Merge pull request #4172 from mfem/mfem-4.7-dev

Final changes for mfem-4.7

.gitignore

@@ -369,7 +369,7 @@ miniapps/dpg/ParaView
 miniapps/spde/generate_random_field
 miniapps/spde/ParaView
 
-miniapps/tribol/ContactPatchTest
+miniapps/tribol/contact-patch-test
 
 # Unit test binary and outputs
 tests/unit/output_meshes

CHANGELOG

@@ -8,93 +8,100 @@
                                https://mfem.org
 
 
-Version 4.6.1 (development)
-===========================
+Version 4.7, released on May 7, 2024
+====================================
+
+- Added support for single precision (with corresponding hypre build). The MFEM
+  floating point type was generalized from `double` to `real_t`. For details see
+  https://github.com/orgs/mfem/discussions/4207.
 
 Meshing improvements
 --------------------
-- Introduced formulas for refinement of patches in NURBS meshes. Refinement by
-  arbitrary integer factors is also enabled, e.g. in the mesh-explorer miniapp.
-  NURBS coarsening and knot removal are also introduced.
-
 - Added the capability to partition (big) serial meshes in serial code, see the
   new classes MeshPartitioner and MeshPart. This capability is also exposed as a
   menu option in the mesh-explorer miniapp in miniapps/meshing.
 
-Discretization improvements
----------------------------
-- Introduced support for higher order non conformal Nedelec elements on
-  simplices in ParMesh.
+- Added named attribute sets and basic supporting methods to the Mesh class as a
+  convenient means of referring to sets of domain or boundary attribute numbers.
+  See the new Example 39/39p and data/compass.mesh.
+
+- Introduced formulas for refinement of patches in NURBS meshes. Refinement by
+  arbitrary integer factors is also enabled, e.g. in the mesh-explorer miniapp.
+  NURBS coarsening and knot removal are also introduced.
 
-- Introduced support for internal boundary elements in nonconformal adapted
-  meshes.
+- Added support for internal boundary elements in nonconforming meshes.
 
-- Added functionality for construction of cut-surface and cut-volume
-  IntegrationRules through a moment-fitting approach. The cut is specified by
-  the zero level set of a Coefficient. See fem/intrules_cut.hpp and Example 38.
+- The ReadCubit Genesis mesh importer has been rewritten to improve readability.
 
-- Added a new nonlinear integrator, `HyperbolicFormIntegrator`. This implements
+Discretization improvements
+---------------------------
+- Added a new nonlinear integrator, `HyperbolicFormIntegrator` that implements
   both element-wise weak divergence and face-wise numerical flux for a general
-  system of hyperbolic conservation laws. To use this integrator for a specific
+  system of hyperbolic conservation laws. To use the integrator for a specific
   flux function, users can define a derived class of `FluxFunction`. Currently,
-  advection, Burgers', shallow-water, Euler equations (see, Example 18) are
+  advection, Burgers, shallow-water and Euler equations (see Example 18/18p) are
   available.
 
-GPU support
-----------------------------
+- Added a capability to construct cut-surface and cut-volume IntegrationRules
+  through a moment-fitting approach. The cut is specified by the zero level set
+  of a Coefficient. See fem/intrules_cut.hpp and the new Example 38.
+
+- Introduced support for high-order nonconforming Nedelec elements on simplices.
+
+GPU computing
+-------------
+- Added partial assembly and GPU support for the DG diffusion integrator.
+
+- Efficient GPU-accelerated LOR assembly is now supported on surface meshes.
+
+- Added functionality to automatically configure hypre's compute policy to match
+  MFEM's compute policy when hypre is built with GPU support. Requires version
+  hypre-2.31.0 or later.
+
 - Added support for full assembly on simplices.
 
-- Added functionality for BilinearFormIntegrators to use kernels that work for both
-  tensor and unstructured elements.
+- Added partial assembly for linear elasticity (no sum factorization for now).
 
-- Added partial assembly for linear elasticity. Does not use sum factorization for now.
-- Added functionality to automatically configure HYPRE's compute policy to match
-  MFEM's compute policy when HYPRE is built with GPU support and HYPRE's version
-  is >= 2.31.0.
+- Added functionality for BilinearFormIntegrators to use kernels that work for
+  both tensor and unstructured elements.
 
-- Added partial assembly and GPU support for the DG diffusion integrator.
+- The RAJA backend will use `seq_exec` for serial loop execution when RAJA
+  v2023.06.00 and beyond is detected as `loop_exec` is deprecated.
+
+- API change: The macro MFEM_HYPRE_FORALL (from hypre.hpp) which was intended
+  for internal use, has been removed and replaced by the function template
+  mfem::hypre_forall in general/forall.hpp.
 
