PetscDMMoose.C File Reference

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Classes
struct	DM_Moose
struct	DM_Moose::SplitInfo

Functions
template<typename I1 , typename I2 >
void	checkSize (const std::string &split_name, const I1 split_size, const I2 size_expected_by_parent)
PetscErrorCode	DMMooseValidityCheck (DM dm)
PetscErrorCode	DMMooseGetContacts (DM dm, std::vector< std::pair< std::string, std::string > > &contact_names, std::vector< PetscBool > &displaced)
PetscErrorCode	DMMooseGetUnContacts (DM dm, std::vector< std::pair< std::string, std::string > > &uncontact_names, std::vector< PetscBool > &displaced)
PetscErrorCode	DMMooseGetSides (DM dm, std::vector< std::string > &side_names)
PetscErrorCode	DMMooseGetUnSides (DM dm, std::vector< std::string > &side_names)
PetscErrorCode	DMMooseGetBlocks (DM dm, std::vector< std::string > &block_names)
PetscErrorCode	DMMooseGetVariables (DM dm, std::vector< std::string > &var_names)
PetscErrorCode	DMMooseSetNonlinearSystem (DM dm, NonlinearSystemBase &nl)
PetscErrorCode	DMMooseSetDofMap (DM dm, const libMesh::DofMapBase &dof_map)
PetscErrorCode	DMMooseSetSystem (DM dm, const System &system)
PetscErrorCode	DMMooseSetName (DM dm, const std::string &dm_name)
PetscErrorCode	DMMooseSetParentDM (DM dm, DM_Moose *parent)
PetscErrorCode	DMMooseSetVariables (DM dm, const std::set< std::string > &vars)
PetscErrorCode	DMMooseSetBlocks (DM dm, const std::set< std::string > &blocks)
PetscErrorCode	DMMooseSetSides (DM dm, const std::set< std::string > &sides)
PetscErrorCode	DMMooseSetUnSides (DM dm, const std::set< std::string > &unsides)
PetscErrorCode	DMMooseSetUnSideByVar (DM dm, const std::set< std::string > &unside_by_var)
PetscErrorCode	DMMooseSetContacts (DM dm, const std::vector< std::pair< std::string, std::string > > &contacts, const std::vector< PetscBool > &displaced)
PetscErrorCode	DMMooseSetUnContacts (DM dm, const std::vector< std::pair< std::string, std::string > > &uncontacts, const std::vector< PetscBool > &displaced)
PetscErrorCode	DMMooseGetNonlinearSystem (DM dm, NonlinearSystemBase *&nl)
PetscErrorCode	DMMooseSetSplitNames (DM dm, const std::vector< std::string > &split_names)
PetscErrorCode	DMMooseGetSplitNames (DM dm, std::vector< std::string > &split_names)
static PetscErrorCode	DMMooseGetEmbedding_Private (DM dm, IS *embedding)
static PetscErrorCode	DMCreateFieldDecomposition_Moose (DM dm, PetscInt *len, char ***namelist, IS **islist, DM **dmlist)
static PetscErrorCode	DMCreateDomainDecomposition_Moose (DM dm, PetscInt *len, char ***namelist, IS **innerislist, IS **outerislist, DM **dmlist)
static PetscErrorCode	DMMooseFunction (DM dm, Vec x, Vec r)
static PetscErrorCode	SNESFunction_DMMoose (SNES, Vec x, Vec r, void *ctx)
static PetscErrorCode	DMMooseJacobian (DM dm, Vec x, Mat jac, Mat pc)
static PetscErrorCode	SNESJacobian_DMMoose (SNES, Vec x, Mat jac, Mat pc, void *ctx)
static PetscErrorCode	DMVariableBounds_Moose (DM dm, Vec xl, Vec xu)
static PetscErrorCode	DMCreateGlobalVector_Moose (DM dm, Vec *x)
static PetscErrorCode	DMCreateMatrix_Moose (DM dm, Mat *A)
static PetscErrorCode	DMView_Moose (DM dm, PetscViewer viewer)
static PetscErrorCode	DMMooseGetMeshBlocks_Private (DM dm, std::set< subdomain_id_type > &blocks)
static PetscErrorCode	DMSetUp_Moose_Pre (DM dm)
PetscErrorCode	DMMooseReset (DM dm)
static PetscErrorCode	DMSetUp_Moose (DM dm)
PetscErrorCode	DMSetFromOptions_Moose (DM dm, PetscOptionItems) PetscErrorCode DMSetFromOptions_Moose(DM dm
PetscErrorCode PetscOptionItems *PetscErrorCode	DMSetFromOptions_Moose (PetscOptionItems *, DM dm) PetscErrorCode DMSetFromOptions_Moose(PetscOptions *
	LibmeshPetscCallQ (DMMooseValidityCheck(dm))
	if (!dmm->_nl) SETERRQ(PETSC_COMM_WORLD
	PetscOptionsBegin (((PetscObject) dm) ->comm,((PetscObject) dm) ->prefix, "DMMoose options", "DM")
	LibmeshPetscCallQ (PetscOptionsBegin(((PetscObject) dm) ->comm,((PetscObject) dm) ->prefix, "DMMoose options", "DM"))
	LibmeshPetscCallQ (PetscMalloc(maxvars *sizeof(char *), &vars))
	LibmeshPetscCallQ (PetscOptionsStringArray(opt.c_str(), help.c_str(), "DMMooseSetVars", vars, &nvars, LIBMESH_PETSC_NULLPTR))
	for (PetscInt i=0;i< nvars;++i)
	LibmeshPetscCallQ (PetscFree(vars))
	if (varset.size()) LibmeshPetscCallQ(DMMooseSetVariables(dm
	LibmeshPetscCallQ (DMMooseGetMeshBlocks_Private(dm, meshblocks))
	LibmeshPetscCallQ (PetscMalloc(maxblocks *sizeof(char *), &blocks))
	LibmeshPetscCallQ (PetscOptionsStringArray(opt.c_str(), help.c_str(), "DMMooseSetBlocks", blocks, &nblocks, LIBMESH_PETSC_NULLPTR))
	LibmeshPetscCallQ (PetscFree(blocks))
	if (blockset.size()) LibmeshPetscCallQ(DMMooseSetBlocks(dm
	LibmeshPetscCallQ (PetscMalloc(maxsides *maxvars *sizeof(char *), &sides))
	LibmeshPetscCallQ (PetscOptionsStringArray(opt.c_str(), help.c_str(), "DMMooseSetSides", sides, &nsides, LIBMESH_PETSC_NULLPTR))
	if (sideset.size()) LibmeshPetscCallQ(DMMooseSetSides(dm
	LibmeshPetscCallQ (PetscOptionsStringArray(opt.c_str(), help.c_str(), "DMMooseSetUnSides", sides, &nsides, LIBMESH_PETSC_NULLPTR))
sideset	clear ()
	LibmeshPetscCallQ (PetscOptionsStringArray(opt.c_str(), help.c_str(), "DMMooseSetUnSideByVar", sides, &nsides, LIBMESH_PETSC_NULLPTR))
	LibmeshPetscCallQ (PetscFree(sides))
	if (displaced_problem)
	if (contacts.size()) LibmeshPetscCallQ(DMMooseSetContacts(dm
	LibmeshPetscCallQ (PetscOptionsInt(opt.c_str(), help.c_str(), "DMMooseSetUnContacts", nuncontacts, &nuncontacts, LIBMESH_PETSC_NULLPTR))
	if (LIBMESH_SETERRQ2(nuncontacts, maxcontacts)
	if (uncontacts.size()) LibmeshPetscCallQ(DMMooseSetUnContacts(dm
	LibmeshPetscCallQ (PetscOptionsInt("-dm_moose_nfieldsplits", fdhelp, "DMMooseSetSplitNames", nsplits, &nsplits, NULL))
	if (nsplits)
	LibmeshPetscCallQ (PetscOptionsBool("-dm_moose_print_embedding", "Print IS embedding DM's dofs", "DMMoose", dmm->_print_embedding, &dmm->_print_embedding, LIBMESH_PETSC_NULLPTR))
	PetscOptionsEnd ()
	LibmeshPetscCallQ (DMSetUp_Moose_Pre(dm))
	PetscFunctionReturn (PETSC_SUCCESS)
static PetscErrorCode	DMDestroy_Moose (DM dm)
PetscErrorCode	DMCreateMoose (MPI_Comm comm, NonlinearSystemBase &nl, const libMesh::DofMapBase &dof_map, const System &system, const std::string &dm_name, DM *dm)
EXTERN_C_BEGIN PetscErrorCode	DMCreate_Moose (DM dm)
PetscErrorCode	SNESUpdateDMMoose (SNES snes, PetscInt iteration)
PetscErrorCode	DMMooseRegisterAll ()

Variables
PetscErrorCode PetscOptionItems *PetscErrorCode DM	dm
	PetscFunctionBegin
	PETSC_ERR_ARG_WRONGSTATE
No Moose system set for	DM_Moose
std::string	opt = "-dm_moose_vars"
std::string	help = "Variables in DMMoose"
PetscInt	maxvars = dmm->_dof_map->n_variables()
char **	vars
std::set< std::string >	varset
PetscInt	nvars = maxvars
std::set< subdomain_id_type >	meshblocks
PetscInt	maxblocks = meshblocks.size()
char **	blocks
std::set< std::string >	blockset
PetscInt	nblocks = maxblocks
PetscInt	maxsides = dmm->_system->get_mesh().get_boundary_info().get_global_boundary_ids().size()
char **	sides
PetscInt	nsides = maxsides
std::set< std::string >	sideset
PetscInt	maxcontacts = dmm->_nl->feProblem().geomSearchData()._penetration_locators.size()
std::shared_ptr< DisplacedProblem >	displaced_problem = dmm->_nl->feProblem().getDisplacedProblem()
	contacts
	contact_displaced
PetscBool	is_include_all_nodes
oopt<< "-dm_moose_includeAllContactNodes";ohelp<< "Whether to include all nodes on the contact surfaces into the subsolver";LibmeshPetscCallQ(PetscOptionsBool(oopt.str().c_str(), ohelp.str().c_str(), "", PETSC_FALSE, &is_include_all_nodes, LIBMESH_PETSC_NULLPTR));dmm->	_include_all_contact_nodes = is_include_all_nodes
std::vector< DM_Moose::ContactName >	uncontacts
std::vector< PetscBool >	uncontact_displaced
PetscInt	nuncontacts = 0
PetscInt	nsplits = 0
const char *	fdhelp

Function Documentation

checkSize()

template<typename I1 , typename I2 >

void checkSize	(	const std::string &	split_name,
		const I1	split_size,
		const I2	size_expected_by_parent
	)

Definition at line 37 of file PetscDMMoose.C.

{
  if (libMesh::cast_int<libMesh::numeric_index_type>(split_size) !=
      libMesh::cast_int<libMesh::numeric_index_type>(size_expected_by_parent))
    mooseError("Split '",
               split_name,
               "' has size ",
               libMesh::cast_int<libMesh::numeric_index_type>(split_size),
               " but the parent split expected size ",
               libMesh::cast_int<libMesh::numeric_index_type>(size_expected_by_parent),
               ". Make sure that you have non-overlapping complete sets for variables and "
               "blocks as well as consistency in sides/unsides, contacts/uncontacts, etc.");
}

Referenced by DM_Moose::checkChildSize(), and DMCreateFieldDecomposition_Moose().

clear()

sideset clear

(

)

Referenced by MooseUtils::CircularBuffer< T >::erase(), MooseUtils::LIFOBuffer< T >::erase(), and SidesetInfoVectorPostprocessor::initialize().

DMCreate_Moose()

EXTERN_C_BEGIN PetscErrorCode DMCreate_Moose

(

DM

dm

)

Definition at line 2078 of file PetscDMMoose.C.

{
  DM_Moose * dmm;
 
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
#if PETSC_RELEASE_LESS_THAN(3, 18, 0)
  LibmeshPetscCallQ(PetscNewLog(dm, &dmm));
#else // PetscNewLog was deprecated
  LibmeshPetscCallQ(PetscNew(&dmm));
#endif
  dm->data = dmm;
 
  dmm->_name = new (std::string);
  dmm->_var_ids = new (std::map<std::string, unsigned int>);
  dmm->_block_ids = new (std::map<std::string, subdomain_id_type>);
  dmm->_var_names = new (std::map<unsigned int, std::string>);
  dmm->_block_names = new (std::map<unsigned int, std::string>);
  dmm->_side_ids = new (std::map<std::string, BoundaryID>);
  dmm->_side_names = new (std::map<BoundaryID, std::string>);
  dmm->_unside_ids = new (std::map<std::string, BoundaryID>);
  dmm->_unside_names = new (std::map<BoundaryID, std::string>);
  dmm->_unside_by_var_set = new (std::set<std::pair<BoundaryID, unsigned int>>);
  dmm->_contact_names = new (std::map<DM_Moose::ContactID, DM_Moose::ContactName>);
  dmm->_uncontact_names = new (std::map<DM_Moose::ContactID, DM_Moose::ContactName>);
  dmm->_contact_displaced = new (std::map<DM_Moose::ContactName, PetscBool>);
  dmm->_uncontact_displaced = new (std::map<DM_Moose::ContactName, PetscBool>);
 
  dmm->_splits = new (std::map<std::string, DM_Moose::SplitInfo>);
 
  dmm->_print_embedding = PETSC_FALSE;
 
  dm->ops->createglobalvector = DMCreateGlobalVector_Moose;
  dm->ops->createlocalvector = 0; // DMCreateLocalVector_Moose;
  dm->ops->getcoloring = 0;       // DMGetColoring_Moose;
  dm->ops->creatematrix = DMCreateMatrix_Moose;
  dm->ops->createinterpolation = 0; // DMCreateInterpolation_Moose;
 
  dm->ops->refine = 0;  // DMRefine_Moose;
  dm->ops->coarsen = 0; // DMCoarsen_Moose;
#if PETSC_RELEASE_LESS_THAN(3, 12, 0)
  dm->ops->getinjection = 0;  // DMGetInjection_Moose;
  dm->ops->getaggregates = 0; // DMGetAggregates_Moose;
#else
  dm->ops->createinjection = 0;
#endif
 
  dm->ops->createfielddecomposition = DMCreateFieldDecomposition_Moose;
  dm->ops->createdomaindecomposition = DMCreateDomainDecomposition_Moose;
 
  dm->ops->destroy = DMDestroy_Moose;
  dm->ops->view = DMView_Moose;
  dm->ops->setfromoptions = DMSetFromOptions_Moose;
  dm->ops->setup = DMSetUp_Moose;
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMMooseRegisterAll().

DMCreateDomainDecomposition_Moose()

static PetscErrorCode DMCreateDomainDecomposition_Moose ( DM  dm, PetscInt *  len, char ***  namelist, IS **  innerislist, IS **  outerislist, DM **  dmlist  )

static

Definition at line 958 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  /* Use DMCreateFieldDecomposition_Moose() to obtain everything but outerislist, which is currently
   * LIBMESH_PETSC_NULLPTR. */
  if (outerislist)
    *outerislist = LIBMESH_PETSC_NULLPTR; /* FIX: allow mesh-based overlap. */
  LibmeshPetscCallQ(DMCreateFieldDecomposition_Moose(dm, len, namelist, innerislist, dmlist));
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreate_Moose().

DMCreateFieldDecomposition_Moose()

static PetscErrorCode DMCreateFieldDecomposition_Moose ( DM  dm, PetscInt *  len, char ***  namelist, IS **  islist, DM **  dmlist  )

static

Definition at line 847 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)(dm->data);
 
  PetscFunctionBegin;
 
  PetscInt split_size_sum = 0;
 
  /* Only called after DMSetUp(). */
  if (!dmm->_splitlocs)
    PetscFunctionReturn(PETSC_SUCCESS);
  *len = dmm->_splitlocs->size();
  if (namelist)
    LibmeshPetscCallQ(PetscMalloc(*len * sizeof(char *), namelist));
  if (islist)
    LibmeshPetscCallQ(PetscMalloc(*len * sizeof(IS), islist));
  if (dmlist)
    LibmeshPetscCallQ(PetscMalloc(*len * sizeof(DM), dmlist));
  for (const auto & dit : *(dmm->_splitlocs))
  {
    unsigned int d = dit.second;
    std::string dname = dit.first;
    DM_Moose::SplitInfo & dinfo = (*dmm->_splits)[dname];
    if (!dinfo._dm)
    {
      LibmeshPetscCallQ(DMCreateMoose(
          ((PetscObject)dm)->comm, *dmm->_nl, *dmm->_dof_map, *dmm->_system, dname, &dinfo._dm));
      LibmeshPetscCallQ(
          PetscObjectSetOptionsPrefix((PetscObject)dinfo._dm, ((PetscObject)dm)->prefix));
      std::string suffix = std::string("fieldsplit_") + dname + "_";
      LibmeshPetscCallQ(PetscObjectAppendOptionsPrefix((PetscObject)dinfo._dm, suffix.c_str()));
      LibmeshPetscCallQ(DMMooseSetParentDM(dinfo._dm, dmm));
    }
    LibmeshPetscCallQ(DMSetFromOptions(dinfo._dm));
    LibmeshPetscCallQ(DMSetUp(dinfo._dm));
    if (namelist)
      LibmeshPetscCallQ(PetscStrallocpy(dname.c_str(), (*namelist) + d));
    if (islist)
    {
      if (!dinfo._rembedding)
      {
        IS dembedding, lembedding;
        LibmeshPetscCallQ(DMMooseGetEmbedding_Private(dinfo._dm, &dembedding));
        if (dmm->_embedding)
        {
          // Create a relative embedding into the parent's index space.
          LibmeshPetscCallQ(ISEmbed(dembedding, dmm->_embedding, PETSC_TRUE, &lembedding));
          const PetscInt * lindices;
          PetscInt len, dlen, llen, *rindices, off, i;
          LibmeshPetscCallQ(ISGetLocalSize(dembedding, &dlen));
          LibmeshPetscCallQ(ISGetLocalSize(lembedding, &llen));
          if (llen != dlen)
            LIBMESH_SETERRQ1(
                ((PetscObject)dm)->comm, PETSC_ERR_PLIB, "Failed to embed split %u", d);
          LibmeshPetscCallQ(ISDestroy(&dembedding));
          // Convert local embedding to global (but still relative) embedding
          LibmeshPetscCallQ(PetscMalloc(llen * sizeof(PetscInt), &rindices));
          LibmeshPetscCallQ(ISGetIndices(lembedding, &lindices));
          LibmeshPetscCallQ(PetscMemcpy(rindices, lindices, llen * sizeof(PetscInt)));
          LibmeshPetscCallQ(ISDestroy(&lembedding));
          // We could get the index offset from a corresponding global vector, but subDMs don't yet
          // have global vectors
          LibmeshPetscCallQ(ISGetLocalSize(dmm->_embedding, &len));
 
          MPI_Scan(&len,
                   &off,
                   1,
#ifdef PETSC_USE_64BIT_INDICES
                   MPI_LONG_LONG_INT,
#else
                   MPI_INT,
#endif
                   MPI_SUM,
                   ((PetscObject)dm)->comm);
 
          off -= len;
          for (i = 0; i < llen; ++i)
            rindices[i] += off;
          LibmeshPetscCallQ(ISCreateGeneral(
              ((PetscObject)dm)->comm, llen, rindices, PETSC_OWN_POINTER, &(dinfo._rembedding)));
        }
        else
        {
          dinfo._rembedding = dembedding;
        }
      }
      LibmeshPetscCallQ(PetscObjectReference((PetscObject)(dinfo._rembedding)));
      (*islist)[d] = dinfo._rembedding;
      PetscInt is_size;
      LibmeshPetscCallQ(ISGetLocalSize(dinfo._rembedding, &is_size));
      split_size_sum += is_size;
    }
    if (dmlist)
    {
      LibmeshPetscCallQ(PetscObjectReference((PetscObject)dinfo._dm));
      (*dmlist)[d] = dinfo._dm;
    }
  }
 
  mooseAssert(islist, "What does it even mean if this is NULL?");
 
  if (dmm->_parent)
    dmm->_parent->checkChildSize(dm, split_size_sum, *dmm->_name);
  else
    checkSize(*dmm->_name, split_size_sum, dmm->_dof_map->n_local_dofs());
 
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreate_Moose(), and DMCreateDomainDecomposition_Moose().

DMCreateGlobalVector_Moose()

static PetscErrorCode DMCreateGlobalVector_Moose ( DM  dm, Vec *  x  )

static

Definition at line 1163 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)(dm->data);
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (!dmm->_nl)
    SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE, "No Moose system set for DM_Moose");
 
  NumericVector<Number> * nv = (dmm->_system->solution).get();
  PetscVector<Number> * pv = dynamic_cast<PetscVector<Number> *>(nv);
  Vec v = pv->vec();
  /* Unfortunately, currently this does not produce a ghosted vector, so nonlinear subproblem solves
   aren't going to be easily available.
   Should work fine for getting vectors out for linear subproblem solvers. */
  if (dmm->_embedding)
  {
    PetscInt n;
    LibmeshPetscCallQ(VecCreate(((PetscObject)v)->comm, x));
    LibmeshPetscCallQ(ISGetLocalSize(dmm->_embedding, &n));
    LibmeshPetscCallQ(VecSetSizes(*x, n, PETSC_DETERMINE));
    LibmeshPetscCallQ(VecSetType(*x, ((PetscObject)v)->type_name));
    LibmeshPetscCallQ(VecSetFromOptions(*x));
    LibmeshPetscCallQ(VecSetUp(*x));
  }
  else
    LibmeshPetscCallQ(VecDuplicate(v, x));
 
#if PETSC_RELEASE_LESS_THAN(3, 13, 0)
  LibmeshPetscCallQ(PetscObjectCompose((PetscObject)*x, "DM", (PetscObject)dm));
#else
  LibmeshPetscCallQ(VecSetDM(*x, dm));
#endif
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreate_Moose().

DMCreateMatrix_Moose()

static PetscErrorCode DMCreateMatrix_Moose ( DM  dm, Mat *  A  )

static

Definition at line 1200 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)(dm->data);
  MatType type;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (!dmm->_nl)
    SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE, "No Moose system set for DM_Moose");
  LibmeshPetscCallQ(DMGetMatType(dm, &type));
 
  /*
   The simplest thing for now: compute the sparsity_pattern using dof_map and init the matrix using
   that info.
   TODO: compute sparsity restricted to this DM's blocks, variables and sides.
   Even fancier: compute the sparsity of the coupling of a contact secondary to the contact primary.
   In any event, here we are in control of the matrix type and structure.
   */
  const auto & dof_map = *dmm->_dof_map;
  PetscInt M, N, m, n;
  MPI_Comm comm;
  M = dof_map.n_dofs();
  N = M;
  m = static_cast<PetscInt>(dof_map.n_local_dofs());
  n = m;
  LibmeshPetscCallQ(PetscObjectGetComm((PetscObject)dm, &comm));
  LibmeshPetscCallQ(MatCreate(comm, A));
  LibmeshPetscCallQ(MatSetSizes(*A, m, n, M, N));
  LibmeshPetscCallQ(MatSetType(*A, type));
  /* TODO: set the prefix for *A and MatSetFromOptions(*A)? Might override the type and other
   * settings made here. */
  LibmeshPetscCallQ(MatSetUp(*A));
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreate_Moose().

DMCreateMoose()

PetscErrorCode DMCreateMoose	(	MPI_Comm	comm,
		NonlinearSystemBase &	nl,
		const libMesh::DofMapBase &	dof_map,
		const System &	system,
		const std::string &	dm_name,
		DM *	dm
	)

Definition at line 2059 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMCreate(comm, dm));
  LibmeshPetscCallQ(DMSetType(*dm, DMMOOSE));
  LibmeshPetscCallQ(DMMooseSetNonlinearSystem(*dm, nl));
  LibmeshPetscCallQ(DMMooseSetDofMap(*dm, dof_map));
  LibmeshPetscCallQ(DMMooseSetSystem(*dm, system));
  LibmeshPetscCallQ(DMMooseSetName(*dm, dm_name));
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreateFieldDecomposition_Moose().

DMDestroy_Moose()

static PetscErrorCode DMDestroy_Moose ( DM  dm )

static

Definition at line 2009 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)(dm->data);
 
  PetscFunctionBegin;
  delete dmm->_name;
  if (dmm->_vars)
    delete dmm->_vars;
  delete dmm->_var_ids;
  delete dmm->_var_names;
  if (dmm->_blocks)
    delete dmm->_blocks;
  delete dmm->_block_ids;
  delete dmm->_block_names;
  if (dmm->_sides)
    delete dmm->_sides;
  delete dmm->_side_ids;
  delete dmm->_side_names;
  if (dmm->_unsides)
    delete dmm->_unsides;
  delete dmm->_unside_ids;
  delete dmm->_unside_names;
  if (dmm->_unside_by_var)
    delete dmm->_unside_by_var;
  delete dmm->_unside_by_var_set;
  if (dmm->_contacts)
    delete dmm->_contacts;
  delete dmm->_contact_names;
  delete dmm->_contact_displaced;
  if (dmm->_uncontacts)
    delete dmm->_uncontacts;
  delete dmm->_uncontact_names;
  delete dmm->_uncontact_displaced;
  if (dmm->_splits)
  {
    for (auto & sit : *(dmm->_splits))
    {
      LibmeshPetscCallQ(DMDestroy(&(sit.second._dm)));
      LibmeshPetscCallQ(ISDestroy(&(sit.second._rembedding)));
    }
    delete dmm->_splits;
  }
  if (dmm->_splitlocs)
    delete dmm->_splitlocs;
  LibmeshPetscCallQ(ISDestroy(&dmm->_embedding));
  LibmeshPetscCallQ(PetscFree(dm->data));
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreate_Moose().

DMMooseFunction()

static PetscErrorCode DMMooseFunction ( DM  dm, Vec  x, Vec  r  )

static

Definition at line 971 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  libmesh_assert(x);
  libmesh_assert(r);
 
  NonlinearSystemBase * nl = NULL;
  LibmeshPetscCallQ(DMMooseGetNonlinearSystem(dm, nl));
  PetscVector<Number> & X_sys = *cast_ptr<PetscVector<Number> *>(nl->system().solution.get());
  PetscVector<Number> X_global(x, nl->comm()), R(r, nl->comm());
 
  // Use the system's update() to get a good local version of the
  // parallel solution.  system.update() does change the residual vector,
  // so there's no reason to swap PETSc's residual into the system for
  // this step.
  X_global.swap(X_sys);
  nl->system().update();
  X_global.swap(X_sys);
 
  // Enforce constraints (if any) exactly on the
  // current_local_solution.  This is the solution vector that is
  // actually used in the computation of the residual below, and is
  // not locked by debug-enabled PETSc the way that "x" is.
  nl->system().get_dof_map().enforce_constraints_exactly(nl->system(),
                                                         nl->system().current_local_solution.get());
 
  // Zero the residual vector before assembling
  R.zero();
 
  // if the user has provided both function pointers and objects only the pointer
  // will be used, so catch that as an error
  if (nl->nonlinearSolver()->residual && nl->nonlinearSolver()->residual_object)
  {
    std::ostringstream err;
    err << "ERROR: cannot specifiy both a function and object to compute the Residual!"
        << std::endl;
    mooseError(err.str());
  }
  if (nl->nonlinearSolver()->matvec && nl->nonlinearSolver()->residual_and_jacobian_object)
  {
    std::ostringstream err;
    err << "ERROR: cannot specifiy both a function and object to compute the combined Residual & "
           "Jacobian!"
        << std::endl;
    mooseError(err.str());
  }
  if (nl->nonlinearSolver()->residual != NULL)
    nl->nonlinearSolver()->residual(
        *(nl->system().current_local_solution.get()), R, nl->nonlinearSolver()->system());
  else if (nl->nonlinearSolver()->residual_object != NULL)
    nl->nonlinearSolver()->residual_object->residual(
        *(nl->system().current_local_solution.get()), R, nl->nonlinearSolver()->system());
  else if (nl->nonlinearSolver()->matvec != NULL)
    nl->nonlinearSolver()->matvec(
        *(nl->system().current_local_solution.get()), &R, NULL, nl->nonlinearSolver()->system());
  else if (nl->nonlinearSolver()->residual_and_jacobian_object != NULL)
    nl->nonlinearSolver()->residual_and_jacobian_object->residual_and_jacobian(
        *(nl->system().current_local_solution.get()), &R, NULL, nl->nonlinearSolver()->system());
  else
  {
    std::ostringstream err;
    err << "No suitable residual computation routine found";
    mooseError(err.str());
  }
  R.close();
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by SNESFunction_DMMoose().

