1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/isimpl.h> 3 #include <petsc/private/vecimpl.h> 4 #include <petsc/private/glvisvecimpl.h> 5 #include <petscsf.h> 6 #include <petscds.h> 7 #include <petscdraw.h> 8 #include <petscdmfield.h> 9 10 /* Logging support */ 11 PetscLogEvent DMPLEX_Interpolate, DMPLEX_Partition, DMPLEX_Distribute, DMPLEX_DistributeCones, DMPLEX_DistributeLabels, DMPLEX_DistributeSF, DMPLEX_DistributeOverlap, DMPLEX_DistributeField, DMPLEX_DistributeData, DMPLEX_Migrate, DMPLEX_InterpolateSF, DMPLEX_GlobalToNaturalBegin, DMPLEX_GlobalToNaturalEnd, DMPLEX_NaturalToGlobalBegin, DMPLEX_NaturalToGlobalEnd, DMPLEX_Stratify, DMPLEX_Symmetrize, DMPLEX_Preallocate, DMPLEX_ResidualFEM, DMPLEX_JacobianFEM, DMPLEX_InterpolatorFEM, DMPLEX_InjectorFEM, DMPLEX_IntegralFEM, DMPLEX_CreateGmsh, DMPLEX_RebalanceSharedPoints, DMPLEX_PartSelf, DMPLEX_PartLabelInvert, DMPLEX_PartLabelCreateSF, DMPLEX_PartStratSF, DMPLEX_CreatePointSF; 12 13 PETSC_EXTERN PetscErrorCode VecView_MPI(Vec, PetscViewer); 14 15 /*@ 16 DMPlexRefineSimplexToTensor - Uniformly refines simplicial cells into tensor product cells. 17 3 quadrilaterals per triangle in 2D and 4 hexahedra per tetrahedron in 3D. 18 19 Collective 20 21 Input Parameters: 22 . dm - The DMPlex object 23 24 Output Parameters: 25 . dmRefined - The refined DMPlex object 26 27 Note: Returns NULL if the mesh is already a tensor product mesh. 28 29 Level: intermediate 30 31 .seealso: DMPlexCreate(), DMPlexSetRefinementUniform() 32 @*/ 33 PetscErrorCode DMPlexRefineSimplexToTensor(DM dm, DM *dmRefined) 34 { 35 PetscInt dim, cMax, fMax, cStart, cEnd, coneSize; 36 CellRefiner cellRefiner; 37 PetscBool lop, allnoop, localized; 38 PetscErrorCode ierr; 39 40 PetscFunctionBegin; 41 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 42 PetscValidPointer(dmRefined, 1); 43 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 44 ierr = DMPlexGetHybridBounds(dm,&cMax,&fMax,NULL,NULL);CHKERRQ(ierr); 45 ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr); 46 if (!(cEnd - cStart)) cellRefiner = REFINER_NOOP; 47 else { 48 ierr = DMPlexGetConeSize(dm,cStart,&coneSize);CHKERRQ(ierr); 49 switch (dim) { 50 case 1: 51 cellRefiner = REFINER_NOOP; 52 break; 53 case 2: 54 switch (coneSize) { 55 case 3: 56 if (cMax >= 0) cellRefiner = REFINER_HYBRID_SIMPLEX_TO_HEX_2D; 57 else cellRefiner = REFINER_SIMPLEX_TO_HEX_2D; 58 break; 59 case 4: 60 if (cMax >= 0) cellRefiner = REFINER_HYBRID_SIMPLEX_TO_HEX_2D; 61 else cellRefiner = REFINER_NOOP; 62 break; 63 default: SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot handle coneSize %D with dimension %D",coneSize,dim); 64 } 65 break; 66 case 3: 67 switch (coneSize) { 68 case 4: 69 if (cMax >= 0) cellRefiner = REFINER_HYBRID_SIMPLEX_TO_HEX_3D; 70 else cellRefiner = REFINER_SIMPLEX_TO_HEX_3D; 71 break; 72 case 5: 73 if (cMax >= 0) cellRefiner = REFINER_HYBRID_SIMPLEX_TO_HEX_3D; 74 else cellRefiner = REFINER_NOOP; 75 break; 76 case 6: 77 if (cMax >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Simplex2Tensor in 3D with Hybrid mesh not yet done"); 78 cellRefiner = REFINER_NOOP; 79 break; 80 default: SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot handle coneSize %D with dimension %D",coneSize,dim); 81 } 82 break; 83 default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot handle dimension %D",dim); 84 } 85 } 86 /* return if we don't need to refine */ 87 lop = (cellRefiner == REFINER_NOOP) ? PETSC_TRUE : PETSC_FALSE; 88 ierr = MPIU_Allreduce(&lop,&allnoop,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 89 if (allnoop) { 90 *dmRefined = NULL; 91 PetscFunctionReturn(0); 92 } 93 ierr = DMPlexRefineUniform_Internal(dm, cellRefiner, dmRefined);CHKERRQ(ierr); 94 ierr = DMCopyBoundary(dm, *dmRefined);CHKERRQ(ierr); 95 ierr = DMGetCoordinatesLocalized(dm, &localized);CHKERRQ(ierr); 96 if (localized) { 97 ierr = DMLocalizeCoordinates(*dmRefined);CHKERRQ(ierr); 98 } 99 PetscFunctionReturn(0); 100 } 101 102 PetscErrorCode DMPlexGetFieldType_Internal(DM dm, PetscSection section, PetscInt field, PetscInt *sStart, PetscInt *sEnd, PetscViewerVTKFieldType *ft) 103 { 104 PetscInt dim, pStart, pEnd, vStart, vEnd, cStart, cEnd, cEndInterior; 105 PetscInt vcdof[2] = {0,0}, globalvcdof[2]; 106 PetscErrorCode ierr; 107 108 PetscFunctionBegin; 109 *ft = PETSC_VTK_POINT_FIELD; 110 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 111 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 112 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 113 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 114 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 115 ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); 116 if (field >= 0) { 117 if ((vStart >= pStart) && (vStart < pEnd)) {ierr = PetscSectionGetFieldDof(section, vStart, field, &vcdof[0]);CHKERRQ(ierr);} 118 if ((cStart >= pStart) && (cStart < pEnd)) {ierr = PetscSectionGetFieldDof(section, cStart, field, &vcdof[1]);CHKERRQ(ierr);} 119 } else { 120 if ((vStart >= pStart) && (vStart < pEnd)) {ierr = PetscSectionGetDof(section, vStart, &vcdof[0]);CHKERRQ(ierr);} 121 if ((cStart >= pStart) && (cStart < pEnd)) {ierr = PetscSectionGetDof(section, cStart, &vcdof[1]);CHKERRQ(ierr);} 122 } 123 ierr = MPI_Allreduce(vcdof, globalvcdof, 2, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 124 if (globalvcdof[0]) { 125 *sStart = vStart; 126 *sEnd = vEnd; 127 if (globalvcdof[0] == dim) *ft = PETSC_VTK_POINT_VECTOR_FIELD; 128 else *ft = PETSC_VTK_POINT_FIELD; 129 } else if (globalvcdof[1]) { 130 *sStart = cStart; 131 *sEnd = cEnd; 132 if (globalvcdof[1] == dim) *ft = PETSC_VTK_CELL_VECTOR_FIELD; 133 else *ft = PETSC_VTK_CELL_FIELD; 134 } else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Could not classify input Vec for VTK"); 135 PetscFunctionReturn(0); 136 } 137 138 static PetscErrorCode VecView_Plex_Local_Draw(Vec v, PetscViewer viewer) 139 { 140 DM dm; 141 PetscSection s; 142 PetscDraw draw, popup; 143 DM cdm; 144 PetscSection coordSection; 145 Vec coordinates; 146 const PetscScalar *coords, *array; 147 PetscReal bound[4] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL}; 148 PetscReal vbound[2], time; 149 PetscBool isnull, flg; 150 PetscInt dim, Nf, f, Nc, comp, vStart, vEnd, cStart, cEnd, c, N, level, step, w = 0; 151 const char *name; 152 char title[PETSC_MAX_PATH_LEN]; 153 PetscErrorCode ierr; 154 155 PetscFunctionBegin; 156 ierr = PetscViewerDrawGetDraw(viewer, 0, &draw);CHKERRQ(ierr); 157 ierr = PetscDrawIsNull(draw, &isnull);CHKERRQ(ierr); 158 if (isnull) PetscFunctionReturn(0); 159 160 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 161 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 162 if (dim != 2) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Cannot draw meshes of dimension %D. Use PETSCVIEWERGLVIS", dim); 163 ierr = DMGetLocalSection(dm, &s);CHKERRQ(ierr); 164 ierr = PetscSectionGetNumFields(s, &Nf);CHKERRQ(ierr); 165 ierr = DMGetCoarsenLevel(dm, &level);CHKERRQ(ierr); 166 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 167 ierr = DMGetLocalSection(cdm, &coordSection);CHKERRQ(ierr); 168 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 169 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 170 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 171 172 ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr); 173 ierr = DMGetOutputSequenceNumber(dm, &step, &time);CHKERRQ(ierr); 174 175 ierr = VecGetLocalSize(coordinates, &N);CHKERRQ(ierr); 176 ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); 177 for (c = 0; c < N; c += dim) { 178 bound[0] = PetscMin(bound[0], PetscRealPart(coords[c])); bound[2] = PetscMax(bound[2], PetscRealPart(coords[c])); 179 bound[1] = PetscMin(bound[1], PetscRealPart(coords[c+1])); bound[3] = PetscMax(bound[3], PetscRealPart(coords[c+1])); 180 } 181 ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); 182 ierr = PetscDrawClear(draw);CHKERRQ(ierr); 183 184 /* Could implement something like DMDASelectFields() */ 185 for (f = 0; f < Nf; ++f) { 186 DM fdm = dm; 187 Vec fv = v; 188 IS fis; 189 char prefix[PETSC_MAX_PATH_LEN]; 190 const char *fname; 191 192 ierr = PetscSectionGetFieldComponents(s, f, &Nc);CHKERRQ(ierr); 193 ierr = PetscSectionGetFieldName(s, f, &fname);CHKERRQ(ierr); 194 195 if (v->hdr.prefix) {ierr = PetscStrncpy(prefix, v->hdr.prefix,sizeof(prefix));CHKERRQ(ierr);} 196 else {prefix[0] = '\0';} 197 if (Nf > 1) { 198 ierr = DMCreateSubDM(dm, 1, &f, &fis, &fdm);CHKERRQ(ierr); 199 ierr = VecGetSubVector(v, fis, &fv);CHKERRQ(ierr); 200 ierr = PetscStrlcat(prefix, fname,sizeof(prefix));CHKERRQ(ierr); 201 ierr = PetscStrlcat(prefix, "_",sizeof(prefix));CHKERRQ(ierr); 202 } 203 for (comp = 0; comp < Nc; ++comp, ++w) { 204 PetscInt nmax = 2; 205 206 ierr = PetscViewerDrawGetDraw(viewer, w, &draw);CHKERRQ(ierr); 207 if (Nc > 1) {ierr = PetscSNPrintf(title, sizeof(title), "%s:%s_%D Step: %D Time: %.4g", name, fname, comp, step, time);CHKERRQ(ierr);} 208 else {ierr = PetscSNPrintf(title, sizeof(title), "%s:%s Step: %D Time: %.4g", name, fname, step, time);CHKERRQ(ierr);} 209 ierr = PetscDrawSetTitle(draw, title);CHKERRQ(ierr); 210 211 /* TODO Get max and min only for this component */ 212 ierr = PetscOptionsGetRealArray(NULL, prefix, "-vec_view_bounds", vbound, &nmax, &flg);CHKERRQ(ierr); 213 if (!flg) { 214 ierr = VecMin(fv, NULL, &vbound[0]);CHKERRQ(ierr); 215 ierr = VecMax(fv, NULL, &vbound[1]);CHKERRQ(ierr); 216 if (vbound[1] <= vbound[0]) vbound[1] = vbound[0] + 1.0; 217 } 218 ierr = PetscDrawGetPopup(draw, &popup);CHKERRQ(ierr); 219 ierr = PetscDrawScalePopup(popup, vbound[0], vbound[1]);CHKERRQ(ierr); 220 ierr = PetscDrawSetCoordinates(draw, bound[0], bound[1], bound[2], bound[3]);CHKERRQ(ierr); 221 222 ierr = VecGetArrayRead(fv, &array);CHKERRQ(ierr); 223 for (c = cStart; c < cEnd; ++c) { 224 PetscScalar *coords = NULL, *a = NULL; 225 PetscInt numCoords, color[4] = {-1,-1,-1,-1}; 226 227 ierr = DMPlexPointLocalRead(fdm, c, array, &a);CHKERRQ(ierr); 228 if (a) { 229 color[0] = PetscDrawRealToColor(PetscRealPart(a[comp]), vbound[0], vbound[1]); 230 color[1] = color[2] = color[3] = color[0]; 231 } else { 232 PetscScalar *vals = NULL; 233 PetscInt numVals, va; 234 235 ierr = DMPlexVecGetClosure(fdm, NULL, fv, c, &numVals, &vals);CHKERRQ(ierr); 236 if (numVals % Nc) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of components %D does not divide the number of values in the closure %D", Nc, numVals); 237 switch (numVals/Nc) { 238 case 3: /* P1 Triangle */ 239 case 4: /* P1 Quadrangle */ 240 for (va = 0; va < numVals/Nc; ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va*Nc+comp]), vbound[0], vbound[1]); 241 break; 242 case 6: /* P2 Triangle */ 243 case 8: /* P2 Quadrangle */ 244 for (va = 0; va < numVals/(Nc*2); ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va*Nc+comp + numVals/(Nc*2)]), vbound[0], vbound[1]); 245 break; 246 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of values for cell closure %D cannot be handled", numVals/Nc); 247 } 248 ierr = DMPlexVecRestoreClosure(fdm, NULL, fv, c, &numVals, &vals);CHKERRQ(ierr); 249 } 250 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, c, &numCoords, &coords);CHKERRQ(ierr); 251 switch (numCoords) { 252 case 6: 253 ierr = PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), color[0], color[1], color[2]);CHKERRQ(ierr); 254 break; 255 case 8: 256 ierr = PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), color[0], color[1], color[2]);CHKERRQ(ierr); 257 ierr = PetscDrawTriangle(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), color[2], color[3], color[0]);CHKERRQ(ierr); 258 break; 259 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %D coordinates", numCoords); 260 } 261 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, &numCoords, &coords);CHKERRQ(ierr); 262 } 263 ierr = VecRestoreArrayRead(fv, &array);CHKERRQ(ierr); 264 ierr = PetscDrawFlush(draw);CHKERRQ(ierr); 265 ierr = PetscDrawPause(draw);CHKERRQ(ierr); 266 ierr = PetscDrawSave(draw);CHKERRQ(ierr); 267 } 268 if (Nf > 1) { 269 ierr = VecRestoreSubVector(v, fis, &fv);CHKERRQ(ierr); 270 ierr = ISDestroy(&fis);CHKERRQ(ierr); 271 ierr = DMDestroy(&fdm);CHKERRQ(ierr); 272 } 273 } 274 PetscFunctionReturn(0); 275 } 276 277 static PetscErrorCode VecView_Plex_Local_VTK(Vec v, PetscViewer viewer) 278 { 279 DM dm; 280 Vec locv; 281 const char *name; 282 PetscSection section; 283 PetscInt pStart, pEnd; 284 PetscViewerVTKFieldType ft; 285 PetscErrorCode ierr; 286 287 PetscFunctionBegin; 288 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 289 ierr = DMCreateLocalVector(dm, &locv);CHKERRQ(ierr); /* VTK viewer requires exclusive ownership of the vector */ 290 ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr); 291 ierr = PetscObjectSetName((PetscObject) locv, name);CHKERRQ(ierr); 292 ierr = VecCopy(v, locv);CHKERRQ(ierr); 293 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 294 ierr = DMPlexGetFieldType_Internal(dm, section, PETSC_DETERMINE, &pStart, &pEnd, &ft);CHKERRQ(ierr); 295 ierr = PetscViewerVTKAddField(viewer, (PetscObject) dm, DMPlexVTKWriteAll, ft, PETSC_TRUE,(PetscObject) locv);CHKERRQ(ierr); 296 PetscFunctionReturn(0); 297 } 298 299 PetscErrorCode VecView_Plex_Local(Vec v, PetscViewer viewer) 300 { 301 DM dm; 302 PetscBool isvtk, ishdf5, isdraw, isglvis; 303 PetscErrorCode ierr; 304 305 PetscFunctionBegin; 306 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 307 if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 308 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);CHKERRQ(ierr); 309 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 310 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW, &isdraw);CHKERRQ(ierr); 311 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);CHKERRQ(ierr); 312 if (isvtk || ishdf5 || isdraw || isglvis) { 313 PetscInt i,numFields; 314 PetscObject fe; 315 PetscBool fem = PETSC_FALSE; 316 Vec locv = v; 317 const char *name; 318 PetscInt step; 319 PetscReal time; 320 321 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 322 for (i=0; i<numFields; i++) { 323 ierr = DMGetField(dm, i, NULL, &fe);CHKERRQ(ierr); 324 if (fe->classid == PETSCFE_CLASSID) { fem = PETSC_TRUE; break; } 325 } 326 if (fem) { 327 ierr = DMGetLocalVector(dm, &locv);CHKERRQ(ierr); 328 ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr); 329 ierr = PetscObjectSetName((PetscObject) locv, name);CHKERRQ(ierr); 330 ierr = VecCopy(v, locv);CHKERRQ(ierr); 331 ierr = DMGetOutputSequenceNumber(dm, NULL, &time);CHKERRQ(ierr); 332 ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL);CHKERRQ(ierr); 333 } 334 if (isvtk) { 335 ierr = VecView_Plex_Local_VTK(locv, viewer);CHKERRQ(ierr); 336 } else if (ishdf5) { 337 #if defined(PETSC_HAVE_HDF5) 338 ierr = VecView_Plex_Local_HDF5_Internal(locv, viewer);CHKERRQ(ierr); 339 #else 340 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 341 #endif 342 } else if (isdraw) { 343 ierr = VecView_Plex_Local_Draw(locv, viewer);CHKERRQ(ierr); 344 } else if (isglvis) { 345 ierr = DMGetOutputSequenceNumber(dm, &step, NULL);CHKERRQ(ierr); 346 ierr = PetscViewerGLVisSetSnapId(viewer, step);CHKERRQ(ierr); 347 ierr = VecView_GLVis(locv, viewer);CHKERRQ(ierr); 348 } 349 if (fem) {ierr = DMRestoreLocalVector(dm, &locv);CHKERRQ(ierr);} 350 } else { 351 PetscBool isseq; 352 353 ierr = PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);CHKERRQ(ierr); 354 if (isseq) {ierr = VecView_Seq(v, viewer);CHKERRQ(ierr);} 355 else {ierr = VecView_MPI(v, viewer);CHKERRQ(ierr);} 356 } 357 PetscFunctionReturn(0); 358 } 359 360 PetscErrorCode VecView_Plex(Vec v, PetscViewer viewer) 361 { 362 DM dm; 363 PetscBool isvtk, ishdf5, isdraw, isglvis; 364 PetscErrorCode ierr; 365 366 PetscFunctionBegin; 367 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 368 if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 369 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);CHKERRQ(ierr); 370 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 371 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW, &isdraw);CHKERRQ(ierr); 372 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);CHKERRQ(ierr); 373 if (isvtk || isdraw || isglvis) { 374 Vec locv; 375 const char *name; 376 377 ierr = DMGetLocalVector(dm, &locv);CHKERRQ(ierr); 378 ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr); 379 ierr = PetscObjectSetName((PetscObject) locv, name);CHKERRQ(ierr); 380 ierr = DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv);CHKERRQ(ierr); 