static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
options->dim = 2;
options->cellSimplex = PETSC_TRUE;
options->filename[0] = '\0';
options->testPartition = PETSC_TRUE;
options->testNum = 0;
ierr = PetscOptionsBegin(comm, "", "Meshing Problem Options", "DMPLEX");
CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex13.c", options->dim, &options->dim, NULL);
CHKERRQ(ierr);
ierr = PetscOptionsBool("-cell_simplex", "Use simplices if true, otherwise hexes", "ex13.c", options->cellSimplex, &options->cellSimplex, NULL);
CHKERRQ(ierr);
ierr = PetscOptionsString("-filename", "The mesh file", "ex13.c", options->filename, options->filename, PETSC_MAX_PATH_LEN, NULL);
CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_partition", "Use a fixed partition for testing", "ex13.c", options->testPartition, &options->testPartition, NULL);
CHKERRQ(ierr);
ierr = PetscOptionsInt("-test_num", "The test partition number", "ex13.c", options->testNum, &options->testNum, NULL);
CHKERRQ(ierr);
ierr = PetscOptionsEnd();
PetscFunctionReturn(0);
};
static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscInt dim;
PetscErrorCode ierr;
PetscFunctionBegin;
options->test = 0;
options->dim = 3;
options->simplex = PETSC_TRUE;
options->interpolate = PETSC_FALSE;
options->filename[0] = '\0';
ierr = PetscOptionsBegin(comm, "", "Zero-sized DMPlexGetCellFields Test Options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsInt("-test", "Test to run", FILENAME, options->test, &options->test, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", FILENAME, options->dim, &options->dim, NULL);CHKERRQ(ierr);
if (options->dim > 3) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "dimension set to %d, must be <= 3", options->dim);
ierr = PetscOptionsBool("-simplex", "Use simplices if true, otherwise hexes", FILENAME, options->simplex, &options->simplex, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-interpolate", "Interpolate the mesh", FILENAME, options->interpolate, &options->interpolate, NULL);CHKERRQ(ierr);
ierr = PetscOptionsString("-filename", "The mesh file", FILENAME, options->filename, options->filename, PETSC_MAX_PATH_LEN, NULL);CHKERRQ(ierr);
options->faces[0] = 1; options->faces[1] = 1; options->faces[2] = 1;
dim = options->dim;
ierr = PetscOptionsIntArray("-faces", "Number of faces per dimension", FILENAME, options->faces, &dim, NULL);CHKERRQ(ierr);
if (dim) options->dim = dim;
ierr = PetscOptionsEnd();
PetscFunctionReturn(0);
}
PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscInt patchSize, commSize, gridSize;
PetscErrorCode ierr;
PetscFunctionBegin;
options->debug = 0;
options->dim = 2;
patchSize = 0;
commSize = 0;
gridSize = 0;
ierr = PetscOptionsBegin(comm, "", "Patch Test Options", "DMPATCH");CHKERRQ(ierr);
ierr = PetscOptionsInt("-debug", "The debugging level", "ex1.c", options->debug, &options->debug, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The spatial dimension", "ex1.c", options->dim, &options->dim, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-patch_size", "The patch size in each dimension", "ex1.c", patchSize, &patchSize, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-comm_size", "The comm size in each dimension", "ex1.c", commSize, &commSize, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-grid_size", "The grid size in each dimension", "ex1.c", gridSize, &gridSize, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
options->patchSize.i = options->patchSize.j = options->patchSize.k = 1;
options->commSize.i = options->commSize.j = options->commSize.k = 1;
options->gridSize.i = options->gridSize.j = options->gridSize.k = 1;
if (options->dim > 0) {options->patchSize.i = patchSize; options->commSize.i = commSize; options->gridSize.i = gridSize;}
if (options->dim > 1) {options->patchSize.j = patchSize; options->commSize.j = commSize; options->gridSize.j = gridSize;}
if (options->dim > 2) {options->patchSize.k = patchSize; options->commSize.k = commSize; options->gridSize.k = gridSize;}
PetscFunctionReturn(0);
};
static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscInt n = 3, sol;
PetscErrorCode ierr;
PetscFunctionBeginUser;
options->dim = 2;
options->cells[0] = 1;
options->cells[1] = 1;
options->cells[2] = 1;
options->simplex = PETSC_TRUE;
options->solType = SOL_VLAP_QUADRATIC;
options->useNearNullspace = PETSC_TRUE;
ierr = PetscStrncpy(options->dmType, DMPLEX, 256);CHKERRQ(ierr);
ierr = PetscOptionsBegin(comm, "", "Linear Elasticity Problem Options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex17.c", options->dim, &options->dim, NULL);CHKERRQ(ierr);
ierr = PetscOptionsIntArray("-cells", "The initial mesh division", "ex17.c", options->cells, &n, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-simplex", "Simplicial (true) or tensor (false) mesh", "ex17.c", options->simplex, &options->simplex, NULL);CHKERRQ(ierr);
sol = options->solType;
ierr = PetscOptionsEList("-sol_type", "Type of exact solution", "ex17.c", solutionTypes, NUM_SOLUTION_TYPES, solutionTypes[options->solType], &sol, NULL);CHKERRQ(ierr);
options->solType = (SolutionType) sol;
ierr = PetscOptionsBool("-near_nullspace", "Use the rigid body modes as an AMG near nullspace", "ex17.c", options->useNearNullspace, &options->useNearNullspace, NULL);CHKERRQ(ierr);
ierr = PetscOptionsFList("-dm_type", "Convert DMPlex to another format", "ex17.c", DMList, options->dmType, options->dmType, 256, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
PetscFunctionReturn(0);
}
dErr dUnitsSetFromOptions(dUnits un)
{
dErr err;
dFunctionBegin;
dValidHeader(un,dUNITS_CLASSID,1);
err = PetscOptionsBegin(((PetscObject)un)->comm,((PetscObject)un)->prefix,"Units manager","dUnits");dCHK(err);
for (dUnitsBaseType btype = 0; btype < dUNITS_MAX; btype++) {
char opt[256],help[256],uspec[256];
dReal commonpersi = 1.0,scale = 1.0;
dBool flg;
err = PetscSNPrintf(opt,sizeof opt,"-units_%s",dUnitsBaseTypes[btype]);dCHK(err);
err = PetscSNPrintf(uspec,sizeof uspec,"%s:%s:%f:%f",dUnitsBaseNamesSI[btype],dUnitsBaseNamesShortSI[btype],commonpersi,scale);
err = PetscSNPrintf(help,sizeof help,"Common name:short name:one common unit of %s expressed in %s:common units per non-dimensionalized",dUnitsBaseTypes[btype],dUnitsBaseNamesSI[btype]);dCHK(err);
err = PetscOptionsString(opt,help,"dUnitsSetBase",uspec,uspec,sizeof uspec,&flg);dCHK(err);
if (flg) {
char *longname,*shortname,*buf1,*buf2;
longname = uspec;
if (!(shortname = strchr(longname,':'))) dERROR(((dObject)un)->comm,PETSC_ERR_USER,"The field specification '%s' is ':' delimited",opt);
*shortname++ = 0;
