int main(int argc,char **argv)
{
PetscErrorCode ierr;
UserCtx user;
DM red,da;
SNES snes;
DM packer;
PetscBool use_monitor = PETSC_FALSE;
ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
ierr = PetscOptionsSetFromOptions(NULL);CHKERRQ(ierr);
/* Hardwire several options; can be changed at command line */
ierr = PetscOptionsInsertString(NULL,common_options);CHKERRQ(ierr);
ierr = PetscOptionsInsertString(NULL,matrix_free_options);CHKERRQ(ierr);
ierr = PetscOptionsInsert(NULL,&argc,&argv,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-use_monitor",&use_monitor,PETSC_IGNORE);CHKERRQ(ierr);
/* Create a global vector that includes a single redundant array and two da arrays */
ierr = DMCompositeCreate(PETSC_COMM_WORLD,&packer);CHKERRQ(ierr);
ierr = DMRedundantCreate(PETSC_COMM_WORLD,0,1,&red);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(red,"red_");CHKERRQ(ierr);
ierr = DMCompositeAddDM(packer,red);CHKERRQ(ierr);
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,-5,2,1,NULL,&da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(red,"da_");CHKERRQ(ierr);
ierr = DMCompositeAddDM(packer,(DM)da);CHKERRQ(ierr);
ierr = DMSetApplicationContext(packer,&user);CHKERRQ(ierr);
packer->ops->creatematrix = DMCreateMatrix_MF;
/* create nonlinear multi-level solver */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes,packer);CHKERRQ(ierr);
ierr = SNESSetFunction(snes,NULL,ComputeFunction,NULL);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,NULL, NULL,ComputeJacobian_MF,NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
if (use_monitor) {
/* create graphics windows */
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"u_lambda - state variables and Lagrange multipliers",-1,-1,-1,-1,&user.u_lambda_viewer);CHKERRQ(ierr);
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"fu_lambda - derivate w.r.t. state variables and Lagrange multipliers",-1,-1,-1,-1,&user.fu_lambda_viewer);CHKERRQ(ierr);
ierr = SNESMonitorSet(snes,Monitor,0,0);CHKERRQ(ierr);
}
ierr = SNESSolve(snes,NULL,NULL);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&red);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = DMDestroy(&packer);CHKERRQ(ierr);
if (use_monitor) {
ierr = PetscViewerDestroy(&user.u_lambda_viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&user.fu_lambda_viewer);CHKERRQ(ierr);
}
ierr = PetscFinalize();
return ierr;
}
PETScLinearSolver::PETScLinearSolver(const std::string /*prefix*/,
BaseLib::ConfigTree const* const option)
{
// Insert options into petsc database. Default options are given in the
// string below.
std::string petsc_options =
"-ksp_type cg -pc_type bjacobi -ksp_rtol 1e-16 -ksp_max_it 10000";
std::string prefix;
if (option)
{
ignoreOtherLinearSolvers(*option, "petsc");
//! \ogs_file_param{prj__linear_solvers__linear_solver__petsc}
if (auto const subtree = option->getConfigSubtreeOptional("petsc"))
{
if (auto const parameters =
//! \ogs_file_param{prj__linear_solvers__linear_solver__petsc__parameters}
subtree->getConfigParameterOptional<std::string>("parameters"))
{
petsc_options = *parameters;
}
if (auto const pre =
//! \ogs_file_param{prj__linear_solvers__linear_solver__petsc__prefix}
subtree->getConfigParameterOptional<std::string>("prefix"))
{
if (!pre->empty())
prefix = *pre + "_";
}
}
}
#if PETSC_VERSION_LT(3, 7, 0)
PetscOptionsInsertString(petsc_options.c_str());
#else
PetscOptionsInsertString(nullptr, petsc_options.c_str());
#endif
KSPCreate(PETSC_COMM_WORLD, &_solver);
KSPGetPC(_solver, &_pc);
if (!prefix.empty())
{
KSPSetOptionsPrefix(_solver, prefix.c_str());
}
KSPSetInitialGuessNonzero(_solver, PETSC_TRUE);
KSPSetFromOptions(_solver); // set run-time options
