Fix another makefile bug

Fixed BlockVector Update method [najlkin:pr5]

.gitignore

@@ -45,6 +45,8 @@ 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
@@ -76,6 +78,13 @@ 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]
@@ -112,6 +121,15 @@ examples/petsc/deformed.*
 examples/petsc/velocity.*
 examples/petsc/elastic_energy.*
 
+examples/pumi/ex1
+examples/pumi/ex[126]p
+
+examples/pumi/refined.mesh
+examples/pumi/sol.gf
+examples/pumi/mesh.*
+examples/pumi/sol.*
+examples/pumi/displaced.mesh
+
 miniapps/electromagnetics/volta
 miniapps/electromagnetics/tesla
 miniapps/electromagnetics/maxwell
@@ -124,16 +142,20 @@ 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*
 
@@ -156,3 +178,7 @@ 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

@@ -8,11 +8,126 @@
                                http://mfem.org
 
 
-Version 3.3.3 (development)
+Version 3.4.1 (development)
 ===========================
 
-More efficient non-conforming adaptive mesh refinement
-------------------------------------------------------
+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(2), 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.
+
+- A boundary in a NURBS mesh can now be connected with another boundary. Such a
+  periodic NURBS mesh is a simple way to impose periodic boundary conditions.
+
+- Added support for reading linear and quadratic 2D quadrilateral and triangular
+  Cubit meshes.
+
+- The TMOP mesh optimization algorithms were extended to support user-defined
+  space-dependent limiting terms. Improved the TMOP objective functions by
+  more accurate normalization of the different terms.
+  
+Discretization improvements
+---------------------------
+- 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.
+
+New and improved solvers and preconditioners
+--------------------------------------------
+- Added support for parallel ILU preconditioning via hypre's Euclid solver.
+
+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 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.
+
+Miscellaneous
+-------------
+- Added unit tests based on the Catch++ library.
+
+- 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.
+
+
+Version 3.4, released on May 29, 2018
+=====================================
+
+More general and efficient mesh adaptivity
+------------------------------------------
+- Added support for PUMI, the Parallel Unstructured Mesh Infrastructure from
+  https://scorec.rpi.edu/pumi. PUMI is an unstructured, distributed mesh data
+  management system that is capable of handling general non-manifold models and
+  effectively supports automated adaptive analysis. PUMI enables for the first
+  time support for parallel unstructured modifications of MFEM meshes.
+
 - Significantly reduced MPI communication in the construction of the parallel
   prolongation matrix in ParFiniteElementSpace, for much improved parallel
   scaling of non-conforming AMR on hundreds of thousands of MPI tasks. The
@@ -81,6 +196,11 @@ New and updated examples and miniapps
   NURBS meshes in the miniapps/nurbs directory. Currently the directory contains
   variable order NURBS versions of examples 1, 1p and 11p.
 
+- Added PUMI versions of examples ex1, ex1p, ex2 and ex6p in a new examples/pumi
+  directory. The new examples demonstrate the PUMI APIs for parallel and serial
+  mesh loading (ex1 and ex1p), applying BCs using classification (ex2), and
+  performing parallel mesh adaptation (ex6p).
+
 - Added two new miniapps related to DataCollection I/O in miniapps/tools:
   load-dc.cpp can be used to visualize fields saved via DataCollection classes;
   convert-dc.cpp demonstrates how to convert between MFEM's different concrete

CMakeLists.txt

@@ -45,7 +45,7 @@ project(mfem NONE)
 # Current version of MFEM, see also `makefile`.
 #   mfem_VERSION = (string)
 #   MFEM_VERSION = (int)   [automatically derived from mfem_VERSION]
-set(${PROJECT_NAME}_VERSION 3.3.3)
+set(${PROJECT_NAME}_VERSION 3.4.1)
 
 # Prohibit in-source build
 if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
@@ -139,7 +139,7 @@ if (MFEM_USE_MPI)
     set(PETSC_INCLUDE_DIRS ${PETSC_INCLUDES})
   endif()
 else()
-  set(PKGS_NEED_MPI SUPERLU PETSC STRUMPACK)
+  set(PKGS_NEED_MPI SUPERLU PETSC STRUMPACK PUMI)
   foreach(PKG IN LISTS PKGS_NEED_MPI)
     if (MFEM_USE_${PKG})
       message(STATUS "Disabling package ${PKG} - requires MPI")
@@ -246,6 +246,22 @@ if (MFEM_USE_SIDRE)
   find_package(Axom REQUIRED Sidre SLIC axom_utils)
 endif()
 
+# PUMI
+if (MFEM_USE_PUMI)
+  # If PUMI_DIR was specified, only link to that directory,
+  # i.e. don't link to another installation in /usr/lib by mistake
+  find_package(SCOREC 2.1.0 REQUIRED OPTIONAL_COMPONENTS gmi_sim
+    CONFIG PATHS ${PUMI_DIR} NO_DEFAULT_PATH)
+  if (SCOREC_FOUND)
+    # Define a header file with the MFEM_USE_SIMMETRIX preprocessor variable
+    set(MFEM_USE_SIMMETRIX ${SCOREC_gmi_sim_FOUND})
+    set(PUMI_FOUND ${SCOREC_FOUND})
+    get_target_property(PUMI_INCLUDE_DIRS
+      SCOREC::apf INTERFACE_INCLUDE_DIRECTORIES)
+    set(PUMI_LIBRARIES SCOREC::core)
+  endif()
+endif()
+
 # MFEM_TIMER_TYPE
 if (NOT DEFINED MFEM_TIMER_TYPE)
   if (APPLE)
@@ -270,8 +286,8 @@ endif()
 #    integers, the METIS header (with 32-bit indices, as used by mfem) needs to
 #    be before SuiteSparse.
 set(MFEM_TPLS MPI_CXX OPENMP BLAS LAPACK METIS HYPRE SuiteSparse SUNDIALS PETSC
-    MESQUITE SuperLUDist STRUMPACK AXOM CONDUIT GECKO GNUTLS NETCDF MPFR POSIXCLOCKS
-    MFEMBacktrace ZLIB)
+    MESQUITE SuperLUDist STRUMPACK AXOM CONDUIT GECKO GNUTLS NETCDF MPFR PUMI
+    POSIXCLOCKS MFEMBacktrace ZLIB)
 # Add all *_FOUND libraries in the variable TPL_LIBRARIES.
 set(TPL_LIBRARIES "")
 set(TPL_INCLUDE_DIRS "")
@@ -296,9 +312,6 @@ 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 ${WIN32})
-
 #-------------------------------------------------------------------------------
 # Define and configure the MFEM library
 #-------------------------------------------------------------------------------
@@ -372,6 +385,9 @@ endif()
 # Enable testing if required
 if (MFEM_ENABLE_TESTING)
   enable_testing()
+  set(MFEM_ALL_TESTS_TARGET_NAME tests)
+  add_mfem_target(${MFEM_ALL_TESTS_TARGET_NAME} OFF)
+  add_subdirectory(tests EXCLUDE_FROM_ALL)
 endif()
 
 # Define a target that all examples and miniapps will depend on.
@@ -391,7 +407,9 @@ 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_EXAMPLES_TARGET_NAME}
+  ${MFEM_ALL_MINIAPPS_TARGET_NAME}
+  ${MFEM_ALL_TESTS_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
@@ -527,3 +545,10 @@ install(FILES
 # Install the export set for use with the install-tree
 install(EXPORT ${PROJECT_NAME_UC}Targets
     DESTINATION ${INSTALL_CMAKE_DIR})
+
+#-------------------------------------------------------------------------------
+# Create 'config.mk' from 'config.mk.in' for the build and install locations and
+# define install rules for 'config.mk' and 'test.mk'
+#-------------------------------------------------------------------------------
+
+mfem_export_mk_files()

CONTRIBUTING.md

@@ -1,3 +1,15 @@
+<p align="center">
+<a href="http://mfem.org/"><img alt="mfem" src="http://mfem.org/img/logo-300.png"></a>
+</p>
+
+<p align="center">
+<a href="https://github.com/mfem/mfem/blob/master/COPYRIGHT"><img alt="License" src="https://img.shields.io/badge/License-LGPL--2.1-brightgreen.svg"></a>
+<a href="https://travis-ci.org/mfem/mfem"><img alt="Build Status" src="https://travis-ci.org/mfem/mfem.svg?branch=master"></a>
+<a href="https://ci.appveyor.com/project/mfem/mfem"><img alt="Build Status" src="https://ci.appveyor.com/api/projects/status/19non9sqm6msi2wy?svg=true"></a>
+<a href="http://mfem.github.io/doxygen/html/index.html"><img alt="Doxygen" src="https://img.shields.io/badge/code-documented-brightgreen.svg"></a>
+</p>
+
+
 # How to Contribute
 
 The MFEM team welcomes contributions at all levels: bugfixes; code
@@ -16,6 +28,7 @@ See the [Quick Summary](#quick-summary) section for the main highlights of our
 GitHub workflow. For more details, consult the following sections and refer
 back to them before issuing pull requests:
 
+- [Code Overview](#code-overview)
 - [GitHub Workflow](#github-workflow)
   - [MFEM Organization](#mfem-organization)
   - [New Feature Development](#new-feature-development)
@@ -53,6 +66,102 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
 - Don't hesitate to [contact us](#contact-information) if you have any questions.
 
 
+### Code Overview
+
+- The MFEM library uses object-orient design principles which reflect, in code,
+  the independent mathematical concepts of meshing, linear algebra and finite
+  element spaces and operators.
+
+- The MFEM source code has the following structure:
+  ```
+  .
+  ├── config
+  │   └── cmake
+  │       └── modules
+  ├── data
+  ├── doc
+  │   └── web
+  │       └── examples
+  ├── examples
+  │   ├── petsc
+  │   ├── pumi
+  │   └── sundials
+  ├── fem
+  ├── general
+  ├── linalg
+  ├── mesh
+  ├── miniapps
+  │   ├── common
+  │   ├── electromagnetics
+  │   ├── meshing
+  │   ├── nurbs
+  │   ├── performance
+  │   └── tools
+  └── tests
+      ├── unit
+      │   ├── ...
+      └── ...
+
+  ```
+
+- The main directories are `fem/`, `mesh/` and `linalg/` containing the C++
+  classes implementing the finite element, mesh and linear algebra concepts
+  respectively.
+
+- The main mesh classes are:
+  + [`Mesh`](http://mfem.github.io/doxygen/html/classmfem_1_1Mesh.html)
+  + [`NCMesh`](http://mfem.github.io/doxygen/html/classmfem_1_1NCMesh.html)
+  + [`Element`](http://mfem.github.io/doxygen/html/classmfem_1_1Element.html)
+  + [`ElementTransformation`](http://mfem.github.io/doxygen/html/classmfem_1_1ElementTransformation.html)
+
+- The main finite element classes are:
+  + [`FiniteElement`](http://mfem.github.io/doxygen/html/classmfem_1_1FiniteElement.html)
+  + [`FiniteElementCollection`](http://mfem.github.io/doxygen/html/classmfem_1_1FiniteElement.html)
+  + [`FiniteElementSpace`](http://mfem.github.io/doxygen/html/classmfem_1_1FiniteElementSpace.html)
+  + [`GridFunction`](http://mfem.github.io/doxygen/html/classmfem_1_1GridFunction.html)
+  + [`BilinearFormIntegrator`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearFormIntegrator.html) and [`LinearFormIntegrator`](http://mfem.github.io/doxygen/html/classmfem_1_1LinearFormIntegrator.html)
+  + [`LinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1LinearFormIntegrator.html), [`BilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html) and [`MixedBilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1MixedBilinearForm.html)
+
+- The main linear algebra classes and sources are
+  + [`Operator`](http://mfem.github.io/doxygen/html/classmfem_1_1Operator.html) and [`BilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html)
+  + [`Vector`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html) and [`LinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1LinearForm.html)
+  + [`DenseMatrix`](http://mfem.github.io/doxygen/html/classmfem_1_1DenseMatrix.html) and [`SparseMatrix`](http://mfem.github.io/doxygen/html/classmfem_1_1SparseMatrix.html)
+  + Sparse [smoothers](http://mfem.github.io/doxygen/html/sparsesmoothers_8hpp.html) and linear [solvers](http://mfem.github.io/doxygen/html/solvers_8hpp.html)
+
+- Parallel MPI objects in MFEM inherit their serial counterparts, so a parallel
+  mesh for example is just a serial mesh on each task plus the information on
+  shared geometric entities between different tasks. The parallel source files
+  have a `p` prefix, e.g. `pmesh.cpp` vs. the serial `mesh.cpp`.
+
+- The main parallel classes are
+  + [`ParMesh`](http://mfem.github.io/doxygen/html/solvers_8hpp.html)
+  + [`ParNCMesh`](http://mfem.github.io/doxygen/html/classmfem_1_1ParMesh.html)
+  + [`ParFiniteElementSpace`](http://mfem.github.io/doxygen/html/classmfem_1_1ParFiniteElementSpace.html)
+  + [`ParGridFunction`](http://mfem.github.io/doxygen/html/classmfem_1_1ParGridFunction.html)
+  + [`ParBilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1ParBilinearForm.html) and [`ParLinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1ParLinearForm.html)
+  + [`HypreParMatrix`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreParMatrix.html) and [`HypreParVector`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreParVector.html)
+  + [`HypreSolver`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreSolver.html) and other [hypre classes](http://mfem.github.io/doxygen/html/hypre_8hpp.html)
+
+- The `general/` directory contains C++ classes that serve as utilities for
+  communication, error handling, arrays, (Boolean) tables, timing, etc.
+
+- The `config/` directory contains build-related files, both for the plain
+  Makefile and the CMake build options.
+
+- The `doc/` directory contains configuration for the Doxygen code documentation
+  that can either be build locally, or browsed online at
+  http://mfem.github.io/doxygen/html/index.html.
+
+- The `data/` directory contains a collection of small mesh files, that are used
+  in the simple example codes and more fully-featured mini applications in the
+  `examples/` and `miniapps/` directories.
+
+- The `tests/` directory contains a unit test suite and will later contain more
+  tests that run example codes.
+
+- See also the [code overview](http://mfem.org/code-overview/) section on the
+  MFEM website.
+
 ## GitHub Workflow
 
 The GitHub organization, https://github.com/mfem, is the main developer hub for
@@ -122,7 +231,7 @@ will allow us to reach you directly with project announcements.
   # Work on "feature-dev", add local commits
   # ...
 
-  # One time only) push the branch to github and setup your local
+  # (One time only) push the branch to github and setup your local
   # branch to track the github branch (for "git pull"):
   git push -u origin feature-dev
 
@@ -215,9 +324,9 @@ 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`:
-    - [ ] Has a new optional library been added? (*Make sure the external library is licensed under LGPL, not GPL!*)
+    - [ ] Had a new optional library been added? (*Make sure the external library is licensed under LGPL, not GPL!*)
     - [ ] Does `make` or `cmake` have a new target?
-    - [ ] Did the requirements or the installation process change? *(rare)*.
+    - [ ] 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.
@@ -257,10 +366,10 @@ 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.
@@ -332,7 +441,7 @@ MFEM uses a `master`/`next`-branch workflow as described below:
     - [ ] `CHANGELOG`
     - [ ] `makefile`
     - [ ] `CMakeLists.txt`
-    - [ ] `doc/CodeDocumentation.conf`
+    - [ ] `doc/CodeDocumentation.conf.in`
 - [ ] (LLNL only) Make sure all `README.html` files in the source repo are up to date.
 - [ ] Tag the repository:
 
@@ -371,7 +480,6 @@ 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

@@ -28,10 +28,13 @@ without GNU make or CMake can be found at the end of this file.
 In addition to the native build systems, MFEM packages are also available in the
 following package managers:
 
-- Spack, https://github.com/LLNL/spack
+- Spack, https://github.com/spack/spack
 - OpenHPC, http://openhpc.community
 - Homebrew/Science, https://github.com/Homebrew/homebrew-science
 
+We also recommend downloading and building the MFEM-based GLVis visualization
+tool which can be used to visualize the meshes and solution in MFEM's examples
+and miniapps. See http://glvis.org and http://mfem.org/building.
 
 Quick start with GNU make
 =========================
@@ -352,6 +355,13 @@ MFEM_USE_GZSTREAM = YES/NO
    before attempting to use it with MFEM.
    When enabled, this option uses the ZLIB_* library options, see below.
 
+MFEM_USE_PUMI = YES/NO
+   Enable the usage of PUMI (https://scorec.rpi.edu/pumi/) in MFEM. The Parallel
+   Unstructured Mesh Infrastructure (PUMI) is an unstructured, distributed mesh
+   data management system that is capable of handling general non-manifold
+   models and effectively supports automated adaptive analysis. PUMI enables
+   support for parallel unstructured mesh modifications in MFEM.
+
 MFEM_BUILD_TAG = (any value)
    An optional tag to characterize the build. Exported to config/config.mk.
    Can be used to identify the MFEM build from other makefiles.
@@ -461,6 +471,10 @@ The specific libraries and their options are:
        https://support.hdfgroup.org/HDF5 (HDF5)
   Options: CONDUIT_OPT, CONDUIT_LIB.
 
+- PUMI, used when MFEM_USE_PUMI = YES.
+  URL: https://scorec.rpi.edu/pumi
+  Options: PUMI_OPT, PUMI_LIB.
+
 - MPFR (optional), used when MFEM_USE_MPFR = YES.
   URL: http://mpfr.org, it depends on the GMP library: https://gmplib.org
   Options: MPFR_OPT, MPFR_LIB.
@@ -593,6 +607,7 @@ MFEM_USE_GNUTLS
 MFEM_USE_NETCDF
 MFEM_USE_MPFR
 MFEM_USE_GZSTREAM
+MFEM_USE_PUMI
 
 The following options are CMake specific:
 
@@ -638,6 +653,7 @@ The CMake build system adds auto-detection for the following packages/libraries:
  - MPFR
  - LIBUNWIND
  - POSIXCLOCKS
+ - PUMI
 
 The following built-in CMake packages are also used:
 

LICENSE

@@ -1,5 +1,5 @@
-		  GNU LESSER GENERAL PUBLIC LICENSE
-		       Version 2.1, February 1999
+                  GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 2.1, February 1999
 
  Copyright (C) 1991, 1999 Free Software Foundation, Inc.
  51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -10,7 +10,7 @@
  as the successor of the GNU Library Public License, version 2, hence
  the version number 2.1.]
 
-			    Preamble
+                            Preamble
 
   The licenses for most software are designed to take away your
 freedom to share and change it.  By contrast, the GNU General Public
@@ -112,7 +112,7 @@ modification follow.  Pay close attention to the difference between a
 former contains code derived from the library, whereas the latter must
 be combined with the library in order to run.
 
-		  GNU LESSER GENERAL PUBLIC LICENSE
+                  GNU LESSER GENERAL PUBLIC LICENSE
    TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
 
   0. This License Agreement applies to any software library or other
@@ -146,7 +146,7 @@ such a program is covered only if its contents constitute a work based
 on the Library (independent of the use of the Library in a tool for
 writing it).  Whether that is true depends on what the Library does
 and what the program that uses the Library does.
-  
+
   1. You may copy and distribute verbatim copies of the Library's
 complete source code as you receive it, in any medium, provided that
 you conspicuously and appropriately publish on each copy an
@@ -432,7 +432,7 @@ decision will be guided by the two goals of preserving the free status
 of all derivatives of our free software and of promoting the sharing
 and reuse of software generally.
 
