Finite Element Discretization Library __ _ __ ___ / _| ___ _ __ ___ | '_  _ \ | |_ / _ \| '_  _ \ | | | | | || _|| __/| | | | | | |_| |_| |_||_| \___||_| |_| |_| http://mfem.org Version 4.1, released on March 10, 2020 ======================================= Starting with this version, the MFEM open source license is changed to BSD-3. Improved GPU capabilities ------------------------- - Added initial support for AMD GPUs based on HIP: a C++ runtime API and kernel language that can run on both AMD and NVIDIA hardware. - Added support for Umpire, a resource management library that allows the discovery, provision, and management of memory on machines with multiple memory devices like NUMA and GPUs, see https://github.com/LLNL/Umpire. - GPU acceleration is now available in 3 additional examples: 3, 9 and 24. - Improved RAJA backend and multi-GPU MPI communications. - Added a "debug" device designed specifically to aid in debugging GPU code by following the "device" code path (using separate host/device memory spaces and host <-> device transfers) without any GPU hardware. - Added support for matrix-free diagonal smoothers on GPUs. - The current list of available device backends is: "ceed-cuda", "occa-cuda", "raja-cuda", "cuda", "hip", "debug", "occa-omp", "raja-omp", "omp", "ceed-cpu", "occa-cpu", "raja-cpu", and "cpu". - The MFEM memory manager now supports different memory types, associated with the following memory backends: * Default host memory, using standard C++ new and delete, * CUDA pointers, using cudaMalloc and HIP pointers, using hipMalloc, * Managed CUDA/HIP memory (UVM), using cudaMallocManaged/hipMallocManaged, * Umpire-managed memory, including memory pools, * 32- or 64-byte aligned memory, using posix_memalign (WIN32 also supported), * Debug memory with mmap/mprotect protection used by the new "debug" device. libCEED support --------------- - Added support for libCEED, the portable library for high-order operator evaluation developed by the Center for Efficient Exascale Discretizations in the Exascale Computing Project, https://github.com/CEED/libCEED. - This initial integration includes Mass and Diffusion integrators. libCEED GPU backends can be used without specific MFEM configuration, however it is highly recommended to use the "cuda" build option to minimize memory transfers. - Both CPU and GPU modes are available as MFEM device backends (ceed-cpu and ceed-cuda), using some of the best performing CPU and GPU backends from libCEED, see the sample runs in examples 1 and 6. - NOTE: The current default libCEED GPU backend (ceed-cuda) uses atomics and therefore is non-deterministic. Partial assembly and matrix-free discretizations ------------------------------------------------ - The support for matrix-free methods on both CPU and GPU devices based on a partially assembled operator decomposition was extended to include: * DG integrators, (for now only in the Gauss-Lobatto basis), see Example 9, * H(curl) bilinear forms, see Example 3, * vector mass and vector diffusion bilinear integrators, * convection integrator with improved performance, * gradient and vector divergence integrators for Stokes problems, * initial partial assembly mode for NonlinearForms. - Diagonals of partially assembled operators can now be computed efficiently. See the new methods AssembleDiagonal in BilinearForm, AssembleDiagonalPA in BilinearFormIntegrator and the implementations in fem/bilininteg_*.cpp. - In many examples, the partial assembly algorithms provide significantly improved performance, particularly in high-order 3D runs on GPUs. Meshing improvements -------------------- - The algorithms for mesh element numbering were changed to have significantly better caching and parallel partitioning properties. Both initial (see e.g. Mesh::GetHilbertElementOrdering) and ordering after uniform refinement were improved. NOTE: new ordering can have a round-off effect on solver results. - Added support for non-conforming AMR on both prisms and tetrahedra, including coarsening and parallel load balancing. Anisotropic prism refinement is only available in the serial version at the moment. - The TMOP mesh optimization algorithms were extended to support r-adaptivity. Target matrices can now be constructed either via a given analytical function (e.g. spatial dependence of size, aspect ratio, etc., for each element) or via a (Par)GridFunction specified on the original mesh. - The TMOP algorithms were also improved to support non-conforming AMR meshes. - Added support for creating refined versions of periodic meshes, making use of the new L2ElementRestriction class. This class also allows for computing geometric factors on periodic meshes using partial assembly. Discretization improvements --------------------------- - Added support for GSLIB-FindPoints, a general high-order interpolation utility that can robustly evaluate a GridFunction in an arbitrary collection of points in physical space. See INSTALL for details on building MFEM with GSLIB, and miniapps/gslib for examples of how to use this feature. - Added support for complex-valued finite element operators and fields using a 2x2 block structured linear system to mimic complex arithmetic. New classes include: ComplexGridFunction, SesquilinearForm, ComplexLinearForm, and their parallel counterparts. - Added second order derivatives of NURBS shape functions. - Added support for serendipity elements of arbitrary order on affinely-mapped square elements. Basis functions for these elements can be visualized using an option in the display-basis miniapp. - Two integrators related to Stokes problems, (Q grad u, v) and (Q div v, u), where u and the components of v are in H1, were added/modified to support full and partial assembly modes. See the new GradientIntegrator and the updated VectorDivergenceIntegrator classes in fem/bilininteg.hpp, as well as the PA kernels in fem/bilininteg_gradient.cpp and fem/bilininteg_divergence.cpp. - Added a nonlinear vector valued convection integrator (Q u \cdot grad u, v) where u_i and v_i are in H1. This form occurs e.g. in the Navier-Stokes equations. The integrator supports the partial assembly mode for its action. In full assembly mode we also provide the GetGradient method that computes the linearized version of the integrator. - Added a new method, MixedBilinearForm::FormRectangularLinearSystem, that can be used to impose boundary conditions on the non-square off-diagonal blocks of a block operator (similar to FormLinearSystem in the square case). Linear and nonlinear solvers ---------------------------- - Added support for Ginkgo, a high-performance linear algebra library for GPU and manycore nodes, with a focus on sparse solution of linear systems. For more details see linalg/ginkgo.hpp and the example code in examples/gingko. - Added support for HiOp, a lightweight HPC solver for nonlinear optimization problems, see class HiOpNLPOptimizer and the example codes in examples/hiop. - Added a general interface for specifying and solving nonlinear constrained optimization problems through the new classes OptimizationProblem and OptimizationSolver, see linalg/solver.hpp. - Added a block ILU(0) preconditioner for DG-type discretizations. Example 9 (DG advection) now takes advantage of this for implicit time integration. - New time integrators: Adams-Bashforth, Adams-Moulton and several integrators for 2nd order ODEs, see the new Example 23. - Added a LinearSolve(A,X) convenience method to solve dense linear systems. In the trivial cases, i.e., square matrices of size 1 or 2, the system is solved directly, otherwise, LU factorization is employed. New and updated examples and miniapps ------------------------------------- - Added a collection of 7 playful miniapps in miniapps/toys that illustrate the meshing and visualization features of the library in more relaxed settings. The toys include simulations of cellular automata, Rubik's cube, Mandelbrot set, a tool to convert any image to mfem mesh, and more. - Added 8 new example codes: * Example 22/22p demonstrates the use of the new complex-valued finite element operators by defining and solving a family of time-harmonic PDEs related to damped harmonic oscillators. * Example 23 solves a simple 2D/3D wave equation with the new second order time integrators. * Example 24/24p demonstrates usage of mixed finite element spaces in bilinear forms. Partial assembly is supported in this example. * A version of Example 1 in examples/ginkgo demonstrating the use of the Gingko interface to solve a linear system. * A version of Example 9/9p in examples/hiop demonstrating the nonlinear constrained optimization interface and use of the SLBQP and HiOp solvers. - Added two new miniapps: Find Points and Field Diff in miniapps/gslib that show how GSLIB-FindPoints can be used to interpolate a (Par) GridFunction in an arbitrary number of physical space points in 2D and 3D. The GridFunction must be in H1 and in the same space as the mesh that is used to find the points. - Added