petsc-3.14.5 2021-03-03
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# Documentation: Changes: 3.13

## CHANGES in the PETSc 3.13 Version

#### General:

- Update `make test` to run the full test suite. Use `make check` to run the short test
- Remove last PetscBool argument from PetscBinaryWrite() and PetscBinarySynchronizedWrite()
- Change PetscLayoutFindOwner() and PetscLayoutFindOwnerIndex() to return a PetscMPIInt instead of a PetscInt
- Support for Compaq F90 is removed along with supporting flags PETSC_HAVE_FORTRAN_STDCALL, PETSC_BLASLAPACK_STDCALL, HAVE_FORTRAN_MIXED_STR_ARG
- Promote all example directories `examples/tutorials/` and `examples/tests/` to `tutorials/` and `tests/` respectively
- Make title argument of PetscOptionsBegin() obligatory

#### Configure/Build:

#### IS:

- Add ISSetInfo(): set local and global properties of an IS (whether the IS is sorted, unique, a permutation, an interval, or identity)
- Add ISGetInfo(): query local and global properties of an IS

#### PetscDraw:

#### PetscSF:

- Fix few bugs in PETSCSFWINDOW when using PETSCSF_WINDOW_SYNC_LOCK or PETSCSF_WINDOW_SYNC_ACTIVE synchronization types
- Add window reusage for PETSCSFWINDOW and support for different creation flavor types. See PetscSFWindowFlavorType man page for details
- Set default of -use_gpu_aware_mpi from false to true

#### PF:

#### Vec:

- VecPinToCPU() is deprecated in favor of VecBindToCPU()
- Add Vec{Set|Get}PinnedMemoryMin() and -vec_pinned_memory_min option. Note that VECCUDA now defaults to using pinned memory for host allocations

#### VecScatter:

#### PetscSection:

#### PetscPartitioner:

- PetscPartitionerPartition() does not longer gets a DM as input. Vertex weights can be specified through PetscSection
- Add support for target partition weights for PETSCPARTITIONERSIMPLE, PETSCPARTITIONERPARMETIS and PETSCPARTITIONERPTSCOTCH

#### Mat:

- Improve the performance of MatConvert_AIJ_BAIJ by preallocating the Mat before dispatching to MatConvert_Basic
- Change the behavior of MatConvert_AIJ_SBAIJ for block size greater than one, the block structure is now preserved (even for the diagonal entries)
- Fix various bugs related with matrix conversions from Hermitian SBAIJ matrices with complex numbers
- Add MatPropagateSymmetryOptions to propagate symmetry information from one matrix to another
- Fix a bug in MATSUPERLU_DIST interface when MATMPIAIJ with commsize 1 is used
- Add MATCHOLMOD support for block solves
- --download-suitesparse now uses the official SuiteSparse repository
- MatPinToCPU() is deprecated in favor of MatBindToCPU()
- Fix MatAXPY for MATSHELL
- MatAXPY(Y,0.0,X,DIFFERENT_NONZERO_PATTERN) no longer modifies the nonzero pattern of Y to include that of X
- Add support of selective 64-bit MUMPS, i.e., the regular/default build of MUMPS. One should still build PETSc --with-64-bit-indices to handle matrices with >2G nonzeros
- Add MatProductCreate(), MatProductCreateWithMat(), MatProductSetType(), MatProductSetAlgorithm(), MatProductSetFill(), MatProductSetFromOptions(), MatProductSymbolic(), MatProductNumeric(), MatProductReplaceMats(), MatProductClear()
- Deprecate MatMatMultSymbolic(), MatMatMultNumeric()
- Deprecate MatMatTransposeMultSymbolic(), MatMatTransposeMultNumeric()
- Deprecate MatPtAPSymbolic(), MatPtAPNumeric()
- Deprecate MatRARtSymbolic(), MatRARtNumeric()
- Fix a deadlock with MATELEMENTAL; if one configures PETSc with Elemental and has PETSC_COMM_WORLD != MPI_COMM_WORLD, it is now one's responsability to explicitly call PetscElementalInitializePackage()/PetscElementalFinalizePackage() outside of PetscInitialize()/PetscFinalize(). PetscElementalInitializePackage()/PetscElementalFinalizePackage() are collective on MPI_COMM_WORLD.

#### PC:

- Change the default behavior of PCASM and PCGASM to not automatically switch to PCASMType BASIC if the matrices are symmetric
- Change the default behavior of PCCHOLESKY to use nested dissection ordering for AIJ matrix

#### KSP:

- Add KSPHPDDMGetDeflationSpace and KSPHPDDMSetDeflationSpace for recycling Krylov methods in KSPHPDDM

#### SNES:

- Deprecate `-snes_test_jacobian_display` and `-snes_test_jacobian_display_threshold`. `-snes_test_jacobian` accepts an optional threshold parameter (since v3.10) and `-snes_test_jacobian_view` should be used in favor of `-snes_test_jacobian_display`

#### SNESLineSearch:

- Add SNESLineSearchGetType() in v3.13.1.