DMMooseGetBlocks()

PetscErrorCode DMMooseGetBlocks	(	DM	dm,
		std::vector< std::string > &	block_names
	)

Definition at line 201 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  DM_Moose * dmm = (DM_Moose *)dm->data;
  for (const auto & it : *(dmm->_block_ids))
    block_names.push_back(it.first);
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseGetContacts()

PetscErrorCode DMMooseGetContacts	(	DM	dm,
		std::vector< std::pair< std::string, std::string > > &	contact_names,
		std::vector< PetscBool > &	displaced
	)

Definition at line 147 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  DM_Moose * dmm = (DM_Moose *)dm->data;
  for (const auto & it : *(dmm->_contact_names))
  {
    contact_names.push_back(it.second);
    displaced.push_back((*dmm->_contact_displaced)[it.second]);
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseGetEmbedding_Private()

static PetscErrorCode DMMooseGetEmbedding_Private ( DM  dm, IS *  embedding  )

static

Definition at line 510 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)dm->data;
 
  PetscFunctionBegin;
  if (!embedding)
    PetscFunctionReturn(PETSC_SUCCESS);
  if (!dmm->_embedding)
  {
    // The rules interpreting the coexistence of blocks (un)sides/(un)contacts are these
    // [sides and contacts behave similarly, so 'sides' means 'sides/contacts']
    // ['ANY' means 'not NONE' and covers 'ALL' as well, unless there is a specific 'ALL' clause,
    // which overrides 'ANY'; 'NOT ALL' means not ALL and not NONE]
    // [there are always some blocks, since by default 'ALL' is assumed, unless it is overridden by
    // a specific list, which implies ANY]
    // In general,
    // (1)  ALL blocks      and ANY sides are interpreted as the INTERSECTION of blocks and sides,
    // equivalent to just the sides (since ALL blocks are assumed to be a cover).
    // (2)  NOT ALL blocks  and ANY or NO sides are interpreted as the UNION of blocks and sides.
    // (3a) ANY unsides and ANY blocks are interpreted as the DIFFERENCE of blocks and unsides.
    // (3b) ANY unsides and ANY sides are interpreted as the DIFFERENCE of sides and unsides.
    // (4)  NO  unsides means NO DIFFERENCE is needed.
    // The result is easily computed by first computing the result of (1 & 2) followed by difference
    // with the result of (3 & 4).
    // To simply (1 & 2) observe the following:
    // - The intersection is computed only if ALL blocks and ANY sides, and the result is the sides,
    // so block dofs do not need to be computed.
    // - Otherwise the union is computed, and initially consists of the blocks' dofs, to which the
    // sides' dofs are added, if ANY.
    // - The result is called 'indices'
    // To satisfy (3 & 4) simply cmpute subtrahend set 'unindices' as all of the unsides' dofs:
    // Then take the set difference of 'indices' and 'unindices', putting the result in 'dindices'.
    if (!dmm->_all_vars || !dmm->_all_blocks || !dmm->_nosides || !dmm->_nounsides ||
        !dmm->_nounside_by_var || !dmm->_nocontacts || !dmm->_nouncontacts)
    {
      auto & dofmap = *dmm->_dof_map;
      // Put this outside the lambda scope to avoid constant memory reallocation
      std::vector<dof_id_type> node_indices;
      auto process_nodal_dof_indices =
          [&dofmap, &node_indices](const Node & node,
                                   const unsigned int var_num,
                                   std::set<dof_id_type> & local_indices,
                                   std::set<dof_id_type> * const nonlocal_indices = nullptr)
      {
        dofmap.dof_indices(&node, node_indices, var_num);
        for (const auto index : node_indices)
        {
          if (index >= dofmap.first_dof() && index < dofmap.end_dof())
            local_indices.insert(index);
          else if (nonlocal_indices)
            nonlocal_indices->insert(index);
        }
      };
 
      auto process_elem_dof_indices =
          [&dofmap](const std::vector<dof_id_type> & elem_indices,
                    std::set<dof_id_type> & local_indices,
                    std::set<dof_id_type> * const nonlocal_indices = nullptr)
      {
        for (const auto index : elem_indices)
        {
          if (index >= dofmap.first_dof() && index < dofmap.end_dof())
            local_indices.insert(index);
          else if (nonlocal_indices)
            nonlocal_indices->insert(index);
        }
      };
 
      std::set<dof_id_type> indices;
      std::set<dof_id_type> unindices;
      std::set<dof_id_type> cached_indices;
      std::set<dof_id_type> cached_unindices;
      auto & lm_mesh = dmm->_system->get_mesh();
      const auto & node_to_elem_map = dmm->_nl->feProblem().mesh().nodeToElemMap();
      for (const auto & vit : *(dmm->_var_ids))
      {
        unsigned int v = vit.second;
        // Iterate only over this DM's blocks.
        if (!dmm->_all_blocks || (dmm->_nosides && dmm->_nocontacts))
          for (const auto & bit : *(dmm->_block_ids))
          {
            subdomain_id_type b = bit.second;
            for (const auto & elem : as_range(lm_mesh.active_local_subdomain_elements_begin(b),
                                              lm_mesh.active_local_subdomain_elements_end(b)))
            {
              // Get the degree of freedom indices for the given variable off the current element.
              std::vector<dof_id_type> evindices;
              dofmap.dof_indices(elem, evindices, v);
              process_elem_dof_indices(evindices, indices);
            }
 
            // Sometime, we own nodes but do not own the elements the nodes are connected to
            {
              bool is_on_current_block = false;
              for (auto & node : lm_mesh.local_node_ptr_range())
              {
                const unsigned int n_comp = node->n_comp(dmm->_system->number(), v);
 
                // skip it if no dof
                if (!n_comp)
                  continue;
 
                auto node_to_elem_pair = node_to_elem_map.find(node->id());
                is_on_current_block = false;
                for (const auto & elem_num : node_to_elem_pair->second)
                {
                  // if one of incident elements belongs to a block, we consider
                  // the node lives in the block
                  const Elem & neighbor_elem = lm_mesh.elem_ref(elem_num);
                  if (neighbor_elem.subdomain_id() == b)
                  {
                    is_on_current_block = true;
                    break;
                  }
                }
                // we add indices for the current block only
                if (!is_on_current_block)
                  continue;
 
                process_nodal_dof_indices(*node, v, indices);
              }
            }
          }
 
        // Iterate over the sides from this split.
        if (dmm->_side_ids->size())
        {
          // For some reason the following may return an empty node list
          // std::vector<dof_id_type> snodes;
          // std::vector<boundary_id_type> sides;
          // dmm->nl->system().get_mesh().get_boundary_info().build_node_list(snodes, sides);
          // // FIXME: make an array of (snode,side) pairs, sort on side and use std::lower_bound
          // from <algorithm>
          // for (dof_id_type i = 0; i < sides.size(); ++i) {
          //   boundary_id_type s = sides[i];
          //   if (!dmm->sidenames->count(s)) continue;
          //  const Node& node = dmm->nl->system().get_mesh().node_ref(snodes[i]);
          //  // determine v's dof on node and insert into indices
          // }
          ConstBndNodeRange & bnodes = *dmm->_nl->mesh().getBoundaryNodeRange();
          for (const auto & bnode : bnodes)
          {
            BoundaryID boundary_id = bnode->_bnd_id;
            if (dmm->_side_names->find(boundary_id) == dmm->_side_names->end())
              continue;
 
            const Node * node = bnode->_node;
            process_nodal_dof_indices(*node, v, indices);
          }
        }
 
        // Iterate over the sides excluded from this split.
        if (dmm->_unside_ids->size())
        {
          ConstBndNodeRange & bnodes = *dmm->_nl->mesh().getBoundaryNodeRange();
          for (const auto & bnode : bnodes)
          {
            BoundaryID boundary_id = bnode->_bnd_id;
            if (dmm->_unside_names->find(boundary_id) == dmm->_unside_names->end())
              continue;
            const Node * node = bnode->_node;
            process_nodal_dof_indices(*node, v, unindices);
          }
        }
        if (dmm->_unside_by_var_set->size())
        {
          std::set<BoundaryID> eligible_bids;
          for (const auto & [bid, var] : *(dmm->_unside_by_var_set))
            if (var == v)
              eligible_bids.insert(bid);
 
          ConstBndNodeRange & bnodes = *dmm->_nl->mesh().getBoundaryNodeRange();
          for (const auto & bnode : bnodes)
          {
            BoundaryID boundary_id = bnode->_bnd_id;
            if (eligible_bids.count(boundary_id))
            {
              const Node * node = bnode->_node;
              process_nodal_dof_indices(*node, v, unindices);
            }
          }
        }
 
        auto process_contact_all_nodes =
            [dmm, process_nodal_dof_indices, v](const auto & contact_names,
                                                auto & indices_to_insert_to)
        {
          std::set<boundary_id_type> bc_id_set;
          // loop over contacts
          for (const auto & [contact_bid_pair, contact_bname_pair] : contact_names)
          {
            libmesh_ignore(contact_bname_pair);
            bc_id_set.insert(contact_bid_pair.first);  // primary
            bc_id_set.insert(contact_bid_pair.second); // secondary
          }
          // loop over boundary elements
          ConstBndElemRange & range = *dmm->_nl->feProblem().mesh().getBoundaryElementRange();
          for (const auto & belem : range)
          {
            const Elem * elem_bdry = belem->_elem;
            const auto side = belem->_side;
            BoundaryID boundary_id = belem->_bnd_id;
 
            if (bc_id_set.find(boundary_id) == bc_id_set.end())
              continue;
 
            for (const auto node_idx : elem_bdry->node_index_range())
              if (elem_bdry->is_node_on_side(node_idx, side))
                process_nodal_dof_indices(elem_bdry->node_ref(node_idx), v, indices_to_insert_to);
          }
        };
 
        auto process_contact_some_nodes =
            [dmm, process_nodal_dof_indices, v, &dofmap, &lm_mesh, process_elem_dof_indices](
                const auto & contact_names,
                auto & indices_to_insert_to,
                auto & nonlocal_indices_to_insert_to)
        {
          std::vector<dof_id_type> evindices;
          for (const auto & it : contact_names)
          {
            PetscBool displaced = (*dmm->_uncontact_displaced)[it.second];
            PenetrationLocator * locator;
            if (displaced)
            {
              std::shared_ptr<DisplacedProblem> displaced_problem =
                  dmm->_nl->feProblem().getDisplacedProblem();
              if (!displaced_problem)
              {
                std::ostringstream err;
                err << "Cannot use a displaced uncontact (" << it.second.first << ","
                    << it.second.second << ") with an undisplaced problem";
                mooseError(err.str());
              }
              locator = displaced_problem->geomSearchData()._penetration_locators[it.first];
            }
            else
              locator = dmm->_nl->feProblem().geomSearchData()._penetration_locators[it.first];
 
            evindices.clear();
            // penetration locator
            auto lend = locator->_penetration_info.end();
            for (auto lit = locator->_penetration_info.begin(); lit != lend; ++lit)
            {
              const dof_id_type secondary_node_num = lit->first;
              PenetrationInfo * pinfo = lit->second;
              if (pinfo && pinfo->isCaptured())
              {
                const Node & secondary_node = lm_mesh.node_ref(secondary_node_num);
                process_nodal_dof_indices(
                    secondary_node, v, indices_to_insert_to, &nonlocal_indices_to_insert_to);
 
                // indices for primary element
                evindices.clear();
                const Elem * primary_side = pinfo->_side;
                dofmap.dof_indices(primary_side, evindices, v);
                process_elem_dof_indices(
                    evindices, indices_to_insert_to, &nonlocal_indices_to_insert_to);
              } // if pinfo
            } // for penetration
          } // for contact name
        };
 
        // Include all nodes on the contact surfaces
        if (dmm->_contact_names->size() && dmm->_include_all_contact_nodes)
          process_contact_all_nodes(*dmm->_contact_names, indices);
 
        // Iterate over the contacts included in this split.
        if (dmm->_contact_names->size() && !(dmm->_include_all_contact_nodes))
          process_contact_some_nodes(*dmm->_contact_names, indices, cached_indices);
 
        // Exclude all nodes on the contact surfaces
        if (dmm->_uncontact_names->size() && dmm->_include_all_contact_nodes)
          process_contact_all_nodes(*dmm->_uncontact_names, unindices);
 
        // Iterate over the contacts excluded from this split.
        if (dmm->_uncontact_names->size() && !(dmm->_include_all_contact_nodes))
          process_contact_some_nodes(*dmm->_uncontact_names, unindices, cached_unindices);
      } // variables
 
      std::vector<dof_id_type> local_vec_indices(cached_indices.size());
      std::copy(cached_indices.begin(), cached_indices.end(), local_vec_indices.begin());
      if (dmm->_contact_names->size() && !(dmm->_include_all_contact_nodes))
        dmm->_nl->feProblem().mesh().comm().allgather(local_vec_indices, false);
      // insert indices
      for (const auto & dof : local_vec_indices)
        if (dof >= dofmap.first_dof() && dof < dofmap.end_dof())
          indices.insert(dof);
 
      local_vec_indices.clear();
      local_vec_indices.resize(cached_unindices.size());
      std::copy(cached_unindices.begin(), cached_unindices.end(), local_vec_indices.begin());
      if (dmm->_uncontact_names->size() && !(dmm->_include_all_contact_nodes))
        dmm->_nl->feProblem().mesh().comm().allgather(local_vec_indices, false);
      // insert unindices
      for (const auto & dof : local_vec_indices)
        if (dof >= dofmap.first_dof() && dof < dofmap.end_dof())
          unindices.insert(dof);
 
      std::set<dof_id_type> dindices;
      std::set_difference(indices.begin(),
                          indices.end(),
                          unindices.begin(),
                          unindices.end(),
                          std::inserter(dindices, dindices.end()));
      PetscInt * darray;
      LibmeshPetscCallQ(PetscMalloc(sizeof(PetscInt) * dindices.size(), &darray));
      dof_id_type i = 0;
      for (const auto & dof : dindices)
      {
        darray[i] = dof;
        ++i;
      }
      LibmeshPetscCallQ(ISCreateGeneral(
          ((PetscObject)dm)->comm, dindices.size(), darray, PETSC_OWN_POINTER, &dmm->_embedding));
    }
    else
    {
      // if (dmm->allblocks && dmm->allvars && dmm->nosides && dmm->nounsides && dmm->nocontacts &&
      // dmm->nouncontacts)
      // DMCreateGlobalVector is defined()
      Vec v;
      PetscInt low, high;
 
      LibmeshPetscCallQ(DMCreateGlobalVector(dm, &v));
      LibmeshPetscCallQ(VecGetOwnershipRange(v, &low, &high));
      LibmeshPetscCallQ(
          ISCreateStride(((PetscObject)dm)->comm, (high - low), low, 1, &dmm->_embedding));
    }
  }
  LibmeshPetscCallQ(PetscObjectReference((PetscObject)(dmm->_embedding)));
  *embedding = dmm->_embedding;
 
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreateFieldDecomposition_Moose(), and DMSetUp_Moose().

