Merge branch 'fusion-ldrd-dev' into epic-dev

.gitignore

@@ -145,14 +145,6 @@ examples/petsc/velocity.*
 examples/petsc/elastic_energy.*
 examples/petsc/mode_*
 
-examples/arpack/ex11
-examples/arpack/mode_*
-examples/arpack/ex11.mesh
-
-examples/spectra/ex11
-examples/spectra/mode_*
-examples/spectra/ex11.mesh
-
 examples/pumi/ex1
 examples/pumi/ex[126]p
 examples/pumi/refined.mesh
@@ -318,13 +310,7 @@ tests/convergence/prates
 tests/par-mesh-format/ex1p
 
 # VPATH builds
-build-*/
-
-# User config
-user-*
-
-# VSCode
-.vscode 
+build-*/*
 
 # PETSc automated build
 petsc-build/*

.gitlab-ci.yml

@@ -50,7 +50,6 @@ variables:
   AUTOTEST_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/autotest.git
   MFEM_DATA_REPO: https://github.com/mfem/data.git
   ARTIFACTS_DIR: artifacts
-  SLURM_OVERLAP: 1
 
 # The pipeline is divided into stages. Usually, jobs in a given stage wait for
 # the preceding stages to complete before to start. However, we sometimes use

.gitlab/lassen.yml

@@ -30,5 +30,5 @@
 
 opt_mpi_cuda_xl_16_1_1_8:
   variables:
-    SPEC: "%xl@16.1.1.8 +mpi +cuda cuda_arch=70"
+    SPEC: "%xl@16.1.1.8 +mpi +cuda cuda_arch=sm_70"
   extends: .build_and_test_on_lassen

CHANGELOG

@@ -10,26 +10,7 @@
 
 Version 4.3.1 (development)
 ===========================
-- Added support for hr-adaptivity using TMOP-based error estimator.
 
-- Adding lowest order Nedelec and Raviart-Thomas basis functions on wedge
-  shaped elements.
-
-- Added initial support for meshes with pyramidal elements, including several
-  pyramidal meshes in the data/ directory and support for the lowest order H1,
-  Nedelec, Raviart-Thomas, and L2 basis functions on pyramids.
-
-- Updated the hypre interface according to changes in hypre-2.22.1. The ADS
-  solver is now fully working on GPUs.
-
-- Tetrahedral meshes no longer need to be reordered to support high order
-  Nedelec basis functions. This will allow future support for Nedelec basis
-  functions on wedges and pyramids which are not amenable to reordering. The
-  ReorientTetMesh method of the Mesh and ParMesh classes has been deprecated.
-
-- Gmsh meshes where all elements have zero physical tag (the default Gmsh
-  output format if no physical groups are defined) are now successfully loaded,
-  and elements are reassigned attribute number 1.
 
 Version 4.3, released on July 29, 2021
 ======================================

CITATION.cff

@@ -1,66 +0,0 @@
-cff-version: 1.2.0
-message: "If you use MFEM, please cite it as follows."
-authors:
-- family-names: "MFEM Team"
-title: "MFEM: Modular Finite Element Methods [Software]"
-doi: 10.11578/dc.20171025.1248
-url: "https://mfem.org"
-preferred-citation:
-  type: article
-  authors:
-  - family-names: "Anderson"
-    given-names: "Robert"
-    orcid: "https://orcid.org/0000-0002-3508-9944"
-  - family-names: "Andrej"
-    given-names: "Julian"
-    orcid: "https://orcid.org/0000-0001-7661-4840"
-  - family-names: "Barker"
-    given-names: "Andrew"
-    orcid: "https://orcid.org/0000-0003-3572-911X"
-  - family-names: "Bramwell"
-    given-names: "Jamie"
-  - family-names: "Camier"
-    given-names: "Jean-Sylvain"
-    orcid: "https://orcid.org/0000-0003-2421-1999"
-  - family-names: "Cerveny"
-    given-names: "Jakub"
-    orcid: "https://orcid.org/0000-0003-4231-2531"
-  - family-names: "Dobrev"
-    given-names: "Veselin"
-    orcid: "https://orcid.org/0000-0003-1793-5622"
-  - family-names: "Dudouit"
-    given-names: "Yohann"
-    orcid: "https://orcid.org/0000-0001-5831-561X"
-  - family-names: "Fisher"
-    given-names: "Aaron"
-  - family-names: "Kolev"
-    given-names: "Tzanio"
-    orcid: "https://orcid.org/0000-0002-2810-3090"
-  - family-names: "Pazner"
-    given-names: "Will"
-    orcid: "https://orcid.org/0000-0003-4885-2934"
-  - family-names: "Stowell"
-    given-names: "Mark"
-    orcid: "https://orcid.org/0000-0002-5389-7435"
-  - family-names: "Tomov"
-    given-names: "Vladimir"
-    orcid: "https://orcid.org/0000-0002-1846-6816"
-  - family-names: "Akkerman"
-    given-names: "Ido"
-    orcid: "https://orcid.org/0000-0002-5937-0300"
-  - family-names: "Dahm"
-    given-names: "Johann"
-    orcid: "https://orcid.org/0000-0001-9657-3564"
-  - family-names: "Medina"
-    given-names: "David"
-  - family-names: "Zampini"
-    given-names: "Stefano"
-    orcid: "https://orcid.org/0000-0002-0435-0433"
-  doi: "10.1016/j.camwa.2020.06.009"
-  journal: "Computers \\& Mathematics with Applications"
-  month: 1
-  start: 42 # First page number
-  end: 74 # Last page number
-  title: "MFEM: A Modular Finite Element Methods Library"
-  volume: 81
-  year: 2021

CMakeLists.txt

@@ -267,6 +267,15 @@ if (MFEM_USE_SUNDIALS)
   find_package(SUNDIALS REQUIRED ${SUNDIALS_COMPONENTS})
 endif()
 
+# EPIC
+if (MFEM_USE_EPIC)
+  if (NOT (MFEM_USE_MPI AND MFEM_USE_SUNDIALS AND MFEM_USE_LAPACK) )
+    message(FATAL_ERROR " *** EPIC requires that MPI, SUNDIALS and LAPACK be enabled.")
+  else()
+    find_package(EPIC REQUIRED SUNDIALS NVector_Serial NVector_Parallel BLAS LAPACK)
+  endif()
+endif()
+
 # Mesquite
 if (MFEM_USE_MESQUITE)
   find_package(Mesquite REQUIRED)
@@ -428,7 +437,7 @@ endif()
 #    With newer versions of SuiteSparse which include METIS header using 64-bit
 #    integers, the METIS header (with 32-bit indices, as used by mfem) needs to
 #    be before SuiteSparse.
-set(MFEM_TPLS MPI_CXX OPENMP HYPRE BLAS LAPACK SuperLUDist METIS SuiteSparse SUNDIALS PETSC
+set(MFEM_TPLS MPI_CXX OPENMP HYPRE BLAS LAPACK SuperLUDist METIS SuiteSparse SUNDIALS EPIC PETSC
     SLEPC MESQUITE MUMPS STRUMPACK AXOM FMS CONDUIT Ginkgo GNUTLS GSLIB NETCDF
     MPFR PUMI HIOP POSIXCLOCKS MFEMBacktrace ZLIB OCCA CEED RAJA UMPIRE ADIOS2
     CUSPARSE MKL_CPARDISO AMGX CALIPER)

INSTALL

@@ -549,7 +549,7 @@ The specific libraries and their options are:
   Options: HYPRE_OPT, HYPRE_LIB.
   Versions: HYPRE >= 2.10.0b  (HYPRE built without CUDA)
             HYPRE >= 2.20.0   (HYPRE built with '--enable-mixedint')
-            HYPRE >= 2.22.1   (HYPRE built with CUDA)
+            HYPRE >= 2.22.0   (HYPRE built with CUDA)
 
 - METIS, used when MFEM_USE_METIS = YES. If using METIS 5, set
   MFEM_USE_METIS_5 = YES (default is to use METIS 4).

config/cmake/MFEMConfig.cmake.in

@@ -29,6 +29,7 @@ set(MFEM_USE_LEGACY_OPENMP @MFEM_USE_LEGACY_OPENMP@)
 set(MFEM_USE_MEMALLOC @MFEM_USE_MEMALLOC@)
 set(MFEM_TIMER_TYPE @MFEM_TIMER_TYPE@)
 set(MFEM_USE_SUNDIALS @MFEM_USE_SUNDIALS@)
+set(MFEM_USE_EPIC @MFEM_USE_EPIC@)
 set(MFEM_USE_MESQUITE @MFEM_USE_MESQUITE@)
 set(MFEM_USE_SUITESPARSE @MFEM_USE_SUITESPARSE@)
 set(MFEM_USE_SUPERLU @MFEM_USE_SUPERLU@)

config/cmake/config.hpp.in

@@ -165,6 +165,9 @@
 // Enable MFEM functionality based on the SUNDIALS libraries.
 #cmakedefine MFEM_USE_SUNDIALS
 
+// Enable MFEM functionality based on the EPIC libraries.
+#cmakedefine MFEM_USE_EPIC
+
 // Version of HYPRE used for building MFEM.
 #cmakedefine MFEM_HYPRE_VERSION @MFEM_HYPRE_VERSION@
 

config/cmake/modules/FindEPIC.cmake

@@ -0,0 +1,21 @@
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
+# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+# LICENSE and NOTICE for details. LLNL-CODE-806117.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability visit https://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the BSD-3 license. We welcome feedback and contributions, see file
+# CONTRIBUTING.md for details.
+
+# Defines the following variables:
+#   - EPIC_FOUND
+#   - EPIC_LIBRARIES
+#   - EPIC_INCLUDE_DIRS
+
+include(MfemCmakeUtilities)
+mfem_find_package(EPIC EPIC EPIC_DIR
+       "include" Epic.h "lib" epic1.0.0
+  "Paths to headers required by EPIC." "Libraries required by EPIC.")
+

config/cmake/modules/MfemCmakeUtilities.cmake

@@ -759,7 +759,7 @@ function(mfem_export_mk_files)
   set(CONFIG_MK_BOOL_VARS MFEM_USE_MPI MFEM_USE_METIS MFEM_USE_METIS_5
       MFEM_DEBUG MFEM_USE_EXCEPTIONS MFEM_USE_ZLIB MFEM_USE_LIBUNWIND
       MFEM_USE_LAPACK MFEM_THREAD_SAFE MFEM_USE_OPENMP MFEM_USE_LEGACY_OPENMP
-      MFEM_USE_MEMALLOC MFEM_USE_SUNDIALS MFEM_USE_MESQUITE MFEM_USE_SUITESPARSE
+      MFEM_USE_MEMALLOC MFEM_USE_SUNDIALS MFEM_USE_EPIC MFEM_USE_MESQUITE MFEM_USE_SUITESPARSE
       MFEM_USE_SUPERLU MFEM_USE_STRUMPACK MFEM_USE_GINKGO MFEM_USE_AMGX
       MFEM_USE_GNUTLS MFEM_USE_GSLIB MFEM_USE_NETCDF MFEM_USE_PETSC
       MFEM_USE_SLEPC MFEM_USE_MPFR MFEM_USE_SIDRE MFEM_USE_CONDUIT MFEM_USE_PUMI

config/config.hpp.in

@@ -85,18 +85,15 @@
 // Enable MFEM functionality based on the SUNDIALS libraries.
 // #define MFEM_USE_SUNDIALS
 
+// Enable MFEM functionality based on the EPIC libraries.
+// #define MFEM_USE_EPIC
+
 // Enable MFEM functionality based on the Mesquite library.
 // #define MFEM_USE_MESQUITE
 
 // Enable MFEM functionality based on the SuiteSparse library.
 // #define MFEM_USE_SUITESPARSE
 
-// Enable MFEM functionality based on the ARPACK library.
-// #define MFEM_USE_ARPACK
-
-// Enable MFEM functionality based on the SPECTRA library.
-// #define MFEM_USE_SPECTRA
-
 // Enable MFEM functionality based on the SuperLU library.
 // #define MFEM_USE_SUPERLU
 // #define MFEM_USE_SUPERLU5

config/config.mk.in

@@ -29,10 +29,9 @@ MFEM_USE_OPENMP        = @MFEM_USE_OPENMP@
 MFEM_USE_MEMALLOC      = @MFEM_USE_MEMALLOC@
 MFEM_TIMER_TYPE        = @MFEM_TIMER_TYPE@
 MFEM_USE_SUNDIALS      = @MFEM_USE_SUNDIALS@
+MFEM_USE_EPIC          = @MFEM_USE_EPIC@
 MFEM_USE_MESQUITE      = @MFEM_USE_MESQUITE@
 MFEM_USE_SUITESPARSE   = @MFEM_USE_SUITESPARSE@
-MFEM_USE_ARPACK        = @MFEM_USE_ARPACK@
-MFEM_USE_SPECTRA       = @MFEM_USE_SPECTRA@
 MFEM_USE_SUPERLU       = @MFEM_USE_SUPERLU@
 MFEM_USE_SUPERLU5      = @MFEM_USE_SUPERLU5@
 MFEM_USE_MUMPS         = @MFEM_USE_MUMPS@

config/defaults.cmake

@@ -30,6 +30,7 @@ option(MFEM_USE_OPENMP "Enable the OpenMP backend" OFF)
 option(MFEM_USE_LEGACY_OPENMP "Enable legacy OpenMP usage" OFF)
 option(MFEM_USE_MEMALLOC "Enable the internal MEMALLOC option." ON)
 option(MFEM_USE_SUNDIALS "Enable SUNDIALS usage" OFF)
+option(MFEM_USE_EPIC "Enable EPIC usage" OFF)
 option(MFEM_USE_MESQUITE "Enable MESQUITE usage" OFF)
 option(MFEM_USE_SUITESPARSE "Enable SuiteSparse usage" OFF)
 option(MFEM_USE_SUPERLU "Enable SuperLU_DIST usage" OFF)
@@ -115,6 +116,9 @@ set(SUNDIALS_DIR "${MFEM_DIR}/../sundials-5.0.0/instdir" CACHE PATH
 # set(SUNDIALS_REQUIRED_PACKAGES "SuiteSparse/KLU/AMD/BTF/COLAMD/config"
 #     CACHE STRING "Additional packages required by SUNDIALS.")
 
+set(EPIC_DIR "${MFEM_DIR}/../epic-cpp/instdir" CACHE PATH
+    "Path to the EPIC library.")
+
 set(MESQUITE_DIR "${MFEM_DIR}/../mesquite-2.99" CACHE PATH
     "Path to the Mesquite library.")
 

config/defaults.mk

@@ -122,6 +122,7 @@ MFEM_USE_LEGACY_OPENMP = NO
 MFEM_USE_MEMALLOC      = YES
 MFEM_TIMER_TYPE        = $(if $(NOTMAC),2,4)
 MFEM_USE_SUNDIALS      = NO
+MFEM_USE_EPIC          = NO
 MFEM_USE_MESQUITE      = NO
 MFEM_USE_SUITESPARSE   = NO
 MFEM_USE_SUPERLU       = NO
@@ -151,8 +152,6 @@ MFEM_USE_UMPIRE        = NO
 MFEM_USE_SIMD          = NO
 MFEM_USE_ADIOS2        = NO
 MFEM_USE_MKL_CPARDISO  = NO
-MFEM_USE_ARPACK        = NO
-MFEM_USE_SPECTRA       = NO
 
 # MPI library compile and link flags
 # These settings are used only when building MFEM with MPI + HIP
@@ -233,6 +232,11 @@ endif
 # If SUNDIALS was built with KLU:
 # MFEM_USE_SUITESPARSE = YES
 
+# EPIC library configuration
+MESQUITE_DIR = @MFEM_DIR@/../epic-cpp/instdir
+MESQUITE_OPT = -I$(EPIC_DIR)/include
+MESQUITE_LIB = -L$(EPIC_DIR)/lib -lepic1.0.0
+
 # MESQUITE library configuration
 MESQUITE_DIR = @MFEM_DIR@/../mesquite-2.99
 MESQUITE_OPT = -I$(MESQUITE_DIR)/include
@@ -330,19 +334,6 @@ NETCDF_LIB = $(XLINKER)-rpath,$(NETCDF_DIR)/lib -L$(NETCDF_DIR)/lib\
  $(XLINKER)-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib\
  -lnetcdf -lhdf5_hl -lhdf5 $(ZLIB_LIB)
 
-# ARPACK library configuration
-ARPACK_DIR = @MFEM_DIR@/../ARPACK
-ARPACK_OPT = -I$(ARPACK_DIR)
-ARPACK_LIB = -L$(ARPACK_DIR) -lparpack -larpack
-
-# EIGEN library configuration
-EIGEN_DIR = @MFEM_DIR@/../eigen
-EIGEN_OPT = -I$(EIGEN_DIR)
-
-# SPECTRA library configuration
-SPECTRA_DIR = @MFEM_DIR@/../spectra/include
-SPECTRA_OPT = -I$(SPECTRA_DIR) $(EIGEN_OPT)
-
 # PETSc library configuration (version greater or equal to 3.8 or the dev branch)
 PETSC_ARCH := arch-linux2-c-debug
 PETSC_DIR  := $(MFEM_DIR)/../petsc/$(PETSC_ARCH)

data/inline-pyramid.mesh

@@ -1,9 +0,0 @@
-MFEM INLINE mesh v1.0
-
-type = pyramid
-nx = 4
-ny = 4
-nz = 4
-sx = 1.0
-sy = 1.0
-sz = 1.0

data/octahedron.mesh

@@ -1,43 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-# PYRAMID     = 7
-#
-
-dimension
-3
-
-elements
-2
-1 7 4 3 2 1 0
-1 7 1 2 3 4 5
-
-boundary
-8
-1 2 0 2 1
-2 2 0 3 2
-3 2 0 4 3
-4 2 0 1 4
-5 2 1 2 5
-6 2 2 3 5
-7 2 3 4 5
-8 2 4 1 5
-
-vertices
-6
-3
-0 0 -1
-1 0 0
-0 1 0
--1 0 0
-0 -1 0
-0 0 1

data/ref-pyramid.mesh

@@ -1,38 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-# PYRAMID     = 7
-#
-
-dimension
-3
-
-elements
-1
-1 7 0 1 2 3 4
-
-boundary
-5
-1 3 3 2 1 0
-2 2 0 1 4
-3 2 1 2 4
-4 2 2 3 4
-5 2 3 0 4
-
-vertices
-5
-3
-0 0 0
-1 0 0
-1 1 0
-0 1 0
-0 0 1

data/sphere.geo

@@ -1,47 +0,0 @@
-Mesh.Algorithm = 6;
-
-lc = 0.1;
-Point(1) = {0.0,0.0,0.0,lc};
-Point(2) = {1,0.0,0.0,lc};
-Point(3) = {0,1,0.0,lc};
-Circle(1) = {2,1,3};
-Point(4) = {-1,0,0.0,lc};
-Point(5) = {0,-1,0.0,lc};
-Circle(2) = {3,1,4};
-Circle(3) = {4,1,5};
-Circle(4) = {5,1,2};
-Point(6) = {0,0,-1,lc};
-Point(7) = {0,0,1,lc};
-Circle(5) = {3,1,6};
-Circle(6) = {6,1,5};
-Circle(7) = {5,1,7};
-Circle(8) = {7,1,3};
-Circle(9) = {2,1,7};
-Circle(10) = {7,1,4};
-Circle(11) = {4,1,6};
-Circle(12) = {6,1,2};
-Curve Loop(13) = {2,8,-10};
-Surface(14) = {13};
-Curve Loop(15) = {10,3,7};
-Surface(16) = {15};
-Curve Loop(17) = {-8,-9,1};
-Surface(18) = {17};
-Curve Loop(19) = {-11,-2,5};
-Surface(20) = {19};
-Curve Loop(21) = {-5,-12,-1};
-Surface(22) = {21};
-Curve Loop(23) = {-3,11,6};
-Surface(24) = {23};
-Curve Loop(25) = {-7,4,9};
-Surface(26) = {25};
-Curve Loop(27) = {-4,12,-6};
-Surface(28) = {27};
-Surface Loop(29) = {28,26,16,14,20,24,22,18};
-Volume(30) = {29};
-
-Physical Surface(1) = {28,26,16,14,20,24,22,18};
-Physical Volume(2) = 30;
-
-// Generate 2D mesh
-Mesh 2;
-Mesh.MshFileVersion = 2.2;

examples/CMakeLists.txt

@@ -159,6 +159,11 @@ if (MFEM_USE_AMGX)
   add_subdirectory(amgx)
 endif()
 
+# Include the examples/epic directory if EPIC is enabled.
+if (MFEM_USE_EPIC)
+  add_subdirectory(epic)
+endif()
+
 # Include the examples/ginkgo directory if GINKGO is enabled.
 if (MFEM_USE_GINKGO)
   add_subdirectory(ginkgo)

examples/arpack/ex11.cpp

@@ -1,286 +0,0 @@
-//                       MFEM Example 11 - Serial Version
-//
-// Compile with: make ex11
-//
-// Sample runs:  ex11 -m ../data/square-disc.mesh
-//               ex11 -m ../data/star.mesh
-//               ex11 -m ../data/star-mixed.mesh
-//               ex11 -m ../data/periodic-annulus-sector.msh
-//               ex11 -m ../data/square-disc-p2.vtk -o 2
-//               ex11 -m ../data/square-disc-p3.mesh -o 3
-//               ex11 -m ../data/square-disc-nurbs.mesh -o -1
-//               ex11 -m ../data/disc-nurbs.mesh -o -1 -n 20
-//               ex11 -m ../data/star-surf.mesh
-//               ex11 -m ../data/square-disc-surf.mesh
-//               ex11 -m ../data/inline-segment.mesh
-//               ex11 -m ../data/inline-quad.mesh
-//               ex11 -m ../data/inline-tri.mesh
-//               ex11 -m ../data/amr-quad.mesh
-//               ex11 -m ../data/amr-hex.mesh
-//               ex11 -m ../data/mobius-strip.mesh -n 8
-//
-// Description:  This example code demonstrates the use of MFEM to solve the
-//               eigenvalue problem -Delta u = lambda u with homogeneous
-//               Dirichlet boundary conditions.
-//
-//               We compute a number of the lowest eigenmodes by discretizing
-//               the Laplacian and Mass operators using a FE space of the
-//               specified order, or an isoparametric/isogeometric space if
-//               order < 1 (quadratic for quadratic curvilinear mesh, NURBS for
-//               NURBS mesh, etc.)
-//
-//               The example highlights the use of the ARPACK eigenvalue solver
-//               (regular inverse mode). Reusing a single GLVis visualization
-//               window for multiple eigenfunctions is also illustrated.
-//
-//               We recommend viewing Example 1 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/star.mesh";
-   int ser_ref_levels = 3;
-   int order = 1;
-   int nev = 5;
-   double dbc_eig = 1e3;
-   bool visualization = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
-                  "Number of times to refine the mesh uniformly in serial.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree) or -1 for"
-                  " isoparametric space.");
-   args.AddOption(&nev, "-n", "--num-eigs",
-                  "Number of desired eigenmodes.");
-   args.AddOption(&dbc_eig, "-d", "--dbc-eig",
-                  "Eigenvalues associated with Dirichlet BC "
-                  "(should be larger than the maximum desired eigenvalue).");
-   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 (serial) mesh from the given mesh file on all processors. We
-   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
-   //    and volume meshes with the same code.
-   Mesh *mesh;
-   ifstream imesh(mesh_file);
-   if (!imesh)
-   {
-      cerr << "\nCan not open mesh file: " << mesh_file << '\n' << endl;
-      return 2;
-   }
-   mesh = new Mesh(imesh, 1, 1);
-   imesh.close();
-   int dim = mesh->Dimension();
-
-   // 3. Refine the serial mesh on all processors to increase the resolution. In
-   //    this example we do 'ref_levels' of uniform refinement (2 by default, or
-   //    specified on the command line with -rs).
-   for (int lev = 0; lev < ser_ref_levels; lev++)
-   {
-      mesh->UniformRefinement();
-   }
-
-   // 4. Define a finite element space on the mesh. Here we
-   //    use continuous Lagrange finite elements of the specified order. If
-   //    order < 1, we instead use an isoparametric/isogeometric space.
-   FiniteElementCollection *fec;
-   if (order > 0)
-   {
-      fec = new H1_FECollection(order, dim);
-   }
-   else if (mesh->GetNodes())
-   {
-      fec = mesh->GetNodes()->OwnFEC();
-   }
-   else
-   {
-      fec = new H1_FECollection(order = 1, dim);
-   }
-   FiniteElementSpace *fespace = new FiniteElementSpace(mesh, fec);
-   int size = fespace->GetVSize();
-
-   cout << "Number of unknowns: " << size << endl;
-
-   // 5. Set up the parallel bilinear forms a(.,.) and m(.,.) on the finite
-   //    element space. The first corresponds to the Laplacian operator -Delta,
-   //    while the second is a simple mass matrix needed on the right hand side
-   //    of the generalized eigenvalue problem below. The boundary conditions
-   //    are implemented by elimination with special values on the diagonal to
-   //    shift the Dirichlet eigenvalues out of the computational range. After
-   //    serial and parallel assembly we extract the corresponding parallel
-   //    matrices A and M.
-   ConstantCoefficient one(1.0);
-   Array<int> ess_bdr;
-   if (mesh->bdr_attributes.Size())
-   {
-      ess_bdr.SetSize(mesh->bdr_attributes.Max());
-      ess_bdr = 1;
-   }
-
-   BilinearForm *a = new BilinearForm(fespace);
-   a->AddDomainIntegrator(new DiffusionIntegrator(one));
-   if (mesh->bdr_attributes.Size() == 0)
-   {
-      // Add a mass term if the mesh has no boundary, e.g. periodic mesh or
-      // closed surface.
-      a->AddDomainIntegrator(new MassIntegrator(one));
-   }
-   a->Assemble();
-   if (mesh->bdr_attributes.Size() != 0)
-   {
-      a->EliminateEssentialBCDiag(ess_bdr, dbc_eig);
-   }
-   a->Finalize();
-
-   BilinearForm *m = new BilinearForm(fespace);
-   m->AddDomainIntegrator(new MassIntegrator(one));
-   m->Assemble();
-   if (mesh->bdr_attributes.Size() != 0)
-   {
-      // shift the eigenvalue corresponding to eliminated dofs to a large value
-      m->EliminateEssentialBCDiag(ess_bdr, 1.0);
-   }
-   m->Finalize();
-
-   // 6. Define and configure the ARPACK eigensolver
-   ArPackSym * arpack = new ArPackSym();
-   Solver    * solver = NULL;
-
-#ifndef MFEM_USE_SUITESPARSE
-   // 7. Define a simple symmetric Gauss-Seidel preconditioner and use it to
-   //    solve the system A X = B with PCG.
-   cout << "Building CGSolver" << endl;
-   GSSmoother M(m->SpMat());
-   CGSolver * cg_solver = new CGSolver;
-   cg_solver->SetPreconditioner(M);
-   cg_solver->SetRelTol(1.0e-12);
-   solver = cg_solver;
-#else
-   // 7. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
-   cout << "Building UMFPackSolver" << endl;
-   UMFPackSolver * umf_solver = new UMFPackSolver;
-   umf_solver->Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-   solver = umf_solver;
-#endif
-   solver->SetOperator(m->SpMat());
-
-   arpack->SetNumModes(nev);
-   arpack->SetMaxIter(400);
-   arpack->SetTol(1e-8);
-   arpack->SetMode(2);
-   arpack->SetPrintLevel(2);
-
-   arpack->SetOperator(*a);
-   arpack->SetMassMatrix(*m);
-   arpack->SetSolver(*solver);
-
-   // 8. Compute the eigenmodes and extract the array of eigenvalues. Define a
-   //    parallel grid function to represent each of the eigenmodes returned by
-   //    the solver.
-   Array<double> eigenvalues;
-   arpack->Solve();
-   arpack->GetEigenvalues(eigenvalues);
-
-   cout << endl;
-   std::ios::fmtflags old_fmt = cout.flags();
-   cout.setf(std::ios::scientific);
-   std::streamsize old_prec = cout.precision(14);
-   for (int i=0; i<nev; i++)
-   {
-      cout << "Eigenvalue lambda   " << eigenvalues[i] << endl;
-   }
-   cout.precision(old_prec);
-   cout.flags(old_fmt);
-   cout << endl;
-
-   GridFunction x(fespace);
-
-   // 9. Save the refined mesh and the modes in parallel. This output can be
-   //    viewed later using GLVis: "glvis -np <np> -m mesh -g mode".
-   {
-      ostringstream mesh_name, mode_name;
-      mesh_name << "ex11.mesh";
-
-      ofstream mesh_ofs(mesh_name.str().c_str());
-      mesh_ofs.precision(8);
-      mesh->Print(mesh_ofs);
-
-      for (int i=0; i<nev; i++)
-      {
-         // convert eigenvector from HypreParVector to ParGridFunction
-         x = arpack->GetEigenvector(i);
-
-         mode_name << "mode_" << setfill('0') << setw(2) << i;
-
-         ofstream mode_ofs(mode_name.str().c_str());
-         mode_ofs.precision(8);
-         x.Save(mode_ofs);
-         mode_name.str("");
-      }
-   }
-
-   // 10. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream mode_sock(vishost, visport);
-      mode_sock.precision(8);
-
-      for (int i=0; i<nev; i++)
-      {
-         cout << "Eigenmode " << i+1 << '/' << nev
-              << ", Lambda = " << eigenvalues[i] << endl;
-
-         // convert eigenvector from HypreParVector to ParGridFunction
-         x = arpack->GetEigenvector(i);
-
-         mode_sock << "solution\n" << *mesh << x << flush
-                   << "window_title 'Eigenmode " << i+1 << '/' << nev
-                   << ", Lambda = " << eigenvalues[i] << "'" << endl;
-
-         char c;
-         cout << "press (q)uit or (c)ontinue --> " << flush;
-         cin >> c;
-
-         if (c != 'c')
-         {
-            break;
-         }
-      }
-      mode_sock.close();
-   }
-
-   // 11. Free the used memory.
-   delete arpack;
-   delete solver;
-   delete m;
-   delete a;
-
-   delete fespace;
-   if (order > 0)
-   {
-      delete fec;
-   }
-   delete mesh;
-
-   return 0;
-}

examples/caliper/ex1.cpp

@@ -206,9 +206,9 @@ int main(int argc, char *argv[])
    cout << "Size of linear system: " << A->Height() << endl;
 
    // 11. Solve the linear system A X = B.
+   MFEM_PERF_BEGIN("Solve A X=B");
    if (!pa)
    {
-      MFEM_PERF_SCOPE("Solve A X=B (FA)");
 #ifndef MFEM_USE_SUITESPARSE
       // Use a simple symmetric Gauss-Seidel preconditioner with PCG.
       GSSmoother M((SparseMatrix&)(*A));
@@ -223,7 +223,6 @@ int main(int argc, char *argv[])
    }
    else // Jacobi preconditioning in partial assembly mode
    {
-      MFEM_PERF_SCOPE("Solve A X=B (PA)");
       if (UsesTensorBasis(fespace))
       {
          OperatorJacobiSmoother M(a, ess_tdof_list);
@@ -234,6 +233,7 @@ int main(int argc, char *argv[])
          CG(*A, B, X, 1, 400, 1e-12, 0.0);
       }
    }
+   MFEM_PERF_END("Solve A X=B");
    // 12. Recover the solution as a finite element grid function.
    a.RecoverFEMSolution(X, b, x);
 

examples/caliper/ex1p.cpp

@@ -231,29 +231,28 @@ int main(int argc, char *argv[])
    // 13. Solve the linear system A X = B.
    //     * With full assembly, use the BoomerAMG preconditioner from hypre.
    //     * With partial assembly, use Jacobi smoothing, for now.
+   MFEM_PERF_BEGIN("Solve A X = B");
+   Solver *prec = NULL;
+   if (pa)
    {
-      MFEM_PERF_SCOPE("Solve A X=B");
-      Solver *prec = NULL;
-      if (pa)
+      if (UsesTensorBasis(fespace))
       {
-         if (UsesTensorBasis(fespace))
-         {
-            prec = new OperatorJacobiSmoother(a, ess_tdof_list);
-         }
+         prec = new OperatorJacobiSmoother(a, ess_tdof_list);
       }
-      else
-      {
-         prec = new HypreBoomerAMG;
-      }
-      CGSolver cg(MPI_COMM_WORLD);
-      cg.SetRelTol(1e-12);
-      cg.SetMaxIter(2000);
-      cg.SetPrintLevel(1);
-      if (prec) { cg.SetPreconditioner(*prec); }
-      cg.SetOperator(*A);
-      cg.Mult(B, X);
-      delete prec;
    }
+   else
+   {
+      prec = new HypreBoomerAMG;
+   }
+   CGSolver cg(MPI_COMM_WORLD);
+   cg.SetRelTol(1e-12);
+   cg.SetMaxIter(2000);
+   cg.SetPrintLevel(1);
+   if (prec) { cg.SetPreconditioner(*prec); }
+   cg.SetOperator(*A);
+   cg.Mult(B, X);
+   delete prec;
+   MFEM_PERF_END("Solve A X = B");
    // 14. Recover the parallel grid function corresponding to X. This is the
    //     local finite element solution on each processor.
    a.RecoverFEMSolution(X, b, x);

examples/epic/CMakeLists.txt

@@ -0,0 +1,64 @@
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
+# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+# LICENSE and NOTICE for details. LLNL-CODE-806117.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability visit https://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the BSD-3 license. We welcome feedback and contributions, see file
+# CONTRIBUTING.md for details.
+
+set(EPIC_EXAMPLES_SRCS)
+list(APPEND EPIC_EXAMPLES_SRCS
+  ex16.cpp
+  )
+
+if (MFEM_USE_MPI)
+list(APPEND EPIC_EXAMPLES_SRCS
+    ex16p.cpp
+    )
+endif()
+
+# Include the source directory where mfem.hpp and mfem-performance.hpp are.
+include_directories(BEFORE ${PROJECT_BINARY_DIR})
+
+# Add "test_epic" target, see below.
+add_custom_target(test_epic
+  ${CMAKE_CTEST_COMMAND} -R epic USES_TERMINAL)
+
+# Add one executable per cpp file, adding "epic_" as prefix. Sets
+# "test_epic" as a target that depends on the given examples.
+set(PFX epic_)
+add_mfem_examples(EPIC_EXAMPLES_SRCS ${PFX} "" test_epic)
+
+# Testing.
+# The EPIC tests can be run separately using the target "test_epic"
+# which builds the examples and runs:
+#   ctest -R epic
+
+# Example 16: use the default options
+
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${EPIC_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: ${THIS_TEST_OPTIONS}")
+
+  if (NOT (${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} ${MFEM_MPI_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()
+

examples/epic/README

@@ -0,0 +1,17 @@
+                    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 EPIC suite of time integration.
+
+To build these examples, make sure that MFEM is configured with the option
+"MFEM_USE_EPIC = YES".
+
+We recommend comparing the original example codes with the corresponding files
+in the current directory.

examples/epic/ex16.cpp

@@ -0,0 +1,610 @@
+//                                MFEM Example 16
+//                               EPIC Modification
+//
+// Compile with: make ex16
+//
+// Sample runs:  ex16
+//               ex16 -m ../../data/inline-tri.mesh
+//               ex16 -m ../../data/disc-nurbs.mesh -tf 2
+//               ex16 -s 8 -a 1.0 -k 0.0 -dt 1e-4 -tf 5e-2 -vs 25
+//               ex16 -m ../../data/fichera-q2.mesh
+//               ex16 -m ../../data/escher.mesh
+//               ex16 -m ../../data/beam-tet.mesh -tf 10 -dt 0.1
+//               ex16 -m ../../data/amr-quad.mesh -o 4 -r 0
+//               ex16 -m ../../data/amr-hex.mesh -o 2 -r 0
+//
+// Description:  This example solves a time dependent nonlinear heat equation
+//               problem of the form du/dt = C(u), with a non-linear diffusion
+//               operator C(u) = \nabla \cdot (\kappa + \alpha u) \nabla u.
+//
+//               We recommend viewing examples 2, 9 and 10 before viewing this
+//               example.
+
+#include "mfem.hpp"
+#include <fstream>
+#include <iostream>
+
+using namespace std;
+using namespace mfem;
+
+class ImplicitSolveOperator;
+class JacobianOperator;
+
+/** After spatial discretization, the conduction model can be written as:
+ *
+ *     du/dt = M^{-1}(-K(u) u)
+ *
+ *  where u is the vector representing the temperature, M is the mass matrix,
+ *  and K is the diffusion operator with diffusivity depending on u:
+ *  (\kappa + \alpha u).
+ *
+ *  Class ConductionOperator represents the right-hand side of the above ODE.
+ */
+class ConductionOperator : public TimeDependentOperator
+{
+protected:
+   FiniteElementSpace &fespace;
+   Array<int> ess_tdof_list; // this list remains empty for pure Neumann b.c.
+
+   BilinearForm *M;
+   mutable BilinearForm *K;
+   mutable BilinearForm *dK;
+   mutable BilinearForm *J_K;
+
+   SparseMatrix Mmat;
+   mutable SparseMatrix J_K_mat;
+
+   mutable CGSolver M_solver; // Krylov solver for inverting the mass matrix M
+   DSmoother M_prec;  // Preconditioner for the mass matrix M
+
+   CGSolver Jg_solver; // Krylov solver for inverting the Jacobian in the nonlinear solve
+   DSmoother Jg_prec;  // Preconditioner for the Jacobian Jg
+
+   NewtonSolver newton_solver;
+   mutable JacobianOperator *jac;
+
+   double alpha, kappa;
+
+   mutable Vector z; // auxiliary vector
+
+   mutable int nRhsMult, nSetJac, nJacMult, nImpSolve, nImpIter, nImpMult, nImpSet;
+
+public:
+   Vector u0;
+
+   ConductionOperator(FiniteElementSpace &f, double alpha, double kappa, const Vector &u);
+
+   void UpdateStats();
+   void PrintStats(ostream& out);
+
+   void ExtractJacobians(const Vector& x, std::ostream &out, std::ostream &out2);
+
+   BilinearForm& GetKLambda(const Vector& u) const;
+   BilinearForm& GetdKLambda(const Vector& u) const;
+
+   virtual void Mult(const Vector &u, Vector &du_dt) const;
+   virtual Operator& GetGradient(const Vector &k) const;
+
+   virtual void ImplicitSolve(const double dt, const Vector &x, Vector &k);
+
+   virtual ~ConductionOperator();
+};
+
+class ImplicitSolveOperator : public Operator
+{
+private:
+   double dt;
+   const Vector* x;
+   ConductionOperator* oper;
+
+   const SparseMatrix* M;
+   mutable SparseMatrix* Jg;
+
+   mutable Vector u, z;
+   mutable int nMult, nSet;
+
+public:
+   ImplicitSolveOperator(ConductionOperator* oper, const SparseMatrix* M, double dt, const Vector* x);
+
+   int GetnMult() { return nMult; }
+   int GetnSet() { return nSet; }
+   virtual void Mult(const Vector &k, Vector &gk) const;
+   virtual Operator &GetGradient(const Vector &k) const;
+};
+
+class JacobianOperator : public Operator
+{
+private:
+   Operator* J;
+   Operator* M_solver;
+
+   mutable int nMult;
+   mutable Vector z;
+public:
+   JacobianOperator(Operator* J, Operator* M_solver);
+
+   int GetnMult() { return nMult; }
+
+   void ExtractJacobian(const Vector& x, std::ostream &out);
+   virtual void Mult(const Vector &k, Vector &gk) const;
+};
+
+double InitialTemperature(const Vector &x);
+
+int main(int argc, char *argv[])
+{
+   // 1. Parse command-line options.
+   const char *mesh_file = "../../data/star.mesh";
+   int ref_levels = 2;
+   int order = 2;
+   int ode_solver_type = 8; // Exponential Euler
+   double t_final = 0.5;
+   double dt = 1.0e-2;
+   double alpha = 1.0e-2;
+   double kappa = 0.5;
+   bool visualization = true;
+   bool visit = false;
+   int vis_steps = 5;
+
+   int precision = 8;
+   cout.precision(precision);
+
+   OptionsParser args(argc, argv);
+   args.AddOption(&mesh_file, "-m", "--mesh",
+                  "Mesh file to use.");
+   args.AddOption(&ref_levels, "-r", "--refine",
+                  "Number of times to refine the mesh uniformly.");
+   args.AddOption(&order, "-o", "--order",
+                  "Order (degree) of the finite elements.");
+   args.AddOption(&ode_solver_type, "-s", "--ode-solver",
+                  "ODE solver:\n\t"
+                  "1  - Forward Euler,\n\t"
+                  "2  - RK2,\n\t"
+                  "3  - RK3 SSP,\n\t"
+                  "4  - RK4,\n\t"
+                  "5  - Backward Euler,\n\t"
+                  "6  - SDIRK 2,\n\t"
+                  "7  - SDIRK 3,\n\t"
+                  "8  - EPIC (exponential euler)\n\t");
+   args.AddOption(&t_final, "-tf", "--t-final",
+                  "Final time; start time is 0.");
+   args.AddOption(&dt, "-dt", "--time-step",
+                  "Time step.");
+   args.AddOption(&alpha, "-a", "--alpha",
+                  "Alpha coefficient.");
+   args.AddOption(&kappa, "-k", "--kappa",
+                  "Kappa coefficient offset.");
+   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
+                  "--no-visualization",
+                  "Enable or disable GLVis visualization.");
+   args.AddOption(&visit, "-visit", "--visit-datafiles", "-no-visit",
+                  "--no-visit-datafiles",
+                  "Save data files for VisIt (visit.llnl.gov) visualization.");
+   args.AddOption(&vis_steps, "-vs", "--visualization-steps",
+                  "Visualize every n-th timestep.");
+   args.Parse();
+   if (!args.Good())
+   {
+      args.PrintUsage(cout);
+      return 1;
+   }
+   if (ode_solver_type < 1 || ode_solver_type > 9)
+   {
+      cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
+      return 3;
+   }
+   args.PrintOptions(cout);
+
+   // 2. Read the mesh from the given mesh file. We can handle triangular,
+   //    quadrilateral, tetrahedral and hexahedral meshes with the same code.
+   Mesh *mesh = new Mesh(mesh_file, 1, 1);
+   int dim = mesh->Dimension();
+
+   // 3. Refine the mesh to increase the resolution. In this example we do
+   //    'ref_levels' of uniform refinement, where 'ref_levels' is a
+   //    command-line parameter.
+   for (int lev = 0; lev < ref_levels; lev++)
+   {
+      mesh->UniformRefinement();
+   }
+
+   // 4. Define the vector finite element space representing the current and the
+   //    initial temperature, u_ref.
+   H1_FECollection fe_coll(order, dim);
+   FiniteElementSpace fespace(mesh, &fe_coll);
+
+   int fe_size = fespace.GetTrueVSize();
+   cout << "Number of temperature unknowns: " << fe_size << endl;
+
+   GridFunction u_gf(&fespace);
+
+   // 5. Set the initial conditions for u. All boundaries are considered
+   //    natural.
+   FunctionCoefficient u_0(InitialTemperature);
+   u_gf.ProjectCoefficient(u_0);
+   Vector u;
+   u_gf.GetTrueDofs(u);
+
+   // 6. Initialize the conduction operator and the visualization.
+   ConductionOperator oper(fespace, alpha, kappa, u);
+
+   u_gf.SetFromTrueDofs(u);
+   {
+      ofstream omesh("ex16.mesh");
+      omesh.precision(precision);
+      mesh->Print(omesh);
+      ofstream osol("ex16-init.gf");
+      osol.precision(precision);
+      u_gf.Save(osol);
+   }
+
+   VisItDataCollection visit_dc("Example16", mesh);
+   visit_dc.RegisterField("temperature", &u_gf);
+   if (visit)
+   {
+      visit_dc.SetCycle(0);
+      visit_dc.SetTime(0.0);
+      visit_dc.Save();
+   }
+
+   socketstream sout;
+   if (visualization)
+   {
+      char vishost[] = "localhost";
+      int  visport   = 19916;
+      sout.open(vishost, visport);
+      if (!sout)
+      {
+         cout << "Unable to connect to GLVis server at "
+              << vishost << ':' << visport << endl;
+         visualization = false;
+         cout << "GLVis visualization disabled.\n";
+      }
+      else
+      {
+         sout.precision(precision);
+         sout << "solution\n" << *mesh << u_gf;
+         sout << "pause\n";
+         sout << flush;
+         cout << "GLVis visualization paused."
+              << " Press space (in the GLVis window) to resume it.\n";
+      }
+   }
+
+   // 7. Define the ODE solver used for time integration.
+   double t = 0.0;
+   ODESolver *ode_solver = NULL;
+   switch (ode_solver_type)
+   {
+      // MFEM explicit methods
+      case 1: ode_solver = new ForwardEulerSolver; break;
+      case 2: ode_solver = new RK2Solver(0.5); break; // midpoint method
+      case 3: ode_solver = new RK3SSPSolver; break;
+      case 4: ode_solver = new RK4Solver; break;
+      // MFEM implicit L-stable methods
+      case 5: ode_solver = new BackwardEulerSolver; break;
+      case 6: ode_solver = new SDIRK23Solver(2); break;
+      case 7: ode_solver = new SDIRK33Solver; break;
+      // EPIC 
+      case 8: ode_solver = new EPI2();break;
+      case 9: ode_solver = new EPIRK4(); break;
+   }
+
+   // Initialize integrators
+   ode_solver->Init(oper);
+
+   // 8. Perform time-integration (looping over the time iterations, ti, with a
+   //    time-step dt).
+   cout << "Integrating the ODE ..." << endl;
+   tic_toc.Clear();
+   tic_toc.Start();
+
+   /*ofstream out_jac_an("jacobian_an.txt");
+   ofstream out_jac_fd("jacobian_fd.txt");
+   oper.ExtractJacobians(u, out_jac_fd, out_jac_an);*/
+
+   bool last_step = false;
+   int ti;
+   for (ti = 1; !last_step; ti++)
+   {
+      double dt_real = min(dt, t_final - t);
+
+      // Note that since we are using the "one-step" mode of the SUNDIALS
+      // solvers, they will, generally, step over the final time and will not
+      // explicitly perform the interpolation to t_final as they do in the
+      // "normal" step mode.
+      ode_solver->Step(u, t, dt_real);
+
+      oper.UpdateStats();
+
+      last_step = (t >= t_final - 1e-8*dt);
+
+      if (last_step || (ti % vis_steps) == 0) {
+         cout << "step " << ti << ", t = " << t << endl;
+
+         u_gf.SetFromTrueDofs(u);
+         if (visualization) {
+            sout << "solution\n" << *mesh << u_gf << flush;
+         }
+
+         if (visit) {
+            visit_dc.SetCycle(ti);
+            visit_dc.SetTime(t);
+            visit_dc.Save();
+         }
+      }
+   }
+   tic_toc.Stop();
+   double comp_time = tic_toc.RealTime();
+   cout << "Done, " << comp_time << "s." << endl;
+
+   // 9. Save the final solution. This output can be viewed later using GLVis:
+   //    "glvis -m ex16.mesh -g ex16-final.gf".
+   {
+      ofstream osol("ex16-final.gf");
+      osol.precision(precision);
+      u_gf.Save(osol);
+
+      ofstream ostats("ex16-stats.txt");
+      ostats << "time " << comp_time << endl;
+      oper.PrintStats(ostats);
+   }
+
+   // 10. Free the used memory.
+   delete ode_solver;
+   delete mesh;
+
+   return 0;
+}
+
+ConductionOperator::ConductionOperator(FiniteElementSpace &f, double al, double kap, const Vector &u)
+   : TimeDependentOperator(f.GetTrueVSize(), 0.0), fespace(f), M(NULL), K(NULL), dK(NULL), J_K(NULL), jac(NULL), z(height), u0(height),
+     nRhsMult(0), nSetJac(0), nJacMult(0), nImpSolve(0), nImpIter(0), nImpMult(0), nImpSet(0)
+{
+   const double rel_tol = 1e-8;
+
+   M = new BilinearForm(&fespace);
+   M->AddDomainIntegrator(new MassIntegrator());
+   M->Assemble();
+   M->FormSystemMatrix(ess_tdof_list, Mmat);
+
+   M_solver.iterative_mode = false;
+   M_solver.SetRelTol(rel_tol);
+   M_solver.SetAbsTol(0.0);
+   M_solver.SetMaxIter(50);
+   M_solver.SetPrintLevel(0);
+   M_solver.SetPreconditioner(M_prec);
+   M_solver.SetOperator(Mmat);
+
+   Jg_solver.SetRelTol(rel_tol);
+   Jg_solver.SetAbsTol(0.0);
+   Jg_solver.SetMaxIter(50);
+   Jg_solver.SetPrintLevel(0);
+   Jg_solver.SetPreconditioner(Jg_prec);
+
+   newton_solver.SetMaxIter(10);
+   newton_solver.SetRelTol(rel_tol);
+   newton_solver.SetPrintLevel(-1);
+   newton_solver.SetSolver(Jg_solver);
+   newton_solver.SetMaxIter(100);
+   newton_solver.iterative_mode = false;
+
+   alpha = al;
+   kappa = kap;
+}
+
+void ConductionOperator::UpdateStats()
+{
+   if (jac)
+   {
+      nJacMult += jac->GetnMult();
+   }
+}
+
+void ConductionOperator::PrintStats(ostream &out)
+{
+   out  << "nRhsMult " << nRhsMult << endl
+        << "nSetJac " << nSetJac << endl
+        << "nJacMult " << nJacMult  << endl
+        << "nImplicitSolve " << nImpSolve  << endl
+        << "nImplicitIter " << nImpIter << endl
+        << "nImplicitMult " << nImpMult << endl
+        << "nImplicitSet " << nImpSet << endl;
+}
+
+BilinearForm& ConductionOperator::GetKLambda(const Vector &u) const
+{
+   GridFunction conductivity_gf(&fespace);
+   conductivity_gf.SetFromTrueDofs(u);
+   for (int i = 0; i < conductivity_gf.Size(); i++)
+   {
+      conductivity_gf(i) = kappa + alpha*conductivity_gf(i);
+   }
+
+   GridFunctionCoefficient conductivity_coeff(&conductivity_gf);
+
+   delete K;
+   K = new BilinearForm(&fespace);
+   K->AddDomainIntegrator(new DiffusionIntegrator(conductivity_coeff));
+   K->Assemble();
+
+   return *K;
+}
+
+BilinearForm& ConductionOperator::GetdKLambda(const Vector &u) const
+{
+   GridFunction conductivity_gf(&fespace);
+   conductivity_gf.SetFromTrueDofs(u);
+   for (int i = 0; i < conductivity_gf.Size(); i++)
+   {
+      conductivity_gf(i) = kappa + alpha*conductivity_gf(i);
+   }
+
+   // Define diffusion form with conductivity = kappa(u0)
+   GridFunctionCoefficient conductivity_coeff(&conductivity_gf);
+
+   // Define advection form with velocity = grad kappa(u0)
+   GridFunction neg_cond_gf(conductivity_gf);
+   neg_cond_gf.Neg();
+   GradientGridFunctionCoefficient velocity_coeff(&neg_cond_gf);
+
+   delete dK;
+   dK = new BilinearForm(&fespace);
+
+   dK->AddDomainIntegrator(new DiffusionIntegrator(conductivity_coeff));
+   dK->AddDomainIntegrator(new MixedScalarWeakDivergenceIntegrator(velocity_coeff));
+   dK->Assemble();
+
+   return *dK;
+}
+
+void ConductionOperator::Mult(const Vector &u, Vector &du_dt) const
+{
+   // Compute:
+   //    du_dt = M^{-1}*-K(u)
+   // for du_dt
+   GetKLambda(u);
+   K->Mult(u, z);
+   z.Neg(); // z = -z
+   M_solver.Mult(z, du_dt);
+   nRhsMult++;
+}
+
+void ConductionOperator::ImplicitSolve(const double dt, const Vector &x, Vector &k)
+{
+   ImplicitSolveOperator imp_oper(this, &this->Mmat, dt, &x);
+   newton_solver.SetOperator(imp_oper);
+
+   Vector zero; // empty vector is interpreted as zero r.h.s. by NewtonSolver
+   newton_solver.Mult(zero, k);
+   MFEM_VERIFY(newton_solver.GetConverged(), "Newton solver did not converge.");
+
+   nImpSolve++;
+   nImpMult += imp_oper.GetnMult();
+   nImpSet  += imp_oper.GetnSet();
+   nImpIter += newton_solver.GetNumIterations();
+}
+
+Operator &ConductionOperator::GetGradient(const Vector &u) const
+{
+   delete jac;
+   GetdKLambda(u);
+   jac = new JacobianOperator(dK, &M_solver);
+
+   nSetJac++;
+
+   return *jac;
+}
+
+ConductionOperator::~ConductionOperator()
+{
+   delete M;
+   delete K;
+   delete dK;
+   delete J_K;
+   delete jac;
+}
+
+ImplicitSolveOperator::ImplicitSolveOperator(ConductionOperator *oper_, const SparseMatrix* M_, double dt_, const Vector* x_):
+   Operator(oper_->Height()), oper(oper_), M(M_), dt(dt_), x(x_), u(height), z(height), Jg(NULL), nMult(0), nSet(0)
+{ }
+
+
+void ImplicitSolveOperator::Mult(const Vector& y, Vector& gy) const
+{
+   // Compute gy = g(y) = My + dt K(lambda(u)) u
+   // with u = x + dt y
+   add(*x, dt, y, u);
+   BilinearForm& K = oper->GetKLambda(u);
+   K.Mult(u, gy);
+
+   M->AddMult(y, gy);
+
+   nMult++;
+}
+
+Operator& ImplicitSolveOperator::GetGradient(const Vector &k) const
+{
+   add(*x, dt, k, u);
+
+   BilinearForm& dK = oper->GetdKLambda(u);
+   Array<int> ess_tdof_list;
+   SparseMatrix dK_mat;
+   dK.FormSystemMatrix(ess_tdof_list, dK_mat);
+
+   delete Jg;
+   Jg = Add(1.0, *M, dt, dK_mat);
+
+   nSet++;
+   return *Jg;
+}
+
+JacobianOperator::JacobianOperator(Operator* J_, Operator* M_solver_):
+   Operator(M_solver_->Height()), J(J_), M_solver(M_solver_), z(height), nMult(0)
+{ }
+
+void JacobianOperator::Mult(const Vector &v, Vector &Jv) const
+{
+   Vector temp(v);
+   J->Mult(v, z);
+   z.Neg(); // z = -z
+   M_solver->Mult(z, Jv);
+   nMult++;
+}
+
+
+void ConductionOperator::ExtractJacobians(const Vector& x, std::ostream &out, std::ostream &out2)
+{
+   int n = x.Size();
+
+   Vector e(n);
+   e = 0.0;
+
+   double eps = 1e-8;
+   Vector fx(n), fx_eps(n), x_eps(n);
+   Mult(x, fx);
+
+   DenseMatrix J(n);
+
+   for (int i = 0; i < n; i++)
+   {
+      e[i] = 1.0;
+      add(x, eps, e, x_eps);
+      Mult(x_eps, fx_eps);
+      fx_eps -= fx;
+      fx_eps /= eps;
+      J.SetCol(i, fx_eps);
+      e[i] = 0.0;
+   }
+
+   J.PrintMatlab(out);
+   GetGradient(x);
+   jac->ExtractJacobian(x, out2);
+}
+
+void JacobianOperator::ExtractJacobian(const Vector& x, std::ostream &out)
+{
+   int n = z.Size();
+
+   Vector e(n);
+   e= 0.0;
+
+   Vector J_i(n);
+   DenseMatrix J(n);
+
+   for (int i = 0; i < n; i++)
+   {
+      e[i] = 1.0;
+      Mult(e, J_i);
+      J.SetCol(i, J_i);
+      e[i] = 0.0;
+   }
+
+   J.PrintMatlab(out);
+}
+
+double InitialTemperature(const Vector &x)
+{
+   if (x.Norml2() < 0.5) { return 2.0; }
+   else                  { return 1.0; }
+}

