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

.gitignore

@@ -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

CHANGELOG

@@ -8,176 +8,17 @@
                                http://mfem.org
 
 
-Version 4.0-RC1, Apr 11, 2019
-=============================
-
-Requirements and Limitations
-----------------------------
-- This is a release candidate for mfem-4.0.
-- Use at your own risk -- not everything will work, the API may change.
-- We are looking for feedback from friendly users.
-- Unlike previous MFEM releases, this version requires a C++11 compiler.
-
-- GPU-related limitations:
-  * NVCC is not supported in the CMake build system yet.
-  * Element batching is currently ignored.
-  * Full-assembly (on device), element assembly, and matrix-free bilinear forms
-    are not supported yet.
-  * FunctionCoefficients do not currently work on GPUs.
-  * Partial assembly kernels are not implemented yet for simplices.
-
-GPU support
------------
-- Added initial support for hardware devices, such as GPUs, and programming
-  models, such as CUDA, OCCA, RAJA and OpenMP.
-
-- The GPU/device support is based on MFEM's new backends and kernels working
-  seamlessly with a new lightweight device/host memory manager. The kernels can
-  be implemented either in OCCA, or as a simple wrapper around for-loops, which
-  can then be dispatched to RAJA and native backends. See the files forall.hpp
-  and mem_manager.hpp in the general/ directory.
-
-- Several of the MFEM example codes (ex1, ex1p, ex6, and ex6p) can now take
-  advantage of GPU acceleration with the backend selectable at runtime. Many of
-  the linear algebra and finite element operations (e.g. partially assembled
-  bilinear forms) have been extended to take advantage of kernel acceleration by
-  simply replacing loops with the MFEM_FORALL() macro.
-
-- In addition to pure CUDA, the library currently supports OCCA, RAJA and OpenMP
-  kernels, which could be mixed and matched in different parts of the same
-  application. We plan on adding support for more programming models and devices
-  in the future, without the need for significant modifications in user code.
-  The list of current backends is: "occa-cuda", "raja-cuda", "cuda", "occa-omp",
-  "raja-omp", "omp", "occa-cpu", "raja-cpu", and "cpu".
-
-Discretization improvements
----------------------------
-- Added support for a general "low-order refined"-to-"high-order" transfer of
-  GridFunction data from a "low-order refined" (LOR) space defined on a refined
-  mesh to a "high-order" (HO) finite element space defined on a coarse mesh. See
-  the new classes InterpolationGridTransfer and L2ProjectionGridTransfer and the
-  new LOR Transfer miniapp: miniapps/tools/lor-transfer.cpp.
-
-- Added support for derefinement of vector (RT + ND) spaces.
-
-- Added element flux, and flux energy computation in class ElasticityIntegrator,
-  allowing for the use of Zienkiewicz-Zhu type error estimators with the
-  integrator. For an illustration of this addition, see the new Example 22.
-
-- Added a variety of coefficients which are sums or products of existing
-  coefficients as well as grid function coefficients which return the
-  divergence, gradient, or curl of their GridFunctions.
-
-Support for wedge elements and meshes with mixed element types
---------------------------------------------------------------
-- Added support for wedge-shaped mesh elements of arbitrary order (with Geometry
-  type PRISM) which have two triangular faces and three quadrilateral faces.
-  Several examples of such meshes can be found in the data/ directory.
-
-- Added H1 and L2 finite elements of arbitrary order for Wedge elements.
-
-- Added support for mixed meshes containing triangles and quadrilaterals in 2D
-  or tetrahedra, wedges, and hexahedra in 3D. This includes support for uniform
-  refinement of such meshes. Several examples of such meshes can be found in the
-  data/ directory.
-
-- Added support for reading and writing linear and quadratic meshes containing
-  wedge elements in VTK mesh format. Several examples of such meshes can be
-  found in the data/ directory.
-
-Other meshing improvements
---------------------------
-- Improved the uniform refinement of tetrahedral meshes (also part of the
-  uniform refinement of mixed 3D meshes). The previous refinement algorithm is
-  still available as an option in Mesh::UniformRefinement. Both can be used in
-  the updated Mesh Explorer miniapp.
-
-- The local tetrahedral mesh refinement algorithm in serial and in parallel now
-  follows precisely the paper:
-
-     D. Arnold, A. Mukherjee, and L. Pouly, "Locally Adapted Tetrahedral Meshes
-     Using Bisection", SIAM J. Sci. Comput. 22 (2000), 431–448.
-
-  This guarantees that the shape regularity of the elements will be preserved
-  under refinement.
-
-- Added support for parallel communication groups on non-conforming meshes.
-
-- Improved parallel partitioning of non-conforming meshes. If the coarse mesh
-  elements are ordered as a sequence of face-neighbors, the parallel partitions
-  are now guaranteed to be continuous. To that end, inline quadrilateral and
-  hexahedral meshes are now by default ordered along a space-filling curve.
-
-- A boundary in a NURBS mesh can now be connected with another boundary. Such a
-  periodic NURBS mesh is a simple way to impose periodic boundary conditions.
-
+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
--------------
-- 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

CMakeLists.txt

@@ -13,11 +13,6 @@ cmake_minimum_required(VERSION 2.8.11)
 set(USER_CONFIG "${CMAKE_CURRENT_SOURCE_DIR}/config/user.cmake" CACHE PATH
   "Path to optional user configuration file.")
 
-# Require C++11 and disable compiler-specific extensions
-set(CMAKE_CXX_STANDARD 11)
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_EXTENSIONS OFF)
-
 # Load user settings before the defaults - this way the defaults will not
 # overwrite the user set options. If the user has not set all options, we still
 # have the defaults.
@@ -175,11 +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)
@@ -316,6 +312,9 @@ message(STATUS "MFEM build type: CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
 message(STATUS "MFEM version: v${MFEM_VERSION_STRING}")
 message(STATUS "MFEM git string: ${MFEM_GIT_STRING}")
 
+# Windows specific
+set(_USE_MATH_DEFINES ${WIN32})
+
 #-------------------------------------------------------------------------------
 # Define and configure the MFEM library
 #-------------------------------------------------------------------------------
@@ -389,9 +388,6 @@ endif()
 # Enable testing if required
 if (MFEM_ENABLE_TESTING)
   enable_testing()
-  set(MFEM_ALL_TESTS_TARGET_NAME tests)
-  add_mfem_target(${MFEM_ALL_TESTS_TARGET_NAME} OFF)
-  add_subdirectory(tests EXCLUDE_FROM_ALL)
 endif()
 
 # Define a target that all examples and miniapps will depend on.
@@ -411,9 +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
@@ -549,10 +543,3 @@ install(FILES
 # Install the export set for use with the install-tree
 install(EXPORT ${PROJECT_NAME_UC}Targets
     DESTINATION ${INSTALL_CMAKE_DIR})
-
-#-------------------------------------------------------------------------------
-# Create 'config.mk' from 'config.mk.in' for the build and install locations and
-# define install rules for 'config.mk' and 'test.mk'
-#-------------------------------------------------------------------------------
-
-mfem_export_mk_files()

CONTRIBUTING.md

@@ -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++
@@ -156,9 +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.
 
@@ -324,9 +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.
@@ -366,10 +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.
@@ -480,6 +472,7 @@ MFEM uses a `master`/`next`-branch workflow as described below:
   - `mfem:gh-next` -- Bleeding-edge development version, may be broken, use at
      your own risk.
 
+
 ## Automated Testing
 
 MFEM has several levels of automated testing running on GitHub, as well as on

INSTALL

@@ -21,24 +21,6 @@ requires an MPI C++ compiler, as well as the following external libraries:
 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.
@@ -65,10 +47,6 @@ Parallel build:
    (build hypre 2.10.0b in ../hypre-2.10.0b relative to mfem/)
    make parallel -j 4
 
-CUDA build:
-   make cuda -j 4
-   (build for a specific compute capability: 'make cuda -j 4 CUDA_ARCH=sm_30')
-
 Example codes (serial/parallel, depending on the build):
    cd examples
    make -j 4
@@ -79,6 +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:
@@ -153,10 +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.
@@ -218,9 +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
@@ -256,7 +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
@@ -276,11 +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.
-
 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.
@@ -391,29 +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.
-
-MFEM_USE_CUDA = YES/NO
-   Enables support for CUDA devices in MFEM. CUDA is a parallel computing
-   platform and programming model for general computing on graphical processing
-   units (GPUs). This option requires MFEM_USE_MM. The variable CUDA_ARCH is
-   used to specify the CUDA compute capability used during compilation (by
-   default, CUDA_ARCH=sm_60). When enabled, this option uses the CUDA_* build
-   options, see below.
-
-MFEM_USE_RAJA = YES/NO
-   Enable support for the RAJA performance portability layer in MFEM. RAJA
-   provides a portable abstraction for loops, supporting different programming
-   model backends. When using the RAJA CUDA backend, MFEM_USE_MM is required.
-
-MFEM_USE_OCCA = YES/NO
-   Enables support for the OCCA library in MFEM. OCCA is an open-source library
-   which aims to make it easy to program different types of devices (e.g. CPU,
-   GPU, FPGA) by providing an unified API for interacting with JIT-compiled
-   backends. When using the OCCA CUDA backend, MFEM_USE_MM is required.
-
 MFEM_BUILD_TAG = (any value)
    An optional tag to characterize the build. Exported to config/config.mk.
    Can be used to identify the MFEM build from other makefiles.
@@ -449,8 +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
@@ -482,8 +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
@@ -529,18 +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.
@@ -662,7 +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.
@@ -676,13 +609,6 @@ MFEM_USE_MPFR
 MFEM_USE_GZSTREAM
 MFEM_USE_PUMI
 
-The following GNU make options are not supported with CMake yet:
-
-MFEM_USE_CUDA
-MFEM_USE_OCCA
-MFEM_USE_RAJA
-MFEM_USE_MM
-
 The following options are CMake specific:
 
 MFEM_ENABLE_TESTING  - Enable the ctest framework for testing.