 New and updated examples and miniapps
 -------------------------------------
-- Added a new block solver in miniapp/solvers for the Darcy problem.
-  The new solver is based on a Bramble-Pasciak preconditioning. User can
-  use and implement their own preconditioner for the mass matrix.
+- Added a new miniapp illustrating elastic contact based on the Tribol library,
+  (https://github.com/LLNL/Tribol). See miniapps/tribol.
 
-- Added miniapp to demonstrate new elasticity integrator and unstructured element GPU support,
-  and a block diagonal preconditioner using low order refinement. Allows comparison with
-  currently existing legacy mode integrator. See miniapps/solvers/lor_elast.
+- Added a miniapp to demonstrate low order refined (LOR) block preconditioning
+  for linear elasticity on GPUs. See miniapps/solvers/lor_elast.
 
-- Added a new mortar contact patch test miniapp using the Tribol interface
-  physics library (see https://github.com/LLNL/Tribol).  See miniapps/tribol.
+- Added a new block solver in miniapp/solvers for the Darcy problem. The new
+  solver is based on a Bramble-Pasciak preconditioning. User can use and
+  implement their own preconditioner for the mass matrix.
 
-Miscellaneous
--------------
-- Added support for single and double precision, with corresponding hypre build.
-  Generalized the floating point type from `double` to `real_t`. For more
-  details see https://github.com/orgs/mfem/discussions/4207.
+- Added a small miniapp for printing the shape functions of a KnotVector. See
+  miniapps/nurbs/nurbs_printfunc.cpp.
 
-- The ReadCubit Genesis mesh importer has been rewritten to improve readability.
+- Added two new example codes: 38 and 39/39p described above. Substantially
+  updated Example 18/18p.
 
+Miscellaneous
+-------------
 - Updated the Doxygen documentation style, which now requires Doxygen version
   1.9.8 or later. See the doc/ directory.
 
-- Improved thread safety for global variables in the library, for example
-  IntegrationRules IntRules, RefinedIntRules, GeometryRefiner
-  GlobGeometryRefiner, and FiniteElement::dof2quad_array.
+- Improved thread safety for global variables in the library, e.g. for IntRules,
+  RefinedIntRules, GlobGeometryRefiner, and FiniteElement::dof2quad_array.
 
 - PETSc integration now generally requires PETSc version 3.21 or later, though
   depending on the functionality older versions may still work.
 
-- RAJA backend will use seq_exec for serial loop execution when RAJA
-  v2023.06.00 and beyond is detected as loop_exec is deprecated.
-
-- API change: The macro MFEM_HYPRE_FORALL (from hypre.hpp) which was intended
-  for internal use, has been removed and replaced by the function template
-  mfem::hypre_forall in general/forall.hpp.
-
-- Adding named attribute sets and basic supporting methods to the Mesh class as
-  a convenient means of referring to sets of domain or boundary attribute
-  numbers. Also adding related serial and parallel examples which illustrate.
+- Various other simplifications, extensions, and bugfixes in the code.
 
 
 Version 4.6, released on September 27, 2023
@@ -116,7 +123,6 @@ Meshing improvements
   * The edge to knot map for NURBS meshes can be determined automatically. It is
     no longer needed to specify this in the NURBS mesh.
   * Added curve interpolation method for NURBS.
-  * Added new small miniapp for printing of shape functions of a KnotVector
   * See miniapps/nurbs for example meshes and miniapps.
 
 Discretization improvements
@@ -163,8 +169,6 @@ Linear and nonlinear solvers
 
 - Added HIP support to the PETSc and SUNDIALS interfaces.
 
-- Efficient GPU-accelerated LOR assembly now supports surface meshes.
-
 New and updated examples and miniapps
 -------------------------------------
 - Added a new H(div) solver miniapp demonstrating the use of a matrix-free

CMakeLists.txt

@@ -58,7 +58,7 @@ project(mfem NONE)
 # Current version of MFEM, see also `makefile`.
 #   mfem_VERSION = (string)
 #   MFEM_VERSION = (int)   [automatically derived from mfem_VERSION]
-set(${PROJECT_NAME}_VERSION 4.6.1)
+set(${PROJECT_NAME}_VERSION 4.7.0)
 
 # Prohibit in-source build
 if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})

INSTALL

@@ -75,6 +75,8 @@ and miniapps. See https://glvis.org and https://mfem.org/building.
 