}
void linearSystemPETSc<scalar>::allocate(int nbRows)
{
int commSize;
MPI_Comm_size(_comm, &commSize);
int blockSize = _getBlockSizeFromParameters();
clear();
_try(MatCreate(_comm, &_a));
_try(MatSetSizes(_a, blockSize * nbRows, blockSize * nbRows, PETSC_DETERMINE, PETSC_DETERMINE));
if (blockSize > 1) {
if (commSize > 1) {
_try(MatSetType(_a, MATMPIBAIJ));
}
else {
_try(MatSetType(_a, MATSEQBAIJ));
}
}
// override the default options with the ones from the option
// database (if any)
if (this->_parameters.count("petscOptions"))
_try(PetscOptionsInsertString(this->_parameters["petscOptions"].c_str()));
if (this->_parameters.count("petscPrefix"))
_try(MatAppendOptionsPrefix(_a, this->_parameters["petscPrefix"].c_str()));
_try(MatSetFromOptions(_a));
//since PETSc 3.3 GetOwnershipRange and MatGetSize cannot be called before MatXXXSetPreallocation
_localSize = nbRows;
#ifdef HAVE_MPI
if (commSize>1){
_localRowStart = 0;
if (Msg::GetCommRank() != 0) {
MPI_Status status;
MPI_Recv((void*)&_localRowStart, 1, MPI_INT, Msg::GetCommRank() - 1, 1, MPI_COMM_WORLD, &status);
}
_localRowEnd = _localRowStart + nbRows;
if (Msg::GetCommRank() != Msg::GetCommSize() - 1) {
MPI_Send((void*)&_localRowEnd, 1, MPI_INT, Msg::GetCommRank() + 1, 1, MPI_COMM_WORLD);
}
MPI_Allreduce((void*)&_localSize, (void*)&_globalSize, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
}
else{
_localRowStart = 0;
_localRowEnd = nbRows;
_globalSize = _localSize;
}
#else
_localRowStart = 0;
_localRowEnd = nbRows;
_globalSize = _localSize;
#endif
// preallocation option must be set after other options
_try(VecCreate(_comm, &_x));
_try(VecSetSizes(_x, blockSize * nbRows, PETSC_DETERMINE));
// override the default options with the ones from the option
// database (if any)
if (this->_parameters.count("petscPrefix"))
_try(VecAppendOptionsPrefix(_x, this->_parameters["petscPrefix"].c_str()));
_try(VecSetFromOptions(_x));
_try(VecDuplicate(_x, &_b));
_isAllocated = true;
_entriesPreAllocated = false;
}
int main(int argc, char *argv[])
{
PetscErrorCode ierr;
PetscInt opts[6] = {0};
PetscBool hascl = PETSC_FALSE,hasstr = PETSC_FALSE;
ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr);
ierr = PetscOptionsSetValue(NULL,"-zero","0");CHKERRQ(ierr);
ierr = PetscOptionsPrefixPush(NULL,"a_");CHKERRQ(ierr);
ierr = PetscOptionsSetValue(NULL,"-one","1");CHKERRQ(ierr);
ierr = PetscOptionsPrefixPush(NULL,"bb_");CHKERRQ(ierr);
ierr = PetscOptionsSetValue(NULL,"-two","2");CHKERRQ(ierr);
ierr = PetscOptionsPrefixPop(NULL);CHKERRQ(ierr);
ierr = PetscOptionsSetValue(NULL,"-three","3");CHKERRQ(ierr);
ierr = PetscOptionsPrefixPush(NULL,"cc_");CHKERRQ(ierr);
ierr = PetscOptionsPrefixPush(NULL,"ddd_");CHKERRQ(ierr);
ierr = PetscOptionsSetValue(NULL,"-four","4");CHKERRQ(ierr);
ierr = PetscOptionsPrefixPop(NULL);CHKERRQ(ierr);
ierr = PetscOptionsPrefixPop(NULL);CHKERRQ(ierr);
ierr = PetscOptionsPrefixPop(NULL);CHKERRQ(ierr);
ierr = PetscOptionsSetValue(NULL,"-five","5");CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-zero",&opts[0],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-a_one",&opts[1],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-a_bb_two",&opts[2],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-a_three",&opts[3],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-a_cc_ddd_four",&opts[4],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-five",&opts[5],0);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"opts = {%D %D %D %D %D %D}\n",opts[0],opts[1],opts[2],opts[3],opts[4],opts[5]);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,0,"-cl",&hascl,0);CHKERRQ(ierr);
if (hascl) {