-			    NO WARRANTY
+                            NO WARRANTY
 
   15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
 WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
@@ -455,7 +455,7 @@ FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
 SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
 DAMAGES.
 
-		     END OF TERMS AND CONDITIONS
+                     END OF TERMS AND CONDITIONS
 
            How to Apply These Terms to Your New Libraries
 
@@ -485,7 +485,8 @@ 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.
 
@@ -494,11 +495,10 @@ school, if any, to sign a "copyright disclaimer" for the library, if
 necessary.  Here is a sample; alter the names:
 
   Yoyodyne, Inc., hereby disclaims all copyright interest in the
-  library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+  library `Frob' (a library for tweaking knobs) written by James Random
+  Hacker.
 
   <signature of Ty Coon>, 1 April 1990
   Ty Coon, President of Vice
 
 That's all there is to it!
-
-

README

@@ -12,11 +12,15 @@ to enable the research and development of scalable finite element discretization
 and solver algorithms through general finite element abstractions, accurate and
 flexible visualization, and tight integration with the hypre library.
 
-For building instructions, see the file INSTALL, or type "make help". Copyright
-information and licensing restrictions can be found in the file COPYRIGHT.
+* For building instructions, see the file INSTALL, or type "make help".
 
-The best starting point for new users interested in MFEM's features is the
-interactive documentation in examples/README.html.
+* Copyright and licensing information can be found in the file COPYRIGHT.
+
+* The best starting point for new users interested in MFEM's features is the
+  interactive documentation in examples/README.html.
+
+* Developers interested in contributing to the library, should read the
+  instructions and documentation in the CONTRIBUTING.md file.
 
 Conceptually, MFEM can be viewed as a finite element toolbox that provides the
 building blocks for developing finite element algorithms in a manner similar to
@@ -56,8 +60,8 @@ time integrators, etc.
 For examples of using MFEM, see the examples/ and miniapps/ directories, as well
 as the OpenGL visualization tool GLVis which is available at http://glvis.org.
 
-This project is released under the LGPL v2.1 license. See LICENSE file for full
-details.
+This project is released under the LGPL v2.1 license with static linking
+exception. See files COPYRIGHT and LICENSE file for full details.
 
 LLNL Release Number: LLNL-CODE-443211
 DOI: 10.11578/dc.20171025.1248

config/XSDKDefaults.cmake

@@ -180,3 +180,75 @@ 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

@@ -39,6 +39,7 @@ set(MFEM_USE_PETSC @MFEM_USE_PETSC@)
 set(MFEM_USE_MPFR @MFEM_USE_MPFR@)
 set(MFEM_USE_SIDRE @MFEM_USE_SIDRE@)
 set(MFEM_USE_CONDUIT @MFEM_USE_CONDUIT@)
+set(MFEM_USE_PUMI @MFEM_USE_PUMI@)
 
 set(MFEM_CXX_COMPILER "@CMAKE_CXX_COMPILER@")
 set(MFEM_CXX_FLAGS "@CMAKE_CXX_FLAGS@")

config/cmake/config.hpp.in

@@ -98,6 +98,9 @@
 // Enable MFEM functionality based on Conduit
 #cmakedefine MFEM_USE_CONDUIT
 
+// Enable MFEM functionality based on the PUMI library
+#cmakedefine MFEM_USE_PUMI
+
 // Which library functions to use in class StopWatch for measuring time.
 // For a list of the available options, see INSTALL.
 // If not defined, an option is selected automatically.
@@ -106,11 +109,11 @@
 // 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@
 
+// Macro defined when PUMI is built with support for the Simmetrix SimModSuite
+// library.
+#cmakedefine MFEM_USE_SIMMETRIX
+
 #endif // MFEM_CONFIG_HEADER

config/cmake/modules/MfemCmakeUtilities.cmake

@@ -229,6 +229,15 @@ 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()
@@ -685,3 +694,162 @@ 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_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

@@ -23,6 +23,18 @@
 #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
@@ -36,4 +48,7 @@
 #ifdef MFEM_USE_PETSC
 #error Building with PETSc (MFEM_USE_PETSC=YES) requires MPI (MFEM_USE_MPI=YES)
 #endif
+#ifdef MFEM_USE_PUMI
+#error Building with PUMI (MFEM_USE_PUMI=YES) requires MPI (MFEM_USE_MPI=YES)
+#endif
 #endif // MFEM_USE_MPI not defined

config/config.hpp.in

@@ -109,13 +109,14 @@
 // Enable functionality based on the MPFR library.
 // #define MFEM_USE_MPFR
 
-// Windows specific options
-#ifdef _WIN32
-// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
-#define _USE_MATH_DEFINES
-#endif
+// Enable MFEM functionality based on the PUMI library
+// #define MFEM_USE_PUMI
 
 // Version of HYPRE used for building MFEM.
 // #define MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@
 
+// Macro defined when PUMI is built with support for the Simmetrix SimModSuite
+// library.
+// #define MFEM_USE_SIMMETRIX
+
 #endif // MFEM_CONFIG_HEADER

config/config.mk.in

@@ -37,6 +37,7 @@ 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@

config/defaults.cmake

@@ -40,6 +40,9 @@ option(MFEM_USE_PETSC "Enable PETSc support." OFF)
 option(MFEM_USE_MPFR "Enable MPFR usage." OFF)
 option(MFEM_USE_SIDRE "Enable Axom/Sidre usage" OFF)
 option(MFEM_USE_CONDUIT "Enable Conduit usage" OFF)
+option(MFEM_USE_PUMI "Enable PUMI" OFF)
+
+set(MFEM_MPI_NP 4 CACHE STRING "Number of processes used for MPI tests")
 
 # 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
@@ -145,6 +148,9 @@ set(AXOM_DIR "${MFEM_DIR}/../axom" CACHE PATH "Path to the Axom library.")
 set(Axom_REQUIRED_PACKAGES "Conduit/relay" CACHE STRING
     "Additional packages required by Axom.")
 
+set(PUMI_DIR "${MFEM_DIR}/../pumi-2.1.0" CACHE STRING
+    "Directory where PUMI is installed")
+
 set(BLAS_INCLUDE_DIRS "" CACHE STRING "Path to BLAS headers.")
 set(BLAS_LIBRARIES "" CACHE STRING "The BLAS library.")
 set(LAPACK_INCLUDE_DIRS "" CACHE STRING "Path to LAPACK headers.")

config/defaults.mk

@@ -106,6 +106,7 @@ 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 =
@@ -271,6 +272,13 @@ SIDRE_LIB = \
    -Wl,-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib \
    -lsidre -lslic -laxom_utils -lconduit -lconduit_relay -lhdf5 $(ZLIB_LIB) -ldl
 
+# PUMI
+# Note that PUMI_DIR is needed -- it is used to check for gmi_sim.h
+PUMI_DIR = @MFEM_DIR@/../pumi-2.1.0
+PUMI_OPT = -I$(PUMI_DIR)/include
+PUMI_LIB = -L$(PUMI_DIR)/lib -lpumi -lcrv -lma -lmds -lapf -lpcu -lgmi -lparma\
+   -llion -lmth -lapf_zoltan -lspr
+
 # If YES, enable some informational messages
 VERBOSE = NO
 

config/makefile

@@ -38,6 +38,9 @@ all: header config-mk
 MPI = $(MFEM_USE_MPI:NO=)
 GHV = get_hypre_version
 GHV_FLAGS = $(subst @MFEM_DIR@,$(if $(MFEM_DIR),$(MFEM_DIR),..),$(HYPRE_OPT))
+SMX = $(if $(MFEM_USE_PUMI:NO=),MFEM_USE_SIMMETRIX)
+SMX_PATH = $(PUMI_DIR)/include/gmi_sim.h
+SMX_FILE = $(subst @MFEM_DIR@,$(if $(MFEM_DIR),$(MFEM_DIR),..),$(SMX_PATH))
 
 $(GHV): $(SRC)$(GHV).cpp
 	$(call mfem-info, Determining HYPRE version ...)
@@ -52,10 +55,16 @@ get-hypre-version: $(GHV).out
 	$(info HYPRE version: $(MFEM_HYPRE_VERSION)),\
 	$(error Unable to determine HYPRE version))
 
-header: $(if $(MPI),get-hypre-version,)
+check-smx:
+	$(call mfem-info, Checking for Simmetrix header [$(SMX_FILE)] ...)
+	$(eval MFEM_USE_SIMMETRIX:=$(if $(wildcard $(SMX_FILE)),YES,NO))
+	$(call mfem-info, MFEM_USE_SIMMETRIX = $(MFEM_USE_SIMMETRIX))
+	$(eval export MFEM_USE_SIMMETRIX)
+
+header: $(if $(MPI),get-hypre-version,) $(if $(SMX),check-smx)
 	$(call mfem-info, Writing $(CONFIG_HPP) ...)
 	@set -- && \
-	for def in $${MFEM_DEFINES} $(if $(MPI),MFEM_HYPRE_VERSION,); do \
+	for def in $${MFEM_DEFINES} $(if $(MPI),MFEM_HYPRE_VERSION) $(SMX); do \
 	   eval var=\$$$$def && \
 	   if [ "NO" != "$${var}" ]; then \
 	      set -- "$$@" -e "s|// \(#define $${def} \)|\1|" && \

config/sample-runs.sh

@@ -30,7 +30,7 @@ groups_serial=(
 '"examples"
    "Examples:"
    "examples"
-   "ex{,1}[0-9].cpp"'
+   "ex{,1,2}[0-9].cpp"'
 #   "ex1.cpp"'
 '"sundials"
    "SUNDIALS examples:"
@@ -44,14 +44,15 @@ groups_serial=(
 '"meshing"
    "Meshing miniapps:"
    "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp mesh-optimizer.cpp"'
+   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
+    mesh-optimizer.cpp"'
 )
 # Parallel groups
 groups_parallel=(
 '"examples"
    "Examples:"
    "examples"
-   "ex{,1}[0-9]p.cpp"'
+   "ex{,1,2}[0-9]p.cpp"'
 #   "ex1p.cpp"'
 '"sundials"
    "SUNDIALS examples:"
@@ -81,7 +82,7 @@ groups_all=(
 '"examples"
    "Examples:"
    "examples"
-   "ex\"{,1}[0-9]\"{,p}.cpp"'
+   "ex\"{,1,2}[0-9]\"{,p}.cpp"'
 '"sundials"
    "SUNDIALS examples:"
    "examples/sundials"
@@ -97,7 +98,8 @@ groups_all=(
 '"meshing"
    "Meshing miniapps:"
    "miniapps/meshing"
-   "mobius-strip.cpp klein-bottle.cpp {,p}mesh-optimizer.cpp"'
+   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
+    {,p}mesh-optimizer.cpp"'
 '"electromagnetics"
    "Electromagnetics miniapps:"
    "miniapps/electromagnetics"
@@ -170,6 +172,9 @@ 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>     [${make_j}] Specify the number of jobs to use for building
       -c|-color   Always use colors for the status messages: OK, FAILED, etc
       -b|-built   Do NOT rebuild the library and the executables
@@ -196,8 +201,8 @@ function help_message()
          Their values can also set using the respective uppercase environment
          variable
       mfem_build_dir [${mfem_build_dir}]
-         Set this variable to something different from <mfem_dir> to use an
-         out-of-source build
+         Same as '-d': set this variable to something different from <mfem_dir>
+         to use an out-of-source build
 
    For other valid variables, see the script source.
 
@@ -266,6 +271,10 @@ case "$1" in
       shift
       output_dir="$1"
       ;;
+   -d)
+      shift
+      mfem_build_dir="$1"
+      ;;
    -j)
       shift
       make_j="-j $1"

config/test.mk

@@ -14,11 +14,13 @@
 # Colors used below:
 # green    '\033[0;32m'
 # red      '\033[0;31m'
+# yellow   '\033[0;33m'
 # no color '\033[0m'
 COLOR_PRINT = if [ -t 1 ]; then \
    printf $(1)$(2)'\033[0m'$(3); else printf $(2)$(3); fi
 PRINT_OK = $(call COLOR_PRINT,'\033[0;32m',OK,"  ($$1 $$2)\n")
 PRINT_FAILED = $(call COLOR_PRINT,'\033[0;31m',FAILED,"  ($$1 $$2)\n")
+PRINT_SKIP = $(call COLOR_PRINT,'\033[0;33m',SKIP,"\n")
 
 # Timing support
 define TIMECMD_detect
@@ -36,7 +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 -- $$($(1) -l $(SHELL) -c "$(2)" 2>&1; echo $$?); \
+set -- $$($(1) -l $(SHELL) -c "{ $(2); } > /dev/null 2>&1" 2>&1; echo $$?); \
 set -- "$$1"s "$$(($$7/1024))"kB "$${60}"
 endef
 define TIMECMD.BASH
@@ -58,7 +60,8 @@ endif
 # Test runs of the examples/miniapps with parameters - check exit code
 mfem-test = \
    printf "   $(3) [$(2) $(1) ... ]: "; \
-   $(call $(TIMEFUN),$(TIMECMD),$(2) ./$(1) -no-vis $(4) > $(1).stderr 2>&1); \
+   $(call $(TIMEFUN),$(TIMECMD),$(2) ./$(1) $(if $(5),,-no-vis )$(4) \
+     > $(1).stderr 2>&1); \
    if [ "$$3" = 0 ]; \
    then $(PRINT_OK); else $(PRINT_FAILED); cat $(1).stderr; fi; \
    rm -f $(1).stderr; exit $$3

data/beam-wedge.mesh

@@ -0,0 +1,87 @@
+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
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+3 3  5 14 15  6
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+3 3 18  0  1 19
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+3 3 15 24 25 16
+3 3 16 25 26 17
+
+vertices
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+0 0 0
+1 0 0
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+0 0.5 1
+1 0.5 1
+2 0.5 1
+3 0.5 1
+4 0.5 1
+5 0.5 1
+6 0.5 1
+7 0.5 1
+8 0.5 1

data/beam-wedge.vtk

@@ -0,0 +1,61 @@
+# 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
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+CELL_TYPES 8
+13
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+13
+13
+CELL_DATA 8
+SCALARS material int
+LOOKUP_TABLE default
+1
+1
+1
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+2
+2
+2
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data/fichera-mixed-p2.mesh

@@ -0,0 +1,192 @@
+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
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+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
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+24 3 20 21 24 23
+
+vertices
+26
+
+nodes
+FiniteElementSpace
+FiniteElementCollection: H1_3D_P2
+VDim: 3
+Ordering: 1
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data/fichera-mixed-p2.vtk

@@ -0,0 +1,168 @@
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+ASCII
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data/fichera-mixed.mesh

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+MFEM mesh v1.0
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data/inline-wedge.mesh

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+MFEM INLINE mesh v1.0
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data/star-mixed-p2.mesh

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data/star-mixed-p2.vtk

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data/star-mixed.mesh

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+MFEM mesh v1.0
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+-0.38291796 0.66323336 0.095745414
+0.21049196 0.88243173 0.38908379
+-0.25356098 1.0629872 0.38908379
+0.32097654 1.3456091 -0.11416557
+-0.29944203 1.2553313 -0.27491822
+0.16461091 0.69008761 -0.27491822
+-0.1430764 0.59980988 -0.11416557
+-1.2341641 6.9922046e-16 -0.095745414
+-0.96583592 -1.1684711e-15 -0.25066475
+-0.8 4.5324311e-16 -0.15491933
+-0.8 9.7971744e-17 0.15491933
+-1.2341641 -3.9693744e-16 0.095745414
+-0.96583592 -1.5973885e-15 0.25066475
+-0.93742781 0.88699007 0.27491822
+-1.3258199 0.3948307 0.11416557
+-0.79379344 0.75108386 -0.38908379
+-0.86945428 0.25892449 -0.38908379
+-0.44791239 0.42381273 0.11416557
+-0.67993886 0.20248658 0.27491822
+-0.51708204 -0.89561236 -0.25066475
+-0.38291796 -0.66323336 -0.095745414
+-0.38291796 -0.66323336 0.095745414
+-0.51708204 -0.89561236 0.25066475
+-0.6 -1.0392305 -0.15491933
+-0.6 -1.0392305 0.15491933
+-1.3258199 -0.3948307 -0.11416557
+-0.93742781 -0.88699007 -0.27491822
+-0.67993886 -0.20248658 -0.27491822
+-0.44791239 -0.42381273 -0.11416557
+-0.86945428 -0.25892449 0.38908379
+-0.79379344 -0.75108386 0.38908379
+0.4 -0.69282032 -0.15491933
+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.conf.in

@@ -38,7 +38,7 @@ PROJECT_NAME           = "MFEM"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v3.3.3
+PROJECT_NUMBER         = v3.4.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -767,6 +767,7 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/fem \
                          @MFEM_SOURCE_DIR@/examples \
                          @MFEM_SOURCE_DIR@/examples/petsc \
+                         @MFEM_SOURCE_DIR@/examples/pumi \
                          @MFEM_SOURCE_DIR@/examples/sundials \
                          @MFEM_SOURCE_DIR@/miniapps/common \
                          @MFEM_SOURCE_DIR@/miniapps/meshing \

doc/CodeDocumentation.dox

@@ -36,8 +36,8 @@ namespace mfem {
  * - HypreSolver and other \link hypre.hpp hypre classes\endlink
  *
  * <H3>Example codes</H3>
- * - <a class="el" href="ex1_8cpp_source.html">Example 1</a>: nodal H1 FEM for the Laplace problem
- * - <a class="el" href="ex1p_8cpp_source.html">Example 1p</a>: parallel nodal H1 FEM for the Laplace problem
+ * - <a class="el" href="examples_2ex1_8cpp_source.html">Example 1</a>: nodal H1 FEM for the Laplace problem
+ * - <a class="el" href="examples_2ex1p_8cpp_source.html">Example 1p</a>: parallel nodal H1 FEM for the Laplace problem
  * - <a class="el" href="ex2_8cpp_source.html">Example 2</a>: vector FEM for linear elasticity
  * - <a class="el" href="ex2p_8cpp_source.html">Example 2p</a>: parallel vector FEM for linear elasticity
  * - <a class="el" href="ex3_8cpp_source.html">Example 3</a>: Nedelec H(curl) FEM for the definite Maxwell problem
@@ -56,7 +56,7 @@ namespace mfem {
  * - <a class="el" href="ex9p_8cpp_source.html">Example 9p</a>: parallel Discontinuous Galerkin (DG) time-dependent advection
  * - <a class="el" href="ex10_8cpp_source.html">Example 10</a>: time-dependent implicit nonlinear elasticity
  * - <a class="el" href="ex10p_8cpp_source.html">Example 10p</a>: parallel time-dependent implicit nonlinear elasticity
- * - <a class="el" href="ex11p_8cpp_source.html">Example 11p</a>: parallel Laplace eigensolver
+ * - <a class="el" href="examples_2ex11p_8cpp_source.html">Example 11p</a>: parallel Laplace eigensolver
  * - <a class="el" href="ex12p_8cpp_source.html">Example 12p</a>: parallel linear elasticity eigensolver
  * - <a class="el" href="ex13p_8cpp_source.html">Example 13p</a>: parallel Maxwell eigensolver
  * - <a class="el" href="ex14_8cpp_source.html">Example 14</a>: Discontinuous Galerkin (DG) for the Laplace problem
@@ -71,6 +71,10 @@ 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
@@ -96,6 +100,15 @@ namespace mfem {
  *   <a class="el" href="petsc_2ex10p_8cpp_source.html">10p</a>
  *   demonstrating the use of MFEM's \link petsc.hpp PETSc classes\endlink
  *
+ * <H4>PUMI Examples</H4>
+ * - Variants of Examples
+ *   <a class="el" href="examples_2pumi_2ex1_8cpp_source.html">1</a>,
+ *   <a class="el" href="examples_2pumi_2ex1p_8cpp_source.html">1p</a>,
+ *   <a class="el" href="pumi_2ex2_8cpp_source.html">2</a>,
+ *   and
+ *   <a class="el" href="pumi_2ex6p_8cpp_source.html">6p</a>
+ *   demonstrating the use of MFEM's \link pumi.hpp PUMI classes\endlink
+ *
  * <H3>Miniapps</H3>
  * - <a class="el" href="volta_8cpp_source.html">Volta</a>: simple electrostatics simulation code
  * - <a class="el" href="tesla_8cpp_source.html">Tesla</a>: simple magnetostatics simulation code
@@ -103,7 +116,9 @@ 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

examples/CMakeLists.txt

@@ -25,6 +25,9 @@ list(APPEND ALL_EXE_SRCS
   ex16.cpp
   ex17.cpp
   ex18.cpp
+  ex19.cpp
+  ex20.cpp
+  ex22.cpp
   )
 
 if (MFEM_USE_MPI)
@@ -47,6 +50,9 @@ if (MFEM_USE_MPI)
     ex16p.cpp
     ex17p.cpp
     ex18p.cpp
+    ex19p.cpp
+    ex20p.cpp
+    ex22p.cpp
     )
 endif()
 