381 ierr = DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv);CHKERRQ(ierr); 382 ierr = VecView_Plex_Local(locv, viewer);CHKERRQ(ierr); 383 ierr = DMRestoreLocalVector(dm, &locv);CHKERRQ(ierr); 384 } else if (ishdf5) { 385 #if defined(PETSC_HAVE_HDF5) 386 ierr = VecView_Plex_HDF5_Internal(v, viewer);CHKERRQ(ierr); 387 #else 388 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 389 #endif 390 } else { 391 PetscBool isseq; 392 393 ierr = PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);CHKERRQ(ierr); 394 if (isseq) {ierr = VecView_Seq(v, viewer);CHKERRQ(ierr);} 395 else {ierr = VecView_MPI(v, viewer);CHKERRQ(ierr);} 396 } 397 PetscFunctionReturn(0); 398 } 399 400 PetscErrorCode VecView_Plex_Native(Vec originalv, PetscViewer viewer) 401 { 402 DM dm; 403 MPI_Comm comm; 404 PetscViewerFormat format; 405 Vec v; 406 PetscBool isvtk, ishdf5; 407 PetscErrorCode ierr; 408 409 PetscFunctionBegin; 410 ierr = VecGetDM(originalv, &dm);CHKERRQ(ierr); 411 ierr = PetscObjectGetComm((PetscObject) originalv, &comm);CHKERRQ(ierr); 412 if (!dm) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 413 ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr); 414 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 415 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);CHKERRQ(ierr); 416 if (format == PETSC_VIEWER_NATIVE) { 417 /* Natural ordering is the common case for DMDA, NATIVE means plain vector, for PLEX is the opposite */ 418 /* this need a better fix */ 419 if (dm->useNatural) { 420 if (dm->sfNatural) { 421 const char *vecname; 422 PetscInt n, nroots; 423 424 ierr = VecGetLocalSize(originalv, &n);CHKERRQ(ierr); 425 ierr = PetscSFGetGraph(dm->sfNatural, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 426 if (n == nroots) { 427 ierr = DMGetGlobalVector(dm, &v);CHKERRQ(ierr); 428 ierr = DMPlexGlobalToNaturalBegin(dm, originalv, v);CHKERRQ(ierr); 429 ierr = DMPlexGlobalToNaturalEnd(dm, originalv, v);CHKERRQ(ierr); 430 ierr = PetscObjectGetName((PetscObject) originalv, &vecname);CHKERRQ(ierr); 431 ierr = PetscObjectSetName((PetscObject) v, vecname);CHKERRQ(ierr); 432 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "DM global to natural SF only handles global vectors"); 433 } else SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "DM global to natural SF was not created"); 434 } else v = originalv; 435 } else v = originalv; 436 437 if (ishdf5) { 438 #if defined(PETSC_HAVE_HDF5) 439 ierr = VecView_Plex_HDF5_Native_Internal(v, viewer);CHKERRQ(ierr); 440 #else 441 SETERRQ(comm, PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 442 #endif 443 } else if (isvtk) { 444 SETERRQ(comm, PETSC_ERR_SUP, "VTK format does not support viewing in natural order. Please switch to HDF5."); 445 } else { 446 PetscBool isseq; 447 448 ierr = PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);CHKERRQ(ierr); 449 if (isseq) {ierr = VecView_Seq(v, viewer);CHKERRQ(ierr);} 450 else {ierr = VecView_MPI(v, viewer);CHKERRQ(ierr);} 451 } 452 if (v != originalv) {ierr = DMRestoreGlobalVector(dm, &v);CHKERRQ(ierr);} 453 PetscFunctionReturn(0); 454 } 455 456 PetscErrorCode VecLoad_Plex_Local(Vec v, PetscViewer viewer) 457 { 458 DM dm; 459 PetscBool ishdf5; 460 PetscErrorCode ierr; 461 462 PetscFunctionBegin; 463 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 464 if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 465 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 466 if (ishdf5) { 467 DM dmBC; 468 Vec gv; 469 const char *name; 470 471 ierr = DMGetOutputDM(dm, &dmBC);CHKERRQ(ierr); 472 ierr = DMGetGlobalVector(dmBC, &gv);CHKERRQ(ierr); 473 ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr); 474 ierr = PetscObjectSetName((PetscObject) gv, name);CHKERRQ(ierr); 475 ierr = VecLoad_Default(gv, viewer);CHKERRQ(ierr); 476 ierr = DMGlobalToLocalBegin(dmBC, gv, INSERT_VALUES, v);CHKERRQ(ierr); 477 ierr = DMGlobalToLocalEnd(dmBC, gv, INSERT_VALUES, v);CHKERRQ(ierr); 478 ierr = DMRestoreGlobalVector(dmBC, &gv);CHKERRQ(ierr); 479 } else { 480 ierr = VecLoad_Default(v, viewer);CHKERRQ(ierr); 481 } 482 PetscFunctionReturn(0); 483 } 484 485 PetscErrorCode VecLoad_Plex(Vec v, PetscViewer viewer) 486 { 487 DM dm; 488 PetscBool ishdf5; 489 PetscErrorCode ierr; 490 491 PetscFunctionBegin; 492 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 493 if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 494 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 495 if (ishdf5) { 496 #if defined(PETSC_HAVE_HDF5) 497 ierr = VecLoad_Plex_HDF5_Internal(v, viewer);CHKERRQ(ierr); 498 #else 499 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 500 #endif 501 } else { 502 ierr = VecLoad_Default(v, viewer);CHKERRQ(ierr); 503 } 504 PetscFunctionReturn(0); 505 } 506 507 PetscErrorCode VecLoad_Plex_Native(Vec originalv, PetscViewer viewer) 508 { 509 DM dm; 510 PetscViewerFormat format; 511 PetscBool ishdf5; 512 PetscErrorCode ierr; 513 514 PetscFunctionBegin; 515 ierr = VecGetDM(originalv, &dm);CHKERRQ(ierr); 516 if (!dm) SETERRQ(PetscObjectComm((PetscObject) originalv), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 517 ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr); 518 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 519 if (format == PETSC_VIEWER_NATIVE) { 520 if (dm->useNatural) { 521 if (dm->sfNatural) { 522 if (ishdf5) { 523 #if defined(PETSC_HAVE_HDF5) 524 Vec v; 525 const char *vecname; 526 527 ierr = DMGetGlobalVector(dm, &v);CHKERRQ(ierr); 528 ierr = PetscObjectGetName((PetscObject) originalv, &vecname);CHKERRQ(ierr); 529 ierr = PetscObjectSetName((PetscObject) v, vecname);CHKERRQ(ierr); 530 ierr = VecLoad_Plex_HDF5_Native_Internal(v, viewer);CHKERRQ(ierr); 531 ierr = DMPlexNaturalToGlobalBegin(dm, v, originalv);CHKERRQ(ierr); 532 ierr = DMPlexNaturalToGlobalEnd(dm, v, originalv);CHKERRQ(ierr); 533 ierr = DMRestoreGlobalVector(dm, &v);CHKERRQ(ierr); 534 #else 535 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 536 #endif 537 } else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Reading in natural order is not supported for anything but HDF5."); 538 } 539 } else { 540 ierr = VecLoad_Default(originalv, viewer);CHKERRQ(ierr); 541 } 542 } 543 PetscFunctionReturn(0); 544 } 545 546 PETSC_UNUSED static PetscErrorCode DMPlexView_Ascii_Geometry(DM dm, PetscViewer viewer) 547 { 548 PetscSection coordSection; 549 Vec coordinates; 550 DMLabel depthLabel; 551 const char *name[4]; 552 const PetscScalar *a; 553 PetscInt dim, pStart, pEnd, cStart, cEnd, c; 554 PetscErrorCode ierr; 555 556 PetscFunctionBegin; 557 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 558 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 559 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 560 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 561 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 562 ierr = PetscSectionGetChart(coordSection, &pStart, &pEnd);CHKERRQ(ierr); 563 ierr = VecGetArrayRead(coordinates, &a);CHKERRQ(ierr); 564 name[0] = "vertex"; 565 name[1] = "edge"; 566 name[dim-1] = "face"; 567 name[dim] = "cell"; 568 for (c = cStart; c < cEnd; ++c) { 569 PetscInt *closure = NULL; 570 PetscInt closureSize, cl; 571 572 ierr = PetscViewerASCIIPrintf(viewer, "Geometry for cell %D:\n", c);CHKERRQ(ierr); 573 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 574 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 575 for (cl = 0; cl < closureSize*2; cl += 2) { 576 PetscInt point = closure[cl], depth, dof, off, d, p; 577 578 if ((point < pStart) || (point >= pEnd)) continue; 579 ierr = PetscSectionGetDof(coordSection, point, &dof);CHKERRQ(ierr); 580 if (!dof) continue; 581 ierr = DMLabelGetValue(depthLabel, point, &depth);CHKERRQ(ierr); 582 ierr = PetscSectionGetOffset(coordSection, point, &off);CHKERRQ(ierr); 583 ierr = PetscViewerASCIIPrintf(viewer, "%s %D coords:", name[depth], point);CHKERRQ(ierr); 584 for (p = 0; p < dof/dim; ++p) { 585 ierr = PetscViewerASCIIPrintf(viewer, " (");CHKERRQ(ierr); 586 for (d = 0; d < dim; ++d) { 587 if (d > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 588 ierr = PetscViewerASCIIPrintf(viewer, "%g", PetscRealPart(a[off+p*dim+d]));CHKERRQ(ierr); 589 } 590 ierr = PetscViewerASCIIPrintf(viewer, ")");CHKERRQ(ierr); 