
-      {
-         case 0:
-            err_r = u.real().ComputeL2Error(u0_r);
-            err_i = u.imag().ComputeL2Error(u0_i);
-            break;
-         case 1:
-            err_r = u.real().ComputeL2Error(u1_r);
-            err_i = u.imag().ComputeL2Error(u1_i);
-            break;
-         case 2:
-            err_r = u.real().ComputeL2Error(u2_r);
-            err_i = u.imag().ComputeL2Error(u2_i);
-            break;
-         default: break; // This should be unreachable
-      }
-
-      if ( myid == 0 )
-      {
-         cout << endl;
-         cout << "|| Re (u_h - u) ||_{L^2} = " << err_r << endl;
-         cout << "|| Im (u_h - u) ||_{L^2} = " << err_i << endl;
-         cout << endl;
-      }
-   }
-
-   // 14. Save the refined mesh and the solution in parallel. This output can be
-   //     viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
-   {
-      ostringstream mesh_name, sol_r_name, sol_i_name;
-      mesh_name << "mesh." << setfill('0') << setw(6) << myid;
-      sol_r_name << "sol_r." << setfill('0') << setw(6) << myid;
-      sol_i_name << "sol_i." << setfill('0') << setw(6) << myid;
-
-      ofstream mesh_ofs(mesh_name.str().c_str());
-      mesh_ofs.precision(8);
-      pmesh->Print(mesh_ofs);
-
-      ofstream sol_r_ofs(sol_r_name.str().c_str());
-      ofstream sol_i_ofs(sol_i_name.str().c_str());
-      sol_r_ofs.precision(8);
-      sol_i_ofs.precision(8);
-      u.real().Save(sol_r_ofs);
-      u.imag().Save(sol_i_ofs);
-   }
-
-   // 15. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *pmesh << u.real()
-                 << "window_title 'Solution: Real Part'" << flush;
-      sol_sock_i << "solution\n" << *pmesh << u.imag()
-                 << "window_title 'Solution: Imaginary Part'" << flush;
-   }
-   if (visualization && exact_sol)
-   {
-      *u_exact -= u;
-
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock_r(vishost, visport);
-      socketstream sol_sock_i(vishost, visport);
-      sol_sock_r << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_i << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock_r.precision(8);
-      sol_sock_i.precision(8);
-      sol_sock_r << "solution\n" << *pmesh << u_exact->real()
-                 << "window_title 'Error: Real Part'" << flush;
-      sol_sock_i << "solution\n" << *pmesh << u_exact->imag()
-                 << "window_title 'Error: Imaginary Part'" << flush;
-   }
-   if (visualization)
-   {
-      ParGridFunction u_t(fespace);
-      u_t = u.real();
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << *pmesh << u_t
-               << "window_title 'Harmonic Solution (t = 0.0 T)'"
-               << "pause\n" << flush;
-      if (myid == 0)
-         cout << "GLVis visualization paused."
-              << " Press space (in the GLVis window) to resume it.\n";
-      int num_frames = 32;
-      int i = 0;
-      while (sol_sock)
-      {
-         double t = (double)(i % num_frames) / num_frames;
-         ostringstream oss;
-         oss << "Harmonic Solution (t = " << t << " T)";
-
-         add(cos( 2.0 * M_PI * t), u.real(),
-             sin(-2.0 * M_PI * t), u.imag(), u_t);
-         sol_sock << "parallel " << num_procs << " " << myid << "\n";
-         sol_sock << "solution\n" << *pmesh << u_t
-                  << "window_title '" << oss.str() << "'" << flush;
-         i++;
-      }
-   }
-
-   // 16. Free the used memory.
-   delete a;
-   delete u_exact;
-   delete pcOp;
-   delete fespace;
-   delete fec;
-   delete pmesh;
-
-   MPI_Finalize();
-
-   return 0;
-}
-
-bool check_for_inline_mesh(const char * mesh_file)
-{
-   string file(mesh_file);
-   size_t p0 = file.find_last_of("/");
-   string s0 = file.substr((p0==string::npos)?0:(p0+1),7);
-   return s0 == "inline-";
-}
-
-complex<double> u0_exact(const Vector &x)
-{
-   int dim = x.Size();
-   complex<double> i(0.0, 1.0);
-   complex<double> alpha = (epsilon_ * omega_ - i * sigma_);
-   complex<double> kappa = std::sqrt(mu_ * omega_* alpha);
-   return std::exp(-i * kappa * x[dim - 1]);
-}
-
-double u0_real_exact(const Vector &x)
-{
-   return u0_exact(x).real();
-}
-
-double u0_imag_exact(const Vector &x)
-{
-   return u0_exact(x).imag();
-}
-
-void u1_real_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[0] = u0_real_exact(x);
-}
-
-void u1_imag_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[0] = u0_imag_exact(x);
-}
-
-void u2_real_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[dim-1] = u0_real_exact(x);
-}
-
-void u2_imag_exact(const Vector &x, Vector &v)
-{
-   int dim = x.Size();
-   v.SetSize(dim); v = 0.0; v[dim-1] = u0_imag_exact(x);
-}

examples/ex2p.cpp

@@ -6,7 +6,6 @@
 //               mpirun -np 4 ex2p -m ../data/beam-quad.mesh
 //               mpirun -np 4 ex2p -m ../data/beam-tet.mesh
 //               mpirun -np 4 ex2p -m ../data/beam-hex.mesh
-//               mpirun -np 4 ex2p -m ../data/beam-wedge.mesh
 //               mpirun -np 4 ex2p -m ../data/beam-tri.mesh -o 2 -sys
 //               mpirun -np 4 ex2p -m ../data/beam-quad.mesh -o 3 -elast
 //               mpirun -np 4 ex2p -m ../data/beam-quad.mesh -o 3 -sc

examples/ex3.cpp

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

examples/ex3p.cpp

@@ -7,7 +7,6 @@
 //               mpirun -np 4 ex3p -m ../data/beam-tet.mesh
 //               mpirun -np 4 ex3p -m ../data/beam-hex.mesh
 //               mpirun -np 4 ex3p -m ../data/escher.mesh
-//               mpirun -np 4 ex3p -m ../data/escher.mesh -o 2
 //               mpirun -np 4 ex3p -m ../data/fichera.mesh
 //               mpirun -np 4 ex3p -m ../data/fichera-q2.vtk
 //               mpirun -np 4 ex3p -m ../data/fichera-q3.mesh
@@ -102,7 +101,8 @@ int main(int argc, char *argv[])
    //    'ref_levels' to be the largest number that gives a final mesh with no
    //    more than 1,000 elements.
    {
-      int ref_levels = (int)floor(log(1000./mesh->GetNE())/log(2.)/dim);
+      int ref_levels =
+         (int)floor(log(1000./mesh->GetNE())/log(2.)/dim);
       for (int l = 0; l < ref_levels; l++)
       {
          mesh->UniformRefinement();

examples/ex5.cpp

@@ -21,7 +21,7 @@
 //
 //               The example demonstrates the use of the BlockMatrix class, as
 //               well as the collective saving of several grid functions in a
-//               VisIt (visit.llnl.gov) and ParaView (paraview.org) formats.
+//               VisIt (visit.llnl.gov) visualization format.
 //
 //               We recommend viewing examples 1-4 before viewing this example.
 
@@ -264,16 +264,7 @@ int main(int argc, char *argv[])
    visit_dc.RegisterField("pressure", &p);
    visit_dc.Save();
 
-   // 14. Save data in the ParaView format
-   ParaViewDataCollection paraview_dc("PVExample5S", mesh);
-   paraview_dc.SetLevelsOfDetail(2);
-   paraview_dc.SetCycle(1);
-   paraview_dc.SetTime(0.0); // set the time
-   paraview_dc.RegisterField("velocity",&u);
-   paraview_dc.RegisterField("pressure",&p);
-   paraview_dc.Save();
-
-   // 15. Send the solution by socket to a GLVis server.
+   // 14. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       char vishost[] = "localhost";
@@ -286,7 +277,7 @@ int main(int argc, char *argv[])
       p_sock << "solution\n" << *mesh << p << "window_title 'Pressure'" << endl;
    }
 
-   // 16. Free the used memory.
+   // 15. Free the used memory.
    delete fform;
    delete gform;
    delete invM;

examples/ex5p.cpp

@@ -21,7 +21,7 @@
 //
 //               The example demonstrates the use of the BlockMatrix class, as
 //               well as the collective saving of several grid functions in a
-//               VisIt (visit.llnl.gov) and ParaView (paraview.org) formats.
+//               VisIt (visit.llnl.gov) visualization format.
 //
 //               We recommend viewing examples 1-4 before viewing this example.
 