#### TS:

#### TAO:

- TAOPDIPM: A new solver in TAO for general NLP problems

#### DM/DA:

- DMCopyLabels(): add two additional input flags
- DMPlexDistribute(): fix a bug associated with vertex partition weights and overlapped meshes
- DMPlexDistribute(): vertex partition weights are now computed by summing all the local section dofs in the transitive closure of each cell
- Add PetscTabulation to hold function tabulation data
- Add DMEnclosureType to describe relations between meshes
- Add DMGetEnclosureRelation() and DMGetEnclosurePoint() to discover relations between meshes
- Add DMPolytopeType to describe different cell constructions

#### DMPlex:

- DMPlexInterpolate() now works correctly for distributed DMPlex
- The idea of hybrid and ghost cells has been removed from Plex in favor of cell type
- Plex can now classify points by cell type, stored in a DMLabel. This is useful for operations that require more than topological data, such as mesh interpolation, geometric calculations, and is also used an index to avoid repeated topological queries
- Add DMPlexSetCellType() and DMPlexCreateReferenceCellByType()
- Distribution sorts strata by cell type.
- Plex can now allow any number of cell types in a single mesh. Interpolation, refinement, and extraction of submeshes mixed meshes work smoothly. Both oriented and tensor-product prisms can be used in the same mesh
- Cell refiners have been abstracted. Currently there are two (regular refinement, and conversion to hexes). The plan is to add more, such as local extrusion and conversion to simplices
- Remove SimplexToTensor in favor of DM_REFINER_TO_BOX
- DMForest now responds to DMPlexGetOverlap() and propagates its overlap to the underlying Plex
- Add DMPlexGetSimplexOrBoxCells() to replace DMPlexGetInteriorCellStratum()
- Add DMPolytopTypeGetDim(), DMPolyTopeTypeGetConeSize(), DMPolytopeTypeGetNumVertices()
- Add DMLabelSetStratumBounds()
- Add DMPlexOrientCell() which orients a single cell
- Add DMPlexCompareOrientations() which compares the cone point order of a single cell with the given reference cone
- Add DMPlexIsInterpolated() which finds out whether the plex is interpolated
- Add DMPlexIsInterpolatedCollective() which finds out whether the plex is interpolated on all ranks
- Add DMPlexIsDistributed() which finds out whether the plex is distributed

#### DMNetwork:

- Add DMNetworkSetComponentNumVariables(), DMNetworkGetComponentVariableOffset(), and DMNetworkGetComponentVariableGlobalOffset() to set number of variables for a component, and retrieve its local/global offsets.

#### DT:

- All tabulated data is now stored in PetscTabulation structures. This changes interfaces in PetscDS, PetscFE, and PetscFV
- Rename DefaultTabulation to CellTabulation everywhere
- PetscDTGaussJacobiQuadrature() is now truly Gauss-Jacobi quadrature. The quadrature for the simplex (without weight function) is now called PetscDTStroudConicalQuadrature()
- Add PetscDTJacobiEval(), PetscDTGaussLobattoJacobiQuadrature()
- Add PetscDTIndexToBary() and PetscDTBaryToIndex() for barycentric lattice calculations
- Add PetscDTNodeType to enumerate methods of defining interpolation nodes
- PetscDualSpace now has PetscDualSpaceSetFormDegree() and PetscDualSpaceGetFormDegree() for governing functional pushforward/pullback behavior
- PETSCDUALSPACELAGRANGE now has PetscDualSpaceGetTrimmed() and PetscDualSpaceSetTrimmed() for creating degrees of freedom for trimmed polynomial spaces
- PETSCDUALSPACELAGRANGE now has PetscDualSpaceGetNodeType() and PetscDualSpaceSetNodType() for controlling the placement of interpolation nodes
- PETSCDUALSPACEBDM is no longer a standalone type of PetscDualSpace: it is now a constructor alias for PETSCDUALSPACELAGRANGE

#### PetscViewer:

- Remove last PetscBool argument from PetscViewerBinaryWrite()
- Add "fieldnum" argument to PetscViewerVTKAddField() to indicate only one field of the vector should be viewed

#### SYS:

- Rename PetscSignalSegvCheckPointer() to PetscSignalSegvCheckPointerOrMpi()
- Extend -info option controlling PetscInfo(). It now takes takes optional arguments `-info [filename][:[~]list,of,classnames[:[~]self]]`. See PetscInfo() manpage
- Add new API to control PetscInfo() programatically:
  - Add PetscInfoEnabled() - Indicate whether a given PETSc class is allowed in PetscInfo()
  - Add PetscInfoSetFile() - Set output destination of PetscInfo()
  - Add PetscInfoGetFile() - Get output destination of PetscInfo()
  - Add PetscInfoSetClasses() - Sets the classes which PetscInfo() is filtered for/against
  - Add PetscInfoGetClass() - Indicates whether the provided classname is marked as a filter in PetscInfo() as set by PetscInfoSetClasses()
  - Add PetscInfoProcessClass() - Activates or deactivates a class based on the filtering status of PetscInfo()
  - Add PetscInfoGetInfo() - Returns the current state of several indicator flags for PetscInfo()
  - Add PetscInfoSetFilterCommSelf() - Sets PetscInfoCommFlag enum to control communicator size filtering for PetscInfo()
  - Add PetscInfoDestroy() - Destroys and resets internal PetscInfo() filter options
  - Change PetscInfoAllow() to only activate/deactivate PetscInfo(), file setting is now handled separately by PetscInfoSetFile()
- Add PetscSubcommGetParent() - Gets the communicator that was used to create the PetscSubcomm
- Add PetscSubcommGetContiguousParent() - Gets a communicator that that is a duplicate of the parent but has the ranks reordered by the order they are in the children
- Add PetscSubcommGetChild() - Gets the communicator created by the PetscSubcomm
- Change the default option of -build_twosided from ibarrier to allreduce for communicators with no more than 1024 ranks

#### AO:

#### Sieve:

#### Fortran: