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Function Documentation
| static PetscErrorCode DMCreateDomainDecomposition_libMesh | ( | DM | dm, |
| PetscInt * | len, | ||
| char *** | namelist, | ||
| IS ** | innerislist, | ||
| IS ** | outerislist, | ||
| DM ** | dmlist | ||
| ) | [static] |
Definition at line 350 of file petscdmlibmeshimpl.C.
References libMesh::MeshBase::active_local_subdomain_elements_begin(), libMesh::MeshBase::active_local_subdomain_elements_end(), DM_libMesh::blockids, DM_libMesh::blocknames, DM_libMesh::decomposition, DM_libMesh::decomposition_type, DMlibMeshSetUpName_Private(), libMesh::DofMap::dof_indices(), DM_libMesh::embedding, DM_libMesh::embedding_type, end, libMesh::DofMap::end_dof(), libMesh::DofMap::first_dof(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::ierr, PETSC_OWN_POINTER, DM_libMesh::sys, libMesh::sys, DM_libMesh::varids, and DM_libMesh::varnames.
{
PetscFunctionBegin;
PetscErrorCode ierr;
DM_libMesh *dlm = (DM_libMesh *)(dm->data);
NonlinearImplicitSystem *sys = dlm->sys;
IS emb;
if(dlm->decomposition_type != DMLIBMESH_DOMAIN_DECOMPOSITION) PetscFunctionReturn(0);
*len = dlm->decomposition->size();
if(namelist) {ierr = PetscMalloc(*len*sizeof(char*), namelist); CHKERRQ(ierr);}
if(innerislist) {ierr = PetscMalloc(*len*sizeof(IS), innerislist); CHKERRQ(ierr);}
if(outerislist) *outerislist = PETSC_NULL; /* FIX: allow mesh-based overlap. */
if(dmlist) {ierr = PetscMalloc(*len*sizeof(DM), dmlist); CHKERRQ(ierr);}
for(unsigned int d = 0; d < dlm->decomposition->size(); ++d) {
std::set<numeric_index_type> dindices;
std::string dname;
std::map<std::string, unsigned int> dblockids;
std::map<unsigned int,std::string> dblocknames;
unsigned int dbcount = 0;
for(std::set<unsigned int>::const_iterator bit = (*dlm->decomposition)[d].begin(); bit != (*dlm->decomposition)[d].end(); ++bit){
unsigned int b = *bit;
std::string bname = (*dlm->blocknames)[b];
dblockids.insert(std::pair<std::string, unsigned int>(bname,b));
dblocknames.insert(std::pair<unsigned int,std::string>(b,bname));
if(!dbcount) dname = bname;
else dname += "_" + bname;
++dbcount;
if(!innerislist) continue;
MeshBase::const_element_iterator el = sys->get_mesh().active_local_subdomain_elements_begin(b);
const MeshBase::const_element_iterator end_el = sys->get_mesh().active_local_subdomain_elements_end(b);
for ( ; el != end_el; ++el) {
const Elem* elem = *el;
std::vector<numeric_index_type> evindices;
/* Iterate only over this DM's variables. */
for(std::map<std::string, unsigned int>::const_iterator vit = dlm->varids->begin(); vit != dlm->varids->end(); ++vit) {
unsigned int v = vit->second;
// Get the degree of freedom indices for the given variable off the current element.
sys->get_dof_map().dof_indices(elem, evindices, v);
for(unsigned int i = 0; i < evindices.size(); ++i) {
numeric_index_type dof = evindices[i];
if(dof >= sys->get_dof_map().first_dof() && dof < sys->get_dof_map().end_dof()) /* might want to use variable_first/last_local_dof instead */
dindices.insert(dof);
}
}
}
}
if(namelist) {
ierr = PetscStrallocpy(dname.c_str(),(*namelist)+d); CHKERRQ(ierr);
}
if(innerislist) {
PetscInt *darray;
IS dis;
ierr = PetscMalloc(sizeof(PetscInt)*dindices.size(), &darray); CHKERRQ(ierr);
numeric_index_type i = 0;
for(std::set<numeric_index_type>::const_iterator it = dindices.begin(); it != dindices.end(); ++it) {
darray[i] = *it;
++i;
}
ierr = ISCreateGeneral(((PetscObject)dm)->comm, dindices.size(),darray, PETSC_OWN_POINTER, &dis); CHKERRQ(ierr);
if(dlm->embedding) {
/* Create a relative embedding into the parent's index space. */
#if PETSC_RELEASE_LESS_THAN(3,3,1)
ierr = ISMapFactorRight(dis,dlm->embedding, PETSC_TRUE, &emb); CHKERRQ(ierr);
#else
ierr = ISEmbed(dis,dlm->embedding, PETSC_TRUE, &emb); CHKERRQ(ierr);
#endif
PetscInt elen, dlen;
ierr = ISGetLocalSize(emb, &elen); CHKERRQ(ierr);
ierr = ISGetLocalSize(dis, &dlen); CHKERRQ(ierr);
if(elen != dlen) SETERRQ1(((PetscObject)dm)->comm, PETSC_ERR_PLIB, "Failed to embed field %D", d);
ierr = ISDestroy(&dis); CHKERRQ(ierr);
dis = emb;
}
else {
emb = dis;
}
if(innerislist) {
ierr = PetscObjectReference((PetscObject)dis); CHKERRQ(ierr);
(*innerislist)[d] = dis;
}
