PetscErrorCode SetupDiscretization(DM dm, AppCtx *user)
{
DM cdm = dm;
const PetscInt dim = 2;
PetscFE fe[3];
PetscQuadrature q;
PetscInt f;
MPI_Comm comm;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* Create finite element */
ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr);
ierr = PetscFECreateDefault(comm, dim, 1, PETSC_TRUE, "potential_", -1, &fe[0]);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) fe[0], "potential");CHKERRQ(ierr);
ierr = PetscFEGetQuadrature(fe[0], &q);CHKERRQ(ierr);
ierr = PetscFECreateDefault(comm, dim, 1, PETSC_TRUE, "charge_", -1, &fe[1]);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) fe[1], "charge");CHKERRQ(ierr);
ierr = PetscFESetQuadrature(fe[1], q);CHKERRQ(ierr);
ierr = PetscFECreateDefault(comm, dim, 1, PETSC_TRUE, "multiplier_", -1, &fe[2]);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) fe[2], "multiplier");CHKERRQ(ierr);
ierr = PetscFESetQuadrature(fe[2], q);CHKERRQ(ierr);
/* Set discretization and boundary conditions for each mesh */
for (f = 0; f < 3; ++f) {ierr = DMSetField(dm, f, NULL, (PetscObject) fe[f]);CHKERRQ(ierr);}
ierr = DMCreateDS(cdm);CHKERRQ(ierr);
ierr = SetupProblem(dm, user);CHKERRQ(ierr);
while (cdm) {
ierr = DMCopyDisc(dm, cdm);CHKERRQ(ierr);
ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
for (f = 0; f < 3; ++f) {ierr = PetscFEDestroy(&fe[f]);CHKERRQ(ierr);}
PetscFunctionReturn(0);
}
PetscErrorCode SetupDiscretization(DM dm, AppCtx *user)
{
DM cdm = dm;
const PetscInt dim = user->dim;
PetscFE fe[2];
PetscQuadrature q;
Parameter *param;
MPI_Comm comm;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* Create finite element */
ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr);
ierr = PetscFECreateDefault(comm, dim, dim, user->simplex, "vel_", PETSC_DEFAULT, &fe[0]);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) fe[0], "velocity");CHKERRQ(ierr);
ierr = PetscFEGetQuadrature(fe[0], &q);CHKERRQ(ierr);
ierr = PetscFECreateDefault(comm, dim, 1, user->simplex, "pres_", PETSC_DEFAULT, &fe[1]);CHKERRQ(ierr);
ierr = PetscFESetQuadrature(fe[1], q);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) fe[1], "pressure");CHKERRQ(ierr);
/* Set discretization and boundary conditions for each mesh */
ierr = DMSetField(dm, 0, NULL, (PetscObject) fe[0]);CHKERRQ(ierr);
ierr = DMSetField(dm, 1, NULL, (PetscObject) fe[1]);CHKERRQ(ierr);
ierr = DMCreateDS(dm);CHKERRQ(ierr);
ierr = SetupProblem(dm, user);CHKERRQ(ierr);
ierr = PetscBagGetData(user->bag, (void **) ¶m);CHKERRQ(ierr);
while (cdm) {
ierr = DMCopyDisc(dm, cdm);CHKERRQ(ierr);
ierr = DMPlexCreateBasisRotation(cdm, param->alpha, 0.0, 0.0);CHKERRQ(ierr);
ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe[0]);CHKERRQ(ierr);
ierr = PetscFEDestroy(&fe[1]);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;
}
void PETSc::Create(
MPI_Comm Comm,
int ilower,
int iupper,
int d_nz,
int o_nz)
{
int n = iupper - ilower +1;
comm = Comm;
iLower = ilower;
iUpper = iupper;
MatCreateAIJ(PETSC_COMM_WORLD,n,n,PETSC_DECIDE,PETSC_DECIDE,
d_nz,PETSC_NULL,o_nz,PETSC_NULL,&A);
ierr = PetscObjectSetName((PetscObject) A, "A");
ierr = MatSetFromOptions(A);
// b
ierr = VecCreate(PETSC_COMM_WORLD, &b);
ierr = PetscObjectSetName((PetscObject) b, "b");
ierr = VecSetSizes(b, n, PETSC_DECIDE);
ierr = VecSetFromOptions(b);
ierr = VecCreate(PETSC_COMM_WORLD,&x);
ierr = PetscObjectSetName((PetscObject) x, "X");
ierr = VecSetSizes(x, n, PETSC_DECIDE);
ierr = VecSetFromOptions(x);
}
int main(int argc, char **argv)
{
PetscErrorCode ierr;
DM dm, rdm;
PetscViewer vwr;
PetscBool flg;
char datafile[PETSC_MAX_PATH_LEN];
MPI_Comm comm;
ierr = PetscInitialize(&argc, &argv, NULL, help);
if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = PetscViewerCreate(comm, &vwr);CHKERRQ(ierr);
ierr = PetscViewerSetType(vwr, PETSCVIEWERHDF5);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(vwr, FILE_MODE_READ);CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL, NULL, "-f", datafile, PETSC_MAX_PATH_LEN, &flg);CHKERRQ(ierr);
