PetscDMMoose.C File Reference

Go to the source code of this file.

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	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(((PetscObject) dm) ->comm 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 std::string &dm_name, DM *dm)
	Create a MOOSE DM. More...
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->_nl->system().get_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
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 39 of file PetscDMMoose.C.

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

{
  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.");
}

clear()

sideset clear

(

)

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

DMCreate_Moose()

EXTERN_C_BEGIN PetscErrorCode DMCreate_Moose

(

DM

dm

)

Definition at line 2056 of file PetscDMMoose.C.

Referenced by DMMooseRegisterAll().

{
  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);
}

DMCreateDomainDecomposition_Moose()

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

static

Definition at line 931 of file PetscDMMoose.C.

Referenced by DMCreate_Moose().

{
  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);
}

DMCreateFieldDecomposition_Moose()

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

static

Definition at line 819 of file PetscDMMoose.C.

Referenced by DMCreate_Moose(), and DMCreateDomainDecomposition_Moose().

{
  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, 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->_nl->nonlinearSolver()->system().get_system_matrix().local_m());

  PetscFunctionReturn(PETSC_SUCCESS);
}

DMCreateGlobalVector_Moose()

static PetscErrorCode DMCreateGlobalVector_Moose ( DM  dm, Vec *  x  )

static

Definition at line 1136 of file PetscDMMoose.C.

Referenced by DMCreate_Moose().

{
  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->_nl->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);
}

DMCreateMatrix_Moose()

static PetscErrorCode DMCreateMatrix_Moose ( DM  dm, Mat *  A  )

static

Definition at line 1173 of file PetscDMMoose.C.

Referenced by DMCreate_Moose().

{
  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.
   */
  DofMap & dof_map = dmm->_nl->system().get_dof_map();
  PetscInt M, N, m, n;
  MPI_Comm comm;
  M = dof_map.n_dofs();
  N = M;
  m = static_cast<PetscInt>(dof_map.n_dofs_on_processor(dmm->_nl->system().processor_id()));
  n = m;
  LibmeshPetscCallQ(PetscObjectGetComm((PetscObject)dm, &comm));
  LibmeshPetscCallQ(MatCreate(comm, A));
  LibmeshPetscCallQ(MatSetSizes(*A, m, n, M, N));
  LibmeshPetscCallQ(MatSetType(*A, type));
  /* Set preallocation for the basic sparse matrix types (applies only if *A has the right type. */
  /* For now we ignore blocksize issues, since BAIJ doesn't play well with field decomposition by
   * variable. */
  const std::vector<numeric_index_type> & n_nz = dof_map.get_n_nz();
  const std::vector<numeric_index_type> & n_oz = dof_map.get_n_oz();
  LibmeshPetscCallQ(MatSeqAIJSetPreallocation(*A, 0, (PetscInt *)(n_nz.empty() ? NULL : &n_nz[0])));
  LibmeshPetscCallQ(MatMPIAIJSetPreallocation(*A,
                                              0,
                                              (PetscInt *)(n_nz.empty() ? NULL : &n_nz[0]),
                                              0,
                                              (PetscInt *)(n_oz.empty() ? NULL : &n_oz[0])));
  /* TODO: set the prefix for *A and MatSetFromOptions(*A)? Might override the type and other
   * settings made here. */
  LibmeshPetscCallQ(MatSetUp(*A));
  PetscFunctionReturn(PETSC_SUCCESS);
}

DMCreateMoose()

PetscErrorCode DMCreateMoose	(	MPI_Comm	comm,
		NonlinearSystemBase &	nl,
		const std::string &	dm_name,
		DM *	dm
	)

Create a MOOSE DM.

Parameters

comm	The communicator that the DM should use
nl	The nonlinear system context that the DM is associated with
dm_name	A name to associate with the DM
dm	A pointer to the PETSc DM

Definition at line 2044 of file PetscDMMoose.C.

Referenced by DMCreateFieldDecomposition_Moose(), and Moose::PetscSupport::petscSetupDM().

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

DMDestroy_Moose()

static PetscErrorCode DMDestroy_Moose ( DM  dm )

static

Definition at line 1994 of file PetscDMMoose.C.

Referenced by DMCreate_Moose().

{
  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);
}

DMMooseFunction()

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

static

Definition at line 944 of file PetscDMMoose.C.

Referenced by SNESFunction_DMMoose().

{
  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);
}

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 482 of file PetscDMMoose.C.

Referenced by DMCreateFieldDecomposition_Moose(), and DMSetUp_Moose().