ierr = ISDestroy(&dis); CHKERRQ(ierr);
}
if(dmlist) {
DM ddm;
ierr = DMCreate(((PetscObject)dm)->comm, &ddm); CHKERRQ(ierr);
ierr = DMSetType(ddm, DMLIBMESH); CHKERRQ(ierr);
DM_libMesh *ddlm = (DM_libMesh*)(ddm->data);
ddlm->sys = dlm->sys;
/* copy over the varids and varnames */
*ddlm->varids = *dlm->varids;
*ddlm->varnames = *dlm->varnames;
/* set the blocks from the d-th part of the decomposition. */
*ddlm->blockids = dblockids;
*ddlm->blocknames = dblocknames;
ierr = PetscObjectReference((PetscObject)emb); CHKERRQ(ierr);
ddlm->embedding = emb;
ddlm->embedding_type = DMLIBMESH_DOMAIN_EMBEDDING;
ierr = DMlibMeshSetUpName_Private(ddm); CHKERRQ(ierr);
ierr = DMSetFromOptions(ddm); CHKERRQ(ierr);
(*dmlist)[d] = ddm;
}
}
PetscFunctionReturn(0);
}
| static PetscErrorCode DMCreateDomainDecompositionDM_libMesh | ( | DM | dm, |
| const char * | ddesc, | ||
| DM * | ddm | ||
| ) | [static] |
Definition at line 731 of file petscdmlibmeshimpl.C.
References DMlibMeshCreateDomainDecompositionDM(), DMlibMeshParseDecompositionDescriptor_Private(), and libMesh::ierr.
{
PetscFunctionBegin;
PetscErrorCode ierr;
PetscInt dtype, dcount, *dsizes;
char ***dlists;
PetscFunctionBegin;
*ddm = PETSC_NULL;
ierr = DMlibMeshParseDecompositionDescriptor_Private(dm,ddesc,&dtype,&dcount,&dsizes,&dlists); CHKERRQ(ierr);
if(dtype == DMLIBMESH_DOMAIN_DECOMPOSITION) {
ierr = DMlibMeshCreateDomainDecompositionDM(dm,dcount,dsizes,dlists,ddm); CHKERRQ(ierr);
}
else SETERRQ1(((PetscObject)dm)->comm, PETSC_ERR_PLIB, "Uexpected unknown decomposition type for domain decomposition descriptor %s", ddesc);
PetscFunctionReturn(0);
}
| static PetscErrorCode DMCreateFieldDecomposition_libMesh | ( | DM | dm, |
| PetscInt * | len, | ||
| char *** | namelist, | ||
| IS ** | islist, | ||
| DM ** | dmlist | ||
| ) | [static] |
Definition at line 244 of file petscdmlibmeshimpl.C.
References libMesh::MeshBase::active_local_subdomain_elements_begin(), libMesh::MeshBase::active_local_subdomain_elements_end(), DM_libMesh::blockids, DM_libMesh::blocknames, DM_libMesh::decomposition, DM_libMesh::decomposition_type, DMlibMeshSetUpName_Private(), libMesh::DofMap::dof_indices(), DM_libMesh::embedding, DM_libMesh::embedding_type, end, libMesh::DofMap::end_dof(), libMesh::DofMap::first_dof(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::ierr, PETSC_OWN_POINTER, DM_libMesh::sys, libMesh::sys, DM_libMesh::varids, and DM_libMesh::varnames.
{
PetscFunctionBegin;
PetscErrorCode ierr;
DM_libMesh *dlm = (DM_libMesh *)(dm->data);
NonlinearImplicitSystem *sys = dlm->sys;
IS emb;
if(dlm->decomposition_type != DMLIBMESH_FIELD_DECOMPOSITION) PetscFunctionReturn(0);
*len = dlm->decomposition->size();
if(namelist) {ierr = PetscMalloc(*len*sizeof(char*), namelist); CHKERRQ(ierr);}
if(islist) {ierr = PetscMalloc(*len*sizeof(IS), islist); CHKERRQ(ierr);}
if(dmlist) {ierr = PetscMalloc(*len*sizeof(DM), dmlist); CHKERRQ(ierr);}
DofMap& dofmap = dlm->sys->get_dof_map();
for(unsigned int d = 0; d < dlm->decomposition->size(); ++d) {
std::set<numeric_index_type> dindices;
std::string dname;
std::map<std::string, unsigned int> dvarids;
std::map<unsigned int, std::string> dvarnames;
unsigned int dvcount = 0;
for(std::set<unsigned int>::const_iterator dvit = (*dlm->decomposition)[d].begin(); dvit != (*dlm->decomposition)[d].end(); ++dvit){
unsigned int v = *dvit;
std::string vname = (*dlm->varnames)[v];
dvarids.insert(std::pair<std::string, unsigned int>(vname,v));
dvarnames.insert(std::pair<unsigned int,std::string>(v,vname));
if(!dvcount) dname = vname;
else dname += "_" + vname;
++dvcount;
if(!islist) continue;
/* Iterate only over this DM's blocks. */
for(std::map<std::string, unsigned int>::const_iterator bit = dlm->blockids->begin(); bit != dlm->blockids->end(); ++bit) {
unsigned int b = bit->second;
MeshBase::const_element_iterator el = sys->get_mesh().active_local_subdomain_elements_begin(b);
MeshBase::const_element_iterator end_el = sys->get_mesh().active_local_subdomain_elements_end(b);
for ( ; el != end_el; ++el) {
const Elem* elem = *el;
//unsigned int e_subdomain = elem->subdomain_id();
std::vector<numeric_index_type> evindices;
// Get the degree of freedom indices for the given variable off the current element.