if (!(buf1 = strchr(shortname,':'))) dERROR(((dObject)un)->comm,PETSC_ERR_USER,"The field specification for '%s' needs four arguments, but only two given",longname);
*buf1++ = 0;
if (!(buf2 = strchr(buf1,':'))) dERROR(((dObject)un)->comm,PETSC_ERR_USER,"The field specification for '%s' needs four arguments, but only three given",longname);
*buf2++ = 0;
if (sscanf(buf1,"%lf",&commonpersi) != 1) dERROR(((dObject)un)->comm,PETSC_ERR_USER,"Size of common unit '%s' could not be parsed from '%s'",longname,buf1);
if (sscanf(buf2,"%lf",&scale) != 1) dERROR(((dObject)un)->comm,PETSC_ERR_USER,"Scale for common unit '%s' could not be parsed from '%s'",longname,buf2);
err = dUnitsSetBase(un,btype,longname,shortname,commonpersi,scale,NULL);dCHK(err);
}
}
err = PetscOptionsEnd();dCHK(err);
dFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm;
char typeString[256] = {'\0'};
PetscViewer viewer = NULL;
PetscBool flg;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = DMCreate(PETSC_COMM_WORLD, &dm);CHKERRQ(ierr);
ierr = PetscStrncpy(typeString,DMFOREST,256);CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"DM Forest example options",NULL);CHKERRQ(ierr);
ierr = PetscOptionsString("-dm_type","The type of the dm",NULL,DMFOREST,typeString,sizeof(typeString),NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = DMSetType(dm,(DMType) typeString);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(PETSC_COMM_WORLD,NULL,"-dm_view",&viewer,NULL,&flg);CHKERRQ(ierr);
if (flg) {
ierr = DMView(dm,viewer);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscInt len;
PetscBool flg;
PetscErrorCode ierr;
PetscFunctionBeginUser;
options->dim = 2;
options->Nf = 0;
options->Nc = NULL;
options->k = NULL;
ierr = PetscOptionsBegin(comm, "", "SEM Problem Options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "Problem dimension", "ex6.c", options->dim, &options->dim, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-num_fields", "The number of fields", "ex6.c", options->Nf, &options->Nf, NULL);CHKERRQ(ierr);
if (options->Nf) {
len = options->Nf;
ierr = PetscMalloc1(len, &options->Nc);CHKERRQ(ierr);
ierr = PetscOptionsIntArray("-num_components", "The number of components per field", "ex6.c", options->Nc, &len, &flg);CHKERRQ(ierr);
if (flg && (len != options->Nf)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Length of components array is %d should be %d", len, options->Nf);
len = options->Nf;
ierr = PetscMalloc1(len, &options->k);CHKERRQ(ierr);
ierr = PetscOptionsIntArray("-order", "The spectral order per field", "ex6.c", options->k, &len, &flg);CHKERRQ(ierr);
if (flg && (len != options->Nf)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Length of order array is %d should be %d", len, options->Nf);
}
ierr = PetscOptionsEnd();
PetscFunctionReturn(0);
}
PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscErrorCode ierr;
PetscFunctionBegin;
options->debug = 0;
options->dim = 2;
options->interpolate = PETSC_FALSE;
options->refinementUniform = PETSC_FALSE;
options->refinementLimit = 0.0;
options->cellSimplex = PETSC_TRUE;
options->filename[0] = '\0';
ierr = PetscOptionsBegin(comm, "", "Meshing Problem Options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsInt("-debug", "The debugging level", "ex1.c", options->debug, &options->debug, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex1.c", options->dim, &options->dim, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-interpolate", "Generate intermediate mesh elements", "ex1.c", options->interpolate, &options->interpolate, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-refinement_uniform", "Uniformly refine the mesh", "ex1.c", options->refinementUniform, &options->refinementUniform, NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-refinement_limit", "The largest allowable cell volume", "ex1.c", options->refinementLimit, &options->refinementLimit, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-cell_simplex", "Use simplices if true, otherwise hexes", "ex1.c", options->cellSimplex, &options->cellSimplex, NULL);CHKERRQ(ierr);
ierr = PetscOptionsString("-filename", "The mesh file", "ex7.c", options->filename, options->filename, PETSC_MAX_PATH_LEN, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = PetscLogEventRegister("CreateMesh", DM_CLASSID, &options->createMeshEvent);CHKERRQ(ierr);
PetscFunctionReturn(0);
};
int main(int argc,char **argv) {
PetscErrorCode ierr;
SNES snes; // nonlinear solver context
Vec x, r; // solution, residual vectors
PetscReal x0 = 2.0;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","options to atan","");CHKERRQ(ierr);
ierr = PetscOptionsReal("-x0","initial value","atan.c",x0,&x0,NULL); CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&x); CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,1); CHKERRQ(ierr);
ierr = VecSetFromOptions(x); CHKERRQ(ierr);
ierr = VecSet(x,x0); CHKERRQ(ierr);
ierr = VecDuplicate(x,&r); CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes); CHKERRQ(ierr);
ierr = SNESSetFunction(snes,r,FormFunction,NULL); CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes); CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,x); CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
VecDestroy(&x); VecDestroy(&r); SNESDestroy(&snes);
PetscFinalize();
return 0;
}
PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscErrorCode ierr;
PetscFunctionBegin;
options->debug = 0;
options->dim = 2;
options->cellHybrid = PETSC_TRUE;
options->cellSimplex = PETSC_TRUE;
options->testPartition = PETSC_TRUE;
options->testNum = 0;
options->simplex2tensor = PETSC_FALSE;
options->uninterpolate = PETSC_FALSE;
options->reinterpolate = PETSC_FALSE;
ierr = PetscOptionsBegin(comm, "", "Meshing Problem Options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsInt("-debug", "The debugging level", "ex4.c", options->debug, &options->debug, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex4.c", options->dim, &options->dim, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-cell_hybrid", "Use a hybrid mesh", "ex4.c", options->cellHybrid, &options->cellHybrid, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-cell_simplex", "Use simplices if true, otherwise hexes", "ex4.c", options->cellSimplex, &options->cellSimplex, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_partition", "Use a fixed partition for testing", "ex4.c", options->testPartition, &options->testPartition, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-test_num", "The particular mesh to test", "ex4.c", options->testNum, &options->testNum, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-simplex2tensor", "Refine simplicial cells in tensor product cells", "ex4.c", options->simplex2tensor, &options->simplex2tensor, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-uninterpolate", "Uninterpolate the mesh at the end", "ex4.c", options->uninterpolate, &options->uninterpolate, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-reinterpolate", "Reinterpolate the mesh at the end", "ex4.c", options->reinterpolate, &options->reinterpolate, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