if (!flg) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Must provide meshfile");
ierr = PetscViewerFileSetName(vwr, datafile);CHKERRQ(ierr);
ierr = DMCreate(comm, &dm);CHKERRQ(ierr);
ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr);
ierr = DMLoad(dm, vwr);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&vwr);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)dm, "BaryDM");CHKERRQ(ierr);
ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);
ierr = DMRefine(dm, comm, &rdm);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)rdm, "RefinedDM");CHKERRQ(ierr);
ierr = DMViewFromOptions(rdm, NULL, "-refined_dm_view");CHKERRQ(ierr);
ierr = DMDestroy(&rdm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode MatLUFactorNumeric_Matlab(Mat F,Mat A,const MatFactorInfo *info)
{
PetscErrorCode ierr;
size_t len;
char *_A,*name;
PetscReal dtcol = info->dtcol;
PetscFunctionBegin;
if (F->factortype == MAT_FACTOR_ILU || info->dt > 0) {
/* the ILU form is not currently registered */
if (info->dtcol == PETSC_DEFAULT) dtcol = .01;
F->ops->solve = MatSolve_Matlab;
F->factortype = MAT_FACTOR_LU;
ierr = PetscMatlabEnginePut(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),(PetscObject)A);
CHKERRQ(ierr);
_A = ((PetscObject)A)->name;
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),"info_%s = struct('droptol',%g,'thresh',%g);",_A,info->dt,dtcol);
CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),"[l_%s,u_%s,p_%s] = luinc(%s',info_%s);",_A,_A,_A,_A,_A);
CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),"%s = 0;",_A);
CHKERRQ(ierr);
ierr = PetscStrlen(_A,&len);
CHKERRQ(ierr);
ierr = PetscMalloc1(len+2,&name);
CHKERRQ(ierr);
sprintf(name,"_%s",_A);
ierr = PetscObjectSetName((PetscObject)F,name);
CHKERRQ(ierr);
ierr = PetscFree(name);
CHKERRQ(ierr);
} else {
ierr = PetscMatlabEnginePut(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),(PetscObject)A);
CHKERRQ(ierr);
_A = ((PetscObject)A)->name;
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),"[l_%s,u_%s,p_%s] = lu(%s',%g);",_A,_A,_A,_A,dtcol);
CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),"%s = 0;",_A);
CHKERRQ(ierr);
ierr = PetscStrlen(_A,&len);
CHKERRQ(ierr);
ierr = PetscMalloc1(len+2,&name);
CHKERRQ(ierr);
sprintf(name,"_%s",_A);
ierr = PetscObjectSetName((PetscObject)F,name);
CHKERRQ(ierr);
ierr = PetscFree(name);
CHKERRQ(ierr);
F->ops->solve = MatSolve_Matlab;
}
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
SNES snes; /* nonlinear solver */
DM dm; /* problem definition */
Vec u, r; /* solution and residual */
AppCtx user; /* user-defined work context */
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = PetscBagCreate(PETSC_COMM_WORLD, sizeof(Parameter), &user.bag);CHKERRQ(ierr);
ierr = SetupParameters(&user);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
ierr = DMSetApplicationContext(dm, &user);CHKERRQ(ierr);
/* Setup problem */
ierr = PetscMalloc(2 * sizeof(void (*)(const PetscReal[], PetscScalar *, void *)), &user.exactFuncs);CHKERRQ(ierr);
ierr = SetupDiscretization(dm, &user);CHKERRQ(ierr);
ierr = DMPlexCreateClosureIndex(dm, NULL);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMPlexSetSNESLocalFEM(dm,&user,&user,&user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
{
Parameter *param;
void *ctxs[2];
ierr = PetscBagGetData(user.bag, (void **) ¶m);CHKERRQ(ierr);
ctxs[0] = ctxs[1] = param;
ierr = DMProjectFunction(dm, 0.0, user.exactFuncs, ctxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) u, "Exact Solution");CHKERRQ(ierr);
ierr = VecViewFromOptions(u, NULL, "-exact_vec_view");CHKERRQ(ierr);
}
ierr = DMSNESCheckFromOptions(snes, u, NULL, NULL);CHKERRQ(ierr);
ierr = VecSet(u, 0.0);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) u, "Solution");CHKERRQ(ierr);
