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

First change to interior dof ordering for cubic quad elements.
Default command line behavior wrt glvis visualization fixed. Cubic Edge DoF orientation fixed.
2018-10-07 15:31:13 -04:00 · 2018-10-02 15:05:24 -04:00 · 2018-09-16 17:37:22 -04:00 · 2018-09-16 14:14:16 -04:00 · 2018-09-09 14:47:22 -04:00 · 2018-09-06 17:20:10 -04:00
276 changed files with 75488 additions and 48659 deletions
@@ -43,9 +43,7 @@ before_build:
 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
@@ -45,8 +45,6 @@ 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
@@ -78,13 +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/ex22*.mesh
-examples/ex22*.sol
-examples/ex22p_*.*

 examples/sundials/ex9
 examples/sundials/ex1[06]
@@ -142,20 +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*

@@ -169,7 +156,6 @@ miniapps/performance/sol.*
 miniapps/tools/display-basis
 miniapps/tools/load-dc
 miniapps/tools/convert-dc
-miniapps/tools/lor-transfer

 miniapps/nurbs/ex1
 miniapps/nurbs/ex1p
@@ -179,7 +165,3 @@ miniapps/nurbs/mesh.*
 miniapps/nurbs/sol.*
 miniapps/nurbs/mode_*
 miniapps/nurbs/Example1*
-
-# Unit test binary and outputs
-tests/unit/output_meshes
-tests/unit/unit_tests
@@ -205,7 +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
@@ -8,179 +8,17 @@
                               http://mfem.org


-Version 4.0-RC2, Apr 24, 2019
-=============================
-
-Requirements and Limitations
----------------------------
- This is a release candidate for mfem-4.0.
- Use at your own risk -- not everything will work and the API may change.
- We are looking for feedback from friendly users.
- Unlike previous MFEM releases, this version requires a C++11 compiler.
-
- GPU-related limitations:
-  * Hypre preconditioners are not yet available in GPU mode.
-  * Only constant coefficients are currently supported on GPUs.
-  * Full-assembly (on device), element assembly, and matrix-free bilinear forms
-    are not supported yet. Element batching is currently ignored.
-  * Partial assembly kernels are not implemented yet for simplices.
-
-GPU support
-----------
- Added initial support for hardware devices, such as GPUs, and programming
-  models, such as CUDA, OCCA, RAJA and OpenMP.
-
- The GPU/device support is based on MFEM's new backends and kernels working
-  seamlessly with a new lightweight device/host memory manager. The kernels can
-  be implemented either in OCCA, or as a simple wrapper around for-loops, which
-  can then be dispatched to RAJA and native backends. See the files forall.hpp
-  and mem_manager.hpp in the general/ directory.
-
- Several of the MFEM example codes (ex1, ex1p, ex6, and ex6p) can now take
-  advantage of GPU acceleration with the backend selectable at runtime. Many of
-  the linear algebra and finite element operations (e.g. partially assembled
-  bilinear forms) have been extended to take advantage of kernel acceleration by
-  simply replacing loops with the MFEM_FORALL() macro.
-
- In addition to pure CUDA, the library currently supports OCCA, RAJA and OpenMP
-  kernels, which could be mixed and matched in different parts of the same
-  application. We plan on adding support for more programming models and devices
-  in the future, without the need for significant modifications in user code.
-  The list of current backends is: "occa-cuda", "raja-cuda", "cuda", "occa-omp",
-  "raja-omp", "omp", "occa-cpu", "raja-cpu", and "cpu".
-
-Discretization improvements
---------------------------
- Added support for a general "low-order refined"-to-"high-order" transfer of
-  GridFunction data from a "low-order refined" (LOR) space defined on a refined
-  mesh to a "high-order" (HO) finite element space defined on a coarse mesh. See
-  the new classes InterpolationGridTransfer and L2ProjectionGridTransfer and the
-  new LOR Transfer miniapp: miniapps/tools/lor-transfer.cpp.
-
- Added support for derefinement of vector (RT + ND) spaces.
-
- Added element flux, and flux energy computation in class ElasticityIntegrator,
-  allowing for the use of Zienkiewicz-Zhu type error estimators with the
-  integrator. For an illustration of this addition, see the new Example 22.
-
- Added a variety of coefficients which are sums or products of existing
-  coefficients as well as grid function coefficients which return the
-  divergence, gradient, or curl of their GridFunctions.
-
-Support for wedge elements and meshes with mixed element types
--------------------------------------------------------------
- Added support for wedge-shaped mesh elements of arbitrary order (with Geometry
-  type PRISM) which have two triangular faces and three quadrilateral faces.
-  Several examples of such meshes can be found in the data/ directory.
-
- Added H1 and L2 finite elements of arbitrary order for Wedge elements.
-
- Added support for mixed meshes containing triangles and quadrilaterals in 2D
-  or tetrahedra, wedges, and hexahedra in 3D. This includes support for uniform
-  refinement of such meshes. Several examples of such meshes can be found in the
-  data/ directory.
-
- Added support for reading and writing linear and quadratic meshes containing
-  wedge elements in VTK mesh format. Several examples of such meshes can be
-  found in the data/ directory.
-
-Other meshing improvements
--------------------------
- Improved the uniform refinement of tetrahedral meshes (also part of the
-  uniform refinement of mixed 3D meshes). The previous refinement algorithm is
-  still available as an option in Mesh::UniformRefinement. Both can be used in
-  the updated Mesh Explorer miniapp.
-
- The local tetrahedral mesh refinement algorithm in serial and in parallel now
-  follows precisely the paper:
-
-     D. Arnold, A. Mukherjee, and L. Pouly, "Locally Adapted Tetrahedral Meshes
-     Using Bisection", SIAM J. Sci. Comput. 22 (2000), 431–448.
-
-  This guarantees that the shape regularity of the elements will be preserved
-  under refinement.
-
- Added support for parallel communication groups on non-conforming meshes.
-
- Improved parallel partitioning of non-conforming meshes. If the coarse mesh
-  elements are ordered as a sequence of face-neighbors, the parallel partitions
-  are now guaranteed to be continuous. To that end, inline quadrilateral and
-  hexahedral meshes are now by default ordered along a space-filling curve.
-
- A boundary in a NURBS mesh can now be connected with another boundary. Such a
-  periodic NURBS mesh is a simple way to impose periodic boundary conditions.
-
+Version 3.4.1 (development)
+===========================
 - Added support for reading linear and quadratic 2D quadrilateral and triangular
  Cubit meshes.

- The TMOP mesh optimization algorithms were extended to support user-defined
-  space-dependent limiting terms. Improved the TMOP objective functions by more
-  accurate normalization of the different terms.
-
-New and updated examples and miniapps
-------------------------------------
- Added a new meshing miniapp, Toroid, which can produce a variety of torus
-  shaped meshes by twisting a stack of wedges or hexahedra.
-
- Added a new meshing miniapp, Extruder, that demonstrates the capability to
-  produce 3D meshes by extruding 2D meshes.
-
- Added a simple miniapp, LOR Transfer, for visualizing the actions of the
-  transfer operators between a high-order and a low-order refined spaces.
-
- Added a new example, Example 20/20p, that solves a system of 1D ODEs derived
-  from a Hamiltonian. The example demonstrates the use of the variable order,
-  symplectic integration algorithm implemented in class SIAVSolver.
-
- Added a new example, Example 22/22p, that illustrates the use of AMR to solve
-  a linear elasticity problem. This is an extension of Example 2/2p.
-
-New and improved solvers and preconditioners
--------------------------------------------
- Added support for parallel ILU preconditioning via hypre's Euclid solver.
-
- Added support for STRUMPACK v3 with a small API change in the class
-  STRUMPACKSolver, see "API changes" below.
-
-Miscellaneous
-------------
- 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.
-
- Added unit tests based on the Catch++ library.
-
- Renamed the option MFEM_USE_OPENMP to MFEM_USE_LEGACY_OPENMP. This legacy
-  option is deprecated and planned for removal in a future release. The original
-  option name, MFEM_USE_OPENMP, is now used to enable the new OpenMP backends in
-  the new kernels.
-
- Altered the way FGMRES counts its iterations so that it matches GMRES.
-
- Various other simplifications, extensions, and bugfixes in the code.
-
-API changes
-----------
- In multiple places, use Geometry::Type instead of int, where appropriate.
- In multiple places, use Element::Type instead of int, where appropriate.
- The Mesh methods GetElementBaseGeometry and GetBdrElementBaseGeometry no
-  longer have a default value for their parameter, they only work with an
-  explicitly given index.
- In class Mesh, added methods useful for queries regarding the types of
-  elements present in the mesh: HasGeometry, GetNumGeometries, GetGeometries,
-  and class Mesh::GeometryList.
- The struct CoarseFineTransformations (returned by the Mesh method
-  GetRefinementTransforms) now stores the embedding matrices separately for each
-  Geometry::Type.
- In class ParMesh, replaced the method GroupNFaces with two new methods:
-  GroupNTriangles and GroupNQuadrilaterals. Also, replaced GroupFace with two
-  methods: GroupTriangle and GroupQuadrilateral.
- In class ParMesh, made the two RefineGroups methods protected.
- Removed the virtual method Element::GetRefinementFlag, it is only used by the
-  derived class Tetrahedron.
- Added new methods: Array::CopyTo, Tetrahedron::Init.
- In class STRUMPACKSolver, the method SetMC64Job() was replaced by the new
-  methods: DisableMatching(), EnableMatching(), and EnableParallelMatching().
+- 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
@@ -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.
@@ -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()
@@ -182,11 +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)
@@ -273,32 +262,6 @@ if (MFEM_USE_PUMI)
  endif()
 endif()

-# CUDA
-if (MFEM_USE_CUDA)
-   set(CMAKE_CUDA_STANDARD 11)
-   set(CMAKE_CUDA_STANDARD_REQUIRED ON)
-   set(CMAKE_CUDA_EXTENSIONS OFF)
-   set(CMAKE_CUDA_FLAGS "-arch=${CUDA_ARCH} --expt-extended-lambda"
-       CACHE STRING "CUDA flags set for MFEM" FORCE)
-   if (MFEM_USE_MPI)
-      set(CUDA_CCBIN_COMPILER ${MPI_CXX_COMPILER})
-   else()
-      set(CUDA_CCBIN_COMPILER ${CMAKE_CXX_COMPILER})
-   endif()
-   string(APPEND CMAKE_CUDA_FLAGS " -ccbin ${CUDA_CCBIN_COMPILER}")
-   set(MFEM_USE_MM YES CACHE BOOL "Enable MFEM's memory manager" FORCE)
-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)
@@ -324,7 +287,7 @@ endif()
 #    be before SuiteSparse.
 set(MFEM_TPLS MPI_CXX OPENMP BLAS LAPACK METIS HYPRE SuiteSparse SUNDIALS PETSC
    MESQUITE SuperLUDist STRUMPACK AXOM CONDUIT GECKO GNUTLS NETCDF MPFR PUMI
-    POSIXCLOCKS MFEMBacktrace ZLIB OCCA RAJA)
+    POSIXCLOCKS MFEMBacktrace ZLIB)
 # Add all *_FOUND libraries in the variable TPL_LIBRARIES.
 set(TPL_LIBRARIES "")
 set(TPL_INCLUDE_DIRS "")
@@ -349,6 +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 ${WIN32})
+
 #-------------------------------------------------------------------------------
 # Define and configure the MFEM library
 #-------------------------------------------------------------------------------
@@ -360,13 +326,6 @@ set(MFEM_SOURCE_DIRS general linalg mesh fem)
 foreach(DIR IN LISTS MFEM_SOURCE_DIRS)
  add_subdirectory(${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
  ${PROJECT_SOURCE_DIR}/mfem.hpp
@@ -377,11 +336,6 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON CACHE BOOL "")
 set(CMAKE_INSTALL_RPATH "${_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 = ${TPL_LIBRARIES}")
@@ -434,9 +388,6 @@ endif()
 # Enable testing if required
 if (MFEM_ENABLE_TESTING)
  enable_testing()
-  set(MFEM_ALL_TESTS_TARGET_NAME tests)
-  add_mfem_target(${MFEM_ALL_TESTS_TARGET_NAME} OFF)
-  add_subdirectory(tests EXCLUDE_FROM_ALL)
 endif()

 # Define a target that all examples and miniapps will depend on.
@@ -456,9 +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
@@ -479,12 +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()
@@ -529,13 +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 ${HEADERS}
 # ---
 # foreach (HDR ${HEADERS})
@@ -601,10 +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()
@@ -90,18 +90,13 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
  ├── general
  ├── linalg
  ├── mesh
-  ├── miniapps
-  │   ├── common
-  │   ├── electromagnetics
-  │   ├── meshing
-  │   ├── nurbs
-  │   ├── performance
-  │   └── tools
-  └── tests
-      ├── unit
-      │   ├── ...
-      └── ...
-
+  └── miniapps
+      ├── common
+      ├── electromagnetics
+      ├── meshing
+      ├── nurbs
+      ├── performance
+      └── tools
  ```

 - The main directories are `fem/`, `mesh/` and `linalg/` containing the C++
@@ -142,16 +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.

@@ -166,9 +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.

@@ -334,9 +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.
@@ -376,10 +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.
@@ -490,6 +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
@@ -13,38 +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, OCCA, OpenMP and RAJA.
-
- Starting with version 4.0, MFEM requires a C++11 compiler
-
- CUDA support requires an NVIDIA GPU and an installation of the CUDA Toolkit
-  https://developer.nvidia.com/cuda-toolkit
-
- OCCA support requires the OCCA library
-  https://libocca.org
-
- OpenMP support requires a compiler implementing the OpenMP API
-  https://www.openmp.org
-
- RAJA support requires installation of the RAJA performance portability layer
-  with (optionally) support for CUDA and OpenMP
-  https://github.com/LLNL/RAJA
-
 The library supports two build systems: one based on GNU make, and a second one
 based on CMake. Both build systems are described below. Some hints for building
 without GNU make or CMake can be found at the end of this file.
@@ -54,7 +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
@@ -66,15 +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')
-
 Example codes (serial/parallel, depending on the build):
   cd examples
   make -j 4
@@ -85,6 +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:
@@ -93,19 +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

@@ -165,10 +132,6 @@ are also defined:
   make parallel -> Builds parallel optimized version of the library
   make debug    -> Builds serial debug version of the library
   make pdebug   -> Builds parallel debug version of the library
-   make cuda     -> Builds serial cuda optimized version of the library
-   make pcuda    -> Builds parallel cuda optimized version of the library
-   make cudebug  -> Builds serial cuda debug version of the library
-   make pcudebug -> Builds parallel cuda debug version of the library

 Note that any of the above shortcuts accept configuration options, either at the
 command line or through a user configuration file.
@@ -230,9 +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
@@ -268,7 +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
@@ -288,12 +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.
@@ -404,32 +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_MM = YES/NO
-   Enables support for the MFEM's memory manager (MM), which is required to
-   support devices with different memory spaces. This option is required when
-   CUDA support is enabled, i.e. when MFEM_USE_CUDA=YES.
-
-MFEM_USE_CUDA = YES/NO
-   Enables support for CUDA devices in MFEM. CUDA is a parallel computing
-   platform and programming model for general computing on graphical processing
-   units (GPUs). This option requires MFEM_USE_MM. The variable CUDA_ARCH is
-   used to specify the CUDA compute capability used during compilation (by
-   default, CUDA_ARCH=sm_60). When enabled, this option uses the CUDA_* build
-   options, see below.
-
-MFEM_USE_RAJA = YES/NO
-   Enable support for the RAJA performance portability layer in MFEM. RAJA
-   provides a portable abstraction for loops, supporting different programming
-   model backends. When using 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_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.
@@ -451,7 +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
@@ -465,8 +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
@@ -498,8 +429,7 @@ 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
@@ -545,18 +475,6 @@ The specific libraries and their options are:
  URL: https://scorec.rpi.edu/pumi
  Options: PUMI_OPT, PUMI_LIB.

- CUDA, used when MFEM_USE_CUDA = YES.
-  URL: https://developer.nvidia.com/cuda-toolkit
-  Options: CUDA_CXX, CUDA_ARCH, CUDA_OPT, CUDA_LIB.
-
- OCCA, used when MFEM_USE_OCCA = YES.
-  URL: https://libocca.org
-  Options: OCCA_DIR, OCCA_OPT, OCCA_LIB.
-
- RAJA, used when MFEM_USE_RAJA = YES.
-  URL: https://github.com/LLNL/RAJA
-  Options: RAJA_DIR, RAJA_OPT, RAJA_LIB.
-
 - MPFR (optional), used when MFEM_USE_MPFR = YES.
  URL: http://mpfr.org, it depends on the GMP library: https://gmplib.org
  Options: MPFR_OPT, MPFR_LIB.
@@ -661,8 +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
@@ -680,7 +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.
@@ -693,10 +608,6 @@ MFEM_USE_NETCDF
 MFEM_USE_MPFR
 MFEM_USE_GZSTREAM
 MFEM_USE_PUMI
-MFEM_USE_CUDA
-MFEM_USE_OCCA
-MFEM_USE_RAJA
-MFEM_USE_MM

 The following options are CMake specific:

@@ -743,8 +654,6 @@ The CMake build system adds auto-detection for the following packages/libraries:
 - LIBUNWIND
 - POSIXCLOCKS
 - PUMI
- - OCCA
- - RAJA

 The following built-in CMake packages are also used:

@@ -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!
+
+
@@ -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.
@@ -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()

@@ -166,108 +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_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()
@@ -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@)
@@ -41,10 +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_MM @MFEM_USE_MM@)
-set(MFEM_USE_CUDA @MFEM_USE_CUDA@)
-set(MFEM_USE_OCCA @MFEM_USE_OCCA@)
-set(MFEM_USE_RAJA @MFEM_USE_RAJA@)

 set(MFEM_CXX_COMPILER "@CMAKE_CXX_COMPILER@")
 set(MFEM_CXX_FLAGS "@CMAKE_CXX_FLAGS@")
@@ -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

@@ -110,19 +101,6 @@
 // Enable MFEM functionality based on the PUMI library
 #cmakedefine MFEM_USE_PUMI

-// 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's internal Memory Manager (needed e.g. for MFEM_USE_CUDA)
-#cmakedefine MFEM_USE_MM
-
 // 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.
@@ -131,6 +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@

@@ -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.")
@@ -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()
@@ -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()
@@ -696,164 +685,3 @@ function(mfem_find_library Name Prefix Lib LibDoc CheckVar CheckSrc)
  endif()

 endfunction(mfem_find_library)
-
-
-#
-#   Function that creates 'config.mk' from 'config.mk.in' for the both the
-#   build- and the install-locations and define install rules for 'config.mk'
-#   and 'test.mk'.
-#
-function(mfem_export_mk_files)
-
-  # Define a few auxiliary variables (not written to 'config.mk')
-  string(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE)
-  # CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG -> '-Wl,-rpath,'
-  set(shared_link_flag ${CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG})
-  if (NOT shared_link_flag)
-    set(shared_link_flag "-Wl,-rpath,")
-  endif()
-
-  # Convert Boolean vars to YES/NO without writting the values to cache
-  set(CONFIG_MK_BOOL_VARS MFEM_USE_MPI MFEM_USE_METIS MFEM_USE_METIS_5
-      MFEM_DEBUG MFEM_USE_EXCEPTIONS MFEM_USE_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_MM 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::.*")
-    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()
@@ -15,9 +15,6 @@
 //
 // Otherwise, use the local file: _config.hpp.