examples/epic/ex16p.cpp

@@ -0,0 +1,494 @@
+//                         MFEM Example 16 - Parallel Version
+//                             SUNDIALS Modification
+//
+// Compile with: make ex16p
+//
+// Sample runs:
+//     mpirun -np 4 ex16p
+//     mpirun -np 4 ex16p -m ../../data/inline-tri.mesh
+//     mpirun -np 4 ex16p -m ../../data/disc-nurbs.mesh -tf 2
+//     mpirun -np 4 ex16p -s 12 -a 0.0 -k 1.0
+//     mpirun -np 4 ex16p -s 8 -a 1.0 -k 0.0 -dt 4e-6 -tf 2e-2 -vs 50
+//     mpirun -np 8 ex16p -s 9 -a 0.5 -k 0.5 -o 4 -dt 8e-6 -tf 2e-2 -vs 50
+//     mpirun -np 4 ex16p -s 10 -dt 2.0e-4 -tf 4.0e-2
+//     mpirun -np 16 ex16p -m ../../data/fichera-q2.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
+//     mpirun -np 4 ex16p -m ../../data/amr-hex.mesh -o 2 -rs 0 -rp 0
+//
+// Description:  This example solves a time dependent nonlinear heat equation
+//               problem of the form du/dt = C(u), with a non-linear diffusion
+//               operator C(u) = \nabla \cdot (\kappa + \alpha u) \nabla u.
+//
+//               We recommend viewing examples 2, 9 and 10 before viewing this
+//               example.
+
+#include "mfem.hpp"
+#include <fstream>
+#include <iostream>
+
+using namespace std;
+using namespace mfem;
+
+/** After spatial discretization, the conduction model can be written as:
+ *
+ *     du/dt = M^{-1}(-Ku)
+ *
+ *  where u is the vector representing the temperature, M is the mass matrix,
+ *  and K is the diffusion operator with diffusivity depending on u:
+ *  (\kappa + \alpha u).
+ *
+ *  Class ConductionOperator represents the right-hand side of the above ODE.
+ */
+class ConductionOperator : public TimeDependentOperator
+{
+protected:
+   ParFiniteElementSpace &fespace;
+   Array<int> ess_tdof_list; // this list remains empty for pure Neumann b.c.
+
+   ParBilinearForm *M;
+   ParBilinearForm *K;
+
+   HypreParMatrix Mmat;
+   HypreParMatrix Kmat;
+   HypreParMatrix *T; // T = M + dt K
+   double current_dt;
+
+   CGSolver M_solver;    // Krylov solver for inverting the mass matrix M
+   HypreSmoother M_prec; // Preconditioner for the mass matrix M
+
+   CGSolver T_solver;    // Implicit solver for T = M + dt K
+   HypreSmoother T_prec; // Preconditioner for the implicit solver
+
+   double alpha, kappa;
+
+   mutable Vector z; // auxiliary vector
+
+public:
+   ConductionOperator(ParFiniteElementSpace &f, double alpha, double kappa,
+                      const Vector &u);
+
+   virtual void Mult(const Vector &u, Vector &du_dt) const;
+
+   /** Solve the Backward-Euler equation: k = f(u + dt*k, t), for the unknown k.
+       This is the only requirement for high-order SDIRK implicit integration.*/
+   virtual void ImplicitSolve(const double dt, const Vector &u, Vector &k);
+
+   /** Setup the system (M + dt K) x = M b. This method is used by the implicit
+       SUNDIALS solvers. */
+   virtual int SUNImplicitSetup(const Vector &x, const Vector &fx,
+                                int jok, int *jcur, double gamma);
+
+   /** Solve the system (M + dt K) x = M b. This method is used by the implicit
+       SUNDIALS solvers. */
+   virtual int SUNImplicitSolve(const Vector &b, Vector &x, double tol);
+
+   /// Update the diffusion BilinearForm K using the given true-dof vector `u`.
+   void SetParameters(const Vector &u);
+
+   virtual ~ConductionOperator();
+};
+
+double InitialTemperature(const Vector &x);
+
+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/star.mesh";
+   int ser_ref_levels = 2;
+   int par_ref_levels = 1;
+   int order = 2;
+   int ode_solver_type = 8; // Exponential Euler 
+   double t_final = 0.5;
+   double dt = 1.0e-2;
+   double alpha = 1.0e-2;
+   double kappa = 0.5;
+   bool visualization = true;
+   bool visit = false;
+   int vis_steps = 5;
+
+   int precision = 8;
+   cout.precision(precision);
+
+   OptionsParser args(argc, argv);
+   args.AddOption(&mesh_file, "-m", "--mesh",
+                  "Mesh file to use.");
+   args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
+                  "Number of times to refine the mesh uniformly in serial.");
+   args.AddOption(&par_ref_levels, "-rp", "--refine-parallel",
+                  "Number of times to refine the mesh uniformly in parallel.");
+   args.AddOption(&order, "-o", "--order",
+                  "Order (degree) of the finite elements.");
+   args.AddOption(&ode_solver_type, "-s", "--ode-solver",
+                  "ODE solver:\n\t"
+                  "1  - Forward Euler,\n\t"
+                  "2  - RK2,\n\t"
+                  "3  - RK3 SSP,\n\t"
+                  "4  - RK4,\n\t"
+                  "5  - Backward Euler,\n\t"
+                  "6  - SDIRK 2,\n\t"
+                  "7  - SDIRK 3,\n\t"
+                  "8  - Exponential Euler,\n\t");
+   args.AddOption(&t_final, "-tf", "--t-final",
+                  "Final time; start time is 0.");
+   args.AddOption(&dt, "-dt", "--time-step",
+                  "Time step.");
+   args.AddOption(&alpha, "-a", "--alpha",
+                  "Alpha coefficient.");
+   args.AddOption(&kappa, "-k", "--kappa",
+                  "Kappa coefficient offset.");
+   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
+                  "--no-visualization",
+                  "Enable or disable GLVis visualization.");
+   args.AddOption(&visit, "-visit", "--visit-datafiles", "-no-visit",
+                  "--no-visit-datafiles",
+                  "Save data files for VisIt (visit.llnl.gov) visualization.");
+   args.AddOption(&vis_steps, "-vs", "--visualization-steps",
+                  "Visualize every n-th timestep.");
+   args.Parse();
+   if (!args.Good())
+   {
+      args.PrintUsage(cout);
+      MPI_Finalize();
+      return 1;
+   }
+
+   if (myid == 0)
+   {
+      args.PrintOptions(cout);
+   }
+
+   // check for vaild ODE solver option
+   if (ode_solver_type < 1 || ode_solver_type > 8)
+   {
+      if (myid == 0)
+      {
+         cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
+      }
+      MPI_Finalize();
+      return 1;
+   }
+
+   // 3. Read the serial mesh from the given mesh file on all processors. We can
+   //    handle triangular, quadrilateral, tetrahedral and hexahedral meshes
+   //    with the same code.
+   Mesh *mesh = new Mesh(mesh_file, 1, 1);
+   int dim = mesh->Dimension();
+
+   // 4. Refine the mesh in serial to increase the resolution. In this example
+   //    we do 'ser_ref_levels' of uniform refinement, where 'ser_ref_levels' is
+   //    a command-line parameter.
+   for (int lev = 0; lev < ser_ref_levels; lev++)
+   {
+      mesh->UniformRefinement();
+   }
+
+   // 5. Define a parallel mesh by a partitioning of the serial mesh. Refine
+   //    this mesh further in parallel to increase the resolution. Once the
+   //    parallel mesh is defined, the serial mesh can be deleted.
+   ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
+   delete mesh;
+   for (int lev = 0; lev < par_ref_levels; lev++)
+   {
+      pmesh->UniformRefinement();
+   }
+
+   // 6. Define the vector finite element space representing the current and the
+   //    initial temperature, u_ref.
+   H1_FECollection fe_coll(order, dim);
+   ParFiniteElementSpace fespace(pmesh, &fe_coll);
+
+   int fe_size = fespace.GlobalTrueVSize();
+   if (myid == 0)
+   {
+      cout << "Number of temperature unknowns: " << fe_size << endl;
+   }
+
+   ParGridFunction u_gf(&fespace);
+
+   // 7. Set the initial conditions for u. All boundaries are considered
+   //    natural.
+   FunctionCoefficient u_0(InitialTemperature);
+   u_gf.ProjectCoefficient(u_0);
+   Vector u;
+   u_gf.GetTrueDofs(u);
+
+   // 8. Initialize the conduction operator and the VisIt visualization.
+   ConductionOperator oper(fespace, alpha, kappa, u);
+
+   u_gf.SetFromTrueDofs(u);
+   {
+      ostringstream mesh_name, sol_name;
+      mesh_name << "ex16-mesh." << setfill('0') << setw(6) << myid;
+      sol_name << "ex16-init." << setfill('0') << setw(6) << myid;
+      ofstream omesh(mesh_name.str().c_str());
+      omesh.precision(precision);
+      pmesh->Print(omesh);
+      ofstream osol(sol_name.str().c_str());
+      osol.precision(precision);
+      u_gf.Save(osol);
+   }
+
+   VisItDataCollection visit_dc("Example16-Parallel", pmesh);
+   visit_dc.RegisterField("temperature", &u_gf);
+   if (visit)
+   {
+      visit_dc.SetCycle(0);
+      visit_dc.SetTime(0.0);
+      visit_dc.Save();
+   }
+
+   socketstream sout;
+   if (visualization)
+   {
+      char vishost[] = "localhost";
+      int  visport   = 19916;
+      sout.open(vishost, visport);
+      sout << "parallel " << num_procs << " " << myid << endl;
+      int good = sout.good(), all_good;
+      MPI_Allreduce(&good, &all_good, 1, MPI_INT, MPI_MIN, pmesh->GetComm());
+      if (!all_good)
+      {
+         sout.close();
+         visualization = false;
+         if (myid == 0)
+         {
+            cout << "Unable to connect to GLVis server at "
+                 << vishost << ':' << visport << endl;
+            cout << "GLVis visualization disabled.\n";
+         }
+      }
+      else
+      {
+         sout.precision(precision);
+         sout << "solution\n" << *pmesh << u_gf;
+         sout << "pause\n";
+         sout << flush;
+         if (myid == 0)
+         {
+            cout << "GLVis visualization paused."
+                 << " Press space (in the GLVis window) to resume it.\n";
+         }
+      }
+   }
+
+   // 9. Define the ODE solver used for time integration.
+   double t = 0.0;
+   ODESolver *ode_solver = NULL;
+   EPICSolver *epic_solver = NULL;
+   switch (ode_solver_type)
+   {
+      // MFEM explicit methods
+      case 1: ode_solver = new ForwardEulerSolver; break;
+      case 2: ode_solver = new RK2Solver(0.5); break; // midpoint method
+      case 3: ode_solver = new RK3SSPSolver; break;
+      case 4: ode_solver = new RK4Solver; break;
+      // MFEM implicit L-stable methods
+      case 5: ode_solver = new BackwardEulerSolver; break;
+      case 6: ode_solver = new SDIRK23Solver(2); break;
+      case 7: ode_solver = new SDIRK33Solver; break;
+      // EPIC
+      case 8:
+         epic_solver = new EPICSolver();
+	 epic_solver->Init(oper);
+	 ode_solver = epic_solver;
+	 break;
+   }
+
+   // Initialize MFEM integrators
+   ode_solver->Init(oper);
+
+   // 10. Perform time-integration (looping over the time iterations, ti, with a
+   //     time-step dt).
+   if (myid == 0)
+   {
+      cout << "Integrating the ODE ..." << endl;
+   }
+   tic_toc.Clear();
+   tic_toc.Start();
+
+   bool last_step = false;
+   for (int ti = 1; !last_step; ti++)
+   {
+      double dt_real = min(dt, t_final - t);
+
+      // Note that since we are using the "one-step" mode of the SUNDIALS
+      // solvers, they will, generally, step over the final time and will not
+      // explicitly perform the interpolation to t_final as they do in the
+      // "normal" step mode.
+
+      ode_solver->Step(u, t, dt_real);
+
+      last_step = (t >= t_final - 1e-8*dt);
+
+      if (last_step || (ti % vis_steps) == 0)
+      {
+         if (myid == 0)
+         {
+            cout << "step " << ti << ", t = " << t << endl;
+         }
+
+         u_gf.SetFromTrueDofs(u);
+         if (visualization)
+         {
+            sout << "parallel " << num_procs << " " << myid << "\n";
+            sout << "solution\n" << *pmesh << u_gf << flush;
+         }
+
+         if (visit)
+         {
+            visit_dc.SetCycle(ti);
+            visit_dc.SetTime(t);
+            visit_dc.Save();
+         }
+      }
+      oper.SetParameters(u);
+   }
+   tic_toc.Stop();
+   if (myid == 0)
+   {
+      cout << "Done, " << tic_toc.RealTime() << "s." << endl;
+   }
+
+   // 11. Save the final solution in parallel. This output can be viewed later
+   //     using GLVis: "glvis -np <np> -m ex16-mesh -g ex16-final".
+   {
+      ostringstream sol_name;
+      sol_name << "ex16-final." << setfill('0') << setw(6) << myid;
+      ofstream osol(sol_name.str().c_str());
+      osol.precision(precision);
+      u_gf.Save(osol);
+   }
+
+   // 12. Free the used memory.
+   delete ode_solver;
+   delete pmesh;
+
+   MPI_Finalize();
+
+   return 0;
+}
+
+ConductionOperator::ConductionOperator(ParFiniteElementSpace &f, double al,
+                                       double kap, const Vector &u)
+   : TimeDependentOperator(f.GetTrueVSize(), 0.0), fespace(f), M(NULL), K(NULL),
+     T(NULL),
+     M_solver(f.GetComm()), T_solver(f.GetComm()), z(height)
+{
+   const double rel_tol = 1e-8;
+
+   M = new ParBilinearForm(&fespace);
+   M->AddDomainIntegrator(new MassIntegrator());
+   M->Assemble(0); // keep sparsity pattern of M and K the same
+   M->FormSystemMatrix(ess_tdof_list, Mmat);
+
+   M_solver.iterative_mode = false;
+   M_solver.SetRelTol(rel_tol);
+   M_solver.SetAbsTol(0.0);
+   M_solver.SetMaxIter(100);
+   M_solver.SetPrintLevel(0);
+   M_prec.SetType(HypreSmoother::Jacobi);
+   M_solver.SetPreconditioner(M_prec);
+   M_solver.SetOperator(Mmat);
+
+   alpha = al;
+   kappa = kap;
+
+   T_solver.iterative_mode = false;
+   T_solver.SetRelTol(rel_tol);
+   T_solver.SetAbsTol(0.0);
+   T_solver.SetMaxIter(100);
+   T_solver.SetPrintLevel(0);
+   T_solver.SetPreconditioner(T_prec);
+
+   SetParameters(u);
+}
+
+void ConductionOperator::Mult(const Vector &u, Vector &du_dt) const
+{
+   // Compute:
+   //    du_dt = M^{-1}*-K(u)
+   // for du_dt
+   Kmat.Mult(u, z);
+   z.Neg(); // z = -z
+   M_solver.Mult(z, du_dt);
+}
+
+void ConductionOperator::ImplicitSolve(const double dt,
+                                       const Vector &u, Vector &du_dt)
+{
+   // Solve the equation:
+   //    du_dt = M^{-1}*[-K(u + dt*du_dt)]
+   // for du_dt
+   if (T) { delete T; }
+   T = Add(1.0, Mmat, dt, Kmat);
+   T_solver.SetOperator(*T);
+   Kmat.Mult(u, z);
+   z.Neg();
+   T_solver.Mult(z, du_dt);
+}
+
+int ConductionOperator::SUNImplicitSetup(const Vector &x,
+                                         const Vector &fx, int jok, int *jcur,
+                                         double gamma)
+{
+   // Setup the ODE Jacobian T = M + gamma K.
+   if (T) { delete T; }
+   T = Add(1.0, Mmat, gamma, Kmat);
+   T_solver.SetOperator(*T);
+   *jcur = 1;
+   return (0);
+}
+
+int ConductionOperator::SUNImplicitSolve(const Vector &b, Vector &x, double tol)
+{
+   // Solve the system A x = z => (M - gamma K) x = M b.
+   Mmat.Mult(b, z);
+   T_solver.Mult(z, x);
+   return (0);
+}
+
+void ConductionOperator::SetParameters(const Vector &u)
+{
+   ParGridFunction u_alpha_gf(&fespace);
+   u_alpha_gf.SetFromTrueDofs(u);
+   for (int i = 0; i < u_alpha_gf.Size(); i++)
+   {
+      u_alpha_gf(i) = kappa + alpha*u_alpha_gf(i);
+   }
+
+   delete K;
+   K = new ParBilinearForm(&fespace);
+
+   GridFunctionCoefficient u_coeff(&u_alpha_gf);
+
+   K->AddDomainIntegrator(new DiffusionIntegrator(u_coeff));
+   K->Assemble(0); // keep sparsity pattern of M and K the same
+   K->FormSystemMatrix(ess_tdof_list, Kmat);
+}
+
+ConductionOperator::~ConductionOperator()
+{
+   delete T;
+   delete M;
+   delete K;
+}
+
+double InitialTemperature(const Vector &x)
+{
+   if (x.Norml2() < 0.5)
+   {
+      return 2.0;
+   }
+   else
+   {
+      return 1.0;
+   }
+}

examples/epic/makefile

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -12,7 +12,7 @@
 # Use the MFEM build directory
 MFEM_DIR ?= ../..
 MFEM_BUILD_DIR ?= ../..
-SRC = $(if $(MFEM_DIR:../..=),$(MFEM_DIR)/examples/arpack/,)
+SRC = $(if $(MFEM_DIR:../..=),$(MFEM_DIR)/examples/epic/,)
 CONFIG_MK = $(MFEM_BUILD_DIR)/config/config.mk
 # Use the MFEM install directory
 # MFEM_INSTALL_DIR = ../../mfem
@@ -21,14 +21,13 @@ CONFIG_MK = $(MFEM_BUILD_DIR)/config/config.mk
 MFEM_LIB_FILE = mfem_is_not_built
 -include $(CONFIG_MK)
 
-SEQ_EXAMPLES = ex11
-PAR_EXAMPLES = 
+SEQ_EXAMPLES = ex16
+PAR_EXAMPLES = ex16p
 ifeq ($(MFEM_USE_MPI),NO)
    EXAMPLES = $(SEQ_EXAMPLES)
 else
-   EXAMPLES = $(PAR_EXAMPLES)
+   EXAMPLES = $(PAR_EXAMPLES) $(SEQ_EXAMPLES)
 endif
-RC_FILES = $(patsubst $(SRC)%,%,$(wildcard $(SRC)rc_*))
 
 .SUFFIXES:
 .SUFFIXES: .o .cpp .mk
@@ -43,16 +42,25 @@ RC_FILES = $(patsubst $(SRC)%,%,$(wildcard $(SRC)rc_*))
 
 all: $(EXAMPLES)
 
-# Examples depend on their corresponding rc_* files:
-make-rc-rule = $(1): | $(filter rc_$(1)%,$(RC_FILES))
-$(foreach ex,$(EXAMPLES),$(eval $(call make-rc-rule,$(ex))))
-
-# Rules to copy the rc_* files when building out-of-source:
-ifneq ($(SRC),)
-$(RC_FILES): %: $(SRC)%
-	cp -pf $(<) .
+ifeq ($(MFEM_USE_EPIC),NO)
+$(EXAMPLES):
+	$(error MFEM is not configured with EPIC)
 endif
 
+MFEM_TESTS = EXAMPLES
+include $(MFEM_TEST_MK)
+
+# Testing: Parallel vs. serial runs
+RUN_MPI = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP) $(MFEM_MPI_NP)
+SERIAL_NAME := Serial EPIC example
+PARALLEL_NAME := Parallel EPIC example
+%-test-par: %
+	@$(call mfem-test,$<, $(RUN_MPI), $(PARALLEL_NAME))
+%-test-seq: %
+	@$(call mfem-test,$<,, $(SERIAL_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)
@@ -64,6 +72,5 @@ clean-build:
 	rm -rf *.dSYM *.TVD.*breakpoints
 
 clean-exec:
-	@rm -rf mesh.* sol.* sol_p.* sol_u.* Example5*
-	@rm -f ex9-mesh.* ex9-init.* ex9-final.* Example9*
 	@rm -f deformed.* velocity.* elastic_energy.*
+	@rm -f ex16.mesh ex16-mesh.* ex16-init.* ex16-final.* Example16*

examples/ex1.cpp

@@ -9,7 +9,6 @@
 //               ex1 -m ../data/fichera.mesh
 //               ex1 -m ../data/fichera-mixed.mesh
 //               ex1 -m ../data/toroid-wedge.mesh
-//               ex1 -m ../data/octahedron.mesh -o 1
 //               ex1 -m ../data/periodic-annulus-sector.msh
 //               ex1 -m ../data/periodic-torus-sector.msh
 //               ex1 -m ../data/square-disc-p2.vtk -o 2

examples/ex13p.cpp

@@ -118,6 +118,7 @@ int main(int argc, char *argv[])
    {
       pmesh->UniformRefinement();
    }
+   pmesh->ReorientTetMesh();
 
    // 7. Define a parallel finite element space on the parallel mesh. Here we
    //    use the Nedelec finite elements of the specified order.

examples/ex16.cpp

@@ -24,10 +24,7 @@
 //               class ConductionOperator defining C(u)), as well as their
 //               implicit time integration. Note that implementing the method
 //               ConductionOperator::ImplicitSolve is the only requirement for
-//               high-order implicit (SDIRK) time integration. In this example,
-//               the diffusion operator is linearized by evaluating with the
-//               lagged solution from the previous timestep, so there is only
-//               a linear solve.
+//               high-order implicit (SDIRK) time integration.
 //
 //               We recommend viewing examples 2, 9 and 10 before viewing this
 //               example.
@@ -329,8 +326,8 @@ ConductionOperator::ConductionOperator(FiniteElementSpace &f, double al,
 void ConductionOperator::Mult(const Vector &u, Vector &du_dt) const
 {
    // Compute:
-   //    du_dt = M^{-1}*-Ku
-   // for du_dt, where K is linearized by using u from the previous timestep
+   //    du_dt = M^{-1}*-K(u)
+   // for du_dt
    Kmat.Mult(u, z);
    z.Neg(); // z = -z
    M_solver.Mult(z, du_dt);
@@ -341,7 +338,7 @@ void ConductionOperator::ImplicitSolve(const double dt,
 {
    // Solve the equation:
    //    du_dt = M^{-1}*[-K(u + dt*du_dt)]
-   // for du_dt, where K is linearized by using u from the previous timestep
+   // for du_dt
    if (!T)
    {
       T = Add(1.0, Mmat, dt, Kmat);

examples/ex16p.cpp

@@ -24,11 +24,8 @@
 //               class ConductionOperator defining C(u)), as well as their
 //               implicit time integration. Note that implementing the method
 //               ConductionOperator::ImplicitSolve is the only requirement for
-//               high-order implicit (SDIRK) time integration. In this example,
-//               the diffusion operator is linearized by evaluating with the
-//               lagged solution from the previous timestep, so there is only
-//               a linear solve. Optional saving with ADIOS2
-//               (adios2.readthedocs.io) is also illustrated.
+//               high-order implicit (SDIRK) time integration. Optional saving
+//               with ADIOS2 (adios2.readthedocs.io) is also illustrated.
 //
 //               We recommend viewing examples 2, 9 and 10 before viewing this
 //               example.
@@ -423,8 +420,8 @@ ConductionOperator::ConductionOperator(ParFiniteElementSpace &f, double al,
 void ConductionOperator::Mult(const Vector &u, Vector &du_dt) const
 {
    // Compute:
-   //    du_dt = M^{-1}*-Ku
-   // for du_dt, where K is linearized by using u from the previous timestep
+   //    du_dt = M^{-1}*-K(u)
+   // for du_dt
    Kmat.Mult(u, z);
    z.Neg(); // z = -z
    M_solver.Mult(z, du_dt);
@@ -435,7 +432,7 @@ void ConductionOperator::ImplicitSolve(const double dt,
 {
    // Solve the equation:
    //    du_dt = M^{-1}*[-K(u + dt*du_dt)]
-   // for du_dt, where K is linearized by using u from the previous timestep
+   // for du_dt
    if (!T)
    {
       T = Add(1.0, Mmat, dt, Kmat);

examples/ex1p.cpp

@@ -9,7 +9,6 @@
 //               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/octahedron.mesh -o 1
 //               mpirun -np 4 ex1p -m ../data/periodic-annulus-sector.msh
 //               mpirun -np 4 ex1p -m ../data/periodic-torus-sector.msh
 //               mpirun -np 4 ex1p -m ../data/square-disc-p2.vtk -o 2

examples/ex22.cpp

@@ -13,8 +13,6 @@
 //               ex22 -m ../data/inline-hex.mesh -o 2 -p 1
 //               ex22 -m ../data/inline-hex.mesh -o 2 -p 2
 //               ex22 -m ../data/inline-hex.mesh -o 2 -p 2 -pa
-//               ex22 -m ../data/inline-wedge.mesh -o 1
-//               ex22 -m ../data/inline-pyramid.mesh -o 1
 //               ex22 -m ../data/star.mesh -r 1 -o 2 -sigma 10.0
 //
 // Device sample runs:

examples/ex22p.cpp

@@ -13,8 +13,6 @@
 //               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 2 -p 1
 //               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 2 -p 2
 //               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 1 -p 2 -pa
-//               mpirun -np 4 ex22p -m ../data/inline-wedge.mesh -o 1
-//               mpirun -np 4 ex22p -m ../data/inline-pyramid.mesh -o 1
 //               mpirun -np 4 ex22p -m ../data/star.mesh -o 2 -sigma 10.0
 //
 // Device sample runs:

examples/ex24.cpp

@@ -113,6 +113,7 @@ int main(int argc, char *argv[])
          mesh->UniformRefinement();
       }
    }
+   mesh->ReorientTetMesh();
 
    // 5. Define a finite element space on the mesh. Here we use Nedelec or
    //    Raviart-Thomas finite elements of the specified order.

examples/ex24p.cpp

@@ -141,6 +141,7 @@ int main(int argc, char *argv[])
          pmesh->UniformRefinement();
       }
    }
+   pmesh->ReorientTetMesh();
 
    // 7. Define a parallel finite element space on the parallel mesh. Here we
    //    use Nedelec or Raviart-Thomas finite elements of the specified order.

examples/ex25.cpp

@@ -277,8 +277,10 @@ int main(int argc, char *argv[])
       mesh->UniformRefinement();
    }
 
-   // 6. Set element attributes in order to distinguish elements in the
-   //    PML region
+   // 6. Reorient mesh in case of a tet mesh
+   mesh->ReorientTetMesh();
+
+   // Set element attributes in order to distinguish elements in the PML region
    pml->SetAttributes(mesh);
 
    // 7. Define a finite element space on the mesh. Here we use the Nedelec

examples/ex25p.cpp

@@ -316,6 +316,9 @@ int main(int argc, char *argv[])
       }
    }
 
+   // 7a. Reorient mesh in case of a tet mesh
+   pmesh->ReorientTetMesh();
+
    // 8. Set element attributes in order to distinguish elements in the PML
    pml->SetAttributes(pmesh);
 

examples/ex3.cpp

@@ -16,8 +16,6 @@
 //               ex3 -m ../data/beam-hex-nurbs.mesh
 //               ex3 -m ../data/amr-hex.mesh
 //               ex3 -m ../data/fichera-amr.mesh
-//               ex3 -m ../data/ref-prism.mesh -o 1
-//               ex3 -m ../data/octahedron.mesh -o 1
 //               ex3 -m ../data/star-surf.mesh -o 1
 //               ex3 -m ../data/mobius-strip.mesh -f 0.1
 //               ex3 -m ../data/klein-bottle.mesh -f 0.1
@@ -115,6 +113,7 @@ int main(int argc, char *argv[])
          mesh->UniformRefinement();
       }
    }
+   mesh->ReorientTetMesh();
 
    // 5. Define a finite element space on the mesh. Here we use the Nedelec
    //    finite elements of the specified order.

examples/ex3p.cpp

@@ -16,8 +16,6 @@
 //               mpirun -np 4 ex3p -m ../data/beam-hex-nurbs.mesh
 //               mpirun -np 4 ex3p -m ../data/amr-quad.mesh -o 2
 //               mpirun -np 4 ex3p -m ../data/amr-hex.mesh
-//               mpirun -np 4 ex3p -m ../data/ref-prism.mesh -o 1
-//               mpirun -np 4 ex3p -m ../data/octahedron.mesh -o 1
 //               mpirun -np 4 ex3p -m ../data/star-surf.mesh -o 2
 //               mpirun -np 4 ex3p -m ../data/mobius-strip.mesh -o 2 -f 0.1
 //               mpirun -np 4 ex3p -m ../data/klein-bottle.mesh -o 2 -f 0.1
@@ -141,7 +139,9 @@ int main(int argc, char *argv[])
 
    // 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
    //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
+   //    parallel mesh is defined, the serial mesh can be deleted. Tetrahedral
+   //    meshes need to be reoriented before we can define high-order Nedelec
+   //    spaces on them.
    ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
    delete mesh;
    {
@@ -151,6 +151,7 @@ int main(int argc, char *argv[])
          pmesh->UniformRefinement();
       }
    }
+   pmesh->ReorientTetMesh();
 
    // 7. Define a parallel finite element space on the parallel mesh. Here we
    //    use the Nedelec finite elements of the specified order.

examples/ex4.cpp

@@ -19,8 +19,6 @@
 //               ex4 -m ../data/amr-hex.mesh
 //               ex4 -m ../data/amr-hex.mesh -o 2 -hb
 //               ex4 -m ../data/fichera-amr.mesh -o 2 -sc
-//               ex4 -m ../data/ref-prism.mesh -o 1
-//               ex4 -m ../data/octahedron.mesh -o 1
 //               ex4 -m ../data/star-surf.mesh -o 1
 //
 // Device sample runs:

examples/ex4p.cpp

@@ -19,8 +19,6 @@
 //               mpirun -np 3 ex4p -m ../data/amr-quad.mesh -o 2 -hb
 //               mpirun -np 4 ex4p -m ../data/amr-hex.mesh -o 2 -sc
 //               mpirun -np 4 ex4p -m ../data/amr-hex.mesh -o 2 -hb
-//               mpirun -np 4 ex4p -m ../data/ref-prism.mesh -o 1
-//               mpirun -np 4 ex4p -m ../data/octahedron.mesh -o 1
 //               mpirun -np 4 ex4p -m ../data/star-surf.mesh -o 3 -hb
 //
 // Device sample runs:
@@ -137,7 +135,9 @@ int main(int argc, char *argv[])
 
    // 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
    //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
+   //    parallel mesh is defined, the serial mesh can be deleted. Tetrahedral
+   //    meshes need to be reoriented before we can define high-order Nedelec
+   //    spaces on them (this is needed in the ADS solver below).
    ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
    delete mesh;
    {
@@ -147,6 +147,7 @@ int main(int argc, char *argv[])
          pmesh->UniformRefinement();
       }
    }
+   pmesh->ReorientTetMesh();
 
    // 7. Define a parallel finite element space on the parallel mesh. Here we
    //    use the Raviart-Thomas finite elements of the specified order.

examples/ex8p.cpp

@@ -106,6 +106,7 @@ int main(int argc, char *argv[])
          pmesh->UniformRefinement();
       }
    }
+   pmesh->ReorientTetMesh();
 
    // 6. Define the trial, interfacial (trace) and test DPG spaces:
    //    - The trial space, x0_space, contains the non-interfacial unknowns and

examples/makefile

@@ -45,6 +45,9 @@ endif
 ifeq ($(MFEM_USE_HIOP),YES)
    SUBDIRS += hiop
 endif
+ifeq ($(MFEM_USE_EPIC),YES)
+   SUBDIRS += epic
+endif
 ifeq ($(MFEM_USE_PETSC),YES)
    SUBDIRS += petsc
 endif

examples/petsc/ex3p.cpp

@@ -121,7 +121,9 @@ int main(int argc, char *argv[])
 
    // 5. Define a parallel mesh by a partitioning of the serial mesh. Refine
    //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
+   //    parallel mesh is defined, the serial mesh can be deleted. Tetrahedral
+   //    meshes need to be reoriented before we can define high-order Nedelec
+   //    spaces on them.
    ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
    delete mesh;
    {
@@ -131,6 +133,7 @@ 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/petsc/ex4p.cpp

@@ -122,7 +122,9 @@ int main(int argc, char *argv[])
 
    // 5. Define a parallel mesh by a partitioning of the serial mesh. Refine
    //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
+   //    parallel mesh is defined, the serial mesh can be deleted. Tetrahedral
+   //    meshes need to be reoriented before we can define high-order Nedelec
+   //    spaces on them (this is needed in the ADS solver below).
    ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
    delete mesh;
    {
@@ -132,6 +134,7 @@ 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 Raviart-Thomas finite elements of the specified order.

examples/spectra/ex11.cpp

@@ -1,250 +0,0 @@
-//                       MFEM Example 11 - Serial Version
-//
-// Compile with: make ex11
-//
-// Sample runs:  ex11 -m ../data/square-disc.mesh
-//               ex11 -m ../data/star.mesh
-//               ex11 -m ../data/star-mixed.mesh
-//               ex11 -m ../data/periodic-annulus-sector.msh
-//               ex11 -m ../data/square-disc-p2.vtk -o 2
-//               ex11 -m ../data/square-disc-p3.mesh -o 3
-//               ex11 -m ../data/square-disc-nurbs.mesh -o -1
-//               ex11 -m ../data/disc-nurbs.mesh -o -1 -n 20
-//               ex11 -m ../data/star-surf.mesh
-//               ex11 -m ../data/square-disc-surf.mesh
-//               ex11 -m ../data/inline-segment.mesh
-//               ex11 -m ../data/inline-quad.mesh
-//               ex11 -m ../data/inline-tri.mesh
-//               ex11 -m ../data/amr-quad.mesh
-//               ex11 -m ../data/amr-hex.mesh
-//               ex11 -m ../data/mobius-strip.mesh -n 8
-//
-// Description:  This example code demonstrates the use of MFEM to solve the
-//               eigenvalue problem -Delta u = lambda u with homogeneous
-//               Dirichlet boundary conditions.
-//
-//               We compute a number of the lowest eigenmodes by discretizing
-//               the Laplacian and Mass operators using a FE space of the
-//               specified order, or an isoparametric/isogeometric space if
-//               order < 1 (quadratic for quadratic curvilinear mesh, NURBS for
-//               NURBS mesh, etc.)
-//
-//               The example highlights the use of the ARPACK eigenvalue solver
-//               (regular inverse mode). Reusing a single GLVis visualization
-//               window for multiple eigenfunctions is also illustrated.
-//
-//               We recommend viewing Example 1 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/star.mesh";
-   int ser_ref_levels = 1;
-   int order = 1;
-   int nev = 5;
-   double dbc_eig = 1e3;
-   bool visualization = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
-                  "Number of times to refine the mesh uniformly in serial.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree) or -1 for"
-                  " isoparametric space.");
-   args.AddOption(&nev, "-n", "--num-eigs",
-                  "Number of desired eigenmodes.");
-   args.AddOption(&dbc_eig, "-d", "--dbc-eig",
-                  "Eigenvalues associated with Dirichlet BC "
-                  "(should be larger than the maximum desired eigenvalue).");
-   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 (serial) mesh from the given mesh file on all processors. We
-   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
-   //    and volume meshes with the same code.
-   Mesh *mesh;
-   ifstream imesh(mesh_file);
-   if (!imesh)
-   {
-      cerr << "\nCan not open mesh file: " << mesh_file << '\n' << endl;
-      return 2;
-   }
-   mesh = new Mesh(imesh, 1, 1);
-   imesh.close();
-   int dim = mesh->Dimension();
-
-   // 3. Refine the serial mesh on all processors to increase the resolution. In
-   //    this example we do 'ref_levels' of uniform refinement (2 by default, or
-   //    specified on the command line with -rs). 
-   for (int lev = 0; lev < ser_ref_levels; lev++)
-   {
-      mesh->UniformRefinement();
-   }
-
-   // 4. Define a finite element space on the mesh. Here we
-   //    use continuous Lagrange finite elements of the specified order. If
-   //    order < 1, we instead use an isoparametric/isogeometric space.
-   FiniteElementCollection *fec;
-   if (order > 0)
-   {
-      fec = new H1_FECollection(order, dim);
-   }
-   else if (mesh->GetNodes())
-   {
-      fec = mesh->GetNodes()->OwnFEC();
-   }
-   else
-   {
-      fec = new H1_FECollection(order = 1, dim);
-   }
-   FiniteElementSpace *fespace = new FiniteElementSpace(mesh, fec);
-   int size = fespace->GetVSize();
-
-   cout << "Number of unknowns: " << size << endl;
-
-   // 5. Set up the parallel bilinear forms a(.,.) and m(.,.) on the finite
-   //    element space. The first corresponds to the Laplacian operator -Delta,
-   //    while the second is a simple mass matrix needed on the right hand side
-   //    of the generalized eigenvalue problem below. The boundary conditions
-   //    are implemented by elimination with special values on the diagonal to
-   //    shift the Dirichlet eigenvalues out of the computational range. After
-   //    serial and parallel assembly we extract the corresponding parallel
-   //    matrices A and M.
-   ConstantCoefficient one(1.0);
-   Array<int> ess_bdr;
-   if (mesh->bdr_attributes.Size())
-   {
-      ess_bdr.SetSize(mesh->bdr_attributes.Max());
-      ess_bdr = 1;
-   }
-
-   BilinearForm *a = new BilinearForm(fespace);
-   a->AddDomainIntegrator(new DiffusionIntegrator(one));
-   if (mesh->bdr_attributes.Size() == 0)
-   {
-      // Add a mass term if the mesh has no boundary, e.g. periodic mesh or
-      // closed surface.
-      a->AddDomainIntegrator(new MassIntegrator(one));
-   }
-   a->Assemble();
-   if (mesh->bdr_attributes.Size() != 0)
-   {
-      a->EliminateEssentialBCDiag(ess_bdr, dbc_eig);
-   }
-   a->Finalize();
-
-   BilinearForm *m = new BilinearForm(fespace);
-   m->AddDomainIntegrator(new MassIntegrator(one));
-   m->Assemble();
-   if (mesh->bdr_attributes.Size() != 0)
-   {
-      // shift the eigenvalue corresponding to eliminated dofs to a large value
-      m->EliminateEssentialBCDiag(ess_bdr, 1.0);
-   }
-   m->Finalize();
-
-   // 6. Define and configure the SPECTRA eigensolver and solve problem
-   SpectraEigenSolver spectra;
-
-   spectra.SetNumModes(nev)
-      .SetKrylov(10)
-      .SetMaxIter(5000)
-      .SetTol(1e-5)
-      .SetOperators(*a, *m)
-      .Solve();
-
-   Eigen::VectorXd eigenvalues = spectra.GetEigenvalues(nev);
-
-   // 7. Define a grid function to represent each of the eigenmodes returned by the solver.
-   
-   GridFunction x(fespace);
-
-   // 8. Save the refined mesh and the modes in parallel. 
-   //    This output can be viewed later using GLVis: "glvis -np <np> -m mesh -g mode"
-   {
-      ostringstream mesh_name, mode_name;
-      mesh_name << "ex11.mesh";
-
-      ofstream mesh_ofs(mesh_name.str().c_str());
-      mesh_ofs.precision(8);
-      mesh->Print(mesh_ofs);
-
-      for (int i = 0; i < nev; i++) {
-         // conver Eigen Vector to MFEM Vector
-         Vector eigenvector = VectorConverter<double>::from(spectra.GetEigenvector(i));
-         
-         // convert eigenvector from Vector to GridFunction
-         x = eigenvector;
-
-         mode_name << "mode_" << setfill('0') << setw(2) << i;
-
-         ofstream mode_ofs(mode_name.str().c_str());
-         mode_ofs.precision(8);
-         x.Save(mode_ofs);
-         mode_name.str("");
-      }
-   }
-
-   // 10. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream mode_sock(vishost, visport);
-      mode_sock.precision(8);
-
-      for (int i=0; i<nev; i++)
-      {
-         cout << "Eigenmode " << i+1 << '/' << nev
-              << ", Lambda = " << eigenvalues[i] << endl;
-
-         // convert eigenvector from HypreParVector to ParGridFunction
-         Vector eigenvector = VectorConverter<double>::from(spectra.GetEigenvector(i));
-         x = eigenvector;
-
-         mode_sock << "solution\n" << *mesh << x << flush
-                   << "window_title 'Eigenmode " << i+1 << '/' << nev
-                   << ", Lambda = " << eigenvalues[i] << "'" << endl;
-
-         char c;
-         cout << "press (q)uit or (c)ontinue --> " << flush;
-         cin >> c;
-
-         if (c != 'c')
-         {
-            break;
-         }
-      }
-      mode_sock.close();
-   }
-
-   // 10. Free the used memory.
-   delete m;
-   delete a;
-
-   delete fespace;
-   if (order > 0)
-   {
-      delete fec;
-   }
-   delete mesh;
-
-   return 0;
-}

examples/spectra/makefile

@@ -1,67 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# Use the MFEM build directory
-MFEM_DIR ?= ../..
-MFEM_BUILD_DIR ?= ../..
-SRC = $(if $(MFEM_DIR:../..=),$(MFEM_DIR)/examples/spectra/,)
-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 $(CONFIG_MK)
-
-SEQ_EXAMPLES = ex11
-PAR_EXAMPLES = 
-ifeq ($(MFEM_USE_MPI),NO)
-   EXAMPLES = $(SEQ_EXAMPLES)
-else
-   EXAMPLES = $(PAR_EXAMPLES)
-endif
-RC_FILES = $(patsubst $(SRC)%,%,$(wildcard $(SRC)rc_*))
-
-.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)
-
-# Examples depend on their corresponding rc_* files:
-make-rc-rule = $(1): | $(filter rc_$(1)%,$(RC_FILES))
-$(foreach ex,$(EXAMPLES),$(eval $(call make-rc-rule,$(ex))))
-
-# Rules to copy the rc_* files when building out-of-source:
-ifneq ($(SRC),)
-$(RC_FILES): %: $(SRC)%
-	cp -pf $(<) .
-endif
-
-# Generate an error message if the MFEM library is not built and exit
-$(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 -rf *.mesh mode_*

fem/CMakeLists.txt

@@ -39,7 +39,6 @@ set(SRCS
   complex_fem.cpp
   convergence.cpp
   datacollection.cpp
-  doftrans.cpp
   eltrans.cpp
   estimators.cpp
   fe.cpp
@@ -106,7 +105,6 @@ set(SRCS
   tmop/tmop_pa_w3.cpp
   tmop/tmop_pa_w3_c0.cpp
   tmop_tools.cpp
-  tmop_amr.cpp
   gslib.cpp
   transfer.cpp
   lor.cpp
@@ -120,7 +118,6 @@ set(HDRS
   complex_fem.hpp
   convergence.hpp
   datacollection.hpp
-  doftrans.hpp
   eltrans.hpp
   estimators.hpp
   fe.hpp
@@ -167,7 +164,6 @@ set(HDRS
   tmop.hpp
   tmop/tmop_pa.hpp
   tmop_tools.hpp
-  tmop_amr.hpp
   gslib.hpp
   transfer.hpp
   lor.hpp

fem/bilinearform.cpp

@@ -391,7 +391,6 @@ void BilinearForm::Assemble(int skip_zeros)
    }
 
    ElementTransformation *eltrans;
-   DofTransformation * doftrans;
    Mesh *mesh = fes -> GetMesh();
    DenseMatrix elmat, *elmat_p;
 