591 } 592 ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); 593 } 594 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 595 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 596 } 597 ierr = VecRestoreArrayRead(coordinates, &a);CHKERRQ(ierr); 598 PetscFunctionReturn(0); 599 } 600 601 static PetscErrorCode DMPlexView_Ascii(DM dm, PetscViewer viewer) 602 { 603 DM_Plex *mesh = (DM_Plex*) dm->data; 604 DM cdm; 605 DMLabel markers; 606 PetscSection coordSection; 607 Vec coordinates; 608 PetscViewerFormat format; 609 PetscErrorCode ierr; 610 611 PetscFunctionBegin; 612 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 613 ierr = DMGetLocalSection(cdm, &coordSection);CHKERRQ(ierr); 614 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 615 ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr); 616 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 617 const char *name; 618 PetscInt dim, cellHeight, maxConeSize, maxSupportSize; 619 PetscInt pStart, pEnd, p; 620 PetscMPIInt rank, size; 621 622 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 623 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);CHKERRQ(ierr); 624 ierr = PetscObjectGetName((PetscObject) dm, &name);CHKERRQ(ierr); 625 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 626 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 627 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 628 ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); 629 if (name) {ierr = PetscViewerASCIIPrintf(viewer, "%s in %D dimension%s:\n", name, dim, dim == 1 ? "" : "s");CHKERRQ(ierr);} 630 else {ierr = PetscViewerASCIIPrintf(viewer, "Mesh in %D dimension%s:\n", dim, dim == 1 ? "" : "s");CHKERRQ(ierr);} 631 if (cellHeight) {ierr = PetscViewerASCIIPrintf(viewer, " Cells are at height %D\n", cellHeight);CHKERRQ(ierr);} 632 ierr = PetscViewerASCIIPrintf(viewer, "Supports:\n", name);CHKERRQ(ierr); 633 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 634 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max support size: %D\n", rank, maxSupportSize);CHKERRQ(ierr); 635 for (p = pStart; p < pEnd; ++p) { 636 PetscInt dof, off, s; 637 638 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 639 ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); 640 for (s = off; s < off+dof; ++s) { 641 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %D ----> %D\n", rank, p, mesh->supports[s]);CHKERRQ(ierr); 642 } 643 } 644 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 645 ierr = PetscViewerASCIIPrintf(viewer, "Cones:\n", name);CHKERRQ(ierr); 646 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max cone size: %D\n", rank, maxConeSize);CHKERRQ(ierr); 647 for (p = pStart; p < pEnd; ++p) { 648 PetscInt dof, off, c; 649 650 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 651 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 652 for (c = off; c < off+dof; ++c) { 653 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %D <---- %D (%D)\n", rank, p, mesh->cones[c], mesh->coneOrientations[c]);CHKERRQ(ierr); 654 } 655 } 656 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 657 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 658 if (coordSection && coordinates) { 659 ierr = PetscSectionVecView(coordSection, coordinates, viewer);CHKERRQ(ierr); 660 } 661 ierr = DMGetLabel(dm, "marker", &markers);CHKERRQ(ierr); 662 if (markers) {ierr = DMLabelView(markers,viewer);CHKERRQ(ierr);} 663 if (size > 1) { 664 PetscSF sf; 665 666 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 667 ierr = PetscSFView(sf, viewer);CHKERRQ(ierr); 668 } 669 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 670 } else if (format == PETSC_VIEWER_ASCII_LATEX) { 671 const char *name, *color; 672 const char *defcolors[3] = {"gray", "orange", "green"}; 673 const char *deflcolors[4] = {"blue", "cyan", "red", "magenta"}; 674 char lname[PETSC_MAX_PATH_LEN]; 675 PetscReal scale = 2.0; 676 PetscReal tikzscale = 1.0; 677 PetscBool useNumbers = PETSC_TRUE, useLabels, useColors; 678 double tcoords[3]; 679 PetscScalar *coords; 680 PetscInt numLabels, l, numColors, numLColors, dim, depth, cStart, cEnd, c, vStart, vEnd, v, eStart = 0, eEnd = 0, e, p; 681 PetscMPIInt rank, size; 682 char **names, **colors, **lcolors; 683 PetscBool plotEdges, flg, lflg; 684 PetscBT wp = NULL; 685 PetscInt pEnd, pStart; 686 687 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 688 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 689 ierr = DMGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 690 numLabels = PetscMax(numLabels, 10); 691 numColors = 10; 692 numLColors = 10; 693 ierr = PetscCalloc3(numLabels, &names, numColors, &colors, numLColors, &lcolors);CHKERRQ(ierr); 694 ierr = PetscOptionsGetReal(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_scale", &scale, NULL);CHKERRQ(ierr); 695 ierr = PetscOptionsGetReal(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_tikzscale", &tikzscale, NULL);CHKERRQ(ierr); 696 ierr = PetscOptionsGetBool(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_numbers", &useNumbers, NULL);CHKERRQ(ierr); 697 ierr = PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_labels", names, &numLabels, &useLabels);CHKERRQ(ierr); 698 if (!useLabels) numLabels = 0; 699 ierr = PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_colors", colors, &numColors, &useColors);CHKERRQ(ierr); 700 if (!useColors) { 701 numColors = 3; 702 for (c = 0; c < numColors; ++c) {ierr = PetscStrallocpy(defcolors[c], &colors[c]);CHKERRQ(ierr);} 703 } 704 ierr = PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_lcolors", lcolors, &numLColors, &useColors);CHKERRQ(ierr); 705 if (!useColors) { 706 numLColors = 4; 707 for (c = 0; c < numLColors; ++c) {ierr = PetscStrallocpy(deflcolors[c], &lcolors[c]);CHKERRQ(ierr);} 708 } 709 ierr = PetscOptionsGetString(((PetscObject) viewer)->options, ((PetscObject) viewer)->prefix, "-dm_plex_view_label_filter", lname, PETSC_MAX_PATH_LEN, &lflg);CHKERRQ(ierr); 710 plotEdges = (PetscBool)(depth > 1 && useNumbers && dim < 3); 711 ierr = PetscOptionsGetBool(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_edges", &plotEdges, &flg);CHKERRQ(ierr); 712 if (flg && plotEdges && depth < dim) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Mesh must be interpolated"); 713 if (depth < dim) plotEdges = PETSC_FALSE; 714 715 /* filter points with labelvalue != labeldefaultvalue */ 716 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 717 if (lflg) { 718 DMLabel lbl; 719 720 ierr = DMGetLabel(dm, lname, &lbl);CHKERRQ(ierr); 721 if (lbl) { 722 PetscInt val, defval; 723 724 ierr = DMLabelGetDefaultValue(lbl, &defval);CHKERRQ(ierr); 725 ierr = PetscBTCreate(pEnd-pStart, &wp);CHKERRQ(ierr); 726 for (c = pStart; c < pEnd; c++) { 727 PetscInt *closure = NULL; 728 PetscInt closureSize; 729 730 ierr = DMLabelGetValue(lbl, c, &val);CHKERRQ(ierr); 731 if (val == defval) continue; 732 733 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 734 for (p = 0; p < closureSize*2; p += 2) { 735 ierr = PetscBTSet(wp, closure[p] - pStart);CHKERRQ(ierr); 736 } 737 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 738 } 739 } 740 } 741 742 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 743 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);CHKERRQ(ierr); 744 ierr = PetscObjectGetName((PetscObject) dm, &name);CHKERRQ(ierr); 745 ierr = PetscViewerASCIIPrintf(viewer, "\ 746 \\documentclass[tikz]{standalone}\n\n\ 747 \\usepackage{pgflibraryshapes}\n\ 748 \\usetikzlibrary{backgrounds}\n\ 749 \\usetikzlibrary{arrows}\n\ 750 \\begin{document}\n");CHKERRQ(ierr); 751 if (size > 1) { 752 ierr = PetscViewerASCIIPrintf(viewer, "%s for process ", name);CHKERRQ(ierr); 753 for (p = 0; p < size; ++p) { 754 if (p > 0 && p == size-1) { 755 ierr = PetscViewerASCIIPrintf(viewer, ", and ", colors[p%numColors], p);CHKERRQ(ierr); 756 } else if (p > 0) { 757 ierr = PetscViewerASCIIPrintf(viewer, ", ", colors[p%numColors], p);CHKERRQ(ierr); 758 } 759 ierr = PetscViewerASCIIPrintf(viewer, "{\\textcolor{%s}%D}", colors[p%numColors], p);CHKERRQ(ierr); 760 } 761 ierr = PetscViewerASCIIPrintf(viewer, ".