@@ -239,6 +239,7 @@ int main(int argc, char *argv[])
 
    // 12. Solve the linear system with MINRES.
    //     Check the norm of the unpreconditioned residual.
+
    int maxIter(500);
    double rtol(1.e-6);
    double atol(1.e-10);
@@ -325,16 +326,7 @@ int main(int argc, char *argv[])
                       DataCollection::PARALLEL_FORMAT);
    visit_dc.Save();
 
-   // 16. Save data in the ParaView format
-   ParaViewDataCollection paraview_dc("PVExample5P", pmesh);
-   paraview_dc.SetLevelsOfDetail(1);
-   paraview_dc.SetCycle(1);
-   paraview_dc.SetTime(0.0);
-   paraview_dc.RegisterField("velocity",u);
-   paraview_dc.RegisterField("pressure",p);
-   paraview_dc.Save();
-
-   // 17. Send the solution by socket to a GLVis server.
+   // 16. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       char vishost[] = "localhost";
@@ -354,7 +346,7 @@ int main(int argc, char *argv[])
              << endl;
    }
 
-   // 18. Free the used memory.
+   // 17. Free the used memory.
    delete fform;
    delete gform;
    delete u;

examples/ex6.cpp

@@ -15,19 +15,12 @@
 //               ex6 -m ../data/square-disc-surf.mesh -o 2
 //               ex6 -m ../data/amr-quad.mesh
 //
-// Device sample runs:
-//               ex6 -pa -d cuda
-//               ex6 -pa -d occa-cuda
-//               ex6 -pa -d raja-omp
-//               ex6 -pa -d ceed-cpu
-//               ex6 -pa -d ceed-cuda
-//
 // Description:  This is a version of Example 1 with a simple adaptive mesh
 //               refinement loop. The problem being solved is again the Laplace
 //               equation -Delta u = 1 with homogeneous Dirichlet boundary
 //               conditions. The problem is solved on a sequence of meshes which
 //               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
+//               or non-conforming (quadrilateral, hexahedrons) manner according
 //               to a simple ZZ error estimator.
 //
 //               The example demonstrates MFEM's capability to work with both
@@ -50,19 +43,13 @@ int main(int argc, char *argv[])
    // 1. Parse command-line options.
    const char *mesh_file = "../data/star.mesh";
    int order = 1;
-   bool pa = false;
-   const char *device_config = "cpu";
-   bool visualization = true;
+   bool visualization = 1;
 
    OptionsParser args(argc, argv);
    args.AddOption(&mesh_file, "-m", "--mesh",
                   "Mesh file to use.");
    args.AddOption(&order, "-o", "--order",
                   "Finite element order (polynomial degree).");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device_config, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -74,19 +61,14 @@ int main(int argc, char *argv[])
    }
    args.PrintOptions(cout);
 
-   // 2. Enable hardware devices such as GPUs, and programming models such as
-   //    CUDA, OCCA, RAJA and OpenMP based on command line options.
-   Device device(device_config);
-   device.Print();
-
-   // 3. Read the mesh from the given mesh file. We can handle triangular,
+   // 2. Read the mesh from the given mesh file. We can handle triangular,
    //    quadrilateral, tetrahedral, hexahedral, surface and volume meshes with
    //    the same code.
    Mesh mesh(mesh_file, 1, 1);
    int dim = mesh.Dimension();
    int sdim = mesh.SpaceDimension();
 
-   // 4. Since a NURBS mesh can currently only be refined uniformly, we need to
+   // 3. Since a NURBS mesh can currently only be refined uniformly, we need to
    //    convert it to a piecewise-polynomial curved mesh. First we refine the
    //    NURBS mesh a bit more and then project the curvature to quadratic Nodes.
    if (mesh.NURBSext)
@@ -98,16 +80,15 @@ int main(int argc, char *argv[])
       mesh.SetCurvature(2);
    }
 
-   // 5. Define a finite element space on the mesh. The polynomial order is
+   // 4. Define a finite element space on the mesh. The polynomial order is
    //    one (linear) by default, but this can be changed on the command line.
    H1_FECollection fec(order, dim);
    FiniteElementSpace fespace(&mesh, &fec);
 