DMMooseGetMeshBlocks_Private()

static PetscErrorCode DMMooseGetMeshBlocks_Private ( DM  dm, std::set< subdomain_id_type > &  blocks  )

static

Definition at line 1334 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)(dm->data);
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (!dmm->_nl)
    SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE, "No Moose system set for DM_Moose");
 
  const MeshBase & mesh = dmm->_system->get_mesh();
  /* The following effectively is a verbatim copy of MeshBase::n_subdomains(). */
  // This requires an inspection on every processor
  libmesh_parallel_only(mesh.comm());
  for (const auto & elem : mesh.active_element_ptr_range())
    blocks.insert(elem->subdomain_id());
  // Some subdomains may only live on other processors
  mesh.comm().set_union(blocks);
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMSetUp_Moose_Pre().

DMMooseGetNonlinearSystem()

PetscErrorCode DMMooseGetNonlinearSystem	(	DM	dm,
		NonlinearSystemBase *&	nl
	)

Definition at line 444 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  DM_Moose * dmm = (DM_Moose *)(dm->data);
  nl = dmm->_nl;
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMMooseFunction(), DMMooseJacobian(), and DMVariableBounds_Moose().

DMMooseGetSides()

PetscErrorCode DMMooseGetSides	(	DM	dm,
		std::vector< std::string > &	side_names
	)

Definition at line 179 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  DM_Moose * dmm = (DM_Moose *)dm->data;
  for (const auto & it : *(dmm->_side_ids))
    side_names.push_back(it.first);
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseGetSplitNames()

PetscErrorCode DMMooseGetSplitNames	(	DM	dm,
		std::vector< std::string > &	split_names
	)

Definition at line 490 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  DM_Moose * dmm = (DM_Moose *)(dm->data);
  if (!dm->setupcalled)
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "DM not set up");
  split_names.clear();
  split_names.reserve(dmm->_splitlocs->size());
  if (dmm->_splitlocs && dmm->_splitlocs->size())
    for (const auto & lit : *(dmm->_splitlocs))
    {
      std::string sname = lit.first;
      unsigned int sloc = lit.second;
      split_names[sloc] = sname;
    }
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseGetUnContacts()

PetscErrorCode DMMooseGetUnContacts	(	DM	dm,
		std::vector< std::pair< std::string, std::string > > &	uncontact_names,
		std::vector< PetscBool > &	displaced
	)

Definition at line 163 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  DM_Moose * dmm = (DM_Moose *)dm->data;
  for (const auto & it : *(dmm->_uncontact_names))
  {
    uncontact_names.push_back(it.second);
    displaced.push_back((*dmm->_uncontact_displaced)[it.second]);
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseGetUnSides()

PetscErrorCode DMMooseGetUnSides	(	DM	dm,
		std::vector< std::string > &	side_names
	)

Definition at line 190 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  DM_Moose * dmm = (DM_Moose *)dm->data;
  for (const auto & it : *(dmm->_unside_ids))
    side_names.push_back(it.first);
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseGetVariables()

PetscErrorCode DMMooseGetVariables	(	DM	dm,
		std::vector< std::string > &	var_names
	)

Definition at line 212 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  DM_Moose * dmm = (DM_Moose *)(dm->data);
  for (const auto & it : *(dmm->_var_ids))
    var_names.push_back(it.first);
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseJacobian()

static PetscErrorCode DMMooseJacobian ( DM  dm, Vec  x, Mat  jac, Mat  pc  )

static

Definition at line 1050 of file PetscDMMoose.C.

{
  NonlinearSystemBase * nl = NULL;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseGetNonlinearSystem(dm, nl));
 
  PetscMatrix<Number> the_pc(pc, nl->comm());
  PetscMatrix<Number> Jac(jac, nl->comm());
  PetscVector<Number> & X_sys = *cast_ptr<PetscVector<Number> *>(nl->system().solution.get());
  PetscVector<Number> X_global(x, nl->comm());
 
  // Set the dof maps
  the_pc.attach_dof_map(nl->system().get_dof_map());
  Jac.attach_dof_map(nl->system().get_dof_map());
 
  // Use the system's update() to get a good local version of the
  // parallel solution.  system.update() does change the Jacobian, so
  // there's no reason to swap PETSc's Jacobian into the system for
  // this step.
  X_global.swap(X_sys);
  nl->system().update();
  X_global.swap(X_sys);
 
  // Enforce constraints (if any) exactly on the
  // current_local_solution.  This is the solution vector that is
  // actually used in the computation of the Jacobian below, and is
  // not locked by debug-enabled PETSc the way that "x" is.
  nl->system().get_dof_map().enforce_constraints_exactly(nl->system(),
                                                         nl->system().current_local_solution.get());
 
  // Zero out the preconditioner before computing the Jacobian.
  the_pc.zero();
 
  // if the user has provided both function pointers and objects only the pointer
  // will be used, so catch that as an error
  if (nl->nonlinearSolver()->jacobian && nl->nonlinearSolver()->jacobian_object)
  {
    std::ostringstream err;
    err << "ERROR: cannot specifiy both a function and object to compute the Jacobian!"
        << std::endl;
    mooseError(err.str());
  }
  if (nl->nonlinearSolver()->matvec && nl->nonlinearSolver()->residual_and_jacobian_object)
  {
    std::ostringstream err;
    err << "ERROR: cannot specifiy both a function and object to compute the combined Residual & "
           "Jacobian!"
        << std::endl;
    mooseError(err.str());
  }
  if (nl->nonlinearSolver()->jacobian != NULL)
    nl->nonlinearSolver()->jacobian(
        *(nl->system().current_local_solution.get()), the_pc, nl->nonlinearSolver()->system());
  else if (nl->nonlinearSolver()->jacobian_object != NULL)
    nl->nonlinearSolver()->jacobian_object->jacobian(
        *(nl->system().current_local_solution.get()), the_pc, nl->nonlinearSolver()->system());
  else if (nl->nonlinearSolver()->matvec != NULL)
    nl->nonlinearSolver()->matvec(*(nl->system().current_local_solution.get()),
                                  NULL,
                                  &the_pc,
                                  nl->nonlinearSolver()->system());
  else if (nl->nonlinearSolver()->residual_and_jacobian_object != NULL)
    nl->nonlinearSolver()->residual_and_jacobian_object->residual_and_jacobian(
        *(nl->system().current_local_solution.get()),
        NULL,
        &the_pc,
        nl->nonlinearSolver()->system());
  else
  {
    std::ostringstream err;
    err << "No suitable Jacobian routine or object";
    mooseError(err.str());
  }
  the_pc.close();
  Jac.close();
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by SNESJacobian_DMMoose().

DMMooseRegisterAll()

PetscErrorCode DMMooseRegisterAll

(

)

Definition at line 2178 of file PetscDMMoose.C.

{
  static PetscBool DMMooseRegisterAllCalled = PETSC_FALSE;
 
  PetscFunctionBegin;
  if (!DMMooseRegisterAllCalled)
  {
    LibmeshPetscCallQ(DMRegister(DMMOOSE, DMCreate_Moose));
    DMMooseRegisterAllCalled = PETSC_TRUE;
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by FieldSplitPreconditioner::setupDM(), and StaticCondensationFieldSplitPreconditioner::setupDM().

DMMooseReset()

PetscErrorCode DMMooseReset

(

DM

dm

)

Definition at line 1610 of file PetscDMMoose.C.

{
  PetscBool ismoose;
  DM_Moose * dmm = (DM_Moose *)(dm->data);
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(PetscObjectTypeCompare((PetscObject)dm, DMMOOSE, &ismoose));
  if (!ismoose)
    PetscFunctionReturn(PETSC_SUCCESS);
  if (!dmm->_nl)
    SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE, "No Moose system set for DM_Moose");
  LibmeshPetscCallQ(ISDestroy(&dmm->_embedding));
  for (auto & it : *(dmm->_splits))
  {
    DM_Moose::SplitInfo & split = it.second;
    LibmeshPetscCallQ(ISDestroy(&split._rembedding));
    if (split._dm)
      LibmeshPetscCallQ(DMMooseReset(split._dm));
  }
  dm->setupcalled = PETSC_FALSE;
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMMooseReset(), and SNESUpdateDMMoose().

DMMooseSetBlocks()

PetscErrorCode DMMooseSetBlocks	(	DM	dm,
		const std::set< std::string > &	blocks
	)

Definition at line 323 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)dm->data;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Not for an already setup DM");
  if (dmm->_blocks)
    delete dmm->_blocks;
  dmm->_blocks = new std::set<std::string>(blocks);
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseSetContacts()

PetscErrorCode DMMooseSetContacts	(	DM	dm,
		const std::vector< std::pair< std::string, std::string > > &	contacts,
		const std::vector< PetscBool > &	displaced
	)

Definition at line 383 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)dm->data;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Not for an already setup DM");
  if (contacts.size() != displaced.size())
    LIBMESH_SETERRQ2(PETSC_COMM_SELF,
                     PETSC_ERR_ARG_SIZ,
                     "Nonmatching sizes of the contact and displaced arrays: %" LIBMESH_PETSCINT_FMT
                     " != %" LIBMESH_PETSCINT_FMT,
                     static_cast<PetscInt>(contacts.size()),
                     static_cast<PetscInt>(displaced.size()));
  if (dmm->_contacts)
    delete dmm->_contacts;
  dmm->_contact_displaced->clear();
  dmm->_contacts = new std::set<DM_Moose::ContactName>();
  for (unsigned int i = 0; i < contacts.size(); ++i)
  {
    dmm->_contacts->insert(contacts[i]);
    dmm->_contact_displaced->insert(std::make_pair(contacts[i], displaced[i]));
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseSetDofMap()

PetscErrorCode DMMooseSetDofMap	(	DM	dm,
		const libMesh::DofMapBase &	dof_map
	)

Definition at line 237 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(((PetscObject)dm)->comm,
            PETSC_ERR_ARG_WRONGSTATE,
            "Cannot reset the degree of freedom map after DM has been set up.");
  DM_Moose * dmm = (DM_Moose *)(dm->data);
  dmm->_dof_map = &dof_map;
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreateMoose().

DMMooseSetName()

PetscErrorCode DMMooseSetName	(	DM	dm,
		const std::string &	dm_name
	)

Definition at line 265 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(((PetscObject)dm)->comm,
            PETSC_ERR_ARG_WRONGSTATE,
            "Cannot reset the MOOSE DM name after DM has been set up.");
  DM_Moose * dmm = (DM_Moose *)(dm->data);
  *dmm->_name = dm_name;
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreateMoose().

DMMooseSetNonlinearSystem()

PetscErrorCode DMMooseSetNonlinearSystem	(	DM	dm,
		NonlinearSystemBase &	nl
	)

Definition at line 223 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(((PetscObject)dm)->comm,
            PETSC_ERR_ARG_WRONGSTATE,
            "Cannot reset the NonlinearSystem after DM has been set up.");
  DM_Moose * dmm = (DM_Moose *)(dm->data);
  dmm->_nl = &nl;
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreateMoose().

DMMooseSetParentDM()

PetscErrorCode DMMooseSetParentDM	(	DM	dm,
		DM_Moose *	parent
	)

Definition at line 279 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(((PetscObject)dm)->comm,
            PETSC_ERR_ARG_WRONGSTATE,
            "Cannot reset the parent DM after the child DM has been set up.");
 
  DM_Moose * dmm = (DM_Moose *)(dm->data);
  dmm->_parent = parent;
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreateFieldDecomposition_Moose().