@@ -425,7 +424,7 @@ void BilinearForm::Assemble(int skip_zeros)
       for (int i = 0; i < fes -> GetNE(); i++)
       {
          int elem_attr = fes->GetMesh()->GetAttribute(i);
-         doftrans = fes->GetElementVDofs(i, vdofs);
+         fes->GetElementVDofs(i, vdofs);
          if (element_matrices)
          {
             elmat_p = &(*element_matrices)(i);
@@ -459,11 +458,6 @@ void BilinearForm::Assemble(int skip_zeros)
             {
                elmat_p = &elmat;
             }
-            if (doftrans)
-            {
-               doftrans->TransformDual(elmat);
-            }
-            elmat_p = &elmat;
          }
          if (static_cond)
          {
@@ -509,7 +503,7 @@ void BilinearForm::Assemble(int skip_zeros)
          if (bdr_attr_marker[bdr_attr-1] == 0) { continue; }
 
          const FiniteElement &be = *fes->GetBE(i);
-         doftrans = fes -> GetBdrElementVDofs (i, vdofs);
+         fes -> GetBdrElementVDofs (i, vdofs);
          eltrans = fes -> GetBdrElementTransformation (i);
          int k = 0;
          for (; k < boundary_integs.Size(); k++)
@@ -529,22 +523,17 @@ void BilinearForm::Assemble(int skip_zeros)
             boundary_integs[k]->AssembleElementMatrix(be, *eltrans, elemmat);
             elmat += elemmat;
          }
-         if (doftrans)
-         {
-            doftrans->TransformDual(elmat);
-         }
-         elmat_p = &elmat;
          if (!static_cond)
          {
-            mat->AddSubMatrix(vdofs, vdofs, *elmat_p, skip_zeros);
+            mat->AddSubMatrix(vdofs, vdofs, elmat, skip_zeros);
             if (hybridization)
             {
-               hybridization->AssembleBdrMatrix(i, *elmat_p);
+               hybridization->AssembleBdrMatrix(i, elmat);
             }
          }
          else
          {
-            static_cond->AssembleBdrMatrix(i, *elmat_p);
+            static_cond->AssembleBdrMatrix(i, elmat);
          }
       }
    }
@@ -1329,10 +1318,9 @@ void MixedBilinearForm::Assemble (int skip_zeros)
       return;
    }
 
+   Array<int> tr_vdofs, te_vdofs;
    ElementTransformation *eltrans;
-   DofTransformation * dom_dof_trans;
-   DofTransformation * ran_dof_trans;
-   DenseMatrix elmat;
+   DenseMatrix elemmat;
 
    Mesh *mesh = test_fes -> GetMesh();
 
@@ -1345,24 +1333,16 @@ void MixedBilinearForm::Assemble (int skip_zeros)
    {
       for (int i = 0; i < test_fes -> GetNE(); i++)
       {
-         dom_dof_trans = trial_fes -> GetElementVDofs (i, trial_vdofs);
-         ran_dof_trans = test_fes  -> GetElementVDofs (i, test_vdofs);
+         trial_fes -> GetElementVDofs (i, tr_vdofs);
+         test_fes  -> GetElementVDofs (i, te_vdofs);
          eltrans = test_fes -> GetElementTransformation (i);
-
-         elmat.SetSize(test_vdofs.Size(), trial_vdofs.Size());
-         elmat = 0.0;
          for (int k = 0; k < domain_integs.Size(); k++)
          {
             domain_integs[k] -> AssembleElementMatrix2 (*trial_fes -> GetFE(i),
                                                         *test_fes  -> GetFE(i),
                                                         *eltrans, elemmat);
-            elmat += elemmat;
+            mat -> AddSubMatrix (te_vdofs, tr_vdofs, elemmat, skip_zeros);
          }
-         if (ran_dof_trans || dom_dof_trans)
-         {
-            TransformDual(ran_dof_trans, dom_dof_trans, elmat);
-         }
-         mat -> AddSubMatrix (test_vdofs, trial_vdofs, elmat, skip_zeros);
       }
    }
 
@@ -1394,12 +1374,9 @@ void MixedBilinearForm::Assemble (int skip_zeros)
          const int bdr_attr = mesh->GetBdrAttribute(i);
          if (bdr_attr_marker[bdr_attr-1] == 0) { continue; }
 
-         dom_dof_trans = trial_fes -> GetBdrElementVDofs (i, trial_vdofs);
-         ran_dof_trans = test_fes  -> GetBdrElementVDofs (i, test_vdofs);
+         trial_fes -> GetBdrElementVDofs (i, tr_vdofs);
+         test_fes  -> GetBdrElementVDofs (i, te_vdofs);
          eltrans = test_fes -> GetBdrElementTransformation (i);
-
-         elmat.SetSize(test_vdofs.Size(), trial_vdofs.Size());
-         elmat = 0.0;
          for (int k = 0; k < boundary_integs.Size(); k++)
          {
             if (boundary_integs_marker[k] &&
@@ -1408,34 +1385,29 @@ void MixedBilinearForm::Assemble (int skip_zeros)
             boundary_integs[k]->AssembleElementMatrix2 (*trial_fes -> GetBE(i),
                                                         *test_fes  -> GetBE(i),
                                                         *eltrans, elemmat);
-            elmat += elemmat;
+            mat -> AddSubMatrix (te_vdofs, tr_vdofs, elemmat, skip_zeros);
          }
-         if (ran_dof_trans || dom_dof_trans)
-         {
-            TransformDual(ran_dof_trans, dom_dof_trans, elmat);
-         }
-         mat -> AddSubMatrix (test_vdofs, trial_vdofs, elmat, skip_zeros);
       }
    }
 
    if (trace_face_integs.Size())
    {
       FaceElementTransformations *ftr;
-      Array<int> test_vdofs2;
+      Array<int> te_vdofs2;
       const FiniteElement *trial_face_fe, *test_fe1, *test_fe2;
 
       int nfaces = mesh->GetNumFaces();
       for (int i = 0; i < nfaces; i++)
       {
          ftr = mesh->GetFaceElementTransformations(i);
-         trial_fes->GetFaceVDofs(i, trial_vdofs);
-         test_fes->GetElementVDofs(ftr->Elem1No, test_vdofs);
+         trial_fes->GetFaceVDofs(i, tr_vdofs);
+         test_fes->GetElementVDofs(ftr->Elem1No, te_vdofs);
          trial_face_fe = trial_fes->GetFaceElement(i);
          test_fe1 = test_fes->GetFE(ftr->Elem1No);
          if (ftr->Elem2No >= 0)
          {
-            test_fes->GetElementVDofs(ftr->Elem2No, test_vdofs2);
-            test_vdofs.Append(test_vdofs2);
+            test_fes->GetElementVDofs(ftr->Elem2No, te_vdofs2);
+            te_vdofs.Append(te_vdofs2);
             test_fe2 = test_fes->GetFE(ftr->Elem2No);
          }
          else
@@ -1449,7 +1421,7 @@ void MixedBilinearForm::Assemble (int skip_zeros)
          {
             trace_face_integs[k]->AssembleFaceMatrix(*trial_face_fe, *test_fe1,
                                                      *test_fe2, *ftr, elemmat);
-            mat->AddSubMatrix(test_vdofs, trial_vdofs, elemmat, skip_zeros);
+            mat->AddSubMatrix(te_vdofs, tr_vdofs, elemmat, skip_zeros);
          }
       }
    }
@@ -1489,8 +1461,8 @@ void MixedBilinearForm::Assemble (int skip_zeros)
          ftr = mesh->GetBdrFaceTransformations(i);
          if (ftr)
          {
-            trial_fes->GetFaceVDofs(ftr->ElementNo, trial_vdofs);
-            test_fes->GetElementVDofs(ftr->Elem1No, test_vdofs);
+            trial_fes->GetFaceVDofs(ftr->ElementNo, tr_vdofs);
+            test_fes->GetElementVDofs(ftr->Elem1No, te_vdofs);
             trial_face_fe = trial_fes->GetFaceElement(ftr->ElementNo);
             test_fe1 = test_fes->GetFE(ftr->Elem1No);
             // The test_fe2 object is really a dummy and not used on the
@@ -1507,7 +1479,7 @@ void MixedBilinearForm::Assemble (int skip_zeros)
                                                                  *test_fe1,
                                                                  *test_fe2,
                                                                  *ftr, elemmat);
-               mat->AddSubMatrix(test_vdofs, trial_vdofs, elemmat, skip_zeros);
+               mat->AddSubMatrix(te_vdofs, tr_vdofs, elemmat, skip_zeros);
             }
          }
       }
@@ -1869,8 +1841,6 @@ void DiscreteLinearOperator::Assemble(int skip_zeros)
 
    Array<int> dom_vdofs, ran_vdofs;
    ElementTransformation *T;
-   DofTransformation * dom_dof_trans;
-   DofTransformation * ran_dof_trans;
    const FiniteElement *dom_fe, *ran_fe;
    DenseMatrix totelmat, elmat;
 
@@ -1883,8 +1853,8 @@ void DiscreteLinearOperator::Assemble(int skip_zeros)
    {
       for (int i = 0; i < test_fes->GetNE(); i++)
       {
-         dom_dof_trans = trial_fes->GetElementVDofs(i, dom_vdofs);
-         ran_dof_trans = test_fes->GetElementVDofs(i, ran_vdofs);
+         trial_fes->GetElementVDofs(i, dom_vdofs);
+         test_fes->GetElementVDofs(i, ran_vdofs);
          T = test_fes->GetElementTransformation(i);
          dom_fe = trial_fes->GetFE(i);
          ran_fe = test_fes->GetFE(i);
@@ -1897,10 +1867,6 @@ void DiscreteLinearOperator::Assemble(int skip_zeros)
                                                      elmat);
             totelmat += elmat;
          }
-         if (ran_dof_trans || dom_dof_trans)
-         {
-            TransformPrimal(ran_dof_trans, dom_dof_trans, totelmat);
-         }
          mat->SetSubMatrix(ran_vdofs, dom_vdofs, totelmat, skip_zeros);
       }
    }

fem/doftrans.cpp

@@ -1,358 +0,0 @@
-// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-// LICENSE and NOTICE for details. LLNL-CODE-806117.
-//
-// This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
-//
-// MFEM is free software; you can redistribute it and/or modify it under the
-// terms of the BSD-3 license. We welcome feedback and contributions, see file
-// CONTRIBUTING.md for details.
-
-#include "fem.hpp"
-
-namespace mfem
-{
-
-void DofTransformation::TransformPrimal(Vector &v) const
-{
-   TransformPrimal(v.GetData());
-}
-
-void DofTransformation::TransformPrimalCols(DenseMatrix &V) const
-{
-   for (int c=0; c<V.Width(); c++)
-   {
-      TransformPrimal(V.GetColumn(c));
-   }
-}
-
-void DofTransformation::TransformDual(Vector &v) const
-{
-   TransformDual(v.GetData());
-}
-
-void DofTransformation::TransformDual(DenseMatrix &V) const
-{
-   TransformDualCols(V);
-   TransformDualRows(V);
-}
-
-void DofTransformation::TransformDualRows(DenseMatrix &V) const
-{
-   Vector row;
-   for (int r=0; r<V.Height(); r++)
-   {
-      V.GetRow(r, row);
-      TransformDual(row);
-      V.SetRow(r, row);
-   }
-}
-
-void DofTransformation::TransformDualCols(DenseMatrix &V) const
-{
-   for (int c=0; c<V.Width(); c++)
-   {
-      TransformDual(V.GetColumn(c));
-   }
-}
-
-void DofTransformation::InvTransformPrimal(Vector &v) const
-{
-   InvTransformPrimal(v.GetData());
-}
-
-void TransformPrimal(const DofTransformation *ran_dof_trans,
-                     const DofTransformation *dom_dof_trans,
-                     DenseMatrix &elmat)
-{
-   if (ran_dof_trans && dom_dof_trans)
-   {
-      ran_dof_trans->TransformPrimalCols(elmat);
-      dom_dof_trans->TransformDualRows(elmat);
-   }
-   else if (ran_dof_trans)
-   {
-      ran_dof_trans->TransformPrimalCols(elmat);
-   }
-   else if (dom_dof_trans)
-   {
-      dom_dof_trans->TransformDualRows(elmat);
-   }
-   else
-   {
-      // If both transformations are NULL this function should not be called
-   }
-}
-
-void TransformDual(const DofTransformation *ran_dof_trans,
-                   const DofTransformation *dom_dof_trans,
-                   DenseMatrix &elmat)
-{
-   if (ran_dof_trans && dom_dof_trans)
-   {
-      ran_dof_trans->TransformDualCols(elmat);
-      dom_dof_trans->TransformDualRows(elmat);
-   }
-   else if (ran_dof_trans)
-   {
-      ran_dof_trans->TransformDualCols(elmat);
-   }
-   else if (dom_dof_trans)
-   {
-      dom_dof_trans->TransformDualRows(elmat);
-   }
-   else
-   {
-      // If both transformations are NULL this function should not be called
-   }
-}
-
-void VDofTransformation::TransformPrimal(double *v) const
-{
-   int size = doftrans_->Size();
-
-   if ((Ordering::Type)ordering_ == Ordering::byNODES || vdim_ == 1)
-   {
-      for (int i=0; i<vdim_; i++)
-      {
-         doftrans_->TransformPrimal(&v[i*size]);
-      }
-   }
-   else
-   {
-      Vector vec(size);
-      for (int i=0; i<vdim_; i++)
-      {
-         for (int j=0; j<size; j++)
-         {
-            vec(j) = v[j*vdim_+i];
-         }
-         doftrans_->TransformPrimal(vec);
-         for (int j=0; j<size; j++)
-         {
-            v[j*vdim_+i] = vec(j);
-         }
-      }
-   }
-}
-
-void VDofTransformation::InvTransformPrimal(double *v) const
-{
-   int size = doftrans_->Height();
-
-   if ((Ordering::Type)ordering_ == Ordering::byNODES)
-   {
-      for (int i=0; i<vdim_; i++)
-      {
-         doftrans_->InvTransformPrimal(&v[i*size]);
-      }
-   }
-   else
-   {
-      Vector vec(size);
-      for (int i=0; i<vdim_; i++)
-      {
-         for (int j=0; j<size; j++)
-         {
-            vec(j) = v[j*vdim_+i];
-         }
-         doftrans_->InvTransformPrimal(vec);
-         for (int j=0; j<size; j++)
-         {
-            v[j*vdim_+i] = vec(j);
-         }
-      }
-   }
-}
-
-void VDofTransformation::TransformDual(double *v) const
-{
-   int size = doftrans_->Size();
-
-   if ((Ordering::Type)ordering_ == Ordering::byNODES)
-   {
-      for (int i=0; i<vdim_; i++)
-      {
-         doftrans_->TransformDual(&v[i*size]);
-      }
-   }
-   else
-   {
-      Vector vec(size);
-      for (int i=0; i<vdim_; i++)
-      {
-         for (int j=0; j<size; j++)
-         {
-            vec(j) = v[j*vdim_+i];
-         }
-         doftrans_->TransformDual(vec);
-         for (int j=0; j<size; j++)
-         {
-            v[j*vdim_+i] = vec(j);
-         }
-      }
-   }
-}
-
-const double ND_DofTransformation::T_data[24] =
-{
-   1.0,  0.0,  0.0,  1.0,
-   -1.0, -1.0,  0.0,  1.0,
-   0.0,  1.0, -1.0, -1.0,
-   1.0,  0.0, -1.0, -1.0,
-   -1.0, -1.0,  1.0,  0.0,
-   0.0,  1.0,  1.0,  0.0
-};
-
-const DenseTensor ND_DofTransformation
-::T(const_cast<double*>(ND_DofTransformation::T_data), 2, 2, 6);
-
-const double ND_DofTransformation::TInv_data[24] =
-{
-   1.0,  0.0,  0.0,  1.0,
-   -1.0, -1.0,  0.0,  1.0,
-   -1.0, -1.0,  1.0,  0.0,
-   1.0,  0.0, -1.0, -1.0,
-   0.0,  1.0, -1.0, -1.0,
-   0.0,  1.0,  1.0,  0.0
-};
-
-const DenseTensor ND_DofTransformation
-::TInv(const_cast<double*>(TInv_data), 2, 2, 6);
-
-ND_DofTransformation::ND_DofTransformation(int size, int p)
-   : DofTransformation(size),
-     order(p)
-{
-}
-
-ND_TriDofTransformation::ND_TriDofTransformation(int p)
-   : ND_DofTransformation(p*(p + 2), p)
-{
-}
-
-void ND_TriDofTransformation::TransformPrimal(double *v) const
-{
-   int nedofs = order; // number of DoFs per edge
-   int nfdofs = order*(order-1); // number of DoFs per face
-
-   double data[2];
-   Vector v2(data, 2);
-
-   // Transform face DoFs
-   for (int f=0; f<1; f++)
-   {
-      for (int i=0; i<nfdofs/2; i++)
-      {
-         v2 = &v[3*nedofs + f*nfdofs + 2*i];
-         T(Fo[f]).Mult(v2, &v[3*nedofs + f*nfdofs + 2*i]);
-      }
-   }
-}
-
-void
-ND_TriDofTransformation::InvTransformPrimal(double *v) const
-{
-   int nedofs = order; // number of DoFs per edge
-   int nfdofs = order*(order-1); // number of DoFs per face
-
-   double data[2];
-   Vector v2(data, 2);
-
-   // Transform face DoFs
-   for (int f=0; f<1; f++)
-   {
-      for (int i=0; i<nfdofs/2; i++)
-      {
-         v2 = &v[3*nedofs + f*nfdofs + 2*i];
-         TInv(Fo[f]).Mult(v2, &v[3*nedofs + f*nfdofs + 2*i]);
-      }
-   }
-}
-
-void
-ND_TriDofTransformation::TransformDual(double *v) const
-{
-   int nedofs = order; // number of DoFs per edge
-   int nfdofs = order*(order-1); // number of DoFs per face
-
-   double data[2];
-   Vector v2(data, 2);
-
-   // Transform face DoFs
-   for (int f=0; f<1; f++)
-   {
-      for (int i=0; i<nfdofs/2; i++)
-      {
-         v2 = &v[3*nedofs + f*nfdofs + 2*i];
-         TInv(Fo[f]).MultTranspose(v2, &v[3*nedofs + f*nfdofs + 2*i]);
-      }
-   }
-}
-
-ND_TetDofTransformation::ND_TetDofTransformation(int p)
-   : ND_DofTransformation(p*(p + 2)*(p + 3)/2, p)
-{
-}
-
-void ND_TetDofTransformation::TransformPrimal(double *v) const
-{
-   int nedofs = order; // number of DoFs per edge
-   int nfdofs = order*(order-1); // number of DoFs per face
-
-   double data[2];
-   Vector v2(data, 2);
-
-   // Transform face DoFs
-   for (int f=0; f<4; f++)
-   {
-      for (int i=0; i<nfdofs/2; i++)
-      {
-         v2 = &v[6*nedofs + f*nfdofs + 2*i];
-         T(Fo[f]).Mult(v2, &v[6*nedofs + f*nfdofs + 2*i]);
-      }
-   }
-}
-
-void
-ND_TetDofTransformation::InvTransformPrimal(double *v) const
-{
-   int nedofs = order; // number of DoFs per edge
-   int nfdofs = order*(order-1); // number of DoFs per face
-
-   double data[2];
-   Vector v2(data, 2);
-
-   // Transform face DoFs
-   for (int f=0; f<4; f++)
-   {
-      for (int i=0; i<nfdofs/2; i++)
-      {
-         v2 = &v[6*nedofs + f*nfdofs + 2*i];
-         TInv(Fo[f]).Mult(v2, &v[6*nedofs + f*nfdofs + 2*i]);
-      }
-   }
-}
-
-void
-ND_TetDofTransformation::TransformDual(double *v) const
-{
-   int nedofs = order; // number of DoFs per edge
-   int nfdofs = order*(order-1); // number of DoFs per face
-
-   double data[2];
-   Vector v2(data, 2);
-
-   // Transform face DoFs
-   for (int f=0; f<4; f++)
-   {
-      for (int i=0; i<nfdofs/2; i++)
-      {
-         v2 = &v[6*nedofs + f*nfdofs + 2*i];
-         TInv(Fo[f]).MultTranspose(v2, &v[6*nedofs + f*nfdofs + 2*i]);
-      }
-   }
-}
-
-} // namespace mfem

fem/doftrans.hpp

@@ -1,277 +0,0 @@
-// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-// LICENSE and NOTICE for details. LLNL-CODE-806117.
-//
-// This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
-//
-// MFEM is free software; you can redistribute it and/or modify it under the
-// terms of the BSD-3 license. We welcome feedback and contributions, see file
-// CONTRIBUTING.md for details.
-
-#ifndef MFEM_DOFTRANSFORM
-#define MFEM_DOFTRANSFORM
-
-#include "../config/config.hpp"
-#include "../linalg/linalg.hpp"
-#include "intrules.hpp"
-#include "fe.hpp"
-
-namespace mfem
-{
-
-/** The DofTransformation class is an abstract base class for a family of
-    transformations that map local degrees of freedom (DoFs), contained within
-    individual elements, to global degrees of freedom, stored within
-    GridFunction objects. These transformations are necessary to ensure that
-    basis functions in neighboring elements align correctly. Closely related but
-    complementary transformations are required for the entries stored in
-    LinearForm and BilinearForm objects. The DofTransformation class is designed
-    to apply the action of both of these types of DoF transformations.
-
-    Let the "primal transformation" be given by the operator T. This means that
-    given a local element vector v the data that must be placed into a
-    GridFunction object is v_t = T * v.
-
-    We also need the inverse of the primal transformation T^{-1} so that we can
-    recover the local element vector from data read out of a GridFunction
-    e.g. v = T^{-1} * v_t.
-
-    We need to preserve the action of our linear forms applied to primal
-    vectors. In other words, if f is the local vector computed by a linear
-    form then f * v = f_t * v_t (where "*" represents an inner product of
-    vectors). This requires that f_t = T^{-T} * f i.e. the "dual transform" is
-    given by the transpose of the inverse of the primal transformation.
-
-    For bilinear forms we require that v^T * A * v = v_t^T * A_t * v_t. This
-    implies that A_t = T^{-T} * A * T^{-1}. This can be accomplished by
-    performing dual transformations of the rows and columns of the matrix A.
-
-    For discrete linear operators the range must be modified with the primal
-    transformation rather than the dual transformation because the result is a
-    primal vector rather than a dual vector. This leads to the transformation
-    D_t = T * D * T^{-1}. This can be accomplished by using a primal
-    transformation on the columns of D and a dual transformation on its rows.
-*/
-class DofTransformation
-{
-protected:
-   int size_;
-
-   Array<int> Fo;
-
-   DofTransformation(int size)
-      : size_(size) {}
-
-public:
-
-   inline int Size() const { return size_; }
-   inline int Height() const { return size_; }
-   inline int NumRows() const { return size_; }
-   inline int Width() const { return size_; }
-   inline int NumCols() const { return size_; }
-
-   /** @brief Configure the transformation using face orientations for the
-       current element. */
-   /// The face_orientation array can be obtained from Mesh::GetElementFaces.
-   inline void SetFaceOrientations(const Array<int> & face_orientation)
-   { Fo = face_orientation; }
-
-   inline const Array<int> & GetFaceOrientations() const { return Fo; }
-
-   /** Transform local DoFs to align with the global DoFs. For example, this
-       transformation can be used to map the local vector computed by
-       FiniteElement::Project() to the transformed vector stored within a
-       GridFunction object. */
-   virtual void TransformPrimal(double *v) const = 0;
-   virtual void TransformPrimal(Vector &v) const;
-
-   /// Transform groups of DoFs stored as dense matrices
-   virtual void TransformPrimalCols(DenseMatrix &V) const;
-
-   /** Inverse transform local DoFs. Used to transform DoFs from a global vector
-       back to their element-local form. For example, this must be used to
-       transform the vector obtained using GridFunction::GetSubVector before it
-       can be used to compute a local interpolation.
-   */
-   virtual void InvTransformPrimal(double *v) const = 0;
-   virtual void InvTransformPrimal(Vector &v) const;
-
-   /** Transform dual DoFs as computed by a LinearFormIntegrator before summing
-       into a LinearForm object. */
-   virtual void TransformDual(double *v) const = 0;
-   virtual void TransformDual(Vector &v) const;
-
-   /** Transform a matrix of dual DoFs entries as computed by a
-       BilinearFormIntegrator before summing into a BilinearForm object. */
-   virtual void TransformDual(DenseMatrix &V) const;
-
-   /// Transform groups of dual DoFs stored as dense matrices
-   virtual void TransformDualRows(DenseMatrix &V) const;
-   virtual void TransformDualCols(DenseMatrix &V) const;
-
-   virtual ~DofTransformation() {}
-};
-
-/** Transform a matrix of DoFs entries from different finite element spaces as
-    computed by a DiscreteInterpolator before copying into a
-    DiscreteLinearOperator.
-*/
-void TransformPrimal(const DofTransformation *ran_dof_trans,
-                     const DofTransformation *dom_dof_trans,
-                     DenseMatrix &elmat);
-
-/** Transform a matrix of dual DoFs entries from different finite element spaces
-    as computed by a BilinearFormIntegrator before summing into a
-    MixedBilinearForm object.
-*/
-void TransformDual(const DofTransformation *ran_dof_trans,
-                   const DofTransformation *dom_dof_trans,
-                   DenseMatrix &elmat);
-
-/** The VDofTransformation class implements a nested transformation where an
-    arbitrary DofTransformation is replicated with a vdim >= 1.
-*/
-class VDofTransformation : public DofTransformation
-{
-private:
-   int vdim_;
-   int ordering_;
-   DofTransformation * doftrans_;
-
-public:
-   /** @brief Default constructor which requires that SetDofTransformation be
-       called before use. */
-   VDofTransformation(int vdim = 1, int ordering = 0)
-      : DofTransformation(0),
-        vdim_(vdim), ordering_(ordering),
-        doftrans_(NULL) {}
-
-   /// Constructor with a known DofTransformation
-   VDofTransformation(DofTransformation & doftrans, int vdim = 1,
-                      int ordering = 0)
-      : DofTransformation(vdim * doftrans.Size()),
-        vdim_(vdim), ordering_(ordering),
-        doftrans_(&doftrans) {}
-
-   /// Set or change the vdim parameter
-   inline void SetVDim(int vdim)
-   {
-      vdim_ = vdim;
-      if (doftrans_)
-      {
-         size_ = vdim_ * doftrans_->Size();
-      }
-   }
-
-   /// Return the current vdim value
-   inline int GetVDim() const { return vdim_; }
-
-   /// Set or change the nested DofTransformation object
-   inline void SetDofTransformation(DofTransformation & doftrans)
-   {
-      size_ = vdim_ * doftrans.Size();
-      doftrans_ = &doftrans;
-   }
-
-   /// Return the nested DofTransformation object
-   inline DofTransformation * GetDofTransformation() const { return doftrans_; }
-
-   inline void SetFaceOrientation(const Array<int> & face_orientation)
-   { Fo = face_orientation; doftrans_->SetFaceOrientations(face_orientation); }
-
-   using DofTransformation::TransformPrimal;
-   using DofTransformation::InvTransformPrimal;
-   using DofTransformation::TransformDual;
-
-   void TransformPrimal(double *v) const;
-   void InvTransformPrimal(double *v) const;
-   void TransformDual(double *v) const;
-};
-
-/** Abstract base class for high-order Nedelec spaces on elements with
-    triangular faces.
-
-    The Nedelec DoFs on the interior of triangular faces come in pairs which
-    share an interpolation point but have different vector directions. These
-    directions depend on the orientation of the face and can therefore differ in
-    neighboring elements. The mapping required to transform these DoFs can be
-    implemented as series of 2x2 linear transformations. The raw data for these
-    linear transformations is stored in the T_data and TInv_data arrays and can
-    be accessed as DenseMatrices using the GetFaceTransform() and
-    GetFaceInverseTransform() methods.
-*/
-class ND_DofTransformation : public DofTransformation
-{
-protected:
-   static const double T_data[24];
-   static const double TInv_data[24];
-   static const DenseTensor T, TInv;
-   int order;
-
-   ND_DofTransformation(int size, int order);
-
-public:
-   // Return the 2x2 transformation operator for the given face orientation
-   static const DenseMatrix & GetFaceTransform(int ori) { return T(ori); }
-
-   // Return the 2x2 inverse transformation operator
-   static const DenseMatrix & GetFaceInverseTransform(int ori)
-   { return TInv(ori); }
-};
-
-/// DoF transformation implementation for the Nedelec basis on triangles
-class ND_TriDofTransformation : public ND_DofTransformation
-{
-public:
-   ND_TriDofTransformation(int order);
-
-   using DofTransformation::TransformPrimal;
-   using DofTransformation::InvTransformPrimal;
-   using DofTransformation::TransformDual;
-
-   void TransformPrimal(double *v) const;
-
-   void InvTransformPrimal(double *v) const;
-
-   void TransformDual(double *v) const;
-};
-
-/// DoF transformation implementation for the Nedelec basis on tetrahedra
-class ND_TetDofTransformation : public ND_DofTransformation
-{
-public:
-   ND_TetDofTransformation(int order);
-
-   using DofTransformation::TransformPrimal;
-   using DofTransformation::InvTransformPrimal;
-   using DofTransformation::TransformDual;
-
-   void TransformPrimal(double *v) const;
-
-   void InvTransformPrimal(double *v) const;
-
-   void TransformDual(double *v) const;
-};
-
-/// DoF transformation implementation for the Nedelec basis on wedge elements
-/** TODO: (Under development) */
-class ND_WedgeDofTransformation : public ND_DofTransformation
-{
-public:
-   ND_WedgeDofTransformation(int order);
-
-   using DofTransformation::TransformPrimal;
-   using DofTransformation::InvTransformPrimal;
-   using DofTransformation::TransformDual;
-
-   void TransformPrimal(double *v) const;
-
-   void InvTransformPrimal(double *v) const;
-
-   void TransformDual(double *v) const;
-};
-
-} // namespace mfem
-
-#endif // MFEM_DOFTRANSFORM

fem/eltrans.cpp

@@ -380,7 +380,6 @@ void IsoparametricTransformation::SetIdentityTransformation(
       case Geometry::TETRAHEDRON : FElem = &TetrahedronFE; break;
       case Geometry::CUBE :        FElem = &HexahedronFE; break;
       case Geometry::PRISM :       FElem = &WedgeFE; break;
-      case Geometry::PYRAMID :     FElem = &PyramidFE; break;
       default:
          MFEM_ABORT("unknown Geometry::Type!");
    }

fem/estimators.cpp

@@ -329,7 +329,7 @@ void KellyErrorEstimator::ComputeEstimates()
          error_estimates(e) = sqrt(factor * error_estimates(e));
       }
 
-      total_error = error_estimates.Norml2();
+      total_error = error_estimates.Sum();
       delete flux;
       return;
    }
@@ -452,10 +452,9 @@ void KellyErrorEstimator::ComputeEstimates()
    auto pfes = dynamic_cast<ParFiniteElementSpace*>(xfes);
    MFEM_VERIFY(pfes, "xfes is not a ParFiniteElementSpace pointer");
 
-   double process_local_error = pow(error_estimates.Norml2(),2.0);
+   double process_local_error = error_estimates.Sum();
    MPI_Allreduce(&process_local_error, &total_error, 1, MPI_DOUBLE,
                  MPI_SUM, pfes->GetComm());
-   total_error = sqrt(total_error);
 #endif // MFEM_USE_MPI
 }
 

fem/fe.hpp

@@ -1313,64 +1313,6 @@ public:
                            DenseMatrix &dshape) const;
 };
 
-/// A linear element defined on a triangular prism
-class LinearWedgeFiniteElement : public NodalFiniteElement
-{
-public:
-   /// Construct the LinearWedgeFiniteElement
-   LinearWedgeFiniteElement();
-
-   /** @brief virtual function which evaluates the values of all
-       shape functions at a given point ip and stores
-       them in the vector shape of dimension Dof (4) */
-   virtual void CalcShape(const IntegrationPoint &ip, Vector &shape) const;
-
-   /** @brief virtual function which evaluates the values of all
-       partial derivatives of all shape functions at a given
-       point ip and stores them in the matrix dshape (Dof x Dim) (4 x 3)
-       so that each row contains the derivatives of one shape function */
-   virtual void CalcDShape(const IntegrationPoint &ip,
-                           DenseMatrix &dshape) const;
-
-   virtual void ProjectDelta(int vertex, Vector &dofs) const
-   { dofs = 0.0; dofs(vertex) = 1.0; }
-
-   /** @brief Get the dofs associated with the given @a face.
-       @a *dofs is set to an internal array of the local dofc on the
-       face, while *ndofs is set to the number of dofs on that face.
-   */
-   virtual void GetFaceDofs(int face, int **dofs, int *ndofs) const;
-};
-
-/// A linear element defined on a square pyramid
-class LinearPyramidFiniteElement : public NodalFiniteElement
-{
-public:
-   /// Construct the LinearPyramidFiniteElement
-   LinearPyramidFiniteElement();
-
-   /** @brief virtual function which evaluates the values of all
-       shape functions at a given point ip and stores
-       them in the vector shape of dimension Dof (4) */
-   virtual void CalcShape(const IntegrationPoint &ip, Vector &shape) const;
-
-   /** @brief virtual function which evaluates the values of all
-       partial derivatives of all shape functions at a given
-       point ip and stores them in the matrix dshape (Dof x Dim) (4 x 3)
-       so that each row contains the derivatives of one shape function */
-   virtual void CalcDShape(const IntegrationPoint &ip,
-                           DenseMatrix &dshape) const;
-
-   virtual void ProjectDelta(int vertex, Vector &dofs) const
-   { dofs = 0.0; dofs(vertex) = 1.0; }
-
-   /** @brief Get the dofs associated with the given @a face.
-       @a *dofs is set to an internal array of the local dofc on the
-       face, while *ndofs is set to the number of dofs on that face.
-   */
-   virtual void GetFaceDofs(int face, int **dofs, int *ndofs) const;
-};
-
 /// A 2D constant element on a triangle
 class P0TriangleFiniteElement : public NodalFiniteElement
 {
@@ -1748,32 +1690,6 @@ public:
    { dofs(0) = 1.0; }
 };
 
-/// A 3D constant element on a wedge
-class P0WdgFiniteElement : public NodalFiniteElement
-{
-public:
-   /// Construct the P0WdgFiniteElement
-   P0WdgFiniteElement ();
-   virtual void CalcShape(const IntegrationPoint &ip, Vector &shape) const;
-   virtual void CalcDShape(const IntegrationPoint &ip,
-                           DenseMatrix &dshape) const;
-   virtual void ProjectDelta(int vertex, Vector &dofs) const
-   { dofs(0) = 1.0; }
-};
-
-/// A 3D constant element on a pyramid
-class P0PyrFiniteElement : public NodalFiniteElement
-{
-public:
-   /// Construct the P0PyrFiniteElement
-   P0PyrFiniteElement ();
-   virtual void CalcShape(const IntegrationPoint &ip, Vector &shape) const;
-   virtual void CalcDShape(const IntegrationPoint &ip,
-                           DenseMatrix &dshape) const;
-   virtual void ProjectDelta(int vertex, Vector &dofs) const
-   { dofs(0) = 1.0; }
-};
-
 /** @brief Tensor products of 1D Lagrange1DFiniteElement
     (only degree 2 is functional) */
 class LagrangeHexFiniteElement : public NodalFiniteElement
@@ -1912,10 +1828,6 @@ public:
    using FiniteElement::Project;
    virtual void Project (VectorCoefficient &vc,
                          ElementTransformation &Trans, Vector &dofs) const;
-
-   virtual void ProjectGrad(const FiniteElement &fe,
-                            ElementTransformation &Trans,
-                            DenseMatrix &grad) const;
 };
 
 
@@ -1940,66 +1852,6 @@ public:
    using FiniteElement::Project;
    virtual void Project (VectorCoefficient &vc,
                          ElementTransformation &Trans, Vector &dofs) const;
-
-   virtual void ProjectGrad(const FiniteElement &fe,
-                            ElementTransformation &Trans,
-                            DenseMatrix &grad) const;
-};
-
-
-/// A 3D 1st order Nedelec element on a wedge
-class Nedelec1WdgFiniteElement : public VectorFiniteElement
-{
-private:
-   static const double tk[9][3];
-
-public:
-   /// Construct the Nedelec1WdgFiniteElement
-   Nedelec1WdgFiniteElement();
-   virtual void CalcVShape(const IntegrationPoint &ip,
-                           DenseMatrix &shape) const;
-   virtual void CalcVShape(ElementTransformation &Trans,
-                           DenseMatrix &shape) const
-   { CalcVShape_ND(Trans, shape); }
-   virtual void CalcCurlShape(const IntegrationPoint &ip,
-                              DenseMatrix &curl_shape) const;
-   virtual void GetLocalInterpolation (ElementTransformation &Trans,
-                                       DenseMatrix &I) const;
-   using FiniteElement::Project;
-   virtual void Project (VectorCoefficient &vc,
-                         ElementTransformation &Trans, Vector &dofs) const;
-
-   virtual void ProjectGrad(const FiniteElement &fe,
-                            ElementTransformation &Trans,
-                            DenseMatrix &grad) const;
-};
-
-
-/// A 3D 1st order Nedelec element on a pyramid
-class Nedelec1PyrFiniteElement : public VectorFiniteElement
-{
-private:
-   static const double tk[8][3];
-
-public:
-   /// Construct the Nedelec1PyrFiniteElement
-   Nedelec1PyrFiniteElement();
-   virtual void CalcVShape(const IntegrationPoint &ip,
-                           DenseMatrix &shape) const;
-   virtual void CalcVShape(ElementTransformation &Trans,
-                           DenseMatrix &shape) const
-   { CalcVShape_ND(Trans, shape); }
-   virtual void CalcCurlShape(const IntegrationPoint &ip,
-                              DenseMatrix &curl_shape) const;
-   virtual void GetLocalInterpolation (ElementTransformation &Trans,
-                                       DenseMatrix &I) const;
-   using FiniteElement::Project;
-   virtual void Project (VectorCoefficient &vc,
-                         ElementTransformation &Trans, Vector &dofs) const;
-
-   virtual void ProjectGrad(const FiniteElement &fe,
-                            ElementTransformation &Trans,
-                            DenseMatrix &grad) const;
 };
 
 
@@ -2093,77 +1945,6 @@ public:
 };
 
 
-/// A 3D 0th order Raviert-Thomas element on a wedge
-class RT0WdgFiniteElement : public VectorFiniteElement
-{
-private:
-   static const double nk[5][3];
-
-public:
-   /// Construct the RT0WdgFiniteElement
-   RT0WdgFiniteElement();
-
-   virtual void CalcVShape(const IntegrationPoint &ip,
-                           DenseMatrix &shape) const;
-
-   virtual void CalcVShape(ElementTransformation &Trans,
-                           DenseMatrix &shape) const
-   { CalcVShape_RT(Trans, shape); }
-
-   virtual void CalcDivShape(const IntegrationPoint &ip,
-                             Vector &divshape) const;
-
-   virtual void GetLocalInterpolation (ElementTransformation &Trans,
-                                       DenseMatrix &I) const;
-
-   using FiniteElement::Project;
-
-   virtual void Project (VectorCoefficient &vc,
-                         ElementTransformation &Trans, Vector &dofs) const;
-
-   virtual void ProjectCurl(const FiniteElement &fe,
-                            ElementTransformation &Trans,
-                            DenseMatrix &curl) const;
-};
-
-
-/// A 3D 0th order Raviert-Thomas element on a pyramid
-class RT0PyrFiniteElement : public VectorFiniteElement
-{
-private:
-   static const double nk[5][3];
-
-   // If true match RT0TetFiniteElement rather than RT_TetrahedronElement(0)
-   bool rt0;
-
-public:
-   /// Construct the RT0PyrFiniteElement
-   RT0PyrFiniteElement(bool rt0tets = true);
-
-   virtual void CalcVShape(const IntegrationPoint &ip,
-                           DenseMatrix &shape) const;
-
-   virtual void CalcVShape(ElementTransformation &Trans,
-                           DenseMatrix &shape) const
-   { CalcVShape_RT(Trans, shape); }
-
-   virtual void CalcDivShape(const IntegrationPoint &ip,
-                             Vector &divshape) const;
-
-   virtual void GetLocalInterpolation (ElementTransformation &Trans,
-                                       DenseMatrix &I) const;
-
-   using FiniteElement::Project;
-
-   virtual void Project (VectorCoefficient &vc,
-                         ElementTransformation &Trans, Vector &dofs) const;
-
-   virtual void ProjectCurl(const FiniteElement &fe,
-                            ElementTransformation &Trans,
-                            DenseMatrix &curl) const;
-};
-
-
 class RotTriLinearHexFiniteElement : public NodalFiniteElement
 {
 public:

fem/fe_coll.cpp

@@ -33,9 +33,6 @@ int FiniteElementCollection::HasFaceDofs(Geometry::Type geom, int p) const
       case Geometry::PRISM:
          return max(GetNumDof(Geometry::TRIANGLE, p),
                     GetNumDof(Geometry::SQUARE, p));
-      case Geometry::PYRAMID:
-         return max(GetNumDof(Geometry::TRIANGLE, p),
-                    GetNumDof(Geometry::SQUARE, p));
       default:
          MFEM_ABORT("unknown geometry type");
    }
@@ -577,7 +574,6 @@ LinearFECollection::FiniteElementForGeometry(Geometry::Type GeomType) const
       case Geometry::TETRAHEDRON: return &TetrahedronFE;
       case Geometry::CUBE:        return &ParallelepipedFE;
       case Geometry::PRISM:       return &WedgeFE;
-      case Geometry::PYRAMID:     return &PyramidFE;
       default:
          mfem_error ("LinearFECollection: unknown geometry type.");
    }
@@ -595,7 +591,6 @@ int LinearFECollection::DofForGeometry(Geometry::Type GeomType) const
       case Geometry::TETRAHEDRON: return 0;
       case Geometry::CUBE:        return 0;
       case Geometry::PRISM:       return 0;
-      case Geometry::PYRAMID:     return 0;
       default:
          mfem_error ("LinearFECollection: unknown geometry type.");
    }
@@ -1245,7 +1240,6 @@ Const3DFECollection::FiniteElementForGeometry(Geometry::Type GeomType) const
       case Geometry::TETRAHEDRON: return &TetrahedronFE;
       case Geometry::CUBE:        return &ParallelepipedFE;
       case Geometry::PRISM:       return &WedgeFE;
-      case Geometry::PYRAMID:     return &PyramidFE;
       default:
          mfem_error ("Const3DFECollection: unknown geometry type.");
    }
@@ -1263,7 +1257,6 @@ int Const3DFECollection::DofForGeometry(Geometry::Type GeomType) const
       case Geometry::TETRAHEDRON: return 1;
       case Geometry::CUBE:        return 1;
       case Geometry::PRISM:       return 1;
-      case Geometry::PYRAMID:     return 1;
       default:
          mfem_error ("Const3DFECollection: unknown geometry type.");
    }
@@ -1284,8 +1277,6 @@ LinearDiscont3DFECollection::FiniteElementForGeometry(
    switch (GeomType)
    {
       case Geometry::TETRAHEDRON: return &TetrahedronFE;
-      case Geometry::PYRAMID:     return &PyramidFE;
-      case Geometry::PRISM:       return &WedgeFE;
       case Geometry::CUBE:        return &ParallelepipedFE;
       default:
          mfem_error ("LinearDiscont3DFECollection: unknown geometry type.");
@@ -1302,8 +1293,6 @@ int LinearDiscont3DFECollection::DofForGeometry(Geometry::Type GeomType) const
       case Geometry::TRIANGLE:    return 0;
       case Geometry::SQUARE:      return 0;
       case Geometry::TETRAHEDRON: return 4;
-      case Geometry::PYRAMID:     return 5;
-      case Geometry::PRISM:       return 6;
       case Geometry::CUBE:        return 8;
       default:
          mfem_error ("LinearDiscont3DFECollection: unknown geometry type.");
@@ -1405,8 +1394,6 @@ ND1_3DFECollection::FiniteElementForGeometry(Geometry::Type GeomType) const
    {
       case Geometry::CUBE:        return &HexahedronFE;
       case Geometry::TETRAHEDRON: return &TetrahedronFE;
-      case Geometry::PRISM:       return &WedgeFE;
-      case Geometry::PYRAMID:     return &PyramidFE;
       default:
          mfem_error ("ND1_3DFECollection: unknown geometry type.");
    }
@@ -1423,8 +1410,6 @@ int ND1_3DFECollection::DofForGeometry(Geometry::Type GeomType) const
       case Geometry::SQUARE:      return 0;
       case Geometry::TETRAHEDRON: return 0;
       case Geometry::CUBE:        return 0;
-      case Geometry::PRISM:       return 0;
-      case Geometry::PYRAMID:     return 0;
       default:
          mfem_error ("ND1_3DFECollection: unknown geometry type.");
    }
@@ -1454,8 +1439,6 @@ RT0_3DFECollection::FiniteElementForGeometry(Geometry::Type GeomType) const
       case Geometry::SQUARE:      return &QuadrilateralFE;
       case Geometry::CUBE:        return &HexahedronFE;
       case Geometry::TETRAHEDRON: return &TetrahedronFE;
-      case Geometry::PRISM:       return &WedgeFE;
-      case Geometry::PYRAMID:     return &PyramidFE;
       default:
          mfem_error ("RT0_3DFECollection: unknown geometry type.");
    }
@@ -1472,8 +1455,6 @@ int RT0_3DFECollection::DofForGeometry(Geometry::Type GeomType) const
       case Geometry::SQUARE:      return 1;
       case Geometry::TETRAHEDRON: return 0;
       case Geometry::CUBE:        return 0;
-      case Geometry::PRISM:       return 0;
-      case Geometry::PYRAMID:     return 0;
       default:
          mfem_error ("RT0_3DFECollection: unknown geometry type.");
    }
@@ -1749,7 +1730,6 @@ H1_FECollection::H1_FECollection(const int p, const int dim, const int btype)
          H1_dof[Geometry::TETRAHEDRON] = (TriDof*pm3)/3;
          H1_dof[Geometry::CUBE] = QuadDof*pm1;
          H1_dof[Geometry::PRISM] = TriDof*pm1;
-         H1_dof[Geometry::PYRAMID] = 0;
          if (b_type == BasisType::Positive)
          {
             H1_Elements[Geometry::TETRAHEDRON] = new H1Pos_TetrahedronElement(p);
@@ -1763,7 +1743,6 @@ H1_FECollection::H1_FECollection(const int p, const int dim, const int btype)
             H1_Elements[Geometry::CUBE] = new H1_HexahedronElement(p, btype);
             H1_Elements[Geometry::PRISM] = new H1_WedgeElement(p, btype);
          }
-         H1_Elements[Geometry::PYRAMID] = new LinearPyramidFiniteElement;
 
          const int &TetDof = H1_dof[Geometry::TETRAHEDRON];
          TetDofOrd[0] = new int[24*TetDof];
@@ -1858,21 +1837,6 @@ H1_FECollection::H1_FECollection(const int p, const int dim, const int btype)
    }
 }
 