a simple miniapp, Get Values, that extracts field values at a set of points, from previously saved data via DataCollection classes. - Several examples and miniapps were updated: * Added device support in Example 3/3p and Example 9/9p. * Example 1/1p and Example 3/3p now use diagonal preconditioning in partial assembly mode. * Example 9/9p now supports implicit time integration, using the new block ILU(0) solvers as preconditioners for the linear system. * The mesh-optimizer and pmesh-optimizer miniapps now include the new r-adaptivity capabilities of TMOP. They were also updated to support mesh optimization on non-conforming AMR meshes. * New options to reorder and partition the mesh and boundary attribute visualization (key 'b') are now available in the mesh-explorer miniapp. - Collected object files from the miniapps/common directory into a new library, libmfem-common for the convenience of application developers. The new library is now used in several miniapps in the electromagnetic and tools directories. Improved testing ---------------- - Added a large number of unit tests in the tests/unit directory, including several parallel unit tests. - Added a new directory, tests/scripts, with several shell scripts that perform simple checks on the code including: code styling, documentation formatting, proper use of .gitignore, and preventing the accidental commit of large files. - It is recommended that developers run the above tests scripts (via the runtest script) before pushing to GitHub. See the README file in tests/scripts. - The Travis CI settings have been updated to include an initial Checks stage which currently runs the code-style, documentation and gitignore test scripts, as well as a final stage for optional checks/tests which currently runs the branch-history script. Miscellaneous ------------- - Added support for output in the ParaView XML format. Both low-order and high-order Lagrange elements are supported. Output can be in ASCII or binary format. The binary output can be compressed if MFEM is compiled with zlib support (MFEM_USE_ZLIB). See the new ParaViewDataCollection class and the updated Examples 5/5p and 9/9p. - Upgraded the SUNDIALS interface to utilize SUNDIALS 5.0. This necessitated a complete rework of the interface and requires changes at the application level. Example usage of the new interface can be found in examples/sundials. - Switched from gzstream to zstr for the implementation of zlib-compressed C++ output stream. The build system definition now uses MFEM_USE_ZLIB instead of MFEM_USE_GZSTREAM, but the code interface (e.g. ofgzstream) remains the same. - Various other simplifications, extensions, and bugfixes in the code. API changes ----------- - In the enum classes MemoryType and MemoryClass, "CUDA" was renamed to "DEVICE" which now denotes either "CUDA" or "HIP" depending on the build configuration. In the same enum classes, "CUDA_UVM" was renamed to "MANAGED". Version 4.0, released on May 24, 2019 ===================================== Unlike previous MFEM releases, this version requires a C++11 compiler. GPU support ----------- - Added initial support for hardware devices, such as GPUs, and programming models, such as CUDA, OCCA, RAJA and OpenMP. - The GPU/device support is based on MFEM's new backends and kernels working seamlessly with a new lightweight device/host memory manager. The kernels can be implemented either in OCCA, or as a simple wrapper around for-loops, which can then be dispatched to RAJA and native backends. See the files forall.hpp and mem_manager.hpp in the general/ directory for more details. - Several of the MFEM example codes (ex1, ex1p, ex6, and ex6p) can now take advantage of GPU acceleration with the backend selectable at runtime. Many of the linear algebra and finite element operations (e.g. partially assembled bilinear forms) have been extended to take advantage of kernel acceleration by simply replacing loops with the MFEM_FORALL() macro. - In addition to native CUDA kernels, the library currently supports OCCA, RAJA and OpenMP kernels, which could be mixed and matched in different parts of the same application. We plan on adding support for more programming models and devices in the future, without the need for significant modifications in user code. The list of current backends is: "occa-cuda", "raja-cuda", "cuda", "occa-omp", "raja-omp", "omp", "occa-cpu", "raja-cpu", and "cpu". - GPU-related limitations: * Hypre preconditioners are not yet available in GPU mode, and in particular hypre must be built in CPU mode. * Only constant coefficients are currently supported on GPUs. * Optimized element assembly, and matrix-free bilinear forms are not implemented yet. Element batching is currently ignored. * In device mode, full assembly is performed on the host (but the matvec action is performed on the device). * Partial assembly kernels are not implemented yet for simplices. Discretization improvements --------------------------- - Partial assembled finite element operators are now available in the core library, based on the new classes PABilinearFormExtension, ElementRestriction, DofToQuad and GeometricFactors (associated with the classes BilinearForm, FiniteElementSpace, FiniteElement and Mesh, respectively). The kernels for partial assembled Setup/Assembly and Action/Mult are implemented in the BilinearFormIntegrator methods AssemblePA and AddMultPA. - Added support for a general "low-order refined"-to-"high-order" transfer of GridFunction data from a "low-order refined" (LOR) space defined on a refined mesh to a "high-order" (HO) finite element space defined on a coarse mesh. See the new classes InterpolationGridTransfer and L2ProjectionGridTransfer and the new LOR Transfer miniapp: miniapps/tools/lor-transfer.cpp. - Added element flux, and flux energy computation in class ElasticityIntegrator, allowing for the use of Zienkiewicz-Zhu type error estimators with the integrator. For an illustration of this addition, see the new Example 21. - Added support for derefinement of vector (RT + ND) spaces. - Added a variety of coefficients which are sums or products of existing coefficients as well as grid function coefficients which return the divergence, gradient, or curl of their GridFunctions. Support for wedge elements and meshes with mixed element types -------------------------------------------------------------- - Added support for wedge-shaped mesh elements of arbitrary order (with Geometry type PRISM) which have two triangular faces and three quadrilateral faces. Several examples of such meshes can be found in the data/ directory. - Added support for mixed meshes containing triangles and quadrilaterals in 2D or tetrahedra, wedges, and hexahedra in 3D. This includes support for uniform refinement of such meshes. Several examples of such meshes can be found in the data/ directory. - Added H1 and L2 finite elements of arbitrary order for Wedge elements. - Added support for reading and writing linear and quadratic meshes containing wedge elements in VTK mesh format. Several examples of such meshes can be found in the data/ directory. Other meshing improvements -------------------------- - Improved the uniform refinement of tetrahedral meshes (also part of the uniform refinement of mixed 3D meshes). The previous refinement algorithm is still available as an option in Mesh::UniformRefinement. Both can be used in the updated Mesh Explorer miniapp. - The local tetrahedral mesh refinement algorithm in serial and in parallel now follows precisely the paper: D. Arnold, A. Mukherjee, and L. Pouly, "Locally Adapted Tetrahedral Meshes Using Bisection", SIAM J. Sci. Comput. 