LICENSE

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

config/XSDKDefaults.cmake

@@ -180,75 +180,3 @@ IF (USE_XSDK_DEFAULTS)
   ENDIF()
 
 ENDIF()
-
-IF (DEFINED TPL_ENABLE_MPI)
-  SET(MFEM_USE_MPI ${TPL_ENABLE_MPI} CACHE BOOL "Enable MPI parallel build" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_METIS)
-  SET(MFEM_USE_METIS ${TPL_ENABLE_METIS} CACHE BOOL "Enable METIS usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_GZSTREAM)
-  SET(MFEM_USE_GZSTREAM ${TPL_ENABLE_GZSTREAM} CACHE BOOL "Enable gzstream for compressed data streams." FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_LIBUNWIND)
-  SET(MFEM_USE_LIBUNWIND ${TPL_ENABLE_LIBUNWIND} CACHE BOOL "Enable backtrace for errors." FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_LAPACK)
-  SET(MFEM_USE_LAPACK ${TPL_ENABLE_LAPACK} CACHE BOOL "Enable LAPACK usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_SUNDIALS)
-  SET(MFEM_USE_SUNDIALS ${TPL_ENABLE_SUNDIALS} CACHE BOOL "Enable SUNDIALS usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_MESQUITE)
-  SET(MFEM_USE_MESQUITE ${TPL_ENABLE_MESQUITE} CACHE BOOL "Enable MESQUITE usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_SUITESPARSE)
-  SET(MFEM_USE_SUITESPARSE ${TPL_ENABLE_SUITESPARSE} CACHE BOOL "Enable SuiteSparse usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_SUPERLU)
-  SET(MFEM_USE_SUPERLU ${TPL_ENABLE_SUPERLU} CACHE BOOL "Enable SuperLU_DIST usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_STRUMPACK)
-  SET(MFEM_USE_STRUMPACK ${TPL_ENABLE_STRUMPACK} CACHE BOOL "Enable STRUMPACK usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_GECKO)
-  SET(MFEM_USE_GECKO ${TPL_ENABLE_GECKO} CACHE BOOL "Enable GECKO usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_GNUTLS)
-  SET(MFEM_USE_GNUTLS ${TPL_ENABLE_GNUTLS} CACHE BOOL "Enable GNUTLS usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_NETCDF)
-  SET(MFEM_USE_NETCDF ${TPL_ENABLE_NETCDF} CACHE BOOL "Enable NETCDF usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_PETSC)
-  SET(MFEM_USE_PETSC ${TPL_ENABLE_PETSC} CACHE BOOL "Enable PETSc support." FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_MPFR)
-  SET(MFEM_USE_MPFR ${TPL_ENABLE_MPFR} CACHE BOOL "Enable MPFR usage." FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_SIDRE)
-  SET(MFEM_USE_SIDRE ${TPL_ENABLE_SIDRE} CACHE BOOL "Enable Axom/Sidre usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_CONDUIT)
-  SET(MFEM_USE_CONDUIT ${TPL_ENABLE_CONDUIT} CACHE BOOL "Enable Conduit usage" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_PUMI)
-  SET(MFEM_USE_PUMI ${TPL_ENABLE_PUMI} CACHE BOOL "Enable PUMI" FORCE)
-ENDIF()

config/cmake/MFEMConfig.cmake.in

@@ -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@)

config/cmake/config.hpp.in

@@ -62,12 +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
 
@@ -112,6 +109,10 @@
 // Enable MFEM functionality based on the SUNDIALS libraries.
 #cmakedefine MFEM_USE_SUNDIALS
 
+// Windows specific options
+// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
+#cmakedefine _USE_MATH_DEFINES
+
 // Version of HYPRE used for building MFEM.
 #cmakedefine MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@
 

config/cmake/modules/MfemCmakeUtilities.cmake

@@ -229,15 +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()
@@ -694,162 +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)
-  foreach(var ${CONFIG_MK_BOOL_VARS})
-    if (${var})
-      set(${var} YES)
-    else()
-      set(${var} NO)
-    endif()
-  endforeach()
-  set(MFEM_CXX ${CMAKE_CXX_COMPILER})
-  set(MFEM_CPPFLAGS "")
-  string(STRIP "${CMAKE_CXX_FLAGS_${BUILD_TYPE}} ${CMAKE_CXX_FLAGS}"
-         MFEM_CXXFLAGS)
-  set(MFEM_TPLFLAGS "")
-  foreach(dir ${MFEM_TPL_INCLUDE_DIRS})
-    set(MFEM_TPLFLAGS "${MFEM_TPLFLAGS} -I${dir}")
-  endforeach()
-  # TODO: MFEM_TPLFLAGS: add other TPL flags, in addition to the -I flags.
-  set(MFEM_INCFLAGS "-I\$(MFEM_INC_DIR) \$(MFEM_TPLFLAGS)")
-  set(MFEM_PICFLAG "")
-  if (BUILD_SHARED_LIBS)
-    set(MFEM_PICFLAG "${CMAKE_SHARED_LIBRARY_CXX_FLAGS}")
-  endif()
-  set(MFEM_FLAGS "\$(MFEM_CPPFLAGS) \$(MFEM_CXXFLAGS) \$(MFEM_INCFLAGS)")
-  # TPL link flags: set below
-  set(MFEM_EXT_LIBS "")
-  if (BUILD_SHARED_LIBS)
-    set(MFEM_LIBS "${shared_link_flag}\$(MFEM_LIB_DIR) -L\$(MFEM_LIB_DIR)")
-    set(MFEM_LIBS "${MFEM_LIBS} -lmfem \$(MFEM_EXT_LIBS)")
-    if (APPLE)
-      set(SO_VER ".${mfem_VERSION}${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    else()
-      set(SO_VER "${CMAKE_SHARED_LIBRARY_SUFFIX}.${mfem_VERSION}")
-    endif()
-    set(MFEM_LIB_FILE "\$(MFEM_LIB_DIR)/libmfem${SO_VER}")
-    set(MFEM_SHARED YES)
-    set(MFEM_STATIC NO)
-  else()
-    set(MFEM_LIBS "-L\$(MFEM_LIB_DIR) -lmfem \$(MFEM_EXT_LIBS)")
-    set(MFEM_LIB_FILE "\$(MFEM_LIB_DIR)/libmfem.a")
-    set(MFEM_SHARED NO)
-    set(MFEM_STATIC YES)
-  endif()
-  set(MFEM_BUILD_TAG "${CMAKE_SYSTEM}")
-  set(MFEM_PREFIX "${CMAKE_INSTALL_PREFIX}")
-  # For the next 4 variable, these are the values for the build-tree version of
-  # 'config.mk'
-  set(MFEM_INC_DIR "${PROJECT_BINARY_DIR}")
-  set(MFEM_LIB_DIR "${PROJECT_BINARY_DIR}")
-  set(MFEM_TEST_MK "${PROJECT_SOURCE_DIR}/config/test.mk")
-  set(MFEM_CONFIG_EXTRA "MFEM_BUILD_DIR ?= ${PROJECT_BINARY_DIR}")
-  set(MFEM_MPIEXEC ${MPIEXEC})
-  if (NOT MFEM_MPIEXEC)
-    set(MFEM_MPIEXEC "mpirun")
-  endif()
-  set(MFEM_MPIEXEC_NP ${MPIEXEC_NUMPROC_FLAG})
-  if (NOT MFEM_MPIEXEC_NP)
-    set(MFEM_MPIEXEC_NP "-np")
-  endif()
-  # MFEM_MPI_NP is already set
-  # Define the variable 'MFEM_EXT_LIBS': handle PUMI libs
-  if ("${MFEM_USE_PUMI}" STREQUAL "YES")
-    message(STATUS "simmodsuite_dir = '${SIMMODSUITE_DIR}'")
-    get_target_property(liblist ${PUMI_LIBRARIES} INTERFACE_LINK_LIBRARIES)
-    set(pumi_dep_libs "${liblist}")
-    foreach(pumilib ${liblist})
-      get_target_property(libdeps ${pumilib} INTERFACE_LINK_LIBRARIES)
-      if (NOT "${libdeps}" MATCHES "libdeps-NOTFOUND")
-        list(APPEND pumi_dep_libs ${libdeps})
-      endif()
-    endforeach()
-    list(REMOVE_DUPLICATES pumi_dep_libs)
-    foreach(pumilib ${pumi_dep_libs})
-      unset(lib CACHE)
-      string(REGEX REPLACE "^SCOREC::" "" libname ${pumilib})
-      string(FIND "${pumilib}" ".a" staticlib)
-      string(FIND "${pumilib}" ".so" sharedlib)
-      find_library(lib ${libname} PATHS ${PUMI_DIR}/lib NO_DEFUALT_PATH)
-      if (NOT "${sharedlib}" MATCHES "-1" OR
-          NOT "${staticlib}" MATCHES "-1"   )
-        set(MFEM_EXT_LIBS "${pumilib} ${MFEM_EXT_LIBS}")
-      elseif (NOT "${lib}" MATCHES "lib-NOTFOUND")
-        set(MFEM_EXT_LIBS "${lib} ${MFEM_EXT_LIBS}")
-      elseif ("${lib}" MATCHES "lib-NOTFOUND" AND
-              NOT "${libname}" MATCHES "can" AND
-              NOT "${libname}" MATCHES "pthread")
-        message(FATAL_ERROR "SCOREC lib ${libname} not found")
-      endif()
-    endforeach()
-  endif()
-  # Define the variable 'MFEM_EXT_LIBS': handle other (not PUMI) libs
-  foreach(lib ${TPL_LIBRARIES})
-    get_filename_component(suffix ${lib} EXT)
-    # handle interfaces (e.g., SCOREC::apf)
-    if ("${lib}" MATCHES "SCOREC::.*")
-    elseif (NOT "${lib}" MATCHES "SCOREC::.*" AND "${lib}" MATCHES ".*::.*")
-      message(FATAL_ERROR "***** interface lib found ... exiting *****")
-      # handle static and shared libs
-    elseif ("${suffix}" STREQUAL "${CMAKE_SHARED_LIBRARY_SUFFIX}")
-      get_filename_component(dir ${lib} DIRECTORY)
-      get_filename_component(fullLibName ${lib} NAME_WE)
-      string(REGEX REPLACE "^lib" "" libname ${fullLibName})
-      set(MFEM_EXT_LIBS
-          "${MFEM_EXT_LIBS} ${shared_link_flag}${dir} -L${dir} -l${libname}")
-    else()
-      set(MFEM_EXT_LIBS "${MFEM_EXT_LIBS} ${lib}")
-    endif()
-  endforeach()
-
-  # Create the build-tree version of 'config.mk'
-  configure_file(
-    "${PROJECT_SOURCE_DIR}/config/config.mk.in"
-    "${PROJECT_BINARY_DIR}/config/config.mk")
-  # Copy 'test.mk' from the source-tree to the build-tree
-  configure_file(
-    "${PROJECT_SOURCE_DIR}/config/test.mk"
-    "${PROJECT_BINARY_DIR}/config/test.mk" COPYONLY)
-
-  # Update variables for the install-tree version of 'config.mk'
-  set(MFEM_INC_DIR "${CMAKE_INSTALL_PREFIX}/include")
-  set(MFEM_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib")
-  set(MFEM_TEST_MK "${CMAKE_INSTALL_PREFIX}/share/mfem/test.mk")
-  set(MFEM_CONFIG_EXTRA "")
-
-  # Create the install-tree version of 'config.mk'
-  configure_file(
-    "${PROJECT_SOURCE_DIR}/config/config.mk.in"
-    "${PROJECT_BINARY_DIR}/config/config-install.mk")
-
-  # Install rules for 'config.mk' and 'test.mk'
-  install(FILES ${PROJECT_SOURCE_DIR}/config/test.mk
-    DESTINATION ${CMAKE_INSTALL_PREFIX}/share/mfem/)
-  install(FILES ${PROJECT_BINARY_DIR}/config/config-install.mk
-    DESTINATION ${CMAKE_INSTALL_PREFIX}/share/mfem/ RENAME config.mk)
-
-endfunction()

config/config.hpp

@@ -15,9 +15,6 @@
 //
 // Otherwise, use the local file: _config.hpp.
 