dofmap.dof_indices(elem, evindices, v);
for(unsigned int i = 0; i < evindices.size(); ++i) {
numeric_index_type dof = evindices[i];
if(dof >= dofmap.first_dof() && dof < dofmap.end_dof()) /* might want to use variable_first/last_local_dof instead */
dindices.insert(dof);
}
}
}
}
if(namelist) {
ierr = PetscStrallocpy(dname.c_str(),(*namelist)+d); CHKERRQ(ierr);
}
if(islist) {
IS dis;
PetscInt *darray;
ierr = PetscMalloc(sizeof(PetscInt)*dindices.size(), &darray); CHKERRQ(ierr);
numeric_index_type i = 0;
for(std::set<numeric_index_type>::const_iterator it = dindices.begin(); it != dindices.end(); ++it) {
darray[i] = *it;
++i;
}
ierr = ISCreateGeneral(((PetscObject)dm)->comm, dindices.size(),darray, PETSC_OWN_POINTER, &dis); CHKERRQ(ierr);
if(dlm->embedding) {
/* Create a relative embedding into the parent's index space. */
#if PETSC_RELEASE_LESS_THAN(3,3,1)
ierr = ISMapFactorRight(dis,dlm->embedding, PETSC_TRUE, &emb); CHKERRQ(ierr);
#else
ierr = ISEmbed(dis,dlm->embedding, PETSC_TRUE, &emb); CHKERRQ(ierr);
#endif
PetscInt elen, dlen;
ierr = ISGetLocalSize(emb, &elen); CHKERRQ(ierr);
ierr = ISGetLocalSize(dis, &dlen); CHKERRQ(ierr);
if(elen != dlen) SETERRQ1(((PetscObject)dm)->comm, PETSC_ERR_PLIB, "Failed to embed subdomain %D", d);
ierr = ISDestroy(&dis); CHKERRQ(ierr);
dis = emb;
}
else {
emb = dis;
}
(*islist)[d] = dis;
}
if(dmlist) {
DM ddm;
ierr = DMCreate(((PetscObject)dm)->comm, &ddm); CHKERRQ(ierr);
ierr = DMSetType(ddm, DMLIBMESH); CHKERRQ(ierr);
DM_libMesh *ddlm = (DM_libMesh*)(ddm->data);
ddlm->sys = dlm->sys;
/* copy over the block ids and names */
*ddlm->blockids = *dlm->blockids;
*ddlm->blocknames = *dlm->blocknames;
/* set the vars from the d-th part of the decomposition. */
*ddlm->varids = dvarids;
*ddlm->varnames = dvarnames;
ierr = PetscObjectReference((PetscObject)emb); CHKERRQ(ierr);
ddlm->embedding = emb;
ddlm->embedding_type = DMLIBMESH_FIELD_EMBEDDING;
ierr = DMlibMeshSetUpName_Private(ddm); CHKERRQ(ierr);
ierr = DMSetFromOptions(ddm); CHKERRQ(ierr);
(*dmlist)[d] = ddm;
}
}
PetscFunctionReturn(0);
}
| static PetscErrorCode DMCreateFieldDecompositionDM_libMesh | ( | DM | dm, |
| const char * | ddesc, | ||
| DM * | ddm | ||
| ) | [static] |
Definition at line 713 of file petscdmlibmeshimpl.C.
References DMlibMeshCreateFieldDecompositionDM(), DMlibMeshParseDecompositionDescriptor_Private(), and libMesh::ierr.