-   // 6. As in Example 1, we set up bilinear and linear forms corresponding to
+   // 5. As in Example 1, we set up bilinear and linear forms corresponding to
    //    the Laplace problem -\Delta u = 1. We don't assemble the discrete
    //    problem yet, this will be done in the main loop.
    BilinearForm a(&fespace);
-   if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
    LinearForm b(&fespace);
 
    ConstantCoefficient one(1.0);
@@ -117,18 +98,18 @@ int main(int argc, char *argv[])
    a.AddDomainIntegrator(integ);
    b.AddDomainIntegrator(new DomainLFIntegrator(one));
 
-   // 7. The solution vector x and the associated finite element grid function
+   // 6. The solution vector x and the associated finite element grid function
    //    will be maintained over the AMR iterations. We initialize it to zero.
    GridFunction x(&fespace);
    x = 0.0;
 
-   // 8. All boundary attributes will be used for essential (Dirichlet) BC.
+   // 7. All boundary attributes will be used for essential (Dirichlet) BC.
    MFEM_VERIFY(mesh.bdr_attributes.Size() > 0,
                "Boundary attributes required in the mesh.");
    Array<int> ess_bdr(mesh.bdr_attributes.Max());
    ess_bdr = 1;
 
-   // 9. Connect to GLVis.
+   // 8. Connect to GLVis.
    char vishost[] = "localhost";
    int  visport   = 19916;
    socketstream sol_sock;
@@ -137,23 +118,23 @@ int main(int argc, char *argv[])
       sol_sock.open(vishost, visport);
    }
 
-   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
-   //     that uses the ComputeElementFlux method of the DiffusionIntegrator to
-   //     recover a smoothed flux (gradient) that is subtracted from the element
-   //     flux to get an error indicator. We need to supply the space for the
-   //     smoothed flux: an (H1)^sdim (i.e., vector-valued) space is used here.
+   // 9. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
+   //    that uses the ComputeElementFlux method of the DiffusionIntegrator to
+   //    recover a smoothed flux (gradient) that is subtracted from the element
+   //    flux to get an error indicator. We need to supply the space for the
+   //    smoothed flux: an (H1)^sdim (i.e., vector-valued) space is used here.
    FiniteElementSpace flux_fespace(&mesh, &fec, sdim);
    ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace);
    estimator.SetAnisotropic();
 
-   // 11. A refiner selects and refines elements based on a refinement strategy.
+   // 10. A refiner selects and refines elements based on a refinement strategy.
    //     The strategy here is to refine elements with errors larger than a
    //     fraction of the maximum element error. Other strategies are possible.
    //     The refiner will call the given error estimator.
    ThresholdRefiner refiner(estimator);
    refiner.SetTotalErrorFraction(0.7);
 
-   // 12. The main AMR loop. In each iteration we solve the problem on the
+   // 11. The main AMR loop. In each iteration we solve the problem on the
    //     current mesh, visualize the solution, and refine the mesh.
    const int max_dofs = 50000;
    for (int it = 0; ; it++)
@@ -162,53 +143,44 @@ int main(int argc, char *argv[])
       cout << "\nAMR iteration " << it << endl;
       cout << "Number of unknowns: " << cdofs << endl;
 
-      // 13. Assemble the right-hand side.
+      // 12. Assemble the stiffness matrix and the right-hand side.
+      a.Assemble();
       b.Assemble();
 
-      // 14. Set Dirichlet boundary values in the GridFunction x.
+      // 13. Set Dirichlet boundary values in the GridFunction x.
       //     Determine the list of Dirichlet true DOFs in the linear system.
       Array<int> ess_tdof_list;
       x.ProjectBdrCoefficient(zero, ess_bdr);
       fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
 
-      // 15. Assemble the stiffness matrix.
-      a.Assemble();
-
-      // 16. Create the linear system: eliminate boundary conditions, constrain
+      // 14. Create the linear system: eliminate boundary conditions, constrain
       //     hanging nodes and possibly apply other transformations. The system
       //     will be solved for true (unconstrained) DOFs only.
-      OperatorPtr A;
+      SparseMatrix A;
       Vector B, X;
-
       const int copy_interior = 1;
       a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
 