-#ifndef MFEM_CONFIG_HPP
-#define MFEM_CONFIG_HPP
-
 #ifdef MFEM_BUILD_DIR
 #define MFEM_QUOTE(a) #a
 #define MFEM_MAKE_PATH(x,y) MFEM_QUOTE(x/y)
@@ -26,18 +23,6 @@
 #include "_config.hpp"
 #endif
 
-// Common configuration macros
-
-#if (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 7)) || defined(__clang__)
-#define MFEM_HAVE_GCC_PRAGMA_DIAGNOSTIC
-#endif
-
-// Windows specific options
-#ifdef _WIN32
-// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
-#define _USE_MATH_DEFINES
-#endif
-
 // Check dependencies:
 
 // Options that require MPI
@@ -55,5 +40,3 @@
 #error Building with PUMI (MFEM_USE_PUMI=YES) requires MPI (MFEM_USE_MPI=YES)
 #endif
 #endif // MFEM_USE_MPI not defined
-
-#endif // MFEM_CONFIG_HPP

config/config.hpp.in

@@ -30,12 +30,6 @@
 #define MFEM_VERSION_MINOR (((MFEM_VERSION)/100)%100)
 #define MFEM_VERSION_PATCH ((MFEM_VERSION)%100)
 
-// The absolute path of the MFEM source prefix
-// #define MFEM_SOURCE_DIR "@MFEM_SOURCE_DIR@"
-
-// The absolute path of the MFEM installation prefix
-// #define MFEM_INSTALL_DIR "@MFEM_INSTALL_DIR@"
-
 // Description of the git commit used to build MFEM.
 // #define MFEM_GIT_STRING "@MFEM_GIT_STRING@"
 
@@ -68,12 +62,9 @@
 // allocation and de-allocation.
 // #define MFEM_THREAD_SAFE
 
-// Enable the OpenMP backend.
+// Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
 // #define MFEM_USE_OPENMP
 
-// [Deprecated] Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
-// #define MFEM_USE_LEGACY_OPENMP
-
 // Internal MFEM option: enable group/batch allocation for some small objects.
 // #define MFEM_USE_MEMALLOC
 
@@ -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@

config/config.mk.in

@@ -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@

config/defaults.cmake

@@ -26,8 +26,7 @@ option(MFEM_USE_GZSTREAM "Enable gzstream for compressed data streams." OFF)
 option(MFEM_USE_LIBUNWIND "Enable backtrace for errors." OFF)
 option(MFEM_USE_LAPACK "Enable LAPACK usage" OFF)
 option(MFEM_THREAD_SAFE "Enable thread safety" OFF)
-option(MFEM_USE_OPENMP "Enable the OpenMP backend" OFF)
-option(MFEM_USE_LEGACY_OPENMP "Enable legacy OpenMP usage" OFF)
+option(MFEM_USE_OPENMP "Enable OpenMP usage" OFF)
 option(MFEM_USE_MEMALLOC "Enable the internal MEMALLOC option." ON)
 option(MFEM_USE_SUNDIALS "Enable SUNDIALS usage" OFF)
 option(MFEM_USE_MESQUITE "Enable MESQUITE usage" OFF)
@@ -43,8 +42,6 @@ option(MFEM_USE_SIDRE "Enable Axom/Sidre usage" OFF)
 option(MFEM_USE_CONDUIT "Enable Conduit usage" OFF)
 option(MFEM_USE_PUMI "Enable PUMI" OFF)
 
-set(MFEM_MPI_NP 4 CACHE STRING "Number of processes used for MPI tests")
-
 # Allow a user to disable testing, examples, and/or miniapps at CONFIGURE TIME
 # if they don't want/need them (e.g. if MFEM is "just a dependency" and all they
 # need is the library, building all that stuff adds unnecessary overhead). Note
@@ -103,7 +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.")
@@ -111,8 +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

config/defaults.mk

@@ -21,13 +21,8 @@ NOTMAC := $(subst Darwin,,$(shell uname -s))
 CXX = g++
 MPICXX = mpicxx
 
-BASE_FLAGS  = -std=c++11
-OPTIM_FLAGS = -O3 $(BASE_FLAGS)
-DEBUG_FLAGS = -g $(XCOMPILER)-Wall $(BASE_FLAGS)
-
-# Prefixes for passing flags to the compiler and linker when using CXX or MPICXX
-CXX_XCOMPILER =
-CXX_XLINKER   = -Wl,
+OPTIM_FLAGS = -O3
+DEBUG_FLAGS = -g -Wall
 
 # Destination location of make install
 # PREFIX = $(HOME)/mfem
@@ -38,41 +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 =
@@ -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\
@@ -300,25 +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. Since we compile and link with nvcc (when CUDA is
-# enabled) we only need to explicitly link with the CUDA driver, libcuda.*,
-# which is usually in a system path.
-CUDA_OPT =
-CUDA_LIB = $(if $(NOTMAC),,-L/usr/local/cuda/lib) -lcuda
-
-# OCCA library configuration
-OCCA_DIR ?= @MFEM_DIR@/../occa
-OCCA_OPT = -I$(OCCA_DIR)/include
-OCCA_LIB = $(XLINKER)-rpath,$(OCCA_DIR)/lib -L$(OCCA_DIR)/lib -locca
-
-# RAJA library configuration
-RAJA_DIR ?= @MFEM_DIR@/../raja
-RAJA_OPT = -I$(RAJA_DIR)/include
-ifdef CUB_DIR
-   RAJA_OPT += -I$(CUB_DIR)
-endif
-RAJA_LIB = $(XLINKER)-rpath,$(RAJA_DIR)/lib -L$(RAJA_DIR)/lib -lRAJA
-
 # If YES, enable some informational messages
 VERBOSE = NO
 

config/sample-runs.sh

@@ -30,7 +30,7 @@ groups_serial=(
 '"examples"
    "Examples:"
    "examples"
-   "ex{,1,2}[0-9].cpp"'
+   "ex{,1}[0-9].cpp"'
 #   "ex1.cpp"'
 '"sundials"
    "SUNDIALS examples:"
@@ -44,15 +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:"
@@ -82,7 +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"
@@ -98,8 +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"
@@ -172,9 +170,6 @@ function help_message()
       -v          Enable valgrind
       -o <dir>    [${output_dir:-"<empty>: output goes to stdout"}]
                   If not empty, save output to files inside <dir>
-      -d <dir>    [${mfem_build_dir}]
-                  If <dir> is different from <mfem_dir> then use an
-                  out-of-source build in <dir>
       -j <np>     [${make_j}] Specify the number of jobs to use for building
       -c|-color   Always use colors for the status messages: OK, FAILED, etc
       -b|-built   Do NOT rebuild the library and the executables
@@ -201,8 +196,8 @@ function help_message()
          Their values can also set using the respective uppercase environment
          variable
       mfem_build_dir [${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.
 
@@ -271,10 +266,6 @@ case "$1" in
       shift
       output_dir="$1"
       ;;
-   -d)
-      shift
-      mfem_build_dir="$1"
-      ;;
    -j)
       shift
       make_j="-j $1"