-#ifndef MFEM_CONFIG_HPP
-#define MFEM_CONFIG_HPP
-
 #ifdef MFEM_BUILD_DIR
 #define MFEM_QUOTE(a) #a
 #define MFEM_MAKE_PATH(x,y) MFEM_QUOTE(x/y)
@@ -26,18 +23,6 @@
 #include "_config.hpp"
 #endif

-// Common configuration macros
-
-#if (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 7)) || defined(__clang__)
-#define MFEM_HAVE_GCC_PRAGMA_DIAGNOSTIC
-#endif
-
-// Windows specific options
-#ifdef _WIN32
-// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
-#define _USE_MATH_DEFINES
-#endif
-
 // Check dependencies:

 // Options that require MPI
@@ -55,10 +40,3 @@
 #error Building with PUMI (MFEM_USE_PUMI=YES) requires MPI (MFEM_USE_MPI=YES)
 #endif
 #endif // MFEM_USE_MPI not defined
-
-// CUDA requires the memory manager
-#if defined(MFEM_USE_CUDA) && !defined(MFEM_USE_MM)
-#error Building with CUDA (MFEM_USE_CUDA=YES) requires MFEM_USE_MM=YES
-#endif
-
-#endif // MFEM_CONFIG_HPP
@@ -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

@@ -121,18 +112,11 @@
 // Enable MFEM functionality based on the PUMI library
 // #define MFEM_USE_PUMI

-// Build the GPU/CUDA-enabled version of the MFEM library.
-// Requires a CUDA compiler (nvcc).
-// #define MFEM_USE_CUDA
-
-// Enable functionality based on the RAJA library.
-// #define MFEM_USE_RAJA
-
-// Enable functionality based on the OCCA library.
-// #define MFEM_USE_OCCA
-
-// Enable MFEM's internal Memory Manager (needed e.g. for MFEM_USE_CUDA)
-// #define MFEM_USE_MM
+// 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@
@@ -10,41 +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_GNUTLS        = @MFEM_USE_GNUTLS@
-MFEM_USE_NETCDF        = @MFEM_USE_NETCDF@
-MFEM_USE_PETSC         = @MFEM_USE_PETSC@
-MFEM_USE_MPFR          = @MFEM_USE_MPFR@
-MFEM_USE_SIDRE         = @MFEM_USE_SIDRE@
-MFEM_USE_CONDUIT       = @MFEM_USE_CONDUIT@
-MFEM_USE_PUMI          = @MFEM_USE_PUMI@
-MFEM_USE_CUDA          = @MFEM_USE_CUDA@
-MFEM_USE_RAJA          = @MFEM_USE_RAJA@
-MFEM_USE_OCCA          = @MFEM_USE_OCCA@
-MFEM_USE_MM            = @MFEM_USE_MM@
+MFEM_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@
@@ -72,8 +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@
@@ -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)
@@ -42,12 +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_MM "Enable MFEM's memory manager" OFF)
-option(MFEM_USE_CUDA "Enable CUDA" OFF)
-option(MFEM_USE_OCCA "Enable OCCA" OFF)
-option(MFEM_USE_RAJA "Enable RAJA" 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
@@ -63,16 +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
@@ -110,7 +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.")
@@ -118,8 +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 "${MFEM_DIR}/../scotch_6.0.4" CACHE PATH
    "Path to the Scotch and PT-Scotch libraries.")
 set(Scotch_REQUIRED_PACKAGES "Threads" CACHE STRING
@@ -161,9 +149,6 @@ set(Axom_REQUIRED_PACKAGES "Conduit/relay" CACHE STRING
 set(PUMI_DIR "${MFEM_DIR}/../pumi-2.1.0" CACHE STRING
    "Directory where PUMI is installed")

-set(OCCA_DIR "${MFEM_DIR}/../occa" CACHE PATH "Path to OCCA")
-set(RAJA_DIR "${MFEM_DIR}/../raja" CACHE PATH "Path to RAJA")
-
 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.")
@@ -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
@@ -38,41 +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=$(CUDA_ARCH)
-# Prefixes for passing flags to the host compiler and linker when using CUDA_CXX
-CUDA_XCOMPILER = -Xcompiler=
-CUDA_XLINKER   = -Xlinker=
-
 ifneq ($(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
@@ -95,36 +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_GNUTLS        = NO
-MFEM_USE_NETCDF        = NO
-MFEM_USE_PETSC         = NO
-MFEM_USE_MPFR          = NO
-MFEM_USE_SIDRE         = NO
-MFEM_USE_CONDUIT       = NO
-MFEM_USE_PUMI          = NO
-MFEM_USE_CUDA          = NO
-MFEM_USE_RAJA          = NO
-MFEM_USE_OCCA          = NO
-MFEM_USE_MM            = NO
+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 =
@@ -136,7 +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

@@ -154,8 +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
@@ -167,7 +147,7 @@ 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
@@ -203,8 +183,7 @@ SUPERLU_DIR = @MFEM_DIR@/../SuperLU_DIST_5.1.0
 SUPERLU_OPT = -I$(SUPERLU_DIR)/SRC
 SUPERLU_LIB = -Wl,-rpath,$(SUPERLU_DIR)/SRC -L$(SUPERLU_DIR)/SRC -lsuperlu_dist

-# SCOTCH library configuration (required by STRUMPACK <= v2.1.0, optional in
-# STRUMPACK >= v2.2.0)
+# SCOTCH 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\
@@ -300,23 +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

-# CUDA library configuration (currently not needed)
-CUDA_OPT =
-CUDA_LIB =
-
-# OCCA library configuration
-OCCA_DIR = @MFEM_DIR@/../occa
-OCCA_OPT = -I$(OCCA_DIR)/include
-OCCA_LIB = $(XLINKER)-rpath,$(OCCA_DIR)/lib -L$(OCCA_DIR)/lib -locca
-
-# RAJA library configuration
-RAJA_DIR = @MFEM_DIR@/../raja
-RAJA_OPT = -I$(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

@@ -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 "$0")"/.. && pwd)"
 mfem_build_dir=""
@@ -32,7 +30,7 @@ groups_serial=(
 '"examples"
   "Examples:"
   "examples"
-   "ex{,1,2}[0-9].cpp"'
+   "ex{,1}[0-9].cpp"'
 #   "ex1.cpp"'
 '"sundials"
   "SUNDIALS examples:"
@@ -46,15 +44,14 @@ groups_serial=(
 '"meshing"
   "Meshing miniapps:"
   "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
-    mesh-optimizer.cpp"'
+   "mobius-strip.cpp klein-bottle.cpp mesh-optimizer.cpp"'
 )
 # Parallel groups
 groups_parallel=(
 '"examples"
   "Examples:"
   "examples"
-   "ex{,1,2}[0-9]p.cpp"'
+   "ex{,1}[0-9]p.cpp"'
 #   "ex1p.cpp"'
 '"sundials"
   "SUNDIALS examples:"
@@ -84,7 +81,7 @@ groups_all=(
 '"examples"
   "Examples:"
   "examples"
-   "ex\"{,1,2}[0-9]\"{,p}.cpp"'
+   "ex\"{,1}[0-9]\"{,p}.cpp"'
 '"sundials"
   "SUNDIALS examples:"
   "examples/sundials"
@@ -100,8 +97,7 @@ groups_all=(
 '"meshing"
   "Meshing miniapps:"
   "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
-    {,p}mesh-optimizer.cpp"'
+   "mobius-strip.cpp klein-bottle.cpp {,p}mesh-optimizer.cpp"'
 '"electromagnetics"
   "Electromagnetics miniapps:"
   "miniapps/electromagnetics"
@@ -150,11 +146,6 @@ function extract_sample_runs()
   if [ "$skip_gen_meshes" == "yes" ]; then
      runs=`printf "%s" "$runs" | grep -v ".* -m .*\.gen"`
   fi
-   if [ "$device_runs" == "yes" ]; then
-      runs=`printf "%s" "$runs" | grep ".* -d .*"`
-   else
-      runs=`printf "%s" "$runs" | grep -v ".* -d .*"`
-   fi
   IFS=$'\n'
   runs=(${runs})
   IFS="${old_IFS}"
@@ -176,15 +167,9 @@ function help_message()
      -g <dir> <pattern>
                  Specify explicitly a group (dir + file pattern) to run; This
                  option can be used multiple times to define multiple groups
-      -dev        configure only sample runs using devices.
-                  To test with a parallel build, the parallel (-p|-par) option
-                  should be set first on the command line.
      -v          Enable valgrind
      -o <dir>    [${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
@@ -211,8 +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.

@@ -263,7 +248,7 @@ case "$1" in
   -h|-help)
      opt_help="yes"
      ;;
-   -p|-par)
+   -p|-parallel)
      mfem_config="MFEM_USE_MPI=YES MFEM_DEBUG=NO"
      ;;
   -g)
@@ -274,11 +259,6 @@ case "$1" in
      groups=("${groups[@]}" "${test_group}")
      shift 2
      ;;
-   -dev)
-       device_runs="yes"
-       mfem_config+=" MFEM_USE_CUDA=YES MFEM_USE_MM=YES \
-MFEM_USE_OCCA=YES MFEM_USE_RAJA=YES MFEM_USE_OPENMP=YES"
-      ;;
   -v)
      valgrind="yes"
      ;;
@@ -286,10 +266,6 @@ MFEM_USE_OCCA=YES MFEM_USE_RAJA=YES MFEM_USE_OPENMP=YES"
      shift
      output_dir="$1"
      ;;
-   -d)
-      shift
-      mfem_build_dir="$1"
-      ;;
   -j)
      shift
      make_j="-j $1"
@@ -309,10 +285,6 @@ MFEM_USE_OCCA=YES MFEM_USE_RAJA=YES MFEM_USE_OPENMP=YES"
   -n)
      run_prefix="echo"
      ;;
-   -*)
-      echo "unknown option: '$1'"
-      exit 1
-      ;;
   *=*)
      eval $1
      ;;
@@ -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
@@ -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
@@ -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
@@ -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
-
-0.028213666146621 -1.0129124616273 -1.0197422793601
-0.99151103207842 -0.97408353323117 -1.0219424221199
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+1 2 18 15 19
+1 2 21 18 22
+1 2 2 4 7
+1 2 6 7 10
+1 2 9 10 13
+1 2 12 13 16
+1 2 15 16 19
+1 2 18 19 22
+
+boundary
+17
+1 1 0 1
+1 1 1 5
+1 1 5 8
+1 1 8 11
+1 1 11 14
+1 1 14 17
+1 1 17 20
+1 1 20 21
+1 1 21 22
+1 1 22 19
+1 1 19 16
+1 1 16 13
+1 1 13 10
+1 1 10 7
+1 1 7 4
+1 1 4 3
+1 1 3 0
+
+vertices
+23
+2
+1.11408460164 0.0
+0.557042300822 0.964825566988
+0.417781725616 0.723619175241
+0.835563451232 0.0
+0.482412783494 0.278521150411
+-0.557042300822 0.964825566988
+-0.417781725616 0.723619175241
+3.41090035345e-17 0.557042300822
+-1.11408460164 1.36436014138e-16
+-0.835563451232 1.02327010604e-16
+-0.482412783494 0.278521150411
+-0.557042300822 -0.964825566988
+-0.417781725616 -0.723619175241
+-0.482412783494 -0.278521150411
+0.557042300822 -0.964825566988
+0.417781725616 -0.723619175241
+-1.02327010604e-16 -0.557042300822
+1.11408460164 -2.72872028276e-16
+0.835563451232 -2.04654021207e-16
+0.482412783494 -0.278521150411
+0.557042300822 0.964825566988
+0.417781725616 0.723619175241
+0.482412783494 0.278521150411
@@ -0,0 +1,924 @@
+#Title:circInSquare.py
+#Author:T. M. McManus
+#Date:10-7-18
+#Purpose: Fill a circular sector with triangles and a bounding region,
+#defined by 3 nodes, with quads.  Then reflect/preserve QuadI twice to
+#create a complete disc bounded in a square.
+
+import scipy as sp
+import argparse
+import sys
+import subprocess
+import time
+
+parser=argparse.ArgumentParser(description='Fill a circular sector with triangles and a bounding region,\
+defined by 3 nodes, with quads.  Then reflect/preserve QuadI twice to create a complete disc bounded in a square.'
+,epilog='Sample run: python circInSquare.py -r 1 -e 2 -n 8 -g ../../../glvis/glvis')
+
+parser.add_argument('-r','--circRad', nargs='?',const=1, default = 1.0, type=float, help='Radius of circle')
+parser.add_argument('-e','--edgeLength', nargs='?',const=1,default=2.0,type=float,help='Edge-length of bounding square')
+parser.add_argument('-n','--numEdges',nargs='?',const=1,default=6,type=int,help='n-gon approximation of internal circle')
+parser.add_argument('-o','--outputFile',nargs='?',const=1,default='circInSquare', help='Output file name.')
+parser.add_argument('-g','--glvis',nargs='?',const=1,default='',type=str,help='Abs. or rel. path of glvis binary.')
+args=parser.parse_args()
+
+r=args.circRad 
+edgeLength=args.edgeLength
+numEdges=args.numEdges
+outputName=args.outputFile
+glvis=args.glvis
+
+visMesh=False;
+
+if glvis!='':
+    visMesh=True
+
+if r >= edgeLength:
+    print("Circle radius must be less than bounding square edge length")
+    sys.exit(1)
+
+if sp.mod(numEdges,2) != 0:
+    print("Currently this mixed element generator only supports an even numbers of edges.")