22 (2000), 431–448. This guarantees that the shape regularity of the elements will be preserved under refinement. - The TMOP mesh optimization algorithms were extended to support user-defined space-dependent limiting terms. Improved the TMOP objective functions by more accurate normalization of the different terms. - Added support for parallel communication groups on non-conforming meshes. - Improved parallel partitioning of non-conforming meshes. If the coarse mesh elements are ordered as a sequence of face-neighbors, the parallel partitions are now guaranteed to be continuous. To that end, inline quadrilateral and hexahedral meshes are now by default ordered along a space-filling curve. - A boundary in a NURBS mesh can now be connected with another boundary. Such a periodic NURBS mesh is a simple way to impose periodic boundary conditions. - Added support for reading linear and quadratic 2D quadrilateral and triangular Cubit meshes. New and updated examples and miniapps ------------------------------------- - Added a new meshing miniapp, Toroid, which can produce a variety of torus shaped meshes by twisting a stack of wedges or hexahedra. - Added a new meshing miniapp, Extruder, that demonstrates the capability to produce 3D meshes by extruding 2D meshes. - Added a simple miniapp, LOR Transfer, for visualizing the actions of the transfer operators between a high-order and a low-order refined spaces. - Added a new example, Example 20/20p, that solves a system of 1D ODEs derived from a Hamiltonian. The example demonstrates the use of the variable order, symplectic integration algorithm implemented in class SIAVSolver. - Added a new example, Example 21/21p, that illustrates the use of AMR to solve a linear elasticity problem. This is an extension of Example 2/2p. New and improved solvers and preconditioners -------------------------------------------- - Added support for parallel ILU preconditioning via hypre's Euclid solver. - Added support for STRUMPACK v3 with a small API change in the class STRUMPACKSolver, see "API changes" below. Miscellaneous ------------- - Added unit tests based on the Catch++ library in the test/ directory. - Renamed the option MFEM_USE_OPENMP to MFEM_USE_LEGACY_OPENMP. This legacy option is deprecated and planned for removal in a future release. The original option name, MFEM_USE_OPENMP, is now used to enable the new OpenMP backends in the new kernels. - In SparseMatrix added the option to perform MultTranspose() by matvec with computed and stored transpose matrix. This is required for deterministic results when using devices such as CUDA and OpenMP. - Altered the way FGMRES counts its iterations so that it matches GMRES. - Various other simplifications, extensions, and bugfixes in the code. - Construct abstract parallel rectangular truedof-to-truedof operators via Operator::FormDiscreteOperator(). API changes ----------- - In multiple places, use Geometry::Type instead of int, where appropriate. - In multiple places, use Element::Type instead of int, where appropriate. - The Mesh methods GetElementBaseGeometry and GetBdrElementBaseGeometry no longer have a default value for their parameter, they only work with an explicitly given index. - In class Mesh, added methods useful for queries regarding the types of elements present in the mesh: HasGeometry, GetNumGeometries, GetGeometries, and class Mesh::GeometryList. - The struct CoarseFineTransformations (returned by the Mesh method GetRefinementTransforms) now stores the embedding matrices separately for each Geometry::Type. - In class ParMesh, replaced the method GroupNFaces with two new methods: GroupNTriangles and GroupNQuadrilaterals. Also, replaced GroupFace with two methods: GroupTriangle and GroupQuadrilateral. - In class ParMesh, made the two RefineGroups methods protected. - Removed the virtual method Element::GetRefinementFlag, it is only used by the derived class Tetrahedron. - Added new methods: Array::CopyTo, Tetrahedron::Init. - In class STRUMPACKSolver, the method SetMC64Job() was replaced by the new methods: DisableMatching(), EnableMatching(), and EnableParallelMatching(). Version 3.4, released on May 29, 2018 ===================================== More general and efficient mesh adaptivity ------------------------------------------ - Added support for PUMI, the Parallel Unstructured Mesh Infrastructure from https://scorec.rpi.edu/pumi. PUMI is an unstructured, distributed mesh data management system that is capable of handling general non-manifold models and effectively supports automated adaptive analysis. PUMI enables for the first time support for parallel unstructured modifications of MFEM meshes. - Significantly reduced MPI communication in the construction of the parallel prolongation matrix in ParFiniteElementSpace, for much improved parallel scaling of non-conforming AMR on hundreds of thousands of MPI tasks. The memory footprint of the ParNCMesh class has also been reduced. - In FiniteElementSpace, the fully assembled refinement matrix is now replaced by default by a specialized refinement operator. The operator option is both faster and more memory efficient than using the fully assembled matrix. The old approach is still available and can be enabled, if needed, using the new method FiniteElementSpace::SetUpdateOperatorType(). Discretization improvements --------------------------- - Added support for a general "high-order"-to-"low-order refined" transfer of GridFunction and true-dof data from a "high-order" finite element space defined on a coarse mesh, to a "low-order refined" space defined on a refined mesh. The new methods, GetTransferOperator and GetTrueTransferOperator in the FiniteElementSpace classes, work in both serial and parallel and support matrix-based as well as matrix-free transfer operator representations. They use a new method, GetTransferMatrix, in the FiniteElement class similar to GetLocalInterpolation, that allows the coarse FiniteElement to be different from the fine FiniteElement. - Added class ComplexOperator, that implements the action of a complex operator through the equivalent 2x2 real formulation. Both symmetric and antisymmetric block structures are supported. - Added classes for general block nonlinear finite element operators (deriving from BlockNonlinearForm and ParBlockNonlinearForm) enabling solution of nonlinear systems with multiple unknowns in different function spaces. Such operators have assemble-based action and also support assembly of the gradient operator to enable inversion with Newton iteration. - Added variable order NURBS: for each space each knot vector in the mesh can have a different order. The order information is now part of the finite element space header in the NURBS mesh output, so NURBS meshes in the old format need to be updated. - In the classes NonlinearForm and ParNonlinearForm, added support for non-conforming AMR meshes; see also the "API changes" section. - New specialized time integrators: symplectic integrators of orders 1-4 for systems of first order ODEs derived from a Hamiltonian and generalized-alpha ODE solver for the filtered Navier–Stokes equations with stabilization. See classes SIASolver and GeneralizedAlphaSolver in linalg/ode.hpp. - Inherit finite element classes from the new base class TensorBasisElement, whenever the basis can be represented by a tensor product of 1D bases. - Added support for elimination of boundary conditions in block matrices. New and updated examples and miniapps ------------------------------------- - Added a new serial and parallel example (ex19) that solves the quasi-static incompressible hyperelastic equations. The example demonstrates the use of block nonlinear forms as well as custom block preconditioners. - Added a new serial example (ex23) to demonstrate the use of second order time integration to solve the wave equation. - Added a new electromagnetics miniapp, Maxwell, for simulating time-domain electromagnetics phenomena as a coupled first order system of equations. - A simple local refinement option has been added to the mesh-explorer miniapp (menu option 'r', sub-option 'l') that selects elements for refinement based on their spatial location - see the function 'region()' in the source file. - Added a set of miniapps specifically focused on Isogeometric Analysis (IGA) on NURBS meshes in the miniapps/nurbs directory. Currently the directory contains variable order NURBS versions of examples 1, 1p and 11p. - Added PUMI versions of examples ex1, ex1p, ex2 and ex6p in a new examples/pumi directory. The new examples demonstrate the PUMI APIs for parallel and serial mesh loading (ex1 and ex1p), applying BCs using classification (ex2), and performing parallel mesh adaptation (ex6p). - Added two new miniapps related to DataCollection I/O in miniapps/tools: load-dc.cpp can be used to visualize fields saved via DataCollection classes; convert-dc.cpp demonstrates how to convert between MFEM's different concrete DataCollection options. - Example 10p with its SUNDIALS and PETSc versions have been updated to reflect the change in the behavior of the method ParNonlinearForm::GetLocalGradient() (see the "API changes" section) and now works correctly on non-conforming AMR meshes. Example 10 and its SUNDIALS version have also been updated to support non-conforming ARM meshes. Miscellaneous ------------- - Documented project workflow and provided contribution guidelines in the new top-level file, CONTRIBUTING.md. - Added (optional) Conduit Mesh Blueprint support of MFEM data for both in-core and I/O use cases. This includes a new ConduitDataCollection that provides json, simple binary, and HDF5-based I/O. Support requires Conduit >= v0.3.1 and VisIt >= v2.13.1 will read the new Data Collection outputs. - Added a new developer tool, config/sample-runs.sh, that extracts the sample runs from all examples and miniapps and runs them. Optionally, it can save the output from the execution to files, allowing comparison between different versions and builds of the library. - Support for building a shared version of the MFEM library with GNU make. - Added a build option, MFEM_USE_EXCEPTIONS=YES, to throw an exception instead of calling abort on mfem errors. - When building with the GnuTLS library, switch to using X.509 certificates for secure socket authentication. Support for the previously used