@@ -61,8 +67,6 @@ foreach(SRC_FILE ${ALL_EXE_SRCS})
   get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
   string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
 
-  string(FIND ${TEST_NAME} "p" is_parallel_test)
-
   set(THIS_TEST_OPTIONS "-no-vis")
   if (${TEST_NAME} MATCHES "ex10p*")
     list(APPEND THIS_TEST_OPTIONS "-tf" "5")
@@ -70,12 +74,12 @@ foreach(SRC_FILE ${ALL_EXE_SRCS})
     list(APPEND THIS_TEST_OPTIONS "-e" "1")
   endif()
 
-  if (is_parallel_test EQUAL -1)
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
     add_test(NAME ${TEST_NAME}_ser
       COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
   else()
     add_test(NAME ${TEST_NAME}_np=4
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
       ${MPIEXEC_PREFLAGS}
       $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
       ${MPIEXEC_POSTFLAGS})
@@ -91,3 +95,8 @@ endif()
 if (MFEM_USE_PETSC)
   add_subdirectory(petsc)
 endif()
+
+# Include the examples/pumi directory if PUMI is enabled
+if (MFEM_USE_PUMI)
+  add_subdirectory(pumi)
+endif()

examples/ex1.cpp

@@ -4,13 +4,18 @@
 //
 // 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

examples/ex10.cpp

@@ -7,6 +7,7 @@
 //    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

@@ -7,6 +7,7 @@
 //    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

@@ -4,8 +4,11 @@
 //
 // 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
@@ -15,6 +18,11 @@
 //               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

examples/ex12p.cpp

@@ -5,9 +5,10 @@
 // Sample runs:
 //    mpirun -np 4 ex12p -m ../data/beam-tri.mesh
 //    mpirun -np 4 ex12p -m ../data/beam-quad.mesh
-//    mpirun -np 4 ex12p -m ../data/beam-tet.mesh -n 10 -o 2 -elast
+//    mpirun -np 4 ex12p -m ../data/beam-tet.mesh -s 79 -n 10 -o 2 -elast
 //    mpirun -np 4 ex12p -m ../data/beam-hex.mesh -s 3876
-//    mpirun -np 4 ex12p -m ../data/beam-tri.mesh -o 2 -sys
+//    mpirun -np 4 ex12p -m ../data/beam-wedge.mesh -s 79
+//    mpirun -np 4 ex12p -m ../data/beam-tri.mesh -s 3876 -o 2 -sys
 //    mpirun -np 4 ex12p -m ../data/beam-quad.mesh -s 4526 -n 6 -o 3 -elast
 //    mpirun -np 4 ex12p -m ../data/beam-quad-nurbs.mesh
 //    mpirun -np 4 ex12p -m ../data/beam-hex-nurbs.mesh

examples/ex13p.cpp

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

examples/ex14.cpp

@@ -4,8 +4,10 @@
 //
 // 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

@@ -4,8 +4,10 @@
 //
 // 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

@@ -135,6 +135,8 @@ 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

@@ -151,6 +151,8 @@ 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

@@ -10,6 +10,7 @@
 //               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

@@ -10,6 +10,7 @@
 //               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

@@ -8,6 +8,7 @@
 //       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

@@ -8,6 +8,7 @@
 //       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

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

examples/ex19.cpp

@@ -7,6 +7,7 @@
 //    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
@@ -50,7 +51,7 @@ using namespace mfem;
 //
 // and K^-1 is an approximation of the inverse of the displacement part of the
 // Jacobian and S^-1 is an approximation of the inverse of the Schur
-// complement S = B K^-1 B^T. The Schur complement is approximiated using
+// complement S = B K^-1 B^T. The Schur complement is approximated using
 // a mass matrix of the pressure variables.
 class JacobianPreconditioner : public Solver
 {

examples/ex19p.cpp

@@ -7,6 +7,7 @@
 //    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
@@ -50,7 +51,7 @@ using namespace mfem;
 //
 // and K^-1 is an approximation of the inverse of the displacement part of the
 // Jacobian and S^-1 is an approximation of the inverse of the Schur
-// complement S = B K^-1 B^T. The Schur complement is approximiated using
+// complement S = B K^-1 B^T. The Schur complement is approximated using
 // a mass matrix of the pressure variables.
 class JacobianPreconditioner : public Solver
 {

examples/ex1p.cpp

@@ -4,14 +4,19 @@
 //
 // 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

examples/ex2.cpp

@@ -6,6 +6,7 @@
 //               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

@@ -0,0 +1,298 @@
+//                                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

@@ -0,0 +1,364 @@
+//                       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/ex22.cpp

@@ -0,0 +1,310 @@
+//                                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

@@ -0,0 +1,366 @@
+//                                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

@@ -6,6 +6,7 @@
 //               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

@@ -7,6 +7,7 @@
 //               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

@@ -7,6 +7,7 @@
 //               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/ex6.cpp

@@ -20,7 +20,7 @@
 //               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 (quadrilateral, hexahedrons) manner according
+//               or non-conforming (quadrilaterals, hexahedra) manner according
 //               to a simple ZZ error estimator.
 //
 //               The example demonstrates MFEM's capability to work with both

examples/ex6p.cpp

@@ -20,7 +20,7 @@
 //               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 (quadrilateral, hexahedrons) manner according
+//               or non-conforming (quadrilaterals, hexahedra) manner according
 //               to a simple ZZ error estimator.
 //
 //               The example demonstrates MFEM's capability to work with both

examples/ex8.cpp

@@ -4,8 +4,10 @@
 //
 // 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

@@ -4,8 +4,10 @@
 //
 // 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
@@ -123,9 +125,13 @@ 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

@@ -10,6 +10,7 @@
 //    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

examples/ex9p.cpp

@@ -10,6 +10,7 @@
 //    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
+  ex18 ex19 ex20 ex22
 PAR_EXAMPLES = ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex8p ex9p ex10p ex11p ex12p\
- ex13p ex14p ex15p ex16p ex17p ex18p ex19p
+ ex13p ex14p ex15p ex16p ex17p ex18p ex19p ex20p ex22p
 
 ifeq ($(MFEM_USE_MPI),NO)
    EXAMPLES = $(SEQ_EXAMPLES)
@@ -38,6 +38,9 @@ endif
 ifeq ($(MFEM_USE_PETSC),YES)
    SUBDIRS += petsc
 endif
+ifeq ($(MFEM_USE_PUMI),YES)
+   SUBDIRS += pumi
+endif
 SUBDIRS_ALL = $(addsuffix /all,$(SUBDIRS))
 SUBDIRS_TEST = $(addsuffix /test,$(SUBDIRS))
 SUBDIRS_CLEAN = $(addsuffix /clean,$(SUBDIRS))
@@ -115,3 +118,5 @@ clean-exec:
 	@rm -f ex16.mesh ex16-mesh.* ex16-init.* ex16-final.*
 	@rm -f vortex-mesh.* vortex.mesh vortex-?-init.* vortex-?-final.*
 	@rm -f deformation.* pressure.*
+	@rm -f ex20.dat ex20p_?????.dat gnuplot_ex20.inp gnuplot_ex20p.inp
+	@rm -f ex22*.mesh ex22*.sol ex22p_*.*

examples/petsc/CMakeLists.txt

@@ -63,31 +63,29 @@ add_mfem_examples(PETSC_EXAMPLES_SRCS ${PFX} copy_petsc_rc_files test_petsc)
 #   ctest -R petsc
 
 # Command line options for the tests.
-set(EX1P_ARGS -m ../../data/amr-quad.mesh --usepetsc --petscopts rc_ex1p)
-set(EX2P_ARGS -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex2p)
-set(EX3P_ARGS -m ../../data/klein-bottle.mesh
-    -o 2 -f 0.1 --usepetsc --petscopts rc_ex3p_bddc --nonoverlapping)
-set(EX4P_ARGS -m ../../data/klein-bottle.mesh
-    -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping)
-set(EX5P_BDDC_ARGS -m ../../data/star.mesh
-    --usepetsc --petscopts rc_ex5p_bddc --nonoverlapping)
-set(EX5P_FSPL_ARGS -m ../../data/beam-tet.mesh
-    --usepetsc --petscopts rc_ex5p_fieldsplit)
-set(EX6P_ARGS -m ../../data/amr-quad.mesh --usepetsc)
-set(EX9P_E_ARGS -m ../../data/periodic-hexagon.mesh
-    --usepetsc --petscopts rc_ex9p_expl -dt 0.1)
-set(EX9P_ES_ARGS -m ../../data/periodic-hexagon.mesh
-    --usepetsc --petscopts rc_ex9p_expl --no-step)
-set(EX9P_IS_ARGS -m ../../data/periodic-hexagon.mesh
-    --usepetsc --petscopts rc_ex9p_impl --implicit -tf 0.5)
-set(EX10P_ARGS -m ../../data/beam-quad.mesh
-    -tf 30 -s 3 -rs 2 -dt 3 --usepetsc --petscopts rc_ex10p)
+set(EX1_ARGS_W       -m ../../data/amr-quad.mesh --usepetsc)
+set(EX1_ARGS_P       -m ../../data/amr-quad.mesh --usepetsc --petscopts rc_ex1p)
+set(EX2_ARGS         -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex2p)
+set(EX3_ARGS         -m ../../data/klein-bottle.mesh -o 2 -f 0.1 --usepetsc --petscopts rc_ex3p_bddc --nonoverlapping)
+set(EX4_ARGS         -m ../../data/klein-bottle.mesh -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping)
+set(EX4_HYB_ARGS     -m ../../data/klein-bottle.mesh -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping --hybridization)
+set(EX5_BDDC_LB_ARGS -m ../../data/star.mesh --usepetsc -o 0 --petscopts rc_ex5p_bddc --nonoverlapping --local-bdr)
+set(EX5_BDDC_GB_ARGS -m ../../data/star.mesh --usepetsc -o 0 --petscopts rc_ex5p_bddc --nonoverlapping)
+set(EX5_FSPL_ARGS    -m ../../data/beam-tet.mesh --usepetsc -o 0 --petscopts rc_ex5p_fieldsplit)
+set(EX6_ARGS         -m ../../data/amr-quad.mesh --usepetsc)
+set(EX6_NONOVL_ARGS  -m ../../data/amr-quad.mesh --usepetsc --nonoverlapping)
+set(EX9_E_ARGS       -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl -dt 0.1)
+set(EX9_ES_ARGS      -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl --no-step)
+set(EX9_IS_ARGS      -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_impl --implicit -tf 0.5)
+set(EX10_ARGS        -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex10p -tf 30 -s 3 -rs 2 -dt 3)
 
 # Add the tests: one test per command-line-variable.
 foreach(TEST_OPTIONS_VAR
-        EX1P_ARGS EX2P_ARGS EX3P_ARGS EX4P_ARGS EX5P_BDDC_ARGS EX5P_FSPL_ARGS
-        EX6P_ARGS EX9P_E_ARGS EX9P_ES_ARGS EX9P_IS_ARGS EX10P_ARGS)
+        EX1_ARGS_W EX1_ARGS_P EX2_ARGS EX3_ARGS EX4_ARGS EX4_HYB_ARGS
+        EX5_BDDC_LB_ARGS EX5_BDDC_GB_ARGS EX5_FSPL_ARGS EX6_ARGS EX6_NONOVL_ARGS
+        EX9_E_ARGS EX9_ES_ARGS EX9_IS_ARGS EX10_ARGS)
   string(REGEX REPLACE "^(.+)_ARGS" "\\1" TEST_NAME_UC ${TEST_OPTIONS_VAR})
+  string(REGEX REPLACE "^([^_]+)" "\\1P" TEST_NAME_UC ${TEST_NAME_UC})
   string(TOLOWER ${TEST_NAME_UC} TEST_NAME_FULL)
   string(REGEX REPLACE "^([^_]+).*" "\\1" TEST_NAME ${TEST_NAME_FULL})
   set(TEST_NAME_FULL ${PFX}${TEST_NAME_FULL})
@@ -98,7 +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} 4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
       ${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)
    {
-      PetscInitialize(NULL,NULL,petscrc_file,NULL);
+      MFEMInitializePetsc(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) { PetscFinalize(); }
+   if (use_petsc) { MFEMFinalizePetsc(); }
 
    MPI_Finalize();
 

examples/petsc/ex1p.cpp

@@ -123,7 +123,7 @@ int main(int argc, char *argv[])
    }
 
    // 2b. We initialize PETSc
-   PetscInitialize(NULL,NULL,petscrc_file,NULL);
+   MFEMInitializePetsc(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
@@ -266,7 +266,6 @@ int main(int argc, char *argv[])
       if (visualization && petscmonitor)
       {
          pcg->SetMonitor(&mymon);
-         pcg->SetPrintLevel(4);
          pcg->iterative_mode = true;
          X.Randomize();
       }
@@ -314,7 +313,7 @@ int main(int argc, char *argv[])
    delete pmesh;
 
    // We finalize PETSc
-   PetscFinalize();
+   MFEMFinalizePetsc();
 
    MPI_Finalize();
 

examples/petsc/ex2p.cpp

@@ -101,7 +101,7 @@ int main(int argc, char *argv[])
    }
 
    // 2b. We initialize PETSc
-   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { MFEMInitializePetsc(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) { PetscFinalize(); }
+   if (use_petsc) { MFEMFinalizePetsc(); }
 
    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) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { MFEMInitializePetsc(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) { PetscFinalize(); }
+   if (use_petsc) { MFEMFinalizePetsc(); }
 
    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) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { MFEMInitializePetsc(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) { PetscFinalize(); }
+   if (use_petsc) { MFEMFinalizePetsc(); }
 
    MPI_Finalize();
 

examples/petsc/ex5p.cpp

@@ -64,6 +64,7 @@ int main(int argc, char *argv[])
    bool visualization = 1;
    bool use_petsc = true;
    bool use_nonoverlapping = false;
+   bool local_bdr_spec = false;
    const char *petscrc_file = "";
 
    OptionsParser args(argc, argv);
@@ -86,6 +87,9 @@ int main(int argc, char *argv[])
                   "-no-nonoverlapping", "--no-nonoverlapping",
                   "Use or not the block diagonal PETSc's matrix format "
                   "for non-overlapping domain decomposition.");
+   args.AddOption(&local_bdr_spec, "-local-bdr", "--local-bdr", "-no-local-bdr",
+                  "--no-local-bdr",
+                  "Specify boundary dofs in local (Vdofs) ordering.");
    args.Parse();
    if (!args.Good())
    {
@@ -101,7 +105,7 @@ int main(int argc, char *argv[])
       args.PrintOptions(cout);
    }
    // 2b. We initialize PETSc
-   if (use_petsc) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { MFEMInitializePetsc(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
@@ -306,33 +310,38 @@ int main(int argc, char *argv[])
    {
       if (use_nonoverlapping)
       {
+         PetscBDDCSolverParams opts;
+
          // For saddle point problems, we need to provide BDDC the list of
          // boundary dofs either essential or natural.
          // Since R_space is the only space that may have boundary dofs and it
          // is ordered first then W_space, we don't need any local offset when
          // specifying the dofs.
          Array<int> bdr_tdof_list;
-         bool local = false;
          if (pmesh->bdr_attributes.Size())
          {
             Array<int> bdr(pmesh->bdr_attributes.Max());
             bdr = 1;
 
-            R_space->GetEssentialTrueDofs(bdr, bdr_tdof_list);
-            local = false;
-            // Alternatively, you can also provide the list of dofs in local
-            // ordering:
-            // R_space->GetEssentialVDofs(bdr, bdr_tdof_list);
-            // bdr_tdof_list.SetSize(R_space->GetVSize()+W_space->GetVSize(),0);
-            // local = true;
+            if (!local_bdr_spec)
+            {
+               // Essential dofs in global ordering
+               R_space->GetEssentialTrueDofs(bdr, bdr_tdof_list);
+            }
+            else
+            {
+               // Alternatively, you can also provide the list of dofs in local
+               // ordering
+               R_space->GetEssentialVDofs(bdr, bdr_tdof_list);
+               bdr_tdof_list.SetSize(R_space->GetVSize()+W_space->GetVSize(),0);
+            }
+            opts.SetNatBdrDofs(&bdr_tdof_list,local_bdr_spec);
          }
          else
          {
-            MFEM_ABORT("Need to know the boundary dofs");
+            MFEM_WARNING("Missing boundary dofs. This may cause solver failures.");
          }
 
-         PetscBDDCSolverParams opts;
-         opts.SetNatBdrDofs(&bdr_tdof_list,local);
          // See also command line options rc_ex5p_bddc
          pdarcyPr = new PetscBDDCSolver(MPI_COMM_WORLD,*darcyOp,opts,"prec_");
       }
@@ -535,7 +544,7 @@ int main(int argc, char *argv[])
    delete pmesh;
 
    // We finalize PETSc
-   if (use_petsc) { PetscFinalize(); }
+   if (use_petsc) { MFEMFinalizePetsc(); }
 
    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 (quadrilateral, hexahedrons) manner according
+//               or non-conforming (quadrilaterals, hexahedra) 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) { PetscInitialize(NULL,NULL,petscrc_file,NULL); }
+   if (use_petsc) { MFEMInitializePetsc(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) { PetscFinalize(); }
+   if (use_petsc) { MFEMFinalizePetsc(); }
 
    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.
-      PetscInitialize(NULL, NULL, petscrc_file, NULL);
+      MFEMInitializePetsc(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) { PetscFinalize(); }
+   if (use_petsc) { MFEMFinalizePetsc(); }
 