ierr = PetscMemzero(opts,sizeof(opts));CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-cl_zero",&opts[0],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-cl_a_one",&opts[1],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-cl_a_bb_two",&opts[2],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-cl_a_three",&opts[3],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-cl_a_cc_ddd_four",&opts[4],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-cl_five",&opts[5],0);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"cl_opts = {%D %D %D %D %D %D}\n",opts[0],opts[1],opts[2],opts[3],opts[4],opts[5]);CHKERRQ(ierr);
}
ierr = PetscOptionsGetBool(NULL,0,"-str",&hasstr,0);CHKERRQ(ierr);
if (hasstr) {
ierr = PetscOptionsInsertString(NULL,"-prefix_push str_ -zero 100 -prefix_push a_ -one 101 -prefix_push bb_ -two 102 -prefix_pop -three 103 -prefix_push cc_ -prefix_push ddd_ -four 104 -prefix_pop -prefix_pop -prefix_pop -five 105 -prefix_pop");CHKERRQ(ierr);
ierr = PetscMemzero(opts,sizeof(opts));CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-str_zero",&opts[0],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-str_a_one",&opts[1],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-str_a_bb_two",&opts[2],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-str_a_three",&opts[3],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-str_a_cc_ddd_four",&opts[4],0);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,0,"-str_five",&opts[5],0);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"str_opts = {%D %D %D %D %D %D}\n",opts[0],opts[1],opts[2],opts[3],opts[4],opts[5]);CHKERRQ(ierr);
}
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
PetscErrorCode PetscParseLayerYAML(yaml_parser_t *parser,int *lvl)
{
yaml_event_t event;
int storage = VAR; /* mapping cannot start with VAL definition w/o VAR key */
char key[PETSC_MAX_PATH_LEN],option[PETSC_MAX_PATH_LEN],prefix[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscSNPrintf(option,PETSC_MAX_PATH_LEN,"%s"," ");CHKERRQ(ierr);
do {
yaml_parser_parse(parser,&event);
/* Parse value either as a new leaf in the mapping */
/* or as a leaf value (one of them, in case it's a sequence) */
switch (event.type) {
case YAML_SCALAR_EVENT:
if (storage) {
ierr = PetscSNPrintf(option,PETSC_MAX_PATH_LEN,"-%s %s",key,(char*)event.data.scalar.value);CHKERRQ(ierr);
ierr = PetscOptionsInsertString(option);CHKERRQ(ierr);
} else {
ierr = PetscStrncpy(key,(char*)event.data.scalar.value,event.data.scalar.length+1);CHKERRQ(ierr);
}
storage ^= VAL; /* Flip VAR/VAL switch for the next event */
break;
case YAML_SEQUENCE_START_EVENT:
/* Sequence - all the following scalars will be appended to the last_leaf */
storage = SEQ;
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP ,"Unable to open YAML option file: sequences not supported");
yaml_event_delete(&event);
break;
case YAML_SEQUENCE_END_EVENT:
storage = VAR;
yaml_event_delete(&event);
break;
case YAML_MAPPING_START_EVENT:
ierr = PetscSNPrintf(prefix,PETSC_MAX_PATH_LEN,"%s_",key);CHKERRQ(ierr);
if (*lvl > 0) {
ierr = PetscOptionsPrefixPush(prefix);CHKERRQ(ierr);
}
(*lvl)++;
ierr = PetscParseLayerYAML(parser,lvl);CHKERRQ(ierr);
(*lvl)--;
if (*lvl > 0) {
ierr = PetscOptionsPrefixPop();CHKERRQ(ierr);
}
storage ^= VAL; /* Flip VAR/VAL, w/o touching SEQ */
yaml_event_delete(&event);
break;
default:
break;
}
}
while ((event.type != YAML_MAPPING_END_EVENT) && (event.type != YAML_STREAM_END_EVENT));
PetscFunctionReturn(0);
}
/**
*
*
* @param comm
* @param props
*
* @return PETSc options prefix to use
*/
void
PETScConfigurable::p_processOptions(utility::Configuration::CursorPtr props)