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = VecViewFromOptions(u, NULL, "-sol_vec_view");CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = PetscBagDestroy(&user.bag);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode CheckMat(Mat A, Mat B, PetscBool usemult, const char* func)
{
Mat Bcheck;
PetscReal error;
PetscErrorCode ierr;
PetscFunctionBeginUser;
if (!usemult) {
if (B) {
MatType Btype;
ierr = MatGetType(B,&Btype);CHKERRQ(ierr);
ierr = MatConvert(A,Btype,MAT_INITIAL_MATRIX,&Bcheck);CHKERRQ(ierr);
} else {
ierr = MatConvert(A,MATAIJ,MAT_INITIAL_MATRIX,&Bcheck);CHKERRQ(ierr);
}
if (B) { /* if B is present, subtract it */
ierr = MatAXPY(Bcheck,-1.,B,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
}
ierr = MatNorm(Bcheck,NORM_INFINITY,&error);CHKERRQ(ierr);
if (error > PETSC_SQRT_MACHINE_EPSILON) {
ISLocalToGlobalMapping rl2g,cl2g;
ierr = PetscObjectSetName((PetscObject)Bcheck,"Assembled Bcheck");CHKERRQ(ierr);
ierr = MatView(Bcheck,NULL);CHKERRQ(ierr);
if (B) {
ierr = PetscObjectSetName((PetscObject)B,"Assembled AIJ");CHKERRQ(ierr);
ierr = MatView(B,NULL);CHKERRQ(ierr);
ierr = MatDestroy(&Bcheck);CHKERRQ(ierr);
ierr = MatConvert(A,MATAIJ,MAT_INITIAL_MATRIX,&Bcheck);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)Bcheck,"Assembled IS");CHKERRQ(ierr);
ierr = MatView(Bcheck,NULL);CHKERRQ(ierr);
}
ierr = MatDestroy(&Bcheck);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)A,"MatIS");CHKERRQ(ierr);
ierr = MatView(A,NULL);CHKERRQ(ierr);
ierr = MatGetLocalToGlobalMapping(A,&rl2g,&cl2g);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingView(rl2g,NULL);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingView(cl2g,NULL);CHKERRQ(ierr);
SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"ERROR ON %s: %g",func,error);
}
ierr = MatDestroy(&Bcheck);CHKERRQ(ierr);
} else {
PetscBool ok,okt;
ierr = MatMultEqual(A,B,3,&ok);CHKERRQ(ierr);
ierr = MatMultTransposeEqual(A,B,3,&okt);CHKERRQ(ierr);
if (!ok || !okt) SETERRQ3(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"ERROR ON %s: mult ok ? %d, multtranspose ok ? %d",func,ok,okt);
}
PetscFunctionReturn(0);
}
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *newdm)
{
PetscInt dim = user->dim;
PetscBool cellSimplex = user->cellSimplex;
PetscErrorCode ierr;
PetscFunctionBegin;
switch (dim) {
case 2:
if (cellSimplex) {
ierr = CreateSimplex_2D(comm, newdm);CHKERRQ(ierr);
} else {
ierr = CreateQuad_2D(comm, newdm);CHKERRQ(ierr);
}
break;
case 3:
if (cellSimplex) {
ierr = CreateSimplex_3D(comm, newdm);CHKERRQ(ierr);
} else {
ierr = CreateHex_3D(comm, newdm);CHKERRQ(ierr);
}
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
}
if (user->refinementLimit > 0.0) {
DM rdm;
const char *name;
ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr);
ierr = DMPlexSetRefinementLimit(*newdm, user->refinementLimit);CHKERRQ(ierr);
ierr = DMRefine(*newdm, PETSC_COMM_SELF, &rdm);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr);
ierr = DMDestroy(newdm);CHKERRQ(ierr);
*newdm = rdm;
}
if (user->interpolate) {
DM idm = NULL;
const char *name;
ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) idm, name);CHKERRQ(ierr);
ierr = DMPlexCopyCoordinates(*newdm, idm);CHKERRQ(ierr);
ierr = DMDestroy(newdm);CHKERRQ(ierr);
*newdm = idm;
}
ierr = DMSetFromOptions(*newdm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode EvaluateJacobian(Tao tao, Vec X, Mat J, Mat JPre, void *ptr)
{
AppCtx *user = (AppCtx *)ptr;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectSetName((PetscObject)X,"X");CHKERRQ(ierr);
ierr = PetscMatlabEnginePut(user->mengine,(PetscObject)X);CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(user->mengine,"J = jac(X);");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)J,"J");CHKERRQ(ierr);
ierr = PetscMatlabEngineGet(user->mengine,(PetscObject)J);CHKERRQ(ierr);
ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode TaoPounders(AppCtx *user)
{
PetscErrorCode ierr;
Tao tao;
Vec X, F;
Mat J;
char buf[1024];
PetscFunctionBegin;
/* Set the values for the algorithm options we want to use */