DMMooseSetSides()

PetscErrorCode DMMooseSetSides	(	DM	dm,
		const std::set< std::string > &	sides
	)

Definition at line 338 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)dm->data;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Not for an already setup DM");
  if (dmm->_sides)
    delete dmm->_sides;
  dmm->_sides = new std::set<std::string>(sides);
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseSetSplitNames()

PetscErrorCode DMMooseSetSplitNames	(	DM	dm,
		const std::vector< std::string > &	split_names
	)

Definition at line 454 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  DM_Moose * dmm = (DM_Moose *)(dm->data);
 
  if (dmm->_splits)
  {
    for (auto & it : *(dmm->_splits))
    {
      LibmeshPetscCallQ(DMDestroy(&(it.second._dm)));
      LibmeshPetscCallQ(ISDestroy(&(it.second._rembedding)));
    }
    delete dmm->_splits;
    dmm->_splits = LIBMESH_PETSC_NULLPTR;
  }
  if (dmm->_splitlocs)
  {
    delete dmm->_splitlocs;
    dmm->_splitlocs = LIBMESH_PETSC_NULLPTR;
  }
  dmm->_splits = new std::map<std::string, DM_Moose::SplitInfo>();
  dmm->_splitlocs = new std::multimap<std::string, unsigned int>();
  for (unsigned int i = 0; i < split_names.size(); ++i)
  {
    DM_Moose::SplitInfo info;
    info._dm = LIBMESH_PETSC_NULLPTR;
    info._rembedding = LIBMESH_PETSC_NULLPTR;
    std::string name = split_names[i];
    (*dmm->_splits)[name] = info;
    dmm->_splitlocs->insert(std::make_pair(name, i));
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by if().

DMMooseSetSystem()

PetscErrorCode DMMooseSetSystem	(	DM	dm,
		const System &	system
	)

Definition at line 251 of file PetscDMMoose.C.

{
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(((PetscObject)dm)->comm,
            PETSC_ERR_ARG_WRONGSTATE,
            "Cannot reset the degree of freedom map after DM has been set up.");
  DM_Moose * dmm = (DM_Moose *)(dm->data);
  dmm->_system = &system;
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreateMoose().

DMMooseSetUnContacts()

PetscErrorCode DMMooseSetUnContacts	(	DM	dm,
		const std::vector< std::pair< std::string, std::string > > &	uncontacts,
		const std::vector< PetscBool > &	displaced
	)

Definition at line 413 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)dm->data;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Not for an already setup DM");
  if (uncontacts.size() != displaced.size())
    LIBMESH_SETERRQ2(
        PETSC_COMM_SELF,
        PETSC_ERR_ARG_SIZ,
        "Nonmatching sizes of the uncontact and displaced arrays: %" LIBMESH_PETSCINT_FMT
        " != %" LIBMESH_PETSCINT_FMT,
        static_cast<PetscInt>(uncontacts.size()),
        static_cast<PetscInt>(displaced.size()));
  if (dmm->_uncontacts)
    delete dmm->_uncontacts;
  dmm->_uncontact_displaced->clear();
  dmm->_uncontacts = new std::set<DM_Moose::ContactName>();
  for (unsigned int i = 0; i < uncontacts.size(); ++i)
  {
    dmm->_uncontacts->insert(uncontacts[i]);
    dmm->_uncontact_displaced->insert(std::make_pair(uncontacts[i], displaced[i]));
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseSetUnSideByVar()

PetscErrorCode DMMooseSetUnSideByVar	(	DM	dm,
		const std::set< std::string > &	unside_by_var
	)

Definition at line 368 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)dm->data;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Not for an already setup DM");
  if (dmm->_unside_by_var)
    delete dmm->_unside_by_var;
  dmm->_unside_by_var = new std::set<std::string>(unside_by_var);
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseSetUnSides()

PetscErrorCode DMMooseSetUnSides	(	DM	dm,
		const std::set< std::string > &	unsides
	)

Definition at line 353 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)dm->data;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Not for an already setup DM");
  if (dmm->_unsides)
    delete dmm->_unsides;
  dmm->_unsides = new std::set<std::string>(unsides);
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseSetVariables()

PetscErrorCode DMMooseSetVariables	(	DM	dm,
		const std::set< std::string > &	vars
	)

Definition at line 294 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)dm->data;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (dm->setupcalled)
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Not for an already setup DM");
  if (dmm->_vars)
    delete dmm->_vars;
  std::set<std::string> processed_vars;
  for (const auto & var_name : vars)
  {
    const auto * const var =
        dmm->_nl->hasVariable(var_name)
            ? cast_ptr<MooseVariableBase *>(&dmm->_nl->getVariable(0, var_name))
            : cast_ptr<MooseVariableBase *>(&dmm->_nl->getScalarVariable(0, var_name));
    if (var->isArray())
      for (const auto i : make_range(var->count()))
        processed_vars.insert(var->arrayVariableComponent(i));
    else
      processed_vars.insert(var_name);
  }
 
  dmm->_vars = new std::set<std::string>(std::move(processed_vars));
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMMooseValidityCheck()

PetscErrorCode DMMooseValidityCheck

(

DM

dm

)

Definition at line 130 of file PetscDMMoose.C.

{
  PetscBool ismoose;
 
  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  LibmeshPetscCallQ(PetscObjectTypeCompare((PetscObject)dm, DMMOOSE, &ismoose));
  if (!ismoose)
    LIBMESH_SETERRQ2(((PetscObject)dm)->comm,
                     PETSC_ERR_ARG_WRONG,
                     "Got DM of type %s, not of type %s",
                     ((PetscObject)dm)->type_name,
                     DMMOOSE);
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreateGlobalVector_Moose(), DMCreateMatrix_Moose(), DMMooseGetBlocks(), DMMooseGetContacts(), DMMooseGetMeshBlocks_Private(), DMMooseGetNonlinearSystem(), DMMooseGetSides(), DMMooseGetSplitNames(), DMMooseGetUnContacts(), DMMooseGetUnSides(), DMMooseGetVariables(), DMMooseSetBlocks(), DMMooseSetContacts(), DMMooseSetDofMap(), DMMooseSetName(), DMMooseSetNonlinearSystem(), DMMooseSetParentDM(), DMMooseSetSides(), DMMooseSetSplitNames(), DMMooseSetSystem(), DMMooseSetUnContacts(), DMMooseSetUnSideByVar(), DMMooseSetUnSides(), DMMooseSetVariables(), DMSetUp_Moose(), and DMSetUp_Moose_Pre().

DMSetFromOptions_Moose() [1/2]

PetscErrorCode DMSetFromOptions_Moose	(	DM	dm,
		PetscOptionItems
	)

Referenced by DMCreate_Moose().

DMSetFromOptions_Moose() [2/2]

PetscErrorCode PetscOptionItems *PetscErrorCode DMSetFromOptions_Moose	(	PetscOptionItems *	,
		DM	dm
	)

DMSetUp_Moose()

static PetscErrorCode DMSetUp_Moose ( DM  dm )

static

Definition at line 1634 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)(dm->data);
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (!dmm->_nl)
    SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE, "No Moose system set for DM_Moose");
  if (dmm->_print_embedding)
  {
    const char *name, *prefix;
    IS embedding;
 
    LibmeshPetscCallQ(PetscObjectGetName((PetscObject)dm, &name));
    LibmeshPetscCallQ(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix));
    LibmeshPetscCallQ(PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_(((PetscObject)dm)->comm),
                                             "DM Moose with name %s and prefix %s\n",
                                             name,
                                             prefix));
    if (dmm->_all_vars && dmm->_all_blocks && dmm->_nosides && dmm->_nounsides &&
        dmm->_nocontacts && dmm->_nouncontacts)
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_(((PetscObject)dm)->comm),
                                               "\thas a trivial embedding\n"));
    else
    {
      LibmeshPetscCallQ(DMMooseGetEmbedding_Private(dm, &embedding));
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(PETSC_VIEWER_STDOUT_(((PetscObject)dm)->comm),
                                               "\thas embedding defined by IS:\n"));
      LibmeshPetscCallQ(ISView(embedding, PETSC_VIEWER_STDOUT_(((PetscObject)dm)->comm)));
      LibmeshPetscCallQ(ISDestroy(&embedding));
    }
  }
  /*
   Do not evaluate function, Jacobian or bounds for an embedded DM -- the subproblem might not have
   enough information for that.
   */
  if (dmm->_all_vars && dmm->_all_blocks && dmm->_nosides && dmm->_nounsides && dmm->_nocontacts &&
      dmm->_nouncontacts)
  {
    LibmeshPetscCallQ(DMSNESSetFunction(dm, SNESFunction_DMMoose, (void *)dm));
    LibmeshPetscCallQ(DMSNESSetJacobian(dm, SNESJacobian_DMMoose, (void *)dm));
    if (dmm->_nl->nonlinearSolver()->bounds || dmm->_nl->nonlinearSolver()->bounds_object)
      LibmeshPetscCallQ(DMSetVariableBounds(dm, DMVariableBounds_Moose));
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreate_Moose().

DMSetUp_Moose_Pre()

static PetscErrorCode DMSetUp_Moose_Pre ( DM  dm )

static

Definition at line 1355 of file PetscDMMoose.C.

{
  DM_Moose * dmm = (DM_Moose *)(dm->data);
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseValidityCheck(dm));
  if (!dmm->_nl)
    SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONGSTATE, "No Moose system set for DM_Moose");
 
  /* Set up variables, blocks and sides. */
  const auto & dofmap = *dmm->_dof_map;
  /* libMesh mesh */
  const MeshBase & mesh = dmm->_system->get_mesh();
 
  // Do sides
  dmm->_nosides = PETSC_TRUE;
  dmm->_side_ids->clear();
  dmm->_side_names->clear();
  if (dmm->_sides)
  {
    dmm->_nosides = PETSC_FALSE;
    for (const auto & name : *(dmm->_sides))
    {
      boundary_id_type id = dmm->_nl->mesh().getBoundaryID(name);
      dmm->_side_names->insert(std::make_pair(id, name));
      dmm->_side_ids->insert(std::make_pair(name, id));
    }
    delete dmm->_sides;
    dmm->_sides = LIBMESH_PETSC_NULLPTR;
  }
 
  // Do unsides
  dmm->_nounsides = PETSC_TRUE;
  dmm->_unside_ids->clear();
  dmm->_unside_names->clear();
  if (dmm->_unsides)
  {
    dmm->_nounsides = PETSC_FALSE;
    for (const auto & name : *(dmm->_unsides))
    {
      boundary_id_type id = dmm->_nl->mesh().getBoundaryID(name);
      dmm->_unside_names->insert(std::make_pair(id, name));
      dmm->_unside_ids->insert(std::make_pair(name, id));
    }
    delete dmm->_unsides;
    dmm->_unsides = LIBMESH_PETSC_NULLPTR;
  }
 
  // Do unside by var
  dmm->_nounside_by_var = PETSC_TRUE;
  dmm->_unside_by_var_set->clear();
  if (dmm->_unside_by_var)
  {
    dmm->_nounside_by_var = PETSC_FALSE;
    for (const auto & name : *(dmm->_unside_by_var))
    {
      const auto colon_pos = name.find(":");
      auto unside_name = name.substr(0, colon_pos);
      auto var_name = name.substr(colon_pos + 1);
      boundary_id_type id = dmm->_nl->mesh().getBoundaryID(unside_name);
      bool var_found = false;
      for (unsigned int v = 0; v < dofmap.n_variables(); ++v)
      {
        const auto & vname = dofmap.variable(v).name();
        if (vname == var_name)
        {
          dmm->_unside_by_var_set->insert(std::make_pair(id, v));
          var_found = true;
          break;
        }
      }
      if (!var_found)
        mooseError("No variable named '", var_name, "' found");
    }
    delete dmm->_unside_by_var;
    dmm->_unside_by_var = LIBMESH_PETSC_NULLPTR;
  }
 
  dmm->_nocontacts = PETSC_TRUE;
 
  if (dmm->_contacts)
  {
    dmm->_nocontacts = PETSC_FALSE;
    for (const auto & cpair : *(dmm->_contacts))
    {
      try
      {
        if ((*dmm->_contact_displaced)[cpair])
          dmm->_nl->feProblem().getDisplacedProblem()->geomSearchData().getPenetrationLocator(
              cpair.first, cpair.second);
        else
          dmm->_nl->feProblem().geomSearchData().getPenetrationLocator(cpair.first, cpair.second);
      }
      catch (...)
      {
        std::ostringstream err;
        err << "Problem retrieving contact for PenetrationLocator with primary " << cpair.first
            << " and secondary " << cpair.second;
        mooseError(err.str());
      }
      BoundaryID primary_id = dmm->_nl->mesh().getBoundaryID(cpair.first);
      BoundaryID secondary_id = dmm->_nl->mesh().getBoundaryID(cpair.second);
      DM_Moose::ContactID cid(primary_id, secondary_id);
      dmm->_contact_names->insert(std::make_pair(cid, cpair));
    }
  }
 
  dmm->_nouncontacts = PETSC_TRUE;
  if (dmm->_uncontacts)
  {
    dmm->_nouncontacts = PETSC_FALSE;
    for (const auto & cpair : *(dmm->_uncontacts))
    {
      try
      {
        if ((*dmm->_uncontact_displaced)[cpair])
          dmm->_nl->feProblem().getDisplacedProblem()->geomSearchData().getPenetrationLocator(
              cpair.first, cpair.second);
        else
          dmm->_nl->feProblem().geomSearchData().getPenetrationLocator(cpair.first, cpair.second);
      }
      catch (...)
      {
        std::ostringstream err;
        err << "Problem retrieving uncontact for PenetrationLocator with primary " << cpair.first
            << " and secondary " << cpair.second;
        mooseError(err.str());
      }
      BoundaryID primary_id = dmm->_nl->mesh().getBoundaryID(cpair.first);
      BoundaryID secondary_id = dmm->_nl->mesh().getBoundaryID(cpair.second);
      DM_Moose::ContactID cid(primary_id, secondary_id);
      dmm->_uncontact_names->insert(std::make_pair(cid, cpair));
    }
  }
 