-      // 17. Solve the linear system A X = B.
-      if (!pa)
-      {
 #ifndef MFEM_USE_SUITESPARSE
-         // Use a simple symmetric Gauss-Seidel preconditioner with PCG.
-         GSSmoother M((SparseMatrix&)(*A));
-         PCG(*A, M, B, X, 3, 200, 1e-12, 0.0);
+      // 15. Define a simple symmetric Gauss-Seidel preconditioner and use it to
+      //     solve the linear system with PCG.
+      GSSmoother M(A);
+      PCG(A, M, B, X, 3, 200, 1e-12, 0.0);
 #else
-         // If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
-         UMFPackSolver umf_solver;
-         umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-         umf_solver.SetOperator(*A);
-         umf_solver.Mult(B, X);
+      // 15. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the
+      //     the linear system.
+      UMFPackSolver umf_solver;
+      umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
+      umf_solver.SetOperator(A);
+      umf_solver.Mult(B, X);
 #endif
-      }
-      else // No preconditioning for now in partial assembly mode.
-      {
-         CG(*A, B, X, 3, 2000, 1e-12, 0.0);
-      }
 
-      // 18. After solving the linear system, reconstruct the solution as a
+      // 16. After solving the linear system, reconstruct the solution as a
       //     finite element GridFunction. Constrained nodes are interpolated
       //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
       a.RecoverFEMSolution(X, b, x);
 
-      // 19. Send solution by socket to the GLVis server.
+      // 17. Send solution by socket to the GLVis server.
       if (visualization && sol_sock.good())
       {
          sol_sock.precision(8);
@@ -221,7 +193,7 @@ int main(int argc, char *argv[])
          break;
       }
 
-      // 20. Call the refiner to modify the mesh. The refiner calls the error
+      // 18. Call the refiner to modify the mesh. The refiner calls the error
       //     estimator to obtain element errors, then it selects elements to be
       //     refined and finally it modifies the mesh. The Stop() method can be
       //     used to determine if a stopping criterion was met.
@@ -232,7 +204,7 @@ int main(int argc, char *argv[])
          break;
       }
 
-      // 21. Update the space to reflect the new state of the mesh. Also,
+      // 19. Update the space to reflect the new state of the mesh. Also,
       //     interpolate the solution x so that it lies in the new space but
       //     represents the same function. This saves solver iterations later
       //     since we'll have a good initial guess of x in the next step.
@@ -241,7 +213,7 @@ int main(int argc, char *argv[])
       fespace.Update();
       x.Update();
 
-      // 22. Inform also the bilinear and linear forms that the space has
+      // 20. Inform also the bilinear and linear forms that the space has
       //     changed.
       a.Update();
       b.Update();

examples/ex6p.cpp

@@ -15,19 +15,12 @@
 //               mpirun -np 4 ex6p -m ../data/square-disc-surf.mesh -o 2
 //               mpirun -np 4 ex6p -m ../data/amr-quad.mesh
 //
-// Device sample runs:
-//               mpirun -np 4 ex6p -pa -d cuda
-//               mpirun -np 4 ex6p -pa -d occa-cuda
-//               mpirun -np 4 ex6p -pa -d raja-omp
-//               mpirun -np 4 ex6p -pa -d ceed-cpu
-//               mpirun -np 4 ex6p -pa -d ceed-cuda
-//
 // Description:  This is a version of Example 1 with a simple adaptive mesh
 //               refinement loop. The problem being solved is again the Laplace
 //               equation -Delta u = 1 with homogeneous Dirichlet boundary
 //               conditions. The problem is solved on a sequence of meshes which
 //               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
+//               or non-conforming (quadrilateral, hexahedrons) manner according
 //               to a simple ZZ error estimator.
 //
 //               The example demonstrates MFEM's capability to work with both
@@ -56,8 +49,6 @@ int main(int argc, char *argv[])
    // 2. Parse command-line options.
    const char *mesh_file = "../data/star.mesh";
    int order = 1;
-   bool pa = false;
-   const char *device_config = "cpu";
    bool visualization = true;
 
    OptionsParser args(argc, argv);
@@ -65,10 +56,6 @@ int main(int argc, char *argv[])
                   "Mesh file to use.");
    args.AddOption(&order, "-o", "--order",
                   "Finite element order (polynomial degree).");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device_config, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -87,19 +74,14 @@ int main(int argc, char *argv[])
       args.PrintOptions(cout);
    }
 