OpenPGP keys has been deprecated in GnuTLS 3.5.x and removed in 3.6.0. For secure communication with the visualization tool GLVis, a new set of certificates can be generated using the latest version of the script 'glvis-keygen.sh' from GLVis. - Upgraded MFEM to support Axom 0.2.8. Prior versions are no longer supported. API changes ----------- - Introduced a new enum, Matrix::DiagonalPolicy, that replaces the integer parameters in many methods that perform elimination of rows and/or columns in matrices. Some examples of such methods are: * class SparseMatrix: EliminateRow(), EliminateCol(), EliminateRowCol(), ... * class BilinearForm: EliminateEssentialBC(), EliminateVDofs(), ... * class StaticCondensation: EliminateReducedTrueDofs() * class BlockMatrix: EliminateRowCol() Calling these methods with an explicitly given (integer) constants, will now generate compilation errors, please use one of the new enum constants instead. - Modified the virtual method AbstractSparseMatrix::EliminateZeroRows() and its implementations in derived classes, to accept an optional 'threshold' parameter, replacing previously hard-coded threshold values. - In the classes NonlinearForm and ParNonlinearForm: * The method GetLocalGradient() no longer imposes boundary conditions. The motivation for the change is that, in the case of non-conforming AMR, performing the elimination at the local level is incorrect - it must be applied at the true-dof level. * The method SetEssentialVDofs() is now deprecated. Version 3.3.2, released on Nov 10, 2017 ======================================= High-order mesh optimization ---------------------------- - Added support for mesh optimization via node-movement based on the Target- Matrix Optimization Paradigm (TMOP) developed by P.Knupp et al. A variety of mesh quality metrics, with their first and second derivatives have been implemented. The combination of targets & quality metrics is used to optimize the physical node positions, i.e., they must be as close as possible to the shape, size and/or alignment of their targets. The optimization of arbitrary high-order meshes in 2D, 3D, serial and parallel is supported. - The new Mesh Optimizer miniapp can be used to perform mesh optimization with TMOP in serial and parallel versions. The miniapp also demonstrates the use of nonlinear operators and their coupling to Newton methods for solving minimization problems. New and improved solvers and preconditioners -------------------------------------------- - MFEM is now included in the xSDK project, the Extreme-scale Scientific Software Development Kit, as of xSDK-0.3.0. Various changes were made to comply with xSDK's community policies, https://xsdk.info/policies, including: xSDK-specific options in CMake, support for user-provided MPI communicators, runtime API for version number, and the ability to disable/redirect output. For more details, see general/globals.hpp and in particular the mfem::err and mfem::out streams replacing std::err and std::out respectively. - Added (optional) support for the STRUMPACK parallel sparse direct solver and preconditioner. STRUMPACK uses Hierarchically Semi-Separable (HSS) compression in a fully algebraic manner, with interface similar to SuperLU_DIST. See http://portal.nersc.gov/project/sparse/strumpack for more details. - Added a block lower triangular preconditioner based (only) on the actions of each block, see class BlockLowerTriangularPreconditioner. - Added an optional operator in LOBPCG to projects vectors onto a desired subspace (e.g. divergence-free). Other small changes in LOBPCG include the ability to set the starting vectors and support for relative tolerance. - The Newton solver supports an optional scaling factor, that can limit the increment in the Newton step, see e.g. the Mesh Optimizer miniapp. - Updated MFEM integration to support the new SUNDIALS 3.0.0 interface. New and updated examples and miniapps ------------------------------------- - Added a new serial and parallel example (ex18) that solves the transient Euler equations on a periodic domain with explicit time integrators. In the process extended the NonlinearForm class to allow for integrals over faces and exchanging face-neighbor data in parallel. - Added a new meshing miniapp, Shaper, that can be used to resolve complicated material interfaces by mesh refinement, e.g. as a tool for initial mesh generation from prescribed "material()" function. Both conforming and non-conforming (isotropic and anisotropic) refinements are supported. - Added a new meshing miniapp, Mesh Optimizer, that demonstrates the use of TMOP for mesh optimization (serial and parallel version.) - Added SUNDIALS version of Example 16/16p. Discretization improvements --------------------------- - Added a FindPoints method of the Mesh and ParMesh classes that returns the elements that contain a given set of points, together with the coordinates of the points in the reference space of the corresponding element. In parallel, if a point is shared by multiple processors, only one of them will mark that point as found. Note that the current implementation of this method is not optimal and/or 100% reliable. See the mesh-explorer miniapp for an example. - Added a new class InverseElementTransformation, that supports a number of algorithms for inversion of general ElementTransformations. This class can be used as a more flexible and extensible alternative to ElementTransformation's TransformBack method. It is also used in the FindPoints methods as a tunable and customizable inversion algorithm. - Memory optimizations in the NCMesh class, which now uses 50% less memory than before. The average cost of an element in a uniformly refined mesh (including the refinement hierarchy, but excluding the temporary face_list and edge_list) is now only about 290 bytes. This also makes the class faster. - Added the ability to integrate delta functions on the right-hand side (by sampling the test function at the center of the delta coefficient). Currently this is supported in the DomainLFIntegrator, VectorDomainLFIntegrator and VectorFEDomainLFIntegrator classes. - Added five new linear interpolators in fem/bilininteg.cpp to compute products of scalar and vector fields or products with arbitrary coefficients. - Added matrix coefficient support to CurlCurlIntegrator. - Extend the method NodalFiniteElement::Project for VectorCoefficient to work with arbitrary number of vector components. Miscellaneous ------------- - Added a .gitignore file that ignores all files erased by "make distclean", i.e. the files that can be generated from the source but we don't want to track in the repository, as well as a few platform-specific files. - Added Linux, Mac and Windows CI testing on GitHub with Travis CI and Appveyor. - Added a new macro, MFEM_VERSION, defined as a single integer of the form (major*100 + minor)*100 + patch. The convention is that an even number (i.e. even patch number) denotes a "release" version, while an odd number denotes a "development" version. See config/config.hpp.in. - Added an option for building in parallel without a METIS dependency. This is used for example the Laghos miniapp, https://github.com/CEED/Laghos. - Modified the installation layout: all headers, except the master headers (mfem.hpp and mfem-performance.hpp), are installed in /include/mfem; the master headers are installed in both /include/mfem and in /include. The mfem configuration and testing makefiles (config.mk and test.mk) are installed in /share/mfem, instead of . - Add three more options for MFEM_TIMER_TYPE. - Support independent number of digits for cycle and rank in DataCollection. - Converted Sidre usage from "asctoolkit" to "axom" namespace. - Various small fixes and styling updates. API changes ----------- - The methods GetCoeff of VectorArrayCoefficient and MatrixArrayCoefficient now return a pointer to Coefficient (instead of reference). Note that NULL pointer is a valid entry for these two classes - it is treated as the zero function. - When building with PETSc, the required PETSc version is now 3.8.0. Newer versions may work too, as long as there are no interface changes in PETSc. - The class GeometryRefiner now uses the enum in Quadrature1D for its type specification. In particular, this will affect older versions of GLVis. A simple upgrade to the latest version of GLVis should resolve this issue. Version 3.3, released on Jan 28, 2017 ===================================== FEM <-> linear system interface for action-only linear operators ---------------------------------------------------------------- - Added a new class, ConstrainedOperator, which can impose essential boundary conditions using only the action, Mult(), of a given square linear Operator. - Added a FormLinearSystem + RecoverFEMSolution functionality for square linear Operators that are available only through their action. This includes all necessary transformations, such as: parallel assembly, conforming constraints for non-conforming AMR and