{
PetscFunctionBegin;
PetscErrorCode ierr;
PetscInt dtype, dcount, *dsizes;
char ***dlists;
PetscFunctionBegin;
*ddm = PETSC_NULL;
ierr = DMlibMeshParseDecompositionDescriptor_Private(dm,ddesc,&dtype,&dcount,&dsizes,&dlists); CHKERRQ(ierr);
if(dtype == DMLIBMESH_FIELD_DECOMPOSITION){
ierr = DMlibMeshCreateFieldDecompositionDM(dm,dcount,dsizes,dlists,ddm); CHKERRQ(ierr);
}
else SETERRQ1(((PetscObject)dm)->comm, PETSC_ERR_PLIB, "Uexpected unknown decomposition type for field decomposition descriptor %s", ddesc);
PetscFunctionReturn(0);
}
| PetscErrorCode DMlibMeshCreateDomainDecompositionDM | ( | DM | dm, |
| PetscInt | dnumber, | ||
| PetscInt * | dsizes, | ||
| char *** | dblocklists, | ||
| DM * | ddm | ||
| ) |
Definition at line 512 of file petscdmlibmeshimpl.C.
References DM_libMesh::blockids, DM_libMesh::blocknames, DM_libMesh::decomposition, DM_libMesh::decomposition_type, DMlibMeshSetUpName_Private(), libMesh::ierr, PetscBool, DM_libMesh::sys, DM_libMesh::varids, and DM_libMesh::varnames.
Referenced by DMCreateDomainDecompositionDM_libMesh().
{
PetscErrorCode ierr;
PetscBool islibmesh;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
ierr = PetscObjectTypeCompare((PetscObject)dm, DMLIBMESH,&islibmesh);
if(!islibmesh) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Got DM oftype %s, not of type %s", ((PetscObject)dm)->type_name, DMLIBMESH);
if(dnumber < 0) SETERRQ1(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Negative number %D of decomposition parts", dnumber);
PetscValidPointer(ddm,5);
DM_libMesh *dlm = (DM_libMesh *)(dm->data);
ierr = DMCreate(((PetscObject)dm)->comm, ddm); CHKERRQ(ierr);
ierr = DMSetType(*ddm, DMLIBMESH); CHKERRQ(ierr);
DM_libMesh *ddlm = (DM_libMesh *)((*ddm)->data);
ddlm->sys = dlm->sys;
ddlm->varids = dlm->varids;
ddlm->varnames = dlm->varnames;
ddlm->blockids = dlm->blockids;
ddlm->blocknames = dlm->blocknames;
ddlm->decomposition = new(std::vector<std::set<unsigned int> >);
ddlm->decomposition_type = DMLIBMESH_DOMAIN_DECOMPOSITION;
if(dnumber) {
for(PetscInt d = 0; d < dnumber; ++d) {
if(dsizes[d] < 0) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Negative size %D of decomposition part %D", dsizes[d],d);
ddlm->decomposition->push_back(std::set<unsigned int>());
for(PetscInt b = 0; b < dsizes[d]; ++b) {
std::string bname(dblocklists[d][b]);
std::map<std::string, unsigned int>::const_iterator bit = dlm->blockids->find(bname);
if(bit == dlm->blockids->end())
SETERRQ3(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Block %D on the %D-th list with name %s is not owned by this DM", b, d, dblocklists[d][b]);
unsigned int bid = bit->second;
(*ddlm->decomposition)[d].insert(bid);
}
}
}
else { /* Empty splits indicate default: split all blocks with one per split. */
PetscInt d = 0;
for(std::map<std::string, unsigned int>::const_iterator bit = ddlm->blockids->begin(); bit != ddlm->blockids->end(); ++bit) {
ddlm->decomposition->push_back(std::set<unsigned int>());
unsigned int bid = bit->second;
std::string bname = bit->first;
(*ddlm->decomposition)[d].insert(bid);
++d;
}
}
ierr = DMlibMeshSetUpName_Private(*ddm); CHKERRQ(ierr);
ierr = DMSetFromOptions(*ddm); CHKERRQ(ierr);
ierr = DMSetUp(*ddm); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
| PetscErrorCode DMlibMeshCreateFieldDecompositionDM | ( | DM | dm, |
| PetscInt | dnumber, | ||
| PetscInt * | dsizes, | ||
| char *** | dvarlists, | ||
| DM * | ddm | ||
| ) |
Definition at line 459 of file petscdmlibmeshimpl.C.
References DM_libMesh::blockids, DM_libMesh::blocknames, DM_libMesh::decomposition, DM_libMesh::decomposition_type, DMlibMeshSetUpName_Private(), libMesh::ierr, PetscBool, DM_libMesh::sys, DM_libMesh::varids, and DM_libMesh::varnames.
Referenced by DMCreateFieldDecompositionDM_libMesh().