-   // 3. Enable hardware devices such as GPUs, and programming models such as
-   //    CUDA, OCCA, RAJA and OpenMP based on command line options.
-   Device device(device_config);
-   if (myid == 0) { device.Print(); }
-
-   // 4. Read the (serial) mesh from the given mesh file on all processors.  We
+   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
    //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
    //    and volume meshes with the same code.
    Mesh *mesh = new Mesh(mesh_file, 1, 1);
    int dim = mesh->Dimension();
    int sdim = mesh->SpaceDimension();
 
-   // 5. Refine the serial mesh on all processors to increase the resolution.
+   // 4. Refine the serial mesh on all processors to increase the resolution.
    //    Also project a NURBS mesh to a piecewise-quadratic curved mesh. Make
    //    sure that the mesh is non-conforming.
    if (mesh->NURBSext)
@@ -109,7 +91,7 @@ int main(int argc, char *argv[])
    }
    mesh->EnsureNCMesh();
 
-   // 6. Define a parallel mesh by partitioning the serial mesh.
+   // 5. Define a parallel mesh by partitioning the serial mesh.
    //    Once the parallel mesh is defined, the serial mesh can be deleted.
    ParMesh pmesh(MPI_COMM_WORLD, *mesh);
    delete mesh;
@@ -119,16 +101,15 @@ int main(int argc, char *argv[])
    Array<int> ess_bdr(pmesh.bdr_attributes.Max());
    ess_bdr = 1;
 
-   // 7. Define a finite element space on the mesh. The polynomial order is
+   // 6. Define a finite element space on the mesh. The polynomial order is
    //    one (linear) by default, but this can be changed on the command line.
    H1_FECollection fec(order, dim);
    ParFiniteElementSpace fespace(&pmesh, &fec);
 
-   // 8. As in Example 1p, we set up bilinear and linear forms corresponding to
+   // 7. As in Example 1p, we set up bilinear and linear forms corresponding to
    //    the Laplace problem -\Delta u = 1. We don't assemble the discrete
    //    problem yet, this will be done in the main loop.
    ParBilinearForm a(&fespace);
-   if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
    ParLinearForm b(&fespace);
 
    ConstantCoefficient one(1.0);
@@ -137,12 +118,12 @@ int main(int argc, char *argv[])
    a.AddDomainIntegrator(integ);
    b.AddDomainIntegrator(new DomainLFIntegrator(one));
 
-   // 9. The solution vector x and the associated finite element grid function
+   // 8. The solution vector x and the associated finite element grid function
    //    will be maintained over the AMR iterations. We initialize it to zero.
    ParGridFunction x(&fespace);
    x = 0;
 
-   // 10. Connect to GLVis.
+   // 9. Connect to GLVis.
    char vishost[] = "localhost";
    int  visport   = 19916;
 
@@ -164,7 +145,7 @@ int main(int argc, char *argv[])
       sout.precision(8);
    }
 
-   // 11. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
+   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
    //     with L2 projection in the smoothing step to better handle hanging
    //     nodes and parallel partitioning. We need to supply a space for the
    //     discontinuous flux (L2) and a space for the smoothed flux (H(div) is
@@ -178,14 +159,14 @@ int main(int argc, char *argv[])
    // ParFiniteElementSpace smooth_flux_fes(&pmesh, &smooth_flux_fec, dim);
    L2ZienkiewiczZhuEstimator estimator(*integ, x, flux_fes, smooth_flux_fes);
 
-   // 12. A refiner selects and refines elements based on a refinement strategy.
+   // 11. A refiner selects and refines elements based on a refinement strategy.
    //     The strategy here is to refine elements with errors larger than a
    //     fraction of the maximum element error. Other strategies are possible.
    //     The refiner will call the given error estimator.
    ThresholdRefiner refiner(estimator);
    refiner.SetTotalErrorFraction(0.7);
 
-   // 13. The main AMR loop. In each iteration we solve the problem on the
+   // 12. The main AMR loop. In each iteration we solve the problem on the
    //     current mesh, visualize the solution, and refine the mesh.
    const int max_dofs = 100000;
    for (int it = 0; ; it++)
@@ -197,46 +178,41 @@ int main(int argc, char *argv[])
          cout << "Number of unknowns: " << global_dofs << endl;
       }
 