  dmm->_var_ids->clear();
  dmm->_var_names->clear();
  // FIXME: would be nice to invert this nested loop structure so we could iterate over the
  // potentially smaller dmm->vars,
  // but checking against dofmap.variable would still require a linear search, hence, no win.  Would
  // be nice to endow dofmap.variable
  // with a fast search capability.
  for (unsigned int v = 0; v < dofmap.n_variables(); ++v)
  {
    std::string vname = dofmap.variable(v).name();
    if (dmm->_vars && dmm->_vars->size() && dmm->_vars->find(vname) == dmm->_vars->end())
      continue;
    dmm->_var_ids->insert(std::pair<std::string, unsigned int>(vname, v));
    dmm->_var_names->insert(std::pair<unsigned int, std::string>(v, vname));
  }
  if (dmm->_var_ids->size() == dofmap.n_variables())
    dmm->_all_vars = PETSC_TRUE;
  else
    dmm->_all_vars = PETSC_FALSE;
  if (dmm->_vars)
  {
    delete dmm->_vars;
    dmm->_vars = LIBMESH_PETSC_NULLPTR;
  }
 
  dmm->_block_ids->clear();
  dmm->_block_names->clear();
  std::set<subdomain_id_type> blocks;
  LibmeshPetscCallQ(DMMooseGetMeshBlocks_Private(dm, blocks));
  if (blocks.empty())
    SETERRQ(((PetscObject)dm)->comm, PETSC_ERR_PLIB, "No mesh blocks found.");
 
  for (const auto & bid : blocks)
  {
    std::string bname = mesh.subdomain_name(bid);
    if (!bname.length())
    {
      // Block names are currently implemented for Exodus meshes
      // only, so we might have to make up our own block names and
      // maintain our own mapping of block ids to names.
      std::ostringstream ss;
      ss << bid;
      bname = ss.str();
    }
    if (dmm->_nosides && dmm->_nocontacts)
    {
      // If no sides and no contacts have been specified, by default (null or empty dmm->blocks) all
      // blocks are included in the split Thus, skip this block only if it is explicitly excluded
      // from a nonempty dmm->blocks.
      if (dmm->_blocks && dmm->_blocks->size() &&
          (dmm->_blocks->find(bname) ==
               dmm->_blocks->end() && // We should allow users to use subdomain IDs
           dmm->_blocks->find(std::to_string(bid)) == dmm->_blocks->end()))
        continue;
    }
    else
    {
      // If sides or contacts have been specified, only the explicitly-specified blocks (those in
      // dmm->blocks, if it's non-null) are in the split. Thus, include this block only if it is
      // explicitly specified in a nonempty dmm->blocks. Equivalently, skip this block if
      // dmm->blocks is dmm->blocks is null or empty or excludes this block.
      if (!dmm->_blocks || !dmm->_blocks->size() ||
          (dmm->_blocks->find(bname) ==
               dmm->_blocks->end() // We should allow users to use subdomain IDs
           && dmm->_blocks->find(std::to_string(bid)) == dmm->_blocks->end()))
        continue;
    }
    dmm->_block_ids->insert(std::make_pair(bname, bid));
    dmm->_block_names->insert(std::make_pair(bid, bname));
  }
 
  if (dmm->_block_ids->size() == blocks.size())
    dmm->_all_blocks = PETSC_TRUE;
  else
    dmm->_all_blocks = PETSC_FALSE;
  if (dmm->_blocks)
  {
    delete dmm->_blocks;
    dmm->_blocks = LIBMESH_PETSC_NULLPTR;
  }
 
  std::string name = dmm->_system->name();
  name += "_vars";
  for (const auto & vit : *(dmm->_var_names))
    name += "_" + vit.second;
 
  name += "_blocks";
 
  for (const auto & bit : *(dmm->_block_names))
    name += "_" + bit.second;
 
  if (dmm->_side_names && dmm->_side_names->size())
  {
    name += "_sides";
    for (const auto & sit : *(dmm->_side_names))
      name += "_" + sit.second;
  }
  if (dmm->_unside_names && dmm->_unside_names->size())
  {
    name += "_unsides";
    for (const auto & sit : *(dmm->_unside_names))
      name += "_" + sit.second;
  }
  if (dmm->_contact_names && dmm->_contact_names->size())
  {
    name += "_contacts";
    for (const auto & cit : *(dmm->_contact_names))
      name += "_primary_" + cit.second.first + "_secondary_" + cit.second.second;
  }
  if (dmm->_uncontact_names && dmm->_uncontact_names->size())
  {
    name += "_uncontacts";
    for (const auto & cit : *(dmm->_uncontact_names))
      name += "_primary_" + cit.second.first + "_secondary_" + cit.second.second;
  }
  LibmeshPetscCallQ(PetscObjectSetName((PetscObject)dm, name.c_str()));
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMVariableBounds_Moose()

static PetscErrorCode DMVariableBounds_Moose ( DM  dm, Vec  xl, Vec  xu  )

static

Definition at line 1140 of file PetscDMMoose.C.

{
  NonlinearSystemBase * nl = NULL;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseGetNonlinearSystem(dm, nl));
 
  PetscVector<Number> XL(xl, nl->comm());
  PetscVector<Number> XU(xu, nl->comm());
 
  LibmeshPetscCallQ(VecSet(xl, PETSC_NINFINITY));
  LibmeshPetscCallQ(VecSet(xu, PETSC_INFINITY));
  if (nl->nonlinearSolver()->bounds != NULL)
    nl->nonlinearSolver()->bounds(XL, XU, nl->nonlinearSolver()->system());
  else if (nl->nonlinearSolver()->bounds_object != NULL)
    nl->nonlinearSolver()->bounds_object->bounds(XL, XU, nl->nonlinearSolver()->system());
  else
    SETERRQ(
        ((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "No bounds calculation in this Moose object");
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMSetUp_Moose().

DMView_Moose()

static PetscErrorCode DMView_Moose ( DM  dm, PetscViewer  viewer  )

static

Definition at line 1236 of file PetscDMMoose.C.

{
  PetscBool isascii;
  const char *name, *prefix;
  DM_Moose * dmm = (DM_Moose *)dm->data;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &isascii));
  if (isascii)
  {
    LibmeshPetscCallQ(PetscObjectGetName((PetscObject)dm, &name));
    LibmeshPetscCallQ(PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix));
    LibmeshPetscCallQ(
        PetscViewerASCIIPrintf(viewer, "DM Moose with name %s and prefix %s\n", name, prefix));
    LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "variables:"));
    for (const auto & vit : *(dmm->_var_ids))
    {
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "(%s,%u) ", vit.first.c_str(), vit.second));
    }
    LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "\n"));
    LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "blocks:"));
    for (const auto & bit : *(dmm->_block_ids))
    {
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "(%s,%d) ", bit.first.c_str(), bit.second));
    }
    LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "\n"));
 
    if (dmm->_side_ids->size())
    {
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "sides:"));
      for (const auto & sit : *(dmm->_side_ids))
      {
        LibmeshPetscCallQ(
            PetscViewerASCIIPrintf(viewer, "(%s,%d) ", sit.first.c_str(), sit.second));
      }
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "\n"));
    }
 
    if (dmm->_unside_ids->size())
    {
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "unsides:"));
      for (const auto & sit : *(dmm->_unside_ids))
      {
        LibmeshPetscCallQ(
            PetscViewerASCIIPrintf(viewer, "(%s,%d) ", sit.first.c_str(), sit.second));
      }
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "\n"));
    }
 
    if (dmm->_contact_names->size())
    {
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "contacts:"));
      for (const auto & cit : *(dmm->_contact_names))
      {
        LibmeshPetscCallQ(PetscViewerASCIIPrintf(
            viewer, "(%s,%s,", cit.second.first.c_str(), cit.second.second.c_str()));
        if ((*dmm->_contact_displaced)[cit.second])
          LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "displaced) "));
        else
          LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "undisplaced) "));
      }
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "\n"));
    }
 
    if (dmm->_uncontact_names->size())
    {
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "_uncontacts:"));
      for (const auto & cit : *(dmm->_uncontact_names))
      {
        LibmeshPetscCallQ(PetscViewerASCIIPrintf(
            viewer, "(%s,%s,", cit.second.first.c_str(), cit.second.second.c_str()));
        if ((*dmm->_uncontact_displaced)[cit.second])
          LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "displaced) "));
        else
          LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "undisplaced) "));
      }
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "\n"));
    }
 
    if (dmm->_splitlocs && dmm->_splitlocs->size())
    {
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "Field decomposition:"));
      // FIX: decompositions might have different sizes and components on different ranks.
      for (const auto & dit : *(dmm->_splitlocs))
      {
        std::string dname = dit.first;
        LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, " %s", dname.c_str()));
      }
      LibmeshPetscCallQ(PetscViewerASCIIPrintf(viewer, "\n"));
    }
  }
  else
    SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Non-ASCII viewers are not supported");
 
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMCreate_Moose().

for()

for

(

)

Definition at line 1719 of file PetscDMMoose.C.

  {
    varset.insert(std::string(vars[i]));
    LibmeshPetscCallQ(PetscFree(vars[i]));
  }

if() [1/9]

if

(

!dmm->

_nl

)

if() [2/9]

if

(

blockset.

size()

)

if() [3/9]

if

(

contacts.

size()

)

if() [4/9]

if

(

displaced_problem

)

Definition at line 1799 of file PetscDMMoose.C.

  {
    {
      char * primary_secondary[2];
      PetscInt sz = 2;
      std::ostringstream oopt, ohelp;
      oopt << "-dm_moose_contact_" << i;
      ohelp << "Primary and secondary for contact " << i;
      LibmeshPetscCallQ(PetscOptionsStringArray(oopt.str().c_str(),
                                                ohelp.str().c_str(),
                                                "DMMooseSetContacts",
                                                primary_secondary,
                                                &sz,
                                                LIBMESH_PETSC_NULLPTR));
      if (sz != 2)
        LIBMESH_SETERRQ2(
            ((PetscObject)dm)->comm,
            PETSC_ERR_ARG_SIZ,
            "Expected 2 sideset IDs (primary & secondary) for contact %" LIBMESH_PETSCINT_FMT
            ", got %" LIBMESH_PETSCINT_FMT " instead",
            i,
            sz);
      contacts.push_back(DM_Moose::ContactName(std::string(primary_secondary[0]),
                                               std::string(primary_secondary[1])));
      LibmeshPetscCallQ(PetscFree(primary_secondary[0]));
      LibmeshPetscCallQ(PetscFree(primary_secondary[1]));
    }
    {
      PetscBool displaced = PETSC_FALSE;
      std::ostringstream oopt, ohelp;
      oopt << "-dm_moose_contact_" << i << "_displaced";
      ohelp << "Whether contact " << i << " is determined using displaced mesh or not";
      LibmeshPetscCallQ(PetscOptionsBool(oopt.str().c_str(),
                                         ohelp.str().c_str(),
                                         "DMMooseSetContacts",
                                         PETSC_FALSE,
                                         &displaced,
                                         LIBMESH_PETSC_NULLPTR));
      contact_displaced.push_back(displaced);
    }
  }

if() [5/9]

if	(	LIBMESH_SETERRQ2(	nuncontacts,
		maxcontacts
	)

Definition at line 1898 of file PetscDMMoose.C.

  {
    {
      char * primary_secondary[2];
      PetscInt sz = 2;
      std::ostringstream oopt, ohelp;
      oopt << "-dm_moose_uncontact_" << i;
      ohelp << "Primary and secondary for uncontact " << i;
      LibmeshPetscCallQ(PetscOptionsStringArray(oopt.str().c_str(),
                                                ohelp.str().c_str(),
                                                "DMMooseSetUnContacts",
                                                primary_secondary,
                                                &sz,
                                                LIBMESH_PETSC_NULLPTR));
      if (sz != 2)
        LIBMESH_SETERRQ2(
            ((PetscObject)dm)->comm,
            PETSC_ERR_ARG_SIZ,
            "Expected 2 sideset IDs (primary & secondary) for uncontact %" LIBMESH_PETSCINT_FMT
            ", got %" LIBMESH_PETSCINT_FMT " instead",
            i,
            sz);
      uncontacts.push_back(DM_Moose::ContactName(std::string(primary_secondary[0]),
                                                 std::string(primary_secondary[1])));
      LibmeshPetscCallQ(PetscFree(primary_secondary[0]));
      LibmeshPetscCallQ(PetscFree(primary_secondary[1]));
    }
    {
      PetscBool displaced = PETSC_FALSE;
      std::ostringstream oopt, ohelp;
      oopt << "-dm_moose_uncontact_" << i << "_displaced";
      ohelp << "Whether uncontact " << i << " is determined using displaced mesh or not";
      LibmeshPetscCallQ(PetscOptionsBool(oopt.str().c_str(),
                                         ohelp.str().c_str(),
                                         "DMMooseSetUnContact",
                                         PETSC_FALSE,
                                         &displaced,
                                         LIBMESH_PETSC_NULLPTR));
      uncontact_displaced.push_back(displaced);
    }
  }

if() [6/9]

if

(

nsplits

)

Definition at line 1957 of file PetscDMMoose.C.