+    sys.exit(1)
+
+    
+#The basic idea:
+#1. Construct topology for regions
+#2. Combine topologies
+#3. Construct boundary
+#4. Construct geometry for regions
+#5. Combine geometries
+#6. Output
+
+def eleMatCirc(numEdges):
+    
+    nNodesSeq=sp.zeros([numEdges])
+    nNodesSeq[0]=3
+    if numEdges != 1:
+        for n in range(1,numEdges):
+            nNodesSeq[n]=nNodesSeq[n-1]+(2+n)
+            
+    numCircNodesTot =int(((numEdges+1)*(numEdges+2))/2)
+    
+    b=range(numCircNodesTot)
+    row_size=1
+    A=sp.zeros([numEdges+1,numEdges+1])
+    start=0;stop=1;
+    for m in range(numEdges+1):
+        if m==0:
+            A[m,range(m+1)]=b[0:1]
+            start=0
+            stop=1
+        else:
+            start=stop
+            stop=stop+m+1
+            A[m,range(m+1)]=b[start:stop]
+
+    M=sp.ones([numEdges**2,5])
+    m_row=0
+    for m in range(numEdges):
+        if m==0:
+            M[0,:]=[1,2,0,1,2]
+            m_row+=1
+        else:
+           holder=sp.size(sp.nonzero(A[m,:]))
+           for n in range(holder):
+               if n!=holder-1:
+                   M[m_row,:]=[1,2,A[m,n],A[m,n+1],A[m+1,n+1]]
+                   m_row+=1
+                   M[m_row,:]=[1,2,A[m,n],A[m+1,n],A[m+1,n+1]]
+                   m_row+=1
+               else:
+                   M[m_row,:]=[1,2,A[m,n],A[m+1,n],A[m+1,n+1]]
+                   m_row+=1
+            
+    return M.astype(int),numCircNodesTot
+
+def eleMatQuad(numEdges):
+    S0=numEdges*(numEdges+1)/(2.0)
+    A=sp.linspace(S0,(S0+(numEdges+1)**2)-1,(numEdges+1)**2)
+    A=A.reshape([numEdges+1,numEdges+1])
+    quadNode=sp.delete(A,-1,1)
+    quadNode=sp.delete(quadNode,-1,0)
+    quadNode=quadNode.flatten()
+    M=sp.zeros([numEdges**2,6])
+    for n in range(numEdges**2):
+        M[n,:]=[2,3,quadNode[n],quadNode[n]+1,quadNode[n]+numEdges+2,quadNode[n]+numEdges+1]
+    return M.astype(int)
+
+def boundMatTot(numEdges):
+    triS1=sp.zeros(numEdges+1)
+    triS3=sp.zeros(numEdges+1)
+    quadS1=sp.zeros(numEdges)
+    quadS2=sp.zeros(numEdges-1)
+    quadS3=sp.zeros(numEdges)
+
+    triS1[0]=0;
+    triS3[0]=0;
+    for n in range(1,numEdges+1):
+        triS1[n]=triS1[n-1]+n
+        triS3[n]=triS1[n]+n
+    ref1=triS3
+    
+    triS3=sp.flipud(triS3)
+    quadS1[0]=triS1[-1]+numEdges+1
+    quadS3[0]=triS1[-1]+2*numEdges+1
+
+    for n in range(1,numEdges):
+        quadS1[n]=quadS1[n-1]+(numEdges+1)
+        quadS3[n]=quadS3[n-1]+(numEdges+1)    
+    ref2=quadS3
+    xAxisRootRef=sp.concatenate([triS1.copy(),quadS1],axis=0)
+    quadS3=sp.flipud(quadS3)
+    quadS2=range(int(quadS1[-1]+1),int(quadS3[0]),1)
+    STOT=sp.concatenate([triS1,quadS1,quadS2,quadS3,triS3],axis=0)
+
+    filler=sp.zeros(1)
+    filler[0]=quadS3[0]
+    fillerFirst=sp.zeros(1)
+    fillerFirst[0]=quadS1[-1]
+    sTotRef=sp.concatenate([triS1,quadS1,quadS2,filler],axis=0)
+    newsTotRef=sp.concatenate([fillerFirst,quadS2,filler],axis=0)
+    boundMat=sp.zeros([STOT.size-1,4])
+    boundMatRef=sp.zeros([sTotRef.size-1,4])
+    new_boundMat_ref=sp.zeros([newsTotRef.size-1,4])
+    
+    for n in range(STOT.size-1):
+        boundMat[n,:]=[1,1,STOT[n],STOT[n+1]]
+    for n in range(sTotRef.size-1):
+        boundMatRef[n,:]=[1,1,sTotRef[n],sTotRef[n+1]]
+    for n in range(newsTotRef.size-1):
+        new_boundMat_ref[n,:]=[1,1,newsTotRef[n],newsTotRef[n+1]]
+        
+    ref=sp.concatenate([ref1,ref2],axis=0).astype(int)
+    return boundMat.astype(int),ref,boundMatRef.astype(int),xAxisRootRef.astype(int),new_boundMat_ref.astype(int)
+
+def vertMatCirc(numEdges):
+    r_o=sp.linspace(0,r,numEdges+1)
+    counter=0
+    vertMat=sp.zeros([numCircNodesTot,2])
+    for m in range(numEdges+1):
+        theta=sp.linspace(0,sp.pi/2.0,m+1)
+        for n in range(sp.size(theta)):
+            vertMat[counter,:]=[r_o[m]*sp.cos(theta[n]),r_o[m]*sp.sin(theta[n])]
+            counter+=1
+    return vertMat
+
+def vertMatQuad(numEdges):
+
+    theta=sp.linspace(0,sp.pi/2.0,numEdges+1)
+    AX=sp.zeros([numEdges+1,numEdges+1])
+    AY=sp.zeros([numEdges+1,numEdges+1])
+    AX[0,:]=r*sp.cos(theta)
+    AY[0,:]=r*sp.sin(theta)
+
+    vertLinSpace=sp.linspace(0,edgeLength,(numEdges/2)+1)
+    horzLineSpace=sp.linspace(edgeLength,0,(numEdges/2)+1)
+
+    #Assigning node locations along the boundary
+    vertCount=0
+    horzCount=1
+    for n in range(numEdges+1):
+        if n < (numEdges/2):
+            AX[-1,n]=edgeLength
+            AY[-1,n]=vertLinSpace[vertCount]
+            vertCount+=1
+        elif n == int(numEdges/2):
+            AX[-1,n]=edgeLength
+            AY[-1,n]=edgeLength
+        else:
+            AX[-1,n]=horzLineSpace[horzCount]
+            AY[-1,n]=edgeLength
+            horzCount+=1
+
+    #Linearly spacing nodes between the inner/outer boundaries
+    #One could then smooth this via r-based adaptivity
+    for col in range(numEdges+1):
+        for row in range(1,numEdges):
+            AX[row,col]=sp.linspace(AX[0,col],AX[-1,col],numEdges+1)[row]
+            AY[row,col]=sp.linspace(AY[0,col],AY[-1,col],numEdges+1)[row]
+
+    AX=sp.delete(AX,0,0)
+    AY=sp.delete(AY,0,0)
+    AX=AX.flatten()
+    AY=AY.flatten()
+    AX_reshape = AX.flatten()
+    
+    numQuadNodesTot=numEdges*(numEdges+1)
+    vertMat=sp.zeros([numQuadNodesTot,2])
+    for n in range(numQuadNodesTot):
+        vertMat[n,:]=[AX[n],AY[n]]    
+    return vertMat
+
+def orient(A):
+    aOrient=sp.zeros([A.shape[0],A.shape[1]])
+    triCounter=0
+    quadCounter=0
+    #Determine the number of triangle and quad elments in the given element matrix
+    for n in range(A.shape[0]):
+        if A[n,1]==2:
+            triCounter+=1
+        else:
+            quadCounter+=1
+    edgeMatTotal=sp.zeros([3*triCounter+4*quadCounter,2])
+    counter=0
+    for n in range(A.shape[0]):
+        detected=0
+        if A[n,1]==2:
+            for m in range(edgeMatTotal.shape[0]):
+                if detected != 1:
+                    if edgeMatTotal[m,0]==A[n,2] and edgeMatTotal[m,1]==A[n,3]:
+                        aOrient[n,:]=[1,2,A[n,2],A[n,4],A[n,3],0]
+                        detected=1
+                        #print("reorder:[{} {} {}] to [{} {} {}]".format(A[n,2],A[n,3],A[n,4],int(aOrient[n,2]),int(aOrient[n,3]),int(aOrient[n,4])))
+                    elif edgeMatTotal[m,0]==A[n,4] and edgeMatTotal[m,1]==A[n,2]:
+                        aOrient[n,:]=[1,2,A[n,2],A[n,4],A[n,3],0]
+                        detected=1
+                    else:
+                        aOrient[n,:]=A[n,:]
+
+            edgeMatTotal[counter,:]=[aOrient[n,2],aOrient[n,3]]
+            counter+=1
+            edgeMatTotal[counter,:]=[aOrient[n,3],aOrient[n,4]]
+            counter+=1
+            edgeMatTotal[counter,:]=[aOrient[n,4],aOrient[n,2]]
+            counter+=1
+        else:
+            for m in range(edgeMatTotal.shape[0]):
+                if detected != 1: 
+                    if edgeMatTotal[m,0]==A[n,2] and edgeMatTotal[m,1]==A[n,3]:
+                        aOrient[n,:]=[2,3,A[n,2],A[n,5],A[n,4],A[n,3]]
+                        detected=1
+                        #print("reorder:[{} {} {} {}] to [{} {} {} {}]".format(A[n,2],A[n,3],A[n,4],A[n,5],int(aOrient[n,2]),int(aOrient[n,3]),int(aOrient[n,4]),int(aOrient[n,5])))
+                    elif edgeMatTotal[m,0]==A[n,5] and edgeMatTotal[m,1]==A[n,2]:
+                        aOrient[n,:]=[2,3,A[n,2],A[n,5],A[n,4],A[n,3]]
+                        detected=1
+                    else:
+                        aOrient[n,:]=A[n,:]
+            edgeMatTotal[counter,:]=[aOrient[n,2],aOrient[n,3]]
+            counter+=1
+            edgeMatTotal[counter,:]=[aOrient[n,3],aOrient[n,4]]
+            counter+=1
+            edgeMatTotal[counter,:]=[aOrient[n,4],aOrient[n,5]]
+            counter+=1
+            edgeMatTotal[counter,:]=[aOrient[n,5],aOrient[n,2]]
+            counter+=1
+    return aOrient.astype(int)
+
+def gVis(_glvis,_meshFile):
+
+    if(_glvis==''):
+        print("Failure: Set glvis location via -g switch")
+        sys.exit(1)
+
+    colFuncFileName=_meshFile.replace('.mesh','.gf')
+    glvsScriptFileName=_meshFile.replace('.mesh','.glvs')
+    imageFileName=_meshFile.replace('.mesh','.png')
+    
+    #Create Coloring Function for mesh
+    _colFuncCommand=_glvis+ ' -m '+ _meshFile +' -sc -k q'
+    args=_colFuncCommand.split()
+    p=subprocess.Popen(args)#Create 'GLVis_coloring.gf'
+
+    _renameCommand='mv GLVis_coloring.gf {}'.format(colFuncFileName)
+    args=_renameCommand.split()
+    p=subprocess.Popen(args)
+
+    #Glvis script template
+    f=open(glvsScriptFileName,'w')
+    f.write('window 0 0 800 800\n'+'\n')
+    f.write('solution {} {}\n'.format(_meshFile,colFuncFileName)+'\n')
+    f.write('{\n'+'perspective off\n'+'zoom 1.5\n'+'keys gAeeRM\n'+'solution {} {} screenshot {}\n'.format(_meshFile,colFuncFileName,imageFileName)+'keys q\n'+'}\n')
+    f.close()
+
+    _runGlvisCommand=_glvis+' -run {}'.format(glvsScriptFileName)
+    args=_runGlvisCommand.split()
+    p=subprocess.Popen(args)
+    p.wait()
+    
+    return 0
+def quadInterDof(_edge,_linEleMat,_linVertMatRound):
+    _state=False
+    for n in range(_linEleMat.shape[0]):
+        if _linEleMat[n,1]==3:
+            if sp.any(_edge[0]==_linEleMat[n,2:6]) and sp.any(_edge[1]==_linEleMat[n,2:6]):
+                print("{} is possibly in {}".format(_edge,_linEleMat[n,2:6]))
+                _n1Loc=sp.where(_edge[0]==_linEleMat[n,2:6])[0][0]
+                _n2Loc=sp.where(_edge[1]==_linEleMat[n,2:6])[0][0]
+                if _n1Loc==sp.mod(_n2Loc+1,4) or _n1Loc==sp.mod(_n2Loc-1,4):
+                    _state=True
+                    xcent=(_linVertMatRound[_linEleMat[n,2],0]+_linVertMatRound[_linEleMat[n,3],0]+_linVertMatRound[_linEleMat[n,4],0]+_linVertMatRound[_linEleMat[n,5],0])/4.0
+                    ycent=(_linVertMatRound[_linEleMat[n,2],1]+_linVertMatRound[_linEleMat[n,3],1]+_linVertMatRound[_linEleMat[n,4],1]+_linVertMatRound[_linEleMat[n,5],1])/4.0
+                    _interDof=sp.zeros(2)
+                    _interDof[0]=sp.round_((_linVertMatRound[_edge[0],0]+_linVertMatRound[_edge[1],0]+xcent)/3.0,5)
+                    _interDof[1]=sp.round_((_linVertMatRound[_edge[0],1]+_linVertMatRound[_edge[1],1]+ycent)/3.0,5)
+                    print("dof loc is {},{}".format(_interDof[0],_interDof[1]))
+                    return(_state,_interDof[0],_interDof[1])
+
+    return(_state,0,0)
+
+[eleMatTriHolder,numCircNodesTot]=eleMatCirc(numEdges) #Construct tri element matrix for the region inside circular sector
+eleMatQuadHolder=eleMatQuad(numEdges) #Construct quad element matrix for region outside the circular sector
+
+#Combining eleMatTriHolder and eleMatQuadHolder
+linEleMat=sp.zeros([eleMatTriHolder.shape[0]+eleMatQuadHolder.shape[0],6])
+counter=0
+for n in range(eleMatTriHolder.shape[0]):
+    linEleMat[n,[0,1,2,3,4]]=eleMatTriHolder[n,:]
+    counter+=1
+for n in range(eleMatQuadHolder.shape[0]):
+    linEleMat[counter+n,:]=eleMatQuadHolder[n,:]
+
+linEleMat=linEleMat.astype(int)
+linBoundMat=boundMatTot(numEdges)[0] #Construct the boundary
+vertMatCircHolder = vertMatCirc(numEdges) #Construct vertex matrix for triang region
+vertMatQuadHolder = vertMatQuad(numEdges) #Construct vertex matrix for the quad region
+
+
+#Combining the two vertex matrices in Quadrant I (q1)
+linVertMat=sp.zeros([vertMatCircHolder.shape[0]+vertMatQuadHolder.shape[0],2])
+counter=0
+for n in range(vertMatCircHolder.shape[0]):
+    linVertMat[n,:]=vertMatCircHolder[n,:]
+    counter+=1
+for n in range(vertMatQuadHolder.shape[0]):
+    linVertMat[counter+n,:]=vertMatQuadHolder[n,:]
+
+#Outputting P1/Q1 mesh to a .mesh file
+g=open(outputName+'Lin.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(linEleMat.shape[0]))
+for n in range(linEleMat.shape[0]):
+    if linEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4],linEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(linBoundMat.shape[0]))
+for n in range(linBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(linBoundMat[n,0],linBoundMat[n,1],linBoundMat[n,2],linBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(linVertMat.shape[0])+'2\n')
+for n in range(linVertMat.shape[0]):
+    g.write('{} {}\n'.format(linVertMat[n,0],linVertMat[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'Lin.mesh')
+
+#Quadratic (P2/Q2) Element Generation
+
+#1.)Create Edge list from previously generated linear elements
+edgeMat=sp.zeros([3*eleMatTriHolder.shape[0]+4*eleMatQuadHolder.shape[0],2])
+linEleMat=orient(linEleMat)#Make sure that element orientation is in agreement with MFEM requirements
+
+counter=0
+for n in range(linEleMat.shape[0]):
+    if linEleMat[n,1]==2:
+        edgeMat[counter,:]=[linEleMat[n,2],linEleMat[n,3]]
+        counter+=1
+        edgeMat[counter,:]=[linEleMat[n,3],linEleMat[n,4]]
+        counter+=1
+        edgeMat[counter,:]=[linEleMat[n,4],linEleMat[n,2]]
+        counter+=1
+    else:
+        edgeMat[counter,:]=[linEleMat[n,2],linEleMat[n,3]]
+        counter+=1
+        edgeMat[counter,:]=[linEleMat[n,3],linEleMat[n,4]]
+        counter+=1
+        edgeMat[counter,:]=[linEleMat[n,4],linEleMat[n,5]]
+        counter+=1
+        edgeMat[counter,:]=[linEleMat[n,5],linEleMat[n,2]]
+        counter+=1
+
+#Remove duplicates
+holder=[]
+for n in range(edgeMat.shape[0]):
+    counter=0
+    for m in range(edgeMat.shape[0]):
+        if edgeMat[n,0]==edgeMat[m,0] and edgeMat[n,1]==edgeMat[m,1] and m!=n:
+            holder.append([n,m])
+        elif edgeMat[n,1]==edgeMat[m,0] and edgeMat[n,0]==edgeMat[m,1] and m!=n:
+            holder.append([n,m])
+
+removeIndices=sp.zeros(len(holder))
+for n in range(len(holder)):
+    if holder[n][0]>holder[n][1]:
+        removeIndices[n]=holder[n][0]
+    else:
+        removeIndices[n]=holder[n][1]
+removeIndices=sp.unique(removeIndices).astype(int)
+edgeMat=sp.delete(edgeMat,removeIndices,0)
+edgeMat=edgeMat.astype(int)
+
+edgeDofMat=sp.zeros([edgeMat.shape[0],2])#These will be the new DoFs that appear after the Element Vertices within the .mesh file
+linVertMatRound=sp.round_(linVertMat,5) 
+ 
+counter=0
+
+for n in edgeMat:
+    if linVertMatRound[n[0],1] == linVertMatRound[n[1],1]:
+        xmid=(linVertMatRound[n[0],0]+linVertMatRound[n[1],0])/2.0
+        ymid=linVertMatRound[n[0],1]
+        edgeDofMat[counter,:]=[xmid,ymid]
+    elif linVertMatRound[n[0],0] == linVertMatRound[n[1],0]:
+        xmid=linVertMatRound[n[0],0]
+        ymid=(linVertMatRound[n[0],1]+linVertMatRound[n[1],1])/2.0
+        edgeDofMat[counter,:]=[xmid,ymid]
+    else:
+        r0=sp.sqrt(linVertMatRound[n[0],0]**2+linVertMatRound[n[0],1]**2)
+        r1=sp.sqrt(linVertMatRound[n[1],0]**2+linVertMatRound[n[1],1]**2)
+        rmid = (r0+r1)/2.0 #should not be needed
+        xmidOld=(linVertMatRound[n[0],0]+linVertMatRound[n[1],0])/2.0
+        ymidOld=(linVertMatRound[n[0],1]+linVertMatRound[n[1],1])/2.0
+        midtheta=sp.arctan(ymidOld/xmidOld)
+        xmid=rmid*sp.cos(midtheta)
+        ymid=rmid*sp.sin(midtheta)
+        edgeDofMat[counter,:]=[xmid,ymid]
+    counter+=1
+edgeDofMat = sp.round_(edgeDofMat,5)
+
+#Determine midpoints of all Q1 elements:
+quadCentroidLoc=sp.zeros([eleMatQuadHolder.shape[0],2])
+for n in range(eleMatQuadHolder.shape[0]):
+    quadCentroidLoc[n,0]=(linVertMatRound[eleMatQuadHolder[n,2],0]+linVertMatRound[eleMatQuadHolder[n,3],0]+linVertMatRound[eleMatQuadHolder[n,4],0]+linVertMatRound[eleMatQuadHolder[n,5],0])/4.0
+    quadCentroidLoc[n,1]=(linVertMatRound[eleMatQuadHolder[n,2],1]+linVertMatRound[eleMatQuadHolder[n,3],1]+linVertMatRound[eleMatQuadHolder[n,4],1]+linVertMatRound[eleMatQuadHolder[n,5],1])/4.0
+
+quadCentroidLoc = sp.round_(quadCentroidLoc,5)
+
+#3.)Populate nodes section
+g=open(outputName+'Quad.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(linEleMat.shape[0]))
+for n in range(linEleMat.shape[0]):
+    if linEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4],linEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(linBoundMat.shape[0]))
+for n in range(linBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(linBoundMat[n,0],linBoundMat[n,1],linBoundMat[n,2],linBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(linVertMat.shape[0]))
+g.write('\n'+'nodes'+'\n'+'FiniteElementSpace'+'\n'+'FiniteElementCollection: H1_2D_P2'+'\n'+'VDim: 2'+'\n'+'Ordering: 1' +'\n\n')
+for n in range(linVertMatRound.shape[0]):
+    g.write('{} {}\n'.format(linVertMatRound[n,0],linVertMatRound[n,1]))
+for n in range(edgeDofMat.shape[0]):
+    g.write('{} {}\n'.format(edgeDofMat[n,0],edgeDofMat[n,1]))
+for n in range(quadCentroidLoc.shape[0]):
+    g.write('{} {}\n'.format(quadCentroidLoc[n,0],quadCentroidLoc[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'Quad.mesh')
+
+#Cubic (P3/Q3) Element Generation
+
+cubeDofMat=sp.zeros([2*edgeMat.shape[0],2])#These will be the new DoFs that appear after the Element Vertices within the .mesh file
+
+counter=0
+for n in edgeMat: #Here DoF ordering matters. 