    MPI_Finalize();
    return 0;

examples/petsc/makefile

@@ -69,18 +69,21 @@ TESTNAME = Parallel PETSc example
 
 
 # Testing PETSc execution options.
-EX1_ARGS_W    := -m ../../data/amr-quad.mesh --usepetsc
-EX1_ARGS_P    := -m ../../data/amr-quad.mesh --usepetsc --petscopts rc_ex1p
-EX2_ARGS      := -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex2p
-EX3_ARGS      := -m ../../data/klein-bottle.mesh -o 2 -f 0.1 --usepetsc --petscopts rc_ex3p_bddc --nonoverlapping
-EX4_ARGS      := -m ../../data/klein-bottle.mesh -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping
-EX5_BDDC_ARGS := -m ../../data/star.mesh --usepetsc -o 0 --petscopts rc_ex5p_bddc --nonoverlapping
-EX5_FSPL_ARGS := -m ../../data/beam-tet.mesh --usepetsc -o 0 --petscopts rc_ex5p_fieldsplit
-EX6_ARGS      := -m ../../data/amr-quad.mesh --usepetsc
-EX9_E_ARGS    := -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl -dt 0.1
-EX9_ES_ARGS   := -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl --no-step
-EX9_IS_ARGS   := -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_impl --implicit -tf 0.5
-EX10_ARGS     := -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex10p -tf 30 -s 3 -rs 2 -dt 3
+EX1_ARGS_W       := -m ../../data/amr-quad.mesh --usepetsc
+EX1_ARGS_P       := -m ../../data/amr-quad.mesh --usepetsc --petscopts rc_ex1p
+EX2_ARGS         := -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex2p
+EX3_ARGS         := -m ../../data/klein-bottle.mesh -o 2 -f 0.1 --usepetsc --petscopts rc_ex3p_bddc --nonoverlapping
+EX4_ARGS         := -m ../../data/klein-bottle.mesh -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping
+EX4_HYB_ARGS     := -m ../../data/klein-bottle.mesh -o 2 --usepetsc --petscopts rc_ex4p_bddc --nonoverlapping --hybridization
+EX5_BDDC_LB_ARGS := -m ../../data/star.mesh --usepetsc -o 0 --petscopts rc_ex5p_bddc --nonoverlapping --local-bdr
+EX5_BDDC_GB_ARGS := -m ../../data/star.mesh --usepetsc -o 0 --petscopts rc_ex5p_bddc --nonoverlapping
+EX5_FSPL_ARGS    := -m ../../data/beam-tet.mesh --usepetsc -o 0 --petscopts rc_ex5p_fieldsplit
+EX6_ARGS         := -m ../../data/amr-quad.mesh --usepetsc
+EX6_NONOVL_ARGS  := -m ../../data/amr-quad.mesh --usepetsc --nonoverlapping
+EX9_E_ARGS       := -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl -dt 0.1
+EX9_ES_ARGS      := -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_expl --no-step
+EX9_IS_ARGS      := -m ../../data/periodic-hexagon.mesh --usepetsc --petscopts rc_ex9p_impl --implicit -tf 0.5
+EX10_ARGS        := -m ../../data/beam-quad.mesh --usepetsc --petscopts rc_ex10p -tf 30 -s 3 -rs 2 -dt 3
 ex1p-test-par: ex1p
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX1_ARGS_W))
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX1_ARGS_P))
@@ -90,11 +93,14 @@ ex3p-test-par: ex3p
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX3_ARGS))
 ex4p-test-par: ex4p
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX4_ARGS))
+	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX4_HYB_ARGS))
 ex5p-test-par: ex5p
-	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX5_BDDC_ARGS))
+	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX5_BDDC_LB_ARGS))
+	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX5_BDDC_GB_ARGS))
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX5_FSPL_ARGS))
 ex6p-test-par: ex6p
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX6_ARGS))
+	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX6_NONOVL_ARGS))
 ex9p-test-par: ex9p
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX9_E_ARGS))
 	@$(call mfem-test,$<, $(RUN_MPI), $(TESTNAME),$(EX9_ES_ARGS))

examples/petsc/rc_ex3p

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

examples/petsc/rc_ex3p_bddc

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

examples/petsc/rc_ex4p

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

examples/petsc/rc_ex4p_bddc

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

examples/petsc/rc_ex5p_bddc

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

examples/pumi/CMakeLists.txt

@@ -0,0 +1,73 @@
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability see http://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
+
+set(PUMI_EXAMPLES_SRCS)
+# All PUMI examples require MPI
+if (MFEM_USE_MPI)
+  list(APPEND PUMI_EXAMPLES_SRCS
+    ex1.cpp
+    ex1p.cpp
+    ex2.cpp
+    ex6p.cpp
+    )
+endif()
+
+# Include the source directory where mfem.hpp and mfem-performance.hpp are.
+include_directories(BEFORE ${PROJECT_BINARY_DIR})
+
+# Add "test_pumi" target, see below.
+add_custom_target(test_pumi
+  ${CMAKE_CTEST_COMMAND} -R pumi USES_TERMINAL)
+
+# Add one executable per cpp file, adding "pumi_" as prefix. Sets
+# "test_pumi" as a target that depends on the given examples.
+set(PFX pumi_)
+add_mfem_examples(PUMI_EXAMPLES_SRCS ${PFX} "" test_pumi)
+
+# Testing.
+# The PUMI tests can be run separately using the target "test_pumi"
+# which builds the examples and runs:
+#   ctest -R pumi
+
+# Command line options for the tests.
+# TODO...
+
+# Set the number of processors for the parallel examples. The value of
+# MFEM_MPI_NP is ignored.
+set(EX1_TEST_NP 1)
+set(EX1P_TEST_NP 8)
+set(EX2_TEST_NP 1)
+set(EX6P_TEST_NP 8)
+
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${PUMI_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
+  set(TEST_NAME ${PFX}${TEST_NAME})
+
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+
+  # All PUMI examples require MPI
+  if (FALSE)
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    set(TEST_NP ${${UP_TEST_NAME}_TEST_NP})
+    add_test(NAME ${TEST_NAME}_np=${TEST_NP}
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${TEST_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

examples/pumi/README

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

examples/pumi/ex1.cpp

@@ -0,0 +1,262 @@
+//                                MFEM Example 1
+//                              PUMI Modification
+//
+// Compile with: make ex1
+//
+// Sample runs:
+//    ex1 -m ../../data/pumi/serial/Kova.smb -p ../../data/pumi/geom/Kova.dmg
+//
+// Note:         Example models + meshes for the PUMI examples can be downloaded
+//               from github.com/mfem/data/pumi. After downloading we recommend
+//               creating a symbolic link to the above directory in ../../data.
+//
+// Description:  This example code demonstrates the use of MFEM to define a
+//               simple finite element discretization of the Laplace problem
+//               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
+//               Specifically, we discretize using a FE space of the specified
+//               order, or if order < 1 using an isoparametric/isogeometric
+//               space (i.e. quadratic for quadratic curvilinear mesh, NURBS for
+//               NURBS mesh, etc.)
+//
+//               The example highlights the use of mesh refinement, finite
+//               element grid functions, as well as linear and bilinear forms
+//               corresponding to the left-hand side and right-hand side of the
+//               discrete linear system. We also cover the explicit elimination
+//               of essential boundary conditions, static condensation, and the
+//               optional connection to the GLVis tool for visualization.
+//
+//               This PUMI modification demonstrates how PUMI's API can be used
+//               to load a PUMI mesh classified on a geometric model and then
+//               convert it to the MFEM mesh format. The inputs are a Parasolid
+//               model, "*.xmt_txt" and a SCOREC mesh "*.smb". The option "-o"
+//               is used for the Finite Element order and "-go" is used for the
+//               geometry order. Note that they can be used independently, i.e.
+//               "-o 8 -go 3" solves for 8th order FE on a third order geometry.
+
+#include "mfem.hpp"
+#include <fstream>
+#include <iostream>
+
+#ifdef MFEM_USE_SIMMETRIX
+#include <SimUtil.h>
+#include <gmi_sim.h>
+#endif
+#include <apfMDS.h>
+#include <gmi_null.h>
+#include <PCU.h>
+#include <apfConvert.h>
+#include <gmi_mesh.h>
+#include <crv.h>
+
+using namespace std;
+using namespace mfem;
+
+int main(int argc, char *argv[])
+{
+   // 1. Initialize MPI (required by PUMI).
+   int num_procs, myid;
+   MPI_Init(&argc, &argv);
+   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
+   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
+
+   // 2. Parse command-line options.
+   const char *mesh_file = "../../data/pumi/serial/Kova.smb";
+#ifdef MFEM_USE_SIMMETRIX
+   const char *model_file = "../../data/pumi/geom/Kova.x_t";
+#else
+   const char *model_file = "../../data/pumi/geom/Kova.dmg";
+#endif
+   int order = 1;
+   bool static_cond = false;
+   bool visualization = 1;
+   int geom_order = 1;
+
+   OptionsParser args(argc, argv);
+   args.AddOption(&mesh_file, "-m", "--mesh",
+                  "Mesh file to use.");
+   args.AddOption(&order, "-o", "--order",
+                  "Finite element order (polynomial degree) or -1 for"
+                  " isoparametric space.");
+   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
+                  "--no-static-condensation", "Enable static condensation.");
+   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
+                  "--no-visualization",
+                  "Enable or disable GLVis visualization.");
+   args.AddOption(&model_file, "-p", "--parasolid",
+                  "Parasolid model to use.");
+   args.AddOption(&geom_order, "-go", "--geometry_order",
+                  "Geometric order of the model");
+   args.Parse();
+   if (!args.Good())
+   {
+      if (myid == 0)
+      {
+         args.PrintUsage(cout);
+      }
+      MPI_Finalize();
+      return 1;
+   }
+   if (myid == 0)
+   {
+      args.PrintOptions(cout);
+   }
+
+   // 3. Read the SCOREC Mesh.
+   PCU_Comm_Init();
+#ifdef MFEM_USE_SIMMETRIX
+   Sim_readLicenseFile(0);
+   gmi_sim_start();
+   gmi_register_sim();
+#endif
+   gmi_register_mesh();
+
+   apf::Mesh2* pumi_mesh;
+   pumi_mesh = apf::loadMdsMesh(model_file, mesh_file);
+
+   // 4. Increase the geometry order if necessary.
+   if (geom_order > 1)
+   {
+      crv::BezierCurver bc(pumi_mesh, geom_order, 2);
+      bc.run();
+   }
+
+   pumi_mesh->verify();
+
+   // 5. Create the MFEM mesh object from the PUMI mesh. We can handle
+   //    triangular and tetrahedral meshes. Other inputs are the same as the
+   //    MFEM default constructor.
+   Mesh *mesh = new PumiMesh(pumi_mesh, 1, 1);
+   int dim = mesh->Dimension();
+
+   // 6. Refine the mesh to increase the resolution. In this example we do
+   //    'ref_levels' of uniform refinement. We choose 'ref_levels' to be the
+   //    largest number that gives a final mesh with no more than 50,000
+   //    elements.
+   {
+      int ref_levels =
+         (int)floor(log(50000./mesh->GetNE())/log(2.)/dim);
+      for (int l = 0; l < ref_levels; l++)
+      {
+         mesh->UniformRefinement();
+      }
+   }
+
+   // 7. Define a finite element space on the mesh. Here we use continuous
+   //    Lagrange finite elements of the specified order. If order < 1, we
+   //    instead use an isoparametric/isogeometric space.
+   FiniteElementCollection *fec;
+   if (order > 0)
+   {
+      fec = new H1_FECollection(order, dim);
+   }
+   else if (mesh->GetNodes())
+   {
+      fec = mesh->GetNodes()->OwnFEC();
+      cout << "Using isoparametric FEs: " << fec->Name() << endl;
+   }
+   else
+   {
+      fec = new H1_FECollection(order = 1, dim);
+   }
+   FiniteElementSpace *fespace = new FiniteElementSpace(mesh, fec);
+   cout << "Number of finite element unknowns: "
+        << fespace->GetTrueVSize() << endl;
+
+   // 8. Determine the list of true (i.e. conforming) essential boundary dofs.
+   //    In this example, the boundary conditions are defined by marking all
+   //    the boundary attributes from the mesh as essential (Dirichlet) and
+   //    converting them to a list of true dofs.
+   Array<int> ess_tdof_list;
+   if (mesh->bdr_attributes.Size())
+   {
+      Array<int> ess_bdr(mesh->bdr_attributes.Max());
+      ess_bdr = 1;
+      fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
+   }
+
+   // 9. Set up the linear form b(.) which corresponds to the right-hand side of
+   //    the FEM linear system, which in this case is (1,phi_i) where phi_i are
+   //    the basis functions in the finite element fespace.
+   LinearForm *b = new LinearForm(fespace);
+   ConstantCoefficient one(1.0);
+   b->AddDomainIntegrator(new DomainLFIntegrator(one));
+   b->Assemble();
+
+   // 10. Define the solution vector x as a finite element grid function
+   //     corresponding to fespace. Initialize x with initial guess of zero,
+   //     which satisfies the boundary conditions.
+   GridFunction x(fespace);
+   x = 0.0;
+
+   // 11. Set up the bilinear form a(.,.) on the finite element space
+   //     corresponding to the Laplacian operator -Delta, by adding the
+   //     Diffusion domain integrator.
+   BilinearForm *a = new BilinearForm(fespace);
+   a->AddDomainIntegrator(new DiffusionIntegrator(one));
+
+   // 12. Assemble the bilinear form and the corresponding linear system,
+   //     applying any necessary transformations such as: eliminating boundary
+   //     conditions, applying conforming constraints for non-conforming AMR,
+   //     static condensation, etc.
+   if (static_cond) { a->EnableStaticCondensation(); }
+   a->Assemble();
+
+   SparseMatrix A;
+   Vector B, X;
+   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);
+
+   cout << "Size of linear system: " << A.Height() << endl;
+
+#ifndef MFEM_USE_SUITESPARSE
+   // 13. Define a simple symmetric Gauss-Seidel preconditioner and use it to
+   //     solve the system A X = B with PCG.
+   GSSmoother M(A);
+   PCG(A, M, B, X, 1, 200, 1e-12, 0.0);
+#else
+   // 13. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
+   UMFPackSolver umf_solver;
+   umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
+   umf_solver.SetOperator(A);
+   umf_solver.Mult(B, X);
+#endif
+
+   // 14. Recover the solution as a finite element grid function.
+   a->RecoverFEMSolution(X, *b, x);
+
+   // 15. Save the refined mesh and the solution. This output can be viewed later
+   //     using GLVis: "glvis -m refined.mesh -g sol.gf".
+   ofstream mesh_ofs("refined.mesh");
+   mesh_ofs.precision(8);
+   mesh->Print(mesh_ofs);
+   ofstream sol_ofs("sol.gf");
+   sol_ofs.precision(8);
+   x.Save(sol_ofs);
+
+   // 16. Send the solution by socket to a GLVis server.
+   if (visualization)
+   {
+      char vishost[] = "localhost";
+      int  visport   = 19916;
+      socketstream sol_sock(vishost, visport);
+      sol_sock.precision(8);
+      sol_sock << "solution\n" << *mesh << x << flush;
+   }
+
+   // 17. Free the used memory.
+   delete a;
+   delete b;
+   delete fespace;
+   if (order > 0) { delete fec; }
+   delete mesh;
+
+   pumi_mesh->destroyNative();
+   apf::destroyMesh(pumi_mesh);
+   PCU_Comm_Free();
+#ifdef MFEM_USE_SIMMETRIX
+   gmi_sim_stop();
+   Sim_unregisterAllKeys();
+#endif
+
+   MPI_Finalize();
+   return 0;
+}