\n\n\n");CHKERRQ(ierr); 762 } 763 ierr = PetscViewerASCIIPrintf(viewer, "\\begin{tikzpicture}[scale = %g,font=\\fontsize{8}{8}\\selectfont]\n", tikzscale);CHKERRQ(ierr); 764 765 /* Plot vertices */ 766 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 767 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 768 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 769 for (v = vStart; v < vEnd; ++v) { 770 PetscInt off, dof, d; 771 PetscBool isLabeled = PETSC_FALSE; 772 773 if (wp && !PetscBTLookup(wp,v - pStart)) continue; 774 ierr = PetscSectionGetDof(coordSection, v, &dof);CHKERRQ(ierr); 775 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 776 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "\\path (");CHKERRQ(ierr); 777 if (PetscUnlikely(dof > 3)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"coordSection vertex %D has dof %D > 3",v,dof); 778 for (d = 0; d < dof; ++d) { 779 tcoords[d] = (double) (scale*PetscRealPart(coords[off+d])); 780 tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 781 } 782 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 783 if (dim == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;} 784 for (d = 0; d < dof; ++d) { 785 if (d > 0) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, ",");CHKERRQ(ierr);} 786 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "%g", tcoords[d]);CHKERRQ(ierr); 787 } 788 color = colors[rank%numColors]; 789 for (l = 0; l < numLabels; ++l) { 790 PetscInt val; 791 ierr = DMGetLabelValue(dm, names[l], v, &val);CHKERRQ(ierr); 792 if (val >= 0) {color = lcolors[l%numLColors]; isLabeled = PETSC_TRUE; break;} 793 } 794 if (useNumbers) { 795 ierr = PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D};\n", v, rank, color, v);CHKERRQ(ierr); 796 } else { 797 ierr = PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", v, rank, !isLabeled ? 1 : 2, color);CHKERRQ(ierr); 798 } 799 } 800 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 801 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 802 /* Plot cells */ 803 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 804 ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr); 805 if (dim == 3 || !useNumbers) { 806 for (e = eStart; e < eEnd; ++e) { 807 const PetscInt *cone; 808 809 if (wp && !PetscBTLookup(wp,e - pStart)) continue; 810 color = colors[rank%numColors]; 811 for (l = 0; l < numLabels; ++l) { 812 PetscInt val; 813 ierr = DMGetLabelValue(dm, names[l], e, &val);CHKERRQ(ierr); 814 if (val >= 0) {color = lcolors[l%numLColors]; break;} 815 } 816 ierr = DMPlexGetCone(dm, e, &cone);CHKERRQ(ierr); 817 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] (%D_%d) -- (%D_%d);\n", color, cone[0], rank, cone[1], rank);CHKERRQ(ierr); 818 } 819 } else { 820 for (c = cStart; c < cEnd; ++c) { 821 PetscInt *closure = NULL; 822 PetscInt closureSize, firstPoint = -1; 823 824 if (wp && !PetscBTLookup(wp,c - pStart)) continue; 825 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 826 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] ", colors[rank%numColors]);CHKERRQ(ierr); 827 for (p = 0; p < closureSize*2; p += 2) { 828 const PetscInt point = closure[p]; 829 830 if ((point < vStart) || (point >= vEnd)) continue; 831 if (firstPoint >= 0) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, " -- ");CHKERRQ(ierr);} 832 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "(%D_%d)", point, rank);CHKERRQ(ierr); 833 if (firstPoint < 0) firstPoint = point; 834 } 835 /* Why doesn't this work? ierr = PetscViewerASCIISynchronizedPrintf(viewer, " -- cycle;\n");CHKERRQ(ierr); */ 836 ierr = PetscViewerASCIISynchronizedPrintf(viewer, " -- (%D_%d);\n", firstPoint, rank);CHKERRQ(ierr); 837 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 838 } 839 } 840 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 841 for (c = cStart; c < cEnd; ++c) { 842 double ccoords[3] = {0.0, 0.0, 0.0}; 843 PetscBool isLabeled = PETSC_FALSE; 844 PetscInt *closure = NULL; 845 PetscInt closureSize, dof, d, n = 0; 846 847 if (wp && !PetscBTLookup(wp,c - pStart)) continue; 848 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 849 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "\\path (");CHKERRQ(ierr); 850 for (p = 0; p < closureSize*2; p += 2) { 851 const PetscInt point = closure[p]; 852 PetscInt off; 853 854 if ((point < vStart) || (point >= vEnd)) continue; 855 ierr = PetscSectionGetDof(coordSection, point, &dof);CHKERRQ(ierr); 856 ierr = PetscSectionGetOffset(coordSection, point, &off);CHKERRQ(ierr); 857 for (d = 0; d < dof; ++d) { 858 tcoords[d] = (double) (scale*PetscRealPart(coords[off+d])); 859 tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 860 } 861 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 862 if (dof == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;} 863 for (d = 0; d < dof; ++d) {ccoords[d] += tcoords[d];} 864 ++n; 865 } 866 for (d = 0; d < dof; ++d) {ccoords[d] /= n;} 867 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 868 for (d = 0; d < dof; ++d) { 869 if (d > 0) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, ",");CHKERRQ(ierr);} 870 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "%g", ccoords[d]);CHKERRQ(ierr); 871 } 872 color = colors[rank%numColors]; 873 for (l = 0; l < numLabels; ++l) { 874 PetscInt val; 875 ierr = DMGetLabelValue(dm, names[l], c, &val);CHKERRQ(ierr); 876 if (val >= 0) {color = lcolors[l%numLColors]; isLabeled = PETSC_TRUE; break;} 877 } 878 if (useNumbers) { 879 ierr = PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D};\n", c, rank, color, c);CHKERRQ(ierr); 880 } else { 881 ierr = PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", c, rank, !isLabeled ? 1 : 2, color);CHKERRQ(ierr); 882 } 883 } 884 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 885 /* Plot edges */ 886 if (plotEdges) { 887 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 888 ierr = PetscViewerASCIIPrintf(viewer, "\\path\n");CHKERRQ(ierr); 889 for (e = eStart; e < eEnd; ++e) { 890 const PetscInt *cone; 891 PetscInt coneSize, offA, offB, dof, d; 892 893 if (wp && !PetscBTLookup(wp,e - pStart)) continue; 894 ierr = DMPlexGetConeSize(dm, e, &coneSize);CHKERRQ(ierr); 895 if (coneSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Edge %D cone should have two vertices, not %D", e, coneSize); 896 ierr = DMPlexGetCone(dm, e, &cone);CHKERRQ(ierr); 897 ierr = PetscSectionGetDof(coordSection, cone[0], &dof);CHKERRQ(ierr); 898 ierr = PetscSectionGetOffset(coordSection, cone[0], &offA);CHKERRQ(ierr); 899 ierr = PetscSectionGetOffset(coordSection, cone[1], &offB);CHKERRQ(ierr); 900 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "(");CHKERRQ(ierr); 901 for (d = 0; d < dof; ++d) { 902 tcoords[d] = (double) (0.5*scale*PetscRealPart(coords[offA+d]+coords[offB+d])); 903 tcoords[d] = PetscAbs(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 904 } 905 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 906 if (dim == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;} 907 for (d = 0; d < dof; ++d) { 908 if (d > 0) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, ",");CHKERRQ(ierr);} 909 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)tcoords[d]);CHKERRQ(ierr); 910 } 911 color = colors[rank%numColors]; 912 for (l = 0; l < numLabels; ++l) { 913 PetscInt val; 914 ierr = DMGetLabelValue(dm, names[l], v, &val);CHKERRQ(ierr); 915 if (val >= 0) {color = lcolors[l%numLColors]; break;} 916 } 917 ierr = PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D} --\n", e, rank, color, e);CHKERRQ(ierr); 918 } 919 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 920 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 921 ierr = PetscViewerASCIIPrintf(viewer, "(0,0);\n");CHKERRQ(ierr); 922 } 923 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 924 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 925 ierr = PetscViewerASCIIPrintf(viewer, "\\end{tikzpicture}\n");CHKERRQ(ierr); 926 ierr = PetscViewerASCIIPrintf(viewer, "\\end{document}\n", name);CHKERRQ(ierr); 927 for (l = 0; l < numLabels; ++l) {ierr = PetscFree(names[l]);CHKERRQ(ierr);} 928 for (c = 0; c < numColors; ++c) {ierr = PetscFree(colors[c]);CHKERRQ(ierr);} 929 for (c = 0; c < numLColors; ++c) {ierr = PetscFree(lcolors[c]);CHKERRQ(ierr);} 930 ierr = PetscFree3(names, colors, lcolors);CHKERRQ(ierr); 