{
  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)
    {
      DofMap & dofmap = dmm->_nl->system().get_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->_nl->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 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->_nl->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
                  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())
              {
                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);
}

DMMooseGetMeshBlocks_Private()

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

static

Definition at line 1318 of file PetscDMMoose.C.

Referenced by DMSetUp_Moose_Pre().

{
  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->_nl->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);
}

DMMooseGetNonlinearSystem()

PetscErrorCode DMMooseGetNonlinearSystem	(	DM	dm,
		NonlinearSystemBase *&	nl
	)

Definition at line 416 of file PetscDMMoose.C.

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

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

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 462 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 1023 of file PetscDMMoose.C.

Referenced by SNESJacobian_DMMoose().

{
  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);
}

DMMooseRegisterAll()

PetscErrorCode DMMooseRegisterAll

(

)

Definition at line 2156 of file PetscDMMoose.C.

Referenced by Moose::PetscSupport::petscSetupDM().

{
  static PetscBool DMMooseRegisterAllCalled = PETSC_FALSE;

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

DMMooseReset()

PetscErrorCode DMMooseReset

(

DM

dm

)

Definition at line 1594 of file PetscDMMoose.C.

Referenced by SNESUpdateDMMoose().

{
  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);
}

DMMooseSetBlocks()

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

Definition at line 295 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 355 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);
}

DMMooseSetName()

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

Definition at line 237 of file PetscDMMoose.C.

Referenced by DMCreateMoose().

{
  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);
}

DMMooseSetNonlinearSystem()

PetscErrorCode DMMooseSetNonlinearSystem	(	DM	dm,
		NonlinearSystemBase &	nl
	)

Definition at line 223 of file PetscDMMoose.C.

Referenced by DMCreateMoose().

{
  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);
}

DMMooseSetParentDM()

PetscErrorCode DMMooseSetParentDM	(	DM	dm,
		DM_Moose *	parent
	)

Definition at line 251 of file PetscDMMoose.C.

Referenced by DMCreateFieldDecomposition_Moose().

{
  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);
}

DMMooseSetSides()

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

Definition at line 310 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 426 of file PetscDMMoose.C.

Referenced by if().

{
  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);
}

DMMooseSetUnContacts()

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

Definition at line 385 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 340 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 325 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 266 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)
            ? static_cast<MooseVariableBase *>(&dmm->_nl->getVariable(0, var_name))
            : static_cast<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.

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

{
  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);
}

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 1618 of file PetscDMMoose.C.

Referenced by DMCreate_Moose().

{
  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);
}

DMSetUp_Moose_Pre()

static PetscErrorCode DMSetUp_Moose_Pre ( DM  dm )

static

Definition at line 1339 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. */
  DofMap & dofmap = dmm->_nl->system().get_dof_map();
  /* libMesh mesh */
  const MeshBase & mesh = dmm->_nl->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->_nl->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 1113 of file PetscDMMoose.C.

Referenced by DMSetUp_Moose().

{
  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);
}

DMView_Moose()

static PetscErrorCode DMView_Moose ( DM  dm, PetscViewer  viewer  )

static

Definition at line 1220 of file PetscDMMoose.C.

Referenced by DMCreate_Moose().

{
  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);
}

for()

for

(

)

Definition at line 1703 of file PetscDMMoose.C.

Referenced by ComponentBoundaryConditionInterface::checkBoundaryConditionsAllRequested(), FEProblemBase::checkDependMaterialsHelper(), DMMooseGetBlocks(), DMMooseGetContacts(), DMMooseGetSides(), DMMooseGetUnContacts(), DMMooseGetUnSides(), and MaterialPropertyStorage::initStatefulProps().

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

if() [1/9]

if

(

!dmm->

_nl

)

Referenced by ComponentBoundaryConditionInterface::checkBoundaryConditionsAllRequested(), MooseApp::getExecutor(), operator<<(), NonlinearSystem::solve(), and to_json().

if() [2/9]

if

(

varset.

size()

)

if() [3/9]

if

(

blockset.

size()

)

if() [4/9]

if

(

sideset.

size()

)

if() [5/9]

if

(

displaced_problem

)

Definition at line 1784 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() [6/9]

if

(

contacts.

size()

)

if() [7/9]

if	(	LIBMESH_SETERRQ2(((PetscObject)dm)->comm	nuncontacts,
		maxcontacts
	)

Definition at line 1883 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() [8/9]

if

(

uncontacts.

size()

)

if() [9/9]

if

(

nsplits

)

Definition at line 1942 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));
  }

LibmeshPetscCallQ() [1/18]

LibmeshPetscCallQ

(

DMMooseValidityCheck(dm)

)

LibmeshPetscCallQ() [2/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [3/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [4/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [5/18]