examples/pumi/ex1p.cpp

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

examples/pumi/ex2.cpp

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

examples/pumi/ex6p.cpp

@@ -0,0 +1,387 @@
+//                       MFEM Example 6 - Parallel Version
+//                              PUMI Modification
+//
+// Compile with: make ex1p
+//
+// Sample runs:  mpirun -np 8 ex6p
+//
+// Description:  This is a version of Example 1 with a simple adaptive mesh
+//               refinement loop. The problem being solved is again the Laplace
+//               equation -Delta u = 1 with homogeneous Dirichlet boundary
+//               conditions. The problem is solved on a sequence of meshes which
+//               are adapted in a conforming (tetrahedrons) manner according
+//               to a simple SPR ZZ error estimator.
+//
+//               This PUMI variation also performs a "uniform" refinement,
+//               similar to MFEM examples, for coarse meshes. However, the
+//               refinement is performed using the PUMI API. A new option "-ar"
+//               is added to modify the "adapt_ratio" which is the fraction of
+//               allowable error that scales the output size field of the error
+//               estimator.
+
+#include "mfem.hpp"
+#include <fstream>
+#include <iostream>
+
+#ifdef MFEM_USE_SIMMETRIX
+#include <SimUtil.h>
+#include <gmi_sim.h>
+#endif
+#include <apfMDS.h>
+#include <gmi_null.h>
+#include <PCU.h>
+#include <spr.h>
+#include <apfConvert.h>
+#include <gmi_mesh.h>
+#include <crv.h>
+
+using namespace std;
+using namespace mfem;
+
+int main(int argc, char *argv[])
+{
+   // 1. Initialize MPI.
+   int num_procs, myid;
+   MPI_Init(&argc, &argv);
+   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
+   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
+
+   // 2. Parse command-line options.
+   const char *mesh_file = "../../data/pumi/parallel/Kova/Kova100k_8.smb";
+#ifdef MFEM_USE_SIMMETRIX
+   const char *model_file = "../../data/pumi/geom/Kova.x_t";
+   const char *smd_file = NULL;
+#else
+   const char *model_file = "../../data/pumi/geom/Kova.dmg";
+#endif
+   int order = 1;
+   bool static_cond = false;
+   bool visualization = 1;
+   int geom_order = 1;
+   double adapt_ratio = 0.05;
+
+   OptionsParser args(argc, argv);
+   args.AddOption(&mesh_file, "-m", "--mesh",
+                  "Mesh file to use.");
+   args.AddOption(&order, "-o", "--order",
+                  "Finite element order (polynomial degree) or -1 for"
+                  " isoparametric space.");
+   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
+                  "--no-static-condensation", "Enable static condensation.");
+   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
+                  "--no-visualization",
+                  "Enable or disable GLVis visualization.");
+   args.AddOption(&model_file, "-p", "--model",
+                  "parasolid or .dmg model to use.");
+#ifdef MFEM_USE_SIMMETRIX
+   args.AddOption(&smd_file, "-sm", "--smd_model",
+                  "smd model file to use.");
+#endif
+   args.AddOption(&geom_order, "-go", "--geometry_order",
+                  "Geometric order of the model");
+   args.AddOption(&adapt_ratio, "-ar", "--adapt_ratio",
+                  "adaptation factor used in MeshAdapt");
+   args.Parse();
+   if (!args.Good())
+   {
+      if (myid == 0)
+      {
+         args.PrintUsage(cout);
+      }
+      MPI_Finalize();
+      return 1;
+   }
+   if (myid == 0)
+   {
+      args.PrintOptions(cout);
+   }
+
+   // 3. Read the SCOREC Mesh.
+   PCU_Comm_Init();
+#ifdef MFEM_USE_SIMMETRIX
+   Sim_readLicenseFile(0);
+   gmi_sim_start();
+   gmi_register_sim();
+#endif
+   gmi_register_mesh();
+
+   apf::Mesh2* pumi_mesh;
+#ifdef MFEM_USE_SIMMETRIX
+   if (smd_file)
+   {
+      gmi_model *mixed_model = gmi_sim_load(model_file, smd_file);
+      pumi_mesh = apf::loadMdsMesh(mixed_model, mesh_file);
+   }
+   else
+#endif
+   {
+      pumi_mesh = apf::loadMdsMesh(model_file, mesh_file);
+   }
+
+   // 4. Increase the geometry order and refine the mesh if necessary.  Parallel
+   //    uniform refinement is performed if the total number of elements is less
+   //    than 100,000.
+   int dim = pumi_mesh->getDimension();
+   int nEle = pumi_mesh->count(dim);
+   int ref_levels = (int)floor(log(100000./nEle)/log(2.)/dim);
+
+   if (geom_order > 1)
+   {
+      crv::BezierCurver bc(pumi_mesh, geom_order, 2);
+      bc.run();
+   }
+
+   // Perform Uniform refinement
+   if (myid == 1)
+   {
+      std::cout << " ref level : " <<     ref_levels << std::endl;
+   }
+
+   if (ref_levels > 1)
+   {
+      ma::Input* uniInput = ma::configureUniformRefine(pumi_mesh, ref_levels);
+
+      if ( geom_order > 1)
+      {
+         crv::adapt(uniInput);
+      }
+      else
+      {
+         ma::adapt(uniInput);
+      }
+   }
+
+   pumi_mesh->verify();
+
+   // 5. Create the parallel MFEM mesh object from the parallel PUMI mesh.  We
+   //    can handle triangular and tetrahedral meshes. Note that the mesh
+   //    resolution is performed on the PUMI mesh.
+   ParMesh *pmesh = new ParPumiMesh(MPI_COMM_WORLD, pumi_mesh);
+
+   // 6. Define a parallel finite element space on the parallel mesh. Here we
+   //    use continuous Lagrange finite elements of the specified order. If
+   //    order < 1, we instead use an isoparametric/isogeometric space.
+   FiniteElementCollection *fec;
+   if (order > 0)
+   {
+      fec = new H1_FECollection(order, dim);
+   }
+   else if (pmesh->GetNodes())
+   {
+      fec = pmesh->GetNodes()->OwnFEC();
+      if (myid == 1)
+      {
+         cout << "Using isoparametric FEs: " << fec->Name() << endl;
+      }
+   }
+   else
+   {
+      fec = new H1_FECollection(order = 1, dim);
+   }
+   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
+   HYPRE_Int size = fespace->GlobalTrueVSize();
+   if (myid == 1)
+   {
+      cout << "Number of finite element unknowns: " << size << endl;
+   }
+
+   // 7. Set up the parallel linear form b(.) which corresponds to the
+   //    right-hand side of the FEM linear system, which in this case is
+   //    (1,phi_i) where phi_i are the basis functions in fespace.
+   ParLinearForm *b = new ParLinearForm(fespace);
+   ConstantCoefficient one(1.0);
+   b->AddDomainIntegrator(new DomainLFIntegrator(one));
+
+   // 8. Define the solution vector x as a parallel finite element grid function
+   //    corresponding to fespace. Initialize x with initial guess of zero,
+   //    which satisfies the boundary conditions.
+   ParGridFunction x(fespace);
+   x = 0.0;
+
+   // 9. Connect to GLVis.
+   char vishost[] = "localhost";
+   int  visport   = 19916;
+
+   socketstream sout;
+   if (visualization)
+   {
+      sout.open(vishost, visport);
+      if (!sout)
+      {
+         if (myid == 0)
+         {
+            cout << "Unable to connect to GLVis server at "
+                 << vishost << ':' << visport << endl;
+            cout << "GLVis visualization disabled.\n";
+         }
+         visualization = false;
+      }
+
+      sout.precision(8);
+   }
+
+   // 10. Set up the parallel bilinear form a(.,.) on the finite element space
+   //     corresponding to the Laplacian operator -Delta, by adding the
+   //     Diffusion domain integrator.
+   ParBilinearForm *a = new ParBilinearForm(fespace);
+   a->AddDomainIntegrator(new DiffusionIntegrator(one));
+
+   // 11. Assemble the parallel bilinear form and the corresponding linear
+   //     system, applying any necessary transformations such as: parallel
+   //     assembly, eliminating boundary conditions, applying conforming
+   //     constraints for non-conforming AMR, static condensation, etc.
+   if (static_cond) { a->EnableStaticCondensation(); }
+
+   // 12. The main AMR loop. In each iteration we solve the problem on the
+   //     current mesh, visualize the solution, and adapt the mesh.
+   apf::Field* Tmag_field = 0;
+   apf::Field* temp_field = 0;
+   apf::Field* ipfield = 0;
+   apf::Field* sizefield = 0;
+   int max_iter = 3;
+
+   for (int Itr = 0; Itr < max_iter; Itr++)
+   {
+      HYPRE_Int global_dofs = fespace->GlobalTrueVSize();
+      if (myid == 1)
+      {
+         cout << "\nAMR iteration " << Itr << endl;
+         cout << "Number of unknowns: " << global_dofs << endl;
+      }
+
+      // Assemble.
+      a->Assemble();
+      b->Assemble();
+
+      // Essential boundary condition.
+      Array<int> ess_tdof_list;
+      if (pmesh->bdr_attributes.Size())
+      {
+         Array<int> ess_bdr(pmesh->bdr_attributes.Max());
+         ess_bdr = 1;
+         fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
+      }
+
+      // Form linear system.
+      HypreParMatrix A;
+      Vector B, X;
+      const int copy_interior = 1;
+      a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B, copy_interior);
+
+      // 13. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
+      //     preconditioner from hypre.
+      HypreBoomerAMG amg;
+      amg.SetPrintLevel(0);
+      CGSolver pcg(A.GetComm());
+      pcg.SetPreconditioner(amg);
+      pcg.SetOperator(A);
+      pcg.SetRelTol(1e-6);
+      pcg.SetMaxIter(200);
+      pcg.SetPrintLevel(3); // print the first and the last iterations only
+      pcg.Mult(B, X);
+
+      // 14. Recover the parallel grid function corresponding to X. This is the
+      //     local finite element solution on each processor.
+      a->RecoverFEMSolution(X, *b, x);
+
+      // 15. Save in parallel the displaced mesh and the inverted solution (which
+      //     gives the backward displacements to the original grid). This output
+      //     can be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
+      {
+         ostringstream mesh_name, sol_name;
+         mesh_name << "mesh." << setfill('0') << setw(6) << myid;
+         sol_name << "sol." << setfill('0') << setw(6) << myid;
+
+         ofstream mesh_ofs(mesh_name.str().c_str());
+         mesh_ofs.precision(8);
+         pmesh->Print(mesh_ofs);
+
+         ofstream sol_ofs(sol_name.str().c_str());
+         sol_ofs.precision(8);
+         x.Save(sol_ofs);
+      }
+
+      // 16. Send the above data by socket to a GLVis server.  Use the "n" and "b"
+      //     keys in GLVis to visualize the displacements.
+      if (visualization)
+      {
+         sout << "parallel " << num_procs << " " << myid << "\n";
+         sout << "solution\n" << *pmesh << x << flush;
+      }
+
+      // 17. Field transfer. Scalar solution field and magnitude field for error
+      //     estimation are created the PUMI mesh.
+      if (order > geom_order)
+      {
+         Tmag_field = apf::createField(pumi_mesh, "field_mag",
+                                       apf::SCALAR, apf::getLagrange(order));
+         temp_field = apf::createField(pumi_mesh, "T_field",
+                                       apf::SCALAR, apf::getLagrange(order));
+      }
+      else
+      {
+         Tmag_field = apf::createFieldOn(pumi_mesh, "field_mag",apf::SCALAR);
+         temp_field = apf::createFieldOn(pumi_mesh, "T_field", apf::SCALAR);
+      }
+
+      ParPumiMesh* pPPmesh = dynamic_cast<ParPumiMesh*>(pmesh);
+      pPPmesh->FieldMFEMtoPUMI(pumi_mesh, &x, temp_field, Tmag_field);
+
+      ipfield= spr::getGradIPField(Tmag_field, "MFEM_gradip", 2);
+      sizefield = spr::getSPRSizeField(ipfield, adapt_ratio);
+
+      apf::destroyField(Tmag_field);
+      apf::destroyField(ipfield);
+      apf::destroyNumbering(pumi_mesh->findNumbering("LocalVertexNumbering"));
+
+      // 18. Perform MesAdapt.
+      ma::Input* erinput = ma::configure(pumi_mesh, sizefield);
+      erinput->shouldFixShape = true;
+      erinput->maximumIterations = 2;
+      if ( geom_order > 1)
+      {
+         crv::adapt(erinput);
+      }
+      else
+      {
+         ma::adapt(erinput);
+      }
+
+      ParMesh* Adapmesh = new ParPumiMesh(MPI_COMM_WORLD, pumi_mesh);
+      pPPmesh->UpdateMesh(Adapmesh);
+      delete Adapmesh;
+
+      // 19. Update the FiniteElementSpace, GridFunction, and bilinear form.
+      fespace->Update();
+      x.Update();
+      x = 0.0;
+
+      pPPmesh->FieldPUMItoMFEM(pumi_mesh, temp_field, &x);
+      a->Update();
+      b->Update();
+
+      // Destroy fields.
+      apf::destroyField(temp_field);
+      apf::destroyField(sizefield);
+   }
+
+   // 20. Free the used memory.
+   delete a;
+   delete b;
+   delete fespace;
+   if (order > 0) { delete fec; }
+   delete pmesh;
+
+   pumi_mesh->destroyNative();
+   apf::destroyMesh(pumi_mesh);
+   PCU_Comm_Free();
+
+#ifdef MFEM_USE_SIMMETRIX
+   gmi_sim_stop();
+   Sim_unregisterAllKeys();
+#endif
+
+   MPI_Finalize();
+
+   return 0;
+}

examples/pumi/makefile

@@ -0,0 +1,94 @@
+# Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at the
+# Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights reserved.
+# See file COPYRIGHT for details.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability see http://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
+
+# Use the MFEM build directory
+MFEM_DIR ?= ../..
+MFEM_BUILD_DIR ?= ../..
+SRC = $(if $(MFEM_DIR:../..=),$(MFEM_DIR)/examples/pumi/,)
+CONFIG_MK = $(MFEM_BUILD_DIR)/config/config.mk
+# Use the MFEM install directory
+# MFEM_INSTALL_DIR = ../../mfem
+# CONFIG_MK = $(MFEM_INSTALL_DIR)/share/mfem/config.mk
+
+MFEM_LIB_FILE = mfem_is_not_built
+-include $(CONFIG_MK)
+
+# All PUMI examples require MPI
+SEQ_EXAMPLES =
+PAR_EXAMPLES = ex1 ex1p ex2 ex6p
+ifeq ($(MFEM_USE_MPI),NO)
+   EXAMPLES = $(SEQ_EXAMPLES)
+else
+   EXAMPLES = $(PAR_EXAMPLES) $(SEQ_EXAMPLES)
+endif
+
+.SUFFIXES:
+.SUFFIXES: .o .cpp .mk
+.PHONY: all clean clean-build clean-exec
+
+# Remove built-in rule
+%: %.cpp
+
+# Replace the default implicit rule for *.cpp files
+%: $(SRC)%.cpp $(MFEM_LIB_FILE) $(CONFIG_MK)
+	$(MFEM_CXX) $(MFEM_FLAGS) $< -o $@ $(MFEM_LIBS)
+
+all: $(EXAMPLES)
+
+ifeq ($(MFEM_USE_PUMI),NO)
+$(EXAMPLES):
+	$(error MFEM is not configured with PUMI)
+endif
+
+MFEM_TESTS = EXAMPLES
+include $(MFEM_TEST_MK)
+
+ifneq (,$(filter test%,$(MAKECMDGOALS)))
+   ifeq (,$(wildcard ../../data/pumi))
+      $(info PUMI data directory not found. The PUMI tests will be SKIPPED.)
+      mfem-test = printf "   $(3) [$(2) $(1) ... ]: "; $(PRINT_SKIP)
+   endif
+endif
+
+# Testing: Parallel vs. serial runs
+RUN_MPI_NP = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP)
+RUN_MPI = $(RUN_MPI_NP) $(MFEM_MPI_NP)
+SERIAL_NAME := Serial PUMI example
+PARALLEL_NAME := Parallel PUMI example
+%-test-par: %
+	@$(call mfem-test,$<, $(RUN_MPI), $(PARALLEL_NAME))
+%-test-seq: %
+	@$(call mfem-test,$<,, $(SERIAL_NAME))
+
+# Testing: Example-specific execution options:
+ex1-test-par: ex1
+	@$(call mfem-test,$<, $(RUN_MPI_NP) 1, $(PARALLEL_NAME))
+ex1p-test-par: ex1p
+	@$(call mfem-test,$<, $(RUN_MPI_NP) 8, $(PARALLEL_NAME))
+ex2-test-par: ex2
+	@$(call mfem-test,$<, $(RUN_MPI_NP) 1, $(PARALLEL_NAME))
+ex6p-test-par: ex6p
+	@$(call mfem-test,$<, $(RUN_MPI_NP) 8, $(PARALLEL_NAME))
+
+# Testing: "test" target and mfem-test* variables are defined in config/test.mk
+
+# Generate an error message if the MFEM library is not built and exit
+$(MFEM_LIB_FILE):
+	$(error The MFEM library is not built)
+
+clean: clean-build clean-exec
+
+clean-build:
+	rm -f *.o *~ $(SEQ_EXAMPLES) $(PAR_EXAMPLES)
+	rm -rf *.dSYM *.TVD.*breakpoints
+
+clean-exec:
+	@rm -f refined.mesh sol.gf mesh.* sol.* displaced.mesh

examples/sundials/CMakeLists.txt

@@ -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} 4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
       ${MPIEXEC_PREFLAGS}
       $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
       ${MPIEXEC_POSTFLAGS})

fem/bilinearform.cpp

@@ -79,9 +79,6 @@ BilinearForm::BilinearForm (FiniteElementSpace * f)
 BilinearForm::BilinearForm (FiniteElementSpace * f, BilinearForm * bf, int ps)
    : Matrix (f->GetVSize())
 {
-   int i;
-   Array<BilinearFormIntegrator*> *bfi;
-
    fes = f;
    sequence = f->GetSequence();
    mat_e = NULL;
@@ -92,33 +89,16 @@ BilinearForm::BilinearForm (FiniteElementSpace * f, BilinearForm * bf, int ps)
    precompute_sparsity = ps;
    diag_policy = DIAG_KEEP;
 
-   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;
 
-   bfi = bf->GetBFBFI();
-   bfbfi.SetSize (bfi->Size());
-   for (i = 0; i < bfi->Size(); i++)
-   {
-      bfbfi[i] = (*bfi)[i];
-   }
+   bfbfi = bf->bfbfi;
+   bfbfi_marker = bf->bfbfi_marker;
 
    AllocMat();
 }
@@ -734,7 +714,7 @@ void BilinearForm::ComputeElementMatrices()
 }
 
 void BilinearForm::EliminateEssentialBC(const Array<int> &bdr_attr_is_ess,
-                                        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);
@@ -785,7 +765,7 @@ void BilinearForm::EliminateEssentialBCDiag (const Array<int> &bdr_attr_is_ess,
 }
 
 void BilinearForm::EliminateVDofs(const Array<int> &vdofs,
-                                  Vector &sol, Vector &rhs,
+                                  const Vector &sol, Vector &rhs,
                                   DiagonalPolicy dpolicy)
 {
    for (int i = 0; i < vdofs.Size(); i++)
@@ -825,7 +805,8 @@ void BilinearForm::EliminateVDofs(const Array<int> &vdofs,
 }
 
 void BilinearForm::EliminateEssentialBCFromDofs(
-   const Array<int> &ess_dofs, Vector &sol, Vector &rhs, DiagonalPolicy dpolicy)
+   const Array<int> &ess_dofs, const Vector &sol, Vector &rhs,
+   DiagonalPolicy dpolicy)
 {
    MFEM_ASSERT(ess_dofs.Size() == height, "incorrect dof Array size");
    MFEM_ASSERT(sol.Size() == height, "incorrect sol Vector size");
@@ -940,6 +921,23 @@ 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)
@@ -1118,7 +1116,7 @@ void MixedBilinearForm::ConformingAssemble()
 }
 
 void MixedBilinearForm::EliminateTrialDofs (
-   Array<int> &bdr_attr_is_ess, Vector &sol, Vector &rhs )
+   Array<int> &bdr_attr_is_ess, const Vector &sol, Vector &rhs )
 {
    int i, j, k;
    Array<int> tr_vdofs, cols_marker (trial_fes -> GetVSize());
@@ -1141,7 +1139,7 @@ void MixedBilinearForm::EliminateTrialDofs (
 }
 
 void MixedBilinearForm::EliminateEssentialBCFromTrialDofs (
-   Array<int> &marked_vdofs, Vector &sol, Vector &rhs)
+   Array<int> &marked_vdofs, const Vector &sol, Vector &rhs)
 {
    mat -> EliminateCols (marked_vdofs, &sol, &rhs);
 }
@@ -1176,12 +1174,14 @@ void MixedBilinearForm::Update()
 
 MixedBilinearForm::~MixedBilinearForm()
 {
-   int i;
-
    if (mat) { delete mat; }
-   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]; }
+   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]; }
+   }
 }
 
 

fem/bilinearform.hpp

@@ -29,19 +29,21 @@ namespace mfem
 class BilinearForm : public Matrix
 {
 protected:
-   /// Sparse matrix to be associated with the form.
+   /// Sparse matrix to be associated with the form. Owned.
    SparseMatrix *mat;
 
-   /// Matrix used to eliminate b.c.
+   /// Matrix used to eliminate b.c. Owned.
    SparseMatrix *mat_e;
 
-   /// FE space on which the form lives.
+   /// FE space on which the form lives. Not owned.
    FiniteElementSpace *fes;
 
    /// 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.
@@ -49,22 +51,22 @@ protected:
 
    /// Set of Boundary Integrators to be applied.
    Array<BilinearFormIntegrator*> bbfi;
-   Array<Array<int>*>             bbfi_marker;
+   Array<Array<int>*>             bbfi_marker; ///< Entries are not owned.
 
    /// 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;
+   Array<Array<int>*>             bfbfi_marker; ///< Entries are not owned.
 
    DenseMatrix elemmat;
    Array<int>  vdofs;
 
-   DenseTensor *element_matrices;
+   DenseTensor *element_matrices; ///< Owned.
 
-   StaticCondensation *static_cond;
-   Hybridization *hybridization;
+   StaticCondensation *static_cond; ///< Owned.
+   Hybridization *hybridization; ///< Owned.
 