config/test.mk

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

data/beam-wedge.mesh

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

data/beam-wedge.vtk

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

data/fichera-mixed-p2.mesh

@@ -1,192 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-#
-
-dimension
-3
-
-elements
-14
-1 4 13 15 21 25
-1 4 15 13 21 12
-1 4 21 13 25 22
-1 4 15 21 25 24
-1 4 13 15 25 16
-1 5 0 1 4 3 9 10 13 12
-1 5 8 9 12 11 17 18 21 20
-1 5 2 3 6 5 11 12 15 14
-1 6 3 4 6 12 13 15
-1 6 4 7 6 13 16 15
-1 6 12 13 21 9 10 18
-1 6 13 22 21 10 19 18
-1 6 11 14 20 12 15 21
-1 6 15 21 24 14 20 23
-
-boundary
-30
-1 3 5 6 3 2
-2 2 6 4 3
-2 2 4 6 7
-3 3 3 4 1 0
-4 3 11 12 9 8
-5 3 2 3 12 11
-6 3 0 1 10 9
-7 2 10 18 9
-7 2 18 10 19
-8 3 8 9 18 17
-9 3 1 4 13 10
-10 3 4 7 16 13
-11 2 25 13 16
-11 2 13 25 22
-12 3 10 13 22 19
-13 3 7 6 15 16
-14 3 6 5 14 15
-15 3 15 14 23 24
-16 2 15 25 16
-16 2 25 15 24
-17 3 5 2 11 14
-18 3 3 0 9 12
-19 3 11 8 17 20
-20 2 20 14 11
-20 2 14 20 23
-21 3 17 18 21 20
-22 3 18 19 22 21
-23 2 25 21 22
-23 2 21 25 24
-24 3 20 21 24 23
-
-vertices
-26
-
-nodes
-FiniteElementSpace
-FiniteElementCollection: H1_3D_P2
-VDim: 3
-Ordering: 1
-
-0.028213666146621 -1.0129124616273 -1.0197422793601
-0.99151103207842 -0.97408353323117 -1.0219424221199
--0.98628834960982 -0.048291393648833 -1.0334530425724
--0.045286384224892 -0.028259630873799 -0.95961592583917
-1.0351351283956 0.016103611653671 -1.0465984194074
--0.97963495329022 0.975340601895 -0.95050375238061
--0.016565482225269 0.98394050155766 -1.0119900547434
-0.98232264800655 1.0061312792241 -0.97468885016611
--1.0111163694877 -1.0328216757625 -0.033904406474903
--0.031359497737139 -0.95907832225785 -0.02936147605069
-1.0216721775476 -0.95571139678359 -0.041445003869012
--0.96617995956913 0.013420177670196 -0.047073400672525
-0.03735491973348 0.024136644229293 -0.035419858060777
-0.99844568660483 -0.023344853520393 0.043047091318294
--1.0075354852248 0.95110015915707 0.040374961402267
--0.018023004801944 0.98735854397528 0.035048884851858
-0.96496833880778 0.98624407089765 0.029059857856424
--0.95618249163963 -0.95913625303656 0.99699592567049
-0.010523111699149 -1.0380611987319 1.0054330066312
-1.0131589291349 -0.99133288586241 1.0510169859154
--0.9992929702159 -0.016950021823868 1.0209834648762
--0.030905270343646 -0.024878516234457 0.96677784407511
-1.0369556044533 0.036727200814101 0.97476146325791
--1.0268666699025 0.99100244478387 0.95557046163574
-0.032850918109418 0.9761234538078 0.99340013005027
-0.96517252528448 1.018590816239 0.96241486393546
-0.52641251369336 0.53453492783232 -0.046831832639522
-0.54842095679127 0.012466884090474 0.52264325135947
-1.0546647359835 0.51503200008771 0.47661895657821
-0.008193729444779 0.46320342579585 0.51330736048101
-0.48446121998846 1.0366433051979 0.46910527980021
-0.50338134740858 0.53372671722279 1.0016026703109
--0.0026805294677615 0.54834160562605 -0.022633473388851
-0.4992129677441 -0.027650739811361 -0.025983834639192
--0.010308592952788 0.043478553090245 0.54404251929373
-0.52373361142037 0.017260625417003 1.0190168930687
-0.95156254112601 0.024917951411289 0.48927665714905
-1.0114961385777 0.53988309084877 0.98077339629239
-0.01429600397056 1.0255897320394 0.44945099394948
--0.0037663174125072 0.46114195337251 0.98693741812483
-0.53955416269275 0.95254191223583 0.99345054396648
-1.0344137934711 0.51549308419917 0.0019079259000746
-0.4635900873147 1.0074141174823 -0.025796540646941
-1.0393698821347 0.99823230649269 0.53561992818844
-0.54910938213579 -1.0186136680655 -1.0399189315271
-0.98251790353097 -0.52159510049969 -1.0488538759761
-0.51290647936985 0.019199261348695 -1.0180139709264
-0.039190890220925 -0.51870735888369 -1.0145805133507
-0.54531239252537 -1.0346180800814 -0.026071808021516
-1.0111227696296 -0.45961035727523 0.028725982550532
--0.0024106570985168 -0.51591348233633 0.042102640075609
-0.019072471559048 -1.0489699664991 -0.53822694290429
-1.0197706996463 -1.0138504981995 -0.48532295548357
-0.97708769380115 0.012869927892461 -0.49512141938321
--0.0056951441802084 -0.018287890031934 -0.46456751856022
--0.48628377295099 -0.97137148869224 -0.040609835088253
--0.52949825478718 0.022831952339038 0.036623532185331
--0.9682938832324 -0.51529484749772 0.039498377451673
--0.45076946932822 -0.98247022288851 1.0229644412175
--0.036635886738077 -0.53934830226935 0.97308384231292
--0.47986206617206 -0.041745604947209 0.98161771683954
--0.95103283049539 -0.5087813614402 1.0116585971788
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+-1.21109238238 -1.57832632157
+-1.02980825986 -3.84329674785
+-0.772356194895 -2.88247256089
+-0.761324498753 -1.83799993026
+-7.30907218597e-16 -3.9788735773
+-5.48180413948e-16 -2.98415518297
+-0.259673608685 -1.97241688113
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+2.81348848799 -2.81348848799
+2.11011636599 -2.11011636599
+1.21109238238 -1.57832632157
+3.44580559639 -1.98943678865
+2.58435419729 -1.49207759149
+1.57832632157 -1.21109238238
+3.84329674785 -1.02980825986
+2.88247256089 -0.772356194895
+1.83799993026 -0.761324498753
+3.9788735773 -9.7454295813e-16
+2.98415518297 -7.30907218597e-16
+1.97241688113 -0.259673608685
+3.84329674785 1.02980825986
+2.88247256089 0.772356194895
+1.97241688113 0.259673608685

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

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

data/mixed-ele-meshes/circInSquare.py

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

data/mixed-ele-meshes/comp_tri_quad_4_edges.mesh

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

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

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-0.4 -0.69282032 0.15491933
-0.48291796 -0.83643844 0.25066475
-0.61708204 -1.0688174 0.095745414
-0.48291796 -0.83643844 -0.25066475
-0.61708204 -1.0688174 -0.095745414
--0.25356098 -1.0629872 -0.38908379
-0.21049196 -0.88243173 -0.38908379
--0.1430764 -0.59980988 0.11416557
-0.16461091 -0.69008761 0.27491822
--0.29944203 -1.2553313 0.27491822
-0.32097654 -1.3456091 0.11416557
-0.59098879 -0.17599714 -0.11416557
-0.51532795 -0.48760104 -0.27491822
-1.0473544 -0.31190335 0.38908379
-0.65896232 -0.62350725 0.38908379
-1.2368698 -0.36834126 -0.27491822
-1.0048434 -0.95077837 -0.11416557
-1 2.4196059e-15 -1.3788671e-16
-0.5 0.8660254 -8.6542076e-17
-0.76950592 0.22915975 0.15859651
-1.0583527 0.31517866 0.23048728
-0.65062668 0.6156201 0.23048728
-0.86954463 0.8227593 0.15859651
-1.1844891 0.35274221 0.091392579
-1.0997352 0.32750241 -0.20555815
-0.9092442 0.86032286 -0.024929133
-0.75456149 0.71396276 -0.24998909
-0.92121806 0.2743398 -0.24998909
-0.71712515 0.2135607 -0.024929133
-0.61926276 0.5859437 -0.20555815
-0.55502751 0.52516459 0.091392579
--0.5 0.8660254 5.1344633e-17
-0.24102914 1.0104508 0.24998909
-0.29043935 1.21759 0.024929133
--0.26624219 1.1161498 0.20555815
--0.28676082 1.2021687 -0.091392579
-0.27775814 1.1644274 -0.15859651
-0.20782931 0.87126929 -0.23048728
--0.25622363 1.0741497 -0.23048728
--0.1862948 0.78099155 -0.15859651
-0.17729212 0.74325022 -0.091392579
-0.19781075 0.82926913 0.20555815
--0.17361359 0.72782894 0.024929133
--0.22302379 0.93496814 0.24998909
--1 -1.2098029e-15 1.3788671e-16
--0.89772824 0.84942651 0.091392579
--0.833493 0.78864741 -0.20555815
--1.1996835 0.35726714 -0.024929133
--0.99559063 0.29648804 -0.24998909
--0.69819427 0.66062834 -0.24998909
--0.54351156 0.51426825 -0.024929133
--0.8170735 0.24332543 -0.20555815
--0.73231963 0.21808563 0.091392579
--0.58321113 0.5518318 0.15859651
--0.80212907 0.758971 0.23048728
--0.85845599 0.25564918 0.23048728
--1.1473028 0.34166809 0.15859651
--0.5 -0.8660254 8.6542076e-17
--1.1473028 -0.34166809 -0.15859651
--0.85845599 -0.25564918 -0.23048728
--0.80212907 -0.758971 -0.23048728
--0.58321113 -0.5518318 -0.15859651
--0.73231963 -0.21808563 -0.091392579
--0.8170735 -0.24332543 0.20555815
--0.54351156 -0.51426825 0.024929133
--0.69819427 -0.66062834 0.24998909
--0.99559063 -0.29648804 0.24998909
--1.1996835 -0.35726714 0.024929133
--0.833493 -0.78864741 0.20555815
--0.89772824 -0.84942651 -0.091392579
-0.5 -0.8660254 -5.1344633e-17
--0.22302379 -0.93496814 -0.24998909
--0.17361359 -0.72782894 -0.024929133
-0.19781075 -0.82926913 -0.20555815
-0.17729212 -0.74325022 0.091392579
--0.1862948 -0.78099155 0.15859651
--0.25622363 -1.0741497 0.23048728
-0.20782931 -0.87126929 0.23048728
-0.27775814 -1.1644274 0.15859651
--0.28676082 -1.2021687 0.091392579
--0.26624219 -1.1161498 -0.20555815
-0.29043935 -1.21759 -0.024929133
-0.24102914 -1.0104508 -0.24998909
-0.55502751 -0.52516459 -0.091392579
-0.61926276 -0.5859437 0.20555815
-0.71712515 -0.2135607 0.024929133
-0.92121806 -0.2743398 0.24998909
-0.75456149 -0.71396276 0.24998909
-0.9092442 -0.86032286 0.024929133
-1.0997352 -0.32750241 0.20555815
-1.1844891 -0.35274221 -0.091392579
-0.86954463 -0.8227593 -0.15859651
-0.65062668 -0.6156201 -0.23048728
-1.0583527 -0.31517866 -0.23048728
-0.76950592 -0.22915975 -0.15859651
-0.95840435 0.28541392 -1.3795119e-16
-0.72637788 0.68729555 -1.1412456e-16
-0.23202647 0.97270947 -5.1760042e-17
--0.23202647 0.97270947 1.2226691e-17
--0.72637788 0.68729555 8.6191148e-17
--0.95840435 0.28541392 1.2635125e-16
--0.95840435 -0.28541392 1.3795119e-16
--0.72637788 -0.68729555 1.1412456e-16
--0.23202647 -0.97270947 5.1760042e-17
-0.23202647 -0.97270947 -1.2226691e-17
-0.72637788 -0.68729555 -8.6191148e-17
-0.95840435 -0.28541392 -1.2635125e-16

doc/CodeDocumentation.dox

@@ -71,10 +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
@@ -116,15 +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
  *

examples/CMakeLists.txt

@@ -26,9 +26,6 @@ list(APPEND ALL_EXE_SRCS
   ex17.cpp
   ex18.cpp
   ex19.cpp
-  ex20.cpp
-  ex21.cpp
-  ex22.cpp
   )
 
 if (MFEM_USE_MPI)
@@ -52,9 +49,6 @@ if (MFEM_USE_MPI)
     ex17p.cpp
     ex18p.cpp
     ex19p.cpp
-    ex20p.cpp
-    ex21p.cpp
-    ex22p.cpp
     )
 endif()
 