{
PetscErrorCode ierr;
PetscBool islibmesh;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
ierr = PetscObjectTypeCompare((PetscObject)dm, DMLIBMESH,&islibmesh);
if(!islibmesh) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Got DM oftype %s, not of type %s", ((PetscObject)dm)->type_name, DMLIBMESH);
if(dnumber < 0) SETERRQ1(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Negative number %D of decomposition parts", dnumber);
PetscValidPointer(ddm,5);
DM_libMesh *dlm = (DM_libMesh *)(dm->data);
ierr = DMCreate(((PetscObject)dm)->comm, ddm); CHKERRQ(ierr);
ierr = DMSetType(*ddm, DMLIBMESH); CHKERRQ(ierr);
DM_libMesh *ddlm = (DM_libMesh *)((*ddm)->data);
ddlm->sys = dlm->sys;
ddlm->varids = dlm->varids;
ddlm->varnames = dlm->varnames;
ddlm->blockids = dlm->blockids;
ddlm->blocknames = dlm->blocknames;
ddlm->decomposition = new(std::vector<std::set<unsigned int> >);
ddlm->decomposition_type = DMLIBMESH_FIELD_DECOMPOSITION;
if(dnumber) {
for(PetscInt d = 0; d < dnumber; ++d) {
if(dsizes[d] < 0) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Negative size %D of decomposition part %D", dsizes[d],d);
ddlm->decomposition->push_back(std::set<unsigned int>());
for(PetscInt v = 0; v < dsizes[d]; ++v) {
std::string vname(dvarlists[d][v]);
std::map<std::string, unsigned int>::const_iterator vit = dlm->varids->find(vname);
if(vit == dlm->varids->end())
SETERRQ3(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Variable %D on the %D-th list with name %s is not owned by this DM", v, d, dvarlists[d][v]);
unsigned int vid = vit->second;
(*ddlm->decomposition)[d].insert(vid);
}
}
}
else { /* Empty splits indicate default: split all variables with one per split. */
PetscInt d = 0;
for(std::map<std::string, unsigned int>::const_iterator vit = ddlm->varids->begin(); vit != ddlm->varids->end(); ++vit) {
ddlm->decomposition->push_back(std::set<unsigned int>());
unsigned int vid = vit->second;
std::string vname = vit->first;
(*ddlm->decomposition)[d].insert(vid);
++d;
}
}
ierr = DMlibMeshSetUpName_Private(*ddm); CHKERRQ(ierr);
ierr = DMSetFromOptions(*ddm); CHKERRQ(ierr);
ierr = DMSetUp(*ddm); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
| static PetscErrorCode DMlibMeshFunction | ( | DM | dm, |
| Vec | x, | ||
| Vec | r | ||
| ) | [static] |
Definition at line 752 of file petscdmlibmeshimpl.C.
References libMesh::ParallelObject::comm(), libMesh::System::current_local_solution, DMlibMeshGetSystem(), libMesh::DofMap::enforce_constraints_exactly(), libMesh::System::get_dof_map(), libMesh::ierr, libMesh::libmesh_assert(), libMesh::NonlinearImplicitSystem::nonlinear_solver, libMesh::ExplicitSystem::rhs, libMesh::System::solution, libMesh::sys, libMesh::System::update(), libMesh::X_global(), and libMesh::X_sys.
Referenced by SNESFunction_DMlibMesh().
{
PetscErrorCode ierr;
PetscFunctionBegin;
libmesh_assert(x);
libmesh_assert(r);
NonlinearImplicitSystem* _sys;
ierr = DMlibMeshGetSystem(dm, _sys);CHKERRQ(ierr);
NonlinearImplicitSystem& sys = *_sys;
PetscVector<Number>& X_sys = *libmesh_cast_ptr<PetscVector<Number>* >(sys.solution.get());
PetscVector<Number>& R_sys = *libmesh_cast_ptr<PetscVector<Number>* >(sys.rhs);
PetscVector<Number> X_global(x, _sys->comm()), R(r, _sys->comm());
// Use the systems update() to get a good local version of the parallel solution
X_global.swap(X_sys);
R.swap(R_sys);
_sys->get_dof_map().enforce_constraints_exactly(*_sys);
_sys->update();
// Swap back
X_global.swap(X_sys);
R.swap(R_sys);
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 (_sys->nonlinear_solver->residual && _sys->nonlinear_solver->residual_object)
libmesh_error_msg("ERROR: cannot specifiy both a function and object to compute the Residual!");
if (_sys->nonlinear_solver->matvec && _sys->nonlinear_solver->residual_and_jacobian_object)
libmesh_error_msg("ERROR: cannot specifiy both a function and object to compute the combined Residual & Jacobian!");
if (_sys->nonlinear_solver->residual != NULL)
_sys->nonlinear_solver->residual(*(_sys->current_local_solution.get()), R, *_sys);
else if (_sys->nonlinear_solver->residual_object != NULL)
_sys->nonlinear_solver->residual_object->residual(*(_sys->current_local_solution.get()), R, *_sys);
else if (_sys->nonlinear_solver->matvec != NULL)
_sys->nonlinear_solver->matvec(*(_sys->current_local_solution.get()), &R, NULL, *_sys);
else if (_sys->nonlinear_solver->residual_and_jacobian_object != NULL)
_sys->nonlinear_solver->residual_and_jacobian_object->residual_and_jacobian(*(_sys->current_local_solution.get()), &R, NULL, *_sys);
else
libmesh_error_msg("Error! Unable to compute residual and/or Jacobian!");
R.close();
X_global.close();
PetscFunctionReturn(0);
}
| PetscErrorCode DMlibMeshGetBlocks | ( | DM | dm, |
| PetscInt * | n, | ||
| char *** | blocknames | ||
| ) |
Definition at line 146 of file petscdmlibmeshimpl.C.