eliminating boundary conditions. (Hybridization and static condensation are not supported.) See examples in miniapps/performance. Matrix-free preconditioning and low-order-refined spaces -------------------------------------------------------- - The HPC examples in miniapps/performance now support efficient preconditioning in matrix-free mode based on applying a standard (e.g. AMG) preconditioner to a sparsified version of the operator. The sparsification is obtained by rediscretizing with a low-order refined spaces, currently at the high-order degrees of freedom. - New mesh constructors support the creation of low-order-refined version of a given mesh, both in serial and in parallel. These are illustrated in the HPC examples in miniapp/performance (option -pc lor), as well as in mesh-explorer miniapp, which now supports Gauss-Lobatto refinement and uniform refinement, both for any factor > 1. Comprehensive PETSc and SUNDIALS interfaces ------------------------------------------- - Added support for many linear and nonlinear solvers, preconditioners, time integrators and other features from the PETSc suite (version 3.8 or higher of the PETSc dev branch is required). The new features include: * support for PETSc matrices in MATAIJ, MATIS, MATSHELL and MATNEST formats. * PETSc linear solvers can take any mfem Operator and support user-defined monitoring routines (see examples/petsc/ex1p). * BDDC preconditioners for H1, H(curl) and H(div), including with static condensation/hybridization, FieldSplit preconditioner for BlockOperators. * PETSc non-linear solvers can take any mfem Operator that implements the GetGradient() method. * PETSc ODE solvers are supported for mfem's TimeDependentOperators. The use of these features is illustrated in the new examples/petsc directory. - Added a new class, OperarorHandle, that provides a common interface for global, matrix-type operators to be used in bilinear forms, gradients of nonlinear forms, static condensation, hybridization, etc. The following backends are currently supported: * HYPRE parallel sparse matrix (HYPRE_PARCSR) * PETSC globally assembled parallel sparse matrix (PETSC_MATAIJ) * PETSC parallel matrix assembled on each processor (PETSC_MATIS) - Added support for the time integrators and non-linear solvers from the CVODE, ARKODE and KINSOL libraries of the SUNDIALS suite (version 2.7 or higher of SUNDIALS is required). The use of these features is illustrated in the new examples/sundials directory. Scalable parallel mesh support ------------------------------ - Introduced a new mesh format (v1.2) that can describe/recover MFEM parallel meshes. This way, computations can start directly in parallel without serial refinement and splitting. Non-conforming meshes are currently supported only in serial. General quadrature and nodal finite element basis types ------------------------------------------------------- - Added support for different numerical quadrature schemes and finite element basis points. Different basis points can be selected via optional integer argument(s) to the finite element collection constructor of type BasisType: * H1 elements can use GaussLobatto (default), Positive, or ClosedUniform; * L2 elements can use GaussLegendre (default), GaussLobatto, Positive, ClosedUniform, OpenUniform or OpenHalfUniform; * RT can now use open basis that is GaussLegendre (default), GaussLobatto, ClosedUniform, OpenUniform, or OpenHalfUniform, and closed basis that is GaussLobatto (default) or ClosedUniform; * ND elements can use the same BasisType's as RT elements. - GaussLegendre, GaussLobatto, ClosedUniform, OpenUniform, and OpenHalfUniform integration rules can be directly constructed with an optional parameter of type Quadrature1D: IntegrationRules gl(0, Quadrature1D::GaussLobatto); const IntegrationRule *ir = gl(Geometry::SEGMENT, 5); // 4pt 1D rule The global IntRules object continues to use GaussLegendre. New integrators for common families of operators ------------------------------------------------ - Added MixedScalarIntegrator and 7 derived classes for integrating products of two scalar basis functions and optional scalar coefficients. - Added MixedVectorIntegrator and 16 derived classes for integrating the inner product of two vector basis functions with optional scalar, vector, or matrix coefficients. - Added MixedScalarVectorIntegrator and 13 derived classes for integrating the product of a scalar basis function with the inner product of a vector basis function with a vector coefficient. In 2D the inner product can optionally be replaced with a cross product. - Added a new class DGElasticityIntegrator that supports a few types of DG formulations for linear elasticity and a new linear form integrator, DGElasticityDirichletLFIntegrator, that implements non-homogeneous BCs. - Added support for DG spaces in class VectorBoundaryLFIntegrator. - In classes BilinearForm and LinearForm, added support for boundary face integrators applied to a subset of the boundary, see AddBdrFaceIntegrator. New and updated examples and miniapps ------------------------------------- - Sixteen new serial and parallel example codes that demonstrate: * solution of a time-dependent nonlinear heat equation (Example 16/16p) * DG formulations of static linear elasticity (Example 17/17p) * the use of PETSc solvers and preconditioners (Examples 1p, 2p, 3p, 4p, 5p, 6p, 9p and 10p in examples/petsc) * the use of SUNDIALS time integrators and nonlinear solvers (Examples 9/9p and 10/10p in examples/sundials) - The HPC examples in miniapps/performance now have a -mf/--matrix-free option illustrating optimized "partial assembly" operator evaluation. This is now the default in these examples, to switch to optimized matrix assembly instead use the -asm/--assembly option. - Added a new electromagnetic miniapp, Joule, illustrating the simulation of transient magnetics and joule heating. This is a comprehensive miniapp that uses finite element spaces and solvers for the whole de Rham sequence. - Added a simple miniapp, display-basis, for displaying the various types of finite element basis functions within single elements. This is part of the new miniapps/tools directory. - Rewrote the Volta and Tesla solver classes to avoid using linear algebra objects when possible. This greatly simplifies the code, reduces memory requirements, and eliminates unnecessary computation. It also fixed a bug with divergence cleaning in the Tesla miniapp. - Added an option to Example 9/9p to save a binary visualization file using the Conduit mesh blueprint/hdf5 format. Improved building options ------------------------- - Added a new CMake build system, that can be used as an alternative to the GNU make-based build system (e.g. for out-of-source building). For more details, see the INSTALL file and the config/cmake directory. - Added support for out-of-source builds with GNU make, see the INSTALL file. Improved file output -------------------- - Added on-the-fly compression of file streams input and output via gzstream, see the MFEM_USE_GZSTREAM option. - Added experimental support for an HDF5-based output file format following the Conduit (https://github.com/LLNL/conduit) mesh blueprint specification for visualization and/or restart capability. This functionality is aimed primarily at user of LLNL's axom project (Sidre component) that run problems at extreme scales. Users desiring a small scale binary format may want to look at the gzstream functionality instead. Miscellaneous ------------- - Added optional support for software-based higher-precision arithmetic with the MPFR library. When MFEM_USE_MPFR is enabled, the 1D quadrature rules will be computed precisely, at least for rules with up to 65-points. - Better support for METIS version 5 and above. - Provide an informative backtrace in mfem_error based on the cross-platform libunwind library (requires MFEM_USE_LIBUNWIND=YES). - In class SparseMatrix, added methods PrintInfo and CheckFinite. - GMRESSolver and MINRESSolver now support the same print levels as CGSolver. - Added method MemoryUsage to the classes Stack and MemAlloc. - Improved Doxygen formatting of code comments. - Various other simplifications, extensions, and bugfixes in the code. Version 3.2, released on Jun 30, 2016 ===================================== Dynamic AMR with parallel load balancing, derefinement of non-conforming meshes ------------------------------------------------------------------------------- - Parallel non-conforming meshes can now be load balanced at any time by calling ParMesh::Rebalance(). Elements of the mesh are redistributed in such a way that each processor gets approximately the same number of elements (plus minus one element). Partitioning is done by splitting a sequence of space-filling (Hilbert) curves defined on the refinement octrees. - Isotropically refined non-conforming meshes can now be derefined, both in serial and in parallel, based on a per-element error measure and a derefinement threshold. See the class