+    if linVertMatRound[n[0],1] == linVertMatRound[n[1],1]:
+        xmid=(linVertMatRound[n[0],0]+linVertMatRound[n[1],0])/2.0
+        ymid=linVertMatRound[n[0],1]
+        xmid1=(linVertMatRound[n[0],0]+xmid)/2.0
+        ymid1=linVertMatRound[n[0],1]
+        xmid2=(linVertMatRound[n[1],0]+xmid)/2.0
+        ymid2=linVertMatRound[n[0],1]
+        if n[0] > n[1]:
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+        else:
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+            
+    elif linVertMatRound[n[0],0] == linVertMatRound[n[1],0]:
+        xmid=linVertMatRound[n[0],0]
+        ymid=(linVertMatRound[n[0],1]+linVertMatRound[n[1],1])/2.0
+        xmid1=linVertMatRound[n[0],0]
+        ymid1=(linVertMatRound[n[0],1]+ymid)/2.0
+        xmid2=linVertMatRound[n[0],0]
+        ymid2=(linVertMatRound[n[1],1]+ymid)/2.0
+        if n[0] > n[1]:
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+        else:
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+    else:
+        r0=sp.sqrt(linVertMatRound[n[0],0]**2+linVertMatRound[n[0],1]**2)
+        r1=sp.sqrt(linVertMatRound[n[1],0]**2+linVertMatRound[n[1],1]**2)
+        rmid = (r0+r1)/2.0 #should not be needed
+        xmidOld=(linVertMatRound[n[0],0]+linVertMatRound[n[1],0])/2.0
+        ymidOld=(linVertMatRound[n[0],1]+linVertMatRound[n[1],1])/2.0
+        midtheta=sp.arctan(ymidOld/xmidOld)
+        xmid=rmid*sp.cos(midtheta)
+        ymid=rmid*sp.sin(midtheta)
+        xmid1=(linVertMatRound[n[0],0]+xmid)/2.0
+        ymid1=(linVertMatRound[n[0],1]+ymid)/2.0
+        xmid2=(linVertMatRound[n[1],0]+xmid)/2.0
+        ymid2=(linVertMatRound[n[1],1]+ymid)/2.0
+        if n[0] > n[1]:
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+        else:
+            cubeDofMat[counter,:]=[xmid1,ymid1]
+            counter+=1
+            cubeDofMat[counter,:]=[xmid2,ymid2]
+            counter+=1
+            
+cubeDofMat = sp.round_(cubeDofMat,5)
+
+triCentroidLoc=sp.zeros([eleMatTriHolder.shape[0],2])
+
+for n in range(eleMatTriHolder.shape[0]):
+    triCentroidLoc[n,0]=(linVertMatRound[eleMatTriHolder[n,2],0]+linVertMatRound[eleMatTriHolder[n,3],0]+linVertMatRound[eleMatTriHolder[n,4],0])/3.0
+    triCentroidLoc[n,1]=(linVertMatRound[eleMatTriHolder[n,2],1]+linVertMatRound[eleMatTriHolder[n,3],1]+linVertMatRound[eleMatTriHolder[n,4],1])/3.0
+
+quadCentroidLocCubic=sp.zeros([4*eleMatQuadHolder.shape[0],2])
+
+counter=0
+for n in range(eleMatQuadHolder.shape[0]):
+    xcent=quadCentroidLoc[n,0];ycent=quadCentroidLoc[n,1]
+    a=eleMatQuadHolder[n,2:6]
+    aMinIndex=sp.where(a[:]==a.min())[0][0]
+    dof0=0.5*sp.array([xcent+linVertMatRound[a[aMinIndex],0],ycent+linVertMatRound[a[aMinIndex],1]])
+    quadCentroidLocCubic[counter,:]=dof0
+    counter+=1
+    if aMinIndex==0:
+        aLeft=-1
+        aRight=1
+        aLast=2
+    else:
+        aLeft=aMinIndex-1
+        aRight=aMinIndex+1
+        aLast=sp.delete(a,[aMinIndex,aLeft,aRight])[0]
+    edge1=[a[aMinIndex], a[aLeft]]
+    edge2=[a[aMinIndex], a[aRight]]
+    edge1Index=0
+    edge2Index=0
+    edgeCounter=0
+    for edge in edgeMat:
+        if(edge[0]==edge1[0] and edge[1]==edge1[1]) or (edge[1]==edge1[0] and edge[0]==edge1[1]):
+            edge1Index=edgeCounter
+        if(edge[0]==edge2[0] and edge[1]==edge2[1]) or (edge[1]==edge2[0] and edge[0]==edge2[1]):
+            edge2Index=edgeCounter
+        edgeCounter+=1
+
+    if (edge1Index > edge2Index):
+        dof1=0.5*sp.array([xcent+linVertMatRound[a[aLeft],0],ycent+linVertMatRound[a[aLeft],1]])
+        quadCentroidLocCubic[counter,:]=dof1
+        counter+=1
+        dof2=0.5*sp.array([xcent+linVertMatRound[a[aRight],0],ycent+linVertMatRound[a[aRight],1]])
+        quadCentroidLocCubic[counter,:]=dof2
+        counter+=1
+        dof3=0.5*sp.array([xcent+linVertMatRound[a[aLast],0],ycent+linVertMatRound[a[aLast],1]])
+        quadCentroidLocCubic[counter,:]=dof3
+        counter+=1
+    else:
+        dof1=0.5*sp.array([xcent+linVertMatRound[a[aRight],0],ycent+linVertMatRound[a[aRight],1]])
+        quadCentroidLocCubic[counter,:]=dof1
+        counter+=1
+        dof2=0.5*sp.array([xcent+linVertMatRound[a[aLeft],0],ycent+linVertMatRound[a[aLeft],1]])
+        quadCentroidLocCubic[counter,:]=dof2
+        counter+=1
+        dof3=0.5*sp.array([xcent+linVertMatRound[a[aLast],0],ycent+linVertMatRound[a[aLast],1]])
+        quadCentroidLocCubic[counter,:]=dof3
+        counter+=1
+        
+truCentroidLoc=sp.round_(triCentroidLoc,5)
+    
+#3.)Populate nodes section
+g=open(outputName+'Cub.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(linEleMat.shape[0]))
+for n in range(linEleMat.shape[0]):
+    if linEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(linEleMat[n,0],linEleMat[n,1],linEleMat[n,2],linEleMat[n,3],linEleMat[n,4],linEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(linBoundMat.shape[0]))
+for n in range(linBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(linBoundMat[n,0],linBoundMat[n,1],linBoundMat[n,2],linBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(linVertMat.shape[0]))
+g.write('\n'+'nodes'+'\n'+'FiniteElementSpace'+'\n'+'FiniteElementCollection: H1_2D_P3'+'\n'+'VDim: 2'+'\n'+'Ordering: 1' +'\n\n')
+for n in range(linVertMatRound.shape[0]):
+    g.write('{} {}\n'.format(linVertMatRound[n,0],linVertMatRound[n,1]))
+for n in range(cubeDofMat.shape[0]):
+    g.write('{} {}\n'.format(cubeDofMat[n,0],cubeDofMat[n,1]))
+for n in range(triCentroidLoc.shape[0]):
+    g.write('{} {}\n'.format(triCentroidLoc[n,0],triCentroidLoc[n,1]))
+for n in range(quadCentroidLocCubic.shape[0]):
+    g.write('{} {}\n'.format(quadCentroidLocCubic[n,0],quadCentroidLocCubic[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'Cub.mesh')
+#raw_input()
+#'Reflecting' topology about one of its edges and append it to itself
+upperPlaneEleMat = sp.zeros([2*linEleMat.shape[0],6])
+for n in range(linEleMat.shape[0]):
+    upperPlaneEleMat[n,:]=linEleMat[n,:]
+    
+#Create ele_mat_holder.shape[0]x2 matrix for mapping
+refEdge=boundMatTot(numEdges)[1]
+q1NumNodes=linVertMat.shape[0]
+
+mapping = sp.zeros([q1NumNodes])
+counter=0
+for n in range(q1NumNodes):
+     if (sp.any(refEdge == n)):
+         mapping[n]=n
+     else:
+         mapping[n]=counter+q1NumNodes
+         counter+=1
+
+mapping=mapping.astype(int)
+#Implement mapping
+
+counter=0
+for n in range(linEleMat.shape[0],2*linEleMat.shape[0]):
+    upperPlaneEleMat[n,0]=linEleMat[counter,0]
+    upperPlaneEleMat[n,1]=linEleMat[counter,1]
+    upperPlaneEleMat[n,2]=mapping[linEleMat[counter,2]]
+    upperPlaneEleMat[n,3]=mapping[linEleMat[counter,3]]
+    upperPlaneEleMat[n,4]=mapping[linEleMat[counter,4]]
+    upperPlaneEleMat[n,5]=mapping[linEleMat[counter,5]]
+    counter+=1
+    
+upperPlaneEleMat = upperPlaneEleMat.astype(int)
+
+#Reflecting boundary matrix
+origBound=boundMatTot(numEdges)[2]
+upperPlaneBoundMat=sp.zeros([2*origBound.shape[0],4])
+for n in range(origBound.shape[0]):
+    upperPlaneBoundMat[n,:]=origBound[n,:]
+counter=0
+newOrigBound=origBound.copy()
+newOrigBound[:,2]=sp.flipud(origBound[:,3])
+newOrigBound[:,3]=sp.flipud(origBound[:,2])
+for n in range(newOrigBound.shape[0],upperPlaneBoundMat.shape[0]):
+    upperPlaneBoundMat[n,0]=newOrigBound[counter,0]
+    upperPlaneBoundMat[n,1]=newOrigBound[counter,1]
+    upperPlaneBoundMat[n,2]=mapping[newOrigBound[counter,2]]
+    upperPlaneBoundMat[n,3]=mapping[newOrigBound[counter,3]]
+    counter+=1
+upperPlaneBoundMat=upperPlaneBoundMat.astype(int)
+
+#Reflecting vertex matrix about the y-axis and appending it to itself
+upperPlaneNumNodes=q1NumNodes+(q1NumNodes-refEdge.shape[0])
+upperPlaneVertMat = sp.zeros([upperPlaneNumNodes,2])
+for n in range(linVertMat.shape[0]):
+    upperPlaneVertMat[n,:]=linVertMat[n,:]
+counter=0
+for n in range(linVertMat.shape[0],upperPlaneNumNodes):
+        upperPlaneVertMat[n,0]=-1.0*linVertMat[sp.where(mapping==n)[0][0],0]
+        upperPlaneVertMat[n,1]=linVertMat[sp.where(mapping==n)[0][0],1]
+        counter+=1
+
+upperPlaneEleMat=orient(upperPlaneEleMat)
+g=open(outputName+'UpperPlaneLin.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(upperPlaneEleMat.shape[0]))
+for n in range(upperPlaneEleMat.shape[0]):
+    if upperPlaneEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(upperPlaneEleMat[n,0],upperPlaneEleMat[n,1],upperPlaneEleMat[n,2],upperPlaneEleMat[n,3],upperPlaneEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(upperPlaneEleMat[n,0],upperPlaneEleMat[n,1],upperPlaneEleMat[n,2],upperPlaneEleMat[n,3],upperPlaneEleMat[n,4],upperPlaneEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(upperPlaneBoundMat.shape[0]))
+for n in range(upperPlaneBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(upperPlaneBoundMat[n,0],upperPlaneBoundMat[n,1],upperPlaneBoundMat[n,2],upperPlaneBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(upperPlaneVertMat.shape[0])+'2\n')
+for n in range(upperPlaneVertMat.shape[0]):
+    g.write('{} {}\n'.format(upperPlaneVertMat[n,0],upperPlaneVertMat[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'UpperPlaneLin.mesh')
+
+#'Reflecting' topology about one of its edges and append it to itself
+wholePlaneEleMat = sp.zeros([2*upperPlaneEleMat.shape[0],6])
+for n in range(upperPlaneEleMat.shape[0]):
+    wholePlaneEleMat[n,:]=upperPlaneEleMat[n,:]
+
+quad1Edge=boundMatTot(numEdges)[3]
+newRefEdge=sp.zeros(2*quad1Edge.shape[0]-1)
+for n in range(quad1Edge.shape[0]):
+    newRefEdge[n]=quad1Edge[n]
+counter=0
+for n in range(quad1Edge.shape[0],newRefEdge.shape[0]):
+    newRefEdge[n]=mapping[quad1Edge[counter]]
+    counter+=1
+newRefEdge=sp.unique(newRefEdge)
+newRefEdge=newRefEdge.astype(int)
+newTotNumNodes=upperPlaneVertMat.shape[0]
+
+newMapping=sp.zeros([newTotNumNodes])
+counter=0
+for n in range(newTotNumNodes):
+    if (sp.any(newRefEdge == n)):
+        newMapping[n]=n
+    else:
+        newMapping[n]=counter+newTotNumNodes
+        counter+=1
+newMapping=newMapping.astype(int)
+
+counter=0
+for n in range(upperPlaneEleMat.shape[0],2*upperPlaneEleMat.shape[0]):
+    wholePlaneEleMat[n,0]=upperPlaneEleMat[counter,0]
+    wholePlaneEleMat[n,1]=upperPlaneEleMat[counter,1]
+    wholePlaneEleMat[n,2]=newMapping[upperPlaneEleMat[counter,2]]
+    wholePlaneEleMat[n,3]=newMapping[upperPlaneEleMat[counter,3]]
+    wholePlaneEleMat[n,4]=newMapping[upperPlaneEleMat[counter,4]]
+    wholePlaneEleMat[n,5]=newMapping[upperPlaneEleMat[counter,5]]
+    counter+=1
+
+wholePlaneEleMat=wholePlaneEleMat.astype(int)
+
+#Reflecting boundary matrix
+newOrigBoundQuad1=boundMatTot(numEdges)[4]
+newFirstBoundMatHolder=sp.zeros([2*newOrigBoundQuad1.shape[0],4])
+for n in range(newOrigBoundQuad1.shape[0]):
+    newFirstBoundMatHolder[n,:]=newOrigBoundQuad1[n,:]
+
+newNewOrigBoundQuad1=newOrigBoundQuad1.copy()
+newNewOrigBoundQuad1[:,2]=sp.flipud(newOrigBoundQuad1[:,3])
+newNewOrigBoundQuad1[:,3]=sp.flipud(newOrigBoundQuad1[:,2])
+counter=0
+for n in range(newOrigBoundQuad1.shape[0],newFirstBoundMatHolder.shape[0]):
+    newFirstBoundMatHolder[n,0]=newNewOrigBoundQuad1[counter,0]
+    newFirstBoundMatHolder[n,1]=newNewOrigBoundQuad1[counter,1]
+    newFirstBoundMatHolder[n,2]=mapping[newNewOrigBoundQuad1[counter,2]]
+    newFirstBoundMatHolder[n,3]=mapping[newNewOrigBoundQuad1[counter,3]]
+    counter+=1
+
+upperQuadMat=newFirstBoundMatHolder.copy()
+wholePlaneBoundMat=sp.zeros([2*upperQuadMat.shape[0],4])
+for n in range(upperQuadMat.shape[0]):
+    wholePlaneBoundMat[n,:]=upperQuadMat[n,:]
+
+counter=0
+newNewOrigBound=upperQuadMat.copy()
+newNewOrigBound[:,2]=sp.flipud(upperQuadMat[:,3])
+newNewOrigBound[:,3]=sp.flipud(upperQuadMat[:,2])
+newNewOrigBound=newNewOrigBound.astype(int)
+for n in range(newNewOrigBound.shape[0],wholePlaneBoundMat.shape[0]):
+    wholePlaneBoundMat[n,0]=newNewOrigBound[counter,0]
+    wholePlaneBoundMat[n,1]=newNewOrigBound[counter,1]
+    wholePlaneBoundMat[n,2]=newMapping[newNewOrigBound[counter,2]]
+    wholePlaneBoundMat[n,3]=newMapping[newNewOrigBound[counter,3]]
+    counter+=1
+wholePlaneBoundMat=wholePlaneBoundMat.astype(int)
+
+wholePlaneNumNodes=newTotNumNodes+(newTotNumNodes-newRefEdge.shape[0])
+wholePlaneVertMat = sp.zeros([wholePlaneNumNodes,2])
+for n in range(upperPlaneVertMat.shape[0]):
+    wholePlaneVertMat[n,:]=upperPlaneVertMat[n,:]
+counter=0
+for n in range(upperPlaneVertMat.shape[0],wholePlaneNumNodes):
+        wholePlaneVertMat[n,0]=upperPlaneVertMat[sp.where(newMapping==n)[0][0],0]
+        wholePlaneVertMat[n,1]=-1.0*upperPlaneVertMat[sp.where(newMapping==n)[0][0],1]
+        counter+=1
+
+g=open(outputName+'WholePlaneLin.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(wholePlaneEleMat.shape[0]))
+for n in range(wholePlaneEleMat.shape[0]):
+    if wholePlaneEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(wholePlaneEleMat[n,0],wholePlaneEleMat[n,1],wholePlaneEleMat[n,2],wholePlaneEleMat[n,3],wholePlaneEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(wholePlaneEleMat[n,0],wholePlaneEleMat[n,1],wholePlaneEleMat[n,2],wholePlaneEleMat[n,3],wholePlaneEleMat[n,4],wholePlaneEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(wholePlaneBoundMat.shape[0]))
+for n in range(wholePlaneBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(wholePlaneBoundMat[n,0],wholePlaneBoundMat[n,1],wholePlaneBoundMat[n,2],wholePlaneBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(wholePlaneVertMat.shape[0])+'2\n')
+for n in range(wholePlaneVertMat.shape[0]):
+    g.write('{} {}\n'.format(wholePlaneVertMat[n,0],wholePlaneVertMat[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'WholePlaneLin.mesh')
+
+#1.)Create Edge list from elements
+wholePlaneEleMat=orient(wholePlaneEleMat)
+triCounter=0;quadCounter=0;
+for n in range(wholePlaneEleMat.shape[0]):
+    if wholePlaneEleMat[n,1]==2:
+        triCounter+=1
+    else:
+        quadCounter+=1
+edgeMat=sp.zeros([3*triCounter+4*quadCounter,2])
+counter=0
+for n in range(wholePlaneEleMat.shape[0]):
+    if wholePlaneEleMat[n,1]==2:
+        edgeMat[counter,:]=[wholePlaneEleMat[n,2],wholePlaneEleMat[n,3]]
+        counter+=1
+        edgeMat[counter,:]=[wholePlaneEleMat[n,3],wholePlaneEleMat[n,4]]
+        counter+=1
+        edgeMat[counter,:]=[wholePlaneEleMat[n,4],wholePlaneEleMat[n,2]]
+        counter+=1
+    else:
+        edgeMat[counter,:]=[wholePlaneEleMat[n,2],wholePlaneEleMat[n,3]]
+        counter+=1
+        edgeMat[counter,:]=[wholePlaneEleMat[n,3],wholePlaneEleMat[n,4]]
+        counter+=1
+        edgeMat[counter,:]=[wholePlaneEleMat[n,4],wholePlaneEleMat[n,5]]
+        counter+=1
+        edgeMat[counter,:]=[wholePlaneEleMat[n,5],wholePlaneEleMat[n,2]]
+        counter+=1
+
+#Remove duplicates
+holder=[]
+for n in range(edgeMat.shape[0]):
+    counter=0
+    for m in range(edgeMat.shape[0]):
+        if edgeMat[n,0]==edgeMat[m,0] and edgeMat[n,1]==edgeMat[m,1] and m!=n:
+            holder.append([n,m])
+        elif edgeMat[n,1]==edgeMat[m,0] and edgeMat[n,0]==edgeMat[m,1] and m!=n:
+            holder.append([n,m])
+removeIndices=sp.zeros(len(holder))
+for n in range(len(holder)):
+    if holder[n][0]>holder[n][1]:
+        removeIndices[n]=holder[n][0]
+    else:
+        removeIndices[n]=holder[n][1]
+removeIndices=sp.unique(removeIndices).astype(int)
+edgeMat=sp.delete(edgeMat,removeIndices,0)
+edgeMat=edgeMat.astype(int)
+
+edgeDofMat=sp.zeros([edgeMat.shape[0],2])
+
+wholePlaneVertMatRound=sp.round_(wholePlaneVertMat,5)
+
+counter=0
+for n in edgeMat:
+    if wholePlaneVertMatRound[n[0],1] == wholePlaneVertMatRound[n[1],1]:
+        xmid=(wholePlaneVertMatRound[n[0],0]+wholePlaneVertMatRound[n[1],0])/2.0
+        ymid=wholePlaneVertMatRound[n[0],1]
+        edgeDofMat[counter,:]=[xmid,ymid]
+    elif wholePlaneVertMatRound[n[0],0] == wholePlaneVertMatRound[n[1],0]:
+        xmid=wholePlaneVertMatRound[n[0],0]
+        ymid=(wholePlaneVertMatRound[n[0],1]+wholePlaneVertMatRound[n[1],1])/2.0
+        edgeDofMat[counter,:]=[xmid,ymid]
+    else:
+        r0=sp.sqrt(wholePlaneVertMatRound[n[0],0]**2+wholePlaneVertMatRound[n[0],1]**2)
+        r1=sp.sqrt(wholePlaneVertMatRound[n[1],0]**2+wholePlaneVertMatRound[n[1],1]**2)
+        rmid = (r0+r1)/2.0 #should not be needed
+        xmidOld=(wholePlaneVertMatRound[n[0],0]+wholePlaneVertMatRound[n[1],0])/2.0
+        ymidOld=(wholePlaneVertMatRound[n[0],1]+wholePlaneVertMatRound[n[1],1])/2.0
+        midtheta=sp.arctan2(ymidOld,xmidOld)
+        xmid=rmid*sp.cos(midtheta)
+        ymid=rmid*sp.sin(midtheta)
+        edgeDofMat[counter,:]=[xmid,ymid]
+    counter+=1
+edgeDofMat = sp.round_(edgeDofMat,5)
+
+#2.)Create correct dof locations
+#Determine midpoints of all quads:
+quadCentroidLoc=sp.zeros([quadCounter,2])
+counter=0
+for n in range(wholePlaneEleMat.shape[0]):
+    if wholePlaneEleMat[n,1]==3:
+        quadCentroidLoc[counter,0]=(wholePlaneVertMatRound[wholePlaneEleMat[n,2],0]+wholePlaneVertMatRound[wholePlaneEleMat[n,3],0]+wholePlaneVertMatRound[wholePlaneEleMat[n,4],0]+wholePlaneVertMatRound[wholePlaneEleMat[n,5],0])/4.0
+        quadCentroidLoc[counter,1]=(wholePlaneVertMatRound[wholePlaneEleMat[n,2],1]+wholePlaneVertMatRound[wholePlaneEleMat[n,3],1]+wholePlaneVertMatRound[wholePlaneEleMat[n,4],1]+wholePlaneVertMatRound[wholePlaneEleMat[n,5],1])/4.0
+        counter+=1
+
+quadCentroidLoc = sp.round_(quadCentroidLoc,5)
+
+#3.)Populate nodes section
+g=open(outputName+'WholePlaneQuad.mesh','w')