References DM_libMesh::blockids, libMesh::ierr, and PetscBool.
{
PetscErrorCode ierr;
PetscInt i;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscBool islibmesh;
ierr = PetscObjectTypeCompare((PetscObject)dm, DMLIBMESH,&islibmesh);
if(!islibmesh) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Got DM oftype %s, not of type %s", ((PetscObject)dm)->type_name, DMLIBMESH);
DM_libMesh *dlm = (DM_libMesh *)(dm->data);
PetscValidPointer(n,2);
*n = dlm->blockids->size();
if(!blocknames) PetscFunctionReturn(0);
ierr = PetscMalloc(*n*sizeof(char*), blocknames); CHKERRQ(ierr);
i = 0;
for(std::map<std::string, unsigned int>::const_iterator it = dlm->blockids->begin(); it != dlm->blockids->end(); ++it){
ierr = PetscStrallocpy(it->first.c_str(), *blocknames+i); CHKERRQ(ierr);
++i;
}
PetscFunctionReturn(0);
}
| PetscErrorCode DMlibMeshGetSystem_libMesh | ( | DM | dm, |
| NonlinearImplicitSystem *& | sys | ||
| ) |
Definition at line 129 of file petscdmlibmeshimpl.C.
References libMesh::ierr, PetscBool, and DM_libMesh::sys.
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscBool islibmesh;
ierr = PetscObjectTypeCompare((PetscObject)dm, DMLIBMESH,&islibmesh);CHKERRQ(ierr);
if(!islibmesh) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Got DM oftype %s, not of type %s", ((PetscObject)dm)->type_name, DMLIBMESH);
DM_libMesh *dlm = (DM_libMesh *)(dm->data);
sys = dlm->sys;
PetscFunctionReturn(0);
}
| PetscErrorCode DMlibMeshGetVariables | ( | DM | dm, |
| PetscInt * | n, | ||
| char *** | varnames | ||
| ) |
Definition at line 170 of file petscdmlibmeshimpl.C.
References libMesh::ierr, PetscBool, and DM_libMesh::varids.
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscBool islibmesh;
PetscInt i;
ierr = PetscObjectTypeCompare((PetscObject)dm, DMLIBMESH,&islibmesh);
if(!islibmesh) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Got DM oftype %s, not of type %s", ((PetscObject)dm)->type_name, DMLIBMESH);
DM_libMesh *dlm = (DM_libMesh *)(dm->data);
PetscValidPointer(n,2);
*n = dlm->varids->size();
if(!varnames) PetscFunctionReturn(0);
ierr = PetscMalloc(*n*sizeof(char*), varnames); CHKERRQ(ierr);
i = 0;
for(std::map<std::string, unsigned int>::const_iterator it = dlm->varids->begin(); it != dlm->varids->end(); ++it){
ierr = PetscStrallocpy(it->first.c_str(), *varnames+i); CHKERRQ(ierr);
++i;
}
PetscFunctionReturn(0);
}
| PetscErrorCode DMlibMeshGetVec_Private | ( | DM | , |
| const char * | , | ||
| Vec * | |||
| ) |
Definition at line 53 of file petscdmlibmeshimpl.C.
{
PetscFunctionBegin;
PetscFunctionReturn(0);
}
| static PetscErrorCode DMlibMeshJacobian | ( | DM | dm, |
| Vec | x, | ||
| Mat | jac, | ||
| Mat | pc, | ||
| MatStructure * | msflag | ||
| ) | [static] |
| static PetscErrorCode DMlibMeshParseDecompositionDescriptor_Private | ( | DM | dm, |
| const char * | ddesc, | ||
| PetscInt * | dtype, | ||
| PetscInt * | dcount, | ||
| PetscInt ** | dsizes, | ||
| char **** | dlists | ||
| ) | [static] |
Definition at line 574 of file petscdmlibmeshimpl.C.
References libMesh::ierr, token::next, PetscBool, and token::s.
Referenced by DMCreateDomainDecompositionDM_libMesh(), and DMCreateFieldDecompositionDM_libMesh().
{
PetscFunctionBegin;
PetscErrorCode ierr;
PetscBool eq;
char *s0, *s, *ss;
struct token *llfirst = PETSC_NULL, *lllast = PETSC_NULL, *tok;
PetscInt stcount = 0, brcount = 0, d, i;
size_t len0, count;
/*
Parse the decomposition descriptor.
Decomposition names could be of one of two forms:
var:v1,v2;v3,v4;v4,v5;
block:b1,b2;b3,b4;b4,b5;
resulting in an overlapping decomposition that groups
variables (v1,v2), (v3,v4), (v4,v5) or
blocks (b1,b2), (b3,b4), (b4,b5).