PetscFunctionReturn(0);
}
int main(int argc, char **args) {
PetscErrorCode ierr;
MPI_Comm comm = MPI_COMM_SELF;
ierr = PetscInitialize(&argc, &args, (char*)0, help); CHKERRQ(ierr);
KSP ksp; KSPCreate(comm, &ksp);
WaveFunc wave_func; WaveFuncCreate(comm, &wave_func);
FEMInf fem; FEMInfCreate(comm, &fem);
PetscViewer viewer= PETSC_VIEWER_STDOUT_SELF;
ViewerFunc view_func; ViewerFuncCreate(comm, &view_func);
PetscViewerFormat format;
ierr = PetscOptionsBegin(comm, "", "eig_one.c options", "none");
ierr = WaveFuncSetFromOptions(wave_func); CHKERRQ(ierr);
ierr = FEMInfSetFromOptions(fem); CHKERRQ(ierr);
// ierr = PotSetFromOptions(pot); CHKERRQ(ierr);
ierr = ViewerFuncSetFromOptions(view_func); CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm, NULL, "-viewer", &viewer, &format, NULL);
PetscOptionsEnd();
Vec c; FEMInfCreateVec(fem, 1, &c);
ierr = FEMInfFit(fem, wave_func, ksp, c); CHKERRQ(ierr);
ierr = FEMInfViewFunc(fem, c, view_func); CHKERRQ(ierr);
ierr = PFView(wave_func, viewer); CHKERRQ(ierr);
ierr = FEMInfView(fem, viewer); CHKERRQ(ierr);
ierr = ViewerFuncView(view_func, viewer); CHKERRQ(ierr);
ierr = PetscFinalize(); CHKERRQ(ierr);
return 0;
}
static PetscErrorCode CECreate(Problem p)
{
PetscErrorCode ierr;
CECtx *ce;
PetscFunctionBeginUser;
ierr = PetscMalloc(sizeof(CECtx),&ce);CHKERRQ(ierr);
p->data = (void*)ce;
p->destroy = &CEDestroy;
p->function = &CEFunction;
p->jacobian = &CEJacobian;
p->solution = &CESolution;
p->final_time = 10;
p->n = 1;
p->hasexact = PETSC_TRUE;
ce->lambda = 10;
ierr = PetscOptionsBegin(p->comm,NULL,"CE options","");CHKERRQ(ierr);
{
ierr = PetscOptionsReal("-problem_ce_lambda","Parameter controlling stiffness: xdot + lambda*(x - cos(t))","",ce->lambda,&ce->lambda,NULL);CHKERRQ(ierr);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscErrorCode ierr;
PetscFunctionBegin;
options->debug = 0;
options->dim = 2;
options->interpolate = PETSC_FALSE;
options->refinementLimit = 0.0;
ierr = MPI_Comm_size(comm, &options->numProcs);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &options->rank);CHKERRQ(ierr);
ierr = PetscOptionsBegin(comm, "", "Mesh Distribution Options", "DMMESH");CHKERRQ(ierr);
ierr = PetscOptionsInt("-debug", "The debugging level", "ex1.c", options->debug, &options->debug, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex1.c", options->dim, &options->dim, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-interpolate", "Generate intermediate mesh elements", "ex1.c", options->interpolate, &options->interpolate, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-refinement_limit", "The largest allowable cell volume", "ex1.c", options->refinementLimit, &options->refinementLimit, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscStrcpy(options->filename, "");CHKERRQ(ierr);
ierr = PetscOptionsString("-filename", "The input filename", "ex1.c", options->filename, options->filename, 2048, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscStrcpy(options->partitioner, "chaco");CHKERRQ(ierr);
ierr = PetscOptionsString("-partitioner", "The graph partitioner", "ex1.c", options->partitioner, options->partitioner, 2048, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = PetscLogEventRegister("CreateMesh", DM_CLASSID, &options->createMeshEvent);CHKERRQ(ierr);
PetscFunctionReturn(0);
};
PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscErrorCode ierr;
PetscFunctionBegin;
options->debug = 0;
options->dim = 2;
options->simplex = PETSC_TRUE;
options->interpolate = PETSC_FALSE;
options->refinementLimit = 0.0;
options->qorder = 0;
options->numComponents = 1;
options->porder = 0;
ierr = PetscOptionsBegin(comm, "", "Projection Test Options", "DMPlex");CHKERRQ(ierr);
ierr = PetscOptionsInt("-debug", "The debugging level", "ex3.c", options->debug, &options->debug, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex3.c", options->dim, &options->dim, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-simplex", "Flag for simplices or hexhedra", "ex3.c", options->simplex, &options->simplex, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-interpolate", "Generate intermediate mesh elements", "ex3.c", options->interpolate, &options->interpolate, NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-refinement_limit", "The largest allowable cell volume", "ex3.c", options->refinementLimit, &options->refinementLimit, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-qorder", "The quadrature order", "ex3.c", options->qorder, &options->qorder, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-num_comp", "The number of field components", "ex3.c", options->numComponents, &options->numComponents, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-porder", "The order of polynomials to test", "ex3.c", options->porder, &options->porder, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
spdim = options->dim;
PetscFunctionReturn(0);
};
PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
const char *names[8] = {"none", "ghosted", "mirror", "periodic", "twist", "DMBoundaryType", "DM_BOUNDARY_", NULL};
PetscInt n;
PetscErrorCode ierr;
PetscFunctionBegin;
options->dim = 2;
options->cellSimplex = PETSC_TRUE;
options->faces[0] = 1;
options->faces[1] = 1;
options->faces[2] = 1;
options->periodicity[0] = DM_BOUNDARY_NONE;
options->periodicity[1] = DM_BOUNDARY_NONE;
options->periodicity[2] = DM_BOUNDARY_NONE;
options->filename[0] = '\0';
ierr = PetscOptionsBegin(comm, "", "Meshing Interpolation Test Options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex32.c", options->dim, &options->dim, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-cell_simplex", "Use simplices if true, otherwise hexes", "ex32.c", options->cellSimplex, &options->cellSimplex, NULL);CHKERRQ(ierr);
n = 3;
ierr = PetscOptionsIntArray("-faces", "Faces per direction", "ex32.c", options->faces, &n, NULL);CHKERRQ(ierr);
n = 3;
ierr = PetscOptionsEnumArray("-periodicity", "Periodicity per direction", "ex32.c", names, (PetscEnum *) options->periodicity, &n, &options->isPeriodic);CHKERRQ(ierr);