@@ -81,22 +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)

examples/ex1.cpp

@@ -4,18 +4,13 @@
 //
 // Sample runs:  ex1 -m ../data/square-disc.mesh
 //               ex1 -m ../data/star.mesh
-//               ex1 -m ../data/star-mixed.mesh
 //               ex1 -m ../data/escher.mesh
 //               ex1 -m ../data/fichera.mesh
-//               ex1 -m ../data/fichera-mixed.mesh
-//               ex1 -m ../data/toroid-wedge.mesh
 //               ex1 -m ../data/square-disc-p2.vtk -o 2
 //               ex1 -m ../data/square-disc-p3.mesh -o 3
 //               ex1 -m ../data/square-disc-nurbs.mesh -o -1
-//               ex1 -m ../data/star-mixed-p2.mesh -o 2
 //               ex1 -m ../data/disc-nurbs.mesh -o -1
 //               ex1 -m ../data/pipe-nurbs.mesh -o -1
-//               ex1 -m ../data/fichera-mixed-p2.mesh -o 2
 //               ex1 -m ../data/star-surf.mesh
 //               ex1 -m ../data/square-disc-surf.mesh
 //               ex1 -m ../data/inline-segment.mesh
@@ -25,14 +20,6 @@
 //               ex1 -m ../data/mobius-strip.mesh
 //               ex1 -m ../data/mobius-strip.mesh -o -1 -sc
 //
-// Device sample runs:
-//             > ex1 -pa -d cuda
-//             > ex1 -pa -d raja-cuda
-//             > ex1 -pa -d occa-cuda
-//             > ex1 -pa -d raja-omp
-//             > ex1 -pa -d occa-omp
-//             > ex1 -m ../data/beam-hex.mesh -pa -d cuda
-//
 // Description:  This example code demonstrates the use of MFEM to define a
 //               simple finite element discretization of the Laplace problem
 //               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
@@ -61,9 +48,7 @@ int main(int argc, char *argv[])
    const char *mesh_file = "../data/star.mesh";
    int order = 1;
    bool static_cond = false;
-   bool pa = false;
-   const char *device = "cpu";
-   bool visualization = true;
+   bool visualization = 1;
 
    OptionsParser args(argc, argv);
    args.AddOption(&mesh_file, "-m", "--mesh",
@@ -73,10 +58,6 @@ int main(int argc, char *argv[])
                   " isoparametric space.");
    args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
                   "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
@@ -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;

examples/ex10.cpp

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

examples/ex10p.cpp

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

examples/ex11p.cpp

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

examples/ex12p.cpp

@@ -5,10 +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

examples/ex14.cpp

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

examples/ex14p.cpp

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

examples/ex15.cpp

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

examples/ex15p.cpp

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

examples/ex16.cpp

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

examples/ex16p.cpp

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

examples/ex17.cpp

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

examples/ex17p.cpp

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

examples/ex18.hpp

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

examples/ex19.cpp

@@ -7,7 +7,6 @@
 //    ex19 -m ../data/beam-tri.mesh
 //    ex19 -m ../data/beam-hex.mesh
 //    ex19 -m ../data/beam-tet.mesh
-//    ex19 -m ../data/beam-wedge.mesh
 //
 // Description:  This examples solves a quasi-static incompressible nonlinear
 //               elasticity problem of the form 0 = H(x), where H is an

examples/ex19p.cpp

@@ -7,7 +7,6 @@
 //    mpirun -np 2 ex19p -m ../data/beam-tri.mesh
 //    mpirun -np 2 ex19p -m ../data/beam-hex.mesh
 //    mpirun -np 2 ex19p -m ../data/beam-tet.mesh
-//    mpirun -np 2 ex19p -m ../data/beam-wedge.mesh
 //
 // Description:  This examples solves a quasi-static incompressible nonlinear
 //               elasticity problem of the form 0 = H(x), where H is an

examples/ex1p.cpp

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

examples/ex2.cpp

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

examples/ex20.cpp

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

examples/ex20p.cpp

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

examples/ex21.cpp

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

examples/ex21p.cpp

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

examples/ex22.cpp

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

examples/ex22p.cpp

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

examples/ex2p.cpp

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

examples/ex3.cpp

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

examples/ex3p.cpp

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

examples/ex3p_sp.cpp

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

examples/ex6.cpp

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

examples/ex6p.cpp

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

examples/ex8.cpp

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

examples/ex8p.cpp

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

examples/ex9.cpp

@@ -10,7 +10,6 @@
 //    ex9 -m ../data/periodic-hexagon.mesh -p 1 -r 2 -dt 0.005 -tf 9
 //    ex9 -m ../data/amr-quad.mesh -p 1 -r 2 -dt 0.002 -tf 9
 //    ex9 -m ../data/star-q3.mesh -p 1 -r 2 -dt 0.005 -tf 9
-//    ex9 -m ../data/star-mixed.mesh -p 1 -r 2 -dt 0.005 -tf 9
 //    ex9 -m ../data/disc-nurbs.mesh -p 1 -r 3 -dt 0.005 -tf 9
 //    ex9 -m ../data/disc-nurbs.mesh -p 2 -r 3 -dt 0.005 -tf 9
 //    ex9 -m ../data/periodic-square.mesh -p 3 -r 4 -dt 0.0025 -tf 9 -vs 20
@@ -132,8 +131,8 @@ int main(int argc, char *argv[])
 
    // 2. Read the mesh from the given mesh file. We can handle geometrically
    //    periodic meshes in this code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
+   Mesh *mesh = new Mesh(mesh_file, 1, 1);
+   int dim = mesh->Dimension();
 
    // 3. Define the ODE solver used for time integration. Several explicit
    //    Runge-Kutta methods are available.
@@ -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)

examples/ex9p.cpp

@@ -10,7 +10,6 @@
 //    mpirun -np 4 ex9p -m ../data/periodic-hexagon.mesh -p 1 -dt 0.005 -tf 9
 //    mpirun -np 4 ex9p -m ../data/amr-quad.mesh -p 1 -rp 1 -dt 0.002 -tf 9
 //    mpirun -np 4 ex9p -m ../data/star-q3.mesh -p 1 -rp 1 -dt 0.004 -tf 9
-//    mpirun -np 4 ex9p -m ../data/star-mixed.mesh -p 1 -rp 1 -dt 0.004 -tf 9
 //    mpirun -np 4 ex9p -m ../data/disc-nurbs.mesh -p 1 -rp 1 -dt 0.005 -tf 9
 //    mpirun -np 4 ex9p -m ../data/disc-nurbs.mesh -p 2 -rp 1 -dt 0.005 -tf 9
 //    mpirun -np 4 ex9p -m ../data/periodic-square.mesh -p 3 -rp 2 -dt 0.0025 -tf 9 -vs 20

examples/makefile

@@ -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 ex21 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 ex21p 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
 
@@ -118,11 +112,9 @@ clean-build:
 clean-exec:
 	@rm -f refined.mesh displaced.mesh mesh.* ex5.mesh
 	@rm -rf Example5* Example9* Example15* Example16*
-	@rm -f sphere_refined.* sol.* sol_u.* sol_p.* sol_r.* sol_i.*
+	@rm -f sphere_refined.* sol.* sol_u.* sol_p.*
 	@rm -f ex9.mesh ex9-mesh.* ex9-init.* ex9-final.*
 	@rm -f deformed.* velocity.* elastic_energy.* mode_*
 	@rm -f ex16.mesh ex16-mesh.* ex16-init.* ex16-final.*
 	@rm -f vortex-mesh.* vortex.mesh vortex-?-init.* vortex-?-final.*
 	@rm -f deformation.* pressure.*
-	@rm -f ex20.dat ex20p_?????.dat gnuplot_ex20.inp gnuplot_ex20p.inp
-	@rm -f ex22*.mesh ex22*.sol ex22p_*.*

examples/petsc/CMakeLists.txt

@@ -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})

examples/petsc/ex10p.cpp

@@ -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();
 

examples/petsc/ex1p.cpp

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

examples/petsc/ex2p.cpp

@@ -101,7 +101,7 @@ int main(int argc, char *argv[])
    }
 
    // 2b. We initialize PETSc
-   if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
 
    // 3. Read the (serial) mesh from the given mesh file on all processors.  We
    //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
@@ -359,7 +359,7 @@ int main(int argc, char *argv[])
    delete pmesh;
 
    // We finalize PETSc
-   if (use_petsc) { MFEMFinalizePetsc(); }
+   if (use_petsc) { PetscFinalize(); }
 
    MPI_Finalize();
 

examples/petsc/ex3p.cpp

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

examples/petsc/ex4p.cpp

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

examples/petsc/ex5p.cpp

@@ -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();
 

examples/petsc/ex6p.cpp

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

examples/petsc/ex9p.cpp

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

examples/pumi/CMakeLists.txt

@@ -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)

examples/pumi/ex2.cpp

@@ -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();

examples/sundials/CMakeLists.txt

@@ -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})

fem/CMakeLists.txt

@@ -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

fem/bilinearform.cpp

@@ -12,7 +12,6 @@
 // Implementation of class BilinearForm
 
 #include "fem.hpp"
-#include "../general/device.hpp"
 #include <cmath>
 
 namespace mfem
@@ -55,7 +54,7 @@ void BilinearForm::AllocMat()
 
    int *I = dof_dof.GetI();
    int *J = dof_dof.GetJ();
-   double *data = mfem::New<double>(I[height]);
+   double *data = new double[I[height]];
 
    mat = new SparseMatrix(I, J, data, height, height, true, true, true);
    *mat = 0.0;
@@ -63,7 +62,7 @@ void BilinearForm::AllocMat()
    dof_dof.LoseData();
 }
 
-BilinearForm::BilinearForm(FiniteElementSpace * f)
+BilinearForm::BilinearForm (FiniteElementSpace * f)
    : Matrix (f->GetVSize())
 {
    fes = f;
@@ -75,15 +74,14 @@ BilinearForm::BilinearForm(FiniteElementSpace * f)
    hybridization = NULL;
    precompute_sparsity = 0;
    diag_policy = DIAG_KEEP;
-
-   assembly = AssemblyLevel::FULL;
-   batch = 1;
-   ext = NULL;
 }
 
 BilinearForm::BilinearForm (FiniteElementSpace * f, BilinearForm * bf, int ps)
    : Matrix (f->GetVSize())
 {
+   int i;
+   Array<BilinearFormIntegrator*> *bfi;
+
    fes = f;
    sequence = f->GetSequence();
    mat_e = NULL;
@@ -94,66 +92,40 @@ BilinearForm::BilinearForm (FiniteElementSpace * f, BilinearForm * bf, int ps)
    precompute_sparsity = ps;
    diag_policy = DIAG_KEEP;
 
-   assembly = AssemblyLevel::FULL;
-   batch = 1;
-   ext = NULL;
+   bfi = bf->GetDBFI();
+   dbfi.SetSize (bfi->Size());
+   for (i = 0; i < bfi->Size(); i++)
+   {
+      dbfi[i] = (*bfi)[i];
+   }
 