*/
/* Copy the descriptor so that we can manipulate it in place. */
ierr = PetscStrallocpy(ddesc,&s0); CHKERRQ(ierr);
ierr = PetscStrlen(s0, &len0) ; CHKERRQ(ierr);
ierr = PetscStrstr(s0,":",&ss); CHKERRQ(ierr);
if(!ss) {
ss = s0+len0;
}
else {
*ss = 0;
}
ierr = PetscStrcmp(s0,"var",&eq); CHKERRQ(ierr);
if(eq) {
*dtype=DMLIBMESH_FIELD_DECOMPOSITION;
}
else {
ierr = PetscStrcmp(s0,"block",&eq);CHKERRQ(ierr);
if(!eq)
SETERRQ1(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Could not determine decomposition type from descriptor: %s\n", ddesc); CHKERRQ(ierr);
*dtype=DMLIBMESH_DOMAIN_DECOMPOSITION;
}
ierr = PetscStrlen(s0,&count); CHKERRQ(ierr);
while(count < len0) {
struct token *st, *br;
++ss; ++count;
s=ss;
while(*ss && *ss != ',' && *ss != ';') {
++ss; ++count;
}
st = PETSC_NULL; br = PETSC_NULL;
if(*ss) {
/*
Found a separator, or a break.
Add an appropriate token to the list.
A token separator ',' produces no token.
*/
if(*ss == ';') {
/* Create a break token: a token with a null string. */
#if PETSC_RELEASE_LESS_THAN(3,5,0)
ierr = PetscNew(struct token,&br);CHKERRQ(ierr);
#else
ierr = PetscNew(&br);CHKERRQ(ierr);
#endif
}
*ss = 0;
if(s != ss) {
/* A nonempty string. */
#if PETSC_RELEASE_LESS_THAN(3,5,0)
ierr = PetscNew(struct token, &st);CHKERRQ(ierr);
#else
ierr = PetscNew(&st);CHKERRQ(ierr);
#endif
st->s = s; /* The string will be properly copied below. */
}
/* Add the new tokens to the list. */
if(st) {
if(!lllast) {
llfirst = lllast = st;
}
else {
lllast->next = st; lllast = st;
}
}
if(br) {
if(!lllast) {
llfirst = lllast = br;
}
else {
lllast->next = br; lllast = br;
}
}
}
}
/* The result of parsing is in the linked list ll. */
/* Count up the strings and the breaks. */
tok = llfirst;
while(tok) {
if(tok->s)
++stcount;
else
++brcount;
tok = tok->next;
}
/* Allocate the space for the output. */
*dcount = brcount;
ierr = PetscMalloc(*dcount*sizeof(PetscInt), dsizes); CHKERRQ(ierr);
ierr = PetscMalloc(*dcount*sizeof(char**), dlists); CHKERRQ(ierr);
for(d = 0; d < *dcount; ++d) (*dsizes)[d] = 0;
tok = llfirst; d = 0;
while(tok) {
if(tok->s)
++(*dsizes)[d];
else
++d;
tok = tok->next;
}
for(d = 0; d < *dcount; ++d) {
ierr = PetscMalloc(sizeof(char**)*(*dsizes)[d], (*dlists)+d); CHKERRQ(ierr);
}
/* Now copy strings and destroy tokens. */
tok = llfirst; d = 0; i = 0;
while(tok) {
if(tok->s) {
ierr = PetscStrallocpy(tok->s, (*dlists)[d]+i); CHKERRQ(ierr);
++i;
}
else {
++d;
i = 0;
}
llfirst = tok;
tok = tok->next;
ierr = PetscFree(llfirst); CHKERRQ(ierr);
}
/* Deallocate workspace. */
ierr = PetscFree(s0); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
| PetscErrorCode DMlibMeshSetSystem_libMesh | ( | DM | dm, |
| NonlinearImplicitSystem & | sys | ||
| ) |
Definition at line 66 of file petscdmlibmeshimpl.C.
References libMesh::MeshBase::active_elements_begin(), libMesh::MeshBase::active_elements_end(), DM_libMesh::blockids, DM_libMesh::blocknames, libMesh::ParallelObject::comm(), DMlibMeshSetUpName_Private(), end, libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::ierr, mesh, libMesh::DofMap::n_variables(), libMesh::Variable::name(), PetscBool, libMesh::MeshBase::subdomain_name(), DM_libMesh::sys, libMesh::sys, libMesh::DofMap::variable(), DM_libMesh::varids, and DM_libMesh::varnames.