ierr = PetscOptionsString("-filename", "The mesh file", "ex32.c", options->filename, options->filename, PETSC_MAX_PATH_LEN, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
PetscFunctionReturn(0);
}
PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscErrorCode ierr;
PetscFunctionBegin;
options->debug = 0;
options->dim = 2;
options->interpolate = PETSC_FALSE;
options->refinementLimit = 0.0;
options->cellSimplex = PETSC_TRUE;
options->filename[0] = '\0';
options->testPartition = PETSC_FALSE;
options->overlap = PETSC_FALSE;
options->testShape = PETSC_FALSE;
ierr = PetscOptionsBegin(comm, "", "Meshing Problem Options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsInt("-debug", "The debugging level", "ex1.c", options->debug, &options->debug, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex1.c", options->dim, &options->dim, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-interpolate", "Generate intermediate mesh elements", "ex1.c", options->interpolate, &options->interpolate, NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-refinement_limit", "The largest allowable cell volume", "ex1.c", options->refinementLimit, &options->refinementLimit, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-cell_simplex", "Use simplices if true, otherwise hexes", "ex1.c", options->cellSimplex, &options->cellSimplex, NULL);CHKERRQ(ierr);
ierr = PetscOptionsString("-filename", "The mesh file", "ex1.c", options->filename, options->filename, PETSC_MAX_PATH_LEN, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_partition", "Use a fixed partition for testing", "ex1.c", options->testPartition, &options->testPartition, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-overlap", "The cell overlap for partitioning", "ex1.c", options->overlap, &options->overlap, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_shape", "Report cell shape qualities (Jacobian condition numbers)", "ex1.c", options->testShape, &options->testShape, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = PetscLogEventRegister("CreateMesh", DM_CLASSID, &options->createMeshEvent);CHKERRQ(ierr);
PetscFunctionReturn(0);
};
PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
options->debug = 0;
options->dim = 2;
options->numBatches = 1;
options->numBlocks = 1;
options->showResidual = PETSC_FALSE;
options->showResidual = PETSC_FALSE;
options->showJacobian = PETSC_FALSE;
options->showSolution = PETSC_TRUE;
ierr = MPI_Comm_size(comm, &options->numProcs);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &options->rank);CHKERRQ(ierr);
ierr = PetscOptionsBegin(comm, "", "DMDA Test Problem Options", "DMDA");CHKERRQ(ierr);
ierr = PetscOptionsInt("-debug", "The debugging level", "ex62.c", options->debug, &options->debug, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex62.c", options->dim, &options->dim, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-gpu_batches", "The number of cell batches per kernel", "ex62.c", options->numBatches, &options->numBatches, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-gpu_blocks", "The number of concurrent blocks per kernel", "ex62.c", options->numBlocks, &options->numBlocks, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-show_initial", "Output the initial guess for verification", "ex62.c", options->showInitial, &options->showInitial, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-show_residual", "Output the residual for verification", "ex62.c", options->showResidual, &options->showResidual, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-show_jacobian", "Output the Jacobian for verification", "ex62.c", options->showJacobian, &options->showJacobian, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-show_solution", "Output the solution for verification", "ex62.c", options->showSolution, &options->showSolution, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = PetscLogEventRegister("Residual", SNES_CLASSID, &options->residualEvent);CHKERRQ(ierr);
ierr = PetscLogEventRegister("IntegResBatchCPU", SNES_CLASSID, &options->integrateResCPUEvent);CHKERRQ(ierr);
ierr = PetscLogEventRegister("IntegJacBatchCPU", SNES_CLASSID, &options->integrateJacCPUEvent);CHKERRQ(ierr);
ierr = PetscLogEventRegister("IntegJacActBatchCPU", SNES_CLASSID, &options->integrateJacActionCPUEvent);CHKERRQ(ierr);
ierr = PetscLogEventRegister("Jacobian", SNES_CLASSID, &options->jacobianEvent);CHKERRQ(ierr);
PetscFunctionReturn(0);
};
int main(int argc, char **argv)
{
DM dm, dmAdapt;
DMLabel adaptLabel;
PetscInt dim, nfaces, cStart, cEnd;
PetscBool interpolate;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
dim = 2;
nfaces = 3;
interpolate = PETSC_TRUE;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"ex20",NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim","domain dimension",NULL,dim,&dim,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-nfaces","number of faces per dimension",NULL,nfaces,&nfaces,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD,dim,nfaces,interpolate,&dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)dm,"Pre Adaptation Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(dm,NULL,"-pre_adapt_dm_view");CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr);
ierr = DMLabelCreate("adapt",&adaptLabel);CHKERRQ(ierr);
ierr = DMLabelSetDefaultValue(adaptLabel,DM_ADAPT_COARSEN);CHKERRQ(ierr);
if (cEnd > cStart) {ierr = DMLabelSetValue(adaptLabel,cStart,DM_ADAPT_REFINE);CHKERRQ(ierr);}
ierr = DMAdaptLabel(dm,adaptLabel,&dmAdapt);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)dmAdapt,"Post Adaptation Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(dmAdapt,NULL,"-post_adapt_dm_view");CHKERRQ(ierr);
ierr = DMDestroy(&dmAdapt);CHKERRQ(ierr);
ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/*@
MatSetFromOptions - Creates a matrix where the type is determined
from the options database. Generates a parallel MPI matrix if the
communicator has more than one processor. The default matrix type is
AIJ, using the routines MatCreateSeqAIJ() and MatCreateMPIAIJ() if
you do not select a type in the options database.
Collective on Mat
Input Parameter:
. A - the matrix
Options Database Keys:
+ -mat_type seqaij - AIJ type, uses MatCreateSeqAIJ()
. -mat_type mpiaij - AIJ type, uses MatCreateMPIAIJ()
. -mat_type seqdense - dense type, uses MatCreateSeqDense()
. -mat_type mpidense - dense type, uses MatCreateMPIDense()
. -mat_type seqbaij - block AIJ type, uses MatCreateSeqBAIJ()
- -mat_type mpibaij - block AIJ type, uses MatCreateMPIBAIJ()
Even More Options Database Keys:
See the manpages for particular formats (e.g., MatCreateSeqAIJ())
for additional format-specific options.