ThresholdDerefiner. - Following an arbitrary mesh change (uniform/general conforming/non-conforming refinement, derefinement, load balancing), the FiniteElementSpace and associated GridFunctions can be updated by interpolating or redistributing the previous function values based on the new state of the mesh. (Internally this is implemented through a transformation matrix that is constructed in the FiniteElementSpace.) The user interface is quite simple: pmesh.Rebalance(); // or GeneralRefinement, or GeneralDerefinement fespace.Update(); // calculate a transformation matrix (by default) x.Update(); // apply the transformation to the GridFunction z.Update(); // apply it again - New abstractions are available for error estimation and general mesh operations such as refinement and derefinement. See the base classes ErrorEstimator and MeshOperator and their descendants. - The above features are illustrated in the new Example 15 (see also Example 6). Tensor-based high-performance FEM operator assembly and evaluation ------------------------------------------------------------------ - Added support for high-performance, tensor-based efficient assembly and evaluation of high-order operators. - A number of new header files have been added to the fem/, linalg/ and mesh/ directories. They start with the prefix "t" to indicate the (heavy) use of C++ templating, similar to how the prefix "p" denotes "parallel". All the code for the new HPC FE assembly/evaluation algorithms is fully implemented in these header files. Note that the new interface is optional and only enabled if the mfem-performance.hpp header is included instead of mfem.hpp. This is an initial, reference implementation. - Similarly to the serial-to-parallel (ex1.cpp-to-ex1p.cpp) transition, an existing MFEM-based applications has to be transitioned to the new HPC interface. This is illustrated in two new example codes which are the high-performance versions of Example 1/1p. See miniapps/performance. - The new interface reduces local operator assembly/evaluation to batched small dense tensor contraction operations. For high performance, the sizes of these contractions should be known at compile time, so the BilinearForm object needs to have detailed knowledge about the mesh, the finite element space, the quadrature rule and the integrator to be assembled. This required a new interface, that supports a subset of the current (general) coefficients and bilinear form integrators, including variable coefficients and mass and diffusion integrators. It is possible to use the old and the new HPC interface side-by-side, see the HPC version of Example 1/1p in miniapps/performance. Advanced FEM on parallel non-conforming meshes ---------------------------------------------- - Added support for discontinuous Galerkin methods on parallel non-conforming meshes, see Examples 9p and 14p. - Added support for hybridization on parallel non-conforming meshes, see Example 4p. New and improved linear solvers ------------------------------- - Added a wrapper for the real-valued, double precision solver in SuperLU_DIST which is a sparse direct solver for distributed memory architectures. As such it can only be enabled along with MFEM_USE_MPI. When MFEM is configured with MFEM_USE_SUPERLU, one also needs to alter the version of METIS, since SuperLU requires ParMETIS (which comes packaged with a serial version of METIS). See http://http://crd-legacy.lbl.gov/~xiaoye/SuperLU for SuperLU_DIST details. - Added a wrapper for the KLU solver in SuiteSparse see http://faculty.cse.tamu.edu/davis/suitesparse.html for details of KLU. If MFEM was configured with MFEM_USE_SUITESPARSE, one must now also link against the klu and btf libraries in SuiteSparse, see config/defaults.mk. New and updated examples and miniapps ------------------------------------- - Four new serial and parallel example codes that demonstrate: * high-performance finite element operator assembly/evaluation (Example 1/1p in miniapps/performance) * adaptive refinement, derefinement and load balancing (in parallel) on non-conforming meshes (Example 15/15p) - Examples 4p now supports hybridization on non-conforming meshes. - Examples 9p and 14p now work on non-conforming meshes. - Example 11p now has optional support for the SuperLU parallel direct solver. - Added several new options and example runs in the Volta and Tesla miniapps, including support for Halbach arrays of permanent magnets. Miscellaneous ------------- - Added "check" and "test" targets to the top-level makefile. The former does a quick check by running Example 1/1p, while the latter does a more thorough verification of the build by running all example codes and miniapps. - Added support for 2D and 3D meshes generated by Gmsh (http://gmsh.info), both in ASCII and binary formats. - Added a reader for Cubit meshes in the Genesis (NetCDF) format. Currently supported are linear and quadratic tet and hex meshes. - Added support for boundary bilinear form integrators when using hybridization. - Added support for Robin boundary conditions for DG in BoundaryMassIntegrator. - Moved all reference element connectivity descriptions, such as element-edge, element-face, etc. to the template class Geometry::Constants. - Added support for secure socket communications in class socketstream based on the GnuTLS library, see INSTALL for more details. - Renamed config/user.mk.in to config/defaults.mk and moved all the default build settings from the makefile there. - Added configurable variables AR, ARFLAGS, and RANLIB in the build system. The defaults for Mac OS X will suppress the "has no symbols" warnings. - Various other simplifications, extensions, and bugfixes in the code. API changes ----------- - Changes in class Mesh * Two-level state functionality was removed, including: UseTwoLevelState(int), SetState(int), GetState(), GetNumFineElems(int), GetRefinementType(int), GetFineElem(int, int) and GetFineElemTrans(int, int). - Changes in class FiniteElementSpace * BuildElementToDofTable() is now protected, and it is always called. * GlobalRestrictionMatrix(FiniteElementSpace*, int) was removed, but the prolongation operator can still be accessed via GetUpdateOperator() after mesh refinement and a call to Update(true). - Changes in methods related to non-conforming meshes and spaces * The methods LinearForm::ConformingAssemble, BilinearForm::ConformingAssemble and GridFunction::ConformingProlongate/ConformingProject are now hidden inside (Par)BilinearForm::FormLinearSystem and RecoverFEMSolution. * The conforming prolongation/restriction matrices can still be accessed via FiniteElementSpace::GetConformingProlongation()/GetConformingRestriction(). - Changes in classes GridFunction and ParGridFunction * Renamed Update((Par)FiniteElementSpace*, Vector&, int) to MakeRef. * Renamed Update((Par)FiniteElementSpace*) to SetSpace. Version 3.1, released on Feb 16, 2016 ===================================== Substantially improved non-conforming adaptive mesh refinement -------------------------------------------------------------- - Added support for parallel non-conforming mesh refinement, including a new example code with adaptive mesh refinement for the Laplace problem (Example 6p). Most of the example codes can now work on non-conforming meshes in serial and in parallel. - Added simple ZZ-type error estimators, including an anisotropic one in serial, and one based on Raviart-Thomas flux projection in parallel, to the AMR examples 6 and 6p. These seem to perform quite reasonably, even for higher-order discretizations on 2D, 3D and surface meshes. - The MFEM mesh format has a new version(1.1) that supports non-conforming meshes. The format is an extension of 1.0 that includes a vertex_parents and an optional coarse_elements section. See the example meshes amr-quad.mesh, amr-hex.mesh and fichera-amr.mesh in the data/ directory. - Added support for DG discretizations on non-conforming meshes in serial. See the sample runs in Example 14. - A new function, ParGridFunction::ParallelProject() directly returns a hypre vector restricted to the true degrees of freedom (and supports non-conforming meshes). In most cases, this should be preferred to the ParallelAverage() function. - When using non-conforming meshes, the essential boundary condition elimination has to be applied at the end of the (parallel) assembly. Furthermore, in serial, the bilinear form needs to call ConformingAssemble() after assembly and the solution should call ConformingProlongate() after the solve (these are not necessary in parallel). Note that these could also be handled automatically by the new FEM <-> linear system interface, see below. General finite element spaces and solvers on surfaces/skeletons --------------------------------------------------------------- - Added support for arbitrary high-order finite element spaces on the mesh skeleton (the faces, edges, and vertices between mesh elements) that are the traces of the H1 and H(curl) spaces defined on the mesh. With