-   // Copy the pointers to the integrators
-   dbfi = bf->dbfi;
+   bfi = bf->GetBBFI();
+   bbfi.SetSize (bfi->Size());
+   for (i = 0; i < bfi->Size(); i++)
+   {
+      bbfi[i] = (*bfi)[i];
+   }
 
-   bbfi = bf->bbfi;
-   bbfi_marker = bf->bbfi_marker;
+   bfi = bf->GetFBFI();
+   fbfi.SetSize (bfi->Size());
+   for (i = 0; i < bfi->Size(); i++)
+   {
+      fbfi[i] = (*bfi)[i];
+   }
 
-   fbfi = bf->fbfi;
-
-   bfbfi = bf->bfbfi;
-   bfbfi_marker = bf->bfbfi_marker;
+   bfi = bf->GetBFBFI();
+   bfbfi.SetSize (bfi->Size());
+   for (i = 0; i < bfi->Size(); i++)
+   {
+      bfbfi[i] = (*bfi)[i];
+   }
 
    AllocMat();
 }
 
-void BilinearForm::SetAssemblyLevel(AssemblyLevel assembly_level)
-{
-   if (ext)
-   {
-      MFEM_ABORT("the assembly level has already been set!");
-   }
-   assembly = assembly_level;
-   switch (assembly)
-   {
-      case AssemblyLevel::FULL:
-         if (Device::IsEnabled())
-         {
-            mfem_error("Full assembly not supported yet in device mode!");
-            // ext = new FABilinearFormExtension(this);
-         }
-         // Use the original BilinearForm implementation for now
-         break;
-      case AssemblyLevel::ELEMENT:
-         mfem_error("Element assembly not supported yet... stay tuned!");
-         // ext = new EABilinearFormExtension(this);
-         break;
-      case AssemblyLevel::PARTIAL:
-         ext = new PABilinearFormExtension(this);
-         break;
-      case AssemblyLevel::NONE:
-         mfem_error("Matrix-free action not supported yet... stay tuned!");
-         // ext = new MFBilinearFormExtension(this);
-         break;
-      default:
-         mfem_error("Unknown assembly level");
-   }
-}
-
 void BilinearForm::EnableStaticCondensation()
 {
    delete static_cond;
-   if (assembly != AssemblyLevel::FULL)
-   {
-      static_cond = NULL;
-      MFEM_WARNING("Static condensation not supported for this assembly level");
-      return;
-   }
    static_cond = new StaticCondensation(fes);
    if (static_cond->ReducesTrueVSize())
    {
@@ -173,13 +145,6 @@ void BilinearForm::EnableHybridization(FiniteElementSpace *constr_space,
                                        const Array<int> &ess_tdof_list)
 {
    delete hybridization;
-   if (assembly != AssemblyLevel::FULL)
-   {
-      delete constr_integ;
-      hybridization = NULL;
-      MFEM_WARNING("Hybridization not supported for this assembly level");
-      return;
-   }
    hybridization = new Hybridization(fes, constr_space);
    hybridization->SetConstraintIntegrator(constr_integ);
    hybridization->Init(ess_tdof_list);
@@ -234,9 +199,9 @@ void BilinearForm::Finalize (int skip_zeros)
    if (hybridization) { hybridization->Finalize(); }
 }
 
-void BilinearForm::AddDomainIntegrator(BilinearFormIntegrator *bfi)
+void BilinearForm::AddDomainIntegrator (BilinearFormIntegrator * bfi)
 {
-   dbfi.Append(bfi);
+   dbfi.Append (bfi);
 }
 
 void BilinearForm::AddBoundaryIntegrator (BilinearFormIntegrator * bfi)
@@ -342,29 +307,20 @@ void BilinearForm::AssembleBdrElementMatrix(
    }
 }
 
-void BilinearForm::Assemble(int skip_zeros)
+void BilinearForm::Assemble (int skip_zeros)
 {
-   if (Device::IsEnabled() && (assembly != AssemblyLevel::PARTIAL))
-   {
-      mfem_error("Chosen assembly level not supported yet in device mode!");
-   }
-
-   if (ext)
-   {
-      ext->Assemble();
-      return;
-   }
-
    ElementTransformation *eltrans;
    Mesh *mesh = fes -> GetMesh();
    DenseMatrix elmat, *elmat_p;
 
+   int i;
+
    if (mat == NULL)
    {
       AllocMat();
    }
 
-#ifdef MFEM_USE_LEGACY_OPENMP
+#ifdef MFEM_USE_OPENMP
    int free_element_matrices = 0;
    if (!element_matrices)
    {
@@ -375,7 +331,7 @@ void BilinearForm::Assemble(int skip_zeros)
 
    if (dbfi.Size())
    {
-      for (int i = 0; i < fes -> GetNE(); i++)
+      for (i = 0; i < fes -> GetNE(); i++)
       {
          fes->GetElementVDofs(i, vdofs);
          if (element_matrices)
@@ -432,7 +388,7 @@ void BilinearForm::Assemble(int skip_zeros)
          }
       }
 
-      for (int i = 0; i < fes -> GetNBE(); i++)
+      for (i = 0; i < fes -> GetNBE(); i++)
       {
          const int bdr_attr = mesh->GetBdrAttribute(i);
          if (bdr_attr_marker[bdr_attr-1] == 0) { continue; }
@@ -470,7 +426,7 @@ void BilinearForm::Assemble(int skip_zeros)
       Array<int> vdofs2;
 
       int nfaces = mesh->GetNumFaces();
-      for (int i = 0; i < nfaces; i++)
+      for (i = 0; i < nfaces; i++)
       {
          tr = mesh -> GetInteriorFaceTransformations (i);
          if (tr != NULL)
@@ -515,7 +471,7 @@ void BilinearForm::Assemble(int skip_zeros)
          }
       }
 
-      for (int i = 0; i < fes -> GetNBE(); i++)
+      for (i = 0; i < fes -> GetNBE(); i++)
       {
          const int bdr_attr = mesh->GetBdrAttribute(i);
          if (bdr_attr_marker[bdr_attr-1] == 0) { continue; }
@@ -541,7 +497,7 @@ void BilinearForm::Assemble(int skip_zeros)
       }
    }
 
-#ifdef MFEM_USE_LEGACY_OPENMP
+#ifdef MFEM_USE_OPENMP
    if (free_element_matrices)
    {
       FreeElementMatrices();
@@ -584,16 +540,11 @@ void BilinearForm::ConformingAssemble()
    width = mat->Width();
 }
 
-void BilinearForm::FormLinearSystem(const Array<int> &ess_tdof_list, Vector &x,
-                                    Vector &b, OperatorHandle &A, Vector &X,
-                                    Vector &B, int copy_interior)
+void BilinearForm::FormLinearSystem(const Array<int> &ess_tdof_list,
+                                    Vector &x, Vector &b,
+                                    SparseMatrix &A, Vector &X, Vector &B,
+                                    int copy_interior)
 {
-   if (ext)
-   {
-      ext->FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
-      return;
-   }
-
    const SparseMatrix *P = fes->GetConformingProlongation();
 
    FormSystemMatrix(ess_tdof_list, A);
@@ -656,14 +607,8 @@ void BilinearForm::FormLinearSystem(const Array<int> &ess_tdof_list, Vector &x,
 }
 
 void BilinearForm::FormSystemMatrix(const Array<int> &ess_tdof_list,
-                                    OperatorHandle &A)
+                                    SparseMatrix &A)
 {
-   if (ext)
-   {
-      ext->FormSystemMatrix(ess_tdof_list, A);
-      return;
-   }
-
    // Finish the matrix assembly and perform BC elimination, storing the
    // eliminated part of the matrix.
    if (static_cond)
@@ -675,7 +620,7 @@ void BilinearForm::FormSystemMatrix(const Array<int> &ess_tdof_list,
          static_cond->EliminateReducedTrueDofs(diag_policy);
          static_cond->Finalize(); // finalize eliminated part
       }
-      A.Reset(&static_cond->GetMatrix(), false);
+      A.MakeRef(static_cond->GetMatrix());
    }
    else
    {
@@ -689,11 +634,11 @@ void BilinearForm::FormSystemMatrix(const Array<int> &ess_tdof_list,
       }
       if (hybridization)
       {
-         A.Reset(&hybridization->GetMatrix(), false);
+         A.MakeRef(hybridization->GetMatrix());
       }
       else
       {
-         A.Reset(mat, false);
+         A.MakeRef(*mat);
       }
    }
 }
@@ -701,12 +646,6 @@ void BilinearForm::FormSystemMatrix(const Array<int> &ess_tdof_list,
 void BilinearForm::RecoverFEMSolution(const Vector &X,
                                       const Vector &b, Vector &x)
 {
-   if (ext)
-   {
-      ext->RecoverFEMSolution(X, b, x);
-      return;
-   }
-
    const SparseMatrix *P = fes->GetConformingProlongation();
    if (!P) // conforming space
    {
@@ -768,7 +707,7 @@ void BilinearForm::ComputeElementMatrices()
    DenseMatrix tmp;
    IsoparametricTransformation eltrans;
 
-#ifdef MFEM_USE_LEGACY_OPENMP
+#ifdef MFEM_USE_OPENMP
    #pragma omp parallel for private(tmp,eltrans)
 #endif
    for (int i = 0; i < num_elements; i++)
@@ -795,8 +734,7 @@ void BilinearForm::ComputeElementMatrices()
 }
 
 void BilinearForm::EliminateEssentialBC(const Array<int> &bdr_attr_is_ess,
-                                        const Vector &sol, Vector &rhs,
-                                        DiagonalPolicy dpolicy)
+                                        const Vector &sol, Vector &rhs, DiagonalPolicy dpolicy)
 {
    Array<int> ess_dofs, conf_ess_dofs;
    fes->GetEssentialVDofs(bdr_attr_is_ess, ess_dofs);
@@ -970,8 +908,6 @@ void BilinearForm::Update(FiniteElementSpace *nfes)
    }
 
    height = width = fes->GetVSize();
-
-   if (ext) { ext->Update(); }
 }
 
 void BilinearForm::SetDiagonalPolicy(DiagonalPolicy policy)
@@ -995,8 +931,6 @@ BilinearForm::~BilinearForm()
       for (k=0; k < fbfi.Size(); k++) { delete fbfi[k]; }
       for (k=0; k < bfbfi.Size(); k++) { delete bfbfi[k]; }
    }
-
-   delete ext;
 }
 