LibmeshPetscCallQ

(

PetscFree(vars)

)

LibmeshPetscCallQ() [6/18]

LibmeshPetscCallQ

(

DMMooseGetMeshBlocks_Private(dm, meshblocks)

)

LibmeshPetscCallQ() [7/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [8/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [9/18]

LibmeshPetscCallQ

(

PetscFree(blocks)

)

LibmeshPetscCallQ() [10/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [11/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [12/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [13/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [14/18]

LibmeshPetscCallQ

(

PetscFree(sides)

)

LibmeshPetscCallQ() [15/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [16/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [17/18]

LibmeshPetscCallQ

(

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

)

LibmeshPetscCallQ() [18/18]

LibmeshPetscCallQ

(

DMSetUp_Moose_Pre(dm)

)

PetscFunctionReturn()

PetscFunctionReturn

(

PETSC_SUCCESS

)

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 1013 of file PetscDMMoose.C.

Referenced by DMSetUp_Moose().

{
  DM dm = (DM)ctx;

  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseFunction(dm, x, r));
  PetscFunctionReturn(PETSC_SUCCESS);
}

SNESJacobian_DMMoose()

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

static

Definition at line 1103 of file PetscDMMoose.C.

Referenced by DMSetUp_Moose().

{
  DM dm = (DM)ctx;

  PetscFunctionBegin;
  LibmeshPetscCallQ(DMMooseJacobian(dm, x, jac, pc));
  PetscFunctionReturn(PETSC_SUCCESS);
}

SNESUpdateDMMoose()

PetscErrorCode SNESUpdateDMMoose	(	SNES	snes,
		PetscInt	iteration
	)

Definition at line 2117 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 1865 of file PetscDMMoose.C.

blocks

char** blocks

Definition at line 1715 of file PetscDMMoose.C.

Referenced by Moose::MFEM::CoefficientMap< mfem::MatrixCoefficient, mfem::PWMatrixCoefficient >::addPiecewiseBlocks(), SystemBase::addVariable(), FEProblemBase::checkProblemIntegrity(), FEProblemBase::computeJacobianBlock(), EigenProblem::computeJacobianBlocks(), NonlinearSystemBase::computeJacobianBlocks(), FEProblemBase::computeJacobianBlocks(), Moose::MFEM::CoefficientManager::declareMatrixProperty(), Moose::MFEM::CoefficientManager::declareScalarProperty(), Moose::MFEM::CoefficientManager::declareVectorProperty(), DMMooseGetMeshBlocks_Private(), DMMooseSetBlocks(), DMSetUp_Moose_Pre(), DumpObjectsProblem::dumpVariableHelper(), MultiAppUserObjectTransfer::execute(), ExtraIDIntegralReporter::ExtraIDIntegralReporter(), DiracKernelInfo::findPoint(), SubdomainPerElementGenerator::generate(), MaterialPropertyInterface::getBlockMaterialProperty(), MooseMesh::getBlocksMaxDimension(), SubProblem::getMaterialPropertyBlockNames(), SubProblem::getMaterialPropertyBlocks(), AddVariableAction::getSubdomainIDs(), MooseObjectWarehouseBase< Indicator >::hasObjectsForVariableAndBlocks(), MultiAppGeneralFieldNearestLocationTransfer::inBlocks(), MultiAppGeneralFieldTransfer::initialSetup(), FEProblemBase::setCoordSystem(), MooseMesh::setCoordSystem(), MooseMesh::setGeneralAxisymmetricCoordAxes(), PhysicsBasedPreconditioner::setup(), and GlobalParamsAction::validParams().

blockset

blockset

Definition at line 1717 of file PetscDMMoose.C.

contact_displaced

contact_displaced

Definition at line 1853 of file PetscDMMoose.C.

contacts

contacts

Definition at line 1853 of file PetscDMMoose.C.

Referenced by DMMooseSetContacts().

displaced_problem

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

Definition at line 1783 of file PetscDMMoose.C.