Level: beginner
.keywords: matrix, create
.seealso: MatCreateSeqAIJ((), MatCreateMPIAIJ(),
MatCreateSeqDense(), MatCreateMPIDense(),
MatCreateSeqBAIJ(), MatCreateMPIBAIJ(),
MatCreateSeqSBAIJ(), MatCreateMPISBAIJ(),
MatConvert()
@*/
PetscErrorCode PETSCMAT_DLLEXPORT MatSetFromOptions(Mat B)
{
PetscErrorCode ierr;
const char *deft = MATAIJ;
char type[256];
PetscTruth flg;
PetscFunctionBegin;
PetscValidHeaderSpecific(B,MAT_COOKIE,1);
ierr = PetscOptionsBegin(((PetscObject)B)->comm,((PetscObject)B)->prefix,"Matrix options","Mat");CHKERRQ(ierr);
ierr = PetscOptionsList("-mat_type","Matrix type","MatSetType",MatList,deft,type,256,&flg);CHKERRQ(ierr);
if (flg) {
ierr = MatSetType(B,type);CHKERRQ(ierr);
} else if (!((PetscObject)B)->type_name) {
ierr = MatSetType(B,deft);CHKERRQ(ierr);
}
if (B->ops->setfromoptions) {
ierr = (*B->ops->setfromoptions)(B);CHKERRQ(ierr);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
KSP ksp;
DM da;
UserContext user;
const char *bcTypes[2] = {"dirichlet","neumann"};
PetscErrorCode ierr;
PetscInt bc;
Vec b,x;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);
CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-3,-3,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0,&da);
CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(da,0,1,0,1,0,0);
CHKERRQ(ierr);
ierr = DMDASetFieldName(da,0,"Pressure");
CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "", "Options for the inhomogeneous Poisson equation", "DMqq");
user.rho = 1.0;
ierr = PetscOptionsReal("-rho", "The conductivity", "ex29.c", user.rho, &user.rho, PETSC_NULL);
CHKERRQ(ierr);
user.nu = 0.1;
ierr = PetscOptionsReal("-nu", "The width of the Gaussian source", "ex29.c", user.nu, &user.nu, PETSC_NULL);
CHKERRQ(ierr);
bc = (PetscInt)DIRICHLET;
ierr = PetscOptionsEList("-bc_type","Type of boundary condition","ex29.c",bcTypes,2,bcTypes[0],&bc,PETSC_NULL);
CHKERRQ(ierr);
user.bcType = (BCType)bc;
ierr = PetscOptionsEnd();
ierr = KSPSetComputeRHS(ksp,ComputeRHS,&user);
CHKERRQ(ierr);
ierr = KSPSetComputeOperators(ksp,ComputeMatrix,&user);
CHKERRQ(ierr);
ierr = KSPSetDM(ksp,da);
CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);
CHKERRQ(ierr);
ierr = KSPSetUp(ksp);
CHKERRQ(ierr);
ierr = KSPSolve(ksp,PETSC_NULL,PETSC_NULL);
CHKERRQ(ierr);
ierr = KSPGetSolution(ksp,&x);
CHKERRQ(ierr);
ierr = KSPGetRhs(ksp,&b);
CHKERRQ(ierr);
ierr = DMDestroy(&da);
CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);
CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc, char **args)
{
Mat A;
MatPartitioning part;
IS is;
PetscInt i,m,N,rstart,rend,nemptyranks,*emptyranks,nbigranks,*bigranks;
PetscMPIInt rank,size;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&args,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
nemptyranks = 10;
nbigranks = 10;
ierr = PetscMalloc2(nemptyranks,PetscInt,&emptyranks,nbigranks,PetscInt,&bigranks);CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,PETSC_NULL,"Partitioning example options",PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsIntArray("-emptyranks","Ranks to be skipped by partition","",emptyranks,&nemptyranks,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsIntArray("-bigranks","Ranks to be overloaded","",bigranks,&nbigranks,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
m = 1;
for (i=0; i<nemptyranks; i++) if (rank == emptyranks[i]) m = 0;
for (i=0; i<nbigranks; i++) if (rank == bigranks[i]) m = 5;
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,m,m,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(A,3,PETSC_NULL);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(A,3,PETSC_NULL,2,PETSC_NULL);CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation(A,1,3,PETSC_NULL);CHKERRQ(ierr);
ierr = MatMPIBAIJSetPreallocation(A,1,3,PETSC_NULL,2,PETSC_NULL);CHKERRQ(ierr);
ierr = MatSeqSBAIJSetPreallocation(A,1,2,PETSC_NULL);CHKERRQ(ierr);
ierr = MatMPISBAIJSetPreallocation(A,1,2,PETSC_NULL,1,PETSC_NULL);CHKERRQ(ierr);
ierr = MatGetSize(A,PETSC_NULL,&N);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
const PetscInt cols[] = {(i+N-1)%N,i,(i+1)%N};
const PetscScalar vals[] = {1,1,1};
ierr = MatSetValues(A,1,&i,3,cols,vals,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatPartitioningCreate(PETSC_COMM_WORLD,&part);CHKERRQ(ierr);
ierr = MatPartitioningSetAdjacency(part,A);CHKERRQ(ierr);
ierr = MatPartitioningSetFromOptions(part);CHKERRQ(ierr);
ierr = MatPartitioningApply(part,&is);CHKERRQ(ierr);
ierr = ISView(is,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = MatPartitioningDestroy(&part);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFree2(emptyranks,bigranks);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
static PetscErrorCode ProcessOptions(AppCtx *options)
{
PetscInt len;
PetscBool flg;
PetscErrorCode ierr;
PetscFunctionBegin;
options->dim = 2;
options->cellSimplex = PETSC_TRUE;
options->spectral = PETSC_FALSE;
options->interpolate = PETSC_FALSE;
options->refinementLimit = 0.0;
options->numFields = 0;
options->numComponents = NULL;
options->numDof = NULL;