sprintf(buf,"%d",user->nfmax);
ierr = PetscOptionsSetValue(NULL,"-tao_max_funcs",buf);CHKERRQ(ierr);
sprintf(buf,"%d",user->npmax);
ierr = PetscOptionsSetValue(NULL,"-tao_pounders_npmax",buf);CHKERRQ(ierr);
sprintf(buf,"%5.4e",user->delta);
ierr = PetscOptionsSetValue(NULL,"-tao_pounders_delta",buf);CHKERRQ(ierr);
/* Create the TAO objects and set the type */
ierr = TaoCreate(PETSC_COMM_SELF,&tao);CHKERRQ(ierr);
/* Create starting point and initialize */
ierr = VecCreateSeq(PETSC_COMM_SELF,user->n,&X);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)X,"X0");CHKERRQ(ierr);
ierr = PetscMatlabEngineGet(user->mengine,(PetscObject)X);CHKERRQ(ierr);
ierr = TaoSetInitialVector(tao,X);CHKERRQ(ierr);
/* Create residuals vector and set residual function */
ierr = VecCreateSeq(PETSC_COMM_SELF,user->m,&F);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)F,"F");CHKERRQ(ierr);
ierr = TaoSetResidualRoutine(tao,F,EvaluateResidual,(void*)user);CHKERRQ(ierr);
/* Create Jacobian matrix and set residual Jacobian routine */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,user->m,user->n,user->n,NULL,&J);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)J,"J");CHKERRQ(ierr);
ierr = TaoSetResidualJacobianRoutine(tao,J,J,EvaluateJacobian,(void*)user);CHKERRQ(ierr);
/* Solve the problem */
ierr = TaoSetType(tao,TAOPOUNDERS);CHKERRQ(ierr);
ierr = TaoSetFromOptions(tao);CHKERRQ(ierr);
ierr = TaoSolve(tao);CHKERRQ(ierr);
/* Finish the problem */
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&F);CHKERRQ(ierr);
ierr = TaoDestroy(&tao);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
// Write the sub mesh into a HDF5 file.
PetscErrorCode ProbeVolume::writeSubMeshHDF5(const std::string &filePath)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
// only the first process in the communicator write the sub-mesh into a file
if (commRank == 0)
{
// because only one process is involved in writing the sub-mesh,
// we need to create a temporary viewer
PetscViewer viewer2;
ierr = PetscViewerCreate(PETSC_COMM_SELF, &viewer2); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer2, PETSCVIEWERHDF5); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer2, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(
viewer2, filePath.c_str()); CHKERRQ(ierr);
ierr = PetscViewerHDF5PushGroup(viewer2, "mesh"); CHKERRQ(ierr);
std::vector<std::string> dirs{"x", "y", "z"};
for (unsigned int d = 0; d < coord.size(); ++d)
{
Vec tmp;
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, 1, nPtsDir[d],
&coord[d][0], &tmp); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) tmp,
dirs[d].c_str()); CHKERRQ(ierr);
ierr = VecView(tmp, viewer2); CHKERRQ(ierr);
ierr = VecDestroy(&tmp); CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer2); CHKERRQ(ierr);
}
PetscFunctionReturn(0);
} // ProbeVolume::writeSubMeshHDF5
PetscErrorCode BVResize_Mat(BV bv,PetscInt m,PetscBool copy)
{
PetscErrorCode ierr;
BV_MAT *ctx = (BV_MAT*)bv->data;
PetscScalar *pA,*pnew;
Mat A;
char str[50];
PetscFunctionBegin;
ierr = MatCreateDense(PetscObjectComm((PetscObject)bv->t),bv->n,PETSC_DECIDE,PETSC_DECIDE,m,NULL,&A);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)bv,(PetscObject)A);CHKERRQ(ierr);
if (((PetscObject)bv)->name) {
ierr = PetscSNPrintf(str,50,"%s_0",((PetscObject)bv)->name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)A,str);CHKERRQ(ierr);
}
if (copy) {
ierr = MatDenseGetArray(ctx->A,&pA);CHKERRQ(ierr);
ierr = MatDenseGetArray(A,&pnew);CHKERRQ(ierr);
ierr = PetscMemcpy(pnew,pA,PetscMin(m,bv->m)*bv->n*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(ctx->A,&pA);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(A,&pnew);CHKERRQ(ierr);
}
ierr = MatDestroy(&ctx->A);CHKERRQ(ierr);
ctx->A = A;
PetscFunctionReturn(0);
}
PetscErrorCode PetscViewerGetSingleton_ASCII(PetscViewer viewer,PetscViewer *outviewer)
{
PetscMPIInt rank;
PetscErrorCode ierr;
PetscViewer_ASCII *vascii = (PetscViewer_ASCII*)viewer->data,*ovascii;