931 ierr = PetscBTDestroy(&wp);CHKERRQ(ierr); 932 } else if (format == PETSC_VIEWER_LOAD_BALANCE) { 933 Vec cown,acown; 934 VecScatter sct; 935 ISLocalToGlobalMapping g2l; 936 IS gid,acis; 937 MPI_Comm comm,ncomm = MPI_COMM_NULL; 938 MPI_Group ggroup,ngroup; 939 PetscScalar *array,nid; 940 const PetscInt *idxs; 941 PetscInt *idxs2,*start,*adjacency,*work; 942 PetscInt64 lm[3],gm[3]; 943 PetscInt i,c,cStart,cEnd,cum,numVertices,ect,ectn,cellHeight; 944 PetscMPIInt d1,d2,rank; 945 946 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 947 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 948 #if defined(PETSC_HAVE_MPI_SHARED_COMM) 949 ierr = MPI_Comm_split_type(comm,MPI_COMM_TYPE_SHARED,rank,MPI_INFO_NULL,&ncomm);CHKERRQ(ierr); 950 #endif 951 if (ncomm != MPI_COMM_NULL) { 952 ierr = MPI_Comm_group(comm,&ggroup);CHKERRQ(ierr); 953 ierr = MPI_Comm_group(ncomm,&ngroup);CHKERRQ(ierr); 954 d1 = 0; 955 ierr = MPI_Group_translate_ranks(ngroup,1,&d1,ggroup,&d2);CHKERRQ(ierr); 956 nid = d2; 957 ierr = MPI_Group_free(&ggroup);CHKERRQ(ierr); 958 ierr = MPI_Group_free(&ngroup);CHKERRQ(ierr); 959 ierr = MPI_Comm_free(&ncomm);CHKERRQ(ierr); 960 } else nid = 0.0; 961 962 /* Get connectivity */ 963 ierr = DMPlexGetVTKCellHeight(dm,&cellHeight);CHKERRQ(ierr); 964 ierr = DMPlexCreatePartitionerGraph(dm,cellHeight,&numVertices,&start,&adjacency,&gid);CHKERRQ(ierr); 965 966 /* filter overlapped local cells */ 967 ierr = DMPlexGetHeightStratum(dm,cellHeight,&cStart,&cEnd);CHKERRQ(ierr); 968 ierr = ISGetIndices(gid,&idxs);CHKERRQ(ierr); 969 ierr = ISGetLocalSize(gid,&cum);CHKERRQ(ierr); 970 ierr = PetscMalloc1(cum,&idxs2);CHKERRQ(ierr); 971 for (c = cStart, cum = 0; c < cEnd; c++) { 972 if (idxs[c-cStart] < 0) continue; 973 idxs2[cum++] = idxs[c-cStart]; 974 } 975 ierr = ISRestoreIndices(gid,&idxs);CHKERRQ(ierr); 976 if (numVertices != cum) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Unexpected %D != %D",numVertices,cum); 977 ierr = ISDestroy(&gid);CHKERRQ(ierr); 978 ierr = ISCreateGeneral(comm,numVertices,idxs2,PETSC_OWN_POINTER,&gid);CHKERRQ(ierr); 979 980 /* support for node-aware cell locality */ 981 ierr = ISCreateGeneral(comm,start[numVertices],adjacency,PETSC_USE_POINTER,&acis);CHKERRQ(ierr); 982 ierr = VecCreateSeq(PETSC_COMM_SELF,start[numVertices],&acown);CHKERRQ(ierr); 983 ierr = VecCreateMPI(comm,numVertices,PETSC_DECIDE,&cown);CHKERRQ(ierr); 984 ierr = VecGetArray(cown,&array);CHKERRQ(ierr); 985 for (c = 0; c < numVertices; c++) array[c] = nid; 986 ierr = VecRestoreArray(cown,&array);CHKERRQ(ierr); 987 ierr = VecScatterCreate(cown,acis,acown,NULL,&sct);CHKERRQ(ierr); 988 ierr = VecScatterBegin(sct,cown,acown,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 989 ierr = VecScatterEnd(sct,cown,acown,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 990 ierr = ISDestroy(&acis);CHKERRQ(ierr); 991 ierr = VecScatterDestroy(&sct);CHKERRQ(ierr); 992 ierr = VecDestroy(&cown);CHKERRQ(ierr); 993 994 /* compute edgeCut */ 995 for (c = 0, cum = 0; c < numVertices; c++) cum = PetscMax(cum,start[c+1]-start[c]); 996 ierr = PetscMalloc1(cum,&work);CHKERRQ(ierr); 997 ierr = ISLocalToGlobalMappingCreateIS(gid,&g2l);CHKERRQ(ierr); 998 ierr = ISLocalToGlobalMappingSetType(g2l,ISLOCALTOGLOBALMAPPINGHASH);CHKERRQ(ierr); 999 ierr = ISDestroy(&gid);CHKERRQ(ierr); 1000 ierr = VecGetArray(acown,&array);CHKERRQ(ierr); 1001 for (c = 0, ect = 0, ectn = 0; c < numVertices; c++) { 1002 PetscInt totl; 1003 1004 totl = start[c+1]-start[c]; 1005 ierr = ISGlobalToLocalMappingApply(g2l,IS_GTOLM_MASK,totl,adjacency+start[c],NULL,work);CHKERRQ(ierr); 1006 for (i = 0; i < totl; i++) { 1007 if (work[i] < 0) { 1008 ect += 1; 1009 ectn += (array[i + start[c]] != nid) ? 0 : 1; 1010 } 1011 } 1012 } 1013 ierr = PetscFree(work);CHKERRQ(ierr); 1014 ierr = VecRestoreArray(acown,&array);CHKERRQ(ierr); 1015 lm[0] = numVertices > 0 ? numVertices : PETSC_MAX_INT; 1016 lm[1] = -numVertices; 1017 ierr = MPIU_Allreduce(lm,gm,2,MPIU_INT64,MPI_MIN,comm);CHKERRQ(ierr); 1018 ierr = PetscViewerASCIIPrintf(viewer," Cell balance: %.2f (max %D, min %D",-((double)gm[1])/((double)gm[0]),-(PetscInt)gm[1],(PetscInt)gm[0]);CHKERRQ(ierr); 1019 lm[0] = ect; /* edgeCut */ 1020 lm[1] = ectn; /* node-aware edgeCut */ 1021 lm[2] = numVertices > 0 ? 0 : 1; /* empty processes */ 1022 ierr = MPIU_Allreduce(lm,gm,3,MPIU_INT64,MPI_SUM,comm);CHKERRQ(ierr); 1023 ierr = PetscViewerASCIIPrintf(viewer,", empty %D)\n",(PetscInt)gm[2]);CHKERRQ(ierr); 1024 #if defined(PETSC_HAVE_MPI_SHARED_COMM) 1025 ierr = PetscViewerASCIIPrintf(viewer," Edge Cut: %D (on node %.3f)\n",(PetscInt)(gm[0]/2),gm[0] ? ((double)(gm[1]))/((double)gm[0]) : 1.);CHKERRQ(ierr); 1026 #else 1027 ierr = PetscViewerASCIIPrintf(viewer," Edge Cut: %D (on node %.3f)\n",(PetscInt)(gm[0]/2),0.0);CHKERRQ(ierr); 1028 #endif 1029 ierr = ISLocalToGlobalMappingDestroy(&g2l);CHKERRQ(ierr); 1030 ierr = PetscFree(start);CHKERRQ(ierr); 1031 ierr = PetscFree(adjacency);CHKERRQ(ierr); 1032 ierr = VecDestroy(&acown);CHKERRQ(ierr); 1033 } else { 1034 MPI_Comm comm; 1035 PetscInt *sizes, *hybsizes; 1036 PetscInt locDepth, depth, cellHeight, dim, d, pMax[4]; 1037 PetscInt pStart, pEnd, p; 1038 PetscInt numLabels, l; 1039 const char *name; 1040 PetscMPIInt size; 1041 1042 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1043 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1044 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1045 ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); 1046 ierr = PetscObjectGetName((PetscObject) dm, &name);CHKERRQ(ierr); 1047 if (name) {ierr = PetscViewerASCIIPrintf(viewer, "%s in %D dimension%s:\n", name, dim, dim == 1 ? "" : "s");CHKERRQ(ierr);} 1048 else {ierr = PetscViewerASCIIPrintf(viewer, "Mesh in %D dimension%s:\n", dim, dim == 1 ? "" : "s");CHKERRQ(ierr);} 1049 if (cellHeight) {ierr = PetscViewerASCIIPrintf(viewer, " Cells are at height %D\n", cellHeight);CHKERRQ(ierr);} 1050 ierr = DMPlexGetDepth(dm, &locDepth);CHKERRQ(ierr); 1051 ierr = MPIU_Allreduce(&locDepth, &depth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); 1052 ierr = DMPlexGetHybridBounds(dm, &pMax[depth], depth > 0 ? &pMax[depth-1] : NULL, depth > 1 ? &pMax[depth - 2] : NULL, &pMax[0]);CHKERRQ(ierr); 1053 ierr = PetscCalloc2(size,&sizes,size,&hybsizes);CHKERRQ(ierr); 1054 if (depth == 1) { 1055 ierr = DMPlexGetDepthStratum(dm, 0, &pStart, &pEnd);CHKERRQ(ierr); 1056 pEnd = pEnd - pStart; 1057 pMax[0] -= pStart; 1058 ierr = MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1059 ierr = MPI_Gather(&pMax[0], 1, MPIU_INT, hybsizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1060 ierr = PetscViewerASCIIPrintf(viewer, " %d-cells:", 0);CHKERRQ(ierr); 1061 for (p = 0; p < size; ++p) { 1062 if (hybsizes[p] >= 0) {ierr = PetscViewerASCIIPrintf(viewer, " %D (%D)", sizes[p], sizes[p] - hybsizes[p]);CHKERRQ(ierr);} 1063 else {ierr = PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);CHKERRQ(ierr);} 1064 } 1065 ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); 1066 ierr = DMPlexGetHeightStratum(dm, 0, &pStart, &pEnd);CHKERRQ(ierr); 1067 pEnd = pEnd - pStart; 1068 pMax[depth] -= pStart; 1069 ierr = MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1070 ierr = MPI_Gather(&pMax[depth], 1, MPIU_INT, hybsizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1071 ierr = PetscViewerASCIIPrintf(viewer, " %D-cells:", dim);CHKERRQ(ierr); 1072 for (p = 0; p < size; ++p) { 1073 if (hybsizes[p] >= 0) {ierr = PetscViewerASCIIPrintf(viewer, " %D (%D)", sizes[p], sizes[p] - hybsizes[p]);CHKERRQ(ierr);} 1074 else {ierr = PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);CHKERRQ(ierr);} 1075 } 1076 ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); 1077 } else { 1078 PetscMPIInt rank; 1079 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1080 for (d = 0; d <= dim; d++) { 1081 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 1082 pEnd -= pStart; 1083 pMax[d] -= pStart; 1084 ierr = MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1085 ierr = MPI_Gather(&pMax[d], 1, MPIU_INT, hybsizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1086 ierr = PetscViewerASCIIPrintf(viewer, " %D-cells:", d);CHKERRQ(ierr); 1087 for (p = 0; p < size; ++p) { 1088 