+g.write('MFEM mesh v1.0\n'+'\n')
+g.write('dimension\n'+'2\n'+'\n')
+g.write('elements\n'+'{}\n'.format(wholePlaneEleMat.shape[0]))
+for n in range(wholePlaneEleMat.shape[0]):
+    if wholePlaneEleMat[n,1]==2:
+        g.write('{} {} {} {} {}\n'.format(wholePlaneEleMat[n,0],wholePlaneEleMat[n,1],wholePlaneEleMat[n,2],wholePlaneEleMat[n,3],wholePlaneEleMat[n,4]))
+    else:
+        g.write('{} {} {} {} {} {}\n'.format(wholePlaneEleMat[n,0],wholePlaneEleMat[n,1],wholePlaneEleMat[n,2],wholePlaneEleMat[n,3],wholePlaneEleMat[n,4],wholePlaneEleMat[n,5]))
+g.write('\n'+'boundary\n'+'{}\n'.format(wholePlaneBoundMat.shape[0]))
+for n in range(wholePlaneBoundMat.shape[0]):
+    g.write('{} {} {} {}\n'.format(wholePlaneBoundMat[n,0],wholePlaneBoundMat[n,1],wholePlaneBoundMat[n,2],wholePlaneBoundMat[n,3]))
+g.write('\n'+'vertices\n'+'{}\n'.format(wholePlaneVertMat.shape[0]))
+g.write('\n'+'nodes'+'\n'+'FiniteElementSpace'+'\n'+'FiniteElementCollection: H1_2D_P2'+'\n'+'VDim: 2'+'\n'+'Ordering: 1' +'\n\n')
+for n in range(wholePlaneVertMatRound.shape[0]):
+    g.write('{} {}\n'.format(wholePlaneVertMatRound[n,0],wholePlaneVertMatRound[n,1]))
+for n in range(edgeDofMat.shape[0]):
+    g.write('{} {}\n'.format(edgeDofMat[n,0],edgeDofMat[n,1]))
+for n in range(quadCentroidLoc.shape[0]):
+    g.write('{} {}\n'.format(quadCentroidLoc[n,0],quadCentroidLoc[n,1]))
+g.close()
+
+if(visMesh==True):
+    gVis(glvis,outputName+'WholePlaneQuad.mesh')
@@ -0,0 +1,264 @@
+MFEM mesh v1.0
+
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@@ -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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-1.1996835 0.35726714 -0.024929133
-0.99559063 0.29648804 -0.24998909
-0.69819427 0.66062834 -0.24998909
-0.54351156 0.51426825 -0.024929133
-0.8170735 0.24332543 -0.20555815
-0.73231963 0.21808563 0.091392579
-0.58321113 0.5518318 0.15859651
-0.80212907 0.758971 0.23048728
-0.85845599 0.25564918 0.23048728
-1.1473028 0.34166809 0.15859651
-0.5 -0.8660254 8.6542076e-17
-1.1473028 -0.34166809 -0.15859651
-0.85845599 -0.25564918 -0.23048728
-0.80212907 -0.758971 -0.23048728
-0.58321113 -0.5518318 -0.15859651
-0.73231963 -0.21808563 -0.091392579
-0.8170735 -0.24332543 0.20555815
-0.54351156 -0.51426825 0.024929133
-0.69819427 -0.66062834 0.24998909
-0.99559063 -0.29648804 0.24998909
-1.1996835 -0.35726714 0.024929133
-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
@@ -35,10 +35,6 @@ namespace mfem {
 * - HypreParMatrix and HypreParVector
 * - HypreSolver and other \link hypre.hpp hypre classes\endlink
 *
- * <H3>Main GPU classes</H3>
- * - Device
- * - MemoryManager
- *
 * <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
@@ -75,10 +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="ex22_8cpp_source.html">Example 22</a>: adaptive mesh refinement for linear elasticity
- * - <a class="el" href="ex22p_8cpp_source.html">Example 22p</a>: parallel adaptive mesh refinement for linear elasticity
 *
 * <H4>SUNDIALS Examples</H4>
 * - Variants of Examples
@@ -120,15 +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="load-dc_8cpp_source.html">Load DC</a>: visualize fields saved via DataCollection classes
 * - <a class="el" href="convert-dc_8cpp_source.html">Convert DC</a>: convert between diffirent DataCollection formats
- * - <a class="el" href="lor-transfer_8cpp_source.html">LOR Transfer</a>: map functions between high-order and low-order refined spaces
 * - <a class="el" href="miniapps_2performance_2ex1_8cpp_source.html">HPC Example 1</a>: high-performance nodal H1 FEM for the Laplace problem
 * - <a class="el" href="miniapps_2performance_2ex1p_8cpp_source.html">HPC Example 1p</a>: high-performance parallel nodal H1 FEM for the Laplace problem
 *
@@ -26,8 +26,6 @@ list(APPEND ALL_EXE_SRCS
  ex17.cpp
  ex18.cpp
  ex19.cpp
-  ex20.cpp
-  ex22.cpp
  )

 if (MFEM_USE_MPI)
@@ -51,8 +49,6 @@ if (MFEM_USE_MPI)
    ex17p.cpp
    ex18p.cpp
    ex19p.cpp
-    ex20p.cpp
-    ex22p.cpp
    )
 endif()

@@ -79,22 +75,13 @@ 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)
@@ -4,18 +4,13 @@
 //
 // Sample runs:  ex1 -m ../data/square-disc.mesh
 //               ex1 -m ../data/star.mesh
-//               ex1 -m ../data/star-mixed.mesh
 //               ex1 -m ../data/escher.mesh
 //               ex1 -m ../data/fichera.mesh
-//               ex1 -m ../data/fichera-mixed.mesh
-//               ex1 -m ../data/toroid-wedge.mesh
 //               ex1 -m ../data/square-disc-p2.vtk -o 2
 //               ex1 -m ../data/square-disc-p3.mesh -o 3
 //               ex1 -m ../data/square-disc-nurbs.mesh -o -1
-//               ex1 -m ../data/star-mixed-p2.mesh -o 2
 //               ex1 -m ../data/disc-nurbs.mesh -o -1
 //               ex1 -m ../data/pipe-nurbs.mesh -o -1
-//               ex1 -m ../data/fichera-mixed-p2.mesh -o 2
 //               ex1 -m ../data/star-surf.mesh
 //               ex1 -m ../data/square-disc-surf.mesh
 //               ex1 -m ../data/inline-segment.mesh
@@ -25,14 +20,6 @@
 //               ex1 -m ../data/mobius-strip.mesh
 //               ex1 -m ../data/mobius-strip.mesh -o -1 -sc
 //
-// Device sample runs:
-//               ex1 -pa -d cuda
-//               ex1 -pa -d raja-cuda
-//               ex1 -pa -d occa-cuda
-//               ex1 -pa -d raja-omp
-//               ex1 -pa -d occa-omp
-//               ex1 -m ../data/beam-hex.mesh -pa -d cuda
-//
 // Description:  This example code demonstrates the use of MFEM to define a
 //               simple finite element discretization of the Laplace problem
 //               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
@@ -61,9 +48,7 @@ int main(int argc, char *argv[])
   const char *mesh_file = "../data/star.mesh";
   int order = 1;
   bool static_cond = false;
-   bool pa = false;
-   const char *device = "cpu";
-   bool visualization = true;
+   bool visualization = 1;

   OptionsParser args(argc, argv);
   args.AddOption(&mesh_file, "-m", "--mesh",
@@ -73,10 +58,6 @@ int main(int argc, char *argv[])
                  " isoparametric space.");
   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                  "--no-visualization",
                  "Enable or disable GLVis visualization.");
@@ -99,8 +80,8 @@ int main(int argc, char *argv[])
   //    largest number that gives a final mesh with no more than 50,000
   //    elements.
   {
-      int ref_levels =
-         (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();
@@ -148,65 +129,48 @@ int main(int argc, char *argv[])
   b->AddDomainIntegrator(new DomainLFIntegrator(one));
   b->Assemble();

-   // 7. Set device config parameters from the command line options and switch
-   //    to working on the device.
-   Device::Configure(device);
-   Device::Print();
-   Device::Enable();
-
-   // 8. Define the solution vector x as a finite element grid function
+   // 7. Define the solution vector x as a finite element grid function
   //    corresponding to fespace. Initialize x with initial guess of zero,
   //    which satisfies the boundary conditions.
   GridFunction x(fespace);
   x = 0.0;

-   // 9. Set up the bilinear form a(.,.) on the finite element space
+   // 8. Set up the bilinear form a(.,.) on the finite element space
   //    corresponding to the Laplacian operator -Delta, by adding the Diffusion
   //    domain integrator.
   BilinearForm *a = new BilinearForm(fespace);
-   if (pa) { a->SetAssemblyLevel(AssemblyLevel::PARTIAL); }
   a->AddDomainIntegrator(new DiffusionIntegrator(one));

-   // 10. Assemble the bilinear form and the corresponding linear system,
-   //     applying any necessary transformations such as: eliminating boundary
-   //     conditions, applying conforming constraints for non-conforming AMR,
-   //     static condensation, etc.
+   // 9. Assemble the bilinear form and the corresponding linear system,
+   //    applying any necessary transformations such as: eliminating boundary
+   //    conditions, applying conforming constraints for non-conforming AMR,
+   //    static condensation, etc.
   if (static_cond) { a->EnableStaticCondensation(); }
   a->Assemble();

-   OperatorPtr A;
+   SparseMatrix A;
   Vector B, X;
   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);

-   cout << "Size of linear system: " << A->Height() << endl;
+   cout << "Size of linear system: " << A.Height() << endl;

-   // 11. Solve the linear system A X = B.
-   if (!pa)
-   {
 #ifndef MFEM_USE_SUITESPARSE
-      // Use a simple symmetric Gauss-Seidel preconditioner with PCG.
-      GSSmoother M((SparseMatrix&)(*A));
-      PCG(*A, M, B, X, 1, 200, 1e-12, 0.0);
+   // 10. Define a simple symmetric Gauss-Seidel preconditioner and use it to
+   //     solve the system A X = B with PCG.
+   GSSmoother M(A);
+   PCG(A, M, B, X, 1, 200, 1e-12, 0.0);
 #else
-      // If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
-      UMFPackSolver umf_solver;
-      umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-      umf_solver.SetOperator(*A);
-      umf_solver.Mult(B, X);
+   // 10. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
+   UMFPackSolver umf_solver;
+   umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
+   umf_solver.SetOperator(A);
+   umf_solver.Mult(B, X);
 #endif
-   }
-   else // No preconditioning for now in partial assembly mode.
-   {
-      CG(*A, B, X, 1, 2000, 1e-12, 0.0);
-   }

-   // 12. Recover the solution as a finite element grid function.
+   // 11. Recover the solution as a finite element grid function.
   a->RecoverFEMSolution(X, *b, x);

-   // 13. Switch back to the host.
-   Device::Disable();
-
-   // 14. Save the refined mesh and the solution. This output can be viewed later
+   // 12. Save the refined mesh and the solution. This output can be viewed later
   //     using GLVis: "glvis -m refined.mesh -g sol.gf".
   ofstream mesh_ofs("refined.mesh");
   mesh_ofs.precision(8);
@@ -215,7 +179,7 @@ int main(int argc, char *argv[])
   sol_ofs.precision(8);
   x.Save(sol_ofs);

-   // 15. Send the solution by socket to a GLVis server.
+   // 13. Send the solution by socket to a GLVis server.
   if (visualization)
   {
      char vishost[] = "localhost";
@@ -225,7 +189,7 @@ int main(int argc, char *argv[])
      sol_sock << "solution\n" << *mesh << x << flush;
   }

-   // 16. Free the used memory.
+   // 14. Free the used memory.
   delete a;
   delete b;
   delete fespace;
@@ -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
@@ -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
@@ -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;
@@ -5,10 +5,9 @@
 // Sample runs:
 //    mpirun -np 4 ex12p -m ../data/beam-tri.mesh
 //    mpirun -np 4 ex12p -m ../data/beam-quad.mesh
-//    mpirun -np 4 ex12p -m ../data/beam-tet.mesh -s 79 -n 10 -o 2 -elast
+//    mpirun -np 4 ex12p -m ../data/beam-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-wedge.mesh -s 79
-//    mpirun -np 4 ex12p -m ../data/beam-tri.mesh -s 3876 -o 2 -sys
+//    mpirun -np 4 ex12p -m ../data/beam-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
@@ -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
@@ -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
@@ -135,8 +135,6 @@ int main(int argc, char *argv[])
   {
      mesh.UniformRefinement();
   }
-   // Make sure tet-only meshes are marked for local refinement.
-   mesh.Finalize(true);

   // 4. All boundary attributes will be used for essential (Dirichlet) BC.
   MFEM_VERIFY(mesh.bdr_attributes.Size() > 0,
@@ -151,8 +151,6 @@ int main(int argc, char *argv[])
   {
      mesh->UniformRefinement();
   }
-   // Make sure tet-only meshes are marked for local refinement.
-   mesh->Finalize(true);

   // 5. Define a parallel mesh by partitioning the serial mesh.  Once the
   //    parallel mesh is defined, the serial mesh can be deleted.
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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)
@@ -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
@@ -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
@@ -4,19 +4,14 @@
 //
 // Sample runs:  mpirun -np 4 ex1p -m ../data/square-disc.mesh
 //               mpirun -np 4 ex1p -m ../data/star.mesh
-//               mpirun -np 4 ex1p -m ../data/star-mixed.mesh
 //               mpirun -np 4 ex1p -m ../data/escher.mesh
 //               mpirun -np 4 ex1p -m ../data/fichera.mesh
-//               mpirun -np 4 ex1p -m ../data/fichera-mixed.mesh
-//               mpirun -np 4 ex1p -m ../data/toroid-wedge.mesh
 //               mpirun -np 4 ex1p -m ../data/square-disc-p2.vtk -o 2
 //               mpirun -np 4 ex1p -m ../data/square-disc-p3.mesh -o 3
 //               mpirun -np 4 ex1p -m ../data/square-disc-nurbs.mesh -o -1
-//               mpirun -np 4 ex1p -m ../data/star-mixed-p2.mesh -o 2
 //               mpirun -np 4 ex1p -m ../data/disc-nurbs.mesh -o -1
 //               mpirun -np 4 ex1p -m ../data/pipe-nurbs.mesh -o -1
 //               mpirun -np 4 ex1p -m ../data/ball-nurbs.mesh -o 2
-//               mpirun -np 4 ex1p -m ../data/fichera-mixed-p2.mesh -o 2
 //               mpirun -np 4 ex1p -m ../data/star-surf.mesh
 //               mpirun -np 4 ex1p -m ../data/square-disc-surf.mesh
 //               mpirun -np 4 ex1p -m ../data/inline-segment.mesh
@@ -25,11 +20,6 @@
 //               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh
 //               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh -o -1 -sc
 //
-// Device sample runs:
-//               mpirun -np 4 ex1p -pa -d cuda
-//               mpirun -np 4 ex1p -pa -d occa-cuda
-//               mpirun -np 4 ex1p -pa -d raja-omp
-//
 // Description:  This example code demonstrates the use of MFEM to define a
 //               simple finite element discretization of the Laplace problem
 //               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
@@ -64,9 +54,7 @@ int main(int argc, char *argv[])
   const char *mesh_file = "../data/star.mesh";
   int order = 1;
   bool static_cond = false;
-   bool pa = false;
-   const char *device = "cpu";
-   bool visualization = true;
+   bool visualization = 1;

   OptionsParser args(argc, argv);
   args.AddOption(&mesh_file, "-m", "--mesh",
@@ -76,10 +64,6 @@ int main(int argc, char *argv[])
                  " isoparametric space.");
   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                  "--no-visualization",
                  "Enable or disable GLVis visualization.");
@@ -177,58 +161,49 @@ int main(int argc, char *argv[])
   b->AddDomainIntegrator(new DomainLFIntegrator(one));
   b->Assemble();

-   // 9. Set device config parameters from the command line options and switch
-   //    to working on the device.
-   Device::Configure(device);
-   if (myid == 0) { Device::Print(); }
-   Device::Enable();
-
-   // 10. Define the solution vector x as a parallel finite element grid function
-   //     corresponding to fespace. Initialize x with initial guess of zero,
-   //     which satisfies the boundary conditions.
+   // 9. Define the solution vector x as a parallel finite element grid function
+   //    corresponding to fespace. Initialize x with initial guess of zero,
+   //    which satisfies the boundary conditions.
   ParGridFunction x(fespace);
   x = 0.0;

-   // 11. Set up the parallel bilinear form a(.,.) on the finite element space
+   // 10. Set up the parallel bilinear form a(.,.) on the finite element space
   //     corresponding to the Laplacian operator -Delta, by adding the Diffusion
   //     domain integrator.
   ParBilinearForm *a = new ParBilinearForm(fespace);
-   if (pa) { a->SetAssemblyLevel(AssemblyLevel::PARTIAL); }
   a->AddDomainIntegrator(new DiffusionIntegrator(one));

-   // 12. Assemble the parallel bilinear form and the corresponding linear
+   // 11. Assemble the parallel bilinear form and the corresponding linear
   //     system, applying any necessary transformations such as: parallel
   //     assembly, eliminating boundary conditions, applying conforming
   //     constraints for non-conforming AMR, static condensation, etc.
   if (static_cond) { a->EnableStaticCondensation(); }
   a->Assemble();

-   OperatorPtr A;
+   HypreParMatrix A;
   Vector B, X;
   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);

-   // 13. Solve the linear system A X = B.
-   //     * With full assembly, use the BoomerAMG preconditioner from hypre.
-   //     * With partial assembly, use no preconditioner, for now.
-   Solver *prec = NULL;
-   if (!pa) { prec = new HypreBoomerAMG; }
-   CGSolver cg(MPI_COMM_WORLD);
-   cg.SetRelTol(1e-12);
-   cg.SetMaxIter(2000);
-   cg.SetPrintLevel(1);
-   if (prec) { cg.SetPreconditioner(*prec); }
-   cg.SetOperator(*A);
-   cg.Mult(B, X);
-   delete prec;
+   if (myid == 0)
+   {
+      cout << "Size of linear system: " << A.GetGlobalNumRows() << endl;
+   }

-   // 14. Recover the parallel grid function corresponding to X. This is the
+   // 12. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
+   //     preconditioner from hypre.
+   HypreSolver *amg = new HypreBoomerAMG(A);
+   HyprePCG *pcg = new HyprePCG(A);
+   pcg->SetTol(1e-12);
+   pcg->SetMaxIter(200);
+   pcg->SetPrintLevel(2);
+   pcg->SetPreconditioner(*amg);
+   pcg->Mult(B, X);
+
+   // 13. Recover the parallel grid function corresponding to X. This is the
   //     local finite element solution on each processor.
   a->RecoverFEMSolution(X, *b, x);

-   // 15. Switch back to the host.