-const FiniteElement *
-H1_FECollection::FiniteElementForGeometry(Geometry::Type GeomType) const
-{
-   if (GeomType != Geometry::PYRAMID || this->GetOrder() == 1)
-   {
-      return H1_Elements[GeomType];
-   }
-   else
-   {
-      MFEM_ABORT("H1 Pyramid basis functions are not yet supported "
-                 "for order > 1.");
-      return NULL;
-   }
-}
-
 const int *H1_FECollection::DofOrderForOrientation(Geometry::Type GeomType,
                                                    int Or) const
 {
@@ -2112,12 +2076,9 @@ L2_FECollection::L2_FECollection(const int p, const int dim, const int btype,
          L2_Elements[Geometry::CUBE] = new L2_HexahedronElement(p, btype);
          L2_Elements[Geometry::PRISM] = new L2_WedgeElement(p, btype);
       }
-      L2_Elements[Geometry::PYRAMID] = new P0PyrFiniteElement;
-
       L2_Elements[Geometry::TETRAHEDRON]->SetMapType(map_type);
       L2_Elements[Geometry::CUBE]->SetMapType(map_type);
       L2_Elements[Geometry::PRISM]->SetMapType(map_type);
-      L2_Elements[Geometry::PYRAMID]->SetMapType(map_type);
       // Trace element use the default Gauss-Legendre nodal points for positive basis
       if (b_type == BasisType::Positive)
       {
@@ -2238,21 +2199,6 @@ L2_FECollection::L2_FECollection(const int p, const int dim, const int btype,
    }
 }
 
-const FiniteElement *
-L2_FECollection::FiniteElementForGeometry(Geometry::Type GeomType) const
-{
-   if (GeomType != Geometry::PYRAMID || this->GetOrder() == 0)
-   {
-      return L2_Elements[GeomType];
-   }
-   else
-   {
-      MFEM_ABORT("L2 Pyramid basis functions are not yet supported "
-                 "for order > 0.");
-      return NULL;
-   }
-}
-
 const int *L2_FECollection::DofOrderForOrientation(Geometry::Type GeomType,
                                                    int Or) const
 {
@@ -2344,12 +2290,6 @@ RT_FECollection::RT_FECollection(const int order, const int dim,
 
       RT_Elements[Geometry::CUBE] = new RT_HexahedronElement(p, cb_type, ob_type);
       RT_dof[Geometry::CUBE] = 3*p*pp1*pp1;
-
-      RT_Elements[Geometry::PRISM] = new RT0WdgFiniteElement;
-      RT_dof[Geometry::PRISM] = 0;
-
-      RT_Elements[Geometry::PYRAMID] = new RT0PyrFiniteElement(false);
-      RT_dof[Geometry::PYRAMID] = 0;
    }
    else
    {
@@ -2493,22 +2433,6 @@ void RT_FECollection::InitFaces(const int p, const int dim,
    }
 }
 
-const FiniteElement *
-RT_FECollection::FiniteElementForGeometry(Geometry::Type GeomType) const
-{
-   if ((GeomType != Geometry::PRISM && GeomType != Geometry::PYRAMID) ||
-       this->GetOrder() == 1)
-   {
-      return RT_Elements[GeomType];
-   }
-   else
-   {
-      MFEM_ABORT("RT Wedge and Pyramid basis functions are not yet supported "
-                 "for order > 0.");
-      return NULL;
-   }
-}
-
 const int *RT_FECollection::DofOrderForOrientation(Geometry::Type GeomType,
                                                    int Or) const
 {
@@ -2732,31 +2656,18 @@ ND_FECollection::ND_FECollection(const int p, const int dim,
       {
          for (int i = 0; i + j <= pm2; i++)
          {
-            int k0 = p*pm1 - (p - j)*(pm1 - j) + 2*i;
-            int k1 = 2*pm2 - 2*i + ((2*p-3)-j)*j;
-            int k2 = 2*pm2 - 2*j + ((2*p-3)-i)*i;
-            int k3 = p*pm1 - 2 - 3*j - i - (i+j)*(i+j);
-            int k4 = p*pm1 - 2 - 3*i - j - (i+j)*(i+j);
-            int k5 = p*pm1 - (p - i)*(pm1 - i) + 2*j;
-
+            int k1 = p*pm1 - (p - j)*(pm1 - j) + 2*i;
+            int k2 = p*pm1 - (p - i)*(pm1 - i) + 2*j;
             // (0,1,2)
-            TriDofOrd[0][k0  ] = k0;
-            TriDofOrd[0][k0+1] = k0 + 1;
-            // (1,0,2)
-            TriDofOrd[1][k0  ] = k1;
-            TriDofOrd[1][k0+1] = k1 + 1;
-            // (2,0,1)
-            TriDofOrd[2][k0  ] = k2;
-            TriDofOrd[2][k0+1] = k2 + 1;
-            // (2,1,0)
-            TriDofOrd[3][k0  ] = k3;
-            TriDofOrd[3][k0+1] = k3 + 1;
-            // (1,2,0)
-            TriDofOrd[4][k0  ] = k4;
-            TriDofOrd[4][k0+1] = k4 + 1;
+            TriDofOrd[0][k1  ] = k1;
+            TriDofOrd[0][k1+1] = k1 + 1;
             // (0,2,1)
-            TriDofOrd[5][k0  ] = k5;
-            TriDofOrd[5][k0+1] = k5 + 1;
+            TriDofOrd[5][k1  ] = k2 + 1;
+            TriDofOrd[5][k1+1] = k2;
+
+            // The other orientations can not be supported with the current
+            // interface. The method Mesh::ReorientTetMesh will ensure that
+            // only orientations 0 and 5 are generated.
          }
       }
    }
@@ -2769,28 +2680,6 @@ ND_FECollection::ND_FECollection(const int p, const int dim,
       // TODO: cb_type and ob_type for tets
       ND_Elements[Geometry::TETRAHEDRON] = new ND_TetrahedronElement(p);
       ND_dof[Geometry::TETRAHEDRON] = p*pm1*pm2/2;
-
-      ND_Elements[Geometry::PRISM] = new Nedelec1WdgFiniteElement;
-      ND_dof[Geometry::PRISM] = 0;
-
-      ND_Elements[Geometry::PYRAMID] = new Nedelec1PyrFiniteElement;
-      ND_dof[Geometry::PYRAMID] = 0;
-   }
-}
-
-const FiniteElement *
-ND_FECollection::FiniteElementForGeometry(Geometry::Type GeomType) const
-{
-   if ((GeomType != Geometry::PRISM && GeomType != Geometry::PYRAMID) ||
-       this->GetOrder() == 1)
-   {
-      return ND_Elements[GeomType];
-   }
-   else
-   {
-      MFEM_ABORT("ND Wedge and Pyramid basis functions are not yet supported "
-                 "for order > 1.");
-      return NULL;
    }
 }
 
@@ -2803,6 +2692,11 @@ const int *ND_FECollection::DofOrderForOrientation(Geometry::Type GeomType,
    }
    else if (GeomType == Geometry::TRIANGLE)
    {
+      if (Or != 0 && Or != 5)
+      {
+         MFEM_ABORT("triangle face orientation " << Or << " is not supported! "
+                    "Use Mesh::ReorientTetMesh to fix it.");
+      }
       return TriDofOrd[Or%6];
    }
    else if (GeomType == Geometry::SQUARE)

fem/fe_coll.hpp

@@ -228,7 +228,8 @@ public:
                             const int btype = BasisType::GaussLobatto);
 
    virtual const FiniteElement *FiniteElementForGeometry(
-      Geometry::Type GeomType) const;
+      Geometry::Type GeomType) const
+   { return H1_Elements[GeomType]; }
    virtual int DofForGeometry(Geometry::Type GeomType) const
    { return H1_dof[GeomType]; }
    virtual const int *DofOrderForOrientation(Geometry::Type GeomType,
@@ -301,7 +302,10 @@ public:
                    const int map_type = FiniteElement::VALUE);
 
    virtual const FiniteElement *FiniteElementForGeometry(
-      Geometry::Type GeomType) const;
+      Geometry::Type GeomType) const
+   {
+      return L2_Elements[GeomType];
+   }
    virtual int DofForGeometry(Geometry::Type GeomType) const
    {
       if (L2_Elements[GeomType])
@@ -367,7 +371,8 @@ public:
                    const int ob_type = BasisType::GaussLegendre);
 
    virtual const FiniteElement *FiniteElementForGeometry(
-      Geometry::Type GeomType) const;
+      Geometry::Type GeomType) const
+   { return RT_Elements[GeomType]; }
    virtual int DofForGeometry(Geometry::Type GeomType) const
    { return RT_dof[GeomType]; }
    virtual const int *DofOrderForOrientation(Geometry::Type GeomType,
@@ -425,7 +430,8 @@ public:
                    const int ob_type = BasisType::GaussLegendre);
 
    virtual const FiniteElement *
-   FiniteElementForGeometry(Geometry::Type GeomType) const;
+   FiniteElementForGeometry(Geometry::Type GeomType) const
+   { return ND_Elements[GeomType]; }
 
    virtual int DofForGeometry(Geometry::Type GeomType) const
    { return ND_dof[GeomType]; }
@@ -523,10 +529,9 @@ private:
    const BiLinear2DFiniteElement QuadrilateralFE;
    const Linear3DFiniteElement TetrahedronFE;
    const TriLinear3DFiniteElement ParallelepipedFE;
-   const LinearWedgeFiniteElement WedgeFE;
-   const LinearPyramidFiniteElement PyramidFE;
+   const H1_WedgeElement WedgeFE;
 public:
-   LinearFECollection() : FiniteElementCollection(1) { }
+   LinearFECollection() : FiniteElementCollection(1), WedgeFE(1) { }
 
    virtual const FiniteElement *
    FiniteElementForGeometry(Geometry::Type GeomType) const;
@@ -931,11 +936,10 @@ class Const3DFECollection : public FiniteElementCollection
 private:
    const P0TetFiniteElement TetrahedronFE;
    const P0HexFiniteElement ParallelepipedFE;
-   const P0WdgFiniteElement WedgeFE;
-   const P0PyrFiniteElement PyramidFE;
+   const L2_WedgeElement WedgeFE;
 
 public:
-   Const3DFECollection() : FiniteElementCollection(0) { }
+   Const3DFECollection() : FiniteElementCollection(0), WedgeFE(0) { }
 
    virtual const FiniteElement *
    FiniteElementForGeometry(Geometry::Type GeomType) const;
@@ -956,8 +960,6 @@ class LinearDiscont3DFECollection : public FiniteElementCollection
 {
 private:
    const Linear3DFiniteElement TetrahedronFE;
-   const LinearPyramidFiniteElement PyramidFE;
-   const LinearWedgeFiniteElement WedgeFE;
    const TriLinear3DFiniteElement ParallelepipedFE;
 
 public:
@@ -1034,8 +1036,6 @@ class ND1_3DFECollection : public FiniteElementCollection
 private:
    const Nedelec1HexFiniteElement HexahedronFE;
    const Nedelec1TetFiniteElement TetrahedronFE;
-   const Nedelec1WdgFiniteElement WedgeFE;
-   const Nedelec1PyrFiniteElement PyramidFE;
 
 public:
    ND1_3DFECollection() : FiniteElementCollection(1) { }
@@ -1061,8 +1061,6 @@ private:
    const P0QuadFiniteElement QuadrilateralFE;
    const RT0HexFiniteElement HexahedronFE;
    const RT0TetFiniteElement TetrahedronFE;
-   const RT0WdgFiniteElement WedgeFE;
-   const RT0PyrFiniteElement PyramidFE;
 public:
    RT0_3DFECollection() : FiniteElementCollection(1) { }
 

fem/fem.hpp

@@ -16,7 +16,6 @@
 #include "geom.hpp"
 #include "fe.hpp"
 #include "fe_coll.hpp"
-#include "doftrans.hpp"
 #include "eltrans.hpp"
 #include "coefficient.hpp"
 #include "complex_fem.hpp"
@@ -35,7 +34,6 @@
 #include "staticcond.hpp"
 #include "tmop.hpp"
 #include "tmop_tools.hpp"
-#include "tmop_amr.hpp"
 #include "gslib.hpp"
 #include "restriction.hpp"
 #include "quadinterpolator.hpp"

fem/fespace.cpp

@@ -58,12 +58,9 @@ DofsToVDofs<Ordering::byVDIM>(int ndofs, int vdim, Array<int> &dofs)
 
 FiniteElementSpace::FiniteElementSpace()
    : mesh(NULL), fec(NULL), vdim(0), ordering(Ordering::byNODES),
-     ndofs(0), nvdofs(0), nedofs(0), nfdofs(0), nbdofs(0),
-     bdofs(NULL),
-     elem_dof(NULL), elem_fos(NULL), bdr_elem_dof(NULL), bdr_elem_fos(NULL),
-     face_dof(NULL),
+     ndofs(0), nvdofs(0), nedofs(0), nfdofs(0), nbdofs(0), bdofs(NULL),
+     elem_dof(NULL), bdr_elem_dof(NULL), face_dof(NULL),
      NURBSext(NULL), own_ext(false),
-     DoFTrans(0), VDoFTrans(vdim, ordering),
      cP(NULL), cR(NULL), cR_hp(NULL), cP_is_set(false),
      Th(Operator::ANY_TYPE),
      sequence(0), mesh_sequence(0), orders_changed(false), relaxed_hp(false)
@@ -72,7 +69,6 @@ FiniteElementSpace::FiniteElementSpace()
 FiniteElementSpace::FiniteElementSpace(const FiniteElementSpace &orig,
                                        Mesh *mesh,
                                        const FiniteElementCollection *fec)
-   : VDoFTrans(orig.vdim, orig.ordering)
 {
    mesh = mesh ? mesh : orig.mesh;
    fec = fec ? fec : orig.fec;
@@ -263,36 +259,16 @@ void FiniteElementSpace::AdjustVDofs (Array<int> &vdofs)
    }
 }
 
-DofTransformation *
-FiniteElementSpace::GetElementVDofs(int i, Array<int> &vdofs) const
+void FiniteElementSpace::GetElementVDofs(int i, Array<int> &vdofs) const
 {
-   DofTransformation * doftrans = GetElementDofs(i, vdofs);
+   GetElementDofs(i, vdofs);
    DofsToVDofs(vdofs);
-   if (vdim == 1 || doftrans == NULL)
-   {
-      return doftrans;
-   }
-   else
-   {
-      VDoFTrans.SetDofTransformation(*doftrans);
-      return &VDoFTrans;
-   }
 }
 
-DofTransformation *
-FiniteElementSpace::GetBdrElementVDofs(int i, Array<int> &vdofs) const
+void FiniteElementSpace::GetBdrElementVDofs(int i, Array<int> &vdofs) const
 {
-   DofTransformation * doftrans = GetBdrElementDofs(i, vdofs);
+   GetBdrElementDofs(i, vdofs);
    DofsToVDofs(vdofs);
-   if (vdim == 1 || doftrans == NULL)
-   {
-      return doftrans;
-   }
-   else
-   {
-      VDoFTrans.SetDofTransformation(*doftrans);
-      return &VDoFTrans;
-   }
 }
 
 void FiniteElementSpace::GetFaceVDofs(int i, Array<int> &vdofs) const
@@ -331,39 +307,21 @@ void FiniteElementSpace::BuildElementToDofTable() const
 
    // TODO: can we call GetElementDofs only once per element?
    Table *el_dof = new Table;
-   Table *el_fos = (mesh->Dimension() > 2) ? (new Table) : NULL;
    Array<int> dofs;
-   Array<int> F, Fo;
    el_dof -> MakeI (mesh -> GetNE());
-   if (el_fos) { el_fos -> MakeI (mesh -> GetNE()); }
    for (int i = 0; i < mesh -> GetNE(); i++)
    {
       GetElementDofs (i, dofs);
       el_dof -> AddColumnsInRow (i, dofs.Size());
-
-      if (el_fos)
-      {
-         mesh->GetElementFaces(i, F, Fo);
-         el_fos -> AddColumnsInRow (i, Fo.Size());
-      }
    }
    el_dof -> MakeJ();
-   if (el_fos) { el_fos -> MakeJ(); }
    for (int i = 0; i < mesh -> GetNE(); i++)
    {
       GetElementDofs (i, dofs);
       el_dof -> AddConnections (i, (int *)dofs, dofs.Size());
-
-      if (el_fos)
-      {
-         mesh->GetElementFaces(i, F, Fo);
-         el_fos -> AddConnections (i, (int *)Fo, Fo.Size());
-      }
    }
    el_dof -> ShiftUpI();
-   if (el_fos) { el_fos -> ShiftUpI(); }
    elem_dof = el_dof;
-   elem_fos = el_fos;
 }
 
 void FiniteElementSpace::BuildBdrElementToDofTable() const
@@ -417,9 +375,7 @@ void FiniteElementSpace::BuildFaceToDofTable() const
 void FiniteElementSpace::RebuildElementToDofTable()
 {
    delete elem_dof;
-   delete elem_fos;
    elem_dof = NULL;
-   elem_fos = NULL;
    BuildElementToDofTable();
 }
 
@@ -1359,10 +1315,8 @@ const FaceQuadratureInterpolator
 
 SparseMatrix *FiniteElementSpace::RefinementMatrix_main(
    const int coarse_ndofs, const Table &coarse_elem_dof,
-   const Table *coarse_elem_fos, const DenseTensor localP[]) const
+   const DenseTensor localP[]) const
 {
-   /// TODO: Implement DofTransformation support
-
    MFEM_VERIFY(mesh->GetLastOperation() == Mesh::REFINE, "");
 
    Array<int> dofs, coarse_dofs, coarse_vdofs;
@@ -1445,8 +1399,7 @@ void FiniteElementSpace::GetLocalRefinementMatrices(
 }
 
 SparseMatrix* FiniteElementSpace::RefinementMatrix(int old_ndofs,
-                                                   const Table* old_elem_dof,
-                                                   const Table* old_elem_fos)
+                                                   const Table* old_elem_dof)
 {
    MFEM_VERIFY(GetNE() >= old_elem_dof->Size(),
                "Previous mesh is not coarser.");
@@ -1459,16 +1412,13 @@ SparseMatrix* FiniteElementSpace::RefinementMatrix(int old_ndofs,
       GetLocalRefinementMatrices(elem_geoms[i], localP[elem_geoms[i]]);
    }
 
-   return RefinementMatrix_main(old_ndofs, *old_elem_dof, old_elem_fos,
-                                localP);
+   return RefinementMatrix_main(old_ndofs, *old_elem_dof, localP);
 }
 
 FiniteElementSpace::RefinementOperator::RefinementOperator
-(const FiniteElementSpace* fespace, Table* old_elem_dof, Table* old_elem_fos,
- int old_ndofs)
+(const FiniteElementSpace* fespace, Table* old_elem_dof, int old_ndofs)
    : fespace(fespace)
    , old_elem_dof(old_elem_dof)
-   , old_elem_fos(old_elem_fos)
 {
    MFEM_VERIFY(fespace->GetNE() >= old_elem_dof->Size(),
                "Previous mesh is not coarser.");
@@ -1482,14 +1432,12 @@ FiniteElementSpace::RefinementOperator::RefinementOperator
    {
       fespace->GetLocalRefinementMatrices(elem_geoms[i], localP[elem_geoms[i]]);
    }
-
-   ConstructDoFTrans();
 }
 
 FiniteElementSpace::RefinementOperator::RefinementOperator(
    const FiniteElementSpace *fespace, const FiniteElementSpace *coarse_fes)
    : Operator(fespace->GetVSize(), coarse_fes->GetVSize()),
-     fespace(fespace), old_elem_dof(NULL), old_elem_fos(NULL)
+     fespace(fespace), old_elem_dof(NULL)
 {
    Mesh::GeometryList elem_geoms(*fespace->GetMesh());
 
@@ -1501,50 +1449,11 @@ FiniteElementSpace::RefinementOperator::RefinementOperator(
 
    // Make a copy of the coarse elem_dof Table.
    old_elem_dof = new Table(coarse_fes->GetElementToDofTable());
-
-   // Make a copy of the coarse elem_fos Table if it exists.
-   if (coarse_fes->GetElementToFaceOrientationTable())
-   {
-      old_elem_fos = new Table(*coarse_fes->GetElementToFaceOrientationTable());
-   }
-
-   ConstructDoFTrans();
 }
 
 FiniteElementSpace::RefinementOperator::~RefinementOperator()
 {
    delete old_elem_dof;
-   delete old_elem_fos;
-}
-
-void FiniteElementSpace::RefinementOperator
-::ConstructDoFTrans()
-{
-   old_DoFTrans.SetSize(Geometry::NUM_GEOMETRIES);
-   for (int i=0; i<old_DoFTrans.Size(); i++)
-   {
-      old_DoFTrans[i] = NULL;
-   }
-
-   const FiniteElementCollection *fec = fespace->FEColl();
-   if (dynamic_cast<const ND_FECollection*>(fec))
-   {
-      const FiniteElement * nd_tri =
-         fec->FiniteElementForGeometry(Geometry::TRIANGLE);
-      if (nd_tri)
-      {
-         old_DoFTrans[Geometry::TRIANGLE] =
-            new ND_TriDofTransformation(nd_tri->GetOrder());
-      }
-
-      const FiniteElement * nd_tet =
-         fec->FiniteElementForGeometry(Geometry::TETRAHEDRON);
-      if (nd_tet)
-      {
-         old_DoFTrans[Geometry::TETRAHEDRON] =
-            new ND_TetDofTransformation(nd_tet->GetOrder());
-      }
-   }
 }
 
 void FiniteElementSpace::RefinementOperator
@@ -1553,7 +1462,7 @@ void FiniteElementSpace::RefinementOperator
    Mesh* mesh = fespace->GetMesh();
    const CoarseFineTransformations &rtrans = mesh->GetRefinementTransforms();
 
-   Array<int> dofs, vdofs, old_dofs, old_vdofs, old_Fo;
+   Array<int> dofs, vdofs, old_dofs, old_vdofs;
 
    int vdim = fespace->GetVDim();
    int old_ndofs = width / vdim;
@@ -1568,53 +1477,18 @@ void FiniteElementSpace::RefinementOperator
 
       subY.SetSize(lP.Height());
 
-      DofTransformation *doftrans = fespace->GetElementDofs(k, dofs);
+      fespace->GetElementDofs(k, dofs);
       old_elem_dof->GetRow(emb.parent, old_dofs);
 
-      if (!doftrans)
+      for (int vd = 0; vd < vdim; vd++)
       {
-         for (int vd = 0; vd < vdim; vd++)
-         {
-            dofs.Copy(vdofs);
-            fespace->DofsToVDofs(vd, vdofs);
-            old_dofs.Copy(old_vdofs);
-            fespace->DofsToVDofs(vd, old_vdofs, old_ndofs);
-            x.GetSubVector(old_vdofs, subX);
-            lP.Mult(subX, subY);
-            y.SetSubVector(vdofs, subY);
-         }
-      }
-      else
-      {
-         old_elem_fos->GetRow(emb.parent, old_Fo);
-         old_DoFTrans[geom]->SetFaceOrientations(old_Fo);
-
-         DofTransformation *new_doftrans = NULL;
-         VDofTransformation *vdoftrans =
-            dynamic_cast<VDofTransformation*>(doftrans);
-         if (vdoftrans)
-         {
-            new_doftrans = doftrans;
-            doftrans = vdoftrans->GetDofTransformation();
-         }
-
-         for (int vd = 0; vd < vdim; vd++)
-         {
-            dofs.Copy(vdofs);
-            fespace->DofsToVDofs(vd, vdofs);
-            old_dofs.Copy(old_vdofs);
-            fespace->DofsToVDofs(vd, old_vdofs, old_ndofs);
-            x.GetSubVector(old_vdofs, subX);
-            old_DoFTrans[geom]->InvTransformPrimal(subX);
-            lP.Mult(subX, subY);
-            doftrans->TransformPrimal(subY);
-            y.SetSubVector(vdofs, subY);
-         }
-
-         if (vdoftrans)
-         {
-            doftrans = new_doftrans;
-         }
+         dofs.Copy(vdofs);
+         fespace->DofsToVDofs(vd, vdofs);
+         old_dofs.Copy(old_vdofs);
+         fespace->DofsToVDofs(vd, old_vdofs, old_ndofs);
+         x.GetSubVector(old_vdofs, subX);
+         lP.Mult(subX, subY);
+         y.SetSubVector(vdofs, subY);
       }
    }
 }
@@ -1630,12 +1504,12 @@ void FiniteElementSpace::RefinementOperator
    Array<char> processed(fespace->GetVSize());
    processed = 0;
 
-   Array<int> f_dofs, c_dofs, f_vdofs, c_vdofs, old_Fo;
+   Array<int> f_dofs, c_dofs, f_vdofs, c_vdofs;
 
    int vdim = fespace->GetVDim();
    int old_ndofs = width / vdim;
 
-   Vector subY, subX, subYt, subXt;
+   Vector subY, subX;
 
    for (int k = 0; k < mesh->GetNE(); k++)
    {
@@ -1643,77 +1517,30 @@ void FiniteElementSpace::RefinementOperator
       const Geometry::Type geom = mesh->GetElementBaseGeometry(k);
       const DenseMatrix &lP = localP[geom](emb.matrix);
 
-      DofTransformation * doftrans = fespace->GetElementDofs(k, f_dofs);
+      fespace->GetElementDofs(k, f_dofs);
       old_elem_dof->GetRow(emb.parent, c_dofs);
 
-      if (!doftrans)
+      subY.SetSize(lP.Width());
+
+      for (int vd = 0; vd < vdim; vd++)
       {
-         subY.SetSize(lP.Width());
+         f_dofs.Copy(f_vdofs);
+         fespace->DofsToVDofs(vd, f_vdofs);
+         c_dofs.Copy(c_vdofs);
+         fespace->DofsToVDofs(vd, c_vdofs, old_ndofs);
 
-         for (int vd = 0; vd < vdim; vd++)
+         x.GetSubVector(f_vdofs, subX);
+
+         for (int p = 0; p < f_dofs.Size(); ++p)
          {
-            f_dofs.Copy(f_vdofs);
-            fespace->DofsToVDofs(vd, f_vdofs);
-            c_dofs.Copy(c_vdofs);
-            fespace->DofsToVDofs(vd, c_vdofs, old_ndofs);
-
-            x.GetSubVector(f_vdofs, subX);
-
-            for (int p = 0; p < f_dofs.Size(); ++p)
+            if (processed[DecodeDof(f_dofs[p])])
             {
-               if (processed[DecodeDof(f_dofs[p])])
-               {
-                  subX[p] = 0.0;
-               }
+               subX[p] = 0.0;
             }
-
-            lP.MultTranspose(subX, subY);
-            y.AddElementVector(c_vdofs, subY);
-         }
-      }
-      else
-      {
-         subYt.SetSize(lP.Width());
-
-         old_elem_fos->GetRow(emb.parent, old_Fo);
-         old_DoFTrans[geom]->SetFaceOrientations(old_Fo);
-
-         DofTransformation *new_doftrans = NULL;
-         VDofTransformation *vdoftrans =
-            dynamic_cast<VDofTransformation*>(doftrans);
-         if (vdoftrans)
-         {
-            new_doftrans = doftrans;
-            doftrans = vdoftrans->GetDofTransformation();
          }
 
-         for (int vd = 0; vd < vdim; vd++)
-         {
-            f_dofs.Copy(f_vdofs);
-            fespace->DofsToVDofs(vd, f_vdofs);
-            c_dofs.Copy(c_vdofs);
-            fespace->DofsToVDofs(vd, c_vdofs, old_ndofs);
-
-            x.GetSubVector(f_vdofs, subX);
-            old_DoFTrans[geom]->InvTransformPrimal(subX);
-
-            for (int p = 0; p < f_dofs.Size(); ++p)
-            {
-               if (processed[DecodeDof(f_dofs[p])])
-               {
-                  subX[p] = 0.0;
-               }
-            }
-
-            lP.MultTranspose(subX, subY);
-            doftrans->TransformPrimal(subY);
-            y.AddElementVector(c_vdofs, subY);
-         }
-
-         if (vdoftrans)
-         {
-            doftrans = new_doftrans;
-         }
+         lP.MultTranspose(subX, subY);
+         y.AddElementVector(c_vdofs, subY);
       }
 
       for (int p = 0; p < f_dofs.Size(); ++p)
@@ -1723,7 +1550,6 @@ void FiniteElementSpace::RefinementOperator
    }
 }
 
-/// TODO: Implement DofTransformation support
 FiniteElementSpace::DerefinementOperator::DerefinementOperator(
    const FiniteElementSpace *f_fes, const FiniteElementSpace *c_fes,
    BilinearFormIntegrator *mass_integ)
@@ -1881,11 +1707,8 @@ void FiniteElementSpace::GetLocalDerefinementMatrices(Geometry::Type geom,
 }
 
 SparseMatrix* FiniteElementSpace::DerefinementMatrix(int old_ndofs,
-                                                     const Table* old_elem_dof,
-                                                     const Table* old_elem_fos)
+                                                     const Table* old_elem_dof)
 {
-   /// TODO: Implement DofTransformation support
-
    MFEM_VERIFY(Nonconforming(), "Not implemented for conforming meshes.");
    MFEM_VERIFY(old_ndofs, "Missing previous (finer) space.");
    MFEM_VERIFY(ndofs <= old_ndofs, "Previous space is not finer.");
@@ -1991,7 +1814,6 @@ void FiniteElementSpace::Constructor(Mesh *mesh, NURBSExtension *NURBSext,
    this->ordering = (Ordering::Type) ordering;
 
    elem_dof = NULL;
-   elem_fos = NULL;
    face_dof = NULL;
 
    sequence = 0;
@@ -2019,8 +1841,6 @@ void FiniteElementSpace::Constructor(Mesh *mesh, NURBSExtension *NURBSext,
       UpdateNURBS();
       cP = cR = cR_hp = NULL;
       cP_is_set = false;
-
-      ConstructDoFTrans();
    }
    else
    {
@@ -2028,41 +1848,9 @@ void FiniteElementSpace::Constructor(Mesh *mesh, NURBSExtension *NURBSext,
       own_ext = 0;
       Construct();
    }
-
    BuildElementToDofTable();
 }
 
-void FiniteElementSpace::ConstructDoFTrans()
-{
-   DestroyDoFTrans();
-
-   VDoFTrans.SetVDim(vdim);
-   DoFTrans.SetSize(Geometry::NUM_GEOMETRIES);
-   for (int i=0; i<DoFTrans.Size(); i++)
-   {
-      DoFTrans[i] = NULL;
-   }
-   if (mesh->Dimension() < 3) { return; }
-   if (dynamic_cast<const ND_FECollection*>(fec))
-   {
-      const FiniteElement * nd_tri =
-         fec->FiniteElementForGeometry(Geometry::TRIANGLE);
-      if (nd_tri)
-      {
-         DoFTrans[Geometry::TRIANGLE] =
-            new ND_TriDofTransformation(nd_tri->GetOrder());
-      }
-
-      const FiniteElement * nd_tet =
-         fec->FiniteElementForGeometry(Geometry::TETRAHEDRON);
-      if (nd_tet)
-      {
-         DoFTrans[Geometry::TETRAHEDRON] =
-            new ND_TetDofTransformation(nd_tet->GetOrder());
-      }
-   }
-}
-
 NURBSExtension *FiniteElementSpace::StealNURBSext()
 {
    if (NURBSext && !own_ext)
@@ -2158,9 +1946,7 @@ void FiniteElementSpace::Construct()
                "Variable order space requires a nonconforming mesh.");
 
    elem_dof = NULL;
-   elem_fos = NULL;
    bdr_elem_dof = NULL;
-   bdr_elem_fos = NULL;
    face_dof = NULL;
 
    ndofs = 0;
@@ -2258,8 +2044,6 @@ void FiniteElementSpace::Construct()
 
    ndofs = nvdofs + nedofs + nfdofs + nbdofs;
 
-   ConstructDoFTrans();
-
    // record the current mesh sequence number to detect refinement etc.
    mesh_sequence = mesh->GetSequence();
 
@@ -2511,22 +2295,14 @@ int FiniteElementSpace::GetNVariants(int entity, int index) const
 static const char* msg_orders_changed =
    "Element orders changed, you need to Update() the space first.";
 
-DofTransformation *
-FiniteElementSpace::GetElementDofs(int elem, Array<int> &dofs) const
+void FiniteElementSpace::GetElementDofs(int elem, Array<int> &dofs) const
 {
    MFEM_VERIFY(!orders_changed, msg_orders_changed);
 
    if (elem_dof)
    {
       elem_dof->GetRow(elem, dofs);
-
-      if (DoFTrans[mesh->GetElementBaseGeometry(elem)])
-      {
-         Array<int> Fo;
-         elem_fos -> GetRow (elem, Fo);
-         DoFTrans[mesh->GetElementBaseGeometry(elem)]->SetFaceOrientations(Fo);
-      }
-      return DoFTrans[mesh->GetElementBaseGeometry(elem)];
+      return;
    }
 
    Array<int> V, E, Eo, F, Fo; // TODO: LocalArray
@@ -2550,11 +2326,6 @@ FiniteElementSpace::GetElementDofs(int elem, Array<int> &dofs) const
       {
          nfd += fec->GetNumDof(mesh->GetFaceGeometry(F[i]), order);
       }
-      if (DoFTrans[mesh->GetElementBaseGeometry(elem)])
-      {
-         DoFTrans[mesh->GetElementBaseGeometry(elem)]
-         -> SetFaceOrientations(Fo);
-      }
    }
 
    dofs.SetSize(0);
@@ -2612,7 +2383,6 @@ FiniteElementSpace::GetElementDofs(int elem, Array<int> &dofs) const
          dofs.Append(bbase + j);
       }
    }
-   return DoFTrans[mesh->GetElementBaseGeometry(elem)];
 }
 
 const FiniteElement *FiniteElementSpace::GetFE(int i) const
@@ -2645,27 +2415,18 @@ const FiniteElement *FiniteElementSpace::GetFE(int i) const
    return FE;
 }
 
-DofTransformation *
-FiniteElementSpace::GetBdrElementDofs(int bel, Array<int> &dofs) const
+void FiniteElementSpace::GetBdrElementDofs(int bel, Array<int> &dofs) const
 {
    MFEM_VERIFY(!orders_changed, msg_orders_changed);
 
    if (bdr_elem_dof)
    {
       bdr_elem_dof->GetRow(bel, dofs);
-
-      if (DoFTrans[mesh->GetBdrElementBaseGeometry(bel)])
-      {
-         Array<int> Fo;
-         bdr_elem_fos -> GetRow (bel, Fo);
-         DoFTrans[mesh->GetBdrElementBaseGeometry(bel)]->
-         SetFaceOrientations(Fo);
-      }
-      return DoFTrans[mesh->GetBdrElementBaseGeometry(bel)];
+      return;
    }
 
-   Array<int> V, E, Eo, Fo; // TODO: LocalArray
-   int F, oF;
+   Array<int> V, E, Eo; // TODO: LocalArray
+   int F, Fo;
 
    int dim = mesh->Dimension();
    auto geom = mesh->GetBdrElementGeometry(bel);
@@ -2684,17 +2445,7 @@ FiniteElementSpace::GetBdrElementDofs(int bel, Array<int> &dofs) const
 
    if (nv) { mesh->GetBdrElementVertices(bel, V); }
    if (ne) { mesh->GetBdrElementEdges(bel, E, Eo); }
-   if (nf)
-   {
-      mesh->GetBdrElementFace(bel, &F, &oF);
-
-      if (DoFTrans[mesh->GetBdrElementBaseGeometry(bel)])
-      {
-         Fo.Append(oF);
-         DoFTrans[mesh->GetBdrElementBaseGeometry(bel)]->
-         SetFaceOrientations(Fo);
-      }
-   }
+   if (nf) { mesh->GetBdrElementFace(bel, &F, &Fo); }
 
    dofs.SetSize(0);
    dofs.Reserve(nv*V.Size() + ne*E.Size() + nf);
@@ -2727,15 +2478,13 @@ FiniteElementSpace::GetBdrElementDofs(int bel, Array<int> &dofs) const
    if (nf) // face DOFs
    {
       int fbase = (var_face_dofs.Size() > 0) ? FindFaceDof(F, nf) : F*nf;
-      const int *ind = fec->GetDofOrdering(geom, order, oF);
+      const int *ind = fec->GetDofOrdering(geom, order, Fo);
 
       for (int j = 0; j < nf; j++)
       {
          dofs.Append(EncodeDof(nvdofs + nedofs + fbase, ind[j]));
       }
    }
-
-   return DoFTrans[mesh->GetBdrElementBaseGeometry(bel)];
 }
 
 int FiniteElementSpace::GetFaceDofs(int face, Array<int> &dofs,
@@ -3045,8 +2794,6 @@ void FiniteElementSpace::Destroy()
    }
    E2BFQ_array.SetSize(0);
 
-   DestroyDoFTrans();
-
    dof_elem_array.DeleteAll();
    dof_ldof_array.DeleteAll();
 
@@ -3059,9 +2806,7 @@ void FiniteElementSpace::Destroy()
    else
    {
       delete elem_dof;
-      delete elem_fos;
       delete bdr_elem_dof;
-      delete bdr_elem_fos;
       delete face_dof;
 
       delete [] bdofs;
@@ -3069,15 +2814,6 @@ void FiniteElementSpace::Destroy()
    ceed::RemoveBasisAndRestriction(this);
 }
 
-void FiniteElementSpace::DestroyDoFTrans()
-{
-   for (int i = 0; i < DoFTrans.Size(); i++)
-   {
-      delete DoFTrans[i];
-   }
-   DoFTrans.SetSize(0);
-}
-
 void FiniteElementSpace::GetTransferOperator(
    const FiniteElementSpace &coarse_fes, OperatorHandle &T) const
 {
@@ -3095,8 +2831,6 @@ void FiniteElementSpace::GetTransferOperator(
       }
       T.Reset(RefinementMatrix_main(coarse_fes.GetNDofs(),
                                     coarse_fes.GetElementToDofTable(),
-                                    coarse_fes.
-                                    GetElementToFaceOrientationTable(),
                                     localP));
    }
    else
@@ -3199,7 +2933,6 @@ void FiniteElementSpace::Update(bool want_transform)
    }
 
    Table* old_elem_dof = NULL;
-   Table* old_elem_fos = NULL;
    int old_ndofs;
    bool old_orders_changed = orders_changed;
 
@@ -3207,9 +2940,7 @@ void FiniteElementSpace::Update(bool want_transform)
    if (want_transform)
    {
       old_elem_dof = elem_dof;
-      old_elem_fos = elem_fos;
       elem_dof = NULL;
-      elem_fos = NULL;
       old_ndofs = ndofs;
    }
 
@@ -3235,18 +2966,15 @@ void FiniteElementSpace::Update(bool want_transform)
          {
             if (Th.Type() != Operator::MFEM_SPARSEMAT)
             {
-               Th.Reset(new RefinementOperator(this, old_elem_dof,
-                                               old_elem_fos, old_ndofs));
+               Th.Reset(new RefinementOperator(this, old_elem_dof, old_ndofs));
                // The RefinementOperator takes ownership of 'old_elem_dof', so
                // we no longer own it:
                old_elem_dof = NULL;
-               old_elem_fos = NULL;
             }
             else
             {
                // calculate fully assembled matrix
-               Th.Reset(RefinementMatrix(old_ndofs, old_elem_dof,
-                                         old_elem_fos));
+               Th.Reset(RefinementMatrix(old_ndofs, old_elem_dof));
             }
             break;
          }
@@ -3254,7 +2982,7 @@ void FiniteElementSpace::Update(bool want_transform)
          case Mesh::DEREFINE:
          {
             BuildConformingInterpolation();
-            Th.Reset(DerefinementMatrix(old_ndofs, old_elem_dof, old_elem_fos));
+            Th.Reset(DerefinementMatrix(old_ndofs, old_elem_dof));
             if (cP && cR)
             {
                Th.SetOperatorOwner(false);
@@ -3269,7 +2997,6 @@ void FiniteElementSpace::Update(bool want_transform)
       }
 
       delete old_elem_dof;
-      delete old_elem_fos;
    }
 }
 

fem/fespace.hpp

@@ -16,7 +16,6 @@
 #include "../linalg/sparsemat.hpp"
 #include "../mesh/mesh.hpp"
 #include "fe_coll.hpp"
-#include "doftrans.hpp"
 #include "restriction.hpp"
 #include <iostream>
 #include <unordered_map>
@@ -129,9 +128,7 @@ protected:
 
    // precalculated DOFs for each element, boundary element, and face
    mutable Table *elem_dof; // owned (except in NURBS FE space)
-   mutable Table *elem_fos; // face orientations by element index
    mutable Table *bdr_elem_dof; // owned (except in NURBS FE space)
-   mutable Table *bdr_elem_fos; // bdr face orientations by bdr element index
    mutable Table *face_dof; // owned; in var-order space contains variant 0 DOFs
 
    Array<int> dof_elem_array, dof_ldof_array;
@@ -140,9 +137,6 @@ protected:
    int own_ext;
    mutable Array<int> face_to_be; // NURBS FE space only
 
-   Array<DofTransformation*> DoFTrans;
-   mutable VDofTransformation VDoFTrans;
-
    /** Matrix representing the prolongation from the global conforming dofs to
        a set of intermediate partially conforming dofs, e.g. the dofs associated
        with a "cut" space on a non-conforming mesh. */
@@ -195,9 +189,6 @@ protected:
    void Construct();
    void Destroy();
 
-   void ConstructDoFTrans();
-   void DestroyDoFTrans();
-
    void BuildElementToDofTable() const;
    void BuildBdrElementToDofTable() const;
    void BuildFaceToDofTable() const;
@@ -292,19 +283,12 @@ protected:
       const FiniteElementSpace* fespace;
       DenseTensor localP[Geometry::NumGeom];
       Table* old_elem_dof; // Owned.
-      Table* old_elem_fos; // Owned.
-
-      Array<DofTransformation*> old_DoFTrans;
-      mutable VDofTransformation old_VDoFTrans;
-
-      void ConstructDoFTrans();
 
    public:
       /** Construct the operator based on the elem_dof table of the original
           (coarse) space. The class takes ownership of the table. */
       RefinementOperator(const FiniteElementSpace* fespace,
-                         Table *old_elem_dof/*takes ownership*/,
-                         Table *old_elem_fos/*takes ownership*/, int old_ndofs);
+                         Table *old_elem_dof/*takes ownership*/, int old_ndofs);
       RefinementOperator(const FiniteElementSpace *fespace,
                          const FiniteElementSpace *coarse_fes);
       virtual void Mult(const Vector &x, Vector &y) const;
@@ -318,7 +302,6 @@ protected:
       const FiniteElementSpace *fine_fes; // Not owned.
       DenseTensor localR[Geometry::NumGeom];
       Table *coarse_elem_dof; // Owned.
-      // Table *coarse_elem_fos; // Owned.
       Table coarse_to_fine;
       Array<int> coarse_to_ref_type;
       Array<Geometry::Type> ref_type_to_geom;
@@ -340,7 +323,6 @@ protected:
        the same vector dimension, vdim. */
    SparseMatrix *RefinementMatrix_main(const int coarse_ndofs,
                                        const Table &coarse_elem_dof,
-                                       const Table *coarse_elem_fos,
                                        const DenseTensor localP[]) const;
 
    void GetLocalRefinementMatrices(Geometry::Type geom,
@@ -351,12 +333,10 @@ protected:
    /** Calculate explicit GridFunction interpolation matrix (after mesh
        refinement). NOTE: consider using the RefinementOperator class instead
        of the fully assembled matrix, which can take a lot of memory. */
-   SparseMatrix* RefinementMatrix(int old_ndofs, const Table* old_elem_dof,
-                                  const Table* old_elem_fos);
+   SparseMatrix* RefinementMatrix(int old_ndofs, const Table* old_elem_dof);
 
    /// Calculate GridFunction restriction matrix after mesh derefinement.
-   SparseMatrix* DerefinementMatrix(int old_ndofs, const Table* old_elem_dof,
-                                    const Table* old_elem_fos);
+   SparseMatrix* DerefinementMatrix(int old_ndofs, const Table* old_elem_dof);
 
    /** @brief Return in @a localP the local refinement matrices that map
        between fespaces after mesh refinement. */
@@ -634,11 +614,10 @@ public:
    int GetBdrAttribute(int i) const { return mesh->GetBdrAttribute(i); }
 
    /// Returns indices of degrees of freedom of element 'elem'.
-   virtual DofTransformation *GetElementDofs(int elem, Array<int> &dofs) const;
+   virtual void GetElementDofs(int elem, Array<int> &dofs) const;
 
    /// Returns indices of degrees of freedom for boundary element 'bel'.
-   virtual DofTransformation *GetBdrElementDofs(int bel,
-                                                Array<int> &dofs) const;
+   virtual void GetBdrElementDofs(int bel, Array<int> &dofs) const;
 
    /** @brief Returns the indices of the degrees of freedom for the specified
        face, including the DOFs for the edges and the vertices of the face. */
@@ -687,10 +666,10 @@ public:
    static void AdjustVDofs(Array<int> &vdofs);
 
    /// Returns indexes of degrees of freedom in array dofs for i'th element.
-   DofTransformation *GetElementVDofs(int i, Array<int> &vdofs) const;
+   void GetElementVDofs(int i, Array<int> &vdofs) const;
 
    /// Returns indexes of degrees of freedom for i'th boundary element.
-   DofTransformation *GetBdrElementVDofs(int i, Array<int> &vdofs) const;
+   void GetBdrElementVDofs(int i, Array<int> &vdofs) const;
 
    /// Returns indexes of degrees of freedom for i'th face element (2D and 3D).
    void GetFaceVDofs(int i, Array<int> &vdofs) const;
@@ -716,8 +695,6 @@ public:
        is preserved. */
    void ReorderElementToDofTable();
 
-   const Table *GetElementToFaceOrientationTable() const { return elem_fos; }
-
    /** @brief Return a reference to the internal Table that stores the lists of
        scalar dofs, for each mesh element, as returned by GetElementDofs(). */
    const Table &GetElementToDofTable() const { return *elem_dof; }

fem/geom.cpp

@@ -11,19 +11,15 @@
 
 #include "fem.hpp"
 #include "../mesh/wedge.hpp"
-#include "../mesh/pyramid.hpp"
 
 namespace mfem
 {
 
 const char *Geometry::Name[NumGeom] =
-{
-   "Point", "Segment", "Triangle", "Square", "Tetrahedron", "Cube", "Prism",
-   "Pyramid"
-};
+{ "Point", "Segment", "Triangle", "Square", "Tetrahedron", "Cube", "Prism" };
 
 const double Geometry::Volume[NumGeom] =
-{ 1.0, 1.0, 0.5, 1.0, 1./6, 1.0, 0.5, 1./3 };
+{ 1.0, 1.0, 0.5, 1.0, 1./6, 1.0, 0.5 };
 
 Geometry::Geometry()
 {
@@ -143,28 +139,6 @@ Geometry::Geometry()
    GeomVert[6]->IntPoint(5).y = 1.0;
    GeomVert[6]->IntPoint(5).z = 1.0;
 
-   // Vertices for Geometry::PYRAMID
-   GeomVert[7] = new IntegrationRule(5);
-   GeomVert[7]->IntPoint(0).x = 0.0;
-   GeomVert[7]->IntPoint(0).y = 0.0;
-   GeomVert[7]->IntPoint(0).z = 0.0;
-
-   GeomVert[7]->IntPoint(1).x = 1.0;
-   GeomVert[7]->IntPoint(1).y = 0.0;
-   GeomVert[7]->IntPoint(1).z = 0.0;
-
-   GeomVert[7]->IntPoint(2).x = 1.0;
-   GeomVert[7]->IntPoint(2).y = 1.0;
-   GeomVert[7]->IntPoint(2).z = 0.0;
-
-   GeomVert[7]->IntPoint(3).x = 0.0;
-   GeomVert[7]->IntPoint(3).y = 1.0;
-   GeomVert[7]->IntPoint(3).z = 0.0;
-
-   GeomVert[7]->IntPoint(4).x = 0.0;
-   GeomVert[7]->IntPoint(4).y = 0.0;
-   GeomVert[7]->IntPoint(4).z = 1.0;
-
    GeomCenter[POINT].x = 0.0;
    GeomCenter[POINT].y = 0.0;
    GeomCenter[POINT].z = 0.0;
@@ -193,10 +167,6 @@ Geometry::Geometry()
    GeomCenter[PRISM].y = 1.0 / 3.0;
    GeomCenter[PRISM].z = 0.5;
 
-   GeomCenter[PYRAMID].x = 0.375;
-   GeomCenter[PYRAMID].y = 0.375;
-   GeomCenter[PYRAMID].z = 0.25;
-
    GeomToPerfGeomJac[POINT]       = NULL;
    GeomToPerfGeomJac[SEGMENT]     = new DenseMatrix(1);
    GeomToPerfGeomJac[TRIANGLE]    = new DenseMatrix(2);
@@ -204,7 +174,6 @@ Geometry::Geometry()
    GeomToPerfGeomJac[TETRAHEDRON] = new DenseMatrix(3);
    GeomToPerfGeomJac[CUBE]        = new DenseMatrix(3);
    GeomToPerfGeomJac[PRISM]       = new DenseMatrix(3);
-   GeomToPerfGeomJac[PYRAMID]     = new DenseMatrix(3);
 