 
@@ -1007,23 +941,6 @@ MixedBilinearForm::MixedBilinearForm (FiniteElementSpace *tr_fes,
    trial_fes = tr_fes;
    test_fes = te_fes;
    mat = NULL;
-   extern_bfs = 0;
-}
-
-MixedBilinearForm::MixedBilinearForm (FiniteElementSpace *tr_fes,
-                                      FiniteElementSpace *te_fes,
-                                      MixedBilinearForm * mbf)
-   : Matrix(te_fes->GetVSize(), tr_fes->GetVSize())
-{
-   trial_fes = tr_fes;
-   test_fes = te_fes;
-   mat = NULL;
-   extern_bfs = 1;
-
-   // Copy the pointers to the integrators
-   dom = mbf->dom;
-   bdr = mbf->bdr;
-   skt = mbf->skt;
 }
 
 double & MixedBilinearForm::Elem (int i, int j)
@@ -1260,14 +1177,12 @@ void MixedBilinearForm::Update()
 
 MixedBilinearForm::~MixedBilinearForm()
 {
+   int i;
+
    if (mat) { delete mat; }
-   if (!extern_bfs)
-   {
-      int i;
-      for (i = 0; i < dom.Size(); i++) { delete dom[i]; }
-      for (i = 0; i < bdr.Size(); i++) { delete bdr[i]; }
-      for (i = 0; i < skt.Size(); i++) { delete skt[i]; }
-   }
+   for (i = 0; i < dom.Size(); i++) { delete dom[i]; }
+   for (i = 0; i < bdr.Size(); i++) { delete bdr[i]; }
+   for (i = 0; i < skt.Size(); i++) { delete skt[i]; }
 }
 
 

fem/bilinearform.hpp

@@ -18,60 +18,30 @@
 #include "gridfunc.hpp"
 #include "linearform.hpp"
 #include "bilininteg.hpp"
-#include "bilinearform_ext.hpp"
 #include "staticcond.hpp"
 #include "hybridization.hpp"
 
 namespace mfem
 {
 
-/// Enumeration defining the assembly level for bilinear and nonlinear form
-/// classes derived from Operator.
-enum class AssemblyLevel
-{
-   /// Fully assembled form, i.e. a global sparse matrix in MFEM, Hypre or PETSC
-   /// format.
-   FULL,
-   /// Form assembled at element level, which computes and stores dense element
-   /// matrices.
-   ELEMENT,
-   /// Partially-assembled form, which computes and stores data only at
-   /// quadrature points.
-   PARTIAL,
-   /// "Matrix-free" form that computes all of its action on-the-fly without any
-   /// substantial storage.
-   NONE,
-};
-
-
 /** Class for bilinear form - "Matrix" with associated FE space and
     BLFIntegrators. */
 class BilinearForm : public Matrix
 {
 protected:
-   /// Sparse matrix to be associated with the form. Owned.
+   /// Sparse matrix to be associated with the form.
    SparseMatrix *mat;
 
-   /// Matrix used to eliminate b.c. Owned.
+   /// Matrix used to eliminate b.c.
    SparseMatrix *mat_e;
 
-   /// FE space on which the form lives. Not owned.
+   /// FE space on which the form lives.
    FiniteElementSpace *fes;
 
-   /// The form assembly level (full, partial, etc.)
-   AssemblyLevel assembly;
-   /// Element batch size used in the form action (1, 8, num_elems, etc.)
-   int batch;
-   /** Extension for supporting Full Assembly (FA), Element Assembly (EA),
-       Partial Assembly (PA), or Matrix Free assembly (MF). */
-   BilinearFormExtension *ext;
-
    /// Indicates the Mesh::sequence corresponding to the current state of the
    /// BilinearForm.
    long sequence;
 
-   /** @brief Indicates the BilinearFormIntegrator%s stored in #dbfi, #bbfi,
-       #fbfi, and #bfbfi are owned by another BilinearForm. */
    int extern_bfs;
 
    /// Set of Domain Integrators to be applied.
@@ -79,22 +49,22 @@ protected:
 
    /// Set of Boundary Integrators to be applied.
    Array<BilinearFormIntegrator*> bbfi;
-   Array<Array<int>*>             bbfi_marker; ///< Entries are not owned.
+   Array<Array<int>*>             bbfi_marker;
 
    /// Set of interior face Integrators to be applied.
    Array<BilinearFormIntegrator*> fbfi;
 
    /// Set of boundary face Integrators to be applied.
    Array<BilinearFormIntegrator*> bfbfi;
-   Array<Array<int>*>             bfbfi_marker; ///< Entries are not owned.
+   Array<Array<int>*>             bfbfi_marker;
 
    DenseMatrix elemmat;
    Array<int>  vdofs;
 
-   DenseTensor *element_matrices; ///< Owned.
+   DenseTensor *element_matrices;
 
-   StaticCondensation *static_cond; ///< Owned.
-   Hybridization *hybridization; ///< Owned.
+   StaticCondensation *static_cond;
+   Hybridization *hybridization;
 
    /**
     * This member allows one to specify what should be done
@@ -117,42 +87,17 @@ protected:
       static_cond = NULL; hybridization = NULL;
       precompute_sparsity = 0;
       diag_policy = DIAG_KEEP;
-      assembly = AssemblyLevel::FULL;
-      batch = 1;
-      ext = NULL;
    }
 
-private:
-   /// Copy construction is not supported; body is undefined.
-   BilinearForm(const BilinearForm &);
-
-   /// Copy assignment is not supported; body is undefined.
-   BilinearForm &operator=(const BilinearForm &);
-
 public:
    /// Creates bilinear form associated with FE space @a *f.
-   /** The pointer @a f is not owned by the newly constructed object. */
    BilinearForm(FiniteElementSpace *f);
 
-   /** @brief Create a BilinearForm on the FiniteElementSpace @a f, using the
-       same integrators as the BilinearForm @a bf.
-
-       The pointer @a f is not owned by the newly constructed object.
-
-       The integrators in @a bf are copied as pointers and they are not owned by
-       the newly constructed BilinearForm.
-
-       The optional parameter @a ps is used to initialize the internal flag
-       #precompute_sparsity, see UsePrecomputedSparsity() for details. */
    BilinearForm(FiniteElementSpace *f, BilinearForm *bf, int ps = 0);
 
    /// Get the size of the BilinearForm as a square matrix.
    int Size() const { return height; }
 
-   /// Set the desired assembly level. The default is AssemblyLevel::FULL.
-   /** This method must be called before assembly. */
-   void SetAssemblyLevel(AssemblyLevel assembly_level);
-
    /** Enable the use of static condensation. For details see the description
        for class StaticCondensation in fem/staticcond.hpp This method should be
        called before assembly. If the number of unknowns after static
@@ -198,25 +143,13 @@ public:
        finalized) and the entries are initialized with zeros. */
    void AllocateMatrix() { if (mat == NULL) { AllocMat(); } }
 
-   /// Access all integrators added with AddDomainIntegrator().
    Array<BilinearFormIntegrator*> *GetDBFI() { return &dbfi; }
 
-   /// Access all integrators added with AddBoundaryIntegrator().
    Array<BilinearFormIntegrator*> *GetBBFI() { return &bbfi; }
-   /** @brief Access all boundary markers added with AddBoundaryIntegrator().
-       If no marker was specified when the integrator was added, the
-       corresponding pointer (to Array<int>) will be NULL. */
-   Array<Array<int>*> *GetBBFI_Marker() { return &bbfi_marker; }
 
-   /// Access all integrators added with AddInteriorFaceIntegrator().
    Array<BilinearFormIntegrator*> *GetFBFI() { return &fbfi; }
 
-   /// Access all integrators added with AddBdrFaceIntegrator().
    Array<BilinearFormIntegrator*> *GetBFBFI() { return &bfbfi; }
-   /** @brief Access all boundary markers added with AddBdrFaceIntegrator().
-       If no marker was specified when the integrator was added, the
-       corresponding pointer (to Array<int>) will be NULL. */
-   Array<Array<int>*> *GetBFBFI_Marker() { return &bfbfi_marker; }
 
    const double &operator()(int i, int j) { return (*mat)(i,j); }
 
@@ -242,10 +175,10 @@ public:
                                  const double a = 1.0) const
    { mat->AddMultTranspose(x, y, a); }
 
-   void FullAddMultTranspose(const Vector & x, Vector & y) const
+   void FullAddMultTranspose (const Vector & x, Vector & y) const
    { mat->AddMultTranspose(x, y); mat_e->AddMultTranspose(x, y); }
 
-   virtual void MultTranspose(const Vector & x, Vector & y) const
+   virtual void MultTranspose (const Vector & x, Vector & y) const
    { y = 0.0; AddMultTranspose (x, y); }
 
    double InnerProduct(const Vector &x, const Vector &y) const
@@ -282,31 +215,25 @@ public:
       return *mat_e;
    }
 
-   /// Adds new Domain Integrator. Assumes ownership of @a bfi.
+   /// Adds new Domain Integrator.
    void AddDomainIntegrator(BilinearFormIntegrator *bfi);
 
-   /// Adds new Boundary Integrator. Assumes ownership of @a bfi.
+   /// Adds new Boundary Integrator.
    void AddBoundaryIntegrator(BilinearFormIntegrator *bfi);
 
    /** @brief Adds new Boundary Integrator, restricted to specific boundary
-       attributes.
-
-       Assumes ownership of @a bfi. The array @a bdr_marker is stored internally
-       as a pointer to the given Array<int> object. */
-   void AddBoundaryIntegrator(BilinearFormIntegrator *bfi,
+       attributes. */
+   void AddBoundaryIntegrator(BilinearFormIntegrator * bfi,
                               Array<int> &bdr_marker);
 
-   /// Adds new interior Face Integrator. Assumes ownership of @a bfi.
+   /// Adds new interior Face Integrator.
    void AddInteriorFaceIntegrator(BilinearFormIntegrator *bfi);
 
-   /// Adds new boundary Face Integrator. Assumes ownership of @a bfi.
+   /// Adds new boundary Face Integrator.
    void AddBdrFaceIntegrator(BilinearFormIntegrator *bfi);
 
    /** @brief Adds new boundary Face Integrator, restricted to specific boundary
-       attributes.
-
-       Assumes ownership of @a bfi. The array @a bdr_marker is stored internally
-       as a pointer to the given Array<int> object. */
+       attributes. */
    void AddBdrFaceIntegrator(BilinearFormIntegrator *bfi,
                              Array<int> &bdr_marker);
 
@@ -326,12 +253,11 @@ public:
    virtual const Operator *GetRestriction() const
    { return fes->GetConformingRestriction(); }
 
-   /** @brief Form the linear system A X = B, corresponding to this bilinear
-       form and the linear form @a b(.). */
-   /** This method applies any necessary transformations to the linear system
-       such as: eliminating boundary conditions; applying conforming constraints
-       for non-conforming AMR; parallel assembly; static condensation;
-       hybridization.
+   /// Form a linear system, A X = B.
+   /** Form the linear system A X = B, corresponding to the current bilinear
+       form and b(.), by applying any necessary transformations such as:
+       eliminating boundary conditions; applying conforming constraints for
+       non-conforming AMR; static condensation; hybridization.
 