const char *name;
PetscFunctionBegin;
if (vascii->sviewer) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Singleton already obtained from PetscViewer and not restored");
ierr = PetscViewerCreate(PETSC_COMM_SELF,outviewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(*outviewer,PETSCVIEWERASCII);CHKERRQ(ierr);
ovascii = (PetscViewer_ASCII*)(*outviewer)->data;
ovascii->fd = vascii->fd;
ovascii->tab = vascii->tab;
vascii->sviewer = *outviewer;
(*outviewer)->format = viewer->format;
ierr = PetscObjectGetName((PetscObject)viewer,&name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)(*outviewer),name);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)viewer),&rank);CHKERRQ(ierr);
((PetscViewer_ASCII*)((*outviewer)->data))->bviewer = viewer;
(*outviewer)->ops->destroy = PetscViewerDestroy_ASCII_Singleton;
if (rank) (*outviewer)->ops->flush = 0;
else (*outviewer)->ops->flush = PetscViewerFlush_ASCII_Singleton_0;
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool interpolate = user->interpolate;
PetscReal refinementLimit = user->refinementLimit;
const char *partitioner = "chaco";
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
ierr = DMComplexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr);
{
DM refinedMesh = PETSC_NULL;
DM distributedMesh = PETSC_NULL;
/* Refine mesh using a volume constraint */
ierr = DMComplexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
/* Distribute mesh over processes */
ierr = DMComplexDistribute(*dm, partitioner, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
}
ierr = PetscObjectSetName((PetscObject) *dm, "Simplical Mesh");CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscMPIInt rank;
PetscInt n = 5;
char *output;
Vec x;
PetscInitialize(&argc,&argv,(char *)0,0);
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
ierr = PetscMatlabEngineGetOutput(PETSC_MATLAB_ENGINE_WORLD,&output);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"MPI_Comm_rank");
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d]Processor rank is %s",rank,output);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)x,"x");CHKERRQ(ierr);
ierr = PetscMatlabEnginePut(PETSC_MATLAB_ENGINE_WORLD,(PetscObject)x);CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"x = x + MPI_Comm_rank;\n");
ierr = PetscMatlabEngineGet(PETSC_MATLAB_ENGINE_WORLD,(PetscObject)x);CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"whos\n");
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d]The result is %s",rank,output);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
/*
This takes as input the coordinates for each vertex
*/
PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
{
PetscSection coordSection;
Vec coordinates;
PetscScalar *coords;
PetscInt coordSize, v, d;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
for (v = numCells; v < numCells+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (v = 0; v < numVertices; ++v) {
for (d = 0; d < spaceDim; ++d) {
coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool interpolate = user->interpolate;
PetscReal refinementLimit = user->refinementLimit;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
ierr = DMMeshCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr);
{
DM refinedMesh = PETSC_NULL;
/* Refine mesh using a volume constraint */
ierr = DMMeshRefine(*dm, refinementLimit, interpolate, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
}
ierr = PetscObjectSetName((PetscObject) *dm, "Serial Mesh");CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm; /* Problem specification */
SNES snes; /* Nonlinear solver */
Vec u; /* Solutions */
AppCtx user; /* User-defined work context */
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
/* Primal system */
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
ierr = SetupFE(dm, user.dim, user.simplex, "displacement", SetupPrimalProblem, &user);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = VecSet(u, 0.0);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) u, "displacement");CHKERRQ(ierr);