{
if (!props) return;
p_prefix = props->get(p_prefixKey, p_generatePrefix(p_comm));
if (*p_prefix.rbegin() != '_') {
p_prefix.append("_");
}
std::string optsorig, optsmod, optsfmt;
optsorig = props->get(p_optionsKey, "");
boost::char_separator<char> sep(" \t\f\n\r\v", "");
boost::tokenizer<boost::char_separator<char> >
opttok(optsorig, sep);
boost::tokenizer<boost::char_separator<char> >::iterator o;
for (o = opttok.begin(); o != opttok.end(); ++o) {
optsfmt.append(*o);
optsfmt.append(" ");
optsmod.append(prefixOptionMaybe(p_prefix, *o));
optsmod.append(" ");
}
if (verbose) {
std::cout << "p_processOptions: in: " << optsorig << std::endl;
std::cout << "p_processOptions: fmt: " << optsfmt << std::endl;
std::cout << "p_processOptions: out: " << optsmod << std::endl;
}
p_loadedOptions = optsmod;
PetscErrorCode ierr(0);
try {
ierr = PetscOptionsInsertString(
#if PETSC_VERSION_GE(3,7,0)
NULL,
#endif
p_loadedOptions.c_str()); CHKERRXX(ierr);
} catch (const PETSC_EXCEPTION_TYPE& e) {
throw PETScException(ierr, e);
}
return;
}
void linearSystemPETSc<scalar>::_kspCreate()
{
// Set option given by the user in its (python script) without using argc,argv or .petscrc
if(this->_parameters.count("petsc_solver_options"))
_try(PetscOptionsInsertString(this->_parameters["petsc_solver_options"].c_str()));
_try(KSPCreate(_comm, &_ksp));
PC pc;
_try(KSPGetPC(_ksp, &pc));
// set some default options
//_try(PCSetType(pc, PCLU));//LU for direct solver and PCILU for indirect solver
/* _try(PCFactorSetMatOrderingType(pc, MATORDERING_RCM));
_try(PCFactorSetLevels(pc, 1));*/
_try(KSPSetTolerances(_ksp, 1.e-8, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT));
// override the default options with the ones from the option
// database (if any)
if (this->_parameters.count("petscPrefix"))
_try(KSPAppendOptionsPrefix(_ksp, this->_parameters["petscPrefix"].c_str()));
_try(KSPSetFromOptions(_ksp));
_try(PCSetFromOptions(pc));
_kspAllocated = true;
}
int main(int argc,char **args)
{
Mat Amat;
PetscErrorCode ierr;
SNES snes;
KSP ksp;
MPI_Comm comm;
PetscMPIInt npe,rank;
PetscLogStage stage[7];
PetscBool test_nonzero_cols=PETSC_FALSE,use_nearnullspace=PETSC_TRUE;
Vec xx,bb;
PetscInt iter,i,N,dim=3,cells[3]={1,1,1},max_conv_its,local_sizes[7],run_type=1;
DM dm,distdm,basedm;
PetscBool flg;
char convType[256];
PetscReal Lx,mdisp[10],err[10];
const char * const options[10] = {"-ex56_dm_refine 0",
"-ex56_dm_refine 1",
"-ex56_dm_refine 2",
"-ex56_dm_refine 3",
"-ex56_dm_refine 4",
"-ex56_dm_refine 5",
"-ex56_dm_refine 6",
"-ex56_dm_refine 7",
"-ex56_dm_refine 8",
"-ex56_dm_refine 9"};
PetscFunctionBeginUser;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &npe);CHKERRQ(ierr);
/* options */
ierr = PetscOptionsBegin(comm,NULL,"3D bilinear Q1 elasticity options","");CHKERRQ(ierr);
{
i = 3;
ierr = PetscOptionsIntArray("-cells", "Number of (flux tube) processor in each dimension", "ex56.c", cells, &i, NULL);CHKERRQ(ierr);
Lx = 1.; /* or ne for rod */
max_conv_its = 3;
ierr = PetscOptionsInt("-max_conv_its","Number of iterations in convergence study","",max_conv_its,&max_conv_its,NULL);CHKERRQ(ierr);
if (max_conv_its<=0 || max_conv_its>7) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_USER, "Bad number of iterations for convergence test (%D)",max_conv_its);
ierr = PetscOptionsReal("-lx","Length of domain","",Lx,&Lx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-alpha","material coefficient inside circle","",s_soft_alpha,&s_soft_alpha,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_nonzero_cols","nonzero test","",test_nonzero_cols,&test_nonzero_cols,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-use_mat_nearnullspace","MatNearNullSpace API test","",use_nearnullspace,&use_nearnullspace,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-run_type","0: twisting load on cantalever, 1: 3rd order accurate convergence test","",run_type,&run_type,NULL);CHKERRQ(ierr);