    PerfGeomToGeomJac[POINT]       = NULL;
    PerfGeomToGeomJac[SEGMENT]     = NULL;
@@ -213,7 +182,6 @@ Geometry::Geometry()
    PerfGeomToGeomJac[TETRAHEDRON] = new DenseMatrix(3);
    PerfGeomToGeomJac[CUBE]        = NULL;
    PerfGeomToGeomJac[PRISM]       = new DenseMatrix(3);
-   PerfGeomToGeomJac[PYRAMID]     = new DenseMatrix(3);
 
    GeomToPerfGeomJac[SEGMENT]->Diag(1.0, 1);
    {
@@ -242,14 +210,6 @@ Geometry::Geometry()
       *GeomToPerfGeomJac[PRISM] = pri_T.Jacobian();
       CalcInverse(pri_T.Jacobian(), *PerfGeomToGeomJac[PRISM]);
    }
-   {
-      IsoparametricTransformation pyr_T;
-      pyr_T.SetFE(&PyramidFE);
-      GetPerfPointMat (PYRAMID, pyr_T.GetPointMat());
-      pyr_T.SetIntPoint(&GeomCenter[PYRAMID]);
-      *GeomToPerfGeomJac[PYRAMID] = pyr_T.Jacobian();
-      CalcInverse(pyr_T.Jacobian(), *PerfGeomToGeomJac[PYRAMID]);
-   }
 }
 
 Geometry::~Geometry()
@@ -273,7 +233,6 @@ const IntegrationRule * Geometry::GetVertices(int GeomType)
       case Geometry::TETRAHEDRON: return GeomVert[4];
       case Geometry::CUBE:        return GeomVert[5];
       case Geometry::PRISM:       return GeomVert[6];
-      case Geometry::PYRAMID:     return GeomVert[7];
       default:
          mfem_error ("Geometry::GetVertices(...)");
    }
@@ -351,25 +310,6 @@ void Geometry::GetRandomPoint(int GeomType, IntegrationPoint &ip)
             ip.y = 1.0 - ip.y;
          }
          break;
-      case Geometry::PYRAMID:
-         ip.x = double(rand()) / RAND_MAX;
-         ip.y = double(rand()) / RAND_MAX;
-         ip.z = double(rand()) / RAND_MAX;
-         if (ip.x + ip.z > 1.0 && ip.y < ip.x)
-         {
-            double x = ip.x;
-            ip.x = ip.y;
-            ip.y = 1.0 - ip.z;
-            ip.z = 1.0 - x;
-         }
-         else if (ip.y + ip.z > 1.0)
-         {
-            double z = ip.z;
-            ip.z = 1.0 - ip.y;
-            ip.y = ip.x;
-            ip.x = 1.0 - z;
-         }
-         break;
       default:
          MFEM_ABORT("Unknown type of reference element!");
    }
@@ -431,10 +371,6 @@ bool Geometry::CheckPoint(int GeomType, const IntegrationPoint &ip)
          if (ip.x < 0.0 || ip.y < 0.0 || ip.x+ip.y > 1.0 ||
              ip.z < 0.0 || ip.z > 1.0) { return false; }
          break;
-      case Geometry::PYRAMID:
-         if (ip.x < 0.0 || ip.y < 0.0 || ip.x+ip.z > 1.0 || ip.y+ip.z > 1.0 ||
-             ip.z < 0.0 || ip.z > 1.0) { return false; }
-         break;
       default:
          MFEM_ABORT("Unknown type of reference element!");
    }
@@ -505,17 +441,6 @@ bool Geometry::CheckPoint(int GeomType, const IntegrationPoint &ip, double eps)
             return false;
          }
          break;
-      case Geometry::PYRAMID:
-         if (internal::FuzzyLT(ip.x, 0.0, eps)
-             || internal::FuzzyLT(ip.y, 0.0, eps)
-             || internal::FuzzyGT(ip.x+ip.z, 1.0, eps)
-             || internal::FuzzyGT(ip.y+ip.z, 1.0, eps)
-             || internal::FuzzyLT(ip.z, 0.0, eps)
-             || internal::FuzzyGT(ip.z, 1.0, eps) )
-         {
-            return false;
-         }
-         break;
       default:
          MFEM_ABORT("Unknown type of reference element!");
    }
@@ -630,16 +555,6 @@ bool Geometry::ProjectPoint(int GeomType, const IntegrationPoint &beg,
          double lbeg[5] = { beg.x, beg.y, beg.z, 1.0-beg.x-beg.y, 1.0-beg.z };
          return internal::IntersectSegment<5,3>(lbeg, lend, end);
       }
-      case Geometry::PYRAMID:
-      {
-         double lend[6] = { end.x, end.y, end.z,
-                            1.0-end.x-end.z, 1.0-end.y-end.z, 1.0-end.z
-                          };
-         double lbeg[6] = { beg.x, beg.y, beg.z,
-                            1.0-beg.x-beg.z, 1.0-beg.y-beg.z, 1.0-beg.z
-                          };
-         return internal::IntersectSegment<6,3>(lbeg, lend, end);
-      }
       default:
          MFEM_ABORT("Unknown type of reference element!");
    }
@@ -737,43 +652,6 @@ bool Geometry::ProjectPoint(int GeomType, IntegrationPoint &ip)
          return in_tri && in_z;
       }
 
-      case PYRAMID:
-      {
-         if (ip.x < 0.0)
-         {
-            ip.x = 0.0;
-            internal::ProjectTriangle(ip.y, ip.z);
-            return false;
-         }
-         if (ip.y < 0.0)
-         {
-            ip.y = 0.0;
-            internal::ProjectTriangle(ip.x, ip.z);
-            return false;
-         }
-         if (ip.z < 0.0)
-         {
-            ip.z = 0.0;
-            if (ip.x > 1.0) { ip.x = 1.0; }
-            if (ip.y > 1.0) { ip.y = 1.0; }
-            return false;
-         }
-         if (ip.x >= ip.y)
-         {
-            bool in_y = true;
-            bool in_tri = internal::ProjectTriangle(ip.x, ip.z);
-            if (ip.y > ip.z) { in_y = false; ip.y = ip.z; }
-            return in_tri && in_y;
-         }
-         else
-         {
-            bool in_x = true;
-            bool in_tri = internal::ProjectTriangle(ip.y, ip.z);
-            if (ip.x > ip.z) { in_x = false; ip.x = ip.z; }
-            return in_tri && in_x;
-         }
-      }
-
       default:
          MFEM_ABORT("Reference element type is not supported!");
    }
@@ -848,17 +726,6 @@ void Geometry::GetPerfPointMat(int GeomType, DenseMatrix &pm)
       }
       break;
 
-      case Geometry::PYRAMID:
-      {
-         pm.SetSize (3, 5);
-         pm(0,0) = 0.0;  pm(1,0) = 0.0;  pm(2,0) = 0.0;
-         pm(0,1) = 1.0;  pm(1,1) = 0.0;  pm(2,1) = 0.0;
-         pm(0,2) = 1.0;  pm(1,2) = 1.0;  pm(2,2) = 0.0;
-         pm(0,3) = 0.0;  pm(1,3) = 1.0;  pm(2,3) = 0.0;
-         pm(0,4) = 0.5;  pm(1,4) = 0.5;  pm(2,4) = 0.7071067811865475;
-      }
-      break;
-
       default:
          mfem_error ("Geometry::GetPerfPointMat (...)");
    }
@@ -877,13 +744,13 @@ void Geometry::JacToPerfJac(int GeomType, const DenseMatrix &J,
    }
 }
 
-const int Geometry::NumBdrArray[NumGeom] = { 0, 2, 3, 4, 4, 6, 5, 5 };
-const int Geometry::Dimension[NumGeom] = { 0, 1, 2, 2, 3, 3, 3, 3 };
+const int Geometry::NumBdrArray[NumGeom] = { 0, 2, 3, 4, 4, 6, 5 };
+const int Geometry::Dimension[NumGeom] = { 0, 1, 2, 2, 3, 3, 3 };
 const int Geometry::DimStart[MaxDim+2] =
 { POINT, SEGMENT, TRIANGLE, TETRAHEDRON, NUM_GEOMETRIES };
-const int Geometry::NumVerts[NumGeom] = { 1, 2, 3, 4, 4, 8, 6, 5 };
-const int Geometry::NumEdges[NumGeom] = { 0, 1, 3, 4, 6, 12, 9, 8 };
-const int Geometry::NumFaces[NumGeom] = { 0, 0, 1, 1, 4, 6, 5, 5 };
+const int Geometry::NumVerts[NumGeom] = { 1, 2, 3, 4, 4, 8, 6 };
+const int Geometry::NumEdges[NumGeom] = { 0, 1, 3, 4, 6, 12, 9 };
+const int Geometry::NumFaces[NumGeom] = { 0, 0, 1, 1, 4, 6, 5 };
 
 const int Geometry::
 Constants<Geometry::POINT>::Orient[1][1] = {{0}};
@@ -1030,30 +897,6 @@ Constants<Geometry::PRISM>::VertToVert::J[9][2] =
    {5, 4}                   // 4,5:4
 };
 
-const int Geometry::
-Constants<Geometry::PYRAMID>::Edges[8][2] =
-{{0, 1}, {1, 2}, {3, 2}, {0, 3}, {0, 4}, {1, 4}, {2, 4}, {3, 4}};
-const int Geometry::
-Constants<Geometry::PYRAMID>::FaceTypes[5] =
-{
-   Geometry::SQUARE,
-   Geometry::TRIANGLE, Geometry::TRIANGLE,
-   Geometry::TRIANGLE, Geometry::TRIANGLE
-};
-const int Geometry::
-Constants<Geometry::PYRAMID>::FaceVert[5][4] =
-{{3, 2, 1, 0}, {0, 1, 4, -1}, {1, 2, 4, -1}, {2, 3, 4, -1}, {3, 0, 4, -1}};
-const int Geometry::
-Constants<Geometry::PYRAMID>::VertToVert::I[5] = {0, 3, 5, 7, 8};
-const int Geometry::
-Constants<Geometry::PYRAMID>::VertToVert::J[8][2] =
-{
-   {1, 0}, {3, 3}, {4, 4}, // 0,1:0   0,3:3  0,4:4
-   {2, 1}, {4, 5},         // 1,2:1   1,4:5
-   {3,-3}, {4, 6},         // 2,3:-3  2,4:6
-   {4, 7}                  // 3,4:7
-};
-
 
 GeometryRefiner::GeometryRefiner()
 {
@@ -1419,104 +1262,6 @@ RefinedGeometry * GeometryRefiner::Refine(Geometry::Type Geom,
          return RG;
       }
 
-      case Geometry::PYRAMID:
-      {
-         const int n = Times;
-         RG = new RefinedGeometry ((n+1)*(n+2)*(2*n+3)/6,
-                                   5*n*(2*n-1)*(2*n+1)/3, 0);
-         RG->Times = Times;
-         RG->ETimes = ETimes;
-         RG->Type = type;
-         // enumerate and define the vertices
-         m = 0;
-         for (k = 0; k <= n; k++)
-         {
-            const double *cpij =
-               poly1d.GetPoints(Times - k, BasisType::GetNodalBasis(type));
-            for (j = 0; j <= n - k; j++)
-               for (i = 0; i <= n - k; i++)
-               {
-                  IntegrationPoint &ip = RG->RefPts.IntPoint(m);
-                  if (type == 0)
-                  {
-                     ip.x = (n > k) ? (double(i) / (n - k)) : 0.0;
-                     ip.y = (n > k) ? (double(j) / (n - k)) : 0.0;
-                     ip.z = double(k) / n;
-                  }
-                  else
-                  {
-                     ip.x = cpij[i] * (1.0 - cp[k]);
-                     ip.y = cpij[j] * (1.0 - cp[k]);
-                     ip.z = cp[k];
-                  }
-                  m++;
-               }
-         }
-         if (m != (n+1)*(n+2)*(2*n+3)/6)
-         {
-            mfem_error("GeometryRefiner::Refine() for PYRAMID #1");
-         }
-         // elements
-         Array<int> &G = RG->RefGeoms;
-         m = 0;
-         for (k = 0; k < n; k++)
-         {
-            int lk = k * (k * (2 * k - 6 * n - 9) + 6 * n * (n + 3) + 13) / 6;
-            int lkp1 = (k + 1) *
-                       (k * (2 * k - 6 * n -5) + 6 * n * (n + 2) + 6) / 6;
-            for (j = 0; j < n - k; j++)
-            {
-               for (i = 0; i < n - k; i++)
-               {
-                  G[m++] = lk + j * (n - k + 1) + i;
-                  G[m++] = lk + j * (n - k + 1) + i + 1;
-                  G[m++] = lk + (j + 1) * (n - k + 1) + i + 1;
-                  G[m++] = lk + (j + 1) * (n - k + 1) + i;
-                  G[m++] = lkp1 + j * (n - k) + i;
-               }
-            }
-            for (j = 0; j < n - k - 1; j++)
-            {
-               for (i = 0; i < n - k - 1; i++)
-               {
-                  G[m++] = lkp1 + j * (n - k) + i;
-                  G[m++] = lkp1 + (j + 1) * (n - k) + i;
-                  G[m++] = lkp1 + (j + 1) * (n - k) + i + 1;
-                  G[m++] = lkp1 + j * (n - k) + i + 1;
-                  G[m++] = lk + (j + 1) * (n - k + 1) + i + 1;
-               }
-            }
-            for (j = 0; j < n - k; j++)
-            {
-               for (i = 0; i < n - k - 1; i++)
-               {
-                  G[m++] = lk + j * (n - k + 1) + i + 1;
-                  G[m++] = lk + (j + 1) * (n - k + 1) + i + 1;
-                  G[m++] = lkp1 + j * (n - k) + i;
-                  G[m++] = lkp1 + j * (n - k) + i + 1;
-                  G[m++] = -1;
-               }
-            }
-            for (j = 0; j < n - k - 1; j++)
-            {
-               for (i = 0; i < n - k; i++)
-               {
-                  G[m++] = lk + (j + 1) * (n - k + 1) + i;
-                  G[m++] = lk + (j + 1) * (n - k + 1) + i + 1;
-                  G[m++] = lkp1 + (j + 1) * (n - k) + i;
-                  G[m++] = lkp1 + j * (n - k) + i;
-                  G[m++] = -1;
-               }
-            }
-         }
-         if (m != 5*n*(2*n-1)*(2*n+1)/3)
-         {
-            mfem_error("GeometryRefiner::Refine() for PYRAMID #2");
-         }
-         RGeom[Geometry::PYRAMID].Append(RG);
-         return RG;
-      }
-
       case Geometry::PRISM:
       {
          const int n = Times;

fem/geom.hpp

@@ -27,7 +27,6 @@ namespace mfem
     Geometry::TETRAHEDRON - w/ vert. (0,0,0),(1,0,0),(0,1,0),(0,0,1)
     Geometry::CUBE - the unit cube
     Geometry::PRISM - w/ vert. (0,0,0),(1,0,0),(0,1,0),(0,0,1),(1,0,1),(0,1,1)
-    Geometry::PYRAMID - w/ vert. (0,0,0),(1,0,0),(1,1,0),(0,1,0),(0,0,1)
 */
 class Geometry
 {
@@ -35,7 +34,7 @@ public:
    enum Type
    {
       INVALID = -1,
-      POINT = 0, SEGMENT, TRIANGLE, SQUARE, TETRAHEDRON, CUBE, PRISM, PYRAMID,
+      POINT = 0, SEGMENT, TRIANGLE, SQUARE, TETRAHEDRON, CUBE, PRISM,
       NUM_GEOMETRIES
    };
 
@@ -252,26 +251,7 @@ template <> struct Geometry::Constants<Geometry::PRISM>
    };
 };
 
-template <> struct Geometry::Constants<Geometry::PYRAMID>
-{
-   static const int Dimension = 3;
-   static const int NumVert = 5;
-   static const int NumEdges = 8;
-   static const int Edges[NumEdges][2];
-   static const int NumFaces = 5;
-   static const int FaceTypes[NumFaces];
-   static const int MaxFaceVert = 4;
-   static const int FaceVert[NumFaces][MaxFaceVert];
-   // Upper-triangular part of the local vertex-to-vertex graph.
-   struct VertToVert
-   {
-      static const int I[NumVert];
-      static const int J[NumEdges][2]; // {end,edge_idx}
-   };
-};
-
-// Defined in fe.cpp to ensure construction after 'mfem::TriangleFE' and
-// `mfem::TetrahedronFE`.
+// Defined in fe.cpp to ensure construction after 'mfem::WedgeFE'.
 extern Geometry Geometries;
 
 

fem/gridfunc.cpp

@@ -255,8 +255,6 @@ void GridFunction::SumFluxAndCount(BilinearFormIntegrator &blfi,
    GridFunction &u = *this;
 
    ElementTransformation *Transf;
-   DofTransformation *udoftrans;
-   DofTransformation *fdoftrans;
 
    FiniteElementSpace *ufes = u.FESpace();
    FiniteElementSpace *ffes = flux.FESpace();
@@ -276,23 +274,15 @@ void GridFunction::SumFluxAndCount(BilinearFormIntegrator &blfi,
          continue;
       }
 
-      udoftrans = ufes->GetElementVDofs(i, udofs);
-      fdoftrans = ffes->GetElementVDofs(i, fdofs);
+      ufes->GetElementVDofs(i, udofs);
+      ffes->GetElementVDofs(i, fdofs);
 
       u.GetSubVector(udofs, ul);
-      if (udoftrans)
-      {
-         udoftrans->InvTransformPrimal(ul);
-      }
 
       Transf = ufes->GetElementTransformation(i);
       blfi.ComputeElementFlux(*ufes->GetFE(i), *Transf, ul,
                               *ffes->GetFE(i), fl, wcoef);
 
-      if (fdoftrans)
-      {
-         fdoftrans->TransformPrimal(fl);
-      }
       flux.AddElementVector(fdofs, fl);
 
       FiniteElementSpace::AdjustVDofs(fdofs);
@@ -374,7 +364,7 @@ void GridFunction::GetNodalValues(int i, Array<double> &nval, int vdim) const
 
    int k;
 
-   DofTransformation * doftrans = fes->GetElementVDofs(i, vdofs);
+   fes->GetElementVDofs(i, vdofs);
    const FiniteElement *FElem = fes->GetFE(i);
    const IntegrationRule *ElemVert =
       Geometries.GetVertices(FElem->GetGeomType());
@@ -384,10 +374,6 @@ void GridFunction::GetNodalValues(int i, Array<double> &nval, int vdim) const
    vdim--;
    Vector loc_data;
    GetSubVector(vdofs, loc_data);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(loc_data);
-   }
 
    if (FElem->GetRangeType() == FiniteElement::SCALAR)
    {
@@ -417,7 +403,7 @@ double GridFunction::GetValue(int i, const IntegrationPoint &ip, int vdim)
 const
 {
    Array<int> dofs;
-   DofTransformation * doftrans = fes->GetElementDofs(i, dofs);
+   fes->GetElementDofs(i, dofs);
    fes->DofsToVDofs(vdim-1, dofs);
    Vector DofVal(dofs.Size()), LocVec;
    const FiniteElement *fe = fes->GetFE(i);
@@ -432,10 +418,6 @@ const
       fe->CalcPhysShape(*Tr, DofVal);
    }
    GetSubVector(dofs, LocVec);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(LocVec);
-   }
 
    return (DofVal * LocVec);
 }
@@ -446,13 +428,9 @@ void GridFunction::GetVectorValue(int i, const IntegrationPoint &ip,
    const FiniteElement *FElem = fes->GetFE(i);
    int dof = FElem->GetDof();
    Array<int> vdofs;
-   DofTransformation * doftrans = fes->GetElementVDofs(i, vdofs);
+   fes->GetElementVDofs(i, vdofs);
    Vector loc_data;
    GetSubVector(vdofs, loc_data);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(loc_data);
-   }
    if (FElem->GetRangeType() == FiniteElement::SCALAR)
    {
       Vector shape(dof);
@@ -492,35 +470,30 @@ const
    Array<int> dofs;
    int n = ir.GetNPoints();
    vals.SetSize(n);
-   DofTransformation * doftrans = fes->GetElementDofs(i, dofs);
+   fes->GetElementDofs(i, dofs);
    fes->DofsToVDofs(vdim-1, dofs);
    const FiniteElement *FElem = fes->GetFE(i);
    int dof = FElem->GetDof();
    Vector DofVal(dof), loc_data(dof);
    GetSubVector(dofs, loc_data);
-   if (doftrans)
+   if (FElem->GetMapType() == FiniteElement::VALUE)
    {
-      doftrans->InvTransformPrimal(loc_data);
+      for (int k = 0; k < n; k++)
+      {
+         FElem->CalcShape(ir.IntPoint(k), DofVal);
+         vals(k) = DofVal * loc_data;
+      }
    }
-   for (int k = 0; k < n; k++)
-      if (FElem->GetMapType() == FiniteElement::VALUE)
+   else
+   {
+      ElementTransformation *Tr = fes->GetElementTransformation(i);
+      for (int k = 0; k < n; k++)
       {
-         for (int k = 0; k < n; k++)
-         {
-            FElem->CalcShape(ir.IntPoint(k), DofVal);
-            vals(k) = DofVal * loc_data;
-         }
-      }
-      else
-      {
-         ElementTransformation *Tr = fes->GetElementTransformation(i);
-         for (int k = 0; k < n; k++)
-         {
-            Tr->SetIntPoint(&ir.IntPoint(k));
-            FElem->CalcPhysShape(*Tr, DofVal);
-            vals(k) = DofVal * loc_data;
-         }
+         Tr->SetIntPoint(&ir.IntPoint(k));
+         FElem->CalcPhysShape(*Tr, DofVal);
+         vals(k) = DofVal * loc_data;
       }
+   }
 }
 
 void GridFunction::GetValues(int i, const IntegrationRule &ir, Vector &vals,
@@ -888,12 +861,11 @@ void GridFunction::GetVectorValue(ElementTransformation &T,
 
    Array<int> vdofs;
    const FiniteElement *fe = NULL;
-   DofTransformation * doftrans = NULL;
 
    switch (T.ElementType)
    {
       case ElementTransformation::ELEMENT:
-         doftrans = fes->GetElementVDofs(T.ElementNo, vdofs);
+         fes->GetElementVDofs(T.ElementNo, vdofs);
          fe = fes->GetFE(T.ElementNo);
          break;
       case ElementTransformation::EDGE:
@@ -984,10 +956,6 @@ void GridFunction::GetVectorValue(ElementTransformation &T,
    int dof = fe->GetDof();
    Vector loc_data;
    GetSubVector(vdofs, loc_data);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(loc_data);
-   }
    if (fe->GetRangeType() == FiniteElement::SCALAR)
    {
       Vector shape(dof);
@@ -1030,14 +998,10 @@ void GridFunction::GetVectorValues(ElementTransformation &T,
    int dof = FElem->GetDof();
 
    Array<int> vdofs;
-   DofTransformation * doftrans = fes->GetElementVDofs(T.ElementNo, vdofs);
+   fes->GetElementVDofs(T.ElementNo, vdofs);
+
    Vector loc_data;
    GetSubVector(vdofs, loc_data);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(loc_data);
-   }
-
    int nip = ir.GetNPoints();
 
    if (FElem->GetRangeType() == FiniteElement::SCALAR)
@@ -1125,8 +1089,6 @@ void GridFunction::GetValuesFrom(const GridFunction &orig_func)
    // Without averaging ...
 
    const FiniteElementSpace *orig_fes = orig_func.FESpace();
-   DofTransformation * doftrans;
-   DofTransformation * orig_doftrans;
    Array<int> vdofs, orig_vdofs;
    Vector shape, loc_values, orig_loc_values;
    int i, j, d, ne, dof, odof, vdim;
@@ -1135,13 +1097,9 @@ void GridFunction::GetValuesFrom(const GridFunction &orig_func)
    vdim = fes->GetVDim();
    for (i = 0; i < ne; i++)
    {
-      doftrans = fes->GetElementVDofs(i, vdofs);
-      orig_doftrans = orig_fes->GetElementVDofs(i, orig_vdofs);
+      fes->GetElementVDofs(i, vdofs);
+      orig_fes->GetElementVDofs(i, orig_vdofs);
       orig_func.GetSubVector(orig_vdofs, orig_loc_values);
-      if (orig_doftrans)
-      {
-         orig_doftrans->InvTransformPrimal(orig_loc_values);
-      }
       const FiniteElement *fe = fes->GetFE(i);
       const FiniteElement *orig_fe = orig_fes->GetFE(i);
       dof = fe->GetDof();
@@ -1159,10 +1117,6 @@ void GridFunction::GetValuesFrom(const GridFunction &orig_func)
                shape * ((const double *)orig_loc_values + d * odof) ;
          }
       }
-      if (doftrans)
-      {
-         doftrans->TransformPrimal(loc_values);
-      }
       SetSubVector(vdofs, loc_values);
    }
 }
@@ -1172,10 +1126,8 @@ void GridFunction::GetBdrValuesFrom(const GridFunction &orig_func)
    // Without averaging ...
 
    const FiniteElementSpace *orig_fes = orig_func.FESpace();
-   // DofTransformation * doftrans;
-   // DofTransformation * orig_doftrans;
    Array<int> vdofs, orig_vdofs;
-   Vector shape, loc_values, loc_values_t, orig_loc_values, orig_loc_values_t;
+   Vector shape, loc_values, orig_loc_values;
    int i, j, d, nbe, dof, odof, vdim;
 
    nbe = fes->GetNBE();
@@ -1213,33 +1165,37 @@ void GridFunction::GetVectorFieldValues(
    Array<int> vdofs;
    ElementTransformation *transf;
 
-   int d, k, n, sdim, dof;
+   int d, j, k, n, sdim, dof, ind;
 
    n = ir.GetNPoints();
-   DofTransformation * doftrans = fes->GetElementVDofs(i, vdofs);
+   fes->GetElementVDofs(i, vdofs);
    const FiniteElement *fe = fes->GetFE(i);
    dof = fe->GetDof();
    sdim = fes->GetMesh()->SpaceDimension();
-   // int *dofs = &vdofs[comp*dof];
+   int *dofs = &vdofs[comp*dof];
    transf = fes->GetElementTransformation(i);
    transf->Transform(ir, tr);
    vals.SetSize(n, sdim);
    DenseMatrix vshape(dof, sdim);
-   Vector loc_data, val(sdim);
-   GetSubVector(vdofs, loc_data);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(loc_data);
-   }
+   double a;
    for (k = 0; k < n; k++)
    {
       const IntegrationPoint &ip = ir.IntPoint(k);
       transf->SetIntPoint(&ip);
       fe->CalcVShape(*transf, vshape);
-      vshape.MultTranspose(loc_data, val);
       for (d = 0; d < sdim; d++)
       {
-         vals(k,d) = val(d);
+         a = 0.0;
+         for (j = 0; j < dof; j++)
+            if ( (ind=dofs[j]) >= 0 )
+            {
+               a += vshape(j, d) * data[ind];
+            }
+            else
+            {
+               a -= vshape(j, d) * data[-1-ind];
+            }
+         vals(k, d) = a;
       }
    }
 }
@@ -1409,13 +1365,9 @@ void GridFunction::GetVectorGradientHat(
    const FiniteElement *FElem = fes->GetFE(elNo);
    int dim = FElem->GetDim(), dof = FElem->GetDof();
    Array<int> vdofs;
-   DofTransformation * doftrans = fes->GetElementVDofs(elNo, vdofs);
+   fes->GetElementVDofs(elNo, vdofs);
    Vector loc_data;
    GetSubVector(vdofs, loc_data);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(loc_data);
-   }
    // assuming scalar FE
    int vdim = fes->GetVDim();
    DenseMatrix dshape(dof, dim);
@@ -1454,13 +1406,9 @@ double GridFunction::GetDivergence(ElementTransformation &T) const
          {
             // Assuming RT-type space
             Array<int> dofs;
-            DofTransformation * doftrans = fes->GetElementDofs(elNo, dofs);
+            fes->GetElementDofs(elNo, dofs);
             Vector loc_data, divshape(fe->GetDof());
             GetSubVector(dofs, loc_data);
-            if (doftrans)
-            {
-               doftrans->InvTransformPrimal(loc_data);
-            }
             fe->CalcDivShape(T.GetIntPoint(), divshape);
             return (loc_data * divshape) / T.Weight();
          }
@@ -1551,13 +1499,9 @@ void GridFunction::GetCurl(ElementTransformation &T, Vector &curl) const
          {
             // Assuming ND-type space
             Array<int> dofs;
-            DofTransformation * doftrans = fes->GetElementDofs(elNo, dofs);
+            fes->GetElementDofs(elNo, dofs);
             Vector loc_data;
             GetSubVector(dofs, loc_data);
-            if (doftrans)
-            {
-               doftrans->InvTransformPrimal(loc_data);
-            }
             DenseMatrix curl_shape(fe->GetDof(), fe->GetDim() == 3 ? 3 : 1);
             fe->CalcCurlShape(T.GetIntPoint(), curl_shape);
             curl.SetSize(curl_shape.Width());
@@ -1699,12 +1643,8 @@ void GridFunction::GetGradients(ElementTransformation &tr,
    DenseMatrix dshape(fe->GetDof(), fe->GetDim());
    Vector lval, gh(fe->GetDim()), gcol;
    Array<int> dofs;
-   DofTransformation * doftrans = fes->GetElementDofs(elNo, dofs);
+   fes->GetElementDofs(elNo, dofs);
    GetSubVector(dofs, lval);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(lval);
-   }
    grad.SetSize(fe->GetDim(), ir.GetNPoints());
    for (int i = 0; i < ir.GetNPoints(); i++)
    {
@@ -1784,8 +1724,6 @@ void GridFunction::GetElementAverages(GridFunction &avgs) const
 {
    MassIntegrator Mi;
    DenseMatrix loc_mass;
-   DofTransformation * te_doftrans;
-   DofTransformation * tr_doftrans;
    Array<int> te_dofs, tr_dofs;
    Vector loc_avgs, loc_this;
    Vector int_psi(avgs.Size());
@@ -1796,19 +1734,11 @@ void GridFunction::GetElementAverages(GridFunction &avgs) const
    {
       Mi.AssembleElementMatrix2(*fes->GetFE(i), *avgs.FESpace()->GetFE(i),
                                 *fes->GetElementTransformation(i), loc_mass);
-      tr_doftrans = fes->GetElementDofs(i, tr_dofs);
-      te_doftrans = avgs.FESpace()->GetElementDofs(i, te_dofs);
+      fes->GetElementDofs(i, tr_dofs);
+      avgs.FESpace()->GetElementDofs(i, te_dofs);
       GetSubVector(tr_dofs, loc_this);
-      if (tr_doftrans)
-      {
-         tr_doftrans->InvTransformPrimal(loc_this);
-      }
       loc_avgs.SetSize(te_dofs.Size());
       loc_mass.Mult(loc_this, loc_avgs);
-      if (te_doftrans)
-      {
-         te_doftrans->TransformPrimal(loc_avgs);
-      }
       avgs.AddElementVector(te_dofs, loc_avgs);
       loc_this = 1.0; // assume the local basis for 'this' sums to 1
       loc_mass.Mult(loc_this, loc_avgs);
@@ -1823,12 +1753,8 @@ void GridFunction::GetElementAverages(GridFunction &avgs) const
 void GridFunction::GetElementDofValues(int el, Vector &dof_vals) const
 {
    Array<int> dof_idx;
-   DofTransformation * doftrans = fes->GetElementVDofs(el, dof_idx);
+   fes->GetElementVDofs(el, dof_idx);
    GetSubVector(dof_idx, dof_vals);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(dof_vals);
-   }
 }
 
 void GridFunction::ProjectGridFunction(const GridFunction &src)
@@ -1864,21 +1790,13 @@ void GridFunction::ProjectGridFunction(const GridFunction &src)
          cached_geom = geom;
       }
 
-      DofTransformation * src_doftrans = src.fes->GetElementVDofs(i, src_vdofs);
+      src.fes->GetElementVDofs(i, src_vdofs);
       src.GetSubVector(src_vdofs, src_lvec);
-      if (src_doftrans)
-      {
-         src_doftrans->InvTransformPrimal(src_lvec);
-      }
       for (int vd = 0; vd < vdim; vd++)
       {
          P.Mult(&src_lvec[vd*P.Width()], &dest_lvec[vd*P.Height()]);
       }
-      DofTransformation * doftrans = fes->GetElementVDofs(i, dest_vdofs);
-      if (doftrans)
-      {
-         doftrans->TransformPrimal(dest_lvec);
-      }
+      fes->GetElementVDofs(i, dest_vdofs);
       SetSubVector(dest_vdofs, dest_lvec);
    }
 }
@@ -1887,15 +1805,10 @@ void GridFunction::ImposeBounds(int i, const Vector &weights,
                                 const Vector &lo_, const Vector &hi_)
 {
    Array<int> vdofs;
-   DofTransformation * doftrans = fes->GetElementVDofs(i, vdofs);
+   fes->GetElementVDofs(i, vdofs);
    int size = vdofs.Size();
    Vector vals, new_vals(size);
-
    GetSubVector(vdofs, vals);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(vals);
-   }
 
    MFEM_ASSERT(weights.Size() == size, "Different # of weights and dofs.");
    MFEM_ASSERT(lo_.Size() == size, "Different # of lower bounds and dofs.");
@@ -1912,10 +1825,6 @@ void GridFunction::ImposeBounds(int i, const Vector &weights,
    slbqp.SetPrintLevel(0); // print messages only if not converged
    slbqp.Mult(vals, new_vals);
 
-   if (doftrans)
-   {
-      doftrans->TransformPrimal(new_vals);
-   }
    SetSubVector(vdofs, new_vals);
 }
 
@@ -1923,14 +1832,10 @@ void GridFunction::ImposeBounds(int i, const Vector &weights,
                                 double min_, double max_)
 {
    Array<int> vdofs;
-   DofTransformation * doftrans = fes->GetElementVDofs(i, vdofs);
+   fes->GetElementVDofs(i, vdofs);
    int size = vdofs.Size();
    Vector vals, new_vals(size);
    GetSubVector(vdofs, vals);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(vals);
-   }
 
    double max_val = vals.Max();
    double min_val = vals.Min();
@@ -1938,10 +1843,6 @@ void GridFunction::ImposeBounds(int i, const Vector &weights,
    if (max_val <= min_)
    {
       new_vals = min_;
-      if (doftrans)
-      {
-         doftrans->TransformPrimal(new_vals);
-      }
       SetSubVector(vdofs, new_vals);
       return;
    }
@@ -2377,7 +2278,6 @@ void GridFunction::ProjectDeltaCoefficient(DeltaCoefficient &delta_coeff,
 void GridFunction::ProjectCoefficient(Coefficient &coeff)
 {
    DeltaCoefficient *delta_c = dynamic_cast<DeltaCoefficient *>(&coeff);
-   DofTransformation * doftrans = NULL;
 
    if (delta_c == NULL)
    {
@@ -2386,13 +2286,9 @@ void GridFunction::ProjectCoefficient(Coefficient &coeff)
 
       for (int i = 0; i < fes->GetNE(); i++)
       {
-         doftrans = fes->GetElementVDofs(i, vdofs);
+         fes->GetElementVDofs(i, vdofs);
          vals.SetSize(vdofs.Size());
          fes->GetFE(i)->Project(coeff, *fes->GetElementTransformation(i), vals);
-         if (doftrans)
-         {
-            doftrans->TransformPrimal(vals);
-         }
          SetSubVector(vdofs, vals);
       }
    }
@@ -2438,17 +2334,11 @@ void GridFunction::ProjectCoefficient(VectorCoefficient &vcoeff)
    Array<int> vdofs;
    Vector vals;
 
-   DofTransformation * doftrans = NULL;
-
    for (i = 0; i < fes->GetNE(); i++)
    {
-      doftrans = fes->GetElementVDofs(i, vdofs);
+      fes->GetElementVDofs(i, vdofs);
       vals.SetSize(vdofs.Size());
       fes->GetFE(i)->Project(vcoeff, *fes->GetElementTransformation(i), vals);
-      if (doftrans)
-      {
-         doftrans->TransformPrimal(vals);
-      }
       SetSubVector(vdofs, vals);
    }
 }
@@ -2511,7 +2401,6 @@ void GridFunction::ProjectCoefficient(Coefficient *coeff[])
    double val;
    const FiniteElement *fe;
    ElementTransformation *transf;
-   // DofTransformation * doftrans;
    Array<int> vdofs;
 
    vdim = fes->GetVDim();
@@ -2521,7 +2410,6 @@ void GridFunction::ProjectCoefficient(Coefficient *coeff[])
       fdof = fe->GetDof();
       transf = fes->GetElementTransformation(i);
       const IntegrationRule &ir = fe->GetNodes();
-      // doftrans = fes->GetElementVDofs(i, vdofs);
       fes->GetElementVDofs(i, vdofs);
       for (j = 0; j < fdof; j++)
       {

fem/gridfunc.hpp

@@ -95,12 +95,6 @@ public:
       : Vector(data, f->GetVSize())
    { fes = f; fec = NULL; fes_sequence = f->GetSequence(); UseDevice(true); }
 
-   /** @brief Construct a GridFunction using previously allocated Vector @a base
-       starting at the given offset, @a base_offset. */
-   GridFunction(FiniteElementSpace *f, Vector &base, int base_offset = 0)
-      : Vector(base, base_offset, f->GetVSize())
-   { fes = f; fec = NULL; fes_sequence = f->GetSequence(); UseDevice(true); }
-
    /// Construct a GridFunction on the given Mesh, using the data from @a input.
    /** The content of @a input should be in the format created by the method
        Save(). The reconstructed FiniteElementSpace and FiniteElementCollection

fem/gslib.cpp

@@ -610,12 +610,7 @@ void FindPointsGSLIB::Interpolate(const GridFunction &field_in,
       {
          if (gsl_code[i] == 1) { indl2.Append(i); }
       }
-      int borderPts = indl2.Size();
-#ifdef MFEM_USE_MPI
-      MPI_Allreduce(MPI_IN_PLACE, &borderPts, 1, MPI_INT, MPI_SUM, gsl_comm->c);
-#endif
-      if (borderPts == 0) { return; } // no points on element borders
-
+      if (indl2.Size() == 0) { return; } // no points on element borders
 
       Vector field_out_l2(field_out.Size());
       VectorGridFunctionCoefficient field_in_dg(&field_in);

fem/intrules.cpp

@@ -910,9 +910,6 @@ IntegrationRules::IntegrationRules(int Ref, int type_):
    TetrahedronIntRules.SetSize(32, h_mt);
    TetrahedronIntRules = NULL;
 
-   PyramidIntRules.SetSize(32, h_mt);
-   PyramidIntRules = NULL;
-
    PrismIntRules.SetSize(32, h_mt);
    PrismIntRules = NULL;
 
@@ -933,7 +930,6 @@ const IntegrationRule &IntegrationRules::Get(int GeomType, int Order)
       case Geometry::TETRAHEDRON: ir_array = &TetrahedronIntRules; break;
       case Geometry::CUBE:        ir_array = &CubeIntRules; break;
       case Geometry::PRISM:       ir_array = &PrismIntRules; break;
-      case Geometry::PYRAMID:     ir_array = &PyramidIntRules; break;
       default:
          mfem_error("IntegrationRules::Get(...) : Unknown geometry type!");
          ir_array = NULL;
@@ -980,7 +976,6 @@ void IntegrationRules::Set(int GeomType, int Order, IntegrationRule &IntRule)
       case Geometry::TETRAHEDRON: ir_array = &TetrahedronIntRules; break;
       case Geometry::CUBE:        ir_array = &CubeIntRules; break;
       case Geometry::PRISM:       ir_array = &PrismIntRules; break;
-      case Geometry::PYRAMID:     ir_array = &PyramidIntRules; break;
       default:
          mfem_error("IntegrationRules::Set(...) : Unknown geometry type!");
          ir_array = NULL;
@@ -1024,7 +1019,6 @@ IntegrationRules::~IntegrationRules()
    DeleteIntRuleArray(TetrahedronIntRules);
    DeleteIntRuleArray(CubeIntRules);
    DeleteIntRuleArray(PrismIntRules);
-   DeleteIntRuleArray(PyramidIntRules);
 }
 
 
@@ -1047,8 +1041,6 @@ IntegrationRule *IntegrationRules::GenerateIntegrationRule(int GeomType,
          return CubeIntegrationRule(Order);
       case Geometry::PRISM:
          return PrismIntegrationRule(Order);
-      case Geometry::PYRAMID:
-         return PyramidIntegrationRule(Order);
       default:
          mfem_error("IntegrationRules::Set(...) : Unknown geometry type!");
          return NULL;
@@ -1656,30 +1648,6 @@ IntegrationRule *IntegrationRules::TetrahedronIntegrationRule(int Order)
    }
 }
 
-// Integration rules for reference pyramid
-IntegrationRule *IntegrationRules::PyramidIntegrationRule(int Order)
-{
-   // This is a simple integration rule adapted from an integration
-   // rule for a cube which seems to be adequate for now. When we
-   // implement high order finite elements for pyramids we should
-   // revisit this and see if we can improve upon it.
-   const IntegrationRule &irc = Get(Geometry::CUBE, Order);
-   int npts = irc.GetNPoints();
-   AllocIntRule(PyramidIntRules, Order);
-   PyramidIntRules[Order] = new IntegrationRule(npts);
-
-   for (int k=0; k<npts; k++)
-   {
-      const IntegrationPoint & ipc = irc.IntPoint(k);
-      IntegrationPoint & ipp = PyramidIntRules[Order]->IntPoint(k);
-      ipp.x = ipc.x * (1.0 - ipc.z);
-      ipp.y = ipc.y * (1.0 - ipc.z);
-      ipp.z = ipc.z;
-      ipp.weight = ipc.weight / 3.0;
-   }
-   return PyramidIntRules[Order];
-}
-
 // Integration rules for reference prism
 IntegrationRule *IntegrationRules::PrismIntegrationRule(int Order)
 {

fem/intrules.hpp

@@ -323,7 +323,6 @@ private:
    Array<IntegrationRule *> TriangleIntRules;
    Array<IntegrationRule *> SquareIntRules;
    Array<IntegrationRule *> TetrahedronIntRules;
-   Array<IntegrationRule *> PyramidIntRules;
    Array<IntegrationRule *> PrismIntRules;
    Array<IntegrationRule *> CubeIntRules;
 
@@ -352,7 +351,6 @@ private:
    IntegrationRule *TriangleIntegrationRule(int Order);
    IntegrationRule *SquareIntegrationRule(int Order);
    IntegrationRule *TetrahedronIntegrationRule(int Order);
-   IntegrationRule *PyramidIntegrationRule(int Order);
    IntegrationRule *PrismIntegrationRule(int Order);
    IntegrationRule *CubeIntegrationRule(int Order);
 

fem/linearform.cpp

@@ -103,7 +103,6 @@ void LinearForm::Assemble()
 {
    Array<int> vdofs;
    ElementTransformation *eltrans;
-   DofTransformation *doftrans;
    Vector elemvect;
 
    int i;
@@ -135,14 +134,10 @@ void LinearForm::Assemble()
             if ( domain_integs_marker[k] == NULL ||
                  (*(domain_integs_marker[k]))[elem_attr-1] == 1 )
             {
-               doftrans = fes -> GetElementVDofs (i, vdofs);
+               fes -> GetElementVDofs (i, vdofs);
                eltrans = fes -> GetElementTransformation (i);
                domain_integs[k]->AssembleRHSElementVect(*fes->GetFE(i),
                                                         *eltrans, elemvect);
-               if (doftrans)
-               {
-                  doftrans->TransformDual(elemvect);
-               }
                AddElementVector (vdofs, elemvect);
             }
          }
@@ -179,7 +174,7 @@ void LinearForm::Assemble()
       {
          const int bdr_attr = mesh->GetBdrAttribute(i);
          if (bdr_attr_marker[bdr_attr-1] == 0) { continue; }
-         doftrans = fes -> GetBdrElementVDofs (i, vdofs);
+         fes -> GetBdrElementVDofs (i, vdofs);
          eltrans = fes -> GetBdrElementTransformation (i);
          for (int k=0; k < boundary_integs.Size(); k++)
          {
@@ -189,10 +184,6 @@ void LinearForm::Assemble()
             boundary_integs[k]->AssembleRHSElementVect(*fes->GetBE(i),
                                                        *eltrans, elemvect);
 
-            if (doftrans)
-            {
-               doftrans->TransformDual(elemvect);
-            }
             AddElementVector (vdofs, elemvect);
          }
       }

fem/pbilinearform.cpp

@@ -317,11 +317,14 @@ ParallelEliminateEssentialBC(const Array<int> &bdr_attr_is_ess,
 void ParBilinearForm::TrueAddMult(const Vector &x, Vector &y, const double a)
 const
 {
+   MFEM_VERIFY(interior_face_integs.Size() == 0,
+               "the case of interior face integrators is not"
+               " implemented");
+
    if (X.ParFESpace() != pfes)
    {
       X.SetSpace(pfes);
       Y.SetSpace(pfes);
-      Ytmp.SetSize(pfes->GetTrueVSize());
    }
 
    X.Distribute(&x);
@@ -331,13 +334,9 @@ const
    }
    else
    {
-      MFEM_VERIFY(interior_face_integs.Size() == 0,
-                  "the case of interior face integrators is not"
-                  " implemented");
       mat->Mult(X, Y);
    }
-   pfes->GetProlongationMatrix()->MultTranspose(Y, Ytmp);
-   y.Add(a,Ytmp);
+   pfes->Dof_TrueDof_Matrix()->MultTranspose(a, Y, 1.0, y);
 }
 
 void ParBilinearForm::FormLinearSystem(

fem/pbilinearform.hpp

@@ -33,7 +33,6 @@ protected:
 
    /// Auxiliary objects used in TrueAddMult().
    mutable ParGridFunction X, Y;
-   mutable Vector Ytmp;
 
    OperatorHandle p_mat, p_mat_e;
 

fem/pfespace.cpp

@@ -128,9 +128,6 @@ void ParFiniteElementSpace::ParInit(ParMesh *pm)
    {
       ApplyLDofSigns(*elem_dof);
    }
-
-   // Check for shared trianglular faces with interior Nedelec DoFs
-   CheckNDSTriaDofs();
 }
 
 void ParFiniteElementSpace::Construct()
@@ -467,53 +464,32 @@ void ParFiniteElementSpace::ApplyLDofSigns(Table &el_dof) const
    ApplyLDofSigns(all_dofs);
 }
 
-DofTransformation *
-ParFiniteElementSpace::GetElementDofs(int i, Array<int> &dofs) const
+void ParFiniteElementSpace::GetElementDofs(int i, Array<int> &dofs) const
 {
    if (elem_dof)
    {
       elem_dof->GetRow(i, dofs);
-
-      if (DoFTrans[mesh->GetElementBaseGeometry(i)])
-      {
-         Array<int> Fo;
-         elem_fos->GetRow(i, Fo);
-         DoFTrans[mesh->GetElementBaseGeometry(i)]->SetFaceOrientations(Fo);
-         return DoFTrans[mesh->GetElementBaseGeometry(i)];
-      }
-      return NULL;
+      return;
    }
-   DofTransformation * doftrans = FiniteElementSpace::GetElementDofs(i, dofs);
+   FiniteElementSpace::GetElementDofs(i, dofs);
    if (Conforming())
    {
       ApplyLDofSigns(dofs);
    }
-   return doftrans;
 }
 
-DofTransformation *
-ParFiniteElementSpace::GetBdrElementDofs(int i, Array<int> &dofs) const
+void ParFiniteElementSpace::GetBdrElementDofs(int i, Array<int> &dofs) const
 {
    if (bdr_elem_dof)
    {
       bdr_elem_dof->GetRow(i, dofs);
-
-      if (DoFTrans[mesh->GetBdrElementBaseGeometry(i)])
-      {
-         Array<int> Fo;
-         bdr_elem_fos -> GetRow (i, Fo);
-         DoFTrans[mesh->GetBdrElementBaseGeometry(i)]->SetFaceOrientations(Fo);
-         return DoFTrans[mesh->GetBdrElementBaseGeometry(i)];
-      }
-      return NULL;
+      return;
    }
-   DofTransformation * doftrans =
-      FiniteElementSpace::GetBdrElementDofs(i, dofs);
+   FiniteElementSpace::GetBdrElementDofs(i, dofs);
    if (Conforming())
    {
       ApplyLDofSigns(dofs);
    }
-   return doftrans;
 }
 
 int ParFiniteElementSpace::GetFaceDofs(int i, Array<int> &dofs,
@@ -681,267 +657,60 @@ void ParFiniteElementSpace::GenerateGlobalOffsets() const
    }
 }
 