-   Device::Disable();
-
-   // 16. Save the refined mesh and the solution in parallel. This output can
+   // 14. Save the refined mesh and the solution in parallel. This output can
   //     be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
   {
      ostringstream mesh_name, sol_name;
@@ -244,7 +219,7 @@ int main(int argc, char *argv[])
      x.Save(sol_ofs);
   }

-   // 17. Send the solution by socket to a GLVis server.
+   // 15. Send the solution by socket to a GLVis server.
   if (visualization)
   {
      char vishost[] = "localhost";
@@ -255,7 +230,9 @@ int main(int argc, char *argv[])
      sol_sock << "solution\n" << *pmesh << x << flush;
   }

-   // 18. Free the used memory.
+   // 16. Free the used memory.
+   delete pcg;
+   delete amg;
   delete a;
   delete b;
   delete fespace;
@@ -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
@@ -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;
-   };
-}
@@ -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;
-   };
-}
@@ -1,310 +0,0 @@
-//                                MFEM Example 22
-//
-// Compile with: make ex22
-//
-// Sample runs:  ex22
-//               ex22 -o 3
-//               ex22 -m ../data/beam-quad.mesh
-//               ex22 -m ../data/beam-quad.mesh -o 3
-//               ex22 -m ../data/beam-quad.mesh -o 3 -f 1
-//               ex22 -m ../data/beam-tet.mesh
-//               ex22 -m ../data/beam-tet.mesh -o 2
-//               ex22 -m ../data/beam-hex.mesh
-//               ex22 -m ../data/beam-hex.mesh -o 2
-//
-// Description:  This is a version of Example 2 with a simple adaptive mesh
-//               refinement loop. The problem being solved is again the linear
-//               elasticity describing a multi-material cantilever beam.
-//               The problem is solved on a sequence of meshes which
-//               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
-//               to a simple ZZ error estimator.
-//
-//               The example demonstrates MFEM's capability to work with both
-//               conforming and nonconforming refinements, in 2D and 3D, on
-//               linear and curved meshes. Interpolation of functions from
-//               coarse to fine meshes, as well as persistent GLVis
-//               visualization are also illustrated.
-//
-//               We recommend viewing Examples 2 and 6 before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/beam-tri.mesh";
-   int order = 1;
-   bool static_cond = false;
-   int flux_averaging = 0;
-   bool visualization = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&flux_averaging, "-f", "--flux-averaging",
-                  "Flux averaging: 0 - global, 1 - by mesh attribute.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   // 2. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral, and hexahedral meshes with the same code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
-   MFEM_VERIFY(mesh.SpaceDimension() == dim, "invalid mesh");
-
-   if (mesh.attributes.Max() < 2 || mesh.bdr_attributes.Max() < 2)
-   {
-      cerr << "\nInput mesh should have at least two materials and "
-           << "two boundary attributes! (See schematic in ex2.cpp)\n"
-           << endl;
-      return 3;
-   }
-
-   // 3. Since a NURBS mesh can currently only be refined uniformly, we need to
-   //    convert it to a piecewise-polynomial curved mesh. First we refine the
-   //    NURBS mesh a bit more and then project the curvature to quadratic Nodes.
-   if (mesh.NURBSext)
-   {
-      for (int i = 0; i < 2; i++)
-      {
-         mesh.UniformRefinement();
-      }
-      mesh.SetCurvature(2);
-   }
-
-   // 4. Define a finite element space on the mesh. The polynomial order is
-   //    one (linear) by default, but this can be changed on the command line.
-   H1_FECollection fec(order, dim);
-   FiniteElementSpace fespace(&mesh, &fec, dim);
-
-   // 5. As in Example 2, we set up the linear form b(.) which corresponds to
-   //    the right-hand side of the FEM linear system. In this case, b_i equals
-   //    the boundary integral of f*phi_i where f represents a "pull down"
-   //    force on the Neumann part of the boundary and phi_i are the basis
-   //    functions in the finite element fespace. The force is defined by the
-   //    VectorArrayCoefficient object f, which is a vector of Coefficient
-   //    objects. The fact that f is non-zero on boundary attribute 2 is
-   //    indicated by the use of piece-wise constants coefficient for its last
-   //    component. We don't assemble the discrete problem yet, this will be
-   //    done in the main loop.
-   VectorArrayCoefficient f(dim);
-   for (int i = 0; i < dim-1; i++)
-   {
-      f.Set(i, new ConstantCoefficient(0.0));
-   }
-   {
-      Vector pull_force(mesh.bdr_attributes.Max());
-      pull_force = 0.0;
-      pull_force(1) = -1.0e-2;
-      f.Set(dim-1, new PWConstCoefficient(pull_force));
-   }
-
-   LinearForm b(&fespace);
-   b.AddDomainIntegrator(new VectorBoundaryLFIntegrator(f));
-
-   // 6. Set up the bilinear form a(.,.) on the finite element space
-   //    corresponding to the linear elasticity integrator with piece-wise
-   //    constants coefficient lambda and mu.
-   Vector lambda(mesh.attributes.Max());
-   lambda = 1.0;
-   lambda(0) = lambda(1)*50;
-   PWConstCoefficient lambda_func(lambda);
-   Vector mu(mesh.attributes.Max());
-   mu = 1.0;
-   mu(0) = mu(1)*50;
-   PWConstCoefficient mu_func(mu);
-
-   BilinearForm a(&fespace);
-   BilinearFormIntegrator *integ =
-      new ElasticityIntegrator(lambda_func,mu_func);
-   a.AddDomainIntegrator(integ);
-   if (static_cond) { a.EnableStaticCondensation(); }
-
-   // 7. The solution vector x and the associated finite element grid function
-   //    will be maintained over the AMR iterations. We initialize it to zero.
-   Vector zero_vec(dim);
-   zero_vec = 0.0;
-   VectorConstantCoefficient zero_vec_coeff(zero_vec);
-   GridFunction x(&fespace);
-   x = 0.0;
-
-   // 8. Determine the list of true (i.e. conforming) essential boundary dofs.
-   //    In this example, the boundary conditions are defined by marking only
-   //    boundary attribute 1 from the mesh as essential and converting it to a
-   //    list of true dofs.  The conversion to true dofs will be done in the
-   //    main loop.
-   Array<int> ess_bdr(mesh.bdr_attributes.Max());
-   ess_bdr = 0;
-   ess_bdr[0] = 1;
-
-   // 9. Connect to GLVis.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock;
-   if (visualization)
-   {
-      sol_sock.open(vishost, visport);
-      sol_sock.precision(8);
-   }
-
-   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
-   //     that uses the ComputeElementFlux method of the ElasticityIntegrator to
-   //     recover a smoothed flux (stress) that is subtracted from the element
-   //     flux to get an error indicator. We need to supply the space for the
-   //     smoothed flux: an (H1)^tdim (i.e., vector-valued) space is used here.
-   //     Here, tdim represents the number of components for a symmetric (dim x
-   //     dim) tensor.
-   const int tdim = dim*(dim+1)/2;
-   FiniteElementSpace flux_fespace(&mesh, &fec, tdim);
-   ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace);
-   estimator.SetFluxAveraging(flux_averaging);
-
-   // 11. A refiner selects and refines elements based on a refinement strategy.
-   //     The strategy here is to refine elements with errors larger than a
-   //     fraction of the maximum element error. Other strategies are possible.
-   //     The refiner will call the given error estimator.
-   ThresholdRefiner refiner(estimator);
-   refiner.SetTotalErrorFraction(0.7);
-
-   // 12. The main AMR loop. In each iteration we solve the problem on the
-   //     current mesh, visualize the solution, and refine the mesh.
-   const int max_dofs = 50000;
-   const int max_amr_itr = 20;
-   for (int it = 0; it <= max_amr_itr; it++)
-   {
-      int cdofs = fespace.GetTrueVSize();
-      cout << "\nAMR iteration " << it << endl;
-      cout << "Number of unknowns: " << cdofs << endl;
-
-      // 13. Assemble the stiffness matrix and the right-hand side.
-      a.Assemble();
-      b.Assemble();
-
-      // 14. Set Dirichlet boundary values in the GridFunction x.
-      //     Determine the list of Dirichlet true DOFs in the linear system.
-      Array<int> ess_tdof_list;
-      x.ProjectBdrCoefficient(zero_vec_coeff, ess_bdr);
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-
-      // 15. Create the linear system: eliminate boundary conditions, constrain
-      //     hanging nodes and possibly apply other transformations. The system
-      //     will be solved for true (unconstrained) DOFs only.
-      SparseMatrix A;
-      Vector B, X;
-      const int copy_interior = 1;
-      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
-
-#ifndef MFEM_USE_SUITESPARSE
-      // 16. Define a simple symmetric Gauss-Seidel preconditioner and use it to
-      //     solve the linear system with PCG.
-      GSSmoother M(A);
-      PCG(A, M, B, X, 3, 2000, 1e-12, 0.0);
-#else
-      // 16. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the
-      //     the linear system.
-      UMFPackSolver umf_solver;
-      umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-      umf_solver.SetOperator(A);
-      umf_solver.Mult(B, X);
-#endif
-
-      // 17. After solving the linear system, reconstruct the solution as a
-      //     finite element GridFunction. Constrained nodes are interpolated
-      //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
-      a.RecoverFEMSolution(X, b, x);
-
-      // 18. Send solution by socket to the GLVis server.
-      if (visualization && sol_sock.good())
-      {
-         GridFunction nodes(&fespace), *nodes_p = &nodes;
-         mesh.GetNodes(nodes);
-         nodes += x;
-         int own_nodes = 0;
-         mesh.SwapNodes(nodes_p, own_nodes);
-         x.Neg(); // visualize the backward displacement
-         sol_sock << "solution\n" << mesh << x << flush;
-         x.Neg();
-         mesh.SwapNodes(nodes_p, own_nodes);
-         if (it == 0)
-         {
-            sol_sock << "keys '" << ((dim == 2) ? "Rjl" : "") << "m'" << endl;
-         }
-         sol_sock << "window_title 'AMR iteration: " << it << "'\n"
-                  << "pause" << endl;
-         cout << "Visualization paused. "
-              "Press <space> in the GLVis window to continue." << endl;
-      }
-
-      if (cdofs > max_dofs)
-      {
-         cout << "Reached the maximum number of dofs. Stop." << endl;
-         break;
-      }
-
-      // 19. Call the refiner to modify the mesh. The refiner calls the error
-      //     estimator to obtain element errors, then it selects elements to be
-      //     refined and finally it modifies the mesh. The Stop() method can be
-      //     used to determine if a stopping criterion was met.
-      refiner.Apply(mesh);
-      if (refiner.Stop())
-      {
-         cout << "Stopping criterion satisfied. Stop." << endl;
-         break;
-      }
-
-      // 20. Update the space to reflect the new state of the mesh. Also,
-      //     interpolate the solution x so that it lies in the new space but
-      //     represents the same function. This saves solver iterations later
-      //     since we'll have a good initial guess of x in the next step.
-      //     Internally, FiniteElementSpace::Update() calculates an
-      //     interpolation matrix which is then used by GridFunction::Update().
-      fespace.Update();
-      x.Update();
-
-      // 21. Inform also the bilinear and linear forms that the space has
-      //     changed.
-      a.Update();
-      b.Update();
-   }
-
-   {
-      ofstream mesh_ref_out("ex22_reference.mesh");
-      mesh_ref_out.precision(16);
-      mesh.Print(mesh_ref_out);
-
-      ofstream mesh_out("ex22_deformed.mesh");
-      mesh_out.precision(16);
-      GridFunction nodes(&fespace), *nodes_p = &nodes;
-      mesh.GetNodes(nodes);
-      nodes += x;
-      int own_nodes = 0;
-      mesh.SwapNodes(nodes_p, own_nodes);
-      mesh.Print(mesh_out);
-      mesh.SwapNodes(nodes_p, own_nodes);
-
-      ofstream x_out("ex22_displacement.sol");
-      x_out.precision(16);
-      x.Save(x_out);
-   }
-
-   return 0;
-}
@@ -1,366 +0,0 @@
-//                                MFEM Example 22
-//
-// Compile with: make ex22p
-//
-// Sample runs:  mpirun -np 4 ex22p
-//               mpirun -np 4 ex22p -o 3
-//               mpirun -np 4 ex22p -m ../data/beam-quad.mesh
-//               mpirun -np 4 ex22p -m ../data/beam-quad.mesh -o 3
-//               mpirun -np 4 ex22p -m ../data/beam-tet.mesh
-//               mpirun -np 4 ex22p -m ../data/beam-tet.mesh -o 2
-//               mpirun -np 4 ex22p -m ../data/beam-hex.mesh
-//               mpirun -np 4 ex22p -m ../data/beam-hex.mesh -o 2
-//
-// Description:  This is a version of Example 2p with a simple adaptive mesh
-//               refinement loop. The problem being solved is again the linear
-//               elasticity describing a multi-material cantilever beam.
-//               The problem is solved on a sequence of meshes which
-//               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
-//               to a simple ZZ error estimator.
-//
-//               The example demonstrates MFEM's capability to work with both
-//               conforming and nonconforming refinements, in 2D and 3D, on
-//               linear and curved meshes. Interpolation of functions from
-//               coarse to fine meshes, as well as persistent GLVis
-//               visualization are also illustrated.
-//
-//               We recommend viewing Examples 2p and 6p before viewing this
-//               example.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 0. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/beam-tri.mesh";
-   int serial_ref_levels = 0;
-   int order = 1;
-   bool static_cond = false;
-   bool visualization = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&serial_ref_levels, "-rs", "--refine-serial",
-                  "Number of uniform serial refinements (before parallel"
-                  " partitioning)");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree).");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 2. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral, and hexahedral meshes with the same code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
-   MFEM_VERIFY(mesh.SpaceDimension() == dim, "invalid mesh");
-
-   if (mesh.attributes.Max() < 2 || mesh.bdr_attributes.Max() < 2)
-   {
-      cerr << "\nInput mesh should have at least two materials and "
-           << "two boundary attributes! (See schematic in ex2.cpp)\n"
-           << endl;
-      MPI_Finalize();
-      return 3;
-   }
-
-   // 3. Refine the mesh before parallel partitioning. Since a NURBS mesh can
-   //    currently only be refined uniformly, we need to convert it to a
-   //    piecewise-polynomial curved mesh. First we refine the NURBS mesh a bit
-   //    more and then project the curvature to quadratic Nodes.
-   if (mesh.NURBSext && serial_ref_levels == 0)
-   {
-      serial_ref_levels = 2;
-   }
-   for (int i = 0; i < serial_ref_levels; i++)
-   {
-      mesh.UniformRefinement();
-   }
-   if (mesh.NURBSext)
-   {
-      mesh.SetCurvature(2);
-   }
-   mesh.EnsureNCMesh();
-
-   ParMesh pmesh(MPI_COMM_WORLD, mesh);
-   mesh.Clear();
-
-   // 4. Define a finite element space on the mesh. The polynomial order is
-   //    one (linear) by default, but this can be changed on the command line.
-   H1_FECollection fec(order, dim);
-   ParFiniteElementSpace fespace(&pmesh, &fec, dim);
-
-   // 5. As in Example 2, we set up the linear form b(.) which corresponds to
-   //    the right-hand side of the FEM linear system. In this case, b_i equals
-   //    the boundary integral of f*phi_i where f represents a "pull down"
-   //    force on the Neumann part of the boundary and phi_i are the basis
-   //    functions in the finite element fespace. The force is defined by the
-   //    VectorArrayCoefficient object f, which is a vector of Coefficient
-   //    objects. The fact that f is non-zero on boundary attribute 2 is
-   //    indicated by the use of piece-wise constants coefficient for its last
-   //    component. We don't assemble the discrete problem yet, this will be
-   //    done in the main loop.
-   VectorArrayCoefficient f(dim);
-   for (int i = 0; i < dim-1; i++)
-   {
-      f.Set(i, new ConstantCoefficient(0.0));
-   }
-   {
-      Vector pull_force(pmesh.bdr_attributes.Max());
-      pull_force = 0.0;
-      pull_force(1) = -1.0e-2;
-      f.Set(dim-1, new PWConstCoefficient(pull_force));
-   }
-
-   ParLinearForm b(&fespace);
-   b.AddDomainIntegrator(new VectorBoundaryLFIntegrator(f));
-
-   // 6. Set up the bilinear form a(.,.) on the finite element space
-   //    corresponding to the linear elasticity integrator with piece-wise
-   //    constants coefficient lambda and mu.
-   Vector lambda(pmesh.attributes.Max());
-   lambda = 1.0;
-   lambda(0) = lambda(1)*50;
-   PWConstCoefficient lambda_func(lambda);
-   Vector mu(pmesh.attributes.Max());
-   mu = 1.0;
-   mu(0) = mu(1)*50;
-   PWConstCoefficient mu_func(mu);
-
-   ParBilinearForm a(&fespace);
-   BilinearFormIntegrator *integ =
-      new ElasticityIntegrator(lambda_func,mu_func);
-   a.AddDomainIntegrator(integ);
-   if (static_cond) { a.EnableStaticCondensation(); }
-
-   // 7. The solution vector x and the associated finite element grid function
-   //    will be maintained over the AMR iterations. We initialize it to zero.
-   Vector zero_vec(dim);
-   zero_vec = 0.0;
-   VectorConstantCoefficient zero_vec_coeff(zero_vec);
-   ParGridFunction x(&fespace);
-   x = 0.0;
-
-   // 8. Determine the list of true (i.e. conforming) essential boundary dofs.
-   //    In this example, the boundary conditions are defined by marking only
-   //    boundary attribute 1 from the mesh as essential and converting it to a
-   //    list of true dofs.  The conversion to true dofs will be done in the
-   //    main loop.
-   Array<int> ess_bdr(pmesh.bdr_attributes.Max());
-   ess_bdr = 0;
-   ess_bdr[0] = 1;
-
-   // 9. GLVis visualization.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock;
-
-   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
-   //     that uses the ComputeElementFlux method of the ElasticityIntegrator to
-   //     recover a smoothed flux (stress) that is subtracted from the element
-   //     flux to get an error indicator. We need to supply the space for the
-   //     smoothed flux: an (H1)^tdim (i.e., vector-valued) space is used here.
-   //     Here, tdim represents the number of components for a symmetric (dim x
-   //     dim) tensor.
-   const int tdim = dim*(dim+1)/2;
-   L2_FECollection flux_fec(order, dim);
-   ParFiniteElementSpace flux_fespace(&pmesh, &flux_fec, tdim);
-   ParFiniteElementSpace smooth_flux_fespace(&pmesh, &fec, tdim);
-   L2ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace,
-                                       smooth_flux_fespace);
-
-   // 11. A refiner selects and refines elements based on a refinement strategy.
-   //     The strategy here is to refine elements with errors larger than a
-   //     fraction of the maximum element error. Other strategies are possible.
-   //     The refiner will call the given error estimator.
-   ThresholdRefiner refiner(estimator);
-   refiner.SetTotalErrorFraction(0.7);
-
-   // 12. The main AMR loop. In each iteration we solve the problem on the
-   //     current mesh, visualize the solution, and refine the mesh.