i = 3;
ierr = PetscOptionsInt("-mat_block_size","","",i,&i,&flg);CHKERRQ(ierr);
if (!flg || i!=3) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_USER, "'-mat_block_size 3' must be set (%D) and = 3 (%D)",flg,flg? i : 3);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscLogStageRegister("Mesh Setup", &stage[6]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("1st Setup", &stage[0]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("1st Solve", &stage[1]);CHKERRQ(ierr);
/* create DM, Plex calls DMSetup */
ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr);
{
DMLabel label;
IS is;
ierr = DMCreateLabel(dm, "boundary");CHKERRQ(ierr);
ierr = DMGetLabel(dm, "boundary", &label);CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr);
if (run_type==0) {
ierr = DMGetStratumIS(dm, "boundary", 1, &is);CHKERRQ(ierr);
ierr = DMCreateLabel(dm,"Faces");CHKERRQ(ierr);
if (is) {
PetscInt d, f, Nf;
const PetscInt *faces;
PetscInt csize;
PetscSection cs;
Vec coordinates ;
DM cdm;
ierr = ISGetLocalSize(is, &Nf);CHKERRQ(ierr);
ierr = ISGetIndices(is, &faces);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetDefaultSection(cdm, &cs);CHKERRQ(ierr);
/* Check for each boundary face if any component of its centroid is either 0.0 or 1.0 */
for (f = 0; f < Nf; ++f) {
PetscReal faceCoord;
PetscInt b,v;
PetscScalar *coords = NULL;
PetscInt Nv;
ierr = DMPlexVecGetClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
Nv = csize/dim; /* Calculate mean coordinate vector */
for (d = 0; d < dim; ++d) {
faceCoord = 0.0;
for (v = 0; v < Nv; ++v) faceCoord += PetscRealPart(coords[v*dim+d]);
faceCoord /= Nv;
for (b = 0; b < 2; ++b) {
if (PetscAbs(faceCoord - b) < PETSC_SMALL) { /* domain have not been set yet, still [0,1]^3 */
ierr = DMSetLabelValue(dm, "Faces", faces[f], d*2+b+1);CHKERRQ(ierr);
}
}
}
ierr = DMPlexVecRestoreClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(is, &faces);CHKERRQ(ierr);
}
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = DMGetLabel(dm, "Faces", &label);CHKERRQ(ierr);
ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr);
}
}
{
PetscInt dimEmbed, i;
PetscInt nCoords;
PetscScalar *coords,bounds[] = {0,Lx,-.5,.5,-.5,.5,}; /* x_min,x_max,y_min,y_max */
Vec coordinates;
if (run_type==1) {
for (i = 0; i < 2*dim; i++) bounds[i] = (i%2) ? 1 : 0;
}
ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr);
if (dimEmbed != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"dimEmbed != dim %D",dimEmbed);CHKERRQ(ierr);
ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr);
if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size");CHKERRQ(ierr);
ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr);
for (i = 0; i < nCoords; i += dimEmbed) {
PetscInt j;
PetscScalar *coord = &coords[i];
for (j = 0; j < dimEmbed; j++) {
coord[j] = bounds[2 * j] + coord[j] * (bounds[2 * j + 1] - bounds[2 * j]);
}
}
ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr);
}
/* convert to p4est, and distribute */
ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format (should not be Plex!)","ex56.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
if (flg) {
DM newdm;
ierr = DMConvert(dm,convType,&newdm);CHKERRQ(ierr);
if (newdm) {
const char *prefix;
PetscBool isForest;
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)newdm,prefix);CHKERRQ(ierr);
ierr = DMIsForest(newdm,&isForest);CHKERRQ(ierr);