 Quick start with GNU make
 =========================
+See also: https://mfem.org/building
+
 Serial build:
    make serial -j 4
 
@@ -83,6 +85,7 @@ Parallel build:
    (build METIS 4 in ../metis-4.0 relative to mfem/)
    (build hypre in ../hypre relative to mfem/)
    make parallel -j 4
+(For METIS 5, see https://mfem.org/building/#parallel-build-using-metis-5)
 
 CUDA build:
    make cuda -j 4
@@ -116,6 +119,7 @@ Parallel build:
    mkdir <mfem-build-dir> ; cd <mfem-build-dir>
    cmake <mfem-source-dir> -DMFEM_USE_MPI=YES
    make -j 4
+(For METIS 5, see https://mfem.org/building/#parallel-build-using-metis-5)
 
 CUDA build:
    (this build requires CMake 3.8 or newer)
@@ -615,7 +619,10 @@ The specific libraries and their options are:
             HYPRE >= 2.31.0   (runtime selectable HYPRE execution on CPU/GPU)
 
 - METIS, used when MFEM_USE_METIS = YES. If using METIS 5, set
-  MFEM_USE_METIS_5 = YES (default is to use METIS 4).
+  MFEM_USE_METIS_5 = YES (default is to use METIS 4). For building instructions,
+  see the following:
+    - METIS 4.0.3: https://mfem.org/building/#parallel-mpi-version-of-mfem
+    - METIS 5.1.0: https://mfem.org/building/#parallel-build-using-metis-5
   URL: https://github.com/mfem/tpls (MFEM mirror, see above)
   Options: METIS_OPT, METIS_LIB.
   Versions: METIS 4.0.3 or 5.1.0.

config/config.hpp

@@ -120,6 +120,15 @@ constexpr real_t operator""_r(unsigned long long v)
 
 // Check dependencies:
 
+// Define MFEM_MPI_REAL_T to be the appropriate MPI real type
+#ifdef MFEM_USE_MPI
+#ifdef MFEM_USE_SINGLE
+#define MFEM_MPI_REAL_T MPI_FLOAT
+#elif defined MFEM_USE_DOUBLE
+#define MFEM_MPI_REAL_T MPI_DOUBLE
+#endif
+#endif
+
 // Options that require MPI
 #ifndef MFEM_USE_MPI
 #ifdef MFEM_USE_SUPERLU

config/makefile

@@ -110,4 +110,4 @@ config-mk:
 
 clean:
 	rm -f $(CONFIG_HPP) $(CONFIG_MK) sample-runs-build.log
-	rm -f $(GHV) $(GHV).out $(GMV) $(GMV).out
+	rm -f $(GHV) $(GHV).out $(GMV) $(GMV).out *.dSYM

doc/CodeDocumentation.conf.in

@@ -48,7 +48,7 @@ PROJECT_NAME           = MFEM
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v4.6.1
+PROJECT_NUMBER         = v4.7.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

doc/CodeDocumentation.dox

@@ -110,9 +110,11 @@ namespace mfem {
  * - <a class="el" href="ex35p_8cpp_source.html">Example 35p</a>: parallel multi-domain damped harmonic oscillators
  * - <a class="el" href="ex36_8cpp_source.html">Example 36</a>: Proximal Galerkin FEM for the obstacle problem
  * - <a class="el" href="ex36p_8cpp_source.html">Example 36p</a>: parallel Proximal Galerkin FEM for the obstacle problem
- * - <a class="el" href="ex37_8cpp_source.html">Example 37</a>: Topology optimization
+ * - <a class="el" href="ex37_8cpp_source.html">Example 37</a>: topology optimization
  * - <a class="el" href="ex37p_8cpp_source.html">Example 37p</a>: parallel topology optimization
  * - <a class="el" href="ex38_8cpp_source.html">Example 38</a>: cut-surface and cut-volume integration
+ * - <a class="el" href="ex39_8cpp_source.html">Example 39</a>: named mesh attributes
+ * - <a class="el" href="ex39p_8cpp_source.html">Example 39</a>: parallel named mesh attributes
  *
  * <H4>AmgX Examples</H4>
  * - Variants of Examples
@@ -214,6 +216,8 @@ namespace mfem {
  * - <a class="el" href="miniapps_2performance_2ex1_8cpp_source.html">HPC Example 1</a>: high-performance nodal H1 FEM for the Laplace problem
  * - <a class="el" href="miniapps_2performance_2ex1p_8cpp_source.html">HPC Example 1p</a>: high-performance parallel nodal H1 FEM for the Laplace problem
  * - <a class="el" href="generate__random__field_8cpp_source.html">SPDE Solvers</a>: SPDE solver random field generation
+ * - <a class="el" href="contact-patch-test_8cpp_source.html">Contact</a>: mortar contact patch test for elasticity
+ * - <a class="el" href="multidomain_8cpp_source.html">Multidomain miniapp</a>: Multidomain and Submesh demonstration miniapp
  * - <a class="el" href="pdiffusion_8cpp_source.html">DPG Diffusion example</a>: DPG formulation for the diffusion problem
  * - <a class="el" href="pmaxwell_8cpp_source.html">DPG Maxwell example</a>: DPG formulation for the indefinite Maxwell problem
  * - <a class="el" href="lor__elast_8cpp_source.html">LOR Elasticity</a>: solve linear elasticity with LOR preconditioning on GPUs