  {
    PetscInt nnsplits = nsplits;
    std::vector<std::string> split_names;
    char ** splitnames;
    LibmeshPetscCallQ(PetscMalloc(nsplits * sizeof(char *), &splitnames));
    LibmeshPetscCallQ(PetscOptionsStringArray("-dm_moose_fieldsplit_names",
                                              "Names of fieldsplits defined by the DM",
                                              "DMMooseSetSplitNames",
                                              splitnames,
                                              &nnsplits,
                                              LIBMESH_PETSC_NULLPTR));
    if (!nnsplits)
    {
      for (PetscInt i = 0; i < nsplits; ++i)
      {
        std::ostringstream s;
        s << i;
        split_names.push_back(s.str());
      }
    }
    else if (nsplits != nnsplits)
      LIBMESH_SETERRQ2(((PetscObject)dm)->comm,
                       PETSC_ERR_ARG_SIZ,
                       "Expected %" LIBMESH_PETSCINT_FMT
                       " fieldsplit names, got %" LIBMESH_PETSCINT_FMT " instead",
                       nsplits,
                       nnsplits);
    else
    {
      for (PetscInt i = 0; i < nsplits; ++i)
      {
        split_names.push_back(std::string(splitnames[i]));
        LibmeshPetscCallQ(PetscFree(splitnames[i]));
      }
    }
    LibmeshPetscCallQ(PetscFree(splitnames));
    LibmeshPetscCallQ(DMMooseSetSplitNames(dm, split_names));
  }

if() [7/9]

if

(

sideset.

size()

)

if() [8/9]

if

(

uncontacts.

size()

)

if() [9/9]

if

(

varset.

size()

)

LibmeshPetscCallQ() [1/18]

LibmeshPetscCallQ

(

DMMooseGetMeshBlocks_Private(dm, meshblocks)

)

LibmeshPetscCallQ() [2/18]

LibmeshPetscCallQ

(

DMMooseValidityCheck(dm)

)

Referenced by clear(), DMCreate_Moose(), DMCreateDomainDecomposition_Moose(), DMCreateFieldDecomposition_Moose(), DMCreateGlobalVector_Moose(), DMCreateMatrix_Moose(), DMCreateMoose(), DMDestroy_Moose(), DMMooseFunction(), DMMooseGetBlocks(), DMMooseGetContacts(), DMMooseGetEmbedding_Private(), DMMooseGetMeshBlocks_Private(), DMMooseGetNonlinearSystem(), DMMooseGetSides(), DMMooseGetSplitNames(), DMMooseGetUnContacts(), DMMooseGetUnSides(), DMMooseGetVariables(), DMMooseJacobian(), DMMooseRegisterAll(), DMMooseReset(), DMMooseSetBlocks(), DMMooseSetContacts(), DMMooseSetDofMap(), DMMooseSetName(), DMMooseSetNonlinearSystem(), DMMooseSetParentDM(), DMMooseSetSides(), DMMooseSetSplitNames(), DMMooseSetSystem(), DMMooseSetUnContacts(), DMMooseSetUnSideByVar(), DMMooseSetUnSides(), DMMooseSetVariables(), DMMooseValidityCheck(), DMSetUp_Moose(), DMSetUp_Moose_Pre(), DMVariableBounds_Moose(), DMView_Moose(), for(), if(), Moose::SlepcSupport::mooseEPSFormMatrices(), Moose::SlepcSupport::mooseMatMult_Eigen(), Moose::SlepcSupport::mooseMatMult_NonEigen(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionA(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionAB(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionB(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionMFFD(), Moose::SlepcSupport::mooseSlepcEigenFormJacobianA(), Moose::SlepcSupport::mooseSlepcEigenFormJacobianB(), Moose::SlepcSupport::mooseSlepcEPSGetSNES(), Moose::SlepcSupport::mooseSlepcEPSMonitor(), Moose::SlepcSupport::mooseSlepcEPSSNESKSPSetPCSide(), Moose::SlepcSupport::mooseSlepcEPSSNESSetCustomizePC(), Moose::SlepcSupport::mooseSlepcEPSSNESSetUpOptionPrefix(), Moose::SlepcSupport::mooseSlepcStoppingTest(), Moose::SlepcSupport::PCApply_MoosePC(), Moose::SlepcSupport::PCSetUp_MoosePC(), Moose::SlepcSupport::PCView_MoosePC(), Moose::SlepcSupport::registerPCToPETSc(), SNESFunction_DMMoose(), SNESJacobian_DMMoose(), and SNESUpdateDMMoose().

LibmeshPetscCallQ() [3/18]

LibmeshPetscCallQ

(

DMSetUp_Moose_Pre(dm)

)

LibmeshPetscCallQ() [4/18]

LibmeshPetscCallQ

(

PetscFree(blocks)

)

LibmeshPetscCallQ() [5/18]

LibmeshPetscCallQ

(

PetscFree(sides)

)

LibmeshPetscCallQ() [6/18]

LibmeshPetscCallQ

(

PetscFree(vars)

)

LibmeshPetscCallQ() [7/18]

LibmeshPetscCallQ

(

PetscMalloc(maxblocks *sizeof(char *), &blocks)

)

LibmeshPetscCallQ() [8/18]

LibmeshPetscCallQ

(

PetscMalloc(maxsides *maxvars *sizeof(char *), &sides)

)

LibmeshPetscCallQ() [9/18]

LibmeshPetscCallQ

(

PetscMalloc(maxvars *sizeof(char *), &vars)

)

LibmeshPetscCallQ() [10/18]

LibmeshPetscCallQ

(

PetscOptionsBegin(((PetscObject) dm) ->comm,((PetscObject) dm) ->prefix, "DMMoose options", "DM")

)

LibmeshPetscCallQ() [11/18]

LibmeshPetscCallQ

(

PetscOptionsBool("-dm_moose_print_embedding", "Print IS embedding DM's dofs", "DMMoose", dmm->_print_embedding, &dmm->_print_embedding, LIBMESH_PETSC_NULLPTR)

)

LibmeshPetscCallQ() [12/18]

LibmeshPetscCallQ

(

PetscOptionsInt("-dm_moose_nfieldsplits", fdhelp, "DMMooseSetSplitNames", nsplits, &nsplits, NULL)

)

LibmeshPetscCallQ() [13/18]

LibmeshPetscCallQ

(

PetscOptionsInt(opt.c_str(), help.c_str(), "DMMooseSetUnContacts", nuncontacts, &nuncontacts, LIBMESH_PETSC_NULLPTR)

)

LibmeshPetscCallQ() [14/18]

LibmeshPetscCallQ

(

PetscOptionsStringArray(opt.c_str(), help.c_str(), "DMMooseSetBlocks", blocks, &nblocks, LIBMESH_PETSC_NULLPTR)

)

LibmeshPetscCallQ() [15/18]

LibmeshPetscCallQ

(

PetscOptionsStringArray(opt.c_str(), help.c_str(), "DMMooseSetSides", sides, &nsides, LIBMESH_PETSC_NULLPTR)

)

LibmeshPetscCallQ() [16/18]

LibmeshPetscCallQ

(

PetscOptionsStringArray(opt.c_str(), help.c_str(), "DMMooseSetUnSideByVar", sides, &nsides, LIBMESH_PETSC_NULLPTR)

)

LibmeshPetscCallQ() [17/18]

LibmeshPetscCallQ

(

PetscOptionsStringArray(opt.c_str(), help.c_str(), "DMMooseSetUnSides", sides, &nsides, LIBMESH_PETSC_NULLPTR)

)

LibmeshPetscCallQ() [18/18]

LibmeshPetscCallQ

(

PetscOptionsStringArray(opt.c_str(), help.c_str(), "DMMooseSetVars", vars, &nvars, LIBMESH_PETSC_NULLPTR)

)

PetscFunctionReturn()

PetscFunctionReturn

(

PETSC_SUCCESS

)

Referenced by DMCreate_Moose(), DMCreateDomainDecomposition_Moose(), DMCreateFieldDecomposition_Moose(), DMCreateGlobalVector_Moose(), DMCreateMatrix_Moose(), DMCreateMoose(), DMDestroy_Moose(), DMMooseFunction(), DMMooseGetBlocks(), DMMooseGetContacts(), DMMooseGetEmbedding_Private(), DMMooseGetMeshBlocks_Private(), DMMooseGetNonlinearSystem(), DMMooseGetSides(), DMMooseGetSplitNames(), DMMooseGetUnContacts(), DMMooseGetUnSides(), DMMooseGetVariables(), DMMooseJacobian(), DMMooseRegisterAll(), DMMooseReset(), DMMooseSetBlocks(), DMMooseSetContacts(), DMMooseSetDofMap(), DMMooseSetName(), DMMooseSetNonlinearSystem(), DMMooseSetParentDM(), DMMooseSetSides(), DMMooseSetSplitNames(), DMMooseSetSystem(), DMMooseSetUnContacts(), DMMooseSetUnSideByVar(), DMMooseSetUnSides(), DMMooseSetVariables(), DMMooseValidityCheck(), DMSetUp_Moose(), DMSetUp_Moose_Pre(), DMVariableBounds_Moose(), DMView_Moose(), Moose::SlepcSupport::mooseEPSFormMatrices(), Moose::SlepcSupport::mooseMatMult_Eigen(), Moose::SlepcSupport::mooseMatMult_NonEigen(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionA(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionAB(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionB(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionMFFD(), Moose::SlepcSupport::mooseSlepcEigenFormJacobianA(), Moose::SlepcSupport::mooseSlepcEigenFormJacobianB(), Moose::SlepcSupport::mooseSlepcEigenFormNorm(), Moose::SlepcSupport::mooseSlepcEPSGetSNES(), Moose::SlepcSupport::mooseSlepcEPSMonitor(), Moose::SlepcSupport::mooseSlepcEPSSNESKSPSetPCSide(), Moose::SlepcSupport::mooseSlepcEPSSNESSetCustomizePC(), Moose::SlepcSupport::mooseSlepcEPSSNESSetUpOptionPrefix(), Moose::SlepcSupport::mooseSlepcStoppingTest(), Moose::SlepcSupport::PCApply_MoosePC(), Moose::SlepcSupport::PCCreate_MoosePC(), Moose::SlepcSupport::PCDestroy_MoosePC(), Moose::SlepcSupport::PCSetUp_MoosePC(), Moose::SlepcSupport::PCView_MoosePC(), Moose::PetscSupport::petscLinearConverged(), Moose::PetscSupport::petscNonlinearConverged(), Moose::PetscSupport::petscSetupOutput(), Moose::SlepcSupport::registerPCToPETSc(), SNESFunction_DMMoose(), SNESJacobian_DMMoose(), and SNESUpdateDMMoose().

PetscOptionsBegin()

PetscOptionsBegin	(	((PetscObject) dm) ->	comm,
		((PetscObject) dm) ->	prefix,
		"DMMoose options"	,
		"DM"
	)

PetscOptionsEnd()

PetscOptionsEnd

(

)

SNESFunction_DMMoose()

static PetscErrorCode SNESFunction_DMMoose ( SNES  , Vec  x, Vec  r, void *  ctx  )

static

Definition at line 1040 of file PetscDMMoose.C.

{
  DM dm = (DM)ctx;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseFunction(dm, x, r));
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMSetUp_Moose().

SNESJacobian_DMMoose()

static PetscErrorCode SNESJacobian_DMMoose ( SNES  , Vec  x, Mat  jac, Mat  pc, void *  ctx  )

static

Definition at line 1130 of file PetscDMMoose.C.

{
  DM dm = (DM)ctx;
 
  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseJacobian(dm, x, jac, pc));
  PetscFunctionReturn(PETSC_SUCCESS);
}

Referenced by DMSetUp_Moose().

SNESUpdateDMMoose()

PetscErrorCode SNESUpdateDMMoose	(	SNES	snes,
		PetscInt	iteration
	)

Definition at line 2139 of file PetscDMMoose.C.

{
  /* This is called any time the structure of the problem changes in a way that affects the Jacobian
     sparsity pattern.
     For example, this may happen when NodeFaceConstraints change Jacobian's sparsity pattern based
     on newly-detected Penetration.
     In that case certain preconditioners (e.g., PCASM) will not work, unless we tell them that the
     sparsity pattern has changed.
     For now we are rebuilding the whole KSP, when necessary.
  */
  DM dm;
  KSP ksp;
  const char * prefix;
  MPI_Comm comm;
  PC pc;
 
  PetscFunctionBegin;
  if (iteration)
  {
    /* TODO: limit this only to situations when displaced (un)contact splits are present, as is
     * DisplacedProblem(). */
    LibmeshPetscCallQ(SNESGetDM(snes, &dm));
    LibmeshPetscCallQ(DMMooseReset(dm));
    LibmeshPetscCallQ(DMSetUp(dm));
    LibmeshPetscCallQ(SNESGetKSP(snes, &ksp));
    /* Should we rebuild the whole KSP? */
    LibmeshPetscCallQ(PetscObjectGetOptionsPrefix((PetscObject)ksp, &prefix));
    LibmeshPetscCallQ(PetscObjectGetComm((PetscObject)ksp, &comm));
    LibmeshPetscCallQ(PCCreate(comm, &pc));
    LibmeshPetscCallQ(PCSetDM(pc, dm));
    LibmeshPetscCallQ(PCSetOptionsPrefix(pc, prefix));
    LibmeshPetscCallQ(PCSetFromOptions(pc));
    LibmeshPetscCallQ(KSPSetPC(ksp, pc));
    LibmeshPetscCallQ(PCDestroy(&pc));
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

Variable Documentation

_include_all_contact_nodes

oopt<< "-dm_moose_includeAllContactNodes"; ohelp << "Whether to include all nodes on the contact surfaces into the subsolver"; LibmeshPetscCallQ(PetscOptionsBool(oopt.str().c_str(), ohelp.str().c_str(), "", PETSC_FALSE, &is_include_all_nodes, LIBMESH_PETSC_NULLPTR)); dmm-> _include_all_contact_nodes = is_include_all_nodes

Definition at line 1880 of file PetscDMMoose.C.

blocks

char** blocks

Definition at line 1731 of file PetscDMMoose.C.