-void ParFiniteElementSpace::CheckNDSTriaDofs()
-{
-   // Check for Nedelec basis
-   bool nd_basis = dynamic_cast<const ND_FECollection*>(fec);
-   if (!nd_basis)
-   {
-      nd_strias = false;
-      return;
-   }
-
-   // Check for interior face dofs on triangles (the use of TETRAHEDRON
-   // is not an error)
-   bool nd_fdof  = fec->HasFaceDofs(Geometry::TETRAHEDRON,
-                                    GetMaxElementOrder());
-   if (!nd_fdof)
-   {
-      nd_strias = false;
-      return;
-   }
-
-   // Check for shared triangle faces
-   bool strias   = false;
-   {
-      int ngrps = pmesh->GetNGroups();
-      for (int g = 1; g < ngrps; g++)
-      {
-         strias |= pmesh->GroupNTriangles(g);
-      }
-   }
-
-   // Combine results
-   int loc_nd_strias = strias ? 1 : 0;
-   int glb_nd_strias = 0;
-   MPI_Allreduce(&loc_nd_strias, &glb_nd_strias, 1,
-                 MPI_INTEGER, MPI_SUM, MyComm);
-   nd_strias = glb_nd_strias > 0;
-}
-
 void ParFiniteElementSpace::Build_Dof_TrueDof_Matrix() const // matrix P
 {
    MFEM_ASSERT(Conforming(), "wrong code path");
 
    if (P) { return; }
 
-   if (!nd_strias)
+   int ldof  = GetVSize();
+   int ltdof = TrueVSize();
+
+   HYPRE_Int *i_diag = Memory<HYPRE_Int>(ldof+1);
+   HYPRE_Int *j_diag = Memory<HYPRE_Int>(ltdof);
+   int diag_counter;
+
+   HYPRE_Int *i_offd = Memory<HYPRE_Int>(ldof+1);
+   HYPRE_Int *j_offd = Memory<HYPRE_Int>(ldof-ltdof);
+   int offd_counter;
+
+   HYPRE_BigInt *cmap = Memory<HYPRE_BigInt>(ldof-ltdof);
+
+   HYPRE_BigInt *col_starts = GetTrueDofOffsets();
+   HYPRE_BigInt *row_starts = GetDofOffsets();
+
+   Array<Pair<HYPRE_BigInt, int> > cmap_j_offd(ldof-ltdof);
+
+   i_diag[0] = i_offd[0] = 0;
+   diag_counter = offd_counter = 0;
+   for (int i = 0; i < ldof; i++)
    {
-      // Safe to assume 1-1 correspondence between shared dofs
-      int ldof  = GetVSize();
-      int ltdof = TrueVSize();
-
-      HYPRE_Int *i_diag = Memory<HYPRE_Int>(ldof+1);
-      HYPRE_Int *j_diag = Memory<HYPRE_Int>(ltdof);
-      int diag_counter;
-
-      HYPRE_Int *i_offd = Memory<HYPRE_Int>(ldof+1);
-      HYPRE_Int *j_offd = Memory<HYPRE_Int>(ldof-ltdof);
-      int offd_counter;
-
-      HYPRE_BigInt *cmap   = Memory<HYPRE_BigInt>(ldof-ltdof);
-
-      HYPRE_BigInt *col_starts = GetTrueDofOffsets();
-      HYPRE_BigInt *row_starts = GetDofOffsets();
-
-      Array<Pair<HYPRE_BigInt, int> > cmap_j_offd(ldof-ltdof);
-
-      i_diag[0] = i_offd[0] = 0;
-      diag_counter = offd_counter = 0;
-      for (int i = 0; i < ldof; i++)
+      int ltdof = GetLocalTDofNumber(i);
+      if (ltdof >= 0)
       {
-         int ltdof = GetLocalTDofNumber(i);
-         if (ltdof >= 0)
-         {
-            j_diag[diag_counter++] = ltdof;
-         }
-         else
-         {
-            cmap_j_offd[offd_counter].one = GetGlobalTDofNumber(i);
-            cmap_j_offd[offd_counter].two = offd_counter;
-            offd_counter++;
-         }
-         i_diag[i+1] = diag_counter;
-         i_offd[i+1] = offd_counter;
+         j_diag[diag_counter++] = ltdof;
       }
-
-      SortPairs<HYPRE_BigInt, int>(cmap_j_offd, offd_counter);
-
-      for (int i = 0; i < offd_counter; i++)
+      else
       {
-         cmap[i] = cmap_j_offd[i].one;
-         j_offd[cmap_j_offd[i].two] = i;
+         cmap_j_offd[offd_counter].one = GetGlobalTDofNumber(i);
+         cmap_j_offd[offd_counter].two = offd_counter;
+         offd_counter++;
       }
-
-      P = new HypreParMatrix(MyComm, MyRank, NRanks, row_starts, col_starts,
-                             i_diag, j_diag, i_offd, j_offd,
-                             cmap, offd_counter);
+      i_diag[i+1] = diag_counter;
+      i_offd[i+1] = offd_counter;
    }
-   else
+
+   SortPairs<HYPRE_BigInt, int>(cmap_j_offd, offd_counter);
+
+   for (int i = 0; i < offd_counter; i++)
    {
-      // Some shared dofs will be linear combinations of others
-      int ldof  = GetVSize();
-      int ltdof = TrueVSize();
-
-      HYPRE_Int gdof  = -1;
-      HYPRE_Int gtdof = -1;
-
-      MPI_Allreduce(&ldof, &gdof, 1, HYPRE_MPI_INT, MPI_SUM, MyComm);
-      MPI_Allreduce(&ltdof, &gtdof, 1, HYPRE_MPI_INT, MPI_SUM, MyComm);
-
-      // Ensure face orientations have been communicated
-      pmesh->ExchangeFaceNbrData();
-
-      // Locate and count non-zeros in off-diagonal portion of P
-      int nnz_offd = 0;
-      Array<int> ldsize(ldof); ldsize = 0;
-      Array<int> ltori(ldof);  ltori = 0; // Local triangle orientations
-      {
-         int ngrps = pmesh->GetNGroups();
-         int nedofs = fec->DofForGeometry(Geometry::SEGMENT);
-         Array<int> sdofs;
-         for (int g = 1; g < ngrps; g++)
-         {
-            if (pmesh->gtopo.IAmMaster(g))
-            {
-               continue;
-            }
-            for (int ei=0; ei<pmesh->GroupNEdges(g); ei++)
-            {
-               this->GetSharedEdgeDofs(g, ei, sdofs);
-               for (int i=0; i<sdofs.Size(); i++)
-               {
-                  int ind = (sdofs[i]>=0) ? sdofs[i] : (-sdofs[i]-1);
-                  if (ldsize[ind] == 0) { nnz_offd++; }
-                  ldsize[ind] = 1;
-               }
-            }
-            for (int fi=0; fi<pmesh->GroupNTriangles(g); fi++)
-            {
-               int face, ori, info1, info2;
-               pmesh->GroupTriangle(g, fi, face, ori);
-               pmesh->GetFaceInfos(face, &info1, &info2);
-               this->GetSharedTriangleDofs(g, fi, sdofs);
-               for (int i=0; i<3*nedofs; i++)
-               {
-                  int ind = (sdofs[i]>=0) ? sdofs[i] : (-sdofs[i]-1);
-                  if (ldsize[ind] == 0) { nnz_offd++; }
-                  ldsize[ind] = 1;
-               }
-               for (int i=3*nedofs; i<sdofs.Size(); i++)
-               {
-                  if (ldsize[sdofs[i]] == 0) { nnz_offd += 2; }
-                  ldsize[sdofs[i]] = 2;
-                  ltori[sdofs[i]]  = info2 % 64;
-               }
-            }
-            for (int fi=0; fi<pmesh->GroupNQuadrilaterals(g); fi++)
-            {
-               this->GetSharedQuadrilateralDofs(g, fi, sdofs);
-               for (int i=0; i<sdofs.Size(); i++)
-               {
-                  int ind = (sdofs[i]>=0) ? sdofs[i] : (-sdofs[i]-1);
-                  if (ldsize[ind] == 0) { nnz_offd++; }
-                  ldsize[ind] = 1;
-               }
-            }
-         }
-      }
-
-      HYPRE_Int *i_diag = new HYPRE_Int[ldof+1];
-      HYPRE_Int *j_diag = new HYPRE_Int[ltdof];
-      double    *d_diag = new double[ltdof];
-      int diag_counter;
-
-      HYPRE_Int *i_offd = new HYPRE_Int[ldof+1];
-      HYPRE_Int *j_offd = new HYPRE_Int[nnz_offd];
-      double    *d_offd = new double[nnz_offd];
-      int offd_counter;
-
-      HYPRE_BigInt *cmap   = new HYPRE_BigInt[ldof-ltdof];
-
-      HYPRE_BigInt *col_starts = GetTrueDofOffsets();
-      HYPRE_BigInt *row_starts = GetDofOffsets();
-
-      Array<Pair<HYPRE_BigInt, int> > cmap_j_offd(ldof-ltdof);
-
-      i_diag[0] = i_offd[0] = 0;
-      diag_counter = offd_counter = 0;
-      int offd_col_counter = 0;
-      for (int i = 0; i < ldof; i++)
-      {
-         int ltdof = GetLocalTDofNumber(i);
-         if (ltdof >= 0)
-         {
-            j_diag[diag_counter]   = ltdof;
-            d_diag[diag_counter++] = 1.0;
-         }
-         else
-         {
-            if (ldsize[i] == 1)
-            {
-               cmap_j_offd[offd_col_counter].one = GetGlobalTDofNumber(i);
-               cmap_j_offd[offd_col_counter].two = offd_counter;
-               offd_counter++;
-               offd_col_counter++;
-            }
-            else
-            {
-               cmap_j_offd[offd_col_counter].one = GetGlobalTDofNumber(i);
-               cmap_j_offd[offd_col_counter].two = offd_counter;
-               offd_counter += 2;
-               offd_col_counter++;
-               i_diag[i+1] = diag_counter;
-               i_offd[i+1] = offd_counter;
-               i++;
-               cmap_j_offd[offd_col_counter].one = GetGlobalTDofNumber(i);
-               cmap_j_offd[offd_col_counter].two = offd_counter;
-               offd_counter += 2;
-               offd_col_counter++;
-            }
-         }
-         i_diag[i+1] = diag_counter;
-         i_offd[i+1] = offd_counter;
-      }
-
-      SortPairs<HYPRE_BigInt, int>(cmap_j_offd, offd_col_counter);
-
-      for (int i = 0; i < nnz_offd; i++)
-      {
-         j_offd[i] = -1;
-         d_offd[i] = 0.0;
-      }
-
-      for (int i = 0; i < offd_col_counter; i++)
-      {
-         cmap[i] = cmap_j_offd[i].one;
-         j_offd[cmap_j_offd[i].two] = i;
-      }
-
-      for (int i = 0; i < ldof; i++)
-      {
-         if (i_offd[i+1] == i_offd[i] + 1)
-         {
-            d_offd[i_offd[i]] = 1.0;
-         }
-         else if (i_offd[i+1] == i_offd[i] + 2)
-         {
-            const double * T = ND_DofTransformation
-                               ::GetFaceTransform(ltori[i]).GetData();
-            j_offd[i_offd[i] + 1] = j_offd[i_offd[i]] + 1;
-            d_offd[i_offd[i]] = T[0]; d_offd[i_offd[i] + 1] = T[2];
-            i++;
-            j_offd[i_offd[i] + 1] = j_offd[i_offd[i]];
-            j_offd[i_offd[i]] = j_offd[i_offd[i] + 1] - 1;
-            d_offd[i_offd[i]] = T[1]; d_offd[i_offd[i] + 1] = T[3];
-         }
-      }
-
-      P = new HypreParMatrix(MyComm, gdof, gtdof, row_starts, col_starts,
-                             i_diag, j_diag, d_diag, i_offd, j_offd, d_offd,
-                             offd_col_counter, cmap);
+      cmap[i] = cmap_j_offd[i].one;
+      j_offd[cmap_j_offd[i].two] = i;
    }
 
+   P = new HypreParMatrix(MyComm, MyRank, NRanks, row_starts, col_starts,
+                          i_diag, j_diag, i_offd, j_offd, cmap, offd_counter);
+
    SparseMatrix Pdiag;
    P->GetDiag(Pdiag);
    R = Transpose(Pdiag);
@@ -1144,8 +913,6 @@ const Operator *ParFiniteElementSpace::GetProlongationMatrix() const
    {
       if (Pconf) { return Pconf; }
 
-      if (nd_strias) { return Dof_TrueDof_Matrix(); }
-
       if (NRanks == 1)
       {
          Pconf = new IdentityOperator(GetTrueVSize());
@@ -1449,29 +1216,10 @@ void ParFiniteElementSpace::ExchangeFaceNbrData()
    delete [] requests;
 }
 
-DofTransformation *ParFiniteElementSpace::GetFaceNbrElementVDofs(
+void ParFiniteElementSpace::GetFaceNbrElementVDofs(
    int i, Array<int> &vdofs) const
 {
    face_nbr_element_dof.GetRow(i, vdofs);
-
-   DofTransformation *doftrans = NULL;
-   Geometry::Type geom = GetFaceNbrFE(i)->GetGeomType();
-   if (DoFTrans[geom])
-   {
-      Array<int> F, Fo;
-      pmesh->GetFaceNbrElementFaces(pmesh->GetNE() + i, F, Fo);
-      doftrans = DoFTrans[geom];
-      doftrans->SetFaceOrientations(Fo);
-   }
-   if (vdim == 1 || doftrans == NULL)
-   {
-      return doftrans;
-   }
-   else
-   {
-      VDoFTrans.SetDofTransformation(*doftrans);
-      return &VDoFTrans;
-   }
 }
 
 void ParFiniteElementSpace::GetFaceNbrFaceVDofs(int i, Array<int> &vdofs) const
@@ -1530,17 +1278,12 @@ const FiniteElement *ParFiniteElementSpace::GetFaceNbrFaceFE(int i) const
 
 void ParFiniteElementSpace::Lose_Dof_TrueDof_Matrix()
 {
-   P -> StealData();
-#if MFEM_HYPRE_VERSION <= 22200
    hypre_ParCSRMatrix *csrP = (hypre_ParCSRMatrix*)(*P);
    hypre_ParCSRMatrixOwnsRowStarts(csrP) = 1;
    hypre_ParCSRMatrixOwnsColStarts(csrP) = 1;
+   P -> StealData();
    dof_offsets.LoseData();
    tdof_offsets.LoseData();
-#else
-   dof_offsets.DeleteAll();
-   tdof_offsets.DeleteAll();
-#endif
 }
 
 void ParFiniteElementSpace::ConstructTrueDofs()
@@ -2783,8 +2526,7 @@ static int_type* make_j_array(int_type* I, int nrows)
 
 HypreParMatrix*
 ParFiniteElementSpace::RebalanceMatrix(int old_ndofs,
-                                       const Table* old_elem_dof,
-                                       const Table* old_elem_fos)
+                                       const Table* old_elem_dof)
 {
    MFEM_VERIFY(Nonconforming(), "Only supported for nonconforming meshes.");
    MFEM_VERIFY(old_dof_offsets.Size(), "ParFiniteElementSpace::Update needs to "
@@ -2909,8 +2651,7 @@ struct DerefDofMessage
 
 HypreParMatrix*
 ParFiniteElementSpace::ParallelDerefinementMatrix(int old_ndofs,
-                                                  const Table* old_elem_dof,
-                                                  const Table *old_elem_fos)
+                                                  const Table* old_elem_dof)
 {
    int nrk = HYPRE_AssumedPartitionCheck() ? 2 : NRanks;
 
@@ -3266,16 +3007,13 @@ void ParFiniteElementSpace::Update(bool want_transform)
    }
 
    Table* old_elem_dof = NULL;
-   Table* old_elem_fos = NULL;
    int old_ndofs;
 
    // save old DOF table
    if (want_transform)
    {
       old_elem_dof = elem_dof;
-      old_elem_fos = elem_fos;
       elem_dof = NULL;
-      elem_fos = NULL;
       old_ndofs = ndofs;
       Swap(dof_offsets, old_dof_offsets);
    }
@@ -3297,25 +3035,22 @@ void ParFiniteElementSpace::Update(bool want_transform)
          {
             if (Th.Type() != Operator::MFEM_SPARSEMAT)
             {
-               Th.Reset(new RefinementOperator(this, old_elem_dof,
-                                               old_elem_fos, old_ndofs));
+               Th.Reset(new RefinementOperator(this, old_elem_dof, old_ndofs));
                // The RefinementOperator takes ownership of 'old_elem_dofs', so
                // we no longer own it:
                old_elem_dof = NULL;
-               old_elem_fos = NULL;
             }
             else
             {
                // calculate fully assembled matrix
-               Th.Reset(RefinementMatrix(old_ndofs, old_elem_dof, old_elem_fos));
+               Th.Reset(RefinementMatrix(old_ndofs, old_elem_dof));
             }
             break;
          }
 
          case Mesh::DEREFINE:
          {
-            Th.Reset(ParallelDerefinementMatrix(old_ndofs, old_elem_dof,
-                                                old_elem_fos));
+            Th.Reset(ParallelDerefinementMatrix(old_ndofs, old_elem_dof));
             if (Nonconforming())
             {
                Th.SetOperatorOwner(false);
@@ -3327,7 +3062,7 @@ void ParFiniteElementSpace::Update(bool want_transform)
 
          case Mesh::REBALANCE:
          {
-            Th.Reset(RebalanceMatrix(old_ndofs, old_elem_dof, old_elem_fos));
+            Th.Reset(RebalanceMatrix(old_ndofs, old_elem_dof));
             break;
          }
 
@@ -3336,7 +3071,6 @@ void ParFiniteElementSpace::Update(bool want_transform)
       }
 
       delete old_elem_dof;
-      delete old_elem_fos;
    }
 }
 

fem/pfespace.hpp

@@ -87,12 +87,6 @@ private:
        this is a TransposeOperator wrapping R. */
    mutable Operator *R_transpose;
 
-   /// Flag indicating the existence of shared triangles with interior ND dofs
-   bool nd_strias;
-
-   /// Resets nd_strias flag at constuction or after rebalancing
-   void CheckNDSTriaDofs();
-
    ParNURBSExtension *pNURBSext() const
    { return dynamic_cast<ParNURBSExtension *>(NURBSext); }
 
@@ -180,16 +174,14 @@ private:
        The result is a parallel permutation matrix that can be used to update
        all grid functions defined on this space. */
    HypreParMatrix* RebalanceMatrix(int old_ndofs,
-                                   const Table* old_elem_dof,
-                                   const Table* old_elem_fos);
+                                   const Table* old_elem_dof);
 
    /** Calculate a GridFunction restriction matrix after mesh derefinement.
        The matrix is constructed so that the new grid function interpolates
        the original function, i.e., the original function is evaluated at the
        nodes of the coarse function. */
    HypreParMatrix* ParallelDerefinementMatrix(int old_ndofs,
-                                              const Table *old_elem_dof,
-                                              const Table *old_elem_fos);
+                                              const Table *old_elem_dof);
 
    /// Updates the internal mesh pointer. @warning @a new_mesh must be
    /// <b>topologically identical</b> to the existing mesh. Used if the address
@@ -210,8 +202,6 @@ public:
    int num_face_nbr_dofs;
    // Face-neighbor-element to face-neighbor dof
    Table face_nbr_element_dof;
-   // Face-neighbor-element face orientations
-   Table face_nbr_element_fos;
    // Face-neighbor to ldof in the face-neighbor numbering
    Table face_nbr_ldof;
    // The global ldof indices of the face-neighbor dofs
@@ -289,10 +279,10 @@ public:
    virtual int GetTrueVSize() const { return ltdof_size; }
 
    /// Returns indexes of degrees of freedom in array dofs for i'th element.
-   virtual DofTransformation *GetElementDofs(int i, Array<int> &dofs) const;
+   virtual void GetElementDofs(int i, Array<int> &dofs) const;
 
    /// Returns indexes of degrees of freedom for i'th boundary element.
-   virtual DofTransformation *GetBdrElementDofs(int i, Array<int> &dofs) const;
+   virtual void GetBdrElementDofs(int i, Array<int> &dofs) const;
 
    /** Returns the indexes of the degrees of freedom for i'th face
        including the dofs for the edges and the vertices of the face. */
@@ -392,7 +382,7 @@ public:
    // Face-neighbor functions
    void ExchangeFaceNbrData();
    int GetFaceNbrVSize() const { return num_face_nbr_dofs; }
-   DofTransformation *GetFaceNbrElementVDofs(int i, Array<int> &vdofs) const;
+   void GetFaceNbrElementVDofs(int i, Array<int> &vdofs) const;
    void GetFaceNbrFaceVDofs(int i, Array<int> &vdofs) const;
    const FiniteElement *GetFaceNbrFE(int i) const;
    const FiniteElement *GetFaceNbrFaceFE(int i) const;
@@ -407,8 +397,6 @@ public:
    bool Conforming() const { return pmesh->pncmesh == NULL && !nonconf_P; }
    bool Nonconforming() const { return pmesh->pncmesh != NULL || nonconf_P; }
 
-   bool SharedNDTriangleDofs() const { return nd_strias; }
-
    // Transfer parallel true-dof data from coarse_fes, defined on a coarse mesh,
    // to this FE space, defined on a refined mesh. See full documentation in the
    // base class, FiniteElementSpace::GetTrueTransferOperator.

fem/pgridfunc.cpp

@@ -325,14 +325,9 @@ void ParGridFunction::GetVectorValue(int i, const IntegrationPoint &ip,
    if (nbr_el_no >= 0)
    {
       Array<int> dofs;
-      DofTransformation * doftrans = pfes->GetFaceNbrElementVDofs(nbr_el_no,
-                                                                  dofs);
+      pfes->GetFaceNbrElementVDofs(nbr_el_no, dofs);
       Vector loc_data;
       face_nbr_data.GetSubVector(dofs, loc_data);
-      if (doftrans)
-      {
-         doftrans->InvTransformPrimal(loc_data);
-      }
       const FiniteElement *FElem = pfes->GetFaceNbrFE(nbr_el_no);
       int dof = FElem->GetDof();
       if (FElem->GetRangeType() == FiniteElement::SCALAR)
@@ -442,17 +437,12 @@ void ParGridFunction::GetVectorValue(ElementTransformation &T,
    }
 
    Array<int> vdofs;
-   DofTransformation * doftrans = pfes->GetFaceNbrElementVDofs(nbr_el_no,
-                                                               vdofs);
+   pfes->GetFaceNbrElementVDofs(nbr_el_no, vdofs);
    const FiniteElement *fe = pfes->GetFaceNbrFE(nbr_el_no);
 
    int dof = fe->GetDof();
    Vector loc_data;
    face_nbr_data.GetSubVector(vdofs, loc_data);
-   if (doftrans)
-   {
-      doftrans->InvTransformPrimal(loc_data);
-   }
    if (fe->GetRangeType() == FiniteElement::SCALAR)
    {
       Vector shape(dof);

fem/pgridfunc.hpp

@@ -65,11 +65,6 @@ public:
    ParGridFunction(ParFiniteElementSpace *pf, double *data) :
       GridFunction(pf, data), pfes(pf) { }
 
-   /** @brief Construct a ParGridFunction using previously allocated Vector
-       @a base starting at the given offset, @a base_offset. */
-   ParGridFunction(ParFiniteElementSpace *pf, Vector &base, int base_offset = 0)
-      : GridFunction(pf, base, base_offset), pfes(pf) { }
-
    /// Construct a ParGridFunction using a GridFunction as external data.
    /** The parallel space @a *pf and the space used by @a *gf should match. The
        data from @a *gf is used as the local data of the ParGridFunction on each

fem/prestriction.cpp

@@ -33,10 +33,6 @@ ParL2FaceRestriction::ParL2FaceRestriction(const ParFiniteElementSpace &fes,
    // If fespace == L2
    const ParFiniteElementSpace &pfes =
       static_cast<const ParFiniteElementSpace&>(this->fes);
-
-   // Ensure the face neighbor data is constructed
-   pfes.GetParMesh()->ExchangeFaceNbrData();
-
    const FiniteElement *fe = pfes.GetFE(0);
    const TensorBasisElement *tfe = dynamic_cast<const TensorBasisElement*>(fe);
    MFEM_VERIFY(tfe != NULL &&

fem/restriction.cpp

@@ -15,12 +15,6 @@
 #include "../general/forall.hpp"
 #include <climits>
 
-#ifdef MFEM_USE_MPI
-
-#include "pfespace.hpp"
-
-#endif
-
 namespace mfem
 {
 
@@ -681,19 +675,6 @@ H1FaceRestriction::H1FaceRestriction(const FiniteElementSpace &fes,
      gather_indices(nf*dof)
 {
    if (nf==0) { return; }
-
-#ifdef MFEM_USE_MPI
-
-   // If the underlying finite element space is parallel, ensure the face
-   // neighbor information is generated.
-   if (const ParFiniteElementSpace *pfes
-       = dynamic_cast<const ParFiniteElementSpace*>(&fes))
-   {
-      pfes->GetParMesh()->ExchangeFaceNbrData();
-   }
-
-#endif
-
    // If fespace == H1
    const FiniteElement *fe = fes.GetFE(0);
    const TensorBasisElement *tfe = dynamic_cast<const TensorBasisElement*>(fe);

fem/tmop.cpp

@@ -1314,61 +1314,33 @@ static inline void device_copy(double *d_dest, const double *d_src, int size)
 } // namespace internal
 
 #ifdef MFEM_USE_MPI
-void DiscreteAdaptTC::FinalizeParDiscreteTargetSpec(const ParGridFunction &t)
+void DiscreteAdaptTC::FinalizeParDiscreteTargetSpec(const ParGridFunction
+                                                    &tspec_)
 {
    MFEM_VERIFY(adapt_eval, "SetAdaptivityEvaluator() has not been called!")
    MFEM_VERIFY(ncomp > 0, "No target specifications have been set!");
 
-   ParFiniteElementSpace *ptspec_fes = t.ParFESpace();
+   ParFiniteElementSpace *ptspec_fes = tspec_.ParFESpace();
 
    adapt_eval->SetParMetaInfo(*ptspec_fes->GetParMesh(),
                               *ptspec_fes->FEColl(), ncomp);
-   adapt_eval->SetInitialField(*ptspec_fes->GetMesh()->GetNodes(), tspec);
+   adapt_eval->SetInitialField(*tspec_fes->GetMesh()->GetNodes(), tspec);
 
    tspec_sav = tspec;
 
    delete tspec_fesv;
-   tspec_fesv = new FiniteElementSpace(ptspec_fes->GetMesh(),
-                                       ptspec_fes->FEColl(), ncomp);
-
-   delete ptspec_fesv;
-   ptspec_fesv = new ParFiniteElementSpace(ptspec_fes->GetParMesh(),
-                                           ptspec_fes->FEColl(), ncomp);
-
-   delete tspec_pgf;
-   tspec_pgf = new ParGridFunction(ptspec_fesv, tspec);
-   tspec_gf = tspec_pgf;
-}
-
-void DiscreteAdaptTC::ParUpdateAfterMeshTopologyChange()
-{
-   ptspec_fesv->Update();
-   if (tspec_fesv)
-   {
-      delete tspec_fesv;
-      tspec_fesv = new FiniteElementSpace(ptspec_fesv->GetMesh(),
-                                          ptspec_fesv->FEColl(), ncomp);
-   }
-   tspec_pgf->Update();
-   tspec_gf = tspec_pgf;
-   tspec.SetDataAndSize(tspec_pgf->GetData(), tspec_pgf->Size());
-   tspec_sav = tspec;
-
-   adapt_eval->SetParMetaInfo(*ptspec_fesv->GetParMesh(),
-                              *ptspec_fesv->FEColl(), ncomp);
-   adapt_eval->SetInitialField(*ptspec_fesv->GetMesh()->GetNodes(), tspec);
+   tspec_fesv = new FiniteElementSpace(tspec_fes->GetMesh(),
+                                       tspec_fes->FEColl(), ncomp);
 }
 
 void DiscreteAdaptTC::SetTspecAtIndex(int idx, const ParGridFunction &tspec_)
 {
-   const int vdim = tspec_.FESpace()->GetVDim(),
-             ndof = tspec_.FESpace()->GetNDofs();
-   MFEM_VERIFY(ndof == tspec.Size()/ncomp, "Inconsistency in SetTspecAtIndex.");
-
+   const int vdim     = tspec_.FESpace()->GetVDim(),
+             dof_cnt  = tspec_.Size()/vdim;
    const auto tspec__d = tspec_.Read();
    auto tspec_d = tspec.ReadWrite();
-   const int offset = idx*ndof;
-   internal::device_copy(tspec_d + offset, tspec__d, ndof*vdim);
+   const int offset = idx*dof_cnt;
+   internal::device_copy(tspec_d + offset, tspec__d, dof_cnt*vdim);
    FinalizeParDiscreteTargetSpec(tspec_);
 }
 
@@ -1388,71 +1360,78 @@ void DiscreteAdaptTC::SetParDiscreteTargetSkew(const ParGridFunction &tspec_)
    FinalizeParDiscreteTargetSpec(tspec_);
 }
 
-void DiscreteAdaptTC::SetParDiscreteTargetAspectRatio(const ParGridFunction &ar)
+void DiscreteAdaptTC::SetParDiscreteTargetAspectRatio(const ParGridFunction
+                                                      &tspec_)
 {
-   if (aspectratioidx > -1) { SetTspecAtIndex(aspectratioidx, ar); return; }
+   if (aspectratioidx > -1) { SetTspecAtIndex(aspectratioidx, tspec_); return; }
    aspectratioidx = ncomp;
-   SetDiscreteTargetBase(ar);
-   FinalizeParDiscreteTargetSpec(ar);
+   SetDiscreteTargetBase(tspec_);
+   FinalizeParDiscreteTargetSpec(tspec_);
 }
 
-void DiscreteAdaptTC::SetParDiscreteTargetOrientation(const ParGridFunction &o)
+void DiscreteAdaptTC::SetParDiscreteTargetOrientation(const ParGridFunction
+                                                      &tspec_)
 {
-   if (orientationidx > -1) { SetTspecAtIndex(orientationidx, o); return; }
+   if (orientationidx > -1) { SetTspecAtIndex(orientationidx, tspec_); return; }
    orientationidx = ncomp;
-   SetDiscreteTargetBase(o);
-   FinalizeParDiscreteTargetSpec(o);
+   SetDiscreteTargetBase(tspec_);
+   FinalizeParDiscreteTargetSpec(tspec_);
 }
 
 void DiscreteAdaptTC::SetParDiscreteTargetSpec(const ParGridFunction &tspec_)
 {
    SetParDiscreteTargetSize(tspec_);
+   FinalizeParDiscreteTargetSpec(tspec_);
 }
 #endif // MFEM_USE_MPI
 
 void DiscreteAdaptTC::SetDiscreteTargetBase(const GridFunction &tspec_)
 {
-   const int vdim = tspec_.FESpace()->GetVDim(),
-             ndof = tspec_.FESpace()->GetNDofs();
+   const int vdim     = tspec_.FESpace()->GetVDim(),
+             dof_cnt  = tspec_.Size()/vdim;
 
    ncomp += vdim;
 
+   delete tspec_fes;
+   tspec_fes = new FiniteElementSpace(tspec_.FESpace()->GetMesh(),
+                                      tspec_.FESpace()->FEColl(), 1);
+
    // need to append data to tspec
    // make a copy of tspec->tspec_temp, increase its size, and
    // copy data from tspec_temp -> tspec, then add new entries
    Vector tspec_temp = tspec;
    tspec.UseDevice(true);
    tspec_sav.UseDevice(true);
-   tspec.SetSize(ncomp*ndof);
+   tspec.SetSize(ncomp*dof_cnt);
 
    const auto tspec_temp_d = tspec_temp.Read();
    auto tspec_d = tspec.ReadWrite();
    internal::device_copy(tspec_d, tspec_temp_d, tspec_temp.Size());
 
    const auto tspec__d = tspec_.Read();
-   const int offset = (ncomp-vdim)*ndof;
-   internal::device_copy(tspec_d + offset, tspec__d, ndof*vdim);
+   const int offset = (ncomp-vdim)*dof_cnt;
+   internal::device_copy(tspec_d + offset, tspec__d, dof_cnt*vdim);
 }
 
 void DiscreteAdaptTC::SetTspecAtIndex(int idx, const GridFunction &tspec_)
 {
-   const int vdim = tspec_.FESpace()->GetVDim(),
-             ndof = tspec_.FESpace()->GetNDofs();
-   MFEM_VERIFY(ndof == tspec.Size()/ncomp, "Inconsistency in SetTargetSpec.");
+   const int vdim     = tspec_.FESpace()->GetVDim(),
+             dof_cnt  = tspec_.Size()/vdim;
 
    const auto tspec__d = tspec_.Read();
    auto tspec_d = tspec.ReadWrite();
-   const int offset = idx*ndof;
-   internal::device_copy(tspec_d + offset, tspec__d, ndof*vdim);
-   FinalizeSerialDiscreteTargetSpec(tspec_);
+   const int offset = idx*dof_cnt;
+   internal::device_copy(tspec_d + offset, tspec__d, dof_cnt*vdim);
+   FinalizeSerialDiscreteTargetSpec();
 }
 
 void DiscreteAdaptTC::SetSerialDiscreteTargetSize(const GridFunction &tspec_)
 {
+
    if (sizeidx > -1) { SetTspecAtIndex(sizeidx, tspec_); return; }
    sizeidx = ncomp;
    SetDiscreteTargetBase(tspec_);
-   FinalizeSerialDiscreteTargetSpec(tspec_);
+   FinalizeSerialDiscreteTargetSpec();
 }
 
 void DiscreteAdaptTC::SetSerialDiscreteTargetSkew(const GridFunction &tspec_)
@@ -1460,31 +1439,32 @@ void DiscreteAdaptTC::SetSerialDiscreteTargetSkew(const GridFunction &tspec_)
    if (skewidx > -1) { SetTspecAtIndex(skewidx, tspec_); return; }
    skewidx = ncomp;
    SetDiscreteTargetBase(tspec_);
-   FinalizeSerialDiscreteTargetSpec(tspec_);
+   FinalizeSerialDiscreteTargetSpec();
 }
 
-void DiscreteAdaptTC::SetSerialDiscreteTargetAspectRatio(const GridFunction &ar)
+void DiscreteAdaptTC::SetSerialDiscreteTargetAspectRatio(
+   const GridFunction &tspec_)
 {
-   if (aspectratioidx > -1) { SetTspecAtIndex(aspectratioidx, ar); return; }
+   if (aspectratioidx > -1) { SetTspecAtIndex(aspectratioidx, tspec_); return; }
    aspectratioidx = ncomp;
-   SetDiscreteTargetBase(ar);
-   FinalizeSerialDiscreteTargetSpec(ar);
+   SetDiscreteTargetBase(tspec_);
+   FinalizeSerialDiscreteTargetSpec();
 }
 
-void DiscreteAdaptTC::SetSerialDiscreteTargetOrientation(const GridFunction &o)
+void DiscreteAdaptTC::SetSerialDiscreteTargetOrientation(
+   const GridFunction &tspec_)
 {
-   if (orientationidx > -1) { SetTspecAtIndex(orientationidx, o); return; }
+   if (orientationidx > -1) { SetTspecAtIndex(orientationidx, tspec_); return; }
    orientationidx = ncomp;
-   SetDiscreteTargetBase(o);
-   FinalizeSerialDiscreteTargetSpec(o);
+   SetDiscreteTargetBase(tspec_);
+   FinalizeSerialDiscreteTargetSpec();
 }
 
-void DiscreteAdaptTC::FinalizeSerialDiscreteTargetSpec(const GridFunction &t)
+void DiscreteAdaptTC::FinalizeSerialDiscreteTargetSpec()
 {
    MFEM_VERIFY(adapt_eval, "SetAdaptivityEvaluator() has not been called!")
    MFEM_VERIFY(ncomp > 0, "No target specifications have been set!");
 
-   const FiniteElementSpace *tspec_fes = t.FESpace();
    adapt_eval->SetSerialMetaInfo(*tspec_fes->GetMesh(),
                                  *tspec_fes->FEColl(), ncomp);
    adapt_eval->SetInitialField(*tspec_fes->GetMesh()->GetNodes(), tspec);
@@ -1494,40 +1474,12 @@ void DiscreteAdaptTC::FinalizeSerialDiscreteTargetSpec(const GridFunction &t)
    delete tspec_fesv;
    tspec_fesv = new FiniteElementSpace(tspec_fes->GetMesh(),
                                        tspec_fes->FEColl(), ncomp);
-
-   delete tspec_gf;
-   tspec_gf = new GridFunction(tspec_fesv, tspec);
-}
-
-void DiscreteAdaptTC::GetDiscreteTargetSpec(GridFunction &tspec_, int idx)
-{
-   if (idx < 0) { return; }
-   const int ndof = tspec_.FESpace()->GetNDofs(),
-             vdim = tspec_.FESpace()->GetVDim();
-   MFEM_VERIFY(ndof == tspec.Size()/ncomp,
-               "Inconsistency in GetSerialDiscreteTargetSpec.");
-
-   for (int i = 0; i < ndof*vdim; i++)
-   {
-      tspec_(i) = tspec(i + idx*ndof);
-   }
-}
-
-void DiscreteAdaptTC::UpdateAfterMeshTopologyChange()
-{
-   tspec_fesv->Update();
-   tspec_gf->Update();
-   tspec.SetDataAndSize(tspec_gf->GetData(), tspec_gf->Size());
-   tspec_sav = tspec;
-
-   adapt_eval->SetSerialMetaInfo(*tspec_fesv->GetMesh(),
-                                 *tspec_fesv->FEColl(), ncomp);
-   adapt_eval->SetInitialField(*tspec_fesv->GetMesh()->GetNodes(), tspec);
 }
 
 void DiscreteAdaptTC::SetSerialDiscreteTargetSpec(const GridFunction &tspec_)
 {
    SetSerialDiscreteTargetSize(tspec_);
+   FinalizeSerialDiscreteTargetSpec();
 }
 
 
@@ -1557,7 +1509,7 @@ void DiscreteAdaptTC::UpdateTargetSpecificationAtNode(const FiniteElement &el,
    MFEM_VERIFY(tspec.Size() > 0, "Target specification is not set!");
 
    Array<int> dofs;
-   tspec_fesv->GetElementDofs(T.ElementNo, dofs);
+   tspec_fes->GetElementDofs(T.ElementNo, dofs);
    const int cnt = tspec.Size()/ncomp; // dofs per scalar-field
 
    for (int i = 0; i < ncomp; i++)
@@ -1572,7 +1524,7 @@ void DiscreteAdaptTC::RestoreTargetSpecificationAtNode(ElementTransformation &T,
    MFEM_VERIFY(tspec.Size() > 0, "Target specification is not set!");
 
    Array<int> dofs;
-   tspec_fesv->GetElementDofs(T.ElementNo, dofs);
+   tspec_fes->GetElementDofs(T.ElementNo, dofs);
    const int cnt = tspec.Size()/ncomp;
    for (int i = 0; i < ncomp; i++)
    {
@@ -1580,40 +1532,6 @@ void DiscreteAdaptTC::RestoreTargetSpecificationAtNode(ElementTransformation &T,
    }
 }
 
-void DiscreteAdaptTC::SetTspecFromIntRule(int e_id,
-                                          const IntegrationRule &intrule)
-{
-   switch (target_type)
-   {
-      case IDEAL_SHAPE_GIVEN_SIZE:
-      case GIVEN_SHAPE_AND_SIZE:
-      {
-         const int ndofs = tspec_fesv->GetFE(e_id)->GetDof(),
-                   ntspec_dofs = ndofs*ncomp;
-
-         Vector tspec_vals(ntspec_dofs);
-
-         Array<int> dofs;
-         tspec_fesv->GetElementVDofs(e_id, dofs);
-         tspec.GetSubVector(dofs, tspec_vals);
-         DenseMatrix tr;
-         tspec_gf->GetVectorValues(e_id, intrule, tspec_refine, tr);
-         tspec_refine.Transpose();
-         break;
-      }
-      default:
-         MFEM_ABORT("Incompatible target type for discrete adaptation!");
-   }
-}
-
-void DiscreteAdaptTC::SetTspecDataForDerefinement(FiniteElementSpace *fes)
-{
-   coarse_tspec_fesv = fes;
-   const Operator *c_op = fes->GetUpdateOperator();
-   tspec_derefine.SetSize(c_op->Height());
-   c_op->Mult(tspec, tspec_derefine);
-}
-
 void DiscreteAdaptTC::ComputeElementTargets(int e_id, const FiniteElement &fe,
                                             const IntegrationRule &ir,
                                             const Vector &elfun,
@@ -1624,8 +1542,6 @@ void DiscreteAdaptTC::ComputeElementTargets(int e_id, const FiniteElement &fe,
              nqp = ir.GetNPoints();
    Jtrcomp.SetSize(dim, dim, 4*nqp);
 
-   FiniteElementSpace *src_fes = tspec_fesv;
-
    switch (target_type)
    {
       case IDEAL_SHAPE_GIVEN_SIZE:
@@ -1634,7 +1550,7 @@ void DiscreteAdaptTC::ComputeElementTargets(int e_id, const FiniteElement &fe,
          const DenseMatrix &Wideal =
             Geometries.GetGeomToPerfGeomJac(fe.GetGeomType());
          const int dim = Wideal.Height(),
-                   ndofs = tspec_fesv->GetFE(e_id)->GetDof(),
+                   ndofs = tspec_fes->GetFE(e_id)->GetDof(),
                    ntspec_dofs = ndofs*ncomp;
 
          Vector shape(ndofs), tspec_vals(ntspec_dofs), par_vals,
@@ -1645,29 +1561,11 @@ void DiscreteAdaptTC::ComputeElementTargets(int e_id, const FiniteElement &fe,
          tspec_fesv->GetElementVDofs(e_id, dofs);
          tspec.UseDevice(true);
          tspec.GetSubVector(dofs, tspec_vals);
-         if (tspec_refine.NumCols() > 0) // Refinement
-         {
-            MFEM_VERIFY(amr_el >= 0, " Target being constructed for an AMR element.");
-            for (int i = 0; i < ncomp; i++)
-            {
-               for (int j = 0; j < ndofs; j++)
-               {
-                  tspec_vals(j + i*ndofs) = tspec_refine(j + amr_el*ndofs, i);
-               }
-            }
-         }
-         else if (tspec_derefine.Size() > 0) // Derefinement
-         {
-            dofs.SetSize(0);
-            coarse_tspec_fesv->GetElementVDofs(e_id, dofs);
-            tspec_derefine.GetSubVector(dofs, tspec_vals);
-            src_fes = coarse_tspec_fesv;
-         }
 
          for (int q = 0; q < nqp; q++)
          {
             const IntegrationPoint &ip = ir.IntPoint(q);
-            src_fes->GetFE(e_id)->CalcShape(ip, shape);
+            tspec_fes->GetFE(e_id)->CalcShape(ip, shape);
             Jtr(q) = Wideal; // Initialize to identity
             for (int d = 0; d < 4; d++)
             {
@@ -1678,16 +1576,9 @@ void DiscreteAdaptTC::ComputeElementTargets(int e_id, const FiniteElement &fe,
             if (sizeidx != -1) // Set size
             {
                par_vals.SetDataAndSize(tspec_vals.GetData()+sizeidx*ndofs, ndofs);
-               double min_size = par_vals.Min();//0.001; //
-               if (lim_min_size > 0.)
-               {
-                  min_size = lim_min_size;
-               }
-               else
-               {
-                  MFEM_VERIFY(min_size > 0.0,
-                              "Non-positive size propagated in the target definition.");
-               }
+               const double min_size = par_vals.Min();
+               MFEM_VERIFY(min_size > 0.0,
+                           "Non-positive size propagated in the target definition.");
                const double size = std::max(shape * par_vals, min_size);
                Jtr(q).Set(std::pow(size, 1.0/dim), Jtr(q));
                DenseMatrix Jtrcomp_q(Jtrcomp.GetData(0 + 4*q), dim, dim);
@@ -1702,9 +1593,6 @@ void DiscreteAdaptTC::ComputeElementTargets(int e_id, const FiniteElement &fe,
                {
                   par_vals.SetDataAndSize(tspec_vals.GetData()+
                                           aspectratioidx*ndofs, ndofs);
-                  const double min_size = par_vals.Min();
-                  MFEM_VERIFY(min_size > 0.0,
-                              "Non-positive aspect-ratio propagated in the target definition.");
 
                   const double aspectratio = shape * par_vals;
                   D_rho = 0.;
@@ -1889,7 +1777,7 @@ void DiscreteAdaptTC::ComputeElementTargetsGradient(const IntegrationRule &ir,
 
                grad_phys.Mult(par_vals, grad_ptr_c1);
                Vector grad_q(dim);
-               tspec_fesv->GetFE(e_id)->CalcShape(ip, shape);
+               tspec_fes->GetFE(e_id)->CalcShape(ip, shape);
                grad_e_c1.MultTranspose(shape, grad_q);
 
                const double min_size = par_vals.Min();
@@ -1922,7 +1810,7 @@ void DiscreteAdaptTC::ComputeElementTargetsGradient(const IntegrationRule &ir,
 
                   grad_phys.Mult(par_vals, grad_ptr_c1);
                   Vector grad_q(dim);
-                  tspec_fesv->GetFE(e_id)->CalcShape(ip, shape);
+                  tspec_fes->GetFE(e_id)->CalcShape(ip, shape);
                   grad_e_c1.MultTranspose(shape, grad_q);
 
                   const double aspectratio = shape * par_vals;
@@ -1953,7 +1841,7 @@ void DiscreteAdaptTC::ComputeElementTargetsGradient(const IntegrationRule &ir,
                   grad_phys.Mult(par_vals_c2, grad_ptr_c2);
                   grad_phys.Mult(par_vals_c3, grad_ptr_c3);
                   Vector grad_q1(dim), grad_q2(dim), grad_q3(dim);
-                  tspec_fesv->GetFE(e_id)->CalcShape(ip, shape);
+                  tspec_fes->GetFE(e_id)->CalcShape(ip, shape);
                   grad_e_c1.MultTranspose(shape, grad_q1);
                   grad_e_c2.MultTranspose(shape, grad_q2);
                   grad_e_c3.MultTranspose(shape, grad_q3);
@@ -1992,7 +1880,7 @@ void DiscreteAdaptTC::ComputeElementTargetsGradient(const IntegrationRule &ir,
 
                   grad_phys.Mult(par_vals, grad_ptr_c1);
                   Vector grad_q(dim);
-                  tspec_fesv->GetFE(e_id)->CalcShape(ip, shape);
+                  tspec_fes->GetFE(e_id)->CalcShape(ip, shape);
                   grad_e_c1.MultTranspose(shape, grad_q);
 
                   const double skew = shape * par_vals;
@@ -2025,7 +1913,7 @@ void DiscreteAdaptTC::ComputeElementTargetsGradient(const IntegrationRule &ir,
                   grad_phys.Mult(par_vals_c2, grad_ptr_c2);
                   grad_phys.Mult(par_vals_c3, grad_ptr_c3);
                   Vector grad_q1(dim), grad_q2(dim), grad_q3(dim);
-                  tspec_fesv->GetFE(e_id)->CalcShape(ip, shape);
+                  tspec_fes->GetFE(e_id)->CalcShape(ip, shape);
                   grad_e_c1.MultTranspose(shape, grad_q1);
                   grad_e_c2.MultTranspose(shape, grad_q2);
                   grad_e_c3.MultTranspose(shape, grad_q3);
@@ -2072,7 +1960,7 @@ void DiscreteAdaptTC::ComputeElementTargetsGradient(const IntegrationRule &ir,
 
                   grad_phys.Mult(par_vals, grad_ptr_c1);
                   Vector grad_q(dim);
-                  tspec_fesv->GetFE(e_id)->CalcShape(ip, shape);
+                  tspec_fes->GetFE(e_id)->CalcShape(ip, shape);
                   grad_e_c1.MultTranspose(shape, grad_q);
 
                   const double theta = shape * par_vals;
@@ -2103,7 +1991,7 @@ void DiscreteAdaptTC::ComputeElementTargetsGradient(const IntegrationRule &ir,
                   grad_phys.Mult(par_vals_c2, grad_ptr_c2);
                   grad_phys.Mult(par_vals_c3, grad_ptr_c3);
                   Vector grad_q1(dim), grad_q2(dim), grad_q3(dim);
-                  tspec_fesv->GetFE(e_id)->CalcShape(ip, shape);
+                  tspec_fes->GetFE(e_id)->CalcShape(ip, shape);
                   grad_e_c1.MultTranspose(shape, grad_q1);
                   grad_e_c2.MultTranspose(shape, grad_q2);
                   grad_e_c3.MultTranspose(shape, grad_q3);
@@ -2183,7 +2071,7 @@ void DiscreteAdaptTC::UpdateGradientTargetSpecification(const Vector &x,
 {
    if (use_flag && good_tspec_grad) { return; }
 