if (isForest) {
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Converted to non Forest?");
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = newdm;
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Convert failed?");
} else {
/* Plex Distribute mesh over processes */
ierr = DMPlexDistribute(dm, 0, NULL, &distdm);CHKERRQ(ierr);
if (distdm) {
const char *prefix;
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)distdm,prefix);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = distdm;
}
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
basedm = dm; dm = NULL;
for (iter=0 ; iter<max_conv_its ; iter++) {
ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
/* make new DM */
ierr = DMClone(basedm, &dm);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, "ex56_");CHKERRQ(ierr);
ierr = PetscObjectSetName( (PetscObject)dm,"Mesh");CHKERRQ(ierr);
ierr = PetscOptionsClearValue(NULL,"-ex56_dm_refine");CHKERRQ(ierr);
ierr = PetscOptionsInsertString(NULL,options[iter]);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr); /* refinement done here in Plex, p4est */
/* snes */
ierr = SNESCreate(comm, &snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
/* fem */
{
const PetscInt Ncomp = dim;
const PetscInt components[] = {0,1,2};
const PetscInt Nfid = 1, Npid = 1;
const PetscInt fid[] = {1}; /* The fixed faces (x=0) */
const PetscInt pid[] = {2}; /* The faces with loading (x=L_x) */
PetscFE fe;
PetscDS prob;
DM cdm = dm;
ierr = PetscFECreateDefault(dm, dim, dim, PETSC_FALSE, NULL, PETSC_DECIDE, &fe);CHKERRQ(ierr); /* elasticity */
ierr = PetscObjectSetName((PetscObject) fe, "deformation");CHKERRQ(ierr);
/* FEM prob */
ierr = DMGetDS(dm, &prob);CHKERRQ(ierr);
ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr);
/* setup problem */
if (run_type==1) {
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, f0_u_x4, f1_u_3d);CHKERRQ(ierr);
} else {
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d_alpha);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, f0_u, f1_u_3d_alpha);CHKERRQ(ierr);
ierr = PetscDSSetBdResidual(prob, 0, f0_bd_u_3d, f1_bd_u);CHKERRQ(ierr);
}
/* bcs */
if (run_type==1) {
PetscInt id = 1;
ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "boundary", 0, 0, NULL, (void (*)()) zero, 1, &id, NULL);CHKERRQ(ierr);
} else {
ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "fixed", "Faces", 0, Ncomp, components, (void (*)()) zero, Nfid, fid, NULL);CHKERRQ(ierr);
ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL, "traction", "Faces", 0, Ncomp, components, NULL, Npid, pid, NULL);CHKERRQ(ierr);
}
while (cdm) {
ierr = DMSetDS(cdm,prob);CHKERRQ(ierr);
ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
}
/* vecs & mat */
ierr = DMCreateGlobalVector(dm,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx, &bb);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) bb, "b");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) xx, "u");CHKERRQ(ierr);
ierr = DMCreateMatrix(dm, &Amat);CHKERRQ(ierr);
ierr = VecGetSize(bb,&N);CHKERRQ(ierr);
local_sizes[iter] = N;
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d global equations, %d vertices\n",rank,PETSC_FUNCTION_NAME,N,N/dim);CHKERRQ(ierr);
if (use_nearnullspace && N/dim > 1) {
/* Set up the near null space (a.k.a. rigid body modes) that will be used by the multigrid preconditioner */
DM subdm;
MatNullSpace nearNullSpace;
PetscInt fields = 0;
PetscObject deformation;
ierr = DMCreateSubDM(dm, 1, &fields, NULL, &subdm);CHKERRQ(ierr);
ierr = DMPlexCreateRigidBody(subdm, &nearNullSpace);CHKERRQ(ierr);
ierr = DMGetField(dm, 0, &deformation);CHKERRQ(ierr);