the previously existing H(div) trace space, the full de Rham sequence on the skeleton is now supported. - Updated integrators and discrete interpolators to work correctly for H(curl) and H(div) spaces defined on surface meshes, or the mesh skeleton. Hybridization, static condensation and a new FEM <-> linear system interface ---------------------------------------------------------------------------- - The BilinearForm/ParBilinearForm classes now support static condensation, as well as hybridization (based on given constraint space and trace integrator). These are illustrated in Examples 1-4. - Added a new interface for transitioning between the finite element objects and their corresponding linear algebra objects, which supports abstracts transformations such as: parallel assembly, eliminating boundary conditions, applying conforming constraints for non-conforming AMR, hybridization, static condensation, back substitution, etc. Changed several of the example codes accordingly. New eigensolvers and improved solvers ------------------------------------- - Added support for the scalable Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG) eigenvalue solver and the Auxiliary-space Maxwell Eigensolver (AME) from hypre. - Added 3 new example codes to demonstrate the LOBPCG and AME applications to the Laplace (Example 11p), Elasticity (Example 12p) and Maxwell (Example 13p) eigenproblems. - Updated the HypreAMS and HypreADS solvers to work for H(curl) and H(div) problems defined on surface meshes, or the mesh skeleton. - Added support for a discretization-enhanced version of hypre's BoomerAMG designed specifically for linear elasticity problems, see Example 2p. - The HypreAMS solver can now be used to solve singular curl-curl problems. New and updated examples ------------------------ - Six new serial and parallel example codes that demonstrate: * parallel conforming and non-conforming adaptive mesh refinement (Example 6p) * hypre's LOBPCG eigensolver for the Laplace eigenproblem (Example 11p) * hypre's LOBPCG eigensolver for the elasticity eigenproblem (Example 12p) * hypre's AME eigensolver for the Maxwell eigenproblem (Example 13p) * DG diffusion discretizations for the Laplace equation (Example 14/14p) - Examples 1-4 now support static condensation, and Example 4/4p supports H(div) hybridization, leading to much improved solve times. These examples also illustrate the new interface for linear system assembly (see also Examples 6 and 7). - Significantly improved the DPG preconditioner in Example 8p, which is now scalable in parallel and uses the HypreADS solver to precondition the interfacial block as an H(div) problem reduced to the mesh skeleton. - Example 7/7p has a new option, -amr, showcasing simple local conforming and non-conforming mesh refinements. - Example 3/3p now works in both 2D and 3D. New miniapps ------------ - Electromagnetic miniapps: * Volta - simple electrostatics simulation code. * Tesla - simple magnetostatics simulation code. See also the README file in miniapps/electromagnetics. - Meshing miniapps: * Mobius Strip - generate various Mobius strip-like meshes. * Klein Bottle - generate three types of Klein bottle surfaces. * Mesh Explorer - visualize and manipulate meshes. See also the README file in miniapps/meshing. Miscellaneous ------------- - Moved MFEM from Google Code to GitHub. New website: http://mfem.org. - Formatted the code with Artistic Style, see the "make style" target. - Added support for 64-bit integers in global size variables, enabling simulations with >2B unknowns. (This requires that hypre is configured with the --enable-bigint option.) - Added optional support for the Gecko graph reordering library. - Updated the implementation of some operations in DenseMatrix for better auto-vectorization. Added a new class LUFactors that computes LU factorization (with pivoting) and perform various operations with the factored data. - Various other simplifications, extensions, and bugfixes in the code. Version 3.0, released on Jan 26, 2015 ===================================== Improved documentation and build system --------------------------------------- - Added interactive example documentation in examples/README.html. This should be the starting point for new users interested in MFEM's features. - New Doxygen-based code documentation. Due to its size, users are expected to build this documentation themselves by typing make in the doc/ directory. (Alternatively, the pre-build documentation can be browsed online). - New build system, based on GNU make which consists of configuration and build steps: "make config; make". The MFEM build options are exported, and can be included in external makefiles. Library installation is also supported. See "make help" and the INSTALL file for details. - To build the examples use 'make' or 'make -j ' in the examples/ directory. Based on the current MFEM configuration this will build the serial or the parallel examples using the same config options as the library. New and updated examples ------------------------ - Six new serial/parallel example codes that demonstrate: * mixed pressure-velocity FEM for Darcy (Example 5) * non-conforming adaptive mesh refinement for Laplace (Example 6) * Laplace problem on a surface (Example 7) * Discontinuous Petrov-Galerkin (DPG) for Laplace (Example 8) * Discontinuous Galerkin (DG) time-dependent advection (Example 9) * time-dependent implicit nonlinear elasticity (Example 10) - Added command line options to all examples and modified several of the serial ones to optionally use the serial direct solver UMFPACK. - Simplified the elimination of Dirichlet boundary conditions in parallel. - Grouped and documented the example code features in examples/README.html Serial non-conforming adaptive mesh refinement ---------------------------------------------- - Added support for general, isotropic and anisotropic, local non-conforming mesh refinement (using hanging nodes) in 2D and 3D, on quadrilateral, triangular and hexahedral meshes. High-order curved and surface meshes are also supported. - The current implementation supports serial meshes (see example 6). Extension to parallel meshes is in active development. - The mesh is refined with Mesh::GeneralRefinement. The non-conforming mesh is represented as a mesh that is "cut" along non-conforming edges and faces in the internal NCMesh class. The only thing the user has to do to obtain a continuous solution is to call BilinearForm::ConformingAssemble and GridFunction::ConformingProlongate before and after solving the linear system. The finite element space and grid functions are then updated with FiniteElementSpace::UpdateAndInterpolate(). Time-dependent problems, non-linear operators and ODE integrators ----------------------------------------------------------------- - Added new abstract base class TimeDependentOperator and a set of explicit Runge-Kutta time integration classes in linalg/ode.?pp. - Added classes for diagonally implicit Runge-Kutta (DIRK) time integrators based on the ImplicitSolve() method of TimeDependentOperator. - Extended all coefficient classes to be optionally time-dependent. - Added classes for general nonlinear finite element operators (deriving from NonlinearForm/ParNonlinearForm). Such operators have assemble-based action and also support assembly of the gradient operator to enable inversion with Newton iteration. Discontinuous Galerkin and Discontinuous Petrov-Galerkin methods ---------------------------------------------------------------- - Added support Discontinuous Galerkin (DG) face integrators in parallel by extending ParMesh with information for face-neighboring processors. Added DG support in ParFiniteElementSpace, ParBilinearForm and ParGridFunction. - Introduced a new class of integrators for forms defined on the faces of the mesh (including interior and boundary faces), mainly intended for hybrid methods like HDG and DPG that employ facet (numerical trace) spaces. Block systems and rectangular operators --------------------------------------- - Added classes BlockOperator, BlockVector and BlockMatrix for handling block systems with different components (e.g., pressure and velocity). - New abstract class AbstractSparseMatrix, between Matrix and SparseMatrix - Modified class Operator to have two separate sizes: "height" and "width" for the output and input sizes, respectively. The Size method was removed. - For backward compatibility, the method Size is still present in the classes DenseMatrix (returns width as before), SparseMatrix (returns height as before), DenseMatrixInverse (square matrix) and BilinearForm (square matrix). Linear and non-linear solvers ----------------------------- - New abstract class Solver, with sub-classes for sparse smoothers, dense matrix inverse, iterative solvers (Krylov methods and Newton) and the hypre solvers. All Krylov methods were consolidated in linalg/solver.cpp and extended to work in parallel. - Added several new classes of solvers and