Referenced by AddPeriodicBCAction::act(), FEProblemBase::addDisplacedProblem(), NonlinearSystemBase::assembleScalingVector(), MooseApp::attachRelationshipManagers(), AddPeriodicBCAction::autoTranslationBoundaries(), NonlinearSystemBase::computeJacobianInternal(), NonlinearSystemBase::computeResidualAndJacobianInternal(), NonlinearSystemBase::computeResidualInternal(), NonlinearSystemBase::computeScaling(), MultiApp::createApp(), DMMooseGetEmbedding_Private(), ActivateElementsUserObjectBase::execute(), ActivateElementsUserObjectBase::finalize(), FEProblemBase::initialSetup(), and ActivateElementsUserObjectBase::setNewBoundayName().

dm

PetscErrorCode PetscOptionItems* PetscErrorCode DM dm

Initial value:

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

Definition at line 1677 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(), DMMooseReset(), DMMooseSetBlocks(), DMMooseSetContacts(), DMMooseSetName(), DMMooseSetNonlinearSystem(), DMMooseSetParentDM(), DMMooseSetSides(), DMMooseSetSplitNames(), DMMooseSetUnContacts(), DMMooseSetUnSideByVar(), DMMooseSetUnSides(), DMMooseSetVariables(), DMMooseValidityCheck(), DMSetUp_Moose(), DMSetUp_Moose_Pre(), DMVariableBounds_Moose(), DMView_Moose(), if(), Moose::PetscSupport::petscSetupDM(), SNESFunction_DMMoose(), SNESJacobian_DMMoose(), and SNESUpdateDMMoose().

DM_Moose

No Moose system set for DM_Moose

Definition at line 1683 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 1937 of file PetscDMMoose.C.

help

help = "Variables in DMMoose"

Definition at line 1693 of file PetscDMMoose.C.

is_include_all_nodes

PetscBool is_include_all_nodes

Initial value:

{
    std::ostringstream oopt, ohelp

Definition at line 1854 of file PetscDMMoose.C.

maxblocks

PetscInt maxblocks = meshblocks.size()

Definition at line 1714 of file PetscDMMoose.C.

maxcontacts

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

Definition at line 1782 of file PetscDMMoose.C.

maxsides

PetscInt maxsides

Initial value:

=
      dmm->_nl->system().get_mesh().get_boundary_info().get_global_boundary_ids().size()

Definition at line 1731 of file PetscDMMoose.C.

maxvars

PetscInt maxvars = dmm->_nl->system().get_dof_map().n_variables()

Definition at line 1694 of file PetscDMMoose.C.

meshblocks

std::set<subdomain_id_type> meshblocks

Definition at line 1712 of file PetscDMMoose.C.

nblocks

PetscInt nblocks = maxblocks

Definition at line 1718 of file PetscDMMoose.C.

nsides

nsides = maxsides

Definition at line 1735 of file PetscDMMoose.C.

nsplits

PetscInt nsplits = 0

Definition at line 1934 of file PetscDMMoose.C.

Referenced by if().

nuncontacts

PetscInt nuncontacts = 0

Definition at line 1869 of file PetscDMMoose.C.

nvars

PetscInt nvars = maxvars

Definition at line 1697 of file PetscDMMoose.C.

opt

opt = "-dm_moose_vars"

Definition at line 1693 of file PetscDMMoose.C.

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

PETSC_ERR_ARG_WRONGSTATE

PETSC_ERR_ARG_WRONGSTATE

Definition at line 1683 of file PetscDMMoose.C.

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

PetscFunctionBegin

PetscFunctionBegin

Definition at line 1680 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(), DMMooseSetName(), DMMooseSetNonlinearSystem(), DMMooseSetParentDM(), DMMooseSetSides(), DMMooseSetSplitNames(), 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 1733 of file PetscDMMoose.C.

Referenced by ElementSubdomainModifierBase::applyMovingBoundaryChanges(), PenetrationThread::createInfoForElem(), DMMooseSetSides(), and PenetrationThread::getSidesOnPrimaryBoundary().

sideset

sideset

Definition at line 1736 of file PetscDMMoose.C.

Referenced by LowerDBlockFromSidesetGenerator::generate().

uncontact_displaced

uncontact_displaced

Definition at line 1868 of file PetscDMMoose.C.

uncontacts

uncontacts

Definition at line 1867 of file PetscDMMoose.C.

Referenced by DMMooseSetUnContacts().

vars

char** vars

Definition at line 1695 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(), FunctionMaterialBase< is_ad >::FunctionMaterialBase(), FEProblemBase::getFunction(), AuxiliarySystem::getMinQuadratureOrder(), SystemBase::getMinQuadratureOrder(), TransientBase::getTimeIntegratorNames(), InputParameters::getVecMooseType(), Assembly::init(), SolutionScalarAux::initialSetup(), SolutionAux::initialSetup(), Axisymmetric2D3DSolutionFunction::initialSetup(), Assembly::initNonlocalCoupling(), Moose::isSectionActive(), SystemBase::prepare(), SystemBase::prepareFace(), SystemBase::prepareLowerD(), Assembly::prepareLowerD(), SystemBase::prepareNeighbor(), Assembly::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 1696 of file PetscDMMoose.C.

Referenced by for().