ierr = DMPlexSetSNESLocalFEM(dm, &user, &user, &user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMSNESCheckFromOptions(snes, u, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = SNESGetSolution(snes, &u);CHKERRQ(ierr);
ierr = VecViewFromOptions(u, NULL, "-displacement_view");CHKERRQ(ierr);
/* Cleanup */
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode GetDotMat(MPI_Comm comm, Mat *Bout, int Nx, int Ny, int Nz)
{
int Nxyz=Nx*Ny*Nz, N=6*Nx*Ny*Nz, Nc=3;
Mat B;
int ns,ne,i,j,ic;
double value[3]={1,1,1};
int col[3];
PetscErrorCode ierr;
MatCreate(comm, &B);
MatSetType(B,MATMPIAIJ);
MatSetSizes(B,PETSC_DECIDE, PETSC_DECIDE, N, N);
MatMPIAIJSetPreallocation(B, 3, PETSC_NULL, 3, PETSC_NULL);
ierr = MatGetOwnershipRange(B, &ns, &ne); CHKERRQ(ierr);
for (i = ns; i < ne; ++i) {
j=i;
ic = (j /= Nxyz) % Nc;
if(ic==0){col[0]=i, col[1]=i+Nxyz, col[2]=i+2*Nxyz;}
if(ic==1){col[0]=i-Nxyz, col[1]=i, col[2]=i+Nxyz; }
if(ic==2){col[0]=i-2*Nxyz, col[1]=i-Nxyz, col[2]=i; }
ierr = MatSetValues(B,1,&i,3,col,value,INSERT_VALUES); CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) B,"DotMatrix"); CHKERRQ(ierr);
*Bout = B;
PetscFunctionReturn(0);
}
PetscErrorCode PetscViewerGetSubcomm_ASCII(PetscViewer viewer,MPI_Comm subcomm,PetscViewer *outviewer)
{
PetscErrorCode ierr;
PetscViewer_ASCII *vascii = (PetscViewer_ASCII *)viewer->data,*ovascii;
const char *name;
PetscFunctionBegin;
if (vascii->sviewer) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Subcomm viewer already obtained from PetscViewer and not restored");
/* Note that we need to open vascii->filename for the subcomm:
we can't count on reusing viewer's fd since the root in comm and subcomm may differ.
Further, if the subcomm happens to be the same as comm, PetscViewerASCIIOpen() will
will return the current viewer, having increfed it.
*/
ierr = PetscViewerASCIIOpen(subcomm,vascii->filename, outviewer);CHKERRQ(ierr);
if(*outviewer == viewer) PetscFunctionReturn(0);
ovascii = (PetscViewer_ASCII*)(*outviewer)->data;
ovascii->tab = vascii->tab;
vascii->sviewer = *outviewer;
(*outviewer)->format = viewer->format;
(*outviewer)->iformat = viewer->iformat;
ierr = PetscObjectGetName((PetscObject)viewer,&name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)(*outviewer),name);CHKERRQ(ierr);
((PetscViewer_ASCII*)((*outviewer)->data))->bviewer = viewer;
(*outviewer)->ops->destroy = PetscViewerDestroy_ASCII_Subcomm;
PetscFunctionReturn(0);
}
/*
DMLabelMakeValid_Private - Transfer stratum data from the hash format to the sorted list format
Input parameter:
+ label - The DMLabel
- v - The stratum value
Output parameter:
. label - The DMLabel with stratum in sorted list format
Level: developer
.seealso: DMLabelCreate()
*/
static PetscErrorCode DMLabelMakeValid_Private(DMLabel label, PetscInt v)
{
PetscInt off;
PetscInt *pointArray;
PetscErrorCode ierr;
if (label->validIS[v]) return 0;
if (v >= label->numStrata) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Trying to access invalid stratum %D in DMLabelMakeValid_Private\n", v);
PetscFunctionBegin;
PetscHashISize(label->ht[v], label->stratumSizes[v]);
ierr = PetscMalloc1(label->stratumSizes[v], &pointArray);CHKERRQ(ierr);
off = 0;
ierr = PetscHashIGetKeys(label->ht[v], &off, pointArray);CHKERRQ(ierr);
if (off != label->stratumSizes[v]) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of contributed points %D from value %D should be %D", off, label->stratumValues[v], label->stratumSizes[v]);
PetscHashIClear(label->ht[v]);
ierr = PetscSortInt(label->stratumSizes[v], pointArray);CHKERRQ(ierr);
if (label->bt) {
PetscInt p;
for (p = 0; p < label->stratumSizes[v]; ++p) {
const PetscInt point = pointArray[p];
if ((point < label->pStart) || (point >= label->pEnd)) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Label point %D is not in [%D, %D)", point, label->pStart, label->pEnd);
