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CHANGELOG
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Finite Element Discretization Library
__
_ __ ___ / _| ___ _ __ ___
| '_ ` _ \ | |_ / _ \| '_ ` _ \
| | | | | || _|| __/| | | | | |
|_| |_| |_||_| \___||_| |_| |_|
http://mfem.org
Version 3.4.1 (development)
===========================
Support for wedge elements and meshes with mixed element types
--------------------------------------------------------------
- Added support for wedge shaped mesh elements of arbitrary order (with Geometry
type PRISM) which have two triangular faces and three quadrilateral faces.
Several examples of such meshes can be found in the data/ directory.
- Added H1 and L2 finite elements of arbitrary order for Wedge elements.
- Added support for mixed meshes containing triangles and quadrilaterals in 2D
or tetrahedra, wedges, and hexahedra in 3D. This includes support for uniform
refinement of such meshes. Several examples of such meshes can be found in the
data/ directory.
- Added support for reading and writing linear and quadratic meshes containing
wedge elements in VTK mesh format. Several examples of such meshes can be
found in the data/ directory.
Other meshing improvements
--------------------------
- Improved the uniform refinement of tetrahedral meshes (also part of the
uniform refinement of mixed 3D meshes). The previous refinement algorithm is
still available as an option in Mesh::UniformRefinement. Both can be used in
the updated Mesh Explorer miniapp.
- The local tetrahedral mesh refinement algorithm in serial and in parallel now
follows precisely the paper:
D. Arnold, A. Mukherjee, and L. Pouly, "Locally Adapted Tetrahedral Meshes
Using Bisection", SIAM J. Sci. Comput. 22 (2000), 431–448.
This guarantees that the shape regularity of the elements will be preserved
under refinement.
- Added support for parallel communication groups on non-conforming meshes.
- 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.
- The TMOP mesh optimization algorithms were extended to support user-defined
space-dependent limiting terms. Improved the TMOP objective functions by
more accurate normalization of the different terms.
Discretization improvements
---------------------------
- Added support for 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 support for derefinement of vector (RT + ND) spaces.
- Added element flux, and flux energy computation in class ElasticityIntegrator,
allowing for the use of Zienkiewicz-Zhu type error estimators with the
integrator. For an illustration of this addition, see the new Example 22.
- Added a variety of coefficients which are sums or products of existing
coefficients as well as grid function coefficients which return the
divergence, gradient, or curl of their GridFunctions.
New and improved solvers and preconditioners
--------------------------------------------
- Added support for parallel ILU preconditioning via hypre's Euclid solver.
- Added support for STRUMPACK v3 with a small API change in the class
STRUMPACKSolver, see "API changes" below.
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 22/22p, that illustrates the use of AMR to solve
a linear elasticity problem. This is an extension of Example 2/2p.
Miscellaneous
-------------
- Added unit tests based on the Catch++ library.
- Altered the way FGMRES counts its iterations so that it matches GMRES.
- Various other simplifications, extensions, and bugfixes in the code.
API changes
-----------
- In multiple places, use Geometry::Type instead of int, where appropriate.
- In multiple places, use Element::Type instead of int, where appropriate.
- The Mesh methods GetElementBaseGeometry and GetBdrElementBaseGeometry no
longer have a default value for their parameter, they only work with an
explicitly given index.
- In class Mesh, added methods useful for queries regarding the types of
elements present in the mesh: HasGeometry, GetNumGeometries, GetGeometries,
and class Mesh::GeometryList.
- The struct CoarseFineTransformations (returned by the Mesh method
GetRefinementTransforms) now stores the embedding matrices separately for each
Geometry::Type.
- In class ParMesh, replaced the method GroupNFaces with two new methods:
GroupNTriangles and GroupNQuadrilaterals. Also, replaced GroupFace with two
methods: GroupTriangle and GroupQuadrilateral.
- In class ParMesh, made the two RefineGroups methods protected.
- Removed the virtual method Element::GetRefinementFlag, it is only used by the
derived class Tetrahedron.
- Added new methods: Array::CopyTo, Tetrahedron::Init.
- 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 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
-------------