        The GridFunction-size vector @a x must contain the essential b.c. The
        BilinearForm and the LinearForm-size vector @a b must be assembled.
@@ -352,52 +278,12 @@ public:
 
        NOTE: If there are no transformations, @a X simply reuses the data of
              @a x. */
-   virtual void FormLinearSystem(const Array<int> &ess_tdof_list, Vector &x,
-                                 Vector &b, OperatorHandle &A, Vector &X,
-                                 Vector &B, int copy_interior = 0);
-
-   /** @brief Form the linear system A X = B, corresponding to this bilinear
-       form and the linear form @a b(.). */
-   /** Version of the method FormLinearSystem() where the system matrix is
-       returned in the variable @a A, of type OpType, holding a *reference* to
-       the system matrix (created with the method OpType::MakeRef()). The
-       reference will be invalidated when SetOperatorType(), Update(), or the
-       destructor is called.
-
-       Currently, this method can be used only with AssemblyLevel::FULL. */
-   template <typename OpType>
    void FormLinearSystem(const Array<int> &ess_tdof_list, Vector &x, Vector &b,
-                         OpType &A, Vector &X, Vector &B,
-                         int copy_interior = 0)
-   {
-      OperatorHandle Ah;
-      FormLinearSystem(ess_tdof_list, x, b, Ah, X, B, copy_interior);
-      OpType *A_ptr = Ah.Is<OpType>();
-      MFEM_VERIFY(A_ptr, "invalid OpType used");
-      A.MakeRef(*A_ptr);
-   }
-
-   /// Form the linear system matrix @a A, see FormLinearSystem() for details.
-   virtual void FormSystemMatrix(const Array<int> &ess_tdof_list,
-                                 OperatorHandle &A);
+                         SparseMatrix &A, Vector &X, Vector &B,
+                         int copy_interior = 0);
 
    /// Form the linear system matrix A, see FormLinearSystem() for details.
-   /** Version of the method FormSystemMatrix() where the system matrix is
-       returned in the variable @a A, of type OpType, holding a *reference* to
-       the system matrix (created with the method OpType::MakeRef()). The
-       reference will be invalidated when SetOperatorType(), Update(), or the
-       destructor is called.
-
-       Currently, this method can be used only with AssemblyLevel::FULL. */
-   template <typename OpType>
-   void FormSystemMatrix(const Array<int> &ess_tdof_list, OpType &A)
-   {
-      OperatorHandle Ah;
-      FormSystemMatrix(ess_tdof_list, Ah);
-      OpType *A_ptr = Ah.Is<OpType>();
-      MFEM_VERIFY(A_ptr, "invalid OpType used");
-      A.MakeRef(*A_ptr);
-   }
+   void FormSystemMatrix(const Array<int> &ess_tdof_list, SparseMatrix &A);
 
    /// Recover the solution of a linear system formed with FormLinearSystem().
    /** Call this method after solving a linear system constructed using the
@@ -489,7 +375,6 @@ public:
    virtual ~BilinearForm();
 };
 
-
 /**
    Class for assembling of bilinear forms `a(u,v)` defined on different
    trial and test spaces. The assembled matrix `A` is such that
@@ -508,68 +393,36 @@ public:
 class MixedBilinearForm : public Matrix
 {
 protected:
-   SparseMatrix *mat; ///< Owned.
+   SparseMatrix *mat;
 
-   FiniteElementSpace *trial_fes, ///< Not owned
-                      *test_fes;  ///< Not owned
+   FiniteElementSpace *trial_fes, *test_fes;
 
-   /** @brief Indicates the BilinearFormIntegrator%s stored in #dom, #bdr, and
-       #skt are owned by another MixedBilinearForm. */
-   int extern_bfs;
-
-   /// Domain integrators.
    Array<BilinearFormIntegrator*> dom;
-   /// Boundary integrators.
    Array<BilinearFormIntegrator*> bdr;
-   /// Trace face (skeleton) integrators.
-   Array<BilinearFormIntegrator*> skt;
-
-private:
-   /// Copy construction is not supported; body is undefined.
-   MixedBilinearForm(const MixedBilinearForm &);
-
-   /// Copy assignment is not supported; body is undefined.
-   MixedBilinearForm &operator=(const MixedBilinearForm &);
+   Array<BilinearFormIntegrator*> skt; // trace face integrators
 
 public:
-   /** @brief Construct a MixedBilinearForm on the given trial, @a tr_fes, and
-       test, @a te_fes, FiniteElementSpace%s. */
-   /** The pointers @a tr_fes and @a te_fes are not owned by the newly
-       constructed object. */
-   MixedBilinearForm(FiniteElementSpace *tr_fes,
-                     FiniteElementSpace *te_fes);
+   MixedBilinearForm (FiniteElementSpace *tr_fes,
+                      FiniteElementSpace *te_fes);
 
-   /** @brief Create a MixedBilinearForm on the given trial, @a tr_fes, and
-       test, @a te_fes, FiniteElementSpace%s, using the same integrators as the
-       MixedBilinearForm @a mbf.
+   virtual double& Elem (int i, int j);
 
-       The pointers @a tr_fes and @a te_fes are not owned by the newly
-       constructed object.
+   virtual const double& Elem (int i, int j) const;
 
-       The integrators in @a mbf are copied as pointers and they are not owned
-       by the newly constructed MixedBilinearForm. */
-   MixedBilinearForm(FiniteElementSpace *tr_fes,
-                     FiniteElementSpace *te_fes,
-                     MixedBilinearForm *mbf);
+   virtual void Mult (const Vector & x, Vector & y) const;
 
-   virtual double &Elem(int i, int j);
+   virtual void AddMult (const Vector & x, Vector & y,
+                         const double a = 1.0) const;
 
-   virtual const double &Elem(int i, int j) const;
+   virtual void AddMultTranspose (const Vector & x, Vector & y,
+                                  const double a = 1.0) const;
 
-   virtual void Mult(const Vector & x, Vector & y) const;
-
-   virtual void AddMult(const Vector & x, Vector & y,
-                        const double a = 1.0) const;
-
-   virtual void AddMultTranspose(const Vector & x, Vector & y,
-                                 const double a = 1.0) const;
-
-   virtual void MultTranspose(const Vector & x, Vector & y) const
+   virtual void MultTranspose (const Vector & x, Vector & y) const
    { y = 0.0; AddMultTranspose (x, y); }
 
-   virtual MatrixInverse *Inverse() const;
+   virtual MatrixInverse * Inverse() const;
 
-   virtual void Finalize(int skip_zeros = 1);
+   virtual void Finalize (int skip_zeros = 1);
 
    /** Extract the associated matrix as SparseMatrix blocks. The number of
        block rows and columns is given by the vector dimensions (vdim) of the
@@ -580,31 +433,24 @@ public:
    SparseMatrix &SpMat() { return *mat; }
    SparseMatrix *LoseMat() { SparseMatrix *tmp = mat; mat = NULL; return tmp; }
 
-   /// Adds a domain integrator. Assumes ownership of @a bfi.
-   void AddDomainIntegrator(BilinearFormIntegrator *bfi);
+   void AddDomainIntegrator (BilinearFormIntegrator * bfi);
 
-   /// Adds a boundary integrator. Assumes ownership of @a bfi.
-   void AddBoundaryIntegrator(BilinearFormIntegrator *bfi);
+   void AddBoundaryIntegrator (BilinearFormIntegrator * bfi);
 
-   /** @brief Add a trace face integrator. Assumes ownership of @a bfi.
+   /** Add a trace face integrator. This type of integrator assembles terms
+       over all faces of the mesh using the face FE from the trial space and the
+       two adjacent volume FEs from the test space. */
+   void AddTraceFaceIntegrator (BilinearFormIntegrator * bfi);
 
-       This type of integrator assembles terms over all faces of the mesh using
-       the face FE from the trial space and the two adjacent volume FEs from the
-       test space. */
-   void AddTraceFaceIntegrator(BilinearFormIntegrator *bfi);
-
-   /// Access all integrators added with AddDomainIntegrator().
    Array<BilinearFormIntegrator*> *GetDBFI() { return &dom; }
 
-   /// Access all integrators added with AddBoundaryIntegrator().
    Array<BilinearFormIntegrator*> *GetBBFI() { return &bdr; }
 
-   /// Access all integrators added with AddTraceFaceIntegrator().
    Array<BilinearFormIntegrator*> *GetTFBFI() { return &skt; }
 
-   void operator=(const double a) { *mat = a; }
+   void operator= (const double a) { *mat = a; }
 
-   void Assemble(int skip_zeros = 1);
+   void Assemble (int skip_zeros = 1);
 
    /** For partially conforming trial and/or test FE spaces, complete the
        assembly process by performing A := P2^t A P1 where A is the internal
@@ -659,35 +505,19 @@ public:
 */
 class DiscreteLinearOperator : public MixedBilinearForm
 {
-private:
-   /// Copy construction is not supported; body is undefined.
-   DiscreteLinearOperator(const DiscreteLinearOperator &);
-
-   /// Copy assignment is not supported; body is undefined.
-   DiscreteLinearOperator &operator=(const DiscreteLinearOperator &);
-
 public:
-   /** @brief Construct a DiscreteLinearOperator on the given
-       FiniteElementSpace%s @a domain_fes and @a range_fes. */
-   /** The pointers @a domain_fes and @a range_fes are not owned by the newly
-       constructed object. */
    DiscreteLinearOperator(FiniteElementSpace *domain_fes,
                           FiniteElementSpace *range_fes)
       : MixedBilinearForm(domain_fes, range_fes) { }
 
-   /// Adds a domain interpolator. Assumes ownership of @a di.
    void AddDomainInterpolator(DiscreteInterpolator *di)
    { AddDomainIntegrator(di); }
 
-   /// Adds a trace face interpolator. Assumes ownership of @a di.
    void AddTraceFaceInterpolator(DiscreteInterpolator *di)
    { AddTraceFaceIntegrator(di); }
 
-   /// Access all interpolators added with AddDomainInterpolator().
    Array<BilinearFormIntegrator*> *GetDI() { return &dom; }
 
-   /** @brief Construct the internal matrix representation of the discrete
-       linear operator. */
    virtual void Assemble(int skip_zeros = 1);
 };