options->reuseArray = PETSC_FALSE;
options->errors = PETSC_FALSE;
options->iterations = 1;
options->maxConeTime = 0.0;
options->maxClosureTime = 0.0;
options->maxVecClosureTime = 0.0;
ierr = PetscOptionsBegin(PETSC_COMM_SELF, "", "Meshing Problem Options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex9.c", options->dim, &options->dim, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-cellSimplex", "Flag for simplices", "ex9.c", options->cellSimplex, &options->cellSimplex, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-spectral", "Flag for spectral element layout", "ex9.c", options->spectral, &options->spectral, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-interpolate", "Flag for mesh interpolation", "ex9.c", options->interpolate, &options->interpolate, NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-refinement_limit", "The maximum volume of a refined cell", "ex9.c", options->refinementLimit, &options->refinementLimit, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-num_fields", "The number of section fields", "ex9.c", options->numFields, &options->numFields, NULL);CHKERRQ(ierr);
if (options->numFields) {
len = options->numFields;
ierr = PetscMalloc1(len, &options->numComponents);CHKERRQ(ierr);
ierr = PetscOptionsIntArray("-num_components", "The number of components per field", "ex9.c", options->numComponents, &len, &flg);CHKERRQ(ierr);
if (flg && (len != options->numFields)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Length of components array is %d should be %d", len, options->numFields);
}
len = (options->dim+1) * PetscMax(1, options->numFields);
ierr = PetscMalloc1(len, &options->numDof);CHKERRQ(ierr);
ierr = PetscOptionsIntArray("-num_dof", "The dof signature for the section", "ex9.c", options->numDof, &len, &flg);CHKERRQ(ierr);
if (flg && (len != (options->dim+1) * PetscMax(1, options->numFields))) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Length of dof array is %d should be %d", len, (options->dim+1) * PetscMax(1, options->numFields));
/* We are specifying the scalar dof, so augment it for multiple components */
{
PetscInt f, d;
for (f = 0; f < options->numFields; ++f) {
for (d = 0; d <= options->dim; ++d) options->numDof[f*(options->dim+1)+d] *= options->numComponents[f];
}
}
ierr = PetscOptionsBool("-reuse_array", "Pass in user allocated array to VecGetClosure()", "ex9.c", options->reuseArray, &options->reuseArray, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-errors", "Treat failures as errors", "ex9.c", options->errors, &options->errors, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-iterations", "The number of iterations for a query", "ex9.c", options->iterations, &options->iterations, NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-max_cone_time", "The maximum time per run for DMPlexGetCone()", "ex9.c", options->maxConeTime, &options->maxConeTime, NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-max_closure_time", "The maximum time per run for DMPlexGetTransitiveClosure()", "ex9.c", options->maxClosureTime, &options->maxClosureTime, NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-max_vec_closure_time", "The maximum time per run for DMPlexVecGetClosure()", "ex9.c", options->maxVecClosureTime, &options->maxVecClosureTime, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
PetscFunctionReturn(0);
};
PETSC_EXTERN PetscErrorCode MatGetOrdering_AMD(Mat mat,MatOrderingType type,IS *row,IS *col)
{
PetscErrorCode ierr;
PetscInt nrow,*perm;
const PetscInt *ia,*ja;
int status;
PetscReal val;
double Control[AMD_CONTROL],Info[AMD_INFO];
PetscBool tval,done;
PetscFunctionBegin;
/*
AMD does not require that the matrix be symmetric (it does so internally,
at least in so far as computing orderings for A+A^T.
*/
ierr = MatGetRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,&nrow,&ia,&ja,&done);CHKERRQ(ierr);
if (!done) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot get rows for matrix type %s",((PetscObject)mat)->type_name);
amd_AMD_defaults(Control);
ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)mat),((PetscObject)mat)->prefix,"AMD Options","Mat");CHKERRQ(ierr);
/*
We have to use temporary values here because AMD always uses double, even though PetscReal may be single
*/
val = (PetscReal)Control[AMD_DENSE];
ierr = PetscOptionsReal("-mat_ordering_amd_dense","threshold for \"dense\" rows/columns","None",val,&val,NULL);CHKERRQ(ierr);
Control[AMD_DENSE] = (double)val;
tval = (PetscBool)Control[AMD_AGGRESSIVE];
ierr = PetscOptionsBool("-mat_ordering_amd_aggressive","use aggressive absorption","None",tval,&tval,NULL);CHKERRQ(ierr);
Control[AMD_AGGRESSIVE] = (double)tval;
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscMalloc(nrow*sizeof(PetscInt),&perm);CHKERRQ(ierr);
status = amd_AMD_order(nrow,ia,ja,perm,Control,Info);
switch (status) {
case AMD_OK: break;
case AMD_OK_BUT_JUMBLED:
/* The result is fine, but PETSc matrices are supposed to satisfy stricter preconditions, so PETSc considers a
* matrix that triggers this error condition to be invalid.