doc/js/doxygen-awesome-darkmode-toggle.js

@@ -46,7 +46,7 @@ class DoxygenAwesomeDarkModeToggle extends HTMLElement {
             DoxygenAwesomeDarkModeToggle.onSystemPreferenceChanged()
         })
         // Update the color scheme when the tab is made visible again.
-        // It is possible that the appearance was changed in another tab 
+        // It is possible that the appearance was changed in another tab
         // while this tab was in the background.
         document.addEventListener("visibilitychange", visibilityState => {
             if (document.visibilityState === 'visible') {
@@ -97,7 +97,7 @@ class DoxygenAwesomeDarkModeToggle extends HTMLElement {
      * @returns `true` for dark-mode, `false` for light-mode user preference
      */
     static get userPreference() {
-        return (!DoxygenAwesomeDarkModeToggle.systemPreference && localStorage.getItem(DoxygenAwesomeDarkModeToggle.prefersDarkModeInLightModeKey)) || 
+        return (!DoxygenAwesomeDarkModeToggle.systemPreference && localStorage.getItem(DoxygenAwesomeDarkModeToggle.prefersDarkModeInLightModeKey)) ||
         (DoxygenAwesomeDarkModeToggle.systemPreference && !localStorage.getItem(DoxygenAwesomeDarkModeToggle.prefersLightModeInDarkModeKey))
     }
 

examples/ex18.hpp

@@ -39,8 +39,8 @@ class DGHyperbolicConservationLaws : public TimeDependentOperator
    // Base Nonlinear Form
    std::unique_ptr<NonlinearForm> nonlinearForm;
    // element-wise inverse mass matrix
-   std::vector<DenseMatrix> invmass; // local scalar inverse mass.
-   std::vector<DenseMatrix> weakdiv; // local weakdivergence. Trial space is ByDim.
+   std::vector<DenseMatrix> invmass; // local scalar inverse mass
+   std::vector<DenseMatrix> weakdiv; // local weak divergence (trial space ByDim)
    // global maximum characteristic speed. Updated by form integrators
    mutable real_t max_char_speed;
    // auxiliary variable used in Mult
@@ -169,9 +169,9 @@ void DGHyperbolicConservationLaws::Mult(const Vector &x, Vector &y) const
 {
    // 0. Reset wavespeed computation before operator application.
    formIntegrator->ResetMaxCharSpeed();
-   // 1. Apply Nonlinear form to obtain an axiliary result
+   // 1. Apply Nonlinear form to obtain an auxiliary result
    //         z = - <F̂(u_h,n), [[v]]>_e
-   //    If weak-divergencee is not preassembled, we also have weak-divergence
+   //    If weak-divergence is not preassembled, we also have weak-divergence
    //         z = - <F̂(u_h,n), [[v]]>_e + (F(u_h), ∇v)
    nonlinearForm->Mult(x, z);
    if (!weakdiv.empty()) // if weak divergence is pre-assembled

examples/moonolith/example_utils.hpp

@@ -1,3 +1,14 @@
+// Copyright (c) 2010-2024, 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 <algorithm>
 #include <assert.h>
 #include <cstdlib>

fem/convergence.cpp

@@ -1,8 +1,18 @@
+// Copyright (c) 2010-2024, 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 "convergence.hpp"
 
 using namespace std;
 
-
 namespace mfem
 {
 

fem/fe/fe_base.hpp

@@ -316,7 +316,7 @@ class FiniteElement
    int GetDim() const { return dim; }
 
    /** @brief Returns the vector dimension for vector-valued finite elements,
-       which is also the dimension of the interpolation operatrion. */
+       which is also the dimension of the interpolation operation. */
    int GetRangeDim() const { return vdim; }
 
    /// Returns the dimension of the curl for vector-valued finite elements.