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Mark L. StowellandTzanio Kolev fbcd11dfef Update CHANGELOG 
Co-authored-by: Tzanio Kolev <tzanio@llnl.gov>
2020-06-07 12:03:07 -07:00

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Finite Element Discretization Library
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http://mfem.org
Version 4.1.1 (development)
===========================
Meshing improvements
--------------------
- The graph linear ordering library Gecko, previously an external dependency, is
now included directly in MFEM. As a result, Mesh::GetGeckoElementOrdering is
always available. The interface has also been improved, see for example the
mesh-explorer miniapp.
- Added support for finite difference-based gradient and Hessian approximation
in the TMOP mesh optimization algorithms. This improves the accuracy of the
Hessian for r-adaptivity using discrete fields, and allows use of skewness
and orientation based metrics.
- Added support for r-adaptivity with more than one discrete field. This allows
the user to specify different discrete functions for controlling the
size, aspect-ratio, orientation, and skew of elements in the mesh.
- Added TMOP capability for approximate tangential mesh relaxation.
- Added support for reading periodic meshes in Gmsh format (version 2.2). See
for example the periodic-annulus-sector and periodic-torus-sector files in
the data directory.
Performance improvements
------------------------
- Added support for explicit vectorization in the high-performance templated
code, which can now take advantage of specific intrinsics classes on the
following architectures:
- x86 (SSE/AVX/AVX2/AVX512),
- Power8 & Power9 (VSX),
- BG/Q (QPX).
These are now enabled by default, and can be disabled with MFEM_USE_SIMD=NO.
See the new file linalg/simd.hpp and the new directory linalg/simd.
Improved GPU capabilities
-------------------------
- Added support for Chebyshev accelerated polynomial smoother on GPU.
Discretization improvements
---------------------------
- Added support for matrix-free interpolation and restriction operators between
continuous H1 finite element spaces of different order on the same mesh or
with the same order on uniformly refined meshes.
- Added support for simplices in GSLIB-FindPoints.
- Added support for H1 and L2 element matrix assembly in the mass, convection,
diffusion, transpose, and the face DG trace integrators. This is compatible
with GPU device execution and is illustrated in Example 9/9p, see the option
'-ea'. When enabled, this level of assembly stores independent dense matrices
for the elements, and independent dense matrices for the faces in the DG case.
- Added new partial assembly kernels for H(div) bilinear forms, as well as
VectorFEDivergenceIntegrator.
- Improved the documentation of the GridFunction GetValue and GetVectorValue
methods. Expanded the GetValue and GetVectorValue methods which accept an
ElementTransformation argument to support evaluation on boundary elements
and, in the continuous field case, arbitrary mesh edges and faces.
- Added new coefficient and vector coefficient classes for QuadratureFunctions.
Additionaly, new LinearForm integrators were also added which make use of
these new QuadratureFunction coefficient classes.
Linear and nonlinear solvers
----------------------------
- Added power method to iteratively estimate the largest eigenvalue and the
corresponding eigenvector of an operator.
- Added initial support for h- and p-multigrid solvers and preconditioners for
matrix-based and matrix-free discretizations with basic GPU capability.
- Added a new IterativeSolverMonitor class that allows to monitor the residual
and solution during the solving process of an IterativeSolver after every
iteration.
- Block arrays of parallel matrices can now be merged into a single parallel
matrix with the function HypreParMatrixFromBlocks. This could be useful for
solving block systems with parallel direct solvers such as STRUMPACK.
- In SLISolver, changed the residual inner product from (Br,r) to (Br,Br) so the
solver can work with non-SPD preconditioner B.
New and updated examples and miniapps
-------------------------------------
- Added a new example, Example 25/25p, to demonstrate the use of a Perfectly
Matched Layer (PML) for the simulation of electromagnetic wave propagation.
The example defines and solves several indefinite Maxwell problems.
- Added a new Example 26/26p to demonstrate the construction of a matrix-free
geometric and p-multigrid preconditioner for the Laplace problem.
- Added a new example, Example 27/27p, to demonstrate the enforcement of
various boundary conditions with the Laplace operator. The example shows the
procedures for applying Dirichlet, Neumann (both homogeneous and
inhomogeneous), Robin, and periodic boundary conditions with either H1 or DG
discretizations.
- Added a simple meshing miniapp, Twist, which demonstrates MFEM's strategy of
stitching together opposite surfaces of a mesh to create a topologically
periodic mesh.
- Added a new meshing miniapp, Minimal Surface, which solves Plateau's problem:
the Dirichlet problem for the minimal surface equation.
- Added partial assembly support to examples 4/4p and 5/5p, with diagonal
preconditioning.
- Added a new test problem in example 24/24p, demonstrating a mixed bilinear
form for H(div) and L_2, with partial assembly support.
Improved testing
----------------
- Added a GitLab pipeline that automates PR testing on supercomputing systems
and Linux clusters at Lawrence Livermore National Lab (LLNL). This can be
triggered only by LLNL developers, see .gitlab-ci.yml, the .gitlab directory
and the updated CONTRIBUTING.md file.
Miscellaneous
-------------
- Added support for ADIOS2 for parallel I/O with ParaView visualization. The
classes adios2stream and ADIOS2DataCollection are introduced in mfem as the
interfaces to generate ADIOS2 Binary Pack (BP4) directory datasets for the
entire spatial and temporal data. In addition, ADIOS2 allows for setting a
user-defined number of data substreams/subfiles. See examples 5, 9, 12, 16.
- The integration order used in the ComputeLpError and ComputeElementLpError
methods of class GridFunction has been increased.
- Various other simplifications, extensions, and bugfixes in the code.
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 <PREFIX>/include/mfem;
the master headers are installed in both <PREFIX>/include/mfem and in
<PREFIX>/include. The mfem configuration and testing makefiles (config.mk and
test.mk) are installed in <PREFIX>/share/mfem, instead of <PREFIX>.
- 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<Geometry::Type>.
- 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 <np>' 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.
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