*/
SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_PLIB,"According to AMD, the matrix has unsorted and/or duplicate row indices");
case AMD_INVALID:
amd_info(Info);
SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_PLIB,"According to AMD, the matrix is invalid");
case AMD_OUT_OF_MEMORY:
SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_MEM,"AMD could not compute ordering");
default:
SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_LIB,"Unexpected return value");
}
ierr = MatRestoreRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,NULL,&ia,&ja,&done);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,nrow,perm,PETSC_COPY_VALUES,row);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,nrow,perm,PETSC_OWN_POINTER,col);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
PetscBagSetFromOptions - Allows setting options from a bag
Collective on PetscBag
Input Parameter:
. bag - the bag of values
Level: beginner
.seealso: PetscBag, PetscBagSetName(), PetscBagDestroy(), PetscBagLoad(), PetscBagGetData()
PetscBagRegisterReal(), PetscBagRegisterInt(), PetscBagRegisterBool(), PetscBagRegisterScalar()
PetscBagSetFromOptions(), PetscBagCreate(), PetscBagGetName(), PetscBagView(), PetscBagRegisterEnum()
@*/
PetscErrorCode PetscBagSetFromOptions(PetscBag bag)
{
PetscErrorCode ierr;
PetscBagItem nitem = bag->bagitems;
char name[PETSC_BAG_NAME_LENGTH+1],helpname[PETSC_BAG_NAME_LENGTH+PETSC_BAG_HELP_LENGTH+3];
PetscInt n;
PetscFunctionBegin;
ierr = PetscStrcpy(helpname,bag->bagname);CHKERRQ(ierr);
ierr = PetscStrcat(helpname," ");CHKERRQ(ierr);
ierr = PetscStrcat(helpname,bag->baghelp);CHKERRQ(ierr);
ierr = PetscOptionsBegin(bag->bagcomm,bag->bagprefix,helpname,0);CHKERRQ(ierr);
while (nitem) {
name[0] = '-';
name[1] = 0;
ierr = PetscStrcat(name,nitem->name);CHKERRQ(ierr);
if (nitem->dtype == PETSC_CHAR) { /* special handling for fortran required? [due to space padding vs null termination] */
char *value = (char*)(((char*)bag) + nitem->offset);
ierr = PetscOptionsString(name,nitem->help,"",value,value,nitem->msize,NULL);CHKERRQ(ierr);
} else if (nitem->dtype == PETSC_REAL) {
PetscReal *value = (PetscReal*)(((char*)bag) + nitem->offset);
if (nitem->msize == 1) {
ierr = PetscOptionsReal(name,nitem->help,"",*value,value,NULL);CHKERRQ(ierr);
} else {
n = nitem->msize;
ierr = PetscOptionsRealArray(name,nitem->help,"",value,&n,NULL);CHKERRQ(ierr);
}
} else if (nitem->dtype == PETSC_SCALAR) {
PetscScalar *value = (PetscScalar*)(((char*)bag) + nitem->offset);
ierr = PetscOptionsScalar(name,nitem->help,"",*value,value,NULL);CHKERRQ(ierr);
} else if (nitem->dtype == PETSC_INT) {
PetscInt *value = (PetscInt*)(((char*)bag) + nitem->offset);
if (nitem->msize == 1) {
ierr = PetscOptionsInt(name,nitem->help,"",*value,value,NULL);CHKERRQ(ierr);
} else {
n = nitem->msize;
ierr = PetscOptionsIntArray(name,nitem->help,"",value,&n,NULL);CHKERRQ(ierr);
}
} else if (nitem->dtype == PETSC_ENUM) {
PetscEnum *value = (PetscEnum*)(((char*)bag) + nitem->offset);
PetscInt i = 0;
while (nitem->list[i++]) ;
ierr = PetscOptionsEnum(name,nitem->help,nitem->list[i-3],(const char*const*)nitem->list,*value,value,NULL);CHKERRQ(ierr);
} else if (nitem->dtype == PETSC_BOOL) {
PetscBool *value = (PetscBool*)(((char*)bag) + nitem->offset);
if (nitem->msize == 1) {
ierr = PetscOptionsBool(name,nitem->help,"",*value,value,NULL);CHKERRQ(ierr);
} else {
n = nitem->msize;
ierr = PetscOptionsBoolArray(name,nitem->help,"",value,&n,NULL);CHKERRQ(ierr);
}
}
nitem = nitem->next;
}
PetscOptionsEnd();
PetscFunctionReturn(0);
}
PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
{
const char *bcTypes[2] = {"neumann", "dirichlet"};
const char *runTypes[2] = {"full", "test"};
PetscInt bc, run;
PetscErrorCode ierr;
PetscFunctionBeginUser;
options->debug = 0;
options->runType = RUN_FULL;
options->dim = 2;
options->interpolate = PETSC_FALSE;
options->refinementLimit = 0.0;
options->bcType = DIRICHLET;
options->numBatches = 1;
options->numBlocks = 1;
options->jacobianMF = PETSC_FALSE;
options->showInitial = PETSC_FALSE;
options->showSolution = PETSC_TRUE;
options->fem.f0Funcs = (void (**)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[])) &options->f0Funcs;
options->fem.f1Funcs = (void (**)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[])) &options->f1Funcs;
options->fem.g0Funcs = (void (**)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[])) &options->g0Funcs;
options->fem.g1Funcs = (void (**)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[])) &options->g1Funcs;
options->fem.g2Funcs = (void (**)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[])) &options->g2Funcs;
options->fem.g3Funcs = (void (**)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[])) &options->g3Funcs;
ierr = MPI_Comm_size(comm, &options->numProcs);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &options->rank);CHKERRQ(ierr);
ierr = PetscOptionsBegin(comm, "", "Stokes Problem Options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsInt("-debug", "The debugging level", "ex62.c", options->debug, &options->debug, NULL);CHKERRQ(ierr);
run = options->runType;
ierr = PetscOptionsEList("-run_type", "The run type", "ex62.c", runTypes, 2, runTypes[options->runType], &run, NULL);CHKERRQ(ierr);
options->runType = (RunType) run;
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "ex62.c", options->dim, &options->dim, NULL);CHKERRQ(ierr);
spatialDim = options->dim;
ierr = PetscOptionsBool("-interpolate", "Generate intermediate mesh elements", "ex62.c", options->interpolate, &options->interpolate, NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-refinement_limit", "The largest allowable cell volume", "ex62.c", options->refinementLimit, &options->refinementLimit, NULL);CHKERRQ(ierr);
ierr = PetscStrcpy(options->partitioner, "chaco");CHKERRQ(ierr);
ierr = PetscOptionsString("-partitioner", "The graph partitioner", "pflotran.cxx", options->partitioner, options->partitioner, 2048, NULL);CHKERRQ(ierr);
bc = options->bcType;
ierr = PetscOptionsEList("-bc_type","Type of boundary condition","ex62.c",bcTypes,2,bcTypes[options->bcType],&bc,NULL);CHKERRQ(ierr);
options->bcType = (BCType) bc;
ierr = PetscOptionsInt("-gpu_batches", "The number of cell batches per kernel", "ex62.c", options->numBatches, &options->numBatches, NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-gpu_blocks", "The number of concurrent blocks per kernel", "ex62.c", options->numBlocks, &options->numBlocks, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-jacobian_mf", "Calculate the action of the Jacobian on the fly", "ex62.c", options->jacobianMF, &options->jacobianMF, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-show_initial", "Output the initial guess for verification", "ex62.c", options->showInitial, &options->showInitial, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-show_solution", "Output the solution for verification", "ex62.c", options->showSolution, &options->showSolution, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = PetscLogEventRegister("CreateMesh", DM_CLASSID, &options->createMeshEvent);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt degrees[1000],ndegrees,npoints,two;