Referenced by Moose::MFEM::CoefficientMap< T, Tpw >::addPiecewiseBlocks(), SystemBase::addVariable(), FEProblemBase::checkProblemIntegrity(), FEProblemBase::computeJacobianBlock(), NonlinearSystemBase::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianBlocks(), FEProblemBase::computeJacobianBlocks(), EigenProblem::computeJacobianBlocks(), Moose::MFEM::CoefficientManager::declareMatrixProperty(), Moose::MFEM::CoefficientManager::declareMatrixProperty(), Moose::MFEM::CoefficientManager::declareMatrixProperty(), Moose::MFEM::CoefficientManager::declareScalarProperty(), Moose::MFEM::CoefficientManager::declareScalarProperty(), Moose::MFEM::CoefficientManager::declareScalarProperty(), Moose::MFEM::CoefficientManager::declareVectorProperty(), Moose::MFEM::CoefficientManager::declareVectorProperty(), Moose::MFEM::CoefficientManager::declareVectorProperty(), DMMooseGetMeshBlocks_Private(), DMMooseSetBlocks(), DMSetUp_Moose_Pre(), DumpObjectsProblem::dumpVariableHelper(), MultiAppUserObjectTransfer::execute(), ExtraIDIntegralReporter::ExtraIDIntegralReporter(), DiracKernelInfo::findPoint(), RenumberBySubdomainGenerator::generate(), SubdomainPerElementGenerator::generate(), MaterialPropertyInterface::getBlockMaterialProperty(), MooseMesh::getBlocksMaxDimension(), MaterialPropertyInterface::getKokkosBlockMaterialProperty(), SubProblem::getMaterialPropertyBlockNames(), SubProblem::getMaterialPropertyBlocks(), AddVariableAction::getSubdomainIDs(), MooseObjectWarehouseBase< T >::hasObjectsForVariableAndBlocks(), MultiAppGeneralFieldTransfer::inBlocks(), MultiAppGeneralFieldTransfer::inBlocks(), MultiAppGeneralFieldKDTreeTransferBase::inBlocks(), MultiAppGeneralFieldTransfer::inBlocks(), BlockRestrictionDebugOutput::printBlockRestrictionGroups(), NonlinearSystemBase::reinitNodeFace(), MooseMesh::setCoordSystem(), FEProblemBase::setCoordSystem(), MooseMesh::setGeneralAxisymmetricCoordAxes(), PhysicsBasedPreconditioner::setup(), BreakMeshByBlockGenerator::syncConnectedBlocks(), and GlobalParamsAction::validParams().

blockset

blockset

Definition at line 1733 of file PetscDMMoose.C.

contact_displaced

contact_displaced

Definition at line 1868 of file PetscDMMoose.C.

contacts

contacts

Definition at line 1868 of file PetscDMMoose.C.

Referenced by DMMooseSetContacts().

displaced_problem

std::shared_ptr<DisplacedProblem> displaced_problem = dmm->_nl->feProblem().getDisplacedProblem()

Definition at line 1798 of file PetscDMMoose.C.

Referenced by FEProblemBase::addDisplacedProblem(), NonlinearSystemBase::assembleScalingVector(), MooseApp::attachRelationshipManagers(), NonlinearSystemBase::computeJacobianInternal(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::computeScaling(), MultiApp::createApp(), DMMooseGetEmbedding_Private(), ActivateElementsUserObjectBase::execute(), ActivateElementsUserObjectBase::finalize(), EqualValueBoundaryConstraint::ghostPrimary(), AddPeriodicBCAction::onSetupPeriodicBoundary(), ActivateElementsUserObjectBase::setNewBoundayName(), and Moose::PeriodicBCHelper::setupPeriodicBoundaries().

dm

PetscErrorCode PetscOptionItems *PetscErrorCode DM dm

Initial value:

{
  DM_Moose * dmm = (DM_Moose *)dm->data

Definition at line 1691 of file PetscDMMoose.C.

Referenced by FieldSplitPreconditionerTempl< Base >::createMooseDM(), DMCreate_Moose(), DMCreateDomainDecomposition_Moose(), DMCreateFieldDecomposition_Moose(), DMCreateGlobalVector_Moose(), DMCreateMatrix_Moose(), DMCreateMoose(), DMDestroy_Moose(), DMMooseFunction(), DMMooseGetBlocks(), DMMooseGetContacts(), DMMooseGetEmbedding_Private(), DMMooseGetMeshBlocks_Private(), DMMooseGetNonlinearSystem(), DMMooseGetSides(), DMMooseGetSplitNames(), DMMooseGetUnContacts(), DMMooseGetUnSides(), DMMooseGetVariables(), DMMooseJacobian(), DMMooseReset(), DMMooseSetBlocks(), DMMooseSetContacts(), DMMooseSetDofMap(), DMMooseSetName(), DMMooseSetNonlinearSystem(), DMMooseSetParentDM(), DMMooseSetSides(), DMMooseSetSplitNames(), DMMooseSetSystem(), DMMooseSetUnContacts(), DMMooseSetUnSideByVar(), DMMooseSetUnSides(), DMMooseSetVariables(), DMMooseValidityCheck(), DMSetUp_Moose(), DMSetUp_Moose_Pre(), DMVariableBounds_Moose(), DMView_Moose(), if(), FieldSplitPreconditioner::setupDM(), StaticCondensationFieldSplitPreconditioner::setupDM(), SNESFunction_DMMoose(), SNESJacobian_DMMoose(), and SNESUpdateDMMoose().

DM_Moose

No Moose system set for DM_Moose

Definition at line 1699 of file PetscDMMoose.C.

fdhelp

const char* fdhelp

Initial value:

= "Number of named fieldsplits defined by the DM.\n\
                \tNames of fieldsplits are defined by -dm_moose_fieldsplit_names <splitname1> <splitname2> ...\n\
                \tEach split can be configured with its own variables, blocks and sides, as any DMMoose"

Definition at line 1952 of file PetscDMMoose.C.

help

help = "Variables in DMMoose"

Definition at line 1709 of file PetscDMMoose.C.

Referenced by Moose::internal::Capabilities::registerMooseCapabilities().

is_include_all_nodes

PetscBool is_include_all_nodes

Initial value:

{
    std::ostringstream oopt, ohelp

Definition at line 1871 of file PetscDMMoose.C.

maxblocks

PetscInt maxblocks = meshblocks.size()

Definition at line 1730 of file PetscDMMoose.C.

maxcontacts

PetscInt maxcontacts = dmm->_nl->feProblem().geomSearchData()._penetration_locators.size()

Definition at line 1797 of file PetscDMMoose.C.

maxsides

PetscInt maxsides = dmm->_system->get_mesh().get_boundary_info().get_global_boundary_ids().size()

Definition at line 1747 of file PetscDMMoose.C.

maxvars

PetscInt maxvars = dmm->_dof_map->n_variables()

Definition at line 1710 of file PetscDMMoose.C.

meshblocks

std::set<subdomain_id_type> meshblocks

Definition at line 1728 of file PetscDMMoose.C.

nblocks

PetscInt nblocks = maxblocks

Definition at line 1734 of file PetscDMMoose.C.

nsides

nsides = maxsides

Definition at line 1750 of file PetscDMMoose.C.

nsplits

PetscInt nsplits = 0

Definition at line 1949 of file PetscDMMoose.C.

Referenced by if().

nuncontacts

PetscInt nuncontacts = 0

Definition at line 1884 of file PetscDMMoose.C.

nvars

PetscInt nvars = maxvars

Definition at line 1713 of file PetscDMMoose.C.

opt

opt = "-dm_moose_vars"

Definition at line 1709 of file PetscDMMoose.C.

Referenced by Moose::findSimilar(), and BoundaryDeletionGenerator::validParams().

PETSC_ERR_ARG_WRONGSTATE

PETSC_ERR_ARG_WRONGSTATE

Definition at line 1699 of file PetscDMMoose.C.

Referenced by DMCreateGlobalVector_Moose(), DMCreateMatrix_Moose(), DMMooseGetMeshBlocks_Private(), DMMooseGetSplitNames(), DMMooseReset(), DMMooseSetBlocks(), DMMooseSetContacts(), DMMooseSetDofMap(), DMMooseSetName(), DMMooseSetNonlinearSystem(), DMMooseSetParentDM(), DMMooseSetSides(), DMMooseSetSystem(), DMMooseSetUnContacts(), DMMooseSetUnSideByVar(), DMMooseSetUnSides(), DMMooseSetVariables(), DMSetUp_Moose(), and DMSetUp_Moose_Pre().

PetscFunctionBegin

PetscFunctionBegin

Definition at line 1696 of file PetscDMMoose.C.

Referenced by DMCreate_Moose(), DMCreateDomainDecomposition_Moose(), DMCreateFieldDecomposition_Moose(), DMCreateGlobalVector_Moose(), DMCreateMatrix_Moose(), DMCreateMoose(), DMDestroy_Moose(), DMMooseFunction(), DMMooseGetBlocks(), DMMooseGetContacts(), DMMooseGetEmbedding_Private(), DMMooseGetMeshBlocks_Private(), DMMooseGetNonlinearSystem(), DMMooseGetSides(), DMMooseGetSplitNames(), DMMooseGetUnContacts(), DMMooseGetUnSides(), DMMooseGetVariables(), DMMooseJacobian(), DMMooseRegisterAll(), DMMooseReset(), DMMooseSetBlocks(), DMMooseSetContacts(), DMMooseSetDofMap(), DMMooseSetName(), DMMooseSetNonlinearSystem(), DMMooseSetParentDM(), DMMooseSetSides(), DMMooseSetSplitNames(), DMMooseSetSystem(), DMMooseSetUnContacts(), DMMooseSetUnSideByVar(), DMMooseSetUnSides(), DMMooseSetVariables(), DMMooseValidityCheck(), DMSetUp_Moose(), DMSetUp_Moose_Pre(), DMVariableBounds_Moose(), DMView_Moose(), Moose::SlepcSupport::mooseEPSFormMatrices(), Moose::SlepcSupport::mooseMatMult_Eigen(), Moose::SlepcSupport::mooseMatMult_NonEigen(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionA(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionAB(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionB(), Moose::SlepcSupport::mooseSlepcEigenFormFunctionMFFD(), Moose::SlepcSupport::mooseSlepcEigenFormJacobianA(), Moose::SlepcSupport::mooseSlepcEigenFormJacobianB(), Moose::SlepcSupport::mooseSlepcEigenFormNorm(), Moose::SlepcSupport::mooseSlepcEPSGetSNES(), Moose::SlepcSupport::mooseSlepcEPSMonitor(), Moose::SlepcSupport::mooseSlepcEPSSNESKSPSetPCSide(), Moose::SlepcSupport::mooseSlepcEPSSNESSetCustomizePC(), Moose::SlepcSupport::mooseSlepcEPSSNESSetUpOptionPrefix(), Moose::SlepcSupport::mooseSlepcStoppingTest(), Moose::SlepcSupport::PCApply_MoosePC(), Moose::SlepcSupport::PCCreate_MoosePC(), Moose::SlepcSupport::PCDestroy_MoosePC(), Moose::SlepcSupport::PCSetUp_MoosePC(), Moose::SlepcSupport::PCView_MoosePC(), Moose::PetscSupport::petscLinearConverged(), Moose::PetscSupport::petscNonlinearConverged(), Moose::PetscSupport::petscSetupOutput(), Moose::SlepcSupport::registerPCToPETSc(), SNESFunction_DMMoose(), SNESJacobian_DMMoose(), and SNESUpdateDMMoose().

sides

char** sides

Definition at line 1748 of file PetscDMMoose.C.

Referenced by ElementSubdomainModifierBase::applyMovingBoundaryChanges(), clear(), DMMooseSetSides(), AdvancedExtruderGenerator::generate(), and ElementGenerator::generate().

sideset

sideset

Definition at line 1751 of file PetscDMMoose.C.

Referenced by clear(), MooseMeshUtils::createSubdomainFromSidesets(), and MooseMeshElementConversionUtils::transitionLayerGenerator().

uncontact_displaced

uncontact_displaced

Definition at line 1883 of file PetscDMMoose.C.

uncontacts

uncontacts

Definition at line 1882 of file PetscDMMoose.C.

Referenced by DMMooseSetUnContacts().

vars

char** vars

Definition at line 1711 of file PetscDMMoose.C.

Referenced by AddFunctionAction::act(), VariableWarehouse::addBoundaryVars(), Assembly::addJacobianOffDiagScalar(), MooseVariableDependencyInterface::addMooseVariableDependency(), Assembly::addResidual(), Assembly::addResidualLower(), Assembly::addResidualNeighbor(), Assembly::addResidualScalar(), AllLocalDofIndicesThread::AllLocalDofIndicesThread(), DerivativeParsedMaterialHelperTempl< is_ad >::assembleDerivatives(), Assembly::cacheResidual(), Assembly::cacheResidualLower(), Assembly::cacheResidualNeighbor(), NonlinearSystemBase::checkKernelCoverage(), ComputeFullJacobianThread::computeOnBoundary(), ComputeFullJacobianThread::computeOnElement(), Coupleable::Coupleable(), DMMooseSetVariables(), ADFParser::Eval(), MultiAppPostprocessorInterpolationTransfer::execute(), for(), FEProblemBase::getFunction(), SystemBase::getMinQuadratureOrder(), AuxiliarySystem::getMinQuadratureOrder(), TransientBase::getTimeIntegratorNames(), AddPeriodicBCAction::getVariables(), Coupleable::getVarsHelper(), InputParameters::getVecMooseType(), SolutionAux::initialSetup(), SolutionScalarAux::initialSetup(), Axisymmetric2D3DSolutionFunction::initialSetup(), Assembly::initNonlocalCoupling(), Moose::isSectionActive(), SystemBase::prepare(), SystemBase::prepareFace(), Assembly::prepareLowerD(), SystemBase::prepareLowerD(), Assembly::prepareNeighbor(), SystemBase::prepareNeighbor(), Assembly::prepareOffDiagScalar(), Assembly::prepareResidual(), Assembly::prepareScalar(), ProjectedStatefulMaterialStorageAction::processProperty(), InputParameters::rangeCheck(), SystemBase::reinitElem(), SystemBase::reinitElemFace(), SystemBase::reinitLowerD(), SystemBase::reinitNeighbor(), SystemBase::reinitNeighborFace(), SystemBase::reinitNode(), SystemBase::reinitNodeFace(), SystemBase::reinitNodes(), SystemBase::reinitNodesNeighbor(), SystemBase::reinitScalars(), ScalarCoupleable::ScalarCoupleable(), FixedPointSolve::setMultiAppTransformedVariables(), FEProblemBase::setNonlocalCouplingMatrix(), Assembly::setResidual(), Assembly::setResidualNeighbor(), SingleMatrixPreconditioner::SingleMatrixPreconditioner(), VariableCondensationPreconditioner::VariableCondensationPreconditioner(), and BadActiveWalker::walk().

varset

varset

Definition at line 1712 of file PetscDMMoose.C.

Referenced by for().