    /**
     * This member allows one to specify what should be done
@@ -89,10 +91,28 @@ protected:
       diag_policy = DIAG_KEEP;
    }
 
+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.
@@ -143,13 +163,25 @@ 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); }
 
@@ -175,10 +207,10 @@ 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
@@ -215,25 +247,31 @@ public:
       return *mat_e;
    }
 
-   /// Adds new Domain Integrator.
+   /// Adds new Domain Integrator. Assumes ownership of @a bfi.
    void AddDomainIntegrator(BilinearFormIntegrator *bfi);
 
-   /// Adds new Boundary Integrator.
+   /// Adds new Boundary Integrator. Assumes ownership of @a bfi.
    void AddBoundaryIntegrator(BilinearFormIntegrator *bfi);
 
    /** @brief Adds new Boundary Integrator, restricted to specific boundary
-       attributes. */
-   void AddBoundaryIntegrator(BilinearFormIntegrator * bfi,
+       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,
                               Array<int> &bdr_marker);
 
-   /// Adds new interior Face Integrator.
+   /// Adds new interior Face Integrator. Assumes ownership of @a bfi.
    void AddInteriorFaceIntegrator(BilinearFormIntegrator *bfi);
 
-   /// Adds new boundary Face Integrator.
+   /// Adds new boundary Face Integrator. Assumes ownership of @a bfi.
    void AddBdrFaceIntegrator(BilinearFormIntegrator *bfi);
 
    /** @brief Adds new boundary Face Integrator, restricted to specific boundary
-       attributes. */
+       attributes.
+
+       Assumes ownership of @a bfi. The array @a bdr_marker is stored internally
+       as a pointer to the given Array<int> object. */
    void AddBdrFaceIntegrator(BilinearFormIntegrator *bfi,
                              Array<int> &bdr_marker);
 
@@ -311,7 +349,7 @@ public:
        essential DOFs is set to 1.0. This behavior is controlled by the argument
        @a dpolicy. */
    void EliminateEssentialBC(const Array<int> &bdr_attr_is_ess,
-                             Vector &sol, Vector &rhs,
+                             const Vector &sol, Vector &rhs,
                              DiagonalPolicy dpolicy = DIAG_ONE);
 
    /// Eliminate essential boundary DOFs from the system matrix.
@@ -322,7 +360,7 @@ public:
                                  double value);
 
    /// Eliminate the given @a vdofs. NOTE: here, @a vdofs is a list of DOFs.
-   void EliminateVDofs(const Array<int> &vdofs, Vector &sol, Vector &rhs,
+   void EliminateVDofs(const Array<int> &vdofs, const Vector &sol, Vector &rhs,
                        DiagonalPolicy dpolicy = DIAG_ONE);
 
    /// Eliminate the given @a vdofs, storing the eliminated part internally.
@@ -333,10 +371,10 @@ public:
                        DiagonalPolicy dpolicy = DIAG_ONE);
 
    /** @brief Similar to
-       EliminateVDofs(const Array<int> &, Vector &, Vector &, DiagonalPolicy)
+       EliminateVDofs(const Array<int> &, const Vector &, Vector &, DiagonalPolicy)
        but here @a ess_dofs is a marker (boolean) array on all vector-dofs
        (@a ess_dofs[i] < 0 is true). */
-   void EliminateEssentialBCFromDofs(const Array<int> &ess_dofs, Vector &sol,
+   void EliminateEssentialBCFromDofs(const Array<int> &ess_dofs, const Vector &sol,
                                      Vector &rhs, DiagonalPolicy dpolicy = DIAG_ONE);
 
    /** @brief Similar to EliminateVDofs(const Array<int> &, DiagonalPolicy) but
@@ -393,36 +431,68 @@ public:
 class MixedBilinearForm : public Matrix
 {
 protected:
-   SparseMatrix *mat;
+   SparseMatrix *mat; ///< Owned.
 
-   FiniteElementSpace *trial_fes, *test_fes;
+   FiniteElementSpace *trial_fes, ///< Not owned
+                      *test_fes;  ///< Not owned
 
+   /** @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;
-   Array<BilinearFormIntegrator*> skt; // trace face integrators
+   /// 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 &);
 
 public:
-   MixedBilinearForm (FiniteElementSpace *tr_fes,
-                      FiniteElementSpace *te_fes);
+   /** @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);
 
-   virtual double& Elem (int i, int j);
+   /** @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 const double& Elem (int i, int j) const;
+       The pointers @a tr_fes and @a te_fes are not owned by the newly
+       constructed object.
 
-   virtual void Mult (const Vector & x, Vector & y) 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 AddMult (const Vector & x, Vector & y,
-                         const double a = 1.0) const;
+   virtual double &Elem(int i, int j);
 
-   virtual void AddMultTranspose (const Vector & x, Vector & y,
-                                  const double a = 1.0) const;
+   virtual const double &Elem(int i, int j) const;
 
-   virtual void MultTranspose (const Vector & x, Vector & y) 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
    { 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
@@ -433,24 +503,31 @@ public:
    SparseMatrix &SpMat() { return *mat; }
    SparseMatrix *LoseMat() { SparseMatrix *tmp = mat; mat = NULL; return tmp; }
 
-   void AddDomainIntegrator (BilinearFormIntegrator * bfi);
+   /// Adds a domain integrator. Assumes ownership of @a bfi.
+   void AddDomainIntegrator(BilinearFormIntegrator *bfi);
 
-   void AddBoundaryIntegrator (BilinearFormIntegrator * bfi);
+   /// Adds a boundary integrator. Assumes ownership of @a bfi.
+   void AddBoundaryIntegrator(BilinearFormIntegrator *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);
+   /** @brief Add a trace face integrator. Assumes ownership of @a 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
@@ -460,10 +537,10 @@ public:
    void ConformingAssemble();
 
    void EliminateTrialDofs(Array<int> &bdr_attr_is_ess,
-                           Vector &sol, Vector &rhs);
+                           const Vector &sol, Vector &rhs);
 
    void EliminateEssentialBCFromTrialDofs(Array<int> &marked_vdofs,
-                                          Vector &sol, Vector &rhs);
+                                          const Vector &sol, Vector &rhs);
 
    virtual void EliminateTestDofs(Array<int> &bdr_attr_is_ess);
 
@@ -505,19 +582,35 @@ 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);
 };
 

fem/bilininteg.cpp

@@ -962,8 +962,8 @@ void VectorMassIntegrator::AssembleElementMatrix
 
    double norm;
 
-   // Get vdim from VQ, MQ, or the space dimension
-   int vdim = (VQ) ? (VQ -> GetVDim()) : ((MQ) ? (MQ -> GetVDim()) : spaceDim);
+   // If vdim is not set, set it to the space dimension
+   vdim = (vdim == -1) ? spaceDim : vdim;
 
    elmat.SetSize(nd*vdim);
    shape.SetSize(nd);
@@ -1041,13 +1041,11 @@ void VectorMassIntegrator::AssembleElementMatrix2(
 {
    int tr_nd = trial_fe.GetDof();
    int te_nd = test_fe.GetDof();
-   int dim   = trial_fe.GetDim();
-   int vdim;
 
    double norm;
 
-   // Get vdim from the ElementTransformation Trans ?
-   vdim = (VQ) ? (VQ -> GetVDim()) : ((MQ) ? (MQ -> GetVDim()) : (dim));
+   // If vdim is not set, set it to the space dimension
+   vdim = (vdim == -1) ? Trans.GetSpaceDim() : vdim;
 
    elmat.SetSize(te_nd*vdim, tr_nd*vdim);
    shape.SetSize(tr_nd);
@@ -1626,6 +1624,7 @@ void VectorCurlCurlIntegrator::AssembleElementMatrix(
       ir = &IntRules.Get(el.GetGeomType(), order);
    }
 
+   elmat.SetSize(dof*dim);
    elmat = 0.0;
    for (int i = 0; i < ir->GetNPoints(); i++)
    {
@@ -2179,11 +2178,12 @@ void ElasticityIntegrator::AssembleElementMatrix(
    int dim = el.GetDim();
    double w, L, M;
 
+   MFEM_ASSERT(dim == Trans.GetSpaceDim(), "");
+
 #ifdef MFEM_THREAD_SAFE
-   DenseMatrix dshape(dof, dim), Jinv(dim), gshape(dof, dim), pelmat(dof);
+   DenseMatrix dshape(dof, dim), gshape(dof, dim), pelmat(dof);
    Vector divshape(dim*dof);
 #else
-   Jinv.SetSize(dim);
    dshape.SetSize(dof, dim);
    gshape.SetSize(dof, dim);
    pelmat.SetSize(dof);
@@ -2209,8 +2209,7 @@ void ElasticityIntegrator::AssembleElementMatrix(
 
       Trans.SetIntPoint(&ip);
       w = ip.weight * Trans.Weight();
-      CalcInverse(Trans.Jacobian(), Jinv);
-      Mult(dshape, Jinv, gshape);
+      Mult(dshape, Trans.InverseJacobian(), gshape);
       MultAAt(gshape, pelmat);
       gshape.GradToDiv (divshape);
 
@@ -2245,14 +2244,184 @@ void ElasticityIntegrator::AssembleElementMatrix(
             {
                for (int k = 0; k < dof; k++)
                   for (int l = 0; l < dof; l++)
+                  {
                      elmat(dof*i+k, dof*j+l) +=
                         (M * w) * gshape(k, j) * gshape(l, i);
-               // + (L * w) * gshape(k, i) * gshape(l, j)
+                  }
             }
       }
    }
 }
 
+void ElasticityIntegrator::ComputeElementFlux(
+   const mfem::FiniteElement &el, ElementTransformation &Trans,
+   Vector &u, const mfem::FiniteElement &fluxelem, Vector &flux,
+   int with_coef)
+{
+   const int dof = el.GetDof();
+   const int dim = el.GetDim();
+   const int tdim = dim*(dim+1)/2; // num. entries in a symmetric tensor
+   double L, M;
+
+   MFEM_ASSERT(dim == 2 || dim == 3,
+               "dimension is not supported: dim = " << dim);
+   MFEM_ASSERT(dim == Trans.GetSpaceDim(), "");
+   MFEM_ASSERT(fluxelem.GetMapType() == FiniteElement::VALUE, "");
+   MFEM_ASSERT(dynamic_cast<const NodalFiniteElement*>(&fluxelem), "");
+
+#ifdef MFEM_THREAD_SAFE
+   DenseMatrix dshape(dof, dim);
+#else
+   dshape.SetSize(dof, dim);
+#endif
+
+   double gh_data[9], grad_data[9];
+   DenseMatrix gh(gh_data, dim, dim);
+   DenseMatrix grad(grad_data, dim, dim);
+
+   const IntegrationRule &ir = fluxelem.GetNodes();
+   const int fnd = ir.GetNPoints();
+   flux.SetSize(fnd * tdim);
+
+   DenseMatrix loc_data_mat(u.GetData(), dof, dim);
+   for (int i = 0; i < fnd; i++)
+   {
+      const IntegrationPoint &ip = ir.IntPoint(i);
+      el.CalcDShape(ip, dshape);
+      MultAtB(loc_data_mat, dshape, gh);
+
+      Trans.SetIntPoint(&ip);
+      Mult(gh, Trans.InverseJacobian(), grad);
+
+      M = mu->Eval(Trans, ip);
+      if (lambda)
+      {
+         L = lambda->Eval(Trans, ip);
+      }
+      else
+      {
+         L = q_lambda * M;
+         M = q_mu * M;
+      }
+
+      // stress = 2*M*e(u) + L*tr(e(u))*I, where
+      //   e(u) = (1/2)*(grad(u) + grad(u)^T)
+      const double M2 = 2.0*M;
+      if (dim == 2)
+      {
+         L *= (grad(0,0) + grad(1,1));
+         // order of the stress entries: s_xx, s_yy, s_xy
+         flux(i+fnd*0) = M2*grad(0,0) + L;
+         flux(i+fnd*1) = M2*grad(1,1) + L;
+         flux(i+fnd*2) = M*(grad(0,1) + grad(1,0));
+      }
+      else if (dim == 3)
+      {
+         L *= (grad(0,0) + grad(1,1) + grad(2,2));
+         // order of the stress entries: s_xx, s_yy, s_zz, s_xy, s_xz, s_yz
+         flux(i+fnd*0) = M2*grad(0,0) + L;
+         flux(i+fnd*1) = M2*grad(1,1) + L;
+         flux(i+fnd*2) = M2*grad(2,2) + L;
+         flux(i+fnd*3) = M*(grad(0,1) + grad(1,0));
+         flux(i+fnd*4) = M*(grad(0,2) + grad(2,0));
+         flux(i+fnd*5) = M*(grad(1,2) + grad(2,1));
+      }
+   }
+}
+
+double ElasticityIntegrator::ComputeFluxEnergy(const FiniteElement &fluxelem,
+                                               ElementTransformation &Trans,
+                                               Vector &flux, Vector *d_energy)
+{
+   const int dof = fluxelem.GetDof();
+   const int dim = fluxelem.GetDim();
+   const int tdim = dim*(dim+1)/2; // num. entries in a symmetric tensor
+   double L, M;
+
+   // The MFEM_ASSERT constraints in ElasticityIntegrator::ComputeElementFlux
+   // are assumed here too.
+   MFEM_ASSERT(d_energy == NULL, "anisotropic estimates are not supported");
+   MFEM_ASSERT(flux.Size() == dof*tdim, "invalid 'flux' vector");
+
+#ifndef MFEM_THREAD_SAFE
+   shape.SetSize(dof);
+#else
+   Vector shape(dof);
+#endif
+   double pointstress_data[6];
+   Vector pointstress(pointstress_data, tdim);
+
+   // View of the 'flux' vector as a (dof x tdim) matrix
+   DenseMatrix flux_mat(flux.GetData(), dof, tdim);
+
+   // Use the same integration rule as in AssembleElementMatrix, replacing 'el'
+   // with 'fluxelem' when 'IntRule' is not set.
+   // Should we be using a different (more accurate) rule here?
+   const IntegrationRule *ir = IntRule;
+   if (ir == NULL)
+   {
+      int order = 2 * Trans.OrderGrad(&fluxelem);
+      ir = &IntRules.Get(fluxelem.GetGeomType(), order);
+   }
+
+   double energy = 0.0;
+
+   for (int i = 0; i < ir->GetNPoints(); i++)
+   {
+      const IntegrationPoint &ip = ir->IntPoint(i);
+      fluxelem.CalcShape(ip, shape);
+
+      flux_mat.MultTranspose(shape, pointstress);
+
+      Trans.SetIntPoint(&ip);
+      double w = Trans.Weight() * ip.weight;
+
+      M = mu->Eval(Trans, ip);
+      if (lambda)
+      {
+         L = lambda->Eval(Trans, ip);
+      }
+      else
+      {
+         L = q_lambda * M;
+         M = q_mu * M;
+      }
+
+      // The strain energy density at a point is given by (1/2)*(s : e) where s
+      // and e are the stress and strain tensors, respectively. Since we only
+      // have the stress, we need to compute the strain from the stress:
+      //    s = 2*mu*e + lambda*tr(e)*I
+      // Taking trace on both sides we find:
+      //    tr(s) = 2*mu*tr(e) + lambda*tr(e)*dim = (2*mu + dim*lambda)*tr(e)
+      // which gives:
+      //    tr(e) = tr(s)/(2*mu + dim*lambda)
+      // Then from the first identity above we can find the strain:
+      //    e = (1/(2*mu))*(s - lambda*tr(e)*I)
+
+      double pt_e; // point strain energy density
+      const double *s = pointstress_data;
+      if (dim == 2)
+      {
+         // s entries: s_xx, s_yy, s_xy
+         const double tr_e = (s[0] + s[1])/(2*(M + L));
+         L *= tr_e;
+         pt_e = (0.25/M)*(s[0]*(s[0] - L) + s[1]*(s[1] - L) + 2*s[2]*s[2]);
+      }
+      else // (dim == 3)
+      {
+         // s entries: s_xx, s_yy, s_zz, s_xy, s_xz, s_yz
+         const double tr_e = (s[0] + s[1] + s[2])/(2*M + 3*L);
+         L *= tr_e;
+         pt_e = (0.25/M)*(s[0]*(s[0] - L) + s[1]*(s[1] - L) + s[2]*(s[2] - L) +
+                          2*(s[3]*s[3] + s[4]*s[4] + s[5]*s[5]));
+      }
+
+      energy += w * pt_e;
+   }
+
+   return energy;
+}
+
 void DGTraceIntegrator::AssembleFaceMatrix(const FiniteElement &el1,
                                            const FiniteElement &el2,
                                            FaceElementTransformations &Trans,
@@ -3046,32 +3215,38 @@ void NormalInterpolator::AssembleElementMatrix2(
 }
 
 
+namespace internal
+{
+
+// Scalar shape functions scaled by scalar coefficient.
+// Used in the implementation of class ScalarProductInterpolator below.
+struct ShapeCoefficient : public VectorCoefficient
+{
+   Coefficient &Q;
+   const FiniteElement &fe;
+
+   ShapeCoefficient(Coefficient &q, const FiniteElement &fe_)
+      : VectorCoefficient(fe_.GetDof()), Q(q), fe(fe_) { }
+
+   using VectorCoefficient::Eval;
+   virtual void Eval(Vector &V, ElementTransformation &T,
+                     const IntegrationPoint &ip)
+   {
+      V.SetSize(vdim);
+      fe.CalcPhysShape(T, V);
+      V *= Q.Eval(T, ip);
+   }
+};
+
+}
+
 void
 ScalarProductInterpolator::AssembleElementMatrix2(const FiniteElement &dom_fe,
                                                   const FiniteElement &ran_fe,
                                                   ElementTransformation &Trans,
                                                   DenseMatrix &elmat)
 {
-   // Scalar shape functions scaled by scalar coefficient
-   struct ShapeCoefficient : public VectorCoefficient
-   {
-      Coefficient &Q;
-      const FiniteElement &fe;
-
-      ShapeCoefficient(Coefficient &q, const FiniteElement &fe_)
-         : VectorCoefficient(fe_.GetDof()), Q(q), fe(fe_) { }
-
-      using VectorCoefficient::Eval;
-      virtual void Eval(Vector &V, ElementTransformation &T,
-                        const IntegrationPoint &ip)
-      {
-         V.SetSize(vdim);
-         fe.CalcPhysShape(T, V);
-         V *= Q.Eval(T, ip);
-      }
-   };
-
-   ShapeCoefficient dom_shape_coeff(Q, dom_fe);
+   internal::ShapeCoefficient dom_shape_coeff(Q, dom_fe);
 
    elmat.SetSize(ran_fe.GetDof(),dom_fe.GetDof());
 
@@ -3208,6 +3383,35 @@ VectorCrossProductInterpolator::AssembleElementMatrix2(
 }
 
 
+namespace internal
+{
+
+// Vector shape functions dot product with a vector coefficient.
+// Used in the implementation of class VectorInnerProductInterpolator below.
+struct VDotVShapeCoefficient : public VectorCoefficient
+{
+   VectorCoefficient &VQ;
+   const FiniteElement &fe;
+   DenseMatrix vshape;
+   Vector vc;
+
+   VDotVShapeCoefficient(VectorCoefficient &vq, const FiniteElement &fe_)
+      : VectorCoefficient(fe_.GetDof()), VQ(vq), fe(fe_),
+        vshape(vdim, vq.GetVDim()), vc(vq.GetVDim()) { }
+
+   using VectorCoefficient::Eval;
+   virtual void Eval(Vector &V, ElementTransformation &T,
+                     const IntegrationPoint &ip)
+   {
+      V.SetSize(vdim);
+      VQ.Eval(vc, T, ip);
+      fe.CalcPhysVShape(T, vshape);
+      vshape.Mult(vc, V);
+   }
+};
+
+}
+
 void
 VectorInnerProductInterpolator::AssembleElementMatrix2(
    const FiniteElement &dom_fe,
@@ -3215,30 +3419,7 @@ VectorInnerProductInterpolator::AssembleElementMatrix2(
    ElementTransformation &Trans,
    DenseMatrix &elmat)
 {
-   // Vector shape functions dot product with a vector coefficient
-   struct VDotVShapeCoefficient : public VectorCoefficient
-   {
-      VectorCoefficient &VQ;
-      const FiniteElement &fe;
-      DenseMatrix vshape;
-      Vector vc;
-
-      VDotVShapeCoefficient(VectorCoefficient &vq, const FiniteElement &fe_)
-         : VectorCoefficient(fe_.GetDof()), VQ(vq), fe(fe_),
-           vshape(vdim, vq.GetVDim()), vc(vq.GetVDim()) { }
-
-      using VectorCoefficient::Eval;
-      virtual void Eval(Vector &V, ElementTransformation &T,
-                        const IntegrationPoint &ip)
-      {
-         V.SetSize(vdim);
-         VQ.Eval(vc, T, ip);
-         fe.CalcPhysVShape(T, vshape);
-         vshape.Mult(vc, V);
-      }
-   };
-
-   VDotVShapeCoefficient dom_shape_coeff(VQ, dom_fe);
+   internal::VDotVShapeCoefficient dom_shape_coeff(VQ, dom_fe);
 
    elmat.SetSize(ran_fe.GetDof(),dom_fe.GetDof());
 

fem/bilininteg.hpp

@@ -69,12 +69,60 @@ public:
                                  const Vector &elfun, DenseMatrix &elmat)
    { AssembleFaceMatrix(el1, el2, Tr, elmat); }
 
+   /** @brief Virtual method required for Zienkiewicz-Zhu type error estimators.
+
+       The purpose of the method is to compute a local "flux" finite element
+       function given a local finite element solution. The "flux" function has
+       to be computed in terms of its coefficients (represented by the Vector
+       @a flux) which multiply the basis functions defined by the FiniteElement
+       @a fluxelem. Typically, the "flux" function will have more than one
+       component and consequently @a flux should be store the coefficients of
+       all components: first all coefficient for component 0, then all
+       coefficients for component 1, etc. What the "flux" function represents
+       depends on the specific integrator. For example, in the case of
+       DiffusionIntegrator, the flux is the gradient of the solution multiplied
+       by the diffusion coefficient.
+
+       @param[in] el     FiniteElement of the solution.
+       @param[in] Trans  The ElementTransformation describing the physical
+                         position of the mesh element.
+       @param[in] u      Solution coefficients representing the expansion of the
+                         solution function in the basis of @a el.
+       @param[in] fluxelem  FiniteElement of the "flux".
+       @param[out] flux  "Flux" coefficients representing the expansion of the
+                         "flux" function in the basis of @a fluxelem. The size
+                         of @a flux as a Vector has to be set by this method,
+                         e.g. using Vector::SetSize().
+       @param[in] with_coef  If zero (the default value is 1) the implementation
+                             of the method may choose not to scale the "flux"
+                             function by any coefficients describing the
+                             integrator.
+    */
    virtual void ComputeElementFlux(const FiniteElement &el,
                                    ElementTransformation &Trans,
                                    Vector &u,
                                    const FiniteElement &fluxelem,
                                    Vector &flux, int with_coef = 1) { }
 
+   /** @brief Virtual method required for Zienkiewicz-Zhu type error estimators.
+
+       The purpose of this method is to compute a local number that measures the
+       energy of a given "flux" function (see ComputeElementFlux() for a
+       description of the "flux" function). Typically, the energy of a "flux"
+       function should be equal to a_local(u,u), if the "flux" is defined from
+       a solution u; here a_local(.,.) denotes the element-local bilinear
+       form represented by the integrator.
+
+       @param[in] fluxelem  FiniteElement of the "flux".
+       @param[in] Trans  The ElementTransformation describing the physical
+                         position of the mesh element.
+       @param[in] flux   "Flux" coefficients representing the expansion of the
+                         "flux" function in the basis of @a fluxelem.
+       @param[out] d_energy  If not NULL, the given Vector should be set to
+                             represent directional energy split that can be used
+                             for anisotropic error estimation.
+       @returns The computed energy.
+    */
    virtual double ComputeFluxEnergy(const FiniteElement &fluxelem,
                                     ElementTransformation &Trans,
                                     Vector &flux, Vector *d_energy = NULL)
@@ -1706,6 +1754,7 @@ public:
 class VectorMassIntegrator: public BilinearFormIntegrator
 {
 private:
+   int vdim;
    Vector shape, te_shape, vec;
    DenseMatrix partelmat;
    DenseMatrix mcoeff;
@@ -1718,22 +1767,25 @@ private:
 public:
    /// Construct an integrator with coefficient 1.0
    VectorMassIntegrator()
-   { Q = NULL; VQ = NULL; MQ = NULL; Q_order = 0; }
+      : vdim(-1), Q(NULL), VQ(NULL), MQ(NULL), Q_order(0) { }
    /** Construct an integrator with scalar coefficient q.
        If possible, save memory by using a scalar integrator since
        the resulting matrix is block diagonal with the same diagonal
        block repeated. */
    VectorMassIntegrator(Coefficient &q, int qo = 0)
-      : Q(&q) { VQ = NULL; MQ = NULL; Q_order = qo; }
+      : vdim(-1), Q(&q) { VQ = NULL; MQ = NULL; Q_order = qo; }
    VectorMassIntegrator(Coefficient &q, const IntegrationRule *ir)
-      : BilinearFormIntegrator(ir), Q(&q)
+      : BilinearFormIntegrator(ir), vdim(-1), Q(&q)
    { VQ = NULL; MQ = NULL; Q_order = 0; }
    /// Construct an integrator with diagonal coefficient q
    VectorMassIntegrator(VectorCoefficient &q, int qo = 0)
-      : VQ(&q) { Q = NULL; MQ = NULL; Q_order = qo; }
+      : vdim(q.GetVDim()), VQ(&q) { Q = NULL; MQ = NULL; Q_order = qo; }
    /// Construct an integrator with matrix coefficient q
    VectorMassIntegrator(MatrixCoefficient &q, int qo = 0)
-      : MQ(&q) { Q = NULL; VQ = NULL; Q_order = qo; }
+      : vdim(q.GetVDim()), MQ(&q) { Q = NULL; VQ = NULL; Q_order = qo; }
+
+   int GetVDim() const { return vdim; }
+   void SetVDim(int vdim) { this->vdim = vdim; }
 
    virtual void AssembleElementMatrix(const FiniteElement &el,
                                       ElementTransformation &Trans,
@@ -2018,7 +2070,8 @@ private:
    Coefficient *lambda, *mu;
 
 #ifndef MFEM_THREAD_SAFE
-   DenseMatrix dshape, Jinv, gshape, pelmat;
+   Vector shape;
+   DenseMatrix dshape, gshape, pelmat;
    Vector divshape;
 #endif
 
@@ -2033,6 +2086,33 @@ public:
    virtual void AssembleElementMatrix(const FiniteElement &,
                                       ElementTransformation &,
                                       DenseMatrix &);
+
+   /** Compute the stress corresponding to the local displacement @a u and
+       interpolate it at the nodes of the given @a fluxelem. Only the symmetric
+       part of the stress is stored, so that the size of @a flux is equal to
+       the number of DOFs in @a fluxelem times dim*(dim+1)/2. In 2D, the order
+       of the stress components is: s_xx, s_yy, s_xy. In 3D, it is: s_xx, s_yy,
+       s_zz, s_xy, s_xz, s_yz. In other words, @a flux is the local vector for
+       a FE space with dim*(dim+1)/2 vector components, based on the finite
+       element @a fluxelem. */
+   virtual void ComputeElementFlux(const FiniteElement &el,
+                                   ElementTransformation &Trans,
+                                   Vector &u,
+                                   const FiniteElement &fluxelem,
+                                   Vector &flux, int with_coef = 1);
+
+   /** Compute the element energy (integral of the strain energy density)
+       corresponding to the stress represented by @a flux which is a vector of
+       coefficients multiplying the basis functions defined by @a fluxelem. In
+       other words, @a flux is the local vector for a FE space with
+       dim*(dim+1)/2 vector components, based on the finite element @a fluxelem.
+       The number of components, dim*(dim+1)/2 is such that it represents the
+       symmetric part of the (symmetric) stress tensor. The order of the
+       components is: s_xx, s_yy, s_xy in 2D, and s_xx, s_yy, s_zz, s_xy, s_xz,
+       s_yz in 3D. */
+   virtual double ComputeFluxEnergy(const FiniteElement &fluxelem,
+                                    ElementTransformation &Trans,
+                                    Vector &flux, Vector *d_energy = NULL);
 };
 
 /** Integrator for the DG form:

fem/coefficient.cpp

@@ -87,7 +87,6 @@ double DeltaCoefficient::EvalDelta(ElementTransformation &T,
    return weight ? weight->Eval(T, ip, GetTime())*w : w;
 }
 
-
 void VectorCoefficient::Eval(DenseMatrix &M, ElementTransformation &T,
                              const IntegrationRule &ir)
 {
@@ -153,11 +152,17 @@ void VectorArrayCoefficient::Eval(Vector &V, ElementTransformation &T,
 }
 
 VectorGridFunctionCoefficient::VectorGridFunctionCoefficient (
-   GridFunction *gf) : VectorCoefficient (gf -> VectorDim())
+   GridFunction *gf)
+   : VectorCoefficient ((gf) ? gf -> VectorDim() : 0)
 {
    GridFunc = gf;
 }
 
+void VectorGridFunctionCoefficient::SetGridFunction(GridFunction *gf)
+{
+   GridFunc = gf; vdim = (gf) ? gf -> VectorDim() : 0;
+}
+
 void VectorGridFunctionCoefficient::Eval(Vector &V, ElementTransformation &T,
                                          const IntegrationPoint &ip)
 {
@@ -170,6 +175,64 @@ void VectorGridFunctionCoefficient::Eval(
    GridFunc->GetVectorValues(T, ir, M);
 }
 
+GradientGridFunctionCoefficient::GradientGridFunctionCoefficient (
+   GridFunction *gf)
+   : VectorCoefficient((gf) ?
+                       gf -> FESpace() -> GetMesh() -> SpaceDimension() : 0)
+{
+   GridFunc = gf;
+}
+
+void GradientGridFunctionCoefficient::SetGridFunction(GridFunction *gf)
+{
+   GridFunc = gf; vdim = (gf) ?
+                         gf -> FESpace() -> GetMesh() -> SpaceDimension() : 0;
+}
+
+void GradientGridFunctionCoefficient::Eval(Vector &V, ElementTransformation &T,
+                                           const IntegrationPoint &ip)
+{
+   GridFunc->GetGradient(T, V);
+}
+
+void GradientGridFunctionCoefficient::Eval(
+   DenseMatrix &M, ElementTransformation &T, const IntegrationRule &ir)
+{
+   GridFunc->GetGradients(T, ir, M);
+}
+
+CurlGridFunctionCoefficient::CurlGridFunctionCoefficient (
+   GridFunction *gf)
+   : VectorCoefficient ((gf) ?
+                        gf -> FESpace() -> GetMesh() -> SpaceDimension() : 0)
+{
+   GridFunc = gf;
+}
+
+void CurlGridFunctionCoefficient::SetGridFunction(GridFunction *gf)
+{
+   GridFunc = gf; vdim = (gf) ?
+                         gf -> FESpace() -> GetMesh() -> SpaceDimension() : 0;
+}
+
+void CurlGridFunctionCoefficient::Eval(Vector &V, ElementTransformation &T,
+                                       const IntegrationPoint &ip)
+{
+   GridFunc->GetCurl(T, V);
+}
+
+DivergenceGridFunctionCoefficient::DivergenceGridFunctionCoefficient (
+   GridFunction *gf) : Coefficient()
+{
+   GridFunc = gf;
+}
+
+double DivergenceGridFunctionCoefficient::Eval(ElementTransformation &T,
+                                               const IntegrationPoint &ip)
+{
+   return GridFunc->GetDivergence(T);
+}
+
 void VectorDeltaCoefficient::SetDirection(const Vector &_d)
 {
    dir = _d;
@@ -209,7 +272,7 @@ void VectorRestrictedCoefficient::Eval(
    }
    else
    {
-      M.SetSize(vdim);
+      M.SetSize(vdim, ir.GetNPoints());
       M = 0.0;
    }
 }
@@ -287,6 +350,220 @@ void MatrixRestrictedCoefficient::Eval(DenseMatrix &K, ElementTransformation &T,
    }
 }
 
+InnerProductCoefficient::InnerProductCoefficient(VectorCoefficient &A,
+                                                 VectorCoefficient &B)
+   : a(&A), b(&B)
+{
+   MFEM_ASSERT(A.GetVDim() == B.GetVDim(),
+               "InnerProductCoefficient:  "
+               "Arguments have incompatible dimensions.");
+}
+
+double InnerProductCoefficient::Eval(ElementTransformation &T,
+                                     const IntegrationPoint &ip)
+{
+   a->Eval(va, T, ip);
+   b->Eval(vb, T, ip);
+   return va * vb;
+}
+
+VectorRotProductCoefficient::VectorRotProductCoefficient(VectorCoefficient &A,
+                                                         VectorCoefficient &B)
+   : a(&A), b(&B), va(A.GetVDim()), vb(B.GetVDim())
+{
+   MFEM_ASSERT(A.GetVDim() == 2 && B.GetVDim() == 2,
+               "VectorRotProductCoefficient:  "
+               "Arguments must have dimension equal to two.");
+}
+
+double VectorRotProductCoefficient::Eval(ElementTransformation &T,
+                                         const IntegrationPoint &ip)
+{
+   a->Eval(va, T, ip);
+   b->Eval(vb, T, ip);
+   return va[0] * vb[1] - va[1] * vb[0];
+}
+
+DeterminantCoefficient::DeterminantCoefficient(MatrixCoefficient &A)
+   : a(&A), ma(A.GetHeight(), A.GetWidth())
+{
+   MFEM_ASSERT(A.GetHeight() == A.GetWidth(),
+               "DeterminantCoefficient:  "
+               "Argument must be a square matrix.");
+}
+
+double DeterminantCoefficient::Eval(ElementTransformation &T,
+                                    const IntegrationPoint &ip)
+{
+   a->Eval(ma, T, ip);
+   return ma.Det();
+}
+
+VectorSumCoefficient::VectorSumCoefficient(VectorCoefficient &A,
+                                           VectorCoefficient &B,
+                                           double _alpha, double _beta)
+   : VectorCoefficient(A.GetVDim()), a(&A), b(&B), alpha(_alpha), beta(_beta),
+     va(A.GetVDim())
+{
+   MFEM_ASSERT(A.GetVDim() == B.GetVDim(),
+               "VectorSumCoefficient:  "
+               "Arguments must have the same dimension.");
+}
+
+void VectorSumCoefficient::Eval(Vector &V, ElementTransformation &T,
+                                const IntegrationPoint &ip)
+{
+   b->Eval(V, T, ip);
+   if ( beta != 1.0 ) { V *= beta; }
+   a->Eval(va, T, ip);
+   V.Add(alpha, va);
+}
+
+ScalarVectorProductCoefficient::ScalarVectorProductCoefficient(
+   Coefficient &A,
+   VectorCoefficient &B)
+   : VectorCoefficient(B.GetVDim()), a(&A), b(&B)
+{}
+
+void ScalarVectorProductCoefficient::Eval(Vector &V, ElementTransformation &T,
+                                          const IntegrationPoint &ip)
+{
+   double sa = a->Eval(T, ip);
+   b->Eval(V, T, ip);
+   V *= sa;
+}
+
+VectorCrossProductCoefficient::VectorCrossProductCoefficient(
+   VectorCoefficient &A,
+   VectorCoefficient &B)
+   : VectorCoefficient(3), a(&A), b(&B), va(A.GetVDim()), vb(B.GetVDim())
+{
+   MFEM_ASSERT(A.GetVDim() == 3 && B.GetVDim() == 3,
+               "VectorCrossProductCoefficient:  "
+               "Arguments must have dimension equal to three.");
+}
+
+void VectorCrossProductCoefficient::Eval(Vector &V, ElementTransformation &T,
+                                         const IntegrationPoint &ip)
+{
+   a->Eval(va, T, ip);
+   b->Eval(vb, T, ip);
+   V.SetSize(3);
+   V[0] = va[1] * vb[2] - va[2] * vb[1];
+   V[1] = va[2] * vb[0] - va[0] * vb[2];
+   V[2] = va[0] * vb[1] - va[1] * vb[0];
+}
+
+MatVecCoefficient::MatVecCoefficient(MatrixCoefficient &A,
+                                     VectorCoefficient &B)
+   : VectorCoefficient(A.GetHeight()), a(&A), b(&B),
+     ma(A.GetHeight(), A.GetWidth()), vb(B.GetVDim())
+{
+   MFEM_ASSERT(A.GetWidth() == B.GetVDim(),
+               "MatVecCoefficient:  Arguments have incompatible dimensions.");
+}
+
+void MatVecCoefficient::Eval(Vector &V, ElementTransformation &T,
+                             const IntegrationPoint &ip)
+{
+   a->Eval(ma, T, ip);
+   b->Eval(vb, T, ip);
+   ma.Mult(vb, V);
+}
+
+void IdentityMatrixCoefficient::Eval(DenseMatrix &M, ElementTransformation &T,
+                                     const IntegrationPoint &ip)
+{
+   M.SetSize(dim);
+   M = 0.0;
+   for (int d=0; d<dim; d++) { M(d,d) = 1.0; }
+}
+
+MatrixSumCoefficient::MatrixSumCoefficient(MatrixCoefficient &A,
+                                           MatrixCoefficient &B,
+                                           double _alpha, double _beta)
+   : MatrixCoefficient(A.GetHeight(), A.GetWidth()),
+     a(&A), b(&B), alpha(_alpha), beta(_beta),
+     ma(A.GetHeight(), A.GetWidth())
+{
+   MFEM_ASSERT(A.GetHeight() == B.GetHeight() && A.GetWidth() == B.GetWidth(),
+               "MatrixSumCoefficient:  "
+               "Arguments must have the same dimensions.");
+}
+
+void MatrixSumCoefficient::Eval(DenseMatrix &M, ElementTransformation &T,
+                                const IntegrationPoint &ip)
+{
+   b->Eval(M, T, ip);
+   if ( beta != 1.0 ) { M *= beta; }
+   a->Eval(ma, T, ip);
+   M.Add(alpha, ma);
+}
+
+ScalarMatrixProductCoefficient::ScalarMatrixProductCoefficient(
+   Coefficient &A,
+   MatrixCoefficient &B)
+   : MatrixCoefficient(B.GetHeight(), B.GetWidth()), a(&A), b(&B)
+{}
+
+void ScalarMatrixProductCoefficient::Eval(DenseMatrix &M,
+                                          ElementTransformation &T,
+                                          const IntegrationPoint &ip)
+{
+   double sa = a->Eval(T, ip);
+   b->Eval(M, T, ip);
+   M *= sa;
+}
+
+TransposeMatrixCoefficient::TransposeMatrixCoefficient(MatrixCoefficient &A)
+   : MatrixCoefficient(A.GetWidth(), A.GetHeight()), a(&A)
+{}
+
+void TransposeMatrixCoefficient::Eval(DenseMatrix &M,
+                                      ElementTransformation &T,
+                                      const IntegrationPoint &ip)
+{
+   a->Eval(M, T, ip);
+   M.Transpose();
+}
+
+InverseMatrixCoefficient::InverseMatrixCoefficient(MatrixCoefficient &A)
+   : MatrixCoefficient(A.GetHeight(), A.GetWidth()), a(&A)
+{
+   MFEM_ASSERT(A.GetHeight() == A.GetWidth(),
+               "InverseMatrixCoefficient:  "
+               "Argument must be a square matrix.");
+}
+
+void InverseMatrixCoefficient::Eval(DenseMatrix &M,
+                                    ElementTransformation &T,
+                                    const IntegrationPoint &ip)
+{
+   a->Eval(M, T, ip);
+   M.Invert();
+}
+
+OuterProductCoefficient::OuterProductCoefficient(VectorCoefficient &A,
+                                                 VectorCoefficient &B)
+   : MatrixCoefficient(A.GetVDim(), B.GetVDim()), a(&A), b(&B),
+     va(A.GetVDim()), vb(B.GetVDim())
+{}
+
+void OuterProductCoefficient::Eval(DenseMatrix &M, ElementTransformation &T,
+                                   const IntegrationPoint &ip)
+{
+   a->Eval(va, T, ip);
+   b->Eval(vb, T, ip);
+   M.SetSize(va.Size(), vb.Size());
+   for (int i=0; i<va.Size(); i++)
+   {
+      for (int j=0; j<vb.Size(); j++)
+      {
+         M(i, j) = va[i] * vb[j];
+      }
+   }
+}
+
 double LpNormLoop(double p, Coefficient &coeff, Mesh &mesh,
                   const IntegrationRule *irs[])
 {

fem/coefficient.hpp

@@ -39,9 +39,19 @@ public:
    void SetTime(double t) { time = t; }
    double GetTime() { return time; }
 
+   /** @brief Evaluate the coefficient in the element described by @a T at the
+       point @a ip. */
+   /** @note When this method is called, the caller must make sure that the
+       IntegrationPoint associated with @a T is the same as @a ip. This can be
+       achieved by calling T.SetIntPoint(&ip). */
    virtual double Eval(ElementTransformation &T,
                        const IntegrationPoint &ip) = 0;
 
+   /** @brief Evaluate the coefficient in the element described by @a T at the
+       point @a ip at time @a t. */
+   /** @note When this method is called, the caller must make sure that the
+       IntegrationPoint associated with @a T is the same as @a ip. This can be
+       achieved by calling T.SetIntPoint(&ip). */
    double Eval(ElementTransformation &T,
                const IntegrationPoint &ip, double t)
    {
@@ -157,6 +167,7 @@ private:
    int Component;
 
 public:
+   GridFunctionCoefficient() : GridF(NULL), Component(1) { }
    /** Construct GridFunctionCoefficient from a given GridFunction, and
        optionally specify a component to use if it is a vector GridFunction. */
    GridFunctionCoefficient (GridFunction *gf, int comp = 1)
@@ -242,7 +253,7 @@ public:
    Coefficient *Weight() { return weight; }
    void GetDeltaCenter(Vector& center);
    /// Return the Scale() multiplied by the weight Coefficient, if any.
-   double EvalDelta(ElementTransformation &T, const IntegrationPoint &ip);
+   virtual double EvalDelta(ElementTransformation &T, const IntegrationPoint &ip);
    /** @brief A DeltaFunction cannot be evaluated. Calling this method will
        cause an MFEM error, terminating the application. */
    virtual double Eval(ElementTransformation &T, const IntegrationPoint &ip)
@@ -280,11 +291,26 @@ public:
    /// Returns dimension of the vector.
    int GetVDim() { return vdim; }
 
+   /** @brief Evaluate the vector coefficient in the element described by @a T
+       at the point @a ip, storing the result in @a V. */
+   /** @note When this method is called, the caller must make sure that the
+       IntegrationPoint associated with @a T is the same as @a ip. This can be
+       achieved by calling T.SetIntPoint(&ip). */
    virtual void Eval(Vector &V, ElementTransformation &T,
                      const IntegrationPoint &ip) = 0;
 
-   // General implementation using the Eval method for one IntegrationPoint.
-   // Can be overloaded for more efficient implementation.
+   /** @brief Evaluate the vector coefficient in the element described by @a T
+       at all points of @a ir, storing the result in @a M. */
+   /** The dimensions of @a M are GetVDim() by ir.GetNPoints() and they must be
+       set by the implementation of this method.
+
+       The general implementation provided by the base class (using the Eval
+       method for one IntegrationPoint at a time) can be overloaded for more
+       efficient implementation.
+
+       @note The IntegrationPoint associated with @a T is not used, and this
+       method will generally modify this IntegrationPoint associated with @a T.
+   */
    virtual void Eval(DenseMatrix &M, ElementTransformation &T,
                      const IntegrationRule &ir);
 
@@ -374,9 +400,10 @@ protected:
    GridFunction *GridFunc;
 
 public:
+   VectorGridFunctionCoefficient() : VectorCoefficient(0), GridFunc(NULL) { }
    VectorGridFunctionCoefficient(GridFunction *gf);
 
-   void SetGridFunction(GridFunction *gf) { GridFunc = gf; }
+   void SetGridFunction(GridFunction *gf);
    GridFunction * GetGridFunction() const { return GridFunc; }
 
    virtual void Eval(Vector &V, ElementTransformation &T,
@@ -388,6 +415,63 @@ public:
    virtual ~VectorGridFunctionCoefficient() { }
 };
 
+/// Vector coefficient defined as the Gradient of a scalar GridFunction
+class GradientGridFunctionCoefficient : public VectorCoefficient
+{
+protected:
+   GridFunction *GridFunc;
+
+public:
+   GradientGridFunctionCoefficient(GridFunction *gf);
+
+   void SetGridFunction(GridFunction *gf);
+   GridFunction * GetGridFunction() const { return GridFunc; }
+
+   virtual void Eval(Vector &V, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+
+   virtual void Eval(DenseMatrix &M, ElementTransformation &T,
+                     const IntegrationRule &ir);
+
+   virtual ~GradientGridFunctionCoefficient() { }
+};
+
+/// Vector coefficient defined as the Curl of a vector GridFunction
+class CurlGridFunctionCoefficient : public VectorCoefficient
+{
+protected:
+   GridFunction *GridFunc;
+
+public:
+   CurlGridFunctionCoefficient(GridFunction *gf);
+
+   void SetGridFunction(GridFunction *gf);
+   GridFunction * GetGridFunction() const { return GridFunc; }
+
+   virtual void Eval(Vector &V, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+
+   virtual ~CurlGridFunctionCoefficient() { }
+};
+
+/// Scalar coefficient defined as the Divergence of a vector GridFunction
+class DivergenceGridFunctionCoefficient : public Coefficient
+{
+protected:
+   GridFunction *GridFunc;
+
+public:
+   DivergenceGridFunctionCoefficient(GridFunction *gf);
+
+   void SetGridFunction(GridFunction *gf) { GridFunc = gf; }
+   GridFunction * GetGridFunction() const { return GridFunc; }
+
+   virtual double Eval(ElementTransformation &T,
+                       const IntegrationPoint &ip);
+
+   virtual ~DivergenceGridFunctionCoefficient() { }
+};
+
 /// VectorDeltaCoefficient: DeltaCoefficient with a direction
 class VectorDeltaCoefficient : public VectorCoefficient
 {
@@ -420,8 +504,8 @@ public:
    /** @brief Return the specified direction vector multiplied by the value
        returned by DeltaCoefficient::EvalDelta() of the associated scalar
        DeltaCoefficient. */
-   void EvalDelta(Vector &V, ElementTransformation &T,
-                  const IntegrationPoint &ip);
+   virtual void EvalDelta(Vector &V, ElementTransformation &T,
+                          const IntegrationPoint &ip);
    using VectorCoefficient::Eval;
    /** @brief A VectorDeltaFunction cannot be evaluated. Calling this method
        will cause an MFEM error, terminating the application. */
@@ -470,6 +554,11 @@ public:
    // For backward compatibility
    int GetVDim() const { return width; }
 
+   /** @brief Evaluate the matrix coefficient in the element described by @a T
+       at the point @a ip, storing the result in @a K. */
+   /** @note When this method is called, the caller must make sure that the
+       IntegrationPoint associated with @a T is the same as @a ip. This can be
+       achieved by calling T.SetIntPoint(&ip). */
    virtual void Eval(DenseMatrix &K, ElementTransformation &T,
                      const IntegrationPoint &ip) = 0;
 
@@ -571,6 +660,279 @@ public:
                      const IntegrationPoint &ip);
 };
 
+/// Coefficients based on sums and products of other coefficients
+
+/// Scalar coefficient defined as the sum of two scalar coefficients
+class SumCoefficient : public Coefficient
+{
+private:
+   Coefficient * a;
+   Coefficient * b;
+
+   double alpha;
+   double beta;
+
+public:
+   // Result is _alpha * A + _beta * B
+   SumCoefficient(Coefficient &A, Coefficient &B,
+                  double _alpha = 1.0, double _beta = 1.0)
+      : a(&A), b(&B), alpha(_alpha), beta(_beta) { }
+
+   /// Evaluate the coefficient
+   virtual double Eval(ElementTransformation &T,
+                       const IntegrationPoint &ip)
+   { return alpha * a->Eval(T, ip) + beta * b->Eval(T, ip); }
+};
+
+/// Scalar coefficient defined as the product of two scalar coefficients
+class ProductCoefficient : public Coefficient
+{
+private:
+   Coefficient * a;
+   Coefficient * b;
+
+public:
+   ProductCoefficient(Coefficient &A, Coefficient &B)
+      : a(&A), b(&B) { }
+
+   /// Evaluate the coefficient
+   virtual double Eval(ElementTransformation &T,
+                       const IntegrationPoint &ip)
+   { return a->Eval(T, ip) * b->Eval(T, ip); }
+};
+
+/// Scalar coefficient defined as a scalar raised to a power
+class PowerCoefficient : public Coefficient
+{
+private:
+   Coefficient * a;
+
+   double p;
+
+public:
+   // Result is A^p
+   PowerCoefficient(Coefficient &A, double _p)
+      : a(&A), p(_p) { }
+
+   /// Evaluate the coefficient
+   virtual double Eval(ElementTransformation &T,
+                       const IntegrationPoint &ip)
+   { return pow(a->Eval(T, ip), p); }
+};
+
+/// Scalar coefficient defined as the inner product of two vector coefficients
+class InnerProductCoefficient : public Coefficient
+{
+private:
+   VectorCoefficient * a;
+   VectorCoefficient * b;
+
+   mutable Vector va;
+   mutable Vector vb;
+public:
+   InnerProductCoefficient(VectorCoefficient &A, VectorCoefficient &B);
+
+   /// Evaluate the coefficient
+   virtual double Eval(ElementTransformation &T,
+                       const IntegrationPoint &ip);
+};
+
+/// Scalar coefficient defined as a cross product of two vectors in 2D
+class VectorRotProductCoefficient : public Coefficient
+{
+private:
+   VectorCoefficient * a;
+   VectorCoefficient * b;
+
+   mutable Vector va;
+   mutable Vector vb;
+
+public:
+   VectorRotProductCoefficient(VectorCoefficient &A, VectorCoefficient &B);
+
+   virtual double Eval(ElementTransformation &T,
+                       const IntegrationPoint &ip);
+};
+
+/// Scalar coefficient defined as the determinant of a matrix coefficient
+class DeterminantCoefficient : public Coefficient
+{
+private:
+   MatrixCoefficient * a;
+
+   mutable DenseMatrix ma;
+
+public:
+   DeterminantCoefficient(MatrixCoefficient &A);
+
+   /// Evaluate the coefficient
+   virtual double Eval(ElementTransformation &T,
+                       const IntegrationPoint &ip);
+};
+
+/// Vector coefficient defined as the sum of two vector coefficients
+class VectorSumCoefficient : public VectorCoefficient
+{
+private:
+   VectorCoefficient * a;
+   VectorCoefficient * b;
+
+   double alpha;
+   double beta;
+
+   mutable Vector va;
+
+public:
+   // Result is _alpha * A + _beta * B
+   VectorSumCoefficient(VectorCoefficient &A, VectorCoefficient &B,
+                        double _alpha = 1.0, double _beta = 1.0);
+
+   /// Evaluate the coefficient
+   virtual void Eval(Vector &V, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+};
+
+/// Vector coefficient defined as a product of a scalar and a vector
+class ScalarVectorProductCoefficient : public VectorCoefficient
+{
+private:
+   Coefficient * a;
+   VectorCoefficient * b;
+
+public:
+   ScalarVectorProductCoefficient(Coefficient &A, VectorCoefficient &B);
+
+   virtual void Eval(Vector &V, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+};
+
+/// Vector coefficient defined as a cross product of two vectors
+class VectorCrossProductCoefficient : public VectorCoefficient
+{
+private:
+   VectorCoefficient * a;
+   VectorCoefficient * b;
+
+   mutable Vector va;
+   mutable Vector vb;
+
+public:
+   VectorCrossProductCoefficient(VectorCoefficient &A, VectorCoefficient &B);
+
+   virtual void Eval(Vector &V, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+};
+
+/// Vector coefficient defined as a matrix vector product
+class MatVecCoefficient : public VectorCoefficient
+{
+private:
+   MatrixCoefficient * a;
+   VectorCoefficient * b;
+
+   mutable DenseMatrix ma;
+   mutable Vector vb;
+
+public:
+   MatVecCoefficient(MatrixCoefficient &A, VectorCoefficient &B);
+
+   virtual void Eval(Vector &V, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+};
+
+/// Matrix coefficient defined as the identity of dimension d
+class IdentityMatrixCoefficient : public MatrixCoefficient
+{
+private:
+   int dim;
+
+public:
+   IdentityMatrixCoefficient(int d)
+      : MatrixCoefficient(d, d), dim(d) { }
+
+   virtual void Eval(DenseMatrix &M, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+};
+
+/// Matrix coefficient defined as the sum of two matrix coefficients
+class MatrixSumCoefficient : public MatrixCoefficient
+{
+private:
+   MatrixCoefficient * a;
+   MatrixCoefficient * b;
+
+   double alpha;
+   double beta;
+
+   mutable DenseMatrix ma;
+
+public:
+   // Result is _alpha * A + _beta * B
+   MatrixSumCoefficient(MatrixCoefficient &A, MatrixCoefficient &B,
+                        double _alpha = 1.0, double _beta = 1.0);
+
+   /// Evaluate the coefficient
+   virtual void Eval(DenseMatrix &M, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+};
+
+/// Matrix coefficient defined as a product of a scalar and a matrix
+class ScalarMatrixProductCoefficient : public MatrixCoefficient
+{
+private:
+   Coefficient * a;
+   MatrixCoefficient * b;
+
+public:
+   ScalarMatrixProductCoefficient(Coefficient &A, MatrixCoefficient &B);
+
+   virtual void Eval(DenseMatrix &M, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+};
+
+/// Matrix coefficient defined as the transpose a matrix
+class TransposeMatrixCoefficient : public MatrixCoefficient
+{
+private:
+   MatrixCoefficient * a;
+
+public:
+   TransposeMatrixCoefficient(MatrixCoefficient &A);
+
+   virtual void Eval(DenseMatrix &M, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+};
+
+/// Matrix coefficient defined as the inverse a matrix
+class InverseMatrixCoefficient : public MatrixCoefficient
+{
+private:
+   MatrixCoefficient * a;
+
+public:
+   InverseMatrixCoefficient(MatrixCoefficient &A);
+
+   virtual void Eval(DenseMatrix &M, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+};
+
+/// Matrix coefficient defined as the outer product of two vectors
+class OuterProductCoefficient : public MatrixCoefficient
+{
+private:
+   VectorCoefficient * a;
+   VectorCoefficient * b;
+
+   mutable Vector va;
+   mutable Vector vb;
+
+public:
+   OuterProductCoefficient(VectorCoefficient &A, VectorCoefficient &B);
+
+   virtual void Eval(DenseMatrix &M, ElementTransformation &T,
+                     const IntegrationPoint &ip);
+};
+
 /** Compute the Lp norm of a function f.
     \f$ \| f \|_{Lp} = ( \int_\Omega | f |^p d\Omega)^{1/p} \f$ */
 double ComputeLpNorm(double p, Coefficient &coeff, Mesh &mesh,

fem/conduitdatacollection.cpp

@@ -304,32 +304,43 @@ ConduitDataCollection::BlueprintMeshToMesh(const Node &n_mesh,
    if ( n_mesh_topo.has_child("boundary_topology") )
    {
       std::string bndry_topo_name = n_mesh_topo["boundary_topology"].as_string();
-      const Node &n_bndry_topo    = n_mesh["topologies"][bndry_topo_name];
-      std::string bndry_ele_shape = n_bndry_topo["elements/shape"].as_string();
 
-      bndry_geo = ShapeNameToGeomType(bndry_ele_shape);
-      int num_idxs_per_bndry_ele = Geometry::NumVerts[mesh_geo];
+      // In VisIt, we encountered a case were a mesh specified a boundary
+      // topology, but the boundary topology was omitted from the blueprint
+      // index, so it's data could not be obtained.
+      //
+      // This guard prevents an error in that case, allowing the mesh to be
+      // created without boundary info
 
-      const Node &n_bndry_conn = n_bndry_topo["elements/connectivity"];
-
-      // mfem requires ints, we could have int64s, etc convert if necessary
-      if ( n_bndry_conn.dtype().is_int() &&
-           n_bndry_conn.is_compact())
+      if (n_mesh["topologies"].has_child(bndry_topo_name))
       {
-         bndry_indices = n_bndry_conn.value();
-      }
-      else
-      {
-         Node &(n_bndry_conn_conv) =
-            n_conv["topologies"][bndry_topo_name]["elements/connectivity"];
-         n_bndry_conn.to_int_array(n_bndry_conn_conv);
-         bndry_indices = (n_bndry_conn_conv).value();
+         const Node &n_bndry_topo    = n_mesh["topologies"][bndry_topo_name];
+         std::string bndry_ele_shape = n_bndry_topo["elements/shape"].as_string();
 
-      }
+         bndry_geo = ShapeNameToGeomType(bndry_ele_shape);
+         int num_idxs_per_bndry_ele = Geometry::NumVerts[mesh_geo];
 
-      num_bndry_ele =
-         n_bndry_topo["elements/connectivity"].dtype().number_of_elements();
-      num_bndry_ele = num_bndry_ele / num_idxs_per_bndry_ele;
+         const Node &n_bndry_conn = n_bndry_topo["elements/connectivity"];
+
+         // mfem requires ints, we could have int64s, etc convert if necessary
+         if ( n_bndry_conn.dtype().is_int() &&
+              n_bndry_conn.is_compact())
+         {
+            bndry_indices = n_bndry_conn.value();
+         }
+         else
+         {
+            Node &(n_bndry_conn_conv) =
+               n_conv["topologies"][bndry_topo_name]["elements/connectivity"];
+            n_bndry_conn.to_int_array(n_bndry_conn_conv);
+            bndry_indices = (n_bndry_conn_conv).value();
+
+         }
+
+         num_bndry_ele =
+            n_bndry_topo["elements/connectivity"].dtype().number_of_elements();
+         num_bndry_ele = num_bndry_ele / num_idxs_per_bndry_ele;
+      }
    }
    else
    {
@@ -688,8 +699,7 @@ ConduitDataCollection::MeshToBlueprintMesh(Mesh *mesh,
    n_topo["type"]  = "unstructured";
    n_topo["coordset"] = coordset_name;
 
-   Element::Type ele_type = static_cast<Element::Type>(mesh->GetElement(
-                                                          0)->GetType());
+   Element::Type ele_type = mesh->GetElementType(0);
 
    std::string ele_shape = ElementTypeToShapeName(ele_type);
 
@@ -763,8 +773,7 @@ ConduitDataCollection::MeshToBlueprintMesh(Mesh *mesh,
       n_bndry_topo["type"]     = "unstructured";
       n_bndry_topo["coordset"] = coordset_name;
 
-      Element::Type bndry_ele_type = static_cast<Element::Type>(mesh->GetBdrElement(
-                                                                   0)->GetType());
+      Element::Type bndry_ele_type = mesh->GetBdrElementType(0);
 
       std::string bndry_ele_shape = ElementTypeToShapeName(bndry_ele_type);
 
@@ -1152,6 +1161,8 @@ ConduitDataCollection::ElementTypeToShapeName(Element::Type element_type)
       case Element::QUADRILATERAL:  return "quad";
       case Element::TETRAHEDRON:    return "tet";
       case Element::HEXAHEDRON:     return "hex";
+      case Element::WEDGE:
+      default: ;
    }
 
    return "unknown";