smoothers: * serial sparse direct solvers from the SuiteSparse library (UMFPACK) * HypreSmoother, giving access to the parallel ParCSR smoothers in hypre * polynomial smoothers: Chebyshev, Taubin and FIR * stationary linear iteration (SLI) * quadratic single linearly-constrained optimization problems with bounds Miscellaneous ------------- - Wrapped all classes/functions/objects in a namespace called "mfem". - Automated the creation of quadrature rules to enable on-demand generation of arbitrary order rules for all geometries 1D/2D/3D geometries. - Added support for saving collections of grid functions in format suitable for visualization with VisIt (visit.llnl.gov). See examples 5 and 9. - Added support for 1D, surface and topologically periodic meshes, as well as a simple inline mesh format. See the data/ directory for examples. - Added support for serial mesh optimization using the Mesquite mesh quality improvement toolkit (see mesh/mesquite.?pp and INSTALL for details). - Made sure that MFEM can work in parallel with empty processors and with any MPI communicator. - Improved high-order Bernstein basis support. - Support for high-resolution timers (e.g. POSIX clocks). - Improved error messages with several macros, such as MFEM_ABORT, MFEM_VERIFY, MFEM_ASSERT, MFEM_WARNING, etc. - Improved portability for Windows (Visual Studio) and Mac OS X. - Various simplifications, extensions, and bugfixes in the code. Version 2.0, released on Nov 18, 2011 ===================================== Arbitrary order finite element spaces ------------------------------------- - Added support for arbitrary high-order finite element spaces through the new classes H1_FECollection, L2_FECollection, RT_FECollection and ND_FECollection. These are based on a number of new FiniteElement sub-classes H1_*, L2_*, RT_* and ND_* elements of arbitrary order on all types of reference elements. - The classes implement H1-conforming, L2-discontinuous, H(div)-conforming Raviart-Thomas and H(curl)-conforming Nedelec elements on triangular, quadrilateral, tetrahedral and hexahedral meshes. The only restriction on the order of the spaces is the availability of the required quadrature rules. NURBS meshes and discretization spaces -------------------------------------- - Added a collection of classes for serial and parallel meshes and discretization spaces using Non-uniform rational B-splines (NURBS) basis functions (files mesh/nurbs.?pp). - The Mesh class supports the NURBS-specific refinement functions: KnotInsert and DegreeElevate. Example NURBS meshes can found in the 'data' directory with file names *-nurbs.mesh including an exact non-degenerate disc (disc-nurbs.mesh) and exact non-degenerate ball (ball-nurbs.mesh). - We can handle arbitrary NURBS or standard, non-NURBS, finite element spaces on NURBS meshes. However, a NURBS finite element space requires an underlying NURBS mesh. Refinement of parallel NURBS meshes is not supported yet. Discrete gradient, curl, etc. matrices -------------------------------------- - Added a new class, DiscreteLinearOperator, that facilitates the construction of matrix representations for linear operators like gradient, curl, embedding, projection, etc. The corresponding local "interpolators" are similar to bilinear form integrators and derive from base class DiscreteInterpolator. Current interpolators include GradientInterpolator, IdentityInterpolator, CurlInterpolator and DivergenceInterpolator. - Also available is a parallel version of DiscreteLinearOperator, which assembles parallel topological matrices (such as the discrete gradient, curl, etc.) in hypre's ParCSR format. New integrators --------------- - New linear (r.h.s.) integrator VectorFEBoundaryFluxLFIntegrator for assembling (u, v.n) on the boundary for scalar u and v in an RT space. - New bilinear integrator VectorFECurlIntegrator for assembling (curl u, v) for u in a ND space and v in an RT space. New and updated examples ------------------------ - Added a new serial/parallel Example code 4/4p, which solves a 2D or 3D H(Div) diffusion problem using the Raviart-Thomas finite elements. In parallel, the linear system is solved with the brand-new Auxiliary-space Divergence Solver (ADS) in hypre. - Modified Example 1 to use isoparametric discretization (use the FE space from the mesh) including NURBS meshes and spaces. Updated Example 2 to support arbitrary order spaces. Updated all examples to work with NURBS meshes and spaces, as well as to not use projection onto discontinuous polynomial spaces for visualization (this is now handled directly in GLVis when necessary). - In all examples, switched to a uniform "solution" socket data type instead of the various previous "*_gf_data" data types. - In the parallel examples, switched to parallel mesh and solution output, as well as to the new parallel socket format in place of PrintAsOne/SaveAsOne. New hypre solvers ----------------- - The parallel MFEM build now requires hypre 2.8.0b or newer. - Extended HypreAMS and HypreADS to support (arbitrary) high-order ND/RT spaces, by internally constructing the high-order ParDiscreteLinearOperator gradient, curl and interpolation matrices. This makes the linear solve in Example 3p and 4p significantly faster than before. Extended the HypreAMS object to also work for 2D H(div) problems. Miscellaneous ------------- - Added new class socketstream implementing two-way tcp/ip socket communications in the framework of C++ streams. Added new class socketserver implementing tcp/ip server functionality: listen on a given port for incoming connections, and accept them by assigning the new connection to a socketstream. These new classes are meant to replace the classes isockstream and osockstream. They allow MFEM code to update the mesh and solution via a single socket connection to a GLVis window. - Added new Mesh and GridFunction constructors that combine multiple Mesh and GridFunction objects into one object. These are used in GLVis to visualize data saved in parallel. Removed obsolete code related to reading of parallel disjoint meshes. - Added more quadrature rules on triangles and tetrahedra. - Basic experimental OpenMP support (disabled by default). When enabled, OpenMP code is used for local matrix assembly, sparse matrix-vector product, and some vector operations. - Added support for METIS 5.0 (not the default, see INSTALL). - Various simplifications, extensions, and bugfixes in the code. Version 1.2, released on Apr 08, 2011 ===================================== Parallel MPI-based version of the library based on hypre -------------------------------------------------------- - New MPI parallel version of the library based on the ParCSR parallel matrix format from hypre and the metis graph partitioning library. This version supports parallel local refinement and parallel curved meshes, as well as several solvers from hypre. New serial and parallel examples -------------------------------- - Added a new example code describing an electromagnetic diffusion problem discretized with lowest order Nedelec finite elements (Example 3). - Added parallel versions of all examples codes (files ex1p.cpp, ex2p.cpp and ex3p.cpp) based on hypre's BoomerAMG and AMS preconditioners. Miscellaneous ------------- - Added support for saving and reading linear and curved quadratic meshes in VTK format. The format is automatically recognized when opening a mesh file, and the boundary is reconstructed based on the actual domain boundary. - The 'data' directory now contains a collection of various mesh files in the MFEM and VTK formats, including curved meshes and the mesh files that were previously in the 'examples' directory. - Updated the default integration rule order for most of the linear form integrators. - Added support for cubic hex elements. - Bugfixes in the face orientation of 3D RT0 elements and in the VectorFEDomain linear form integrator. - Various small fixes and styling updates. Version 1.1, released on Sep 13, 2010 ===================================== New MFEM format for general meshes ---------------------------------- - New MFEM mesh v1.0 format with uniform structure for any dimension and support for curved meshes including in 3D. Class Mesh will recognize and read the new format (in addition to all previously used formats) and Mesh::Print uses the new format by default. The old print function was renamed to Mesh::PrintXG. New elasticity example ---------------------- - Added an example code for linear elasticity with (high-order) vector finite elements (Example 2). Miscellaneous ------------- - Added Mesh::PrintVTK and GridFunction::SaveVTK methods for output in VTK format. - Implemented GeometryRefiner::Refine for CUBE and TETRAHEDRON geometries. This allows for saving curved meshes in the VTK format. - Added SConstruct file for mfem/examples. - Various small fixes and styling updates. Version 1.0, released on Jul 21, 2010 ===================================== - Uploaded to http://mfem.googlecode.com. - Initial release.