-      // 14. Assemble the right-hand side and determine the list of true
-      //     (i.e. parallel conforming) essential boundary dofs.
-      Array<int> ess_tdof_list;
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
+      // 13. Assemble the stiffness matrix and the right-hand side. Note that
+      //     MFEM doesn't care at this point that the mesh is nonconforming
+      //     and parallel. The FE space is considered 'cut' along hanging
+      //     edges/faces, and also across processor boundaries.
+      a.Assemble();
       b.Assemble();
 
-      // 15. Assemble the stiffness matrix. Note that MFEM doesn't care at this
-      //     point that the mesh is nonconforming and parallel.  The FE space is
-      //     considered 'cut' along hanging edges/faces, and also across
-      //     processor boundaries.
-      a.Assemble();
-
-      // 16. Create the parallel linear system: eliminate boundary conditions.
+      // 14. Create the parallel linear system: eliminate boundary conditions,
+      //     constrain hanging nodes and nodes across processor boundaries.
       //     The system will be solved for true (unconstrained/unique) DOFs only.
-      OperatorPtr A;
-      Vector B, X;
+      Array<int> ess_tdof_list;
+      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
 
+      HypreParMatrix A;
+      Vector B, X;
       const int copy_interior = 1;
       a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
 
-      // 17. Solve the linear system A X = B.
-      //     * With full assembly, use the BoomerAMG preconditioner from hypre.
-      //     * With partial assembly, use no preconditioner, for now.
-      HypreBoomerAMG *amg = NULL;
-      if (!pa) { amg = new HypreBoomerAMG; amg->SetPrintLevel(0); }
-      CGSolver cg(MPI_COMM_WORLD);
-      cg.SetRelTol(1e-6);
-      cg.SetMaxIter(2000);
-      cg.SetPrintLevel(3); // print the first and the last iterations only
-      if (amg) { cg.SetPreconditioner(*amg); }
-      cg.SetOperator(*A);
-      cg.Mult(B, X);
-      delete amg;
+      // 15. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
+      //     preconditioner from hypre.
+      HypreBoomerAMG amg;
+      amg.SetPrintLevel(0);
+      CGSolver pcg(A.GetComm());
+      pcg.SetPreconditioner(amg);
+      pcg.SetOperator(A);
+      pcg.SetRelTol(1e-6);
+      pcg.SetMaxIter(200);
+      pcg.SetPrintLevel(3); // print the first and the last iterations only
+      pcg.Mult(B, X);
 
-      // 18. Switch back to the host and extract the parallel grid function
-      //     corresponding to the finite element approximation X. This is the
-      //     local solution on each processor.
+      // 16. Extract the parallel grid function corresponding to the finite element
+      //     approximation X. This is the local solution on each processor.
       a.RecoverFEMSolution(X, b, x);
 
-      // 19. Send the solution by socket to a GLVis server.
+      // 17. Send the solution by socket to a GLVis server.
       if (visualization)
       {
          sout << "parallel " << num_procs << " " << myid << "\n";
@@ -252,7 +228,7 @@ int main(int argc, char *argv[])
          break;
       }
 
-      // 20. Call the refiner to modify the mesh. The refiner calls the error
+      // 18. Call the refiner to modify the mesh. The refiner calls the error
       //     estimator to obtain element errors, then it selects elements to be
       //     refined and finally it modifies the mesh. The Stop() method can be
       //     used to determine if a stopping criterion was met.
@@ -266,7 +242,7 @@ int main(int argc, char *argv[])
          break;
       }
 
-      // 21. Update the finite element space (recalculate the number of DOFs,
+      // 19. Update the finite element space (recalculate the number of DOFs,
       //     etc.) and create a grid function update matrix. Apply the matrix
       //     to any GridFunctions over the space. In this case, the update
       //     matrix is an interpolation matrix so the updated GridFunction will
@@ -274,7 +250,7 @@ int main(int argc, char *argv[])
       fespace.Update();
       x.Update();
 
-      // 22. Load balance the mesh, and update the space and solution. Currently
+      // 20. Load balance the mesh, and update the space and solution. Currently
       //     available only for nonconforming meshes.
       if (pmesh.Nonconforming())
       {
@@ -286,7 +262,7 @@ int main(int argc, char *argv[])
          x.Update();
       }
 
-      // 23. Inform also the bilinear and linear forms that the space has
+      // 21. Inform also the bilinear and linear forms that the space has
       //     changed.
       a.Update();
       b.Update();