-   const int max_dofs = 50000;
-   const int max_amr_itr = 20;
-   for (int it = 0; it <= max_amr_itr; it++)
-   {
-      HYPRE_Int global_dofs = fespace.GlobalTrueVSize();
-      if (myid == 0)
-      {
-         cout << "\nAMR iteration " << it << endl;
-         cout << "Number of unknowns: " << global_dofs << endl;
-      }
-
-      // 13. Assemble the stiffness matrix and the right-hand side.
-      a.Assemble();
-      b.Assemble();
-
-      // 14. Set Dirichlet boundary values in the GridFunction x.
-      //     Determine the list of Dirichlet true DOFs in the linear system.
-      Array<int> ess_tdof_list;
-      x.ProjectBdrCoefficient(zero_vec_coeff, ess_bdr);
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-
-      // 15. Create the linear system: eliminate boundary conditions, constrain
-      //     hanging nodes and possibly apply other transformations. The system
-      //     will be solved for true (unconstrained) DOFs only.
-
-      HypreParMatrix A;
-      Vector B, X;
-      const int copy_interior = 1;
-      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
-
-      // 16. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
-      //     preconditioner from hypre.
-      HypreBoomerAMG amg;
-      amg.SetPrintLevel(0);
-      // amg.SetSystemsOptions(dim); // optional
-      CGSolver pcg(A.GetComm());
-      pcg.SetPreconditioner(amg);
-      pcg.SetOperator(A);
-      pcg.SetRelTol(1e-6);
-      pcg.SetMaxIter(500);
-      pcg.SetPrintLevel(3); // print the first and the last iterations only
-      pcg.Mult(B, X);
-
-      // 17. After solving the linear system, reconstruct the solution as a
-      //     finite element GridFunction. Constrained nodes are interpolated
-      //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
-      a.RecoverFEMSolution(X, b, x);
-
-      // 18. Send solution by socket to the GLVis server.
-      if (visualization && it == 0)
-      {
-         sol_sock.open(vishost, visport);
-         sol_sock.precision(8);
-      }
-      if (visualization && sol_sock.good())
-      {
-         GridFunction nodes(&fespace), *nodes_p = &nodes;
-         pmesh.GetNodes(nodes);
-         nodes += x;
-         int own_nodes = 0;
-         pmesh.SwapNodes(nodes_p, own_nodes);
-         x.Neg(); // visualize the backward displacement
-         sol_sock << "parallel " << num_procs << ' ' << myid << '\n';
-         sol_sock << "solution\n" << pmesh << x << flush;
-         x.Neg();
-         pmesh.SwapNodes(nodes_p, own_nodes);
-         if (it == 0)
-         {
-            sol_sock << "keys '" << ((dim == 2) ? "Rjl" : "") << "m'" << endl;
-         }
-         sol_sock << "window_title 'AMR iteration: " << it << "'\n"
-                  << "pause" << endl;
-         if (myid == 0)
-         {
-            cout << "Visualization paused. "
-                 "Press <space> in the GLVis window to continue." << endl;
-         }
-      }
-
-      if (global_dofs > max_dofs)
-      {
-         if (myid == 0)
-         {
-            cout << "Reached the maximum number of dofs. Stop." << endl;
-         }
-         break;
-      }
-
-      // 19. Call the refiner to modify the mesh. The refiner calls the error
-      //     estimator to obtain element errors, then it selects elements to be
-      //     refined and finally it modifies the mesh. The Stop() method can be
-      //     used to determine if a stopping criterion was met.
-      refiner.Apply(pmesh);
-      if (refiner.Stop())
-      {
-         if (myid == 0)
-         {
-            cout << "Stopping criterion satisfied. Stop." << endl;
-         }
-         break;
-      }
-
-      // 20. Update the space to reflect the new state of the mesh. Also,
-      //     interpolate the solution x so that it lies in the new space but
-      //     represents the same function. This saves solver iterations later
-      //     since we'll have a good initial guess of x in the next step.
-      //     Internally, FiniteElementSpace::Update() calculates an
-      //     interpolation matrix which is then used by GridFunction::Update().
-      fespace.Update();
-      x.Update();
-
-      // 21. Load balance the mesh, and update the space and solution. Currently
-      //     available only for nonconforming meshes.
-      if (pmesh.Nonconforming())
-      {
-         pmesh.Rebalance();
-
-         // Update the space and the GridFunction. This time the update matrix
-         // redistributes the GridFunction among the processors.
-         fespace.Update();
-         x.Update();
-      }
-
-      // 22. Inform also the bilinear and linear forms that the space has
-      //     changed.
-      a.Update();
-      b.Update();
-   }
-
-   {
-      ostringstream mref_name, mesh_name, sol_name;
-      mref_name << "ex22p_reference_mesh." << setfill('0') << setw(6) << myid;
-      mesh_name << "ex22p_deformed_mesh." << setfill('0') << setw(6) << myid;
-      sol_name << "ex22p_displacement." << setfill('0') << setw(6) << myid;
-
-      ofstream mesh_ref_out(mref_name.str().c_str());
-      mesh_ref_out.precision(16);
-      pmesh.Print(mesh_ref_out);
-
-      ofstream mesh_out(mesh_name.str().c_str());
-      mesh_out.precision(16);
-      GridFunction nodes(&fespace), *nodes_p = &nodes;
-      pmesh.GetNodes(nodes);
-      nodes += x;
-      int own_nodes = 0;
-      pmesh.SwapNodes(nodes_p, own_nodes);
-      pmesh.Print(mesh_out);
-      pmesh.SwapNodes(nodes_p, own_nodes);
-
-      ofstream x_out(sol_name.str().c_str());
-      x_out.precision(16);
-      x.Save(x_out);
-   }
-
-   MPI_Finalize();
-   return 0;
-}
@@ -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
@@ -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
@@ -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
@@ -15,17 +15,12 @@
 //               ex6 -m ../data/square-disc-surf.mesh -o 2
 //               ex6 -m ../data/amr-quad.mesh
 //
-// Device sample runs:
-//               ex6 -pa -d cuda
-//               ex6 -pa -d occa-cuda
-//               ex6 -pa -d raja-omp
-//
 // Description:  This is a version of Example 1 with a simple adaptive mesh
 //               refinement loop. The problem being solved is again the Laplace
 //               equation -Delta u = 1 with homogeneous Dirichlet boundary
 //               conditions. The problem is solved on a sequence of meshes which
 //               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
+//               or non-conforming (quadrilateral, hexahedrons) manner according
 //               to a simple ZZ error estimator.
 //
 //               The example demonstrates MFEM's capability to work with both
@@ -48,19 +43,13 @@ int main(int argc, char *argv[])
   // 1. Parse command-line options.
   const char *mesh_file = "../data/star.mesh";
   int order = 1;
-   bool pa = false;
-   const char *device = "cpu";
-   bool visualization = true;
+   bool visualization = 1;

   OptionsParser args(argc, argv);
   args.AddOption(&mesh_file, "-m", "--mesh",
                  "Mesh file to use.");
   args.AddOption(&order, "-o", "--order",
                  "Finite element order (polynomial degree).");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                  "--no-visualization",
                  "Enable or disable GLVis visualization.");
@@ -96,15 +85,10 @@ int main(int argc, char *argv[])
   H1_FECollection fec(order, dim);
   FiniteElementSpace fespace(&mesh, &fec);

-   // 5. Set device config parameters from the command line options.
-   Device::Configure(device);
-   Device::Print();
-
-   // 6. As in Example 1, we set up bilinear and linear forms corresponding to
+   // 5. As in Example 1, we set up bilinear and linear forms corresponding to
   //    the Laplace problem -\Delta u = 1. We don't assemble the discrete
   //    problem yet, this will be done in the main loop.
   BilinearForm a(&fespace);
-   if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
   LinearForm b(&fespace);

   ConstantCoefficient one(1.0);
@@ -114,18 +98,18 @@ int main(int argc, char *argv[])
   a.AddDomainIntegrator(integ);
   b.AddDomainIntegrator(new DomainLFIntegrator(one));

-   // 7. The solution vector x and the associated finite element grid function
+   // 6. The solution vector x and the associated finite element grid function
   //    will be maintained over the AMR iterations. We initialize it to zero.
   GridFunction x(&fespace);
   x = 0.0;

-   // 8. All boundary attributes will be used for essential (Dirichlet) BC.
+   // 7. All boundary attributes will be used for essential (Dirichlet) BC.
   MFEM_VERIFY(mesh.bdr_attributes.Size() > 0,
               "Boundary attributes required in the mesh.");
   Array<int> ess_bdr(mesh.bdr_attributes.Max());
   ess_bdr = 1;

-   // 9. Connect to GLVis.
+   // 8. Connect to GLVis.
   char vishost[] = "localhost";
   int  visport   = 19916;
   socketstream sol_sock;
@@ -134,23 +118,23 @@ int main(int argc, char *argv[])
      sol_sock.open(vishost, visport);
   }

-   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
-   //     that uses the ComputeElementFlux method of the DiffusionIntegrator to
-   //     recover a smoothed flux (gradient) that is subtracted from the element
-   //     flux to get an error indicator. We need to supply the space for the
-   //     smoothed flux: an (H1)^sdim (i.e., vector-valued) space is used here.
+   // 9. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
+   //    that uses the ComputeElementFlux method of the DiffusionIntegrator to
+   //    recover a smoothed flux (gradient) that is subtracted from the element
+   //    flux to get an error indicator. We need to supply the space for the
+   //    smoothed flux: an (H1)^sdim (i.e., vector-valued) space is used here.
   FiniteElementSpace flux_fespace(&mesh, &fec, sdim);
   ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace);
   estimator.SetAnisotropic();

-   // 11. A refiner selects and refines elements based on a refinement strategy.
+   // 10. A refiner selects and refines elements based on a refinement strategy.
   //     The strategy here is to refine elements with errors larger than a
   //     fraction of the maximum element error. Other strategies are possible.
   //     The refiner will call the given error estimator.
   ThresholdRefiner refiner(estimator);
   refiner.SetTotalErrorFraction(0.7);

-   // 12. The main AMR loop. In each iteration we solve the problem on the
+   // 11. The main AMR loop. In each iteration we solve the problem on the
   //     current mesh, visualize the solution, and refine the mesh.
   const int max_dofs = 50000;
   for (int it = 0; ; it++)
@@ -159,55 +143,44 @@ int main(int argc, char *argv[])
      cout << "\nAMR iteration " << it << endl;
      cout << "Number of unknowns: " << cdofs << endl;

-      // 13. Assemble the right-hand side.
+      // 12. Assemble the stiffness matrix and the right-hand side.
+      a.Assemble();
      b.Assemble();

-      // 14. Set Dirichlet boundary values in the GridFunction x.
+      // 13. Set Dirichlet boundary values in the GridFunction x.
      //     Determine the list of Dirichlet true DOFs in the linear system.
      Array<int> ess_tdof_list;
      x.ProjectBdrCoefficient(zero, ess_bdr);
      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);

-      // 15. Switch to the device and assemble the stiffness matrix.
-      Device::Enable();
-      a.Assemble();
-
-      // 16. Create the linear system: eliminate boundary conditions, constrain
+      // 14. Create the linear system: eliminate boundary conditions, constrain
      //     hanging nodes and possibly apply other transformations. The system
      //     will be solved for true (unconstrained) DOFs only.
-      OperatorPtr A;
+      SparseMatrix A;
      Vector B, X;
-
      const int copy_interior = 1;
      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);

-      // 17. Solve the linear system A X = B.
-      if (!pa)
-      {
 #ifndef MFEM_USE_SUITESPARSE
-         // Use a simple symmetric Gauss-Seidel preconditioner with PCG.
-         GSSmoother M((SparseMatrix&)(*A));
-         PCG(*A, M, B, X, 3, 200, 1e-12, 0.0);
+      // 15. Define a simple symmetric Gauss-Seidel preconditioner and use it to
+      //     solve the linear system with PCG.
+      GSSmoother M(A);
+      PCG(A, M, B, X, 3, 200, 1e-12, 0.0);
 #else
-         // If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
-         UMFPackSolver umf_solver;
-         umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-         umf_solver.SetOperator(*A);
-         umf_solver.Mult(B, X);
+      // 15. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the
+      //     the linear system.
+      UMFPackSolver umf_solver;
+      umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
+      umf_solver.SetOperator(A);
+      umf_solver.Mult(B, X);
 #endif
-      }
-      else // No preconditioning for now in partial assembly mode.
-      {
-         CG(*A, B, X, 3, 2000, 1e-12, 0.0);
-      }

-      // 18. After solving the linear system, reconstruct the solution as a
+      // 16. After solving the linear system, reconstruct the solution as a
      //     finite element GridFunction. Constrained nodes are interpolated
      //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
-      Device::Disable();
      a.RecoverFEMSolution(X, b, x);

-      // 19. Send solution by socket to the GLVis server.
+      // 17. Send solution by socket to the GLVis server.
      if (visualization && sol_sock.good())
      {
         sol_sock.precision(8);
@@ -220,7 +193,7 @@ int main(int argc, char *argv[])
         break;
      }

-      // 20. Call the refiner to modify the mesh. The refiner calls the error
+      // 18. Call the refiner to modify the mesh. The refiner calls the error
      //     estimator to obtain element errors, then it selects elements to be
      //     refined and finally it modifies the mesh. The Stop() method can be
      //     used to determine if a stopping criterion was met.
@@ -231,7 +204,7 @@ int main(int argc, char *argv[])
         break;
      }

-      // 21. Update the space to reflect the new state of the mesh. Also,
+      // 19. Update the space to reflect the new state of the mesh. Also,
      //     interpolate the solution x so that it lies in the new space but
      //     represents the same function. This saves solver iterations later
      //     since we'll have a good initial guess of x in the next step.
@@ -240,7 +213,7 @@ int main(int argc, char *argv[])
      fespace.Update();
      x.Update();

-      // 22. Inform also the bilinear and linear forms that the space has
+      // 20. Inform also the bilinear and linear forms that the space has
      //     changed.
      a.Update();
      b.Update();
@@ -15,17 +15,12 @@
 //               mpirun -np 4 ex6p -m ../data/square-disc-surf.mesh -o 2
 //               mpirun -np 4 ex6p -m ../data/amr-quad.mesh
 //
-// Device sample runs:
-//               mpirun -np 4 ex6p -pa -d cuda
-//               mpirun -np 4 ex6p -pa -d occa-cuda
-//               mpirun -np 4 ex6p -pa -d raja-omp
-//
 // Description:  This is a version of Example 1 with a simple adaptive mesh
 //               refinement loop. The problem being solved is again the Laplace
 //               equation -Delta u = 1 with homogeneous Dirichlet boundary
 //               conditions. The problem is solved on a sequence of meshes which
 //               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
+//               or non-conforming (quadrilateral, hexahedrons) manner according
 //               to a simple ZZ error estimator.
 //
 //               The example demonstrates MFEM's capability to work with both
@@ -54,8 +49,6 @@ int main(int argc, char *argv[])
   // 2. Parse command-line options.
   const char *mesh_file = "../data/star.mesh";
   int order = 1;
-   bool pa = false;
-   const char *device = "cpu";
   bool visualization = true;

   OptionsParser args(argc, argv);
@@ -63,10 +56,6 @@ int main(int argc, char *argv[])
                  "Mesh file to use.");
   args.AddOption(&order, "-o", "--order",
                  "Finite element order (polynomial degree).");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                  "--no-visualization",
                  "Enable or disable GLVis visualization.");
@@ -117,15 +106,10 @@ int main(int argc, char *argv[])
   H1_FECollection fec(order, dim);
   ParFiniteElementSpace fespace(&pmesh, &fec);

-   // 7. Set device config parameters from the command line options.
-   Device::Configure(device);
-   if (myid == 0) { Device::Print(); }
-
-   // 8. As in Example 1p, we set up bilinear and linear forms corresponding to
+   // 7. As in Example 1p, we set up bilinear and linear forms corresponding to
   //    the Laplace problem -\Delta u = 1. We don't assemble the discrete
   //    problem yet, this will be done in the main loop.
   ParBilinearForm a(&fespace);
-   if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
   ParLinearForm b(&fespace);

   ConstantCoefficient one(1.0);
@@ -134,12 +118,12 @@ int main(int argc, char *argv[])
   a.AddDomainIntegrator(integ);
   b.AddDomainIntegrator(new DomainLFIntegrator(one));

-   // 9. The solution vector x and the associated finite element grid function
+   // 8. The solution vector x and the associated finite element grid function
   //    will be maintained over the AMR iterations. We initialize it to zero.
   ParGridFunction x(&fespace);
   x = 0;

-   // 10. Connect to GLVis.
+   // 9. Connect to GLVis.
   char vishost[] = "localhost";
   int  visport   = 19916;

@@ -161,7 +145,7 @@ int main(int argc, char *argv[])
      sout.precision(8);
   }

-   // 11. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
+   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
   //     with L2 projection in the smoothing step to better handle hanging
   //     nodes and parallel partitioning. We need to supply a space for the
   //     discontinuous flux (L2) and a space for the smoothed flux (H(div) is
@@ -175,14 +159,14 @@ int main(int argc, char *argv[])
   // ParFiniteElementSpace smooth_flux_fes(&pmesh, &smooth_flux_fec, dim);
   L2ZienkiewiczZhuEstimator estimator(*integ, x, flux_fes, smooth_flux_fes);

-   // 12. A refiner selects and refines elements based on a refinement strategy.
+   // 11. A refiner selects and refines elements based on a refinement strategy.
   //     The strategy here is to refine elements with errors larger than a
   //     fraction of the maximum element error. Other strategies are possible.
   //     The refiner will call the given error estimator.
   ThresholdRefiner refiner(estimator);
   refiner.SetTotalErrorFraction(0.7);

-   // 13. The main AMR loop. In each iteration we solve the problem on the
+   // 12. The main AMR loop. In each iteration we solve the problem on the
   //     current mesh, visualize the solution, and refine the mesh.
   const int max_dofs = 100000;
   for (int it = 0; ; it++)
@@ -194,48 +178,41 @@ int main(int argc, char *argv[])
         cout << "Number of unknowns: " << global_dofs << endl;
      }

-      // 14. Assemble the right-hand side and determine the list of true
-      //     (i.e. parallel conforming) essential boundary dofs.
-      Array<int> ess_tdof_list;
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
+      // 13. Assemble the stiffness matrix and the right-hand side. Note that
+      //     MFEM doesn't care at this point that the mesh is nonconforming
+      //     and parallel. The FE space is considered 'cut' along hanging
+      //     edges/faces, and also across processor boundaries.
+      a.Assemble();
      b.Assemble();

-      // 15. Switch to the device and assemble the stiffness matrix. Note that
-      //     MFEM doesn't care at this point that the mesh is nonconforming and
-      //     parallel.  The FE space is considered 'cut' along hanging
-      //     edges/faces, and also across processor boundaries.
-      Device::Enable();
-      a.Assemble();
-
-      // 16. Create the parallel linear system: eliminate boundary conditions.
+      // 14. Create the parallel linear system: eliminate boundary conditions,
+      //     constrain hanging nodes and nodes across processor boundaries.
      //     The system will be solved for true (unconstrained/unique) DOFs only.
-      OperatorPtr A;
-      Vector B, X;
+      Array<int> ess_tdof_list;
+      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);

+      HypreParMatrix A;
+      Vector B, X;
      const int copy_interior = 1;
      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);

-      // 17. Solve the linear system A X = B.