ierr = PetscBTSet(label->bt, point - label->pStart);CHKERRQ(ierr);
}
}
ierr = ISCreateGeneral(PETSC_COMM_SELF,label->stratumSizes[v],pointArray,PETSC_OWN_POINTER,&(label->points[v]));CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) (label->points[v]), "indices");CHKERRQ(ierr);
label->validIS[v] = PETSC_TRUE;
++label->state;
PetscFunctionReturn(0);
}
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *ctx, DM *dm)
{
PetscInt dim = ctx->dim;
PetscBool cellSimplex = ctx->cellSimplex;
const char *filename = ctx->filename;
const PetscInt cells[3] = {1, 1, 1};
size_t len;
PetscMPIInt rank, size;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (len) {ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, dm);CHKERRQ(ierr);}
else {ierr = DMPlexCreateBoxMesh(comm, dim, cellSimplex, cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr);}
{
DM distributedMesh = NULL;
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
}
ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
const char *filename = user->filename;
PetscInt dim = user->dim;
size_t len;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (!len) {ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, dm);CHKERRQ(ierr);}
else {ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, dm);CHKERRQ(ierr);}
ierr = DMViewFromOptions(*dm, NULL, "-orig_dm_view");CHKERRQ(ierr);
{
DM distributedMesh = NULL;
ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
ierr = DMViewFromOptions(*dm, NULL, "-dist_dm_view");CHKERRQ(ierr);
}
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
if (user->uninterpolate) {
DM udm = NULL;
ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = udm;
ierr = DMViewFromOptions(*dm, NULL, "-un_dm_view");CHKERRQ(ierr);
}
ierr = PetscObjectSetName((PetscObject) *dm, "Test Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMLabelClearStratum(DMLabel label, PetscInt value)
{
PetscInt v;
PetscErrorCode ierr;
PetscFunctionBegin;
for (v = 0; v < label->numStrata; ++v) {
if (label->stratumValues[v] == value) break;
}
if (v >= label->numStrata) PetscFunctionReturn(0);
if (label->validIS[v]) {
if (label->bt) {
PetscInt i;
const PetscInt *points;
ierr = ISGetIndices(label->points[v], &points);CHKERRQ(ierr);
for (i = 0; i < label->stratumSizes[v]; ++i) {
const PetscInt point = points[i];
if ((point < label->pStart) || (point >= label->pEnd)) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Label point %D is not in [%D, %D)", point, label->pStart, label->pEnd);
ierr = PetscBTClear(label->bt, point - label->pStart);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(label->points[v], &points);CHKERRQ(ierr);
}
ierr = ISDestroy(&(label->points[v]));CHKERRQ(ierr);
label->stratumSizes[v] = 0;
ierr = ISCreateGeneral(PETSC_COMM_SELF,0,NULL,PETSC_OWN_POINTER,&(label->points[v]));CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) (label->points[v]), "indices");CHKERRQ(ierr);
} else {
PetscHashIClear(label->ht[v]);
}
PetscFunctionReturn(0);
}
int main(int argc, char **argv){
SlepcInitialize(&argc, &argv, PETSC_NULL, PETSC_NULL);
int N[3] = {20, 25, 1}, Npml[3] = {5, 7, 0}, Nc = 2,
b[3][2] = {{-1, 0}, {1, 0}, {0, 0}}, LowerPML = 0, BCPeriod = 3;
double h[3] = {0.2, 0.3, 0.1};
int i, Nxyzr = 2*N[0]*N[1]*N[2];
double sigma[3], *muinv;
Vec muinvpml;
muinv = (double *) malloc(sizeof(double)*3*Nxyzr );
for(i=0; i<3; i++) sigma[i] = pmlsigma(1e-25, Npml[i]*h[i]);
MuinvPMLFull(PETSC_COMM_SELF, &muinvpml, N[0], N[1], N[2], Npml[0],
Npml[1], Npml[2], sigma[0], sigma[1], sigma[2], 1.0, LowerPML);
AddMuAbsorption(muinv, muinvpml, 1e25, 0);
VecDestroy(&muinvpml);
Mat Moperator;
MatCreateAIJ(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE, Nc*Nxyzr,
Nc*Nxyzr, 26, NULL, 26, NULL, &Moperator);
MoperatorGeneralFill(Moperator, N[0], N[1], N[2], h[0], h[1], h[2],
b[0], b[1], b[2], muinv, BCPeriod, 0, Nc);
Assemble(Moperator);
PetscObjectSetName((PetscObject) Moperator, "M");