PetscReal points[1000],weights[1000],interval[2];
PetscBool flg;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Discretization tools test options",NULL);CHKERRQ(ierr);
{
ndegrees = 1000;
degrees[0] = 0;
degrees[1] = 1;
degrees[2] = 2;
ierr = PetscOptionsIntArray("-degrees","list of degrees to evaluate","",degrees,&ndegrees,&flg);CHKERRQ(ierr);
if (!flg) ndegrees = 3;
npoints = 1000;
points[0] = 0.0;
points[1] = -0.5;
points[2] = 1.0;
ierr = PetscOptionsRealArray("-points","list of points at which to evaluate","",points,&npoints,&flg);CHKERRQ(ierr);
if (!flg) npoints = 3;
two = 2;
interval[0] = -1.;
interval[1] = 1.;
ierr = PetscOptionsRealArray("-interval","interval on which to construct quadrature","",interval,&two,NULL);CHKERRQ(ierr);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = CheckPoints("User-provided points",npoints,points,ndegrees,degrees);CHKERRQ(ierr);
ierr = PetscDTGaussQuadrature(npoints,interval[0],interval[1],points,weights);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Quadrature weights\n");CHKERRQ(ierr);
ierr = PetscRealView(npoints,weights,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
{
PetscReal a = interval[0],b = interval[1],zeroth,first,second;
PetscInt i;
zeroth = b - a;
first = (b*b - a*a)/2;
second = (b*b*b - a*a*a)/3;
for (i=0; i<npoints; i++) {
zeroth -= weights[i];
first -= weights[i] * points[i];
second -= weights[i] * PetscSqr(points[i]);
}
if (PetscAbs(zeroth) < 1e-10) zeroth = 0.;
if (PetscAbs(first) < 1e-10) first = 0.;
if (PetscAbs(second) < 1e-10) second = 0.;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Moment error: zeroth=%g, first=%g, second=%g\n",(double)(-zeroth),(double)(-first),(double)(-second));CHKERRQ(ierr);
}
ierr = CheckPoints("Gauss points",npoints,points,ndegrees,degrees);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv) {
PetscErrorCode ierr;
SNES snes;
KSP ksp;
Vec u, uexact;
FishCtx user;
DMDALocalInfo info;
double errnorm;
PetscInitialize(&argc,&argv,NULL,help);
user.printevals = PETSC_FALSE;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "f3_", "options for fish3", ""); CHKERRQ(ierr);
ierr = PetscOptionsBool("-printevals","residual and Jacobian routines report grid",
"fish3.c",user.printevals,&user.printevals,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd(); CHKERRQ(ierr);
ierr = DMDACreate3d(COMM,
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,
DMDA_STENCIL_STAR,
3,3,3,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,
1,1,
NULL,NULL,NULL,&(user.da)); CHKERRQ(ierr);
ierr = DMSetFromOptions(user.da); CHKERRQ(ierr);
ierr = DMSetUp(user.da); CHKERRQ(ierr);
ierr = DMSetApplicationContext(user.da,&user);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(user.da,&info); CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user.da,&u);CHKERRQ(ierr);
ierr = VecDuplicate(u,&uexact);CHKERRQ(ierr);
ierr = VecDuplicate(u,&(user.b));CHKERRQ(ierr);
ierr = formExactRHS(&info,uexact,user.b,&user); CHKERRQ(ierr);
ierr = SNESCreate(COMM,&snes); CHKERRQ(ierr);
ierr = SNESSetDM(snes,user.da); CHKERRQ(ierr);
ierr = DMDASNESSetFunctionLocal(user.da,INSERT_VALUES,
(DMDASNESFunction)FormFunctionLocal,&user); CHKERRQ(ierr);
ierr = DMDASNESSetJacobianLocal(user.da,
(DMDASNESJacobian)FormJacobianLocal,&user); CHKERRQ(ierr);
ierr = SNESGetKSP(snes,&ksp); CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPCG); CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes); CHKERRQ(ierr);
ierr = VecSet(u,0.0); CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,u); CHKERRQ(ierr);
ierr = VecAXPY(u,-1.0,uexact); CHKERRQ(ierr); // u <- u + (-1.0) uexact
ierr = VecNorm(u,NORM_INFINITY,&errnorm); CHKERRQ(ierr);
ierr = PetscPrintf(COMM,"on %d x %d x %d grid: error |u-uexact|_inf = %g\n",
info.mx,info.my,info.mz,errnorm); CHKERRQ(ierr);
VecDestroy(&u); VecDestroy(&uexact); VecDestroy(&(user.b));
SNESDestroy(&snes); DMDestroy(&(user.da));
PetscFinalize();
return 0;
}
/*@
PetscConvEstSetFromOptions - Sets a PetscConvEst object from options
Collective on PetscConvEst
Input Parameters:
. ce - The PetscConvEst object
Level: beginner
.keywords: PetscConvEst, convergence, options
.seealso: PetscConvEstCreate(), PetscConvEstGetConvRate()
@*/
PetscErrorCode PetscConvEstSetFromOptions(PetscConvEst ce)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscOptionsBegin(PetscObjectComm((PetscObject) ce), "", "Convergence Estimator Options", "PetscConvEst");CHKERRQ(ierr);
ierr = PetscOptionsInt("-convest_num_refine", "The number of refinements for the convergence check", "PetscConvEst", ce->Nr, &ce->Nr, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-convest_monitor", "Monitor the error for each convergence check", "PetscConvEst", ce->monitor, &ce->monitor, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
PetscFunctionReturn(0);
}
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* Create box mesh */
ierr = DMPlexCreateBoxMesh(comm, user->dim, user->simplex, user->cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr);
/* Distribute mesh over processes */
{
DM dmDist = NULL;
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
ierr = DMPlexDistribute(*dm, 0, NULL, &dmDist);CHKERRQ(ierr);
if (dmDist) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmDist;
}
}
/* TODO: This should be pulled into the library */
{
char convType[256];
PetscBool flg;
ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsFList("-dm_plex_convert_type","Convert DMPlex to another format","ex12",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
if (flg) {
DM dmConv;
ierr = DMConvert(*dm,convType,&dmConv);CHKERRQ(ierr);
if (dmConv) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmConv;
}
}
}
/* TODO: This should be pulled into the library */
ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr);
ierr = DMSetApplicationContext(*dm, user);CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
/* TODO: Add a hierachical viewer */
if (user->spectral) {
PetscInt planeDir[2] = {0, 1};
PetscReal planeCoord[2] = {0., 1.};
ierr = CreateSpectralPlanes(*dm, 2, planeDir, planeCoord, user);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode configureCtx(Ctx *usr) {
PetscErrorCode ierr;
usr->eps = 1.0;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"glaze_","2D advection-diffusion solver options",""); CHKERRQ(ierr);
ierr = PetscOptionsReal("-eps","diffusion coefficient eps with 0 < eps < infty",
NULL,usr->eps,&(usr->eps),NULL); CHKERRQ(ierr);
if (usr->eps <= 0.0) {
SETERRQ1(PETSC_COMM_WORLD,1,"eps=%.3f invalid ... eps > 0 required",usr->eps);
}
ierr = PetscOptionsEnd(); CHKERRQ(ierr);
return 0;
}