-   const int dim = tspec_fesv->GetFE(0)->GetDim(),
+   const int dim = tspec_fes->GetFE(0)->GetDim(),
              cnt = x.Size()/dim;
 
    tspec_pert1h.SetSize(x.Size()*ncomp);
@@ -2209,7 +2097,7 @@ void DiscreteAdaptTC::UpdateHessianTargetSpecification(const Vector &x,
 
    if (use_flag && good_tspec_hess) { return; }
 
-   const int dim    = tspec_fesv->GetFE(0)->GetDim(),
+   const int dim    = tspec_fes->GetFE(0)->GetDim(),
              cnt    = x.Size()/dim,
              totmix = 1+2*(dim-2);
 
@@ -2257,16 +2145,6 @@ void DiscreteAdaptTC::UpdateHessianTargetSpecification(const Vector &x,
    good_tspec_hess = use_flag;
 }
 
-DiscreteAdaptTC::~DiscreteAdaptTC()
-{
-   delete tspec_gf;
-   delete adapt_eval;
-   delete tspec_fesv;
-#ifdef MFEM_USE_MPI
-   delete ptspec_fesv;
-#endif
-}
-
 void AdaptivityEvaluator::SetSerialMetaInfo(const Mesh &m,
                                             const FiniteElementCollection &fec,
                                             int num_comp)
@@ -2380,7 +2258,6 @@ void TMOP_Integrator::EnableAdaptiveLimiting(const ParGridFunction &z0,
                                              AdaptivityEvaluator &ae)
 {
    zeta_0 = &z0;
-   pzeta_0 = &z0;
    delete zeta;
    zeta   = new GridFunction(z0);
    coeff_zeta = &coeff;
@@ -2393,33 +2270,6 @@ void TMOP_Integrator::EnableAdaptiveLimiting(const ParGridFunction &z0,
 }
 #endif
 
-void TMOP_Integrator::UpdateAfterMeshTopologyChange()
-{
-   if (zeta)
-   {
-      zeta->Update();
-      adapt_eval->SetSerialMetaInfo(*zeta->FESpace()->GetMesh(),
-                                    *zeta->FESpace()->FEColl(), 1);
-      adapt_eval->SetInitialField
-      (*zeta->FESpace()->GetMesh()->GetNodes(), *zeta);
-   }
-}
-
-#ifdef MFEM_USE_MPI
-void TMOP_Integrator::ParUpdateAfterMeshTopologyChange()
-{
-   if (zeta)
-   {
-      zeta->Update();
-      adapt_eval->SetParMetaInfo(*pzeta_0->ParFESpace()->GetParMesh(),
-                                 *pzeta_0->ParFESpace()->FEColl(), 1);
-      adapt_eval->SetInitialField
-      (*zeta->FESpace()->GetMesh()->GetNodes(), *zeta);
-   }
-}
-#endif
-
-
 double TMOP_Integrator::GetElementEnergy(const FiniteElement &el,
                                          ElementTransformation &T,
                                          const Vector &elfun)
@@ -2528,145 +2378,6 @@ double TMOP_Integrator::GetElementEnergy(const FiniteElement &el,
 
    return energy;
 }
-
-double TMOP_Integrator::GetRefinementElementEnergy(const FiniteElement &el,
-                                                   ElementTransformation &T,
-                                                   const Vector &elfun,
-                                                   const IntegrationRule &irule)
-{
-   int dof = el.GetDof(), dim = el.GetDim(),
-       NEsplit = elfun.Size() / (dof*dim), el_id = T.ElementNo;
-   double energy = 0.;
-
-   TargetConstructor *tc = const_cast<TargetConstructor *>(targetC);
-   DiscreteAdaptTC *dtc = dynamic_cast<DiscreteAdaptTC *>(tc);
-   // For DiscreteAdaptTC the GridFunctions used to set the targets must be
-   // mapped onto the fine elements.
-   if (dtc) { dtc->SetTspecFromIntRule(el_id, irule); }
-
-   for (int e = 0; e < NEsplit; e++)
-   {
-      DSh.SetSize(dof, dim);
-      Jrt.SetSize(dim);
-      Jpr.SetSize(dim);
-      Jpt.SetSize(dim);
-      Vector elfun_child(dof*dim);
-      for (int i = 0; i < dof; i++)
-      {
-         for (int d = 0; d < dim; d++)
-         {
-            // elfun is (xe1,xe2,...xen,ye1,ye2...yen) and has nodal coordinates
-            // for all the children element of the parent element being considered.
-            // So we must index and get (xek, yek) i.e. nodal coordinates for
-            // the fine element being considered.
-            elfun_child(i + d*dof) = elfun(i + e*dof + d*dof*NEsplit);
-         }
-      }
-      PMatI.UseExternalData(elfun_child.GetData(), dof, dim);
-
-      const IntegrationRule &ir = EnergyIntegrationRule(el);
-
-      double el_energy = 0;
-      DenseTensor Jtr(dim, dim, ir.GetNPoints());
-      if (dtc)
-      {
-         // This is used to index into the tspec vector inside DiscreteAdaptTC.
-         dtc->SetRefinementSubElement(e);
-      }
-      targetC->ComputeElementTargets(el_id, el, ir, elfun_child, Jtr);
-
-      // Define ref->physical transformation, wn a Coefficient is specified.
-      IsoparametricTransformation *Tpr = NULL;
-      if (coeff1 || coeff0)
-      {
-         Tpr = new IsoparametricTransformation;
-         Tpr->SetFE(&el);
-         Tpr->ElementNo = T.ElementNo;
-         Tpr->ElementType = ElementTransformation::ELEMENT;
-         Tpr->Attribute = T.Attribute;
-         Tpr->GetPointMat().Transpose(PMatI); // PointMat = PMatI^T
-      }
-
-      for (int i = 0; i < ir.GetNPoints(); i++)
-      {
-         const IntegrationPoint &ip = ir.IntPoint(i);
-         const DenseMatrix &Jtr_i = Jtr(i);
-         h_metric->SetTargetJacobian(Jtr_i);
-         CalcInverse(Jtr_i, Jrt);
-         const double weight = ip.weight * Jtr_i.Det();
-
-         el.CalcDShape(ip, DSh);
-         MultAtB(PMatI, DSh, Jpr);
-         Mult(Jpr, Jrt, Jpt);
-
-         double val = metric_normal * h_metric->EvalW(Jpt);
-         if (coeff1) { val *= coeff1->Eval(*Tpr, ip); }
-
-         el_energy += weight * val;
-         delete Tpr;
-      }
-      energy += el_energy;
-   }
-   energy /= NEsplit;
-
-   if (dtc) { dtc->ResetRefinementTspecData(); }
-
-   return energy;
-}
-
-double TMOP_Integrator::GetDerefinementElementEnergy(const FiniteElement &el,
-                                                     ElementTransformation &T,
-                                                     const Vector &elfun)
-{
-   int dof = el.GetDof(), dim = el.GetDim();
-   double energy = 0.;
-
-   DSh.SetSize(dof, dim);
-   Jrt.SetSize(dim);
-   Jpr.SetSize(dim);
-   Jpt.SetSize(dim);
-   PMatI.UseExternalData(elfun.GetData(), dof, dim);
-
-   const IntegrationRule &ir = EnergyIntegrationRule(el);
-
-   energy = 0.0;
-   DenseTensor Jtr(dim, dim, ir.GetNPoints());
-   targetC->ComputeElementTargets(T.ElementNo, el, ir, elfun, Jtr);
-
-   // Define ref->physical transformation, wn a Coefficient is specified.
-   IsoparametricTransformation *Tpr = NULL;
-   if (coeff1)
-   {
-      Tpr = new IsoparametricTransformation;
-      Tpr->SetFE(&el);
-      Tpr->ElementNo = T.ElementNo;
-      Tpr->ElementType = ElementTransformation::ELEMENT;
-      Tpr->Attribute = T.Attribute;
-      Tpr->GetPointMat().Transpose(PMatI); // PointMat = PMatI^T
-   }
-
-   for (int i = 0; i < ir.GetNPoints(); i++)
-   {
-      const IntegrationPoint &ip = ir.IntPoint(i);
-      const DenseMatrix &Jtr_i = Jtr(i);
-      h_metric->SetTargetJacobian(Jtr_i);
-      CalcInverse(Jtr_i, Jrt);
-      const double weight = ip.weight * Jtr_i.Det();
-
-      el.CalcDShape(ip, DSh);
-      MultAtB(PMatI, DSh, Jpr);
-      Mult(Jpr, Jrt, Jpt);
-
-      double val = metric_normal * h_metric->EvalW(Jpt);
-      if (coeff1) { val *= coeff1->Eval(*Tpr, ip); }
-
-      energy += weight * val;
-   }
-
-   delete Tpr;
-   return energy;
-}
-
 void TMOP_Integrator::AssembleElementVector(const FiniteElement &el,
                                             ElementTransformation &T,
                                             const Vector &elfun, Vector &elvect)
@@ -3328,7 +3039,7 @@ void TMOP_Integrator::ComputeMinJac(const Vector &x,
    dx = detv_avg_min / dxscale;
 }
 
-void TMOP_Integrator::UpdateAfterMeshPositionChange(const Vector &new_x)
+void TMOP_Integrator::UpdateAfterMeshChange(const Vector &new_x)
 {
    if (discr_tc)
    {
@@ -3457,32 +3168,6 @@ void TMOPComboIntegrator::AssembleElementGrad(const FiniteElement &el,
    }
 }
 
-double TMOPComboIntegrator::GetRefinementElementEnergy(const FiniteElement &el,
-                                                       ElementTransformation &T,
-                                                       const Vector &elfun,
-                                                       const IntegrationRule &irule)
-{
-   double energy= 0.0;
-   for (int i = 0; i < tmopi.Size(); i++)
-   {
-      energy += tmopi[i]->GetRefinementElementEnergy(el, T, elfun, irule);
-   }
-   return energy;
-}
-
-double TMOPComboIntegrator::GetDerefinementElementEnergy(
-   const FiniteElement &el,
-   ElementTransformation &T,
-   const Vector &elfun)
-{
-   double energy= 0.0;
-   for (int i = 0; i < tmopi.Size(); i++)
-   {
-      energy += tmopi[i]->GetDerefinementElementEnergy(el, T, elfun);
-   }
-   return energy;
-}
-
 void TMOPComboIntegrator::EnableNormalization(const GridFunction &x)
 {
    const int cnt = tmopi.Size();

fem/tmop.hpp

@@ -1057,31 +1057,14 @@ protected:
    // eta1(x+h,y), eta2(x+h,y) ... etan(x+h,y), eta1(x,y+h), eta2(x,y+h) ...
    // same for tspec_pert2h and tspec_pertmix.
 
-   // DenseMatrix to hold target_spec values for the (children of the)
-   // element being refined to consider for h-refinement.
-   DenseMatrix tspec_refine;
-   // Vector to hold the target_spec values for the coarse version of the
-   // current mesh. Used for derefinement decision with hr-adaptivity.
-   Vector tspec_derefine;
-
    // Components of Target Jacobian at each quadrature point of an element. This
    // is required for computation of the derivative using chain rule.
    mutable DenseTensor Jtrcomp;
 
    // Note: do not use the Nodes of this space as they may not be on the
    // positions corresponding to the values of tspec.
-   FiniteElementSpace *tspec_fesv;         //owned
-   FiniteElementSpace *coarse_tspec_fesv;  //not owned, derefinement FESpace
-   GridFunction *tspec_gf;                 //owned, uses tspec and tspec_fes
-   // discrete adaptivity
-#ifdef MFEM_USE_MPI
-   ParFiniteElementSpace *ptspec_fesv;     //owned, needed for derefinement to
-   // get update operator.
-   ParGridFunction *tspec_pgf;             // similar to tspec_gf
-#endif
-
-   int amr_el;
-   double lim_min_size;
+   const FiniteElementSpace *tspec_fes;
+   const FiniteElementSpace *tspec_fesv;
 
    // These flags can be used by outside functions to avoid recomputing the
    // tspec and tspec_perth fields again on the same mesh.
@@ -1093,7 +1076,7 @@ protected:
 
    void SetDiscreteTargetBase(const GridFunction &tspec_);
    void SetTspecAtIndex(int idx, const GridFunction &tspec_);
-   void FinalizeSerialDiscreteTargetSpec(const GridFunction &tspec_);
+   void FinalizeSerialDiscreteTargetSpec();
 #ifdef MFEM_USE_MPI
    void SetTspecAtIndex(int idx, const ParGridFunction &tspec_);
    void FinalizeParDiscreteTargetSpec(const ParGridFunction &tspec_);
@@ -1105,16 +1088,16 @@ public:
         ncomp(0),
         sizeidx(-1), skewidx(-1), aspectratioidx(-1), orientationidx(-1),
         tspec(), tspec_sav(), tspec_pert1h(), tspec_pert2h(), tspec_pertmix(),
-        tspec_refine(), tspec_derefine(),
-        tspec_fesv(NULL), coarse_tspec_fesv(NULL), tspec_gf(NULL),
-#ifdef MFEM_USE_MPI
-        ptspec_fesv(NULL), tspec_pgf(NULL),
-#endif
-        amr_el(-1), lim_min_size(-0.1),
+        tspec_fes(NULL), tspec_fesv(NULL),
         good_tspec(false), good_tspec_grad(false), good_tspec_hess(false),
         adapt_eval(NULL) { }
 
-   virtual ~DiscreteAdaptTC();
+   virtual ~DiscreteAdaptTC()
+   {
+      delete adapt_eval;
+      delete tspec_fes;
+      delete tspec_fesv;
+   }
 
    /** @name Target specification methods.
        The following methods are used to specify geometric parameters of the
@@ -1145,20 +1128,6 @@ public:
    void ResetUpdateFlags()
    { good_tspec = good_tspec_grad = good_tspec_hess = false; }
 
-   /// Get one of the discrete fields from tspec.
-   void GetDiscreteTargetSpec(GridFunction &tspec_, int idx);
-   /// Get the FESpace associated with tspec.
-   FiniteElementSpace *GetTSpecFESpace() { return tspec_fesv; }
-   /// Get the entire tspec.
-   GridFunction *GetTSpecData() { return tspec_gf; }
-   /// Update all discrete fields based on tspec and update for AMR
-   void UpdateAfterMeshTopologyChange();
-
-#ifdef MFEM_USE_MPI
-   ParFiniteElementSpace *GetTSpecParFESpace() { return ptspec_fesv; }
-   void ParUpdateAfterMeshTopologyChange();
-#endif
-
    /** Used to update the target specification after the mesh has changed. The
        new mesh positions are given by new_x. If @a use_flags is true, repeated
        calls won't do anything until ResetUpdateFlags() is called. */
@@ -1215,36 +1184,6 @@ public:
                                               const Vector &elfun,
                                               IsoparametricTransformation &Tpr,
                                               DenseTensor &dJtr) const;
-
-   // Generates tspec_vals for target construction using intrule
-   // Used for the refinement component in hr-adaptivity.
-   void SetTspecFromIntRule(int e_id, const IntegrationRule &intrule);
-
-   // Targets based on discrete functions can result in invalid (negative)
-   // size at the quadrature points. This method can be used to set a
-   // minimum target size.
-   void SetMinSizeForTargets(double min_size_) { lim_min_size = min_size_; }
-
-   /// Computes target specification data with respect to the coarse FE space.
-   void SetTspecDataForDerefinement(FiniteElementSpace *fes);
-
-   // Reset refinement data associated with h-adaptivity component.
-   void ResetRefinementTspecData()
-   {
-      tspec_refine.Clear();
-      amr_el = -1;
-   }
-
-   // Reset derefinement data associated with h-adaptivity component.
-   void ResetDerefinementTspecData()
-   {
-      tspec_derefine.Destroy();
-      coarse_tspec_fesv = NULL;
-   }
-
-   // Used to specify the fine element for determining energy of children of a
-   // parent element.
-   void SetRefinementSubElement(int amr_el_) { amr_el = amr_el_; }
 };
 
 class TMOPNewtonSolver;
@@ -1262,7 +1201,6 @@ protected:
    friend class TMOPNewtonSolver;
    friend class TMOPComboIntegrator;
 
-   TMOP_QualityMetric *h_metric;
    TMOP_QualityMetric *metric;        // not owned
    const TargetConstructor *targetC;  // not owned
 
@@ -1289,9 +1227,6 @@ protected:
 
    // Adaptive limiting.
    const GridFunction *zeta_0;       // Not owned.
-#ifdef MFEM_USE_MPI
-   const ParGridFunction *pzeta_0;
-#endif
    GridFunction *zeta;               // Owned. Updated by adapt_eval.
    Coefficient *coeff_zeta;          // Not owned.
    AdaptivityEvaluator *adapt_eval;  // Not owned.
@@ -1402,7 +1337,7 @@ protected:
 #endif
    void ComputeMinJac(const Vector &x, const FiniteElementSpace &fes);
 
-   void UpdateAfterMeshPositionChange(const Vector &new_x);
+   void UpdateAfterMeshChange(const Vector &new_x);
 
    void DisableLimiting()
    {
@@ -1460,13 +1395,11 @@ protected:
    void ComputeAllElementTargets(const Vector &xe = Vector()) const;
 
 public:
-   /** @param[in] m    TMOP_QualityMetric for r-adaptivity (not owned).
-       @param[in] tc   Target-matrix construction algorithm to use (not owned).
-       @param[in] hm   TMOP_QualityMetric for h-adaptivity (not owned). */
-   TMOP_Integrator(TMOP_QualityMetric *m, TargetConstructor *tc,
-                   TMOP_QualityMetric *hm)
-      : h_metric(hm), metric(m), targetC(tc), IntegRules(NULL),
-        integ_order(-1), coeff1(NULL), metric_normal(1.0),
+   /** @param[in] m  TMOP_QualityMetric that will be integrated (not owned).
+       @param[in] tc Target-matrix construction algorithm to use (not owned). */
+   TMOP_Integrator(TMOP_QualityMetric *m, TargetConstructor *tc)
+      : metric(m), targetC(tc), IntegRules(NULL), integ_order(-1),
+        coeff1(NULL), metric_normal(1.0),
         nodes0(NULL), coeff0(NULL),
         lim_dist(NULL), lim_func(NULL), lim_normal(1.0),
         zeta_0(NULL), zeta(NULL), coeff_zeta(NULL), adapt_eval(NULL),
@@ -1474,9 +1407,6 @@ public:
         fdflag(false), dxscale(1.0e3), fd_call_flag(false), exact_action(false)
    { PA.enabled = false; }
 
-   TMOP_Integrator(TMOP_QualityMetric *m, TargetConstructor *tc)
-      : TMOP_Integrator(m, tc, m) { }
-
    ~TMOP_Integrator();
 
    /// Release the device memory of large PA allocations. This will copy device
@@ -1548,22 +1478,6 @@ public:
                                    ElementTransformation &T,
                                    const Vector &elfun);
 
-   /** @brief Computes the mean of the energies of the given element's children.
-
-       In addition to the inputs for GetElementEnergy, this function requires an
-       IntegrationRule to be specified that will give the decomposition of the
-       given element based on the refinement type being considered. */
-   virtual double GetRefinementElementEnergy(const FiniteElement &el,
-                                             ElementTransformation &T,
-                                             const Vector &elfun,
-                                             const IntegrationRule &irule);
-
-   /// This function is similar to GetElementEnergy, but ignores components
-   /// such as limiting etc. to compute the element energy.
-   virtual double GetDerefinementElementEnergy(const FiniteElement &el,
-                                               ElementTransformation &T,
-                                               const Vector &elfun);
-
    virtual void AssembleElementVector(const FiniteElement &el,
                                       ElementTransformation &T,
                                       const Vector &elfun, Vector &elvect);
@@ -1572,13 +1486,6 @@ public:
                                     ElementTransformation &T,
                                     const Vector &elfun, DenseMatrix &elmat);
 
-   TMOP_QualityMetric &GetAMRQualityMetric() { return *h_metric; }
-
-   void UpdateAfterMeshTopologyChange();
-#ifdef MFEM_USE_MPI
-   void ParUpdateAfterMeshTopologyChange();
-#endif
-
    // PA extension
    using NonlinearFormIntegrator::AssemblePA;
    virtual void AssemblePA(const FiniteElementSpace&);
@@ -1657,15 +1564,6 @@ public:
                                     ElementTransformation &T,
                                     const Vector &elfun, DenseMatrix &elmat);
 
-   virtual double GetRefinementElementEnergy(const FiniteElement &el,
-                                             ElementTransformation &T,
-                                             const Vector &elfun,
-                                             const IntegrationRule &irule);
-
-   virtual double GetDerefinementElementEnergy(const FiniteElement &el,
-                                               ElementTransformation &T,
-                                               const Vector &elfun);
-
    /// Normalization factor that considers all integrators in the combination.
    void EnableNormalization(const GridFunction &x);
 #ifdef MFEM_USE_MPI

fem/tmop_amr.cpp

@@ -1,896 +0,0 @@
-// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-// LICENSE and NOTICE for details. LLNL-CODE-806117.
-//
-// This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
-//
-// MFEM is free software; you can redistribute it and/or modify it under the
-// terms of the BSD-3 license. We welcome feedback and contributions, see file
-// CONTRIBUTING.md for details.
-
-#include "tmop_amr.hpp"
-
-namespace mfem
-{
-
-using namespace mfem;
-
-void TMOPRefinerEstimator::ComputeEstimates()
-{
-   bool iso = false;
-   bool aniso = false;
-   if (amrmetric == 1 || amrmetric == 2 || amrmetric == 58)
-   {
-      aniso = true;
-   }
-   if (amrmetric == 55 || amrmetric == 56 || amrmetric == 77 ||
-       amrmetric == 315 || amrmetric == 316 || amrmetric == 321)
-   {
-      iso = true;
-   }
-   if (amrmetric == 7 || amrmetric == 9)
-   {
-      iso = true; aniso = true;
-   }
-
-   MFEM_VERIFY(iso || aniso, "Metric type not supported in hr-adaptivity.");
-
-   const int dim = mesh->Dimension();
-   const int num_ref_types = 3 + 4*(dim-2);
-   const int NEorig = mesh->GetNE();
-
-   aniso_flags.SetSize(NEorig);
-   error_estimates.SetSize(NEorig);
-   Vector amr_base_energy(NEorig), amr_temp_energy(NEorig);
-   error_estimates = 1.*std::numeric_limits<float>::max();
-   aniso_flags = -1;
-   GetTMOPRefinementEnergy(0, amr_base_energy);
-
-   for (int i = 1; i < num_ref_types+1; i++)
-   {
-      if ( dim == 2 && i < 3  && aniso != true ) { continue; }
-      if ( dim == 2 && i == 3 && iso   != true ) { continue; }
-      if ( dim == 3 && i < 7  && aniso != true ) { continue; }
-      if ( dim == 3 && i == 7 && iso   != true ) { continue; }
-
-      GetTMOPRefinementEnergy(i, amr_temp_energy);
-
-      for (int e = 0; e < NEorig; e++)
-      {
-         if ( amr_temp_energy(e) < error_estimates(e) )
-         {
-            error_estimates(e) = amr_temp_energy(e);
-            aniso_flags[e] = i;
-         }
-      }
-   }
-   error_estimates *= energy_scaling_factor;
-
-   if (spat_gf)
-   {
-      L2_FECollection avg_fec(0, mesh->Dimension());
-      FiniteElementSpace avg_fes(spat_gf->FESpace()->GetMesh(), &avg_fec);
-      GridFunction elem_avg(&avg_fes);
-      spat_gf->GetElementAverages(elem_avg);
-      for (int i = 0; i < amr_base_energy.Size(); i++)
-      {
-         if (elem_avg(i) < spat_gf_critical) { amr_base_energy(i) = 0.; }
-      }
-   }
-
-   error_estimates -= amr_base_energy;
-   error_estimates *= -1; // error = E(parent) - scaling_factor*mean(E(children))
-   current_sequence = mesh->GetSequence();
-}
-
-void TMOPRefinerEstimator::GetTMOPRefinementEnergy(int reftype,
-                                                   Vector &el_energy_vec)
-{
-   const FiniteElementSpace *fes = mesh->GetNodalFESpace();
-   const int NE = fes->GetNE();
-   GridFunction *xdof = mesh->GetNodes();
-   xdof->SetTrueVector();
-   xdof->SetFromTrueVector();
-
-   el_energy_vec.SetSize(NE);
-   el_energy_vec = std::numeric_limits<float>::max();
-
-   for (int e = 0; e < NE; e++)
-   {
-      Geometry::Type gtype = fes->GetFE(e)->GetGeomType();
-      DenseMatrix tr, xsplit;
-      IntegrationRule *irule = NULL;
-
-      if ( (gtype == Geometry::TRIANGLE && reftype > 0 && reftype < 3) ||
-           (gtype == Geometry::CUBE && reftype > 0 && reftype < 7) ||
-           (gtype == Geometry::TETRAHEDRON && reftype > 0 && reftype < 7) )
-      {
-         continue;
-      }
-
-      switch (gtype)
-      {
-         case Geometry::TRIANGLE:
-         {
-            int ref_access = reftype == 0 ? 0 : 1;
-            xdof->GetVectorValues(e, *TriIntRule[ref_access], xsplit, tr);
-            irule = TriIntRule[ref_access];
-            break;
-         }
-         case Geometry::TETRAHEDRON:
-         {
-            int ref_access = reftype == 0 ? 0 : 1;
-            xdof->GetVectorValues(e, *TetIntRule[ref_access], xsplit, tr);
-            irule = TetIntRule[ref_access];
-            break;
-         }
-         case Geometry::SQUARE:
-         {
-            MFEM_VERIFY(QuadIntRule[reftype], " Integration rule does not exist.");
-            xdof->GetVectorValues(e, *QuadIntRule[reftype], xsplit, tr);
-            irule = QuadIntRule[reftype];
-            break;
-         }
-         case Geometry::CUBE:
-         {
-            int ref_access = reftype == 0 ? 0 : 1;
-            xdof->GetVectorValues(e, *HexIntRule[ref_access], xsplit, tr);
-            irule = HexIntRule[ref_access];
-            break;
-         }
-         default:
-            MFEM_ABORT("Incompatible geometry type!");
-      }
-      xsplit.Transpose();
-
-      el_energy_vec(e) = 0.; // Re-set to 0
-
-      // The data format is xe1,xe2,..xen,ye1,ye2..yen.
-      // We will reformat it inside GetRefinementElementEnergy
-      Vector elfun(xsplit.GetData(), xsplit.NumCols()*xsplit.NumRows());
-
-      Array<NonlinearFormIntegrator*> &integs = *(nlf->GetDNFI());
-      TMOP_Integrator *ti  = NULL;
-      TMOPComboIntegrator *co = NULL;
-      for (int i = 0; i < integs.Size(); i++)
-      {
-         ti = dynamic_cast<TMOP_Integrator *>(integs[i]);
-         if (ti)
-         {
-            el_energy_vec(e) = ti->GetRefinementElementEnergy(*fes->GetFE(e),
-                                                              *mesh->GetElementTransformation(e),
-                                                              elfun,
-                                                              *irule);
-         }
-         co = dynamic_cast<TMOPComboIntegrator *>(integs[i]);
-         if (co)
-         {
-            Array<TMOP_Integrator *> ati = co->GetTMOPIntegrators();
-            for (int j = 0; j < ati.Size(); j++)
-            {
-               el_energy_vec(e) += ati[j]->GetRefinementElementEnergy(*fes->GetFE(e),
-                                                                      *mesh->GetElementTransformation(e),
-                                                                      elfun,
-                                                                      *irule);
-            }
-         }
-      }
-   }
-}
-
-void TMOPRefinerEstimator::SetHexIntRules()
-{
-   HexIntRule.SetSize(1+1);
-   // Reftype = 0 -> original element
-   Mesh meshsplit = Mesh::MakeCartesian3D(1, 1, 1, Element::HEXAHEDRON);
-   Mesh base_mesh_copy(meshsplit);
-   HexIntRule[0] = SetIntRulesFromMesh(meshsplit);
-   meshsplit.Clear();
-
-   // Reftype = 7
-   for (int i = 7; i < 8; i++)
-   {
-      Array<Refinement> marked_elements;
-      Mesh mesh_ref(base_mesh_copy);
-      for (int e = 0; e < mesh_ref.GetNE(); e++)
-      {
-         marked_elements.Append(Refinement(e, i));
-      }
-      mesh_ref.GeneralRefinement(marked_elements, 1, 0);
-      HexIntRule[1] = SetIntRulesFromMesh(mesh_ref);
-      mesh_ref.Clear();
-   }
-}
-
-void TMOPRefinerEstimator::SetQuadIntRules()
-{
-   QuadIntRule.SetSize(3+1);
-
-   // Reftype = 0 -> original element
-   Mesh meshsplit = Mesh::MakeCartesian2D(1, 1, Element::QUADRILATERAL);
-   Mesh base_mesh_copy(meshsplit);
-   QuadIntRule[0] = SetIntRulesFromMesh(meshsplit);
-   meshsplit.Clear();
-
-   // Reftype = 1-3
-   for (int i = 1; i < 4; i++)
-   {
-      Array<Refinement> marked_elements;
-      Mesh mesh_ref(base_mesh_copy);
-      for (int e = 0; e < mesh_ref.GetNE(); e++)
-      {
-         marked_elements.Append(Refinement(e, i));
-      }
-      mesh_ref.GeneralRefinement(marked_elements, 1, 0);
-      QuadIntRule[i] = SetIntRulesFromMesh(mesh_ref);
-      mesh_ref.Clear();
-   }
-}
-
-void TMOPRefinerEstimator::SetTriIntRules()
-{
-   TriIntRule.SetSize(1+1);
-
-   // Reftype = 0 // original element
-   const int Nvert = 3, NEsplit = 1;
-   Mesh meshsplit(2, Nvert, NEsplit, 0 ,2);
-   const double tri_v[3][2] =
-   {
-      {0, 0}, {1, 0}, {0, 1}
-   };
-   const int tri_e[1][3] =
-   {
-      {0, 1, 2}
-   };
-
-   for (int j = 0; j < Nvert; j++)
-   {
-      meshsplit.AddVertex(tri_v[j]);
-   }
-   meshsplit.AddTriangle(tri_e[0], 1);
-   meshsplit.FinalizeTriMesh(1, 1, true);
-
-   Mesh base_mesh_copy(meshsplit);
-   TriIntRule[0] = SetIntRulesFromMesh(meshsplit);
-   meshsplit.Clear();
-
-   // no anisotropic refinements for triangle
-   // Reftype = 3
-   for (int i = 1; i < 2; i++)
-   {
-      Array<Refinement> marked_elements;
-      Mesh mesh_ref(base_mesh_copy);
-      for (int e = 0; e < mesh_ref.GetNE(); e++)
-      {
-         marked_elements.Append(Refinement(e, i));
-      }
-      mesh_ref.GeneralRefinement(marked_elements, 1, 0);
-      TriIntRule[i] = SetIntRulesFromMesh(mesh_ref);
-      mesh_ref.Clear();
-   }
-}
-
-void TMOPRefinerEstimator::SetTetIntRules()
-{
-   TetIntRule.SetSize(1+1);
-
-   // Reftype = 0 // original element
-   const int Nvert = 4, NEsplit = 1;
-   Mesh meshsplit(3, Nvert, NEsplit, 0, 3);
-   const double tet_v[4][3] =
-   {
-      {0, 0, 0}, {1, 0, 0}, {0, 1, 0}, {0, 0, 1}
-   };
-   const int tet_e[1][4] =
-   {
-      {0, 1, 2, 3}
-   };
-
-   for (int j = 0; j < Nvert; j++)
-   {
-      meshsplit.AddVertex(tet_v[j]);
-   }
-   meshsplit.AddTet(tet_e[0], 1);
-   meshsplit.FinalizeTetMesh(1, 1, true);
-
-   Mesh base_mesh_copy(meshsplit);
-   TetIntRule[0] = SetIntRulesFromMesh(meshsplit);
-   meshsplit.Clear();
-
-   // no anisotropic refinements for triangle
-   // Reftype = 7
-   for (int i = 1; i < 2; i++)
-   {
-      Array<Refinement> marked_elements;
-      Mesh mesh_ref(base_mesh_copy);
-      for (int e = 0; e < mesh_ref.GetNE(); e++)
-      {
-         marked_elements.Append(Refinement(e, i)); //ref_type will default to 7
-      }
-      mesh_ref.GeneralRefinement(marked_elements, 1, 0);
-      TetIntRule[i] = SetIntRulesFromMesh(mesh_ref);
-      mesh_ref.Clear();
-   }
-}
-
-IntegrationRule* TMOPRefinerEstimator::SetIntRulesFromMesh(Mesh &meshsplit)
-{
-   const int dim = meshsplit.Dimension();
-   H1_FECollection fec(order, dim);
-   FiniteElementSpace nodal_fes(&meshsplit, &fec, dim);
-   meshsplit.SetNodalFESpace(&nodal_fes);
-
-   const int NEsplit = meshsplit.GetNE();
-   const int dof_cnt = nodal_fes.GetFE(0)->GetDof(),
-             pts_cnt = NEsplit * dof_cnt;
-
-   DenseMatrix pos(dof_cnt, dim);
-   Vector posV(pos.Data(), dof_cnt * dim);
-   Array<int> xdofs(dof_cnt * dim);
-
-   // Create an IntegrationRule on the nodes of the reference submesh.
-   IntegrationRule *irule = new IntegrationRule(pts_cnt);
-   GridFunction *nodesplit = meshsplit.GetNodes();
-
-   int pt_id = 0;
-   for (int i = 0; i < NEsplit; i++)
-   {
-      nodal_fes.GetElementVDofs(i, xdofs);
-      nodesplit->GetSubVector(xdofs, posV);
-      for (int j = 0; j < dof_cnt; j++)
-      {
-         if (dim == 2)
-         {
-            irule->IntPoint(pt_id).Set2(pos(j, 0), pos(j, 1));
-         }
-         else if (dim == 3)
-         {
-            irule->IntPoint(pt_id).Set3(pos(j, 0), pos(j, 1), pos(j, 2));
-         }
-         pt_id++;
-      }
-   }
-   return irule;
-}
-
-bool TMOPDeRefinerEstimator::GetDerefineEnergyForIntegrator(
-   TMOP_Integrator &tmopi,
-   Vector &fine_energy)
-{
-   DiscreteAdaptTC *tcd = tmopi.GetDiscreteAdaptTC();
-   fine_energy.SetSize(mesh->GetNE());
-
-   if (serial)
-   {
-      Mesh meshcopy(*mesh);
-      FiniteElementSpace *tcdfes = NULL;
-      if (tcd)
-      {
-         tcdfes = new FiniteElementSpace(*tcd->GetTSpecFESpace(), &meshcopy);
-      }
-
-      Vector local_err(meshcopy.GetNE());
-      local_err = 0.;
-      double threshold = std::numeric_limits<float>::max();
-      meshcopy.DerefineByError(local_err, threshold, 0, 1);
-
-      if (meshcopy.GetGlobalNE() == mesh->GetGlobalNE())
-      {
-         delete tcdfes;
-         return false;
-      }
-
-      if (tcd)
-      {
-         tcdfes->Update();
-         tcd->SetTspecDataForDerefinement(tcdfes);
-      }
-
-      Vector coarse_energy(meshcopy.GetNE());
-      GetTMOPDerefinementEnergy(meshcopy, tmopi, coarse_energy);
-      if (tcd) { tcd->ResetDerefinementTspecData(); }
-      GetTMOPDerefinementEnergy(*mesh, tmopi, fine_energy);
-
-      const CoarseFineTransformations &dtrans =
-         meshcopy.ncmesh->GetDerefinementTransforms();
-      Table coarse_to_fine;
-      dtrans.GetCoarseToFineMap(meshcopy, coarse_to_fine);
-
-      for (int pe = 0; pe < coarse_to_fine.Size(); pe++)
-      {
-         Array<int> tabrow;
-         coarse_to_fine.GetRow(pe, tabrow);
-         int nchild = tabrow.Size();
-         double parent_energy = coarse_energy(pe);
-         for (int fe = 0; fe < nchild; fe++)
-         {
-            int child = tabrow[fe];
-            MFEM_VERIFY(child < mesh->GetNE(), " invalid coarse to fine mapping");
-            fine_energy(child) -= parent_energy;
-         }
-      }
-      delete tcdfes;
-   }
-   else
-   {
-#ifdef MFEM_USE_MPI
-      ParMesh meshcopy(*pmesh);
-      ParFiniteElementSpace *tcdfes = NULL;
-      if (tcd)
-      {
-         tcdfes = new ParFiniteElementSpace(*tcd->GetTSpecParFESpace(), meshcopy);
-      }
-
-      Vector local_err(meshcopy.GetNE());
-      local_err = 0.;
-      double threshold = std::numeric_limits<float>::max();
-      meshcopy.DerefineByError(local_err, threshold, 0, 1);
-
-      if (meshcopy.GetGlobalNE() == pmesh->GetGlobalNE())
-      {
-         delete tcdfes;
-         return false;
-      }
-
-      if (tcd)
-      {
-         tcdfes->Update();
-         tcd->SetTspecDataForDerefinement(tcdfes);
-      }
-
-      Vector coarse_energy(meshcopy.GetNE());
-      GetTMOPDerefinementEnergy(meshcopy, tmopi, coarse_energy);
-      if (tcd) { tcd->ResetDerefinementTspecData(); }
-      GetTMOPDerefinementEnergy(*pmesh, tmopi, fine_energy);
-
-      const CoarseFineTransformations &dtrans =
-         meshcopy.pncmesh->GetDerefinementTransforms();
-      Table coarse_to_fine;
-      dtrans.GetCoarseToFineMap(meshcopy, coarse_to_fine);
-
-      for (int pe = 0; pe < meshcopy.GetNE(); pe++)
-      {
-         Array<int> tabrow;
-         coarse_to_fine.GetRow(pe, tabrow);
-         int nchild = tabrow.Size();
-         double parent_energy = coarse_energy(pe);
-         for (int fe = 0; fe < nchild; fe++)
-         {
-            int child = tabrow[fe];
-            MFEM_VERIFY(child < pmesh->GetNE(), " invalid coarse to fine mapping");
-            fine_energy(child) -= parent_energy;
-         }
-      }
-      delete tcdfes;
-#endif
-   }
-
-   // error_estimate(e) = energy(parent_of_e)-energy(e)
-   // Negative energy means derefinement is desirable.
-   fine_energy *= -1;
-   return true;
-}
-
-void TMOPDeRefinerEstimator::ComputeEstimates()
-{
-   Array<NonlinearFormIntegrator*> &integs = *(nlf->GetDNFI());
-   TMOP_Integrator *ti  = NULL;
-   TMOPComboIntegrator *co = NULL;
-   error_estimates.SetSize(mesh->GetNE());
-   error_estimates = 0.;
-   Vector fine_energy(mesh->GetNE());
-
-   for (int i = 0; i < integs.Size(); i++)
-   {
-      ti = dynamic_cast<TMOP_Integrator *>(integs[i]);
-      if (ti)
-      {
-         bool deref = GetDerefineEnergyForIntegrator(*ti, fine_energy);
-         if (!deref) { error_estimates = 1; return; }
-         error_estimates += fine_energy;
-      }
-      co = dynamic_cast<TMOPComboIntegrator *>(integs[i]);
-      if (co)
-      {
-         Array<TMOP_Integrator *> ati = co->GetTMOPIntegrators();
-         for (int j = 0; j < ati.Size(); j++)
-         {
-            bool deref = GetDerefineEnergyForIntegrator(*ati[j], fine_energy);
-            if (!deref) { error_estimates = 1; return; }
-            error_estimates += fine_energy;
-         }
-      }
-   }
-}
-
-void TMOPDeRefinerEstimator::GetTMOPDerefinementEnergy(Mesh &cmesh,
-                                                       TMOP_Integrator &tmopi,
-                                                       Vector &el_energy_vec)
-{
-   const int cNE = cmesh.GetNE();
-   el_energy_vec.SetSize(cNE);
-   const FiniteElementSpace *fespace = cmesh.GetNodalFESpace();
-
-   GridFunction *cxdof = cmesh.GetNodes();
-
-   Array<int> vdofs;
-   Vector el_x;
-   const FiniteElement *fe;
-   ElementTransformation *T;
-
-   for (int j = 0; j < cNE; j++)
-   {
-      fe = fespace->GetFE(j);
-      fespace->GetElementVDofs(j, vdofs);
-      T = cmesh.GetElementTransformation(j);
-      cxdof->GetSubVector(vdofs, el_x);
-      el_energy_vec(j) = tmopi.GetDerefinementElementEnergy(*fe, *T, el_x);
-   }
-}
-
-
-TMOPHRSolver::TMOPHRSolver(Mesh &mesh_, NonlinearForm &nlf_,
-                           TMOPNewtonSolver &tmopns_, GridFunction &x_,
-                           bool move_bnd_, bool hradaptivity_,
-                           int mesh_poly_deg_, int amr_metric_id_,
-                           int hr_iter_, int h_per_r_iter_) :
-   mesh(&mesh_), nlf(&nlf_), tmopns(&tmopns_), x(&x_),
-   gridfuncarr(), fespacearr(),
-   move_bnd(move_bnd_), hradaptivity(hradaptivity_),
-   mesh_poly_deg(mesh_poly_deg_), amr_metric_id(amr_metric_id_),
-   serial(true), hr_iter(hr_iter_), h_per_r_iter(h_per_r_iter_)
-{
-   if (!hradaptivity) { return; }
-   tmop_r_est = new TMOPRefinerEstimator(*mesh, *nlf, mesh_poly_deg,
-                                         amr_metric_id);
-   tmop_r = new ThresholdRefiner(*tmop_r_est);
-   tmop_r->SetTotalErrorFraction(0.0);
-   tmop_r_est->SetEnergyScalingFactor(1.);
-   tmop_dr_est= new TMOPDeRefinerEstimator(*mesh, *nlf);
-   tmop_dr = new ThresholdDerefiner(*tmop_dr_est);
-   AddGridFunctionForUpdate(x);
-}
-
-#ifdef MFEM_USE_MPI
-TMOPHRSolver::TMOPHRSolver(ParMesh &pmesh_, ParNonlinearForm &pnlf_,
-                           TMOPNewtonSolver &tmopns_, ParGridFunction &px_,
-                           bool move_bnd_, bool hradaptivity_,
-                           int mesh_poly_deg_, int amr_metric_id_,
-                           int hr_iter_, int h_per_r_iter_) :
-   mesh(&pmesh_), nlf(&pnlf_), tmopns(&tmopns_), x(&px_),
-   gridfuncarr(), fespacearr(),
-   move_bnd(move_bnd_), hradaptivity(hradaptivity_),
-   mesh_poly_deg(mesh_poly_deg_), amr_metric_id(amr_metric_id_),
-   pmesh(&pmesh_), pnlf(&pnlf_), pgridfuncarr(), pfespacearr(),
-   serial(false), hr_iter(hr_iter_), h_per_r_iter(h_per_r_iter_)
-{
-   if (!hradaptivity) { return; }
-   tmop_r_est = new TMOPRefinerEstimator(*pmesh, *pnlf, mesh_poly_deg,
-                                         amr_metric_id);
-   tmop_r = new ThresholdRefiner(*tmop_r_est);
-   tmop_r->SetTotalErrorFraction(0.0);
-   tmop_r_est->SetEnergyScalingFactor(1.);
-   tmop_dr_est= new TMOPDeRefinerEstimator(*pmesh, *pnlf);
-   tmop_dr = new ThresholdDerefiner(*tmop_dr_est);
-   AddGridFunctionForUpdate(&px_);
-}
-#endif
-
-void TMOPHRSolver::Mult()
-{
-   Vector b(0);
-   int myid = 0;
-   if (serial)
-   {
-      tmopns->SetOperator(*nlf);
-   }
-   else
-   {
-#ifdef MFEM_USE_MPI
-      myid = pnlf->ParFESpace()->GetMyRank();
-      tmopns->SetOperator(*pnlf);
-#endif
-   }
-   if (!hradaptivity)
-   {
-      tmopns->Mult(b, x->GetTrueVector());
-      if (tmopns->GetConverged() == false)
-      {
-         if (myid == 0) { mfem::out << "Nonlinear solver: rtol not achieved.\n"; }
-      }
-      x->SetFromTrueVector();
-      return;
-   }
-
-   bool radaptivity = true;
-
-   tmop_dr->Reset();
-   tmop_r->Reset();
-
-   if (serial)
-   {
-      for (int i_hr = 0; i_hr < hr_iter; i_hr++)
-      {
-         if (!radaptivity)
-         {
-            break;
-         }
-         mfem::out << i_hr << " r-adaptivity iteration.\n";
-
-         tmopns->SetOperator(*nlf);
-         tmopns->Mult(b, x->GetTrueVector());
-         x->SetFromTrueVector();
-
-         mfem::out << "TMOP energy after r-adaptivity: " <<
-                   nlf->GetGridFunctionEnergy(*x)/mesh->GetNE() <<
-                   ", Elements: " << mesh->GetNE() << std::endl;
-
-         for (int i_h = 0; i_h < h_per_r_iter; i_h++)
-         {
-            // Derefinement step.
-            if (mesh->ncmesh)
-            {
-               tmop_dr->Apply(*mesh);
-               Update();
-            }
-            mfem::out << "TMOP energy after derefinement: " <<
-                      nlf->GetGridFunctionEnergy(*x)/mesh->GetNE() <<
-                      ", Elements: " << mesh->GetNE() << std::endl;
-
-            // Refinement step.
-            tmop_r->Apply(*mesh);
-            Update();
-            mfem::out << "TMOP energy after   refinement: " <<
-                      nlf->GetGridFunctionEnergy(*x)/mesh->GetNE() <<
-                      ", Elements: " << mesh->GetNE() << std::endl;
-
-            if (!tmop_dr->Derefined() && tmop_r->Stop())
-            {
-               radaptivity = false;
-               mfem::out << "AMR stopping criterion satisfied. Stop.\n";
-               break;
-            }
-         } //n_h
-      } //n_hr
-   }
-   else
-   {
-#ifdef MFEM_USE_MPI
-      int NEGlob;
-      double tmopenergy;
-      for (int i_hr = 0; i_hr < hr_iter; i_hr++)
-      {
-         if (!radaptivity)
-         {
-            break;
-         }
-         if (myid == 0) { mfem::out << i_hr << " r-adaptivity iteration.\n"; }
-         tmopns->SetOperator(*pnlf);
-         tmopns->Mult(b, x->GetTrueVector());
-         x->SetFromTrueVector();
-
-         NEGlob = pmesh->GetGlobalNE();
-         tmopenergy = pnlf->GetParGridFunctionEnergy(*x) / NEGlob;
-         if (myid == 0)
-         {
-            mfem::out << "TMOP energy after r-adaptivity: " << tmopenergy <<
-                      ", Elements: " << NEGlob << std::endl;
-         }
-
-         for (int i_h = 0; i_h < h_per_r_iter; i_h++)
-         {
-            // Derefinement step.
-            if (pmesh->pncmesh)
-            {
-               RebalanceParNCMesh();
-               ParUpdate();
-
-               tmop_dr->Apply(*pmesh);
-               ParUpdate();
-            }
-            NEGlob = pmesh->GetGlobalNE();
-            tmopenergy = pnlf->GetParGridFunctionEnergy(*x) / NEGlob;
-            if (myid == 0)
-            {
-               mfem::out << "TMOP energy after derefinement: " << tmopenergy <<
-                         ", Elements: " << NEGlob << std::endl;
-            }
-
-            // Refinement step.
-            tmop_r->Apply(*pmesh);
-            ParUpdate();
-            NEGlob = pmesh->GetGlobalNE();
-            tmopenergy = pnlf->GetParGridFunctionEnergy(*x) / NEGlob;
-            if (myid == 0)
-            {
-               mfem::out << "TMOP energy after   refinement: " << tmopenergy <<
-                         ", Elements: " << NEGlob << std::endl;
-            }
-
-            if (!tmop_dr->Derefined() && tmop_r->Stop())
-            {
-               radaptivity = false;
-               if (myid == 0)
-               {
-                  mfem::out << "AMR stopping criterion satisfied. Stop.\n";
-               }
-               break;
-            }
-         } //n_r limit
-      } //n_hr
-#endif
-   }
-}
-
-#ifdef MFEM_USE_MPI
-void TMOPHRSolver::RebalanceParNCMesh()
-{
-   ParNCMesh *pncmesh = pmesh->pncmesh;
-   if (pncmesh)
-   {
-      const Table &dreftable = pncmesh->GetDerefinementTable();
-      Array<int> drefs, new_ranks;
-      for (int i = 0; i < dreftable.Size(); i++)
-      {
-         drefs.Append(i);
-      }
-      pncmesh->GetFineToCoarsePartitioning(drefs, new_ranks);
-      pmesh->Rebalance(new_ranks);
-   }
-}
-#endif
-
-void TMOPHRSolver::Update()
-{
-   // Update FESpace
-   for (int i = 0; i < fespacearr.Size(); i++)
-   {
-      fespacearr[i]->Update();
-   }
-   // Update nodal GF
-   for (int i = 0; i < gridfuncarr.Size(); i++)
-   {
-      gridfuncarr[i]->Update();
-      gridfuncarr[i]->SetTrueVector();
-      gridfuncarr[i]->SetFromTrueVector();
-   }
-
-   // Update Discrete Indicator for all the TMOP_Integrators in NonLinearForm
-   Array<NonlinearFormIntegrator*> &integs = *(nlf->GetDNFI());
-   TMOP_Integrator *ti  = NULL;
-   TMOPComboIntegrator *co = NULL;
-   DiscreteAdaptTC *dtc = NULL;
-   for (int i = 0; i < integs.Size(); i++)
-   {
-      ti = dynamic_cast<TMOP_Integrator *>(integs[i]);
-      if (ti)
-      {
-         ti->UpdateAfterMeshTopologyChange();
-         dtc = ti->GetDiscreteAdaptTC();
-         if (dtc) { dtc->UpdateAfterMeshTopologyChange(); }
-      }
-      co = dynamic_cast<TMOPComboIntegrator *>(integs[i]);
-      if (co)
-      {
-         Array<TMOP_Integrator *> ati = co->GetTMOPIntegrators();
-         for (int j = 0; j < ati.Size(); j++)
-         {
-            ati[j]->UpdateAfterMeshTopologyChange();
-            dtc = ati[j]->GetDiscreteAdaptTC();
-            if (dtc) { dtc->UpdateAfterMeshTopologyChange(); }
-         }
-      }
-   }
-
-   // Update the Nonlinear form and set Essential BC.
-   UpdateNonlinearFormAndBC(mesh, nlf);
-}
-
-#ifdef MFEM_USE_MPI
-void TMOPHRSolver::ParUpdate()
-{
-   // Update FESpace
-   for (int i = 0; i < pfespacearr.Size(); i++)
-   {
-      pfespacearr[i]->Update();
-   }
-   // Update nodal GF
-   for (int i = 0; i < pgridfuncarr.Size(); i++)
-   {
-      pgridfuncarr[i]->Update();
-      pgridfuncarr[i]->SetTrueVector();
-      pgridfuncarr[i]->SetFromTrueVector();
-   }
-
-   // Update Discrete Indicator
-   Array<NonlinearFormIntegrator*> &integs = *(nlf->GetDNFI());
-   TMOP_Integrator *ti  = NULL;
-   TMOPComboIntegrator *co = NULL;
-   DiscreteAdaptTC *dtc = NULL;
-   for (int i = 0; i < integs.Size(); i++)
-   {
-      ti = dynamic_cast<TMOP_Integrator *>(integs[i]);
-      if (ti)
-      {
-         ti->ParUpdateAfterMeshTopologyChange();
-         dtc = ti->GetDiscreteAdaptTC();
-         if (dtc) { dtc->ParUpdateAfterMeshTopologyChange(); }
-      }
-      co = dynamic_cast<TMOPComboIntegrator *>(integs[i]);
-      if (co)
-      {
-         Array<TMOP_Integrator *> ati = co->GetTMOPIntegrators();
-         for (int j = 0; j < ati.Size(); j++)
-         {
-            ati[j]->ParUpdateAfterMeshTopologyChange();
-            dtc = ati[j]->GetDiscreteAdaptTC();
-            if (dtc) { dtc->ParUpdateAfterMeshTopologyChange(); }
-         }
-      }
-   }
-
-   // Update the Nonlinear form and set Essential BC.
-   UpdateNonlinearFormAndBC(pmesh, pnlf);
-}
-#endif
-
-void TMOPHRSolver::UpdateNonlinearFormAndBC(Mesh *mesh, NonlinearForm *nlf)
-{
-   const FiniteElementSpace &fes = *mesh->GetNodalFESpace();
-
-   // Update Nonlinear form and Set Essential BC
-   nlf->Update();
-   const int dim = fes.GetFE(0)->GetDim();
-   if (move_bnd == false)
-   {
-      Array<int> ess_bdr(mesh->bdr_attributes.Max());
-      ess_bdr = 1;
-      nlf->SetEssentialBC(ess_bdr);
-   }
-   else
-   {
-      const int nd  = fes.GetBE(0)->GetDof();
-      int n = 0;
-      for (int i = 0; i < mesh->GetNBE(); i++)
-      {
-         const int attr = mesh->GetBdrElement(i)->GetAttribute();
-         MFEM_VERIFY(!(dim == 2 && attr == 3),
-                     "Boundary attribute 3 must be used only for 3D meshes. "
-                     "Adjust the attributes (1/2/3/4 for fixed x/y/z/all "
-                     "components, rest for free nodes), or use -fix-bnd.");
-         if (attr == 1 || attr == 2 || attr == 3) { n += nd; }
-         if (attr == 4) { n += nd * dim; }
-      }
-      Array<int> ess_vdofs(n), vdofs;
-      n = 0;
-      for (int i = 0; i < mesh->GetNBE(); i++)
-      {
-         const int attr = mesh->GetBdrElement(i)->GetAttribute();
-         fes.GetBdrElementVDofs(i, vdofs);
-         if (attr == 1) // Fix x components.
-         {
-            for (int j = 0; j < nd; j++)
-            { ess_vdofs[n++] = vdofs[j]; }
-         }
-         else if (attr == 2) // Fix y components.
-         {
-            for (int j = 0; j < nd; j++)
-            { ess_vdofs[n++] = vdofs[j+nd]; }
-         }
-         else if (attr == 3) // Fix z components.
-         {
-            for (int j = 0; j < nd; j++)
-            { ess_vdofs[n++] = vdofs[j+2*nd]; }
-         }
-         else if (attr == 4) // Fix all components.
-         {
-            for (int j = 0; j < vdofs.Size(); j++)
-            { ess_vdofs[n++] = vdofs[j]; }
-         }
-      }
-      nlf->SetEssentialVDofs(ess_vdofs);
-   }
-}
-
-}