OutputMat(PETSC_COMM_WORLD, Moperator, filenameComm, "M.m");
SlepcFinalize();
return 0;
}
PetscErrorCode ImagIMat(MPI_Comm comm, Mat *Dout, int N)
{
Mat D;
int nz = 1; /* max # nonzero elements in each row */
PetscErrorCode ierr;
int ns, ne;
int i;
//ierr = MatCreateAIJ(comm, PETSC_DECIDE, PETSC_DECIDE, N,N,nz, NULL, nz, NULL, &D); CHKERRQ(ierr); // here N is total length;
MatCreate(comm, &D);
MatSetType(D,MATMPIAIJ);
MatSetSizes(D,PETSC_DECIDE, PETSC_DECIDE,N,N);
MatMPIAIJSetPreallocation(D, nz, PETSC_NULL, nz, PETSC_NULL);
ierr = MatGetOwnershipRange(D, &ns, &ne); CHKERRQ(ierr);
for (i = ns; i < ne; ++i) {
int id = (i+N/2)%(N);
double sign = pow(-1.0, (i<N/2));
ierr = MatSetValue(D, i, id, sign, INSERT_VALUES); CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(D, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(D, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) D, "ImaginaryIMatrix"); CHKERRQ(ierr);
*Dout = D;
PetscFunctionReturn(0);
}
static PetscErrorCode CreateHex_3D(MPI_Comm comm, DM *newdm)
{
DM dm;
PetscInt numPoints[2] = {12, 2};
PetscInt coneSize[14] = {8, 8, 0,0,0,0,0,0,0,0,0,0,0,0};
PetscInt cones[16] = {2,5,4,3,6,7,8,9, 3,4,11,10,7,12,13,8};
PetscInt coneOrientations[16] = {0,0,0,0,0,0,0,0, 0,0, 0, 0,0, 0, 0,0};
PetscScalar vertexCoords[36] = {-0.5,0.0,0.0, 0.0,0.0,0.0, 0.0,1.0,0.0, -0.5,1.0,0.0,
-0.5,0.0,1.0, 0.0,0.0,1.0, 0.0,1.0,1.0, -0.5,1.0,1.0,
0.5,0.0,0.0, 0.5,1.0,0.0, 0.5,0.0,1.0, 0.5,1.0,1.0};
PetscInt markerPoints[24] = {2,1,3,1,4,1,5,1,6,1,7,1,8,1,9,1,10,1,11,1,12,1,13,1};
PetscInt dim = 3, depth = 1, p;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMCreate(comm, &dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);
ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr);
ierr = DMSetDimension(dm, dim);CHKERRQ(ierr);
ierr = DMPlexCreateFromDAG(dm, depth, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr);
for(p = 0; p < 12; ++p) {
ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);
}
*newdm = dm;
PetscFunctionReturn(0);
}
PetscErrorCode CongMat(MPI_Comm comm, Mat *Cout, int N)
{
Mat C;
int nz = 1; /* max # nonzero elements in each row */
PetscErrorCode ierr;
int ns, ne;
int i;
//ierr = MatCreateAIJ(comm, PETSC_DECIDE, PETSC_DECIDE, N,N,nz, NULL, nz, NULL, &C); CHKERRQ(ierr);
MatCreate(comm, &C);
MatSetType(C,MATMPIAIJ);
MatSetSizes(C,PETSC_DECIDE, PETSC_DECIDE, N, N);
MatMPIAIJSetPreallocation(C, nz, PETSC_NULL, nz, PETSC_NULL);
ierr = MatGetOwnershipRange(C, &ns, &ne); CHKERRQ(ierr);
for (i = ns; i < ne; ++i) {
double sign = pow(-1.0, (i>(N/2-1)));
ierr = MatSetValue(C, i, i, sign, INSERT_VALUES); CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(C, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(C, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) C,"CongMatrix"); CHKERRQ(ierr);
*Cout = C;
PetscFunctionReturn(0);
}
PetscErrorCode SetupFE(DM dm, PetscInt Nc, PetscBool simplex, const char name[], PetscErrorCode (*setup)(DM, AppCtx *), void *ctx)
{
AppCtx *user = (AppCtx *) ctx;
DM cdm = dm;
PetscFE fe;
char prefix[PETSC_MAX_PATH_LEN];
PetscInt dim;
PetscErrorCode ierr;
PetscFunctionBegin;
/* Create finite element */
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = PetscSNPrintf(prefix, PETSC_MAX_PATH_LEN, "%s_", name);CHKERRQ(ierr);
ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) dm), dim, Nc, simplex, name ? prefix : NULL, -1, &fe);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) fe, name);CHKERRQ(ierr);
/* Set discretization and boundary conditions for each mesh */
ierr = DMSetField(dm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr);
ierr = DMCreateDS(dm);CHKERRQ(ierr);
ierr = (*setup)(dm, user);CHKERRQ(ierr);
while (cdm) {
ierr = DMCopyDisc(dm, cdm);CHKERRQ(ierr);
if (user->useNearNullspace) {ierr = DMSetNearNullSpaceConstructor(cdm, 0, CreateElasticityNullSpace);CHKERRQ(ierr);}
/* TODO: Check whether the boundary of coarse meshes is marked */
ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