-      //     * With full assembly, use the BoomerAMG preconditioner from hypre.
-      //     * With partial assembly, use no preconditioner, for now.
-      HypreBoomerAMG *amg = NULL;
-      if (!pa) { amg = new HypreBoomerAMG; amg->SetPrintLevel(0); }
-      CGSolver cg(MPI_COMM_WORLD);
-      cg.SetRelTol(1e-6);
-      cg.SetMaxIter(2000);
-      cg.SetPrintLevel(3); // print the first and the last iterations only
-      if (amg) { cg.SetPreconditioner(*amg); }
-      cg.SetOperator(*A);
-      cg.Mult(B, X);
-      delete amg;
+      // 15. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
+      //     preconditioner from hypre.
+      HypreBoomerAMG amg;
+      amg.SetPrintLevel(0);
+      CGSolver pcg(A.GetComm());
+      pcg.SetPreconditioner(amg);
+      pcg.SetOperator(A);
+      pcg.SetRelTol(1e-6);
+      pcg.SetMaxIter(200);
+      pcg.SetPrintLevel(3); // print the first and the last iterations only
+      pcg.Mult(B, X);

-      // 18. Switch back to the host and extract the parallel grid function
-      //     corresponding to the finite element approximation X. This is the
-      //     local solution on each processor.
-      Device::Disable();
+      // 16. Extract the parallel grid function corresponding to the finite element
+      //     approximation X. This is the local solution on each processor.
      a.RecoverFEMSolution(X, b, x);

-      // 19. Send the solution by socket to a GLVis server.
+      // 17. Send the solution by socket to a GLVis server.
      if (visualization)
      {
         sout << "parallel " << num_procs << " " << myid << "\n";
@@ -251,7 +228,7 @@ int main(int argc, char *argv[])
         break;
      }

-      // 20. Call the refiner to modify the mesh. The refiner calls the error
+      // 18. Call the refiner to modify the mesh. The refiner calls the error
      //     estimator to obtain element errors, then it selects elements to be
      //     refined and finally it modifies the mesh. The Stop() method can be
      //     used to determine if a stopping criterion was met.
@@ -265,7 +242,7 @@ int main(int argc, char *argv[])
         break;
      }

-      // 21. Update the finite element space (recalculate the number of DOFs,
+      // 19. Update the finite element space (recalculate the number of DOFs,
      //     etc.) and create a grid function update matrix. Apply the matrix
      //     to any GridFunctions over the space. In this case, the update
      //     matrix is an interpolation matrix so the updated GridFunction will
@@ -273,7 +250,7 @@ int main(int argc, char *argv[])
      fespace.Update();
      x.Update();

-      // 22. Load balance the mesh, and update the space and solution. Currently
+      // 20. Load balance the mesh, and update the space and solution. Currently
      //     available only for nonconforming meshes.
      if (pmesh.Nonconforming())
      {
@@ -285,7 +262,7 @@ int main(int argc, char *argv[])
         x.Update();
      }

-      // 23. Inform also the bilinear and linear forms that the space has
+      // 21. Inform also the bilinear and linear forms that the space has
      //     changed.
      a.Update();
      b.Update();
@@ -4,10 +4,8 @@
 //
 // Sample runs:  ex8 -m ../data/square-disc.mesh
 //               ex8 -m ../data/star.mesh
-//               ex8 -m ../data/star-mixed.mesh
 //               ex8 -m ../data/escher.mesh
 //               ex8 -m ../data/fichera.mesh
-//               ex8 -m ../data/fichera-mixed.mesh
 //               ex8 -m ../data/square-disc-p2.vtk
 //               ex8 -m ../data/square-disc-p3.mesh
 //               ex8 -m ../data/star-surf.mesh -o 2
@@ -4,10 +4,8 @@
 //
 // Sample runs:  mpirun -np 4 ex8p -m ../data/square-disc.mesh
 //               mpirun -np 4 ex8p -m ../data/star.mesh
-//               mpirun -np 4 ex8p -m ../data/star-mixed.mesh
 //               mpirun -np 4 ex8p -m ../data/escher.mesh
 //               mpirun -np 4 ex8p -m ../data/fichera.mesh
-//               mpirun -np 4 ex8p -m ../data/fichera-mixed.mesh
 //               mpirun -np 4 ex8p -m ../data/square-disc-p2.vtk
 //               mpirun -np 4 ex8p -m ../data/square-disc-p3.mesh
 //               mpirun -np 4 ex8p -m ../data/star-surf.mesh -o 2
@@ -125,13 +123,9 @@ int main(int argc, char *argv[])
      test_order++;
   }
   if (test_order < trial_order)
-   {
      if (myid == 0)
-      {
         cerr << "Warning, test space not enriched enough to handle primal"
              << " trial space\n";
-      }
-   }

   FiniteElementCollection *x0_fec, *xhat_fec, *test_fec;

@@ -10,7 +10,6 @@
 //    ex9 -m ../data/periodic-hexagon.mesh -p 1 -r 2 -dt 0.005 -tf 9
 //    ex9 -m ../data/amr-quad.mesh -p 1 -r 2 -dt 0.002 -tf 9
 //    ex9 -m ../data/star-q3.mesh -p 1 -r 2 -dt 0.005 -tf 9
-//    ex9 -m ../data/star-mixed.mesh -p 1 -r 2 -dt 0.005 -tf 9
 //    ex9 -m ../data/disc-nurbs.mesh -p 1 -r 3 -dt 0.005 -tf 9
 //    ex9 -m ../data/disc-nurbs.mesh -p 2 -r 3 -dt 0.005 -tf 9
 //    ex9 -m ../data/periodic-square.mesh -p 3 -r 4 -dt 0.0025 -tf 9 -vs 20
@@ -132,8 +131,8 @@ int main(int argc, char *argv[])

   // 2. Read the mesh from the given mesh file. We can handle geometrically
   //    periodic meshes in this code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
+   Mesh *mesh = new Mesh(mesh_file, 1, 1);
+   int dim = mesh->Dimension();

   // 3. Define the ODE solver used for time integration. Several explicit
   //    Runge-Kutta methods are available.
@@ -147,6 +146,7 @@ int main(int argc, char *argv[])
      case 6: ode_solver = new RK6Solver; break;
      default:
         cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
+         delete mesh;
         return 3;
   }

@@ -156,18 +156,18 @@ int main(int argc, char *argv[])
   //    a (piecewise-polynomial) high-order mesh.
   for (int lev = 0; lev < ref_levels; lev++)
   {
-      mesh.UniformRefinement();
+      mesh->UniformRefinement();
   }
-   if (mesh.NURBSext)
+   if (mesh->NURBSext)
   {
-      mesh.SetCurvature(max(order, 1));
+      mesh->SetCurvature(max(order, 1));
   }
-   mesh.GetBoundingBox(bb_min, bb_max, max(order, 1));
+   mesh->GetBoundingBox(bb_min, bb_max, max(order, 1));

   // 5. Define the discontinuous DG finite element space of the given
   //    polynomial order on the refined mesh.
   DG_FECollection fec(order, dim);
-   FiniteElementSpace fes(&mesh, &fec);
+   FiniteElementSpace fes(mesh, &fec);

   cout << "Number of unknowns: " << fes.GetVSize() << endl;

@@ -207,7 +207,7 @@ int main(int argc, char *argv[])
   {
      ofstream omesh("ex9.mesh");
      omesh.precision(precision);
-      mesh.Print(omesh);
+      mesh->Print(omesh);
      ofstream osol("ex9-init.gf");
      osol.precision(precision);
      u.Save(osol);
@@ -221,14 +221,14 @@ int main(int argc, char *argv[])
      if (binary)
      {
 #ifdef MFEM_USE_SIDRE
-         dc = new SidreDataCollection("Example9", &mesh);
+         dc = new SidreDataCollection("Example9", mesh);
 #else
         MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
 #endif
      }
      else
      {
-         dc = new VisItDataCollection("Example9", &mesh);
+         dc = new VisItDataCollection("Example9", mesh);
         dc->SetPrecision(precision);
      }
      dc->RegisterField("solution", &u);
@@ -253,7 +253,7 @@ int main(int argc, char *argv[])
      else
      {
         sout.precision(precision);
-         sout << "solution\n" << mesh << u;
+         sout << "solution\n" << *mesh << u;
         sout << "pause\n";
         sout << flush;
         cout << "GLVis visualization paused."
@@ -285,7 +285,7 @@ int main(int argc, char *argv[])

         if (visualization)
         {
-            sout << "solution\n" << mesh << u << flush;
+            sout << "solution\n" << *mesh << u << flush;
         }

         if (visit)
@@ -10,7 +10,6 @@
 //    mpirun -np 4 ex9p -m ../data/periodic-hexagon.mesh -p 1 -dt 0.005 -tf 9
 //    mpirun -np 4 ex9p -m ../data/amr-quad.mesh -p 1 -rp 1 -dt 0.002 -tf 9
 //    mpirun -np 4 ex9p -m ../data/star-q3.mesh -p 1 -rp 1 -dt 0.004 -tf 9
-//    mpirun -np 4 ex9p -m ../data/star-mixed.mesh -p 1 -rp 1 -dt 0.004 -tf 9
 //    mpirun -np 4 ex9p -m ../data/disc-nurbs.mesh -p 1 -rp 1 -dt 0.005 -tf 9
 //    mpirun -np 4 ex9p -m ../data/disc-nurbs.mesh -p 2 -rp 1 -dt 0.005 -tf 9
 //    mpirun -np 4 ex9p -m ../data/periodic-square.mesh -p 3 -rp 2 -dt 0.0025 -tf 9 -vs 20
@@ -22,9 +22,9 @@ MFEM_LIB_FILE = mfem_is_not_built
 -include $(CONFIG_MK)

 SEQ_EXAMPLES = ex1 ex2 ex3 ex4 ex5 ex6 ex7 ex8 ex9 ex10 ex14 ex15 ex16 ex17\
-  ex18 ex19 ex20 ex22
+  ex18 ex19
 PAR_EXAMPLES = ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex8p ex9p ex10p ex11p ex12p\
- ex13p ex14p ex15p ex16p ex17p ex18p ex19p ex20p ex22p
+ ex13p ex14p ex15p ex16p ex17p ex18p ex19p

 ifeq ($(MFEM_USE_MPI),NO)
   EXAMPLES = $(SEQ_EXAMPLES)
@@ -96,12 +96,6 @@ ex15-test-seq: ex15
 	@$(call mfem-test,$<,, Serial example,-e 1)
 ex15p-test-par: ex15p
 	@$(call mfem-test,$<, $(RUN_MPI), Parallel example,-e 1)
-# Testing: optional tests
-ifeq ($(MFEM_USE_STRUMPACK),YES)
-ex11p-test-strumpack: ex11p
-	@$(call mfem-test,$<, $(RUN_MPI), STRUMPACK example,--strumpack)
-test-par-YES: ex11p-test-strumpack
-endif

 # Testing: "test" target and mfem-test* variables are defined in config/test.mk

@@ -124,5 +118,3 @@ clean-exec:
 	@rm -f ex16.mesh ex16-mesh.* ex16-init.* ex16-final.*
 	@rm -f vortex-mesh.* vortex.mesh vortex-?-init.* vortex-?-final.*
 	@rm -f deformation.* pressure.*
-	@rm -f ex20.dat ex20p_?????.dat gnuplot_ex20.inp gnuplot_ex20p.inp
-	@rm -f ex22*.mesh ex22*.sol ex22p_*.*
@@ -96,7 +96,7 @@ foreach(TEST_OPTIONS_VAR
  # All PETSC tests are parallel.
  if (MFEM_USE_MPI)
    add_test(NAME ${TEST_NAME_FULL}_np=4
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4
      ${MPIEXEC_PREFLAGS}
      $<TARGET_FILE:${TEST_NAME}> ${TEST_OPTIONS}
      ${MPIEXEC_POSTFLAGS})
@@ -239,7 +239,7 @@ int main(int argc, char *argv[])
   // 2b. We initialize PETSc
   if (use_petsc)
   {
-      MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL);
+      PetscInitialize(NULL,NULL,petscrc_file,NULL);
   }

   // 3. Read the serial mesh from the given mesh file on all processors. We can
@@ -446,7 +446,7 @@ int main(int argc, char *argv[])
   delete oper;

   // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }

   MPI_Finalize();

@@ -123,7 +123,7 @@ int main(int argc, char *argv[])
   }

   // 2b. We initialize PETSc
-   MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL);
+   PetscInitialize(NULL,NULL,petscrc_file,NULL);

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

   // We finalize PETSc
-   MFEMFinalizePetsc();
+   PetscFinalize();

   MPI_Finalize();

@@ -101,7 +101,7 @@ int main(int argc, char *argv[])
   }

   // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }

   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
@@ -359,7 +359,7 @@ int main(int argc, char *argv[])
   delete pmesh;

   // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }

   MPI_Finalize();

@@ -96,7 +96,7 @@ int main(int argc, char *argv[])
      args.PrintOptions(cout);
   }
   // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
   kappa = freq * M_PI;

   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
@@ -309,7 +309,7 @@ int main(int argc, char *argv[])
   delete pmesh;

   // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }

   MPI_Finalize();

@@ -97,7 +97,7 @@ int main(int argc, char *argv[])
      args.PrintOptions(cout);
   }
   // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
   kappa = freq * M_PI;

   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
@@ -330,7 +330,7 @@ int main(int argc, char *argv[])
   delete pmesh;

   // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }

   MPI_Finalize();

@@ -105,7 +105,7 @@ int main(int argc, char *argv[])
      args.PrintOptions(cout);
   }
   // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }

   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
@@ -544,7 +544,7 @@ int main(int argc, char *argv[])
   delete pmesh;

   // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }

   MPI_Finalize();

@@ -12,7 +12,7 @@
 //               equation -Delta u = 1 with homogeneous Dirichlet boundary
 //               conditions. The problem is solved on a sequence of meshes which
 //               are locally refined in a conforming (triangles, tetrahedrons)
-//               or non-conforming (quadrilaterals, hexahedra) manner according
+//               or non-conforming (quadrilateral, hexahedrons) manner according
 //               to a simple ZZ error estimator.
 //
 //               The example demonstrates MFEM's capability to work with both
@@ -88,7 +88,7 @@ int main(int argc, char *argv[])
      args.PrintOptions(cout);
   }
   // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }

   // 3. Read the (serial) mesh from the given mesh file on all processors.  We
   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
@@ -315,7 +315,7 @@ int main(int argc, char *argv[])
   }

   // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }

   MPI_Finalize();
   return 0;
@@ -248,7 +248,7 @@ int main(int argc, char *argv[])
   {
      // When using PETSc, we just create the ODE solver. We use command line
      // customization to select a specific solver.
-      MFEMInitializePetsc(NULL, NULL, petscrc_file, NULL);
+      PetscInitialize(NULL, NULL, petscrc_file, NULL);
      ode_solver = pode_solver = new PetscODESolver(MPI_COMM_WORLD);
   }

@@ -481,7 +481,7 @@ int main(int argc, char *argv[])
   delete pmon;

   // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }

   MPI_Finalize();
   return 0;
@@ -40,8 +40,7 @@ add_mfem_examples(PUMI_EXAMPLES_SRCS ${PFX} "" test_pumi)
 # Command line options for the tests.
 # TODO...

-# Set the number of processors for the parallel examples. The value of
-# MFEM_MPI_NP is ignored.
+# Set the number of processors for the parallel examples.
 set(EX1_TEST_NP 1)
 set(EX1P_TEST_NP 8)
 set(EX2_TEST_NP 1)
@@ -209,15 +209,15 @@ int main(int argc, char *argv[])
      Transform(Geometries.GetCenter(mesh->GetElementBaseGeometry(el)),cent);
      if (cent(0) <= -0.05)
      {
-         mesh->SetAttribute(el, 1);
+         mesh->SetAttribute(el , 1);
      }
      else if (cent(0) >= 0.05)
      {
-         mesh->SetAttribute(el, 2);
+         mesh->SetAttribute(el , 2);
      }
      else
      {
-         mesh->SetAttribute(el, 3);
+         mesh->SetAttribute(el , 3);
      }
   }
   mesh->SetAttributes();
@@ -68,7 +68,7 @@ foreach(SRC_FILE ${SUNDIALS_EXAMPLES_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})
@@ -11,9 +11,7 @@

 set(SRCS
  bilinearform.cpp
-  bilinearform_ext.cpp
  bilininteg.cpp
-  bilininteg_ext.cpp
  coefficient.cpp
  datacollection.cpp
  eltrans.cpp
@@ -35,9 +33,7 @@ set(SRCS

 set(HDRS
  bilinearform.hpp
-  bilinearform_ext.hpp
  bilininteg.hpp
-  bilininteg_ext.hpp
  coefficient.hpp
  datacollection.hpp
  eltrans.hpp
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Tim McManus	4d61e4807a	Interior DoF for Cubic Quadrilateral Elements Fixed and currently implemented for Quadrant 1 Mesh	2018-10-07 15:31:13 -04:00
Tim McManus	29bf750349	First change to interior dof ordering for cubic quad elements.	2018-10-02 15:05:24 -04:00
Tim McManus	97368ef77f	Default command line behavior wrt glvis visualization fixed. Cubic Edge DoF orientation fixed.	2018-09-16 17:37:22 -04:00
Tim McManus	2fbe31f57a	Changing variable name for easier readibility and first attempt at P3/Q3 element generation.	2018-09-16 14:14:16 -04:00
Tim McManus	d27ca5e40c	Basic half/whole plane meshes, and glvis autovisualizing.	2018-09-09 14:47:22 -04:00
Tim McManus	fd9aa3afeb	Merge remote-tracking branch 'origin/master' into mixed-elements-dev	2018-09-06 17:20:10 -04:00
Tim McManus	7b3e124613	Updating some file names in gallery	2017-06-28 17:36:05 -07:00
Tim McManus	c09d22b6c0	2nd order quadratic, mixed elements, covering all quadrants. Animation and .mesh file included.	2017-06-09 06:58:18 -07:00
Tim McManus	4b6ab370ca	tri_quad 2nd order jacobian image	2017-06-07 07:12:43 -07:00
Tim McManus	adb40b62f7	Quad 1, 2 edges, 2nd order, mixed-elemnts	2017-06-04 18:41:18 -07:00
Tim McManus	cfcbbfd6cf	Merge branch 'master' into mixed-elements-dev	2017-06-04 18:23:04 -07:00
Tim McManus	f36a7f40f2	Animation of Triangle/Quad element mesh in Quad1 of a circle sector bounded by a square.	2017-05-23 22:08:25 -07:00
Tim McManus	0138d7fbd9	Triangle/Quad element mesh in Quad1 of a circle sector bounded by a square generator. Full 2D problem animation	2017-05-21 21:08:17 -07:00
Tim McManus	2ae20dde47	Triangle and single layer Quad mesh for circle sector bounded by a square	2017-05-16 23:55:36 -07:00
Tim McManus	a360b53521	Circle bounded by a square: triangles.	2017-05-11 22:27:39 -07:00
Tim McManus	fb9a4d61d2	Preliminary mixed element mesh work involving equilateral triangles and squares.	2017-05-02 22:45:29 -07:00