{
const Parallel::Communicator &comm(sys.comm());
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscBool islibmesh;
ierr = PetscObjectTypeCompare((PetscObject)dm, DMLIBMESH,&islibmesh);
if(!islibmesh) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Got DM oftype %s, not of type %s", ((PetscObject)dm)->type_name, DMLIBMESH);
if(dm->setupcalled) SETERRQ(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONGSTATE, "Cannot reset the libMesh system after DM has been set up.");
DM_libMesh *dlm = (DM_libMesh *)(dm->data);
dlm->sys =&sys;
/* Initially populate the sets of active blockids and varids using all of the
existing blocks/variables (only variables are supported at the moment). */
DofMap& dofmap = dlm->sys->get_dof_map();
dlm->varids->clear();
dlm->varnames->clear();
for(unsigned int v = 0; v < dofmap.n_variables(); ++v) {
std::string vname = dofmap.variable(v).name();
dlm->varids->insert(std::pair<std::string,unsigned int>(vname,v));
dlm->varnames->insert(std::pair<unsigned int,std::string>(v,vname));
}
const MeshBase& mesh = dlm->sys->get_mesh();
dlm->blockids->clear();
dlm->blocknames->clear();
std::set<subdomain_id_type> blocks;
/* The following effectively is a verbatim copy of MeshBase::n_subdomains(). */
// This requires an inspection on every processor
libmesh_parallel_only(mesh.comm());
MeshBase::const_element_iterator el = mesh.active_elements_begin();
const MeshBase::const_element_iterator end = mesh.active_elements_end();
for (; el!=end; ++el)
blocks.insert((*el)->subdomain_id());
// Some subdomains may only live on other processors
comm.set_union(blocks);
std::set<subdomain_id_type>::iterator bit = blocks.begin();
std::set<subdomain_id_type>::iterator bend = blocks.end();
if(bit == bend) SETERRQ(((PetscObject)dm)->comm, PETSC_ERR_PLIB, "No mesh blocks found.");
for(; bit != bend; ++bit) {
subdomain_id_type bid = *bit;
std::string bname = mesh.subdomain_name(bid);
if(!bname.length()) {
/* Block names are currently implemented for Exodus II 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 << "dm" << bid;
bname = ss.str();
}
dlm->blockids->insert(std::pair<std::string,unsigned int>(bname,bid));
dlm->blocknames->insert(std::pair<unsigned int,std::string>(bid,bname));
}
ierr = DMlibMeshSetUpName_Private(dm); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
| PetscErrorCode DMlibMeshSetUpName_Private | ( | DM | dm | ) |
Definition at line 194 of file petscdmlibmeshimpl.C.
References DM_libMesh::blocknames, DM_libMesh::decomposition, DM_libMesh::decomposition_type, DM_libMesh::embedding_type, end, libMesh::ierr, libMesh::Quality::name(), libMesh::System::name(), DM_libMesh::sys, and DM_libMesh::varnames.
Referenced by DMCreateDomainDecomposition_libMesh(), DMCreateFieldDecomposition_libMesh(), DMlibMeshCreateDomainDecompositionDM(), DMlibMeshCreateFieldDecompositionDM(), and DMlibMeshSetSystem_libMesh().
{
DM_libMesh* dlm = (DM_libMesh*)dm->data;
PetscErrorCode ierr;
PetscFunctionBegin;
std::string name = dlm->sys->name();
std::map<unsigned int, std::string> *dnames = PETSC_NULL, *enames = PETSC_NULL;
if(dlm->decomposition_type == DMLIBMESH_FIELD_DECOMPOSITION) {
name += ":dec:var:";
dnames = dlm->varnames;
}
if(dlm->decomposition_type == DMLIBMESH_DOMAIN_DECOMPOSITION) {
name += ":dec:block:";
dnames = dlm->blocknames;
}
if(dnames) {
for(unsigned int d = 0; d < dlm->decomposition->size(); ++d) {
for(std::set<unsigned int>::iterator dit = (*dlm->decomposition)[d].begin(); dit != (*dlm->decomposition)[d].end(); ++dit) {
unsigned int id = *dit;
if(dit != (*dlm->decomposition)[d].begin())
name += ",";
name += (*dnames)[id];
}
name += ";";
}
}
if(dlm->embedding_type == DMLIBMESH_FIELD_EMBEDDING) {
name += ":emb:var:";
enames = dlm->varnames;
}
if(dlm->embedding_type == DMLIBMESH_DOMAIN_EMBEDDING) {
name += ":emb:block:";
enames = dlm->blocknames;
}
if(enames) {
for(std::map<unsigned int, std::string>::iterator eit = enames->begin(); eit != enames->end(); ++eit) {
std::string ename = eit->second;
if(eit != enames->begin())
name += ",";
name += ename;
}
name += ";";
}
ierr = PetscObjectSetName((PetscObject)dm, name.c_str()); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
| static PetscErrorCode SNESFunction_DMlibMesh | ( | SNES | , |
| Vec | x, | ||
| Vec | r, | ||
| void * | ctx | ||
| ) | [static] |
Definition at line 809 of file petscdmlibmeshimpl.C.
References DMlibMeshFunction(), and libMesh::ierr.
{
DM dm = (DM)ctx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMlibMeshFunction(dm,x,r);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
Variable Documentation
| PetscErrorCode Vec Mat jac |
Definition at line 825 of file petscdmlibmeshimpl.C.
Referenced by libMesh::PetscDiffSolver::solve().
| PetscErrorCode Vec x |
Definition at line 825 of file petscdmlibmeshimpl.C.
Referenced by GETPOT_NAMESPACE::GetPot::_DBE_expand().
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