ierr = PetscObjectCompose(deformation, "nearnullspace", (PetscObject) nearNullSpace);CHKERRQ(ierr);
ierr = DMDestroy(&subdm);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nearNullSpace);CHKERRQ(ierr); /* created by DM and destroyed by Mat */
}
ierr = DMPlexSetSNESLocalFEM(dm,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, Amat, Amat, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogStagePush(stage[0]);CHKERRQ(ierr);
/* ksp */
ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr);
ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr);
/* test BCs */
ierr = VecZeroEntries(xx);CHKERRQ(ierr);
if (test_nonzero_cols) {
if (rank==0) ierr = VecSetValue(xx,0,1.0,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(xx);CHKERRQ(ierr);
ierr = VecAssemblyEnd(xx);CHKERRQ(ierr);
}
ierr = VecZeroEntries(bb);CHKERRQ(ierr);
ierr = VecGetSize(bb,&i);CHKERRQ(ierr);
local_sizes[iter] = i;
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d equations in vector, %d vertices\n",rank,PETSC_FUNCTION_NAME,i,i/dim);CHKERRQ(ierr);
/* setup solver, dummy solve to really setup */
if (0) {
ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1);CHKERRQ(ierr);
ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,50);CHKERRQ(ierr);
ierr = VecZeroEntries(xx);CHKERRQ(ierr);
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
/* solve */
ierr = PetscLogStagePush(stage[1]);CHKERRQ(ierr);
ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = VecNorm(xx,NORM_INFINITY,&mdisp[iter]);CHKERRQ(ierr);
ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
{
PetscViewer viewer = NULL;
PetscViewerFormat fmt;
ierr = PetscOptionsGetViewer(comm,"ex56_","-vec_view",&viewer,&fmt,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerPushFormat(viewer,fmt);CHKERRQ(ierr);
ierr = VecView(xx,viewer);CHKERRQ(ierr);
ierr = VecView(bb,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
/* Free work space */
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = VecDestroy(&xx);CHKERRQ(ierr);
ierr = VecDestroy(&bb);CHKERRQ(ierr);
ierr = MatDestroy(&Amat);CHKERRQ(ierr);
}
ierr = DMDestroy(&basedm);CHKERRQ(ierr);
if (run_type==1) {
err[0] = 59.975208 - mdisp[0]; /* error with what I think is the exact solution */
} else {
err[0] = 171.038 - mdisp[0];
}
for (iter=1 ; iter<max_conv_its ; iter++) {
if (run_type==1) {
err[iter] = 59.975208 - mdisp[iter];
} else {
err[iter] = 171.038 - mdisp[iter];
}
PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %D) N=%12D, max displ=%9.7e, disp diff=%9.2e, error=%4.3e, rate=%3.2g\n",
rank,PETSC_FUNCTION_NAME,iter,local_sizes[iter],mdisp[iter],
mdisp[iter]-mdisp[iter-1],err[iter],log(err[iter-1]/err[iter])/log(2.));
}
ierr = PetscFinalize();
return ierr;
}
#define petscoptionsinsertfile_ petscoptionsinsertfile
#define petscoptionsclear_ petscoptionsclear
#define petscoptionsinsertstring_ petscoptionsinsertstring
#define petscoptionsview_ petscoptionsview
#endif
EXTERN_C_BEGIN
/* ---------------------------------------------------------------------*/
void PETSC_STDCALL petscoptionsinsertstring_(CHAR file PETSC_MIXED_LEN(len),PetscErrorCode *ierr PETSC_END_LEN(len))
{
char *c1;
FIXCHAR(file,len,c1);
*ierr = PetscOptionsInsertString(c1);
FREECHAR(file,c1);
}
void PETSC_STDCALL petscoptionsinsertfile_(MPI_Fint *comm,CHAR file PETSC_MIXED_LEN(len),PetscBool *require,PetscErrorCode *ierr PETSC_END_LEN(len))
{
char *c1;
FIXCHAR(file,len,c1);
*ierr = PetscOptionsInsertFile(MPI_Comm_f2c(*comm),c1,*require);
FREECHAR(file,c1);
}
void PETSC_STDCALL petscoptionssetvalue_(CHAR name PETSC_MIXED_LEN(len1),CHAR value PETSC_MIXED_LEN(len2),
PetscErrorCode *ierr PETSC_END_LEN(len1) PETSC_END_LEN(len2))
{