fem/tmop_amr.hpp

@@ -1,284 +0,0 @@
-// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-// LICENSE and NOTICE for details. LLNL-CODE-806117.
-//
-// This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
-//
-// MFEM is free software; you can redistribute it and/or modify it under the
-// terms of the BSD-3 license. We welcome feedback and contributions, see file
-// CONTRIBUTING.md for details.
-
-#ifndef MFEM_TMOP_AMR_HPP
-#define MFEM_TMOP_AMR_HPP
-
-#include "tmop_tools.hpp"
-#include "nonlinearform.hpp"
-#include "pnonlinearform.hpp"
-#include "estimators.hpp"
-#include "../mesh/mesh_operators.hpp"
-
-namespace mfem
-{
-
-class TMOPRefinerEstimator : public AnisotropicErrorEstimator
-{
-protected:
-   Mesh *mesh; // not owned
-   NonlinearForm *nlf; // not owned
-   int order;
-   int amrmetric;
-   Array<IntegrationRule *> TriIntRule, QuadIntRule, TetIntRule, HexIntRule;
-   long current_sequence;
-   Vector error_estimates;
-   Array<int> aniso_flags;
-   // An element is refined only if
-   // [mean TMOPEnergy(children)]*energy_scaling_factor < TMOPEnergy(parent)
-   double energy_scaling_factor;
-   GridFunction *spat_gf;   // If specified, can be used to specify the
-   double spat_gf_critical; // region where hr-adaptivity is done.
-
-   /// Check if the mesh of the solution was modified.
-   bool MeshIsModified()
-   {
-      long mesh_sequence = mesh->GetSequence();
-      MFEM_ASSERT(mesh_sequence >= current_sequence, "");
-      return (mesh_sequence > current_sequence);
-   }
-
-   /// Compute the element error estimates. For an element E in the mesh,
-   /// error(E) = TMOPEnergy(E)*energy_scaling_factor-Mean(TMOPEnergy(ChildofE)),
-   /// where TMOPEnergy of Children of E is obtained by assuming the element E
-   /// is refined using the refinement type being considered based on the TMOP
-   /// mesh quality metric.
-   void ComputeEstimates();
-
-   /// Construct the integration rules to model how each element type is split
-   /// using different refinement types. ref_type = 0 is the original element
-   /// and reftype \ in [1, 7] represent different refinement type based on
-   /// NCMesh class.
-   void SetQuadIntRules(); // supports ref_type = 1 to 3.
-   void SetTriIntRules(); // currently supports only isotropic refinement.
-   void SetHexIntRules(); // currently supports only isotropic refinement.
-   void SetTetIntRules(); // currently supports only isotropic refinement.
-
-   /// Get TMOP energy for each element corresponding to the refinement type
-   /// specified.
-   void GetTMOPRefinementEnergy(int reftype, Vector &el_energy_vec);
-
-   /// Use a mesh to setup an integration rule that will mimic the different
-   /// refinement types.
-   IntegrationRule* SetIntRulesFromMesh(Mesh &meshsplit);
-public:
-   TMOPRefinerEstimator(Mesh &mesh_, NonlinearForm &nlf_, int order_,
-                        int amrmetric_) :
-      mesh(&mesh_), nlf(&nlf_), order(order_), amrmetric(amrmetric_),
-      TriIntRule(0), QuadIntRule(0), TetIntRule(0), HexIntRule(0),
-      current_sequence(-1), error_estimates(), aniso_flags(),
-      energy_scaling_factor(1.), spat_gf(NULL), spat_gf_critical(0.)
-   {
-      if (mesh->Dimension() == 2)
-      {
-         SetQuadIntRules();
-         SetTriIntRules();
-      }
-      else
-      {
-         SetHexIntRules();
-         SetTetIntRules();
-      }
-   }
-
-   ~TMOPRefinerEstimator()
-   {
-      for (int i = 0; i < QuadIntRule.Size(); i++) { delete QuadIntRule[i]; }
-      for (int i = 0; i < TriIntRule.Size();  i++) { delete TriIntRule[i]; }
-      for (int i = 0; i < HexIntRule.Size();  i++) { delete HexIntRule[i]; }
-      for (int i = 0; i < TetIntRule.Size();  i++) { delete TetIntRule[i]; }
-   }
-
-   /// Get TMOP-based errors for each element in the mesh computed based on the
-   /// refinement types being considered.
-   virtual const Vector &GetLocalErrors()
-   {
-      if (MeshIsModified()) { ComputeEstimates(); }
-      return error_estimates;
-   }
-   /// For anisotropic refinements, get the refinement type (e.g., x or y)
-   virtual const Array<int> &GetAnisotropicFlags()
-   {
-      if (MeshIsModified()) { ComputeEstimates(); }
-      return aniso_flags;
-   }
-
-   /// Scaling factor for the TMOP refinement energy. An element is refined if
-   /// [mean TMOPEnergy(children)]*energy_scaling_factor < TMOPEnergy(parent)
-   void SetEnergyScalingFactor(double scale) { energy_scaling_factor = scale; }
-
-   /// Spatial indicator function (eta) that can be used to prevent elements
-   /// from being refined even if the energy criterion is met. Using this,
-   /// an element E is not refined if mean(@a spat_gf(E)) < @a spat_gf_critical.
-   void SetSpatialIndicator(GridFunction &spat_gf_,
-                            double spat_gf_critical_ = 0.5)
-   { spat_gf = &spat_gf_; spat_gf_critical = spat_gf_critical_; }
-   void SetSpatialIndicatorCritical(double val_) { spat_gf_critical = val_; }
-
-   /// Reset the error estimator.
-   virtual void Reset() { current_sequence = -1; }
-};
-
-class TMOPDeRefinerEstimator : public ErrorEstimator
-{
-protected:
-   Mesh *mesh;
-   NonlinearForm *nlf;
-#ifdef MFEM_USE_MPI
-   ParMesh *pmesh;
-   ParNonlinearForm *pnlf;
-#endif
-   int order;
-   int amrmetric;
-   long current_sequence;
-   Vector error_estimates;
-   bool serial;
-
-   /// Check if the mesh of the solution was modified.
-   bool MeshIsModified()
-   {
-      long mesh_sequence = mesh->GetSequence();
-      MFEM_ASSERT(mesh_sequence >= current_sequence, "");
-      return (mesh_sequence > current_sequence);
-   }
-
-   /// Compute the element error estimates. For a given element E in the mesh,
-   /// error(E) = TMOPEnergy(parent_of_E)-TMOPEnergy(E). Children element of an
-   /// element are derefined if the mean TMOP energy of children is greated than
-   /// the TMOP energy associated with their parent.
-   void ComputeEstimates();
-
-   void GetTMOPDerefinementEnergy(Mesh &cmesh,
-                                  TMOP_Integrator &tmopi,
-                                  Vector &el_energy_vec);
-
-   bool GetDerefineEnergyForIntegrator(TMOP_Integrator &tmopi,
-                                       Vector &fine_energy);
-public:
-   TMOPDeRefinerEstimator(Mesh &mesh_, NonlinearForm &nlf_) :
-      mesh(&mesh_), nlf(&nlf_),
-      current_sequence(-1), error_estimates(), serial(true)   { }
-#ifdef MFEM_USE_MPI
-   TMOPDeRefinerEstimator(ParMesh &pmesh_, ParNonlinearForm &pnlf_) :
-      mesh(&pmesh_), nlf(&pnlf_), pmesh(&pmesh_), pnlf(&pnlf_),
-      current_sequence(-1), error_estimates(), serial(false) { }
-#endif
-
-   ~TMOPDeRefinerEstimator() { }
-
-   virtual const Vector &GetLocalErrors()
-   {
-      if (MeshIsModified()) { ComputeEstimates(); }
-      return error_estimates;
-   }
-
-   /// Reset the error estimator.
-   virtual void Reset() { current_sequence = -1; }
-};
-
-// hr-adaptivity using TMOP.
-// If hr-adaptivity is disabled, r-adaptivity is done once using the
-// TMOPNewtonSolver.
-// Otherwise, "hr_iter" iterations of r-adaptivity are done followed by
-// "h_per_r_iter" iterations of h-adaptivity after each r-adaptivity iteration.
-// The solver terminates early if an h-adaptivity iteration does not
-// refine/derefine any element in the mesh.
-class TMOPHRSolver
-{
-protected:
-   Mesh *mesh;
-   NonlinearForm *nlf;
-   TMOPNewtonSolver *tmopns;
-   GridFunction *x;
-   Array<GridFunction *> gridfuncarr;
-   Array<FiniteElementSpace *> fespacearr;
-   bool move_bnd, hradaptivity;
-   const int mesh_poly_deg, amr_metric_id;
-#ifdef MFEM_USE_MPI
-   ParMesh *pmesh;
-   ParNonlinearForm *pnlf;
-   Array<ParGridFunction *> pgridfuncarr;
-   Array<ParFiniteElementSpace *> pfespacearr;
-#endif
-   bool serial;
-
-   // All are owned.
-   TMOPRefinerEstimator *tmop_r_est;
-   ThresholdRefiner *tmop_r;
-   TMOPDeRefinerEstimator *tmop_dr_est;
-   ThresholdDerefiner *tmop_dr;
-
-   int hr_iter, h_per_r_iter;
-
-   void Update();
-#ifdef MFEM_USE_MPI
-   void ParUpdate();
-#endif
-   void UpdateNonlinearFormAndBC(Mesh *mesh, NonlinearForm *nlf);
-
-#ifdef MFEM_USE_MPI
-   // Rebalance ParMesh such that all the children elements are moved to the same
-   // MPI rank where the parent will be if the mesh were to be derefined.
-   void RebalanceParNCMesh();
-#endif
-
-public:
-   TMOPHRSolver(Mesh &mesh_, NonlinearForm &nlf_,
-                TMOPNewtonSolver &tmopns_, GridFunction &x_,
-                bool move_bnd_, bool hradaptivity_,
-                int mesh_poly_deg_, int amr_metric_id_,
-                int hr_iter_ = 5, int h_per_r_iter_ = 1);
-#ifdef MFEM_USE_MPI
-   TMOPHRSolver(ParMesh &pmesh_, ParNonlinearForm &pnlf_,
-                TMOPNewtonSolver &tmopns_, ParGridFunction &x_,
-                bool move_bnd_, bool hradaptivity_,
-                int mesh_poly_deg_, int amr_metric_id_,
-                int hr_iter_ = 5, int h_per_r_iter_ = 1);
-#endif
-
-   void Mult();
-
-   /// These are used to update spaces and functions that are not owned by the
-   /// TMOPIntegrator or DiscreteAdaptTC. The owned ones are updated in the
-   /// functions UpdateAfterMeshTopologyChange() of both classes.
-   void AddGridFunctionForUpdate(GridFunction *gf) { gridfuncarr.Append(gf); }
-   void AddFESpaceForUpdate(FiniteElementSpace *fes) { fespacearr.Append(fes); }
-
-#ifdef MFEM_USE_MPI
-   void AddGridFunctionForUpdate(ParGridFunction *pgf_)
-   {
-      pgridfuncarr.Append(pgf_);
-   }
-   void AddFESpaceForUpdate(ParFiniteElementSpace *pfes_)
-   {
-      pfespacearr.Append(pfes_);
-   }
-#endif
-
-   ~TMOPHRSolver()
-   {
-      if (!hradaptivity) { return; }
-      delete tmop_dr;
-      delete tmop_dr_est;
-      delete tmop_r;
-      delete tmop_r_est;
-   }
-
-   /// Total number of hr-adaptivity iterations. At each iteration, we do an
-   /// r-adaptivity iteration followed by a number of h-adaptivity iterations.
-   void SetHRAdaptivityIterations(int iter) { hr_iter = iter; }
-
-   /// Total number of h-adaptivity iterations per r-adaptivity iteration.
-   void SetHAdaptivityIterations(int iter) { h_per_r_iter = iter; }
-};
-
-}
-#endif

fem/tmop_tools.cpp

@@ -407,8 +407,6 @@ double TMOPNewtonSolver::ComputeScalingFactor(const Vector &x,
    {
       // Needed for the line search below. The untangling metrics see this
       // reference to detect deteriorations.
-      MFEM_VERIFY(min_det_ptr != NULL, " Initial mesh was valid, but"
-                  " intermediate mesh is invalid. Contact TMOP Developers.");
       *min_det_ptr = untangle_factor * min_detT_in;
    }
 
@@ -578,7 +576,7 @@ void TMOPNewtonSolver::ProcessNewState(const Vector &x) const
          ti = dynamic_cast<TMOP_Integrator *>(integs[i]);
          if (ti)
          {
-            ti->UpdateAfterMeshPositionChange(x_loc);
+            ti->UpdateAfterMeshChange(x_loc);
             ti->ComputeFDh(x_loc, *pfesc);
             UpdateDiscreteTC(*ti, x_loc);
          }
@@ -588,7 +586,7 @@ void TMOPNewtonSolver::ProcessNewState(const Vector &x) const
             Array<TMOP_Integrator *> ati = co->GetTMOPIntegrators();
             for (int j = 0; j < ati.Size(); j++)
             {
-               ati[j]->UpdateAfterMeshPositionChange(x_loc);
+               ati[j]->UpdateAfterMeshChange(x_loc);
                ati[j]->ComputeFDh(x_loc, *pfesc);
                UpdateDiscreteTC(*ati[j], x_loc);
             }
@@ -615,7 +613,7 @@ void TMOPNewtonSolver::ProcessNewState(const Vector &x) const
          ti = dynamic_cast<TMOP_Integrator *>(integs[i]);
          if (ti)
          {
-            ti->UpdateAfterMeshPositionChange(x_loc);
+            ti->UpdateAfterMeshChange(x_loc);
             ti->ComputeFDh(x_loc, *fesc);
             UpdateDiscreteTC(*ti, x_loc);
          }
@@ -625,7 +623,7 @@ void TMOPNewtonSolver::ProcessNewState(const Vector &x) const
             Array<TMOP_Integrator *> ati = co->GetTMOPIntegrators();
             for (int j = 0; j < ati.Size(); j++)
             {
-               ati[j]->UpdateAfterMeshPositionChange(x_loc);
+               ati[j]->UpdateAfterMeshChange(x_loc);
                ati[j]->ComputeFDh(x_loc, *fesc);
                UpdateDiscreteTC(*ati[j], x_loc);
             }

fem/transfer.cpp

@@ -175,8 +175,7 @@ const Operator &InterpolationGridTransfer::ForwardOperator()
                                             localP[elem_geoms[i]]);
       }
       F.Reset(ran_fes.RefinementMatrix_main(
-                 dom_fes.GetNDofs(), dom_fes.GetElementToDofTable(),
-                 dom_fes.GetElementToFaceOrientationTable(), localP));
+                 dom_fes.GetNDofs(), dom_fes.GetElementToDofTable(), localP));
    }
    else
    {

general/annotation.hpp

@@ -21,16 +21,12 @@
 #define MFEM_PERF_FUNCTION CALI_CXX_MARK_FUNCTION
 #define MFEM_PERF_BEGIN(s) CALI_MARK_BEGIN(s)
 #define MFEM_PERF_END(s) CALI_MARK_END(s)
-#define MFEM_PERF_SCOPE(name) \
-  cali::Annotation::Guard cali_autogenerated_guard_name(cali::Annotation("function").begin(std::string(name).c_str()))
-
 
 #else
 
 #define MFEM_PERF_FUNCTION
 #define MFEM_PERF_BEGIN(s)
 #define MFEM_PERF_END(s)
-#define MFEM_PERF_SCOPE(name)
 
 #endif
 

general/forall.hpp

@@ -13,7 +13,6 @@
 #define MFEM_FORALL_HPP
 
 #include "../config/config.hpp"
-#include "annotation.hpp"
 #include "error.hpp"
 #include "backends.hpp"
 #include "device.hpp"

general/mem_manager.hpp

@@ -494,7 +494,8 @@ public:
    /// Copy @a size entries from @a *this to @a dest.
    /** The given @a size should not exceed the Capacity() of @a *this and the
        destination, @a dest. */
-   inline void CopyTo(Memory &dest, int size) const;
+   inline void CopyTo(Memory &dest, int size) const
+   { dest.CopyFrom(*this, size); }
 
    /// Copy @a size entries from @a *this to the host pointer @a dest.
    /** The given @a size should not exceed the Capacity() of @a *this. */
@@ -922,11 +923,6 @@ inline void Memory<T>::Wrap(T *ptr, T *d_ptr, int size, MemoryType mt, bool own)
 template <typename T>
 inline void Memory<T>::MakeAlias(const Memory &base, int offset, int size)
 {
-   MFEM_ASSERT(0 <= offset, "invalid offset = " << offset);
-   MFEM_ASSERT(0 <= size, "invalid size = " << size);
-   MFEM_ASSERT(offset + size <= base.capacity,
-               "invalid offset + size = " << offset + size
-               << " > base capacity = " << base.capacity);
    capacity = size;
    h_mt = base.h_mt;
    h_ptr = base.h_ptr + offset;
@@ -1140,7 +1136,6 @@ inline bool Memory<T>::DeviceIsValid() const
 template <typename T>
 inline void Memory<T>::CopyFrom(const Memory &src, int size)
 {
-   MFEM_VERIFY(src.capacity>=size && capacity>=size, "Incorrect size");
    if (!(flags & REGISTERED) && !(src.flags & REGISTERED))
    {
       if (h_ptr != src.h_ptr && size != 0)
@@ -1160,7 +1155,6 @@ inline void Memory<T>::CopyFrom(const Memory &src, int size)
 template <typename T>
 inline void Memory<T>::CopyFromHost(const T *src, int size)
 {
-   MFEM_VERIFY(capacity>=size, "Incorrect size");
    if (!(flags & REGISTERED))
    {
       if (h_ptr != src && size != 0)
@@ -1177,17 +1171,9 @@ inline void Memory<T>::CopyFromHost(const T *src, int size)
    }
 }
 
-template <typename T>
-inline void Memory<T>::CopyTo(Memory &dest, int size) const
-{
-   MFEM_VERIFY(capacity>=size, "Incorrect size");
-   dest.CopyFrom(*this, size);
-}
-
 template <typename T>
 inline void Memory<T>::CopyToHost(T *dest, int size) const
 {
-   MFEM_VERIFY(capacity>=size, "Incorrect size");
    if (!(flags & REGISTERED))
    {
       if (h_ptr != dest && size != 0)

general/stable3d.cpp

@@ -118,11 +118,6 @@ int STable3D::Index (int r, int c, int f) const
 {
    STable3DNode *node;
 
-   if (r >= Size)
-   {
-      return -1;
-   }
-
    Sort3 (r, c, f);
 
    for (node = Rows[r]; node != NULL; node = node->Prev)

general/version.cpp

@@ -82,6 +82,9 @@ const char *GetConfigStr()
 #ifdef MFEM_USE_CUDA
       "MFEM_USE_CUDA\n"
 #endif
+#ifdef MFEM_USE_EPIC
+      "MFEM_USE_EPIC\n"
+#endif
 #ifdef MFEM_USE_EXCEPTIONS
       "MFEM_USE_EXCEPTIONS\n"
 #endif

linalg/CMakeLists.txt

@@ -78,21 +78,16 @@ if (MFEM_USE_MPI)
   endif()
 endif()
 
-if (MFEM_USE_ARPACK)
-  list(APPEND SRCS eigensolvers.cpp arpack.cpp)
-  list(APPEND HDRS eigensolvers.hpp arpack.hpp)
-endif()
-
-if (MFEM_USE_SPECTRA)
-  list(APPEND SRCS spectra.cpp)
-  list(APPEND HDRS eigen.hpp spectra.hpp)
-endif()
-
 if (MFEM_USE_SUNDIALS)
   list(APPEND SRCS sundials.cpp)
   list(APPEND HDRS sundials.hpp)
 endif()
 
+if (MFEM_USE_EPIC)
+  list(APPEND SRCS epic.cpp)
+  list(APPEND HDRS epic.hpp)
+endif()
+
 if (MFEM_USE_SUPERLU)
   list(APPEND SRCS superlu.cpp)
   # If this list (HDRS -> HEADERS) is used for install, we probably want the

linalg/arpack.hpp

@@ -1,240 +0,0 @@
-// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
-// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-// LICENSE and NOTICE for details. LLNL-CODE-806117.
-//
-// This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
-//
-// MFEM is free software; you can redistribute it and/or modify it under the
-// terms of the BSD-3 license. We welcome feedback and contributions, see file
-// CONTRIBUTING.md for details.
-
-#ifndef MFEM_ARPACK
-#define MFEM_ARPACK
-
-#include "../config/config.hpp"
-
-#ifdef MFEM_USE_ARPACK
-
-#include <string>
-
-using namespace std;
-
-#ifdef MFEM_USE_MPI
-#include <mpi.h>
-#include "hypre.hpp"
-#endif
-
-#include "operator.hpp"
-
-#define DSAUPD  dsaupd_
-#define DSEUPD  dseupd_
-
-#ifdef MFEM_USE_MPI
-#define PDSAUPD pdsaupd_
-#define PDSEUPD pdseupd_
-#endif
-
-extern "C" void DSAUPD(int *ido,char *bmat, int *n,
-                       char *which, int *nev,double *tol,double *resid,
-                       int *ncv,double *v, int *ldv,
-                       int *iparam, int *ipntr,
-                       double *workd, double *workl, int *lworkl, int *info);
-
-extern "C" void DSEUPD(int *, char *,int *, double *,
-                       double *,int *, double *,char *, int *, char *,
-                       int *,double *,double *,int *, double *,
-                       int *, int  *,int *, double *,
-                       double *,int *, int *);
-
-#ifdef MFEM_USE_MPI
-
-extern "C" void PDSAUPD(int *comm, int *ido,char *bmat, int *n,
-                        char *which, int *nev,double *tol,double *resid,
-                        int *ncv,double *v, int *ldv,
-                        int *iparam, int *ipntr,
-                        double *workd, double *workl, int *lworkl, int *info);
-
-extern "C" void PDSEUPD(int *comm, int *, char *,int *, double *,
-                        double *,int *, double *,char *, int *, char *,
-                        int *,double *,double *,int *, double *,
-                        int *, int  *,int *, double *,
-                        double *,int *, int *);
-
-#endif
-
-extern "C" {
-   void arpackgetcommdbg_(int *,int *,int *);
-   void arpacksetcommdbg_(int *,int *,int *);
-   void arpacksymdbg_(int *,int *,int *,int *,int *,int *,int *);
-   void arpacknonsymdbg_(int *,int *,int *,int *,int *,int *,int *);
-   void arpackcmplxdbg_(int *,int *,int *,int *,int *,int *,int *);
-}
-
-namespace mfem
-{
-
-class ArPackSym : public Eigensolver
-{
-public:
-
-   ArPackSym();
-   virtual ~ArPackSym();
-
-   /** ARPACK modes are described in section 3.5 of the ARPACK manual.
-       Mode 1: regular mode to solve A x = lambda x
-               No solver and no mass matrix are needed.
-       Mode 2: regular inverse mode to solve A x = lambda M x
-               Both A and M are needed and the solver should compute M^{-1}.
-       Mode 3: shift-invert mode to solve either A x = lambda x
-               or A x = lambda M x
-               Mass matrix is optional.  The solver should compute
-               (A-sigma I)^{-1} or (A-sigma M)^{-1}.  The shift parameter,
-               sigma, also needs to be set with SetShift().
-       Mode 4: Buckling mode to solve K x = lambda K_G x
-               K is set using SetMassMatrix(), K_G is set using SetOperator(),
-          and the solver should compute (K-sigma K_G)^{-1}.  The shift
-               parameter, sigma, also needs to be set with SetShift().
-       Mode 5: Cayley mode to solve A x = lambda M x
-               Both A and M are needed and the solver should compute
-               (A - sigma M)^{-1}.  The shift parameter, sigma, also needs
-               to be set with SetShift().
-    */
-   void SetMode(int mode);
-
-   inline void SetTol(double tol)         {      tol_ = tol;      }
-   inline void SetMaxIter(int max_iter)   { max_iter_ = max_iter; }
-   inline void SetPrintLevel(int logging) {  logging_ = logging;  }
-   inline void SetShift(double sigma)     {    sigma_ = sigma;    }
-   inline void SetNumModes(int num_eigs)  {      nev_ = num_eigs; }
-
-   virtual void SetSolver(Solver & solver);
-   virtual void SetOperator(Operator & A);
-   virtual void SetMassMatrix(Operator & M);
-
-   void Solve();
-
-   /// Collect the converged eigenvalues
-   virtual void GetEigenvalues(Array<double> & eigenvalues);
-
-   /// Extract a single eigenvector
-   virtual Vector & GetEigenvector(unsigned int i);
-
-   /// Transfer ownership of the converged eigenvectors
-   Vector ** StealEigenvectors();
-
-protected:
-
-   int myid_;       // Index of this processor
-   int max_iter_;
-   int logging_;
-
-   // The following variables are for ARPACK
-   int nloc_;       // number of items stored locally
-   int nev_;        // number of requested eigenvalues
-   int ncv_;        // number of ritz vectors
-   int rvec_;       // boolean to return eigenvectors as well
-   int mode_;       // 1 = standard, 2 = generalized, 3 = shift invert,
-   // 4 = buckling, 5 = Cayley
-   int lworkl_;     // length of lworkl_ work array
-   int iparam_[12]; // arpack parameters
-   int ipntr_[12];  // arpack pointers
-
-   char bmat_;      // I for standard problem, G for generalized
-   char which_[3];  // spectrum portion: LA, SA, LM, SM, BE
-   char hwmny_;     // DSEUPD: A for all eigenvalues, S for some
-
-   double tol_;     // relative accuracy bound for Ritz values
-   double sigma_;   // eigenvalue shift parameter
-
-   int    * select_;// workspace used during eigenvalue computation
-   double * dv_;    // Ritz values
-   double * v_;     // ncv Lanczos basis vectors
-   double * resid_; // residual vector
-   double * workd_; // work array for 3 vectors used in Arnoldi iteration
-   double * workl_; // work array
-
-   // Operators and Vectors needed outside of ARPACK
-   Solver   * solver_;
-   Operator * A_;
-   Operator * B_;
-
-   Vector * w_;
-   Vector * x_;
-   Vector * y_;
-   Vector * z_;
-
-   Vector ** eigenvectors_;
-
-   string solverName_;
-
-   void reverseComm();
-
-   int reverseCommMode1();
-   int reverseCommMode2();
-   int reverseCommMode3();
-   int reverseCommMode4();
-   int reverseCommMode5();
-
-   virtual void prepareEigenvectors();
-
-   void printErrors(const int & info, const int iparam[],
-                    const char & bmat, const int & n,
-                    const char which[],
-                    const int & nev, const int & ncv,
-                    const int & lworkl );
-
-private:
-
-   virtual int computeNlocf() { return nloc_; }
-   virtual int computeIter(int & ido);
-   virtual int computeEigs();
-
-};
-
-#ifdef MFEM_USE_MPI
-
-class ParArPackSym : public ArPackSym
-{
-public:
-   ParArPackSym(MPI_Comm comm);
-   virtual ~ParArPackSym() {}
-
-   void SetOperator(Operator & A);
-   void SetMassMatrix(Operator & M);
-
-   /// Collect the converged eigenvalues
-   void GetEigenvalues(Array<double> & eigenvalues);
-
-   /// Extract a single eigenvector
-   Vector & GetEigenvector(unsigned int i);
-
-   /// Transfer ownership of the converged eigenvectors
-   // HypreParVector ** StealEigenvectors();
-   Vector ** StealEigenvectors();
-
-protected:
-
-   void prepareEigenvectors();
-
-private:
-
-   MPI_Comm comm_;
-   MPI_Fint commf_; // Fortran style MPI communicator
-   int numProcs_;   // Number of processors
-
-   HYPRE_Int * part_; // parallel partitioning for eigenvectors
-
-   int computeNlocf();
-   int computeIter(int & ido);
-   int computeEigs();
-
-};
-
-#endif // MFEM_USE_MPI
-
-};
-
-#endif // MFEM_USE_ARPACK
-
-#endif // MFEM_ARPACK

linalg/complex_operator.cpp

@@ -787,16 +787,10 @@ HypreParMatrix * ComplexHypreParMatrix::GetSystemMatrix() const
                                            2 * num_cols_offd, cmap,
                                            true);
 
-#if MFEM_HYPRE_VERSION <= 22200
    // Give the new matrix ownership of row_starts and col_starts
    hypre_ParCSRMatrix *hA = (hypre_ParCSRMatrix*)(*A);
-
    hypre_ParCSRMatrixSetRowStartsOwner(hA,1);
    hypre_ParCSRMatrixSetColStartsOwner(hA,1);
-#else
-   mfem_hypre_TFree_host(row_starts);
-   mfem_hypre_TFree_host(col_starts);
-#endif
 
    return A;
 }

linalg/densemat.hpp

@@ -763,13 +763,6 @@ public:
       tdata.New(i*j*k);
    }
 
-   DenseTensor(double *d, int i, int j, int k)
-      : Mk(NULL, i, j)
-   {
-      nk = k;
-      tdata.Wrap(d, i*j*k, false);
-   }
-
    DenseTensor(int i, int j, int k, MemoryType mt)
       : Mk(NULL, i, j)
    {

linalg/eigen.hpp

@@ -1,94 +0,0 @@
-#ifndef MFEM_EIGEN_HPP
-#define MFEM_EIGEN_HPP
-
-#include <vector>
-#include <Eigen/Sparse>
-
-#include "vector.hpp"
-#include "sparsemat.hpp"
-#include "densemat.hpp"
-
-namespace mfem{
-    /** @brief Eigen template specialization for vector conversion */
-    template <typename T>
-    struct VectorConverter {
-        static Vector from(const Eigen::Matrix<T, Eigen::Dynamic, 1>& other)
-        {
-            Vector v(other.rows());
-
-            for (size_t i = 0; i < v.Size(); i++)
-                v(i) = other(i);
-
-            return std::move(v);
-        }
-
-        static Eigen::Matrix<T, Eigen::Dynamic, 1> to(const Vector& other)
-        {
-            Eigen::Matrix<T, Eigen::Dynamic, 1> v(other.Size());
-
-            for (size_t i = 0; i < v.Size(); i++)
-                v(i) = other(i);
-
-            return std::move(v);
-        }
-    };
-
-    /** @brief Eigen template specialization for dense matrix conversion */
-    template <typename T>
-    struct DenseMatrixConverter {
-        static DenseMatrix from(const Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic>& other)
-        {
-            DenseMatrix mat(other.rows(), other.cols());
-
-            for (size_t j = 0; j < mat.Width(); j++)
-                for (size_t i = 0; i < mat.Height(); i++)
-                    mat(i, j) = other(i, j);
-
-            return mat;
-        }
-
-        static Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic> to(const DenseMatrix& other)
-        {
-            Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic> mat(other.Height(), other.Width());
-
-            for (size_t j = 0; j < mat.cols(); j++)
-                for (size_t i = 0; i < mat.rows(); i++)
-                    mat(i, j) = other(i, j);
-
-            return mat;
-        }
-    };
-
-    /** @brief Eigen template specialization for sparse matrix conversion */
-    template <class T>
-    struct SparseMatrixConverter {
-        static SparseMatrix from(const Eigen::SparseMatrix<T, Eigen::RowMajor>& other)
-        {
-            return SparseMatrix(other.outerIndexPtr(), other.innerIndexPtr(), other.valuePtr(), other.rows(), other.cols());
-        }
-
-        static Eigen::SparseMatrix<T, Eigen::RowMajor> to(const SparseMatrix& other)
-        {
-            // MFEM memory info
-            const int *I = other.GetI(), *J = other.GetJ();
-            const T* Data = other.GetData();
-
-            // Eigen triplet
-            std::vector<Eigen::Triplet<double>> tripletList;
-            tripletList.reserve(other.GetMemoryData().Capacity());
-
-            for (size_t i = 0; i < other.Size(); i++) {
-                for (size_t k = I[i], end = I[i + 1]; k < end; k++)
-                    tripletList.push_back(Eigen::Triplet<double>(i, J[k], Data[k]));
-            }
-
-            // Create Eigen sparse matrix
-            Eigen::SparseMatrix<T, Eigen::RowMajor> mat(other.Height(), other.Width());
-            mat.setFromTriplets(tripletList.begin(), tripletList.end());
-
-            return mat;
-        }
-    };   
-}
-
-#endif // MFEM_EIGEN_HPP

linalg/eigensolver.cpp

@@ -1,23 +0,0 @@
-// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
-// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-// LICENSE and NOTICE for details. LLNL-CODE-806117.
-//
-// This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
-//
-// MFEM is free software; you can redistribute it and/or modify it under the
-// terms of the BSD-3 license. We welcome feedback and contributions, see file
-// CONTRIBUTING.md for details.
-
-#include "linalg.hpp"
-#include "eigensolver.hpp"
-
-using namespace std;
-
-namespace mfem
-{
-
-Eigensolver::Eigensolver()
-{}
-
-};

linalg/eigensolver.hpp

@@ -1,53 +0,0 @@
-// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
-// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-// LICENSE and NOTICE for details. LLNL-CODE-806117.
-//
-// This file is part of the MFEM library. For more information and source code
-// availability visit https://mfem.org.
-//
-// MFEM is free software; you can redistribute it and/or modify it under the
-// terms of the BSD-3 license. We welcome feedback and contributions, see file
-// CONTRIBUTING.md for details.
-
-#ifndef MFEM_EIGENSOLVERS
-#define MFEM_EIGENSOLVERS
-
-#include "vector.hpp"
-#include "operator.hpp"
-
-namespace mfem
-{
-
-/// Abstract Eigensolver
-class Eigensolver
-{
-public:
-
-   Eigensolver();
-   virtual ~Eigensolver() {}
-
-   virtual void SetTol(double tol) = 0;
-   virtual void SetMaxIter(int max_iter) = 0;
-   virtual void SetPrintLevel(int logging) = 0;
-   virtual void SetNumModes(int num_eigs) = 0;
-
-   virtual void SetOperator(Operator & A) = 0;
-   virtual void SetMassMatrix(Operator & M) = 0;
-
-   /// Perform the eigenvalue solve
-   virtual void Solve() = 0;
-
-   /// Collect the converged eigenvalues
-   virtual void GetEigenvalues(Array<double> & eigenvalues) = 0;
-
-   /// Extract a single eigenvector
-   virtual Vector & GetEigenvector(unsigned int i) = 0;
-
-   /// Transfer ownership of the converged eigenvectors
-   virtual Vector ** StealEigenvectors() = 0;
-
-};
-
-}
-
-#endif

linalg/epic.cpp

@@ -0,0 +1,171 @@
+// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
+// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+// LICENSE and NOTICE for details. LLNL-CODE-806117.
+//
+// This file is part of the MFEM library. For more information and source code
+// availability visit https://mfem.org.
+//
+// MFEM is free software; you can redistribute it and/or modify it under the
+// terms of the BSD-3 license. We welcome feedback and contributions, see file
+// CONTRIBUTING.md for details.
+
+#include "epic.hpp"
+
+#ifdef MFEM_USE_EPIC
+
+namespace mfem
+{
+
+EPICSolver::EPICSolver(bool exactJacobian_, EPICNumJacDelta delta)
+{
+   // Allocate an empty serial N_Vector
+   temp = N_VNewEmpty_Serial(0);
+   m[0] = 10;
+   m[1] = 10;
+   MFEM_VERIFY(temp, "error in N_VNewEmpty_Serial()");
+   exactJacobian = exactJacobian_;
+   Jtv = NULL;
+   Delta = delta;
+}
+
+#ifdef MFEM_USE_MPI
+EPICSolver::EPICSolver(MPI_Comm comm)
+{
+   m[0] = 10;
+   m[1] = 10;
+
+   // Allocate an empty vector
+   if (comm == MPI_COMM_NULL)
+   {
+      // Allocate an empty serial N_Vector
+      temp = N_VNewEmpty_Serial(0);
+      MFEM_VERIFY(temp, "error in N_VNewEmpty_Serial()");
+   }
+   else
+   {
+      // Allocate an empty parallel N_Vector
+      temp = N_VNewEmpty_Parallel(comm, 0, 0);  // calls MPI_Allreduce()
+      MFEM_VERIFY(temp, "error in N_VNewEmpty_Parallel()");
+   }
+}
+#endif
+
+int EPICSolver::RHS(realtype t, const N_Vector y, N_Vector ydot, void *user_data)
+{
+   // Get data from N_Vectors
+   const Vector mfem_y(y);
+   Vector mfem_ydot(ydot);
+   EPICSolver *self = static_cast<EPICSolver*>(user_data);
+
+   // Compute y' = f(t, y)
+   self->f->SetTime(t);
+   self->f->Mult(mfem_y, mfem_ydot);
+
+   // Return success
+   return 0;
+}
+
+
+int EPICSolver::Jacobian(N_Vector v, N_Vector Jv, realtype t, N_Vector y, N_Vector fy, void *user_data, N_Vector tmp)
+{
+    // Get data from N_Vectors
+   const Vector mfem_v(v);
+   Vector mfem_Jv(Jv);
+   EPICSolver *self = static_cast<EPICSolver*>(user_data);
+
+   // Compute J(t, y) v
+   self->Jtv->Mult(mfem_v, mfem_Jv);
+
+   return 0;
+}
+
+void EPICSolver::Init(TimeDependentOperator &f)
+{
+    ODESolver::Init(f);
+	    
+    long local_size = f.Height();
+    long global_size = 0;
+#ifdef MFEM_USE_MPI
+    if (Parallel())
+    {
+        MPI_Allreduce(&local_size, &global_size, 1, MPI_LONG, MPI_SUM,
+                      NV_COMM_P(temp));
+    }
+#endif
+
+    Vector mfem_temp(local_size);
+    mfem_temp.ToNVector(temp, global_size);
+}
+
+EPI2::EPI2(bool exactJacobian, EPICNumJacDelta delta) : EPICSolver(exactJacobian, delta) {}
+
+void EPI2::Init(TimeDependentOperator &f)
+{
+    EPICSolver::Init(f);
+    long local_size = f.Height();
+    if (exactJacobian) {
+       integrator = new Epi2_KIOPS(EPICSolver::RHS, EPICSolver::Jacobian, this, 100, temp ,local_size);
+    } else {
+       integrator = new Epi2_KIOPS(EPICSolver::RHS, Delta, this, 100, temp ,local_size);
+    }
+
+}
+
+EPIRK4::EPIRK4(bool exactJacobian, EPICNumJacDelta delta) : EPICSolver(exactJacobian, delta) {}
+
+void EPIRK4::Init(TimeDependentOperator &f)
+{
+    EPICSolver::Init(f);
+    long local_size = f.Height();
+    if (exactJacobian) {
+       integrator = new EpiRK4SC_KIOPS(EPICSolver::RHS, EPICSolver::Jacobian, this, 100, temp ,local_size);
+    } else {
+       integrator = new EpiRK4SC_KIOPS(EPICSolver::RHS, Delta, this, 100, temp ,local_size);
+    }
+}
+
+void EPICSolver::Step(Vector &x, double &t, double &dt)
+{
+   if (!Parallel())
+   {
+      NV_DATA_S(temp) = x.GetData();
+      MFEM_VERIFY(NV_LENGTH_S(temp) == x.Size(), "");
+   }
+   else
+   {
+#ifdef MFEM_USE_MPI
+      NV_DATA_P(temp) = x.GetData();
+      MFEM_VERIFY(NV_LOCLENGTH_P(temp) == x.Size(), "");
+#endif
+   }
+
+   Jtv = &(this->f->GetGradient(x));
+}
+
+void EPI2::Step(Vector &x, double &t, double &dt)
+{
+    EPICSolver::Step(x, t, dt);
+    integrator->Integrate(dt, t, t+dt, 0, temp, 1e-10, m);
+    t += dt;
+}
+
+void EPIRK4::Step(Vector &x, double &t, double &dt)
+{
+    EPICSolver::Step(x, t, dt);
+    integrator->Integrate(dt, t, t+dt, 0, temp, 1e-10, m);
+    t += dt;
+}
+
+EPI2::~EPI2()
+{
+    delete integrator;
+}
+
+EPIRK4::~EPIRK4()
+{
+    delete integrator;
+}
+
+}
+
+#endif

linalg/epic.hpp

@@ -0,0 +1,98 @@
+// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
+// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+// LICENSE and NOTICE for details. LLNL-CODE-806117.
+//
+// This file is part of the MFEM library. For more information and source code
+// availability visit https://mfem.org.
+//
+// MFEM is free software; you can redistribute it and/or modify it under the
+// terms of the BSD-3 license. We welcome feedback and contributions, see file
+// CONTRIBUTING.md for details.
+
+#ifndef MFEM_EPIC
+#define MFEM_EPIC
+
+#include "../config/config.hpp"
+
+#ifdef MFEM_USE_EPIC
+
+// SUNDIALS vectors
+#include <nvector/nvector_serial.h>
+#ifdef MFEM_USE_MPI
+#include <mpi.h>
+#include <nvector/nvector_parallel.h>
+#endif
+
+#include "ode.hpp"
+#include "solvers.hpp"
+#include <Epic.h>
+
+namespace mfem
+{
+
+typedef void (*JacobianFun)(const realtype t, const Vector &y, const Vector& v, Vector& Jv, void* user_data);
+// ---------------------------------------------------------------------------
+// Interface to the EPIC library -- exponential methods
+// ---------------------------------------------------------------------------
+
+class EPICSolver : public ODESolver
+{
+protected:
+    EPICNumJacDelta Delta;
+    Operator* Jtv;
+    N_Vector temp;
+    int m[2];
+
+    bool exactJacobian;
+
+    #ifdef MFEM_USE_MPI
+    bool Parallel() const
+    {
+        return (N_VGetVectorID(temp) != SUNDIALS_NVEC_SERIAL);
+    }
+    #else
+    bool Parallel() const { return false; }
+    #endif
+
+public:
+    EPICSolver(bool exactJacobian, EPICNumJacDelta delta=&DefaultDelta);
+    EPICSolver(MPI_Comm comm);
+
+    static int RHS(realtype t, const N_Vector y, N_Vector ydot, void *user_data);
+    static int Jacobian(N_Vector v, N_Vector Jv, realtype t,
+                         N_Vector y, N_Vector fy, void *user_data, N_Vector tmp);
+    virtual void Init(TimeDependentOperator &f);
+    virtual void Step(Vector &x, double &t, double &dt);
+
+    virtual ~EPICSolver() {}
+};
+
+class EPI2 : public EPICSolver
+{
+protected:
+    Epi2_KIOPS* integrator;
+public:
+    EPI2(bool exactJacobian=true, EPICNumJacDelta delta=&DefaultDelta);
+    virtual void Init(TimeDependentOperator &f);
+    virtual void Step(Vector &x, double &t, double &dt);
+
+    virtual ~EPI2();
+};
+
+class EPIRK4 : public EPICSolver
+{
+protected:
+    EpiRK4SC_KIOPS* integrator;
+public:
+    EPIRK4(bool exactJacobian=true, EPICNumJacDelta delta=&DefaultDelta);
+    virtual void Init(TimeDependentOperator &f);
+    virtual void Step(Vector &x, double &t, double &dt);
+
+    virtual ~EPIRK4();
+};
+
+} // namespace mfem
+
+#endif // MFEM_USE_EPIC
+
+#endif // MFEM_EPIC