if (!rank) { 1089 if (hybsizes[p] >= 0) {ierr = PetscViewerASCIIPrintf(viewer, " %D (%D)", sizes[p], sizes[p] - hybsizes[p]);CHKERRQ(ierr);} 1090 else {ierr = PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);CHKERRQ(ierr);} 1091 } 1092 } 1093 ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); 1094 } 1095 } 1096 ierr = PetscFree2(sizes,hybsizes);CHKERRQ(ierr); 1097 ierr = DMGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 1098 if (numLabels) {ierr = PetscViewerASCIIPrintf(viewer, "Labels:\n");CHKERRQ(ierr);} 1099 for (l = 0; l < numLabels; ++l) { 1100 DMLabel label; 1101 const char *name; 1102 IS valueIS; 1103 const PetscInt *values; 1104 PetscInt numValues, v; 1105 1106 ierr = DMGetLabelName(dm, l, &name);CHKERRQ(ierr); 1107 ierr = DMGetLabel(dm, name, &label);CHKERRQ(ierr); 1108 ierr = DMLabelGetNumValues(label, &numValues);CHKERRQ(ierr); 1109 ierr = PetscViewerASCIIPrintf(viewer, " %s: %D strata with value/size (", name, numValues);CHKERRQ(ierr); 1110 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 1111 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 1112 ierr = PetscViewerASCIIUseTabs(viewer, PETSC_FALSE);CHKERRQ(ierr); 1113 for (v = 0; v < numValues; ++v) { 1114 PetscInt size; 1115 1116 ierr = DMLabelGetStratumSize(label, values[v], &size);CHKERRQ(ierr); 1117 if (v > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 1118 ierr = PetscViewerASCIIPrintf(viewer, "%D (%D)", values[v], size);CHKERRQ(ierr); 1119 } 1120 ierr = PetscViewerASCIIPrintf(viewer, ")\n");CHKERRQ(ierr); 1121 ierr = PetscViewerASCIIUseTabs(viewer, PETSC_TRUE);CHKERRQ(ierr); 1122 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 1123 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 1124 } 1125 /* If no fields are specified, people do not want to see adjacency */ 1126 if (dm->Nf) { 1127 PetscInt f; 1128 1129 for (f = 0; f < dm->Nf; ++f) { 1130 const char *name; 1131 1132 ierr = PetscObjectGetName(dm->fields[f].disc, &name);CHKERRQ(ierr); 1133 if (numLabels) {ierr = PetscViewerASCIIPrintf(viewer, "Field %s:\n", name);CHKERRQ(ierr);} 1134 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 1135 if (dm->fields[f].label) {ierr = DMLabelView(dm->fields[f].label, viewer);CHKERRQ(ierr);} 1136 if (dm->fields[f].adjacency[0]) { 1137 if (dm->fields[f].adjacency[1]) {ierr = PetscViewerASCIIPrintf(viewer, "adjacency FVM++\n");CHKERRQ(ierr);} 1138 else {ierr = PetscViewerASCIIPrintf(viewer, "adjacency FVM\n");CHKERRQ(ierr);} 1139 } else { 1140 if (dm->fields[f].adjacency[1]) {ierr = PetscViewerASCIIPrintf(viewer, "adjacency FEM\n");CHKERRQ(ierr);} 1141 else {ierr = PetscViewerASCIIPrintf(viewer, "adjacency FUNKY\n");CHKERRQ(ierr);} 1142 } 1143 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 1144 } 1145 } 1146 ierr = DMGetCoarseDM(dm, &cdm);CHKERRQ(ierr); 1147 if (cdm) { 1148 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 1149 ierr = DMPlexView_Ascii(cdm, viewer);CHKERRQ(ierr); 1150 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 1151 } 1152 } 1153 PetscFunctionReturn(0); 1154 } 1155 1156 static PetscErrorCode DMPlexView_Draw(DM dm, PetscViewer viewer) 1157 { 1158 PetscDraw draw; 1159 DM cdm; 1160 PetscSection coordSection; 1161 Vec coordinates; 1162 const PetscScalar *coords; 1163 PetscReal xyl[2],xyr[2],bound[4] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL}; 1164 PetscBool isnull; 1165 PetscInt dim, vStart, vEnd, cStart, cEnd, c, N; 1166 PetscMPIInt rank; 1167 PetscErrorCode ierr; 1168 1169 PetscFunctionBegin; 1170 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 1171 if (dim != 2) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Cannot draw meshes of dimension %D", dim); 1172 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 1173 ierr = DMGetLocalSection(cdm, &coordSection);CHKERRQ(ierr); 1174 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1175 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1176 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1177 1178 ierr = PetscViewerDrawGetDraw(viewer, 0, &draw);CHKERRQ(ierr); 1179 ierr = PetscDrawIsNull(draw, &isnull);CHKERRQ(ierr); 1180 if (isnull) PetscFunctionReturn(0); 1181 ierr = PetscDrawSetTitle(draw, "Mesh");CHKERRQ(ierr); 1182 1183 ierr = VecGetLocalSize(coordinates, &N);CHKERRQ(ierr); 1184 ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); 1185 for (c = 0; c < N; c += dim) { 1186 bound[0] = PetscMin(bound[0], PetscRealPart(coords[c])); bound[2] = PetscMax(bound[2], PetscRealPart(coords[c])); 1187 bound[1] = PetscMin(bound[1], PetscRealPart(coords[c+1])); bound[3] = PetscMax(bound[3], PetscRealPart(coords[c+1])); 1188 } 1189 ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); 1190 ierr = MPIU_Allreduce(&bound[0],xyl,2,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 1191 ierr = MPIU_Allreduce(&bound[2],xyr,2,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 1192 ierr = PetscDrawSetCoordinates(draw, xyl[0], xyl[1], xyr[0], xyr[1]);CHKERRQ(ierr); 1193 ierr = PetscDrawClear(draw);CHKERRQ(ierr); 1194 1195 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 1196 for (c = cStart; c < cEnd; ++c) { 1197 PetscScalar *coords = NULL; 1198 PetscInt numCoords,coneSize; 1199 1200 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1201 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, c, &numCoords, &coords);CHKERRQ(ierr); 1202 switch (coneSize) { 1203 case 3: 1204 ierr = PetscDrawTriangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), 1205 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2, 1206 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2, 1207 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2);CHKERRQ(ierr); 1208 break; 1209 case 4: 1210 ierr = PetscDrawRectangle(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), 1211 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2, 1212 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2, 1213 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2, 1214 PETSC_DRAW_WHITE + rank % (PETSC_DRAW_BASIC_COLORS-2) + 2);CHKERRQ(ierr); 1215 break; 1216 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %D facets", coneSize); 1217 } 1218 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, &numCoords, &coords);CHKERRQ(ierr); 1219 } 1220 for (c = cStart; c < cEnd; ++c) { 1221 PetscScalar *coords = NULL; 1222 PetscInt numCoords,coneSize; 1223 1224 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 1225 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, c, &numCoords, &coords);CHKERRQ(ierr); 1226 switch (coneSize) { 1227 case 3: 1228 ierr = PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 1229 ierr = PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 1230 ierr = PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 1231 break; 1232 case 4: 1233 ierr = PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 1234 ierr = PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 1235 ierr = PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 1236 ierr = PetscDrawLine(draw, PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 1237 break; 1238 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %D facets", coneSize); 1239 } 1240 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, &numCoords, &coords);CHKERRQ(ierr); 1241 } 1242 ierr = PetscDrawFlush(draw);CHKERRQ(ierr); 1243 ierr = PetscDrawPause(draw);CHKERRQ(ierr); 1244 ierr = PetscDrawSave(draw);CHKERRQ(ierr); 1245 PetscFunctionReturn(0); 1246 } 1247 1248 PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer) 1249 { 1250 PetscBool iascii, ishdf5, isvtk, isdraw, flg, isglvis; 1251 char name[PETSC_MAX_PATH_LEN]; 1252 PetscErrorCode ierr; 1253 1254 PetscFunctionBegin; 1255 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1256 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 1257 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);CHKERRQ(ierr); 1258 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);CHKERRQ(ierr); 1259 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 1260 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW, &isdraw);CHKERRQ(ierr); 1261 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);CHKERRQ(ierr); 1262 if (iascii) { 1263 PetscViewerFormat format; 1264 ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr); 1265 if (format == PETSC_VIEWER_ASCII_GLVIS) { 1266 ierr = DMPlexView_GLVis(dm, viewer);CHKERRQ(ierr); 1267 } else { 1268 ierr = DMPlexView_Ascii(dm, viewer);CHKERRQ(ierr); 1269 } 1270 } else if (ishdf5) { 1271 #if defined(PETSC_HAVE_HDF5) 1272 ierr = DMPlexView_HDF5_Internal(dm, viewer);CHKERRQ(ierr); 1273 #else 1274 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 1275 #endif 1276 } else if (isvtk) { 1277 ierr = DMPlexVTKWriteAll((PetscObject) dm,viewer);CHKERRQ(ierr); 1278 } else if (isdraw) { 1279 ierr = DMPlexView_Draw(dm, viewer);CHKERRQ(ierr); 1280 } else if (isglvis) { 1281 ierr = DMPlexView_GLVis(dm, viewer);CHKERRQ(ierr); 1282 } else { 1283 SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMPlex writing", ((PetscObject)viewer)->type_name); 1284 } 1285 /* Optionally view the partition */ 1286 ierr = PetscOptionsHasName(((PetscObject) dm)->options, ((PetscObject) dm)->prefix, "-dm_partition_view", &flg);CHKERRQ(ierr); 1287 if (flg) { 1288 Vec ranks; 1289 ierr = DMPlexCreateRankField(dm, &ranks);CHKERRQ(ierr); 1290 ierr = VecView(ranks, viewer);CHKERRQ(ierr); 1291 ierr = VecDestroy(&ranks);CHKERRQ(ierr); 1292 } 1293 /* Optionally view a label */ 1294 ierr = PetscOptionsGetString(((PetscObject) dm)->options, ((PetscObject) dm)->prefix, "-dm_label_view", name, PETSC_MAX_PATH_LEN, &flg);CHKERRQ(ierr); 1295 if (flg) { 1296 DMLabel label; 1297 Vec val; 1298 1299 ierr = DMGetLabel(dm, name, &label);CHKERRQ(ierr); 1300 if (!label) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Label %s provided to -dm_label_view does not exist in this DM", name); 1301 ierr = DMPlexCreateLabelField(dm, label, &val);CHKERRQ(ierr); 1302 ierr = VecView(val, viewer);CHKERRQ(ierr); 1303 ierr = VecDestroy(&val);CHKERRQ(ierr); 1304 } 1305 PetscFunctionReturn(0); 1306 } 1307 1308 PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer) 1309 { 1310 PetscBool ishdf5; 1311 PetscErrorCode ierr; 1312 1313 PetscFunctionBegin; 1314 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1315 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 1316 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 1317 if (ishdf5) { 1318 #if defined(PETSC_HAVE_HDF5) 1319 PetscViewerFormat format; 1320 ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr); 1321 if (format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) { 1322 ierr = DMPlexLoad_HDF5_Xdmf_Internal(dm, viewer);CHKERRQ(ierr); 1323 } else if (format == PETSC_VIEWER_HDF5_PETSC || format == PETSC_VIEWER_DEFAULT || format == PETSC_VIEWER_NATIVE) { 1324 ierr = DMPlexLoad_HDF5_Internal(dm, viewer);CHKERRQ(ierr); 1325 } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 input.", PetscViewerFormats[format]); 1326 #else 1327 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 1328 #endif 1329 } else { 1330 SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Viewer type %s not yet supported for DMPlex loading", ((PetscObject)viewer)->type_name); 1331 } 1332 PetscFunctionReturn(0); 1333 } 1334 1335 PetscErrorCode DMDestroy_Plex(DM dm) 1336 { 1337 DM_Plex *mesh = (DM_Plex*) dm->data; 1338 PetscErrorCode ierr; 1339 1340 PetscFunctionBegin; 1341 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",NULL);CHKERRQ(ierr); 1342 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C", NULL);CHKERRQ(ierr); 1343 if (--mesh->refct > 0) PetscFunctionReturn(0); 1344 ierr = PetscSectionDestroy(&mesh->coneSection);CHKERRQ(ierr); 1345 ierr = PetscFree(mesh->cones);CHKERRQ(ierr); 1346 ierr = PetscFree(mesh->coneOrientations);CHKERRQ(ierr); 1347 ierr = PetscSectionDestroy(&mesh->supportSection);CHKERRQ(ierr); 1348 ierr = PetscSectionDestroy(&mesh->subdomainSection);CHKERRQ(ierr); 1349 ierr = PetscFree(mesh->supports);CHKERRQ(ierr); 1350 ierr = PetscFree(mesh->facesTmp);CHKERRQ(ierr); 1351 ierr = PetscFree(mesh->tetgenOpts);CHKERRQ(ierr); 1352 ierr = PetscFree(mesh->triangleOpts);CHKERRQ(ierr); 1353 ierr = PetscPartitionerDestroy(&mesh->partitioner);CHKERRQ(ierr); 1354 ierr = DMLabelDestroy(&mesh->subpointMap);CHKERRQ(ierr); 1355 ierr = ISDestroy(&mesh->globalVertexNumbers);CHKERRQ(ierr); 1356 ierr = ISDestroy(&mesh->globalCellNumbers);CHKERRQ(ierr); 1357 ierr = PetscSectionDestroy(&mesh->anchorSection);CHKERRQ(ierr); 1358 ierr = ISDestroy(&mesh->anchorIS);CHKERRQ(ierr); 1359 ierr = PetscSectionDestroy(&mesh->parentSection);CHKERRQ(ierr); 1360 ierr = PetscFree(mesh->parents);CHKERRQ(ierr); 1361 ierr = PetscFree(mesh->childIDs);CHKERRQ(ierr); 1362 ierr = PetscSectionDestroy(&mesh->childSection);CHKERRQ(ierr); 1363 ierr = PetscFree(mesh->children);CHKERRQ(ierr); 1364 ierr = DMDestroy(&mesh->referenceTree);CHKERRQ(ierr); 1365 ierr = PetscGridHashDestroy(&mesh->lbox);CHKERRQ(ierr); 1366 /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */ 1367 ierr = PetscFree(mesh);CHKERRQ(ierr); 1368 PetscFunctionReturn(0); 1369 } 1370 1371 PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J) 1372 { 1373 PetscSection sectionGlobal; 1374 PetscInt bs = -1, mbs; 1375 PetscInt localSize; 1376 PetscBool isShell, isBlock, isSeqBlock, isMPIBlock, isSymBlock, isSymSeqBlock, isSymMPIBlock, isMatIS; 1377 PetscErrorCode ierr; 1378 MatType mtype; 1379 ISLocalToGlobalMapping ltog; 1380 1381 PetscFunctionBegin; 1382 ierr = MatInitializePackage();CHKERRQ(ierr); 1383 mtype = dm->mattype; 1384 ierr = DMGetGlobalSection(dm, §ionGlobal);CHKERRQ(ierr); 1385 /* ierr = PetscSectionGetStorageSize(sectionGlobal, &localSize);CHKERRQ(ierr); */ 1386 ierr = PetscSectionGetConstrainedStorageSize(sectionGlobal, &localSize);CHKERRQ(ierr); 1387 ierr = MatCreate(PetscObjectComm((PetscObject)dm), J);CHKERRQ(ierr); 1388 ierr = MatSetSizes(*J, localSize, localSize, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 1389 ierr = MatSetType(*J, mtype);CHKERRQ(ierr); 1390 ierr = MatSetFromOptions(*J);CHKERRQ(ierr); 1391 ierr = MatGetBlockSize(*J, &mbs);CHKERRQ(ierr); 1392 if (mbs > 1) bs = mbs; 1393 ierr = PetscStrcmp(mtype, MATSHELL, &isShell);CHKERRQ(ierr); 1394 ierr = PetscStrcmp(mtype, MATBAIJ, &isBlock);CHKERRQ(ierr); 1395 ierr = PetscStrcmp(mtype, MATSEQBAIJ, &isSeqBlock);CHKERRQ(ierr); 1396 ierr = PetscStrcmp(mtype, MATMPIBAIJ, &isMPIBlock);CHKERRQ(ierr); 1397 ierr = PetscStrcmp(mtype, MATSBAIJ, &isSymBlock);CHKERRQ(ierr); 1398 ierr = PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock);CHKERRQ(ierr); 1399 ierr = PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock);CHKERRQ(ierr); 1400 ierr = PetscStrcmp(mtype, MATIS, &isMatIS);CHKERRQ(ierr); 1401 if (!isShell) { 1402 PetscSection subSection; 1403 PetscBool fillMatrix = (PetscBool)(!dm->prealloc_only && !isMatIS); 1404 PetscInt *dnz, *onz, *dnzu, *onzu, bsLocal[2], bsMinMax[2], *ltogidx, lsize; 1405 PetscInt pStart, pEnd, p, dof, cdof; 1406 1407 /* Set localtoglobalmapping on the matrix for MatSetValuesLocal() to work (it also creates the local matrices in case of MATIS) */ 1408 if (isMatIS) { /* need a different l2g map than the one computed by DMGetLocalToGlobalMapping */ 1409 PetscSection section; 1410 PetscInt size; 1411 1412 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1413 ierr = PetscSectionGetStorageSize(section, &size);CHKERRQ(ierr); 1414 ierr = PetscMalloc1(size,<ogidx);CHKERRQ(ierr); 1415 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 1416 } else { 1417 ierr = DMGetLocalToGlobalMapping(dm,<og);CHKERRQ(ierr); 1418 } 1419 ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr); 1420 for (p = pStart, lsize = 0; p < pEnd; ++p) { 1421 PetscInt bdof; 1422 1423 ierr = PetscSectionGetDof(sectionGlobal, p, &dof);CHKERRQ(ierr); 1424 ierr = PetscSectionGetConstraintDof(sectionGlobal, p, &cdof);CHKERRQ(ierr); 1425 dof = dof < 0 ? -(dof+1) : dof; 1426 bdof = cdof && (dof-cdof) ? 1 : dof; 1427 if (dof) { 1428 if (bs < 0) {bs = bdof;} 1429 else if (bs != bdof) {bs = 1; if (!isMatIS) break;} 1430 } 1431 if (isMatIS) { 1432 PetscInt loff,c,off; 1433 ierr = PetscSectionGetOffset(subSection, p, &loff);CHKERRQ(ierr); 1434 ierr = PetscSectionGetOffset(sectionGlobal, p, &off);CHKERRQ(ierr); 1435 for (c = 0; c < dof-cdof; ++c, ++lsize) ltogidx[loff+c] = off > -1 ? off+c : -(off+1)+c; 1436 } 1437 } 1438 /* Must have same blocksize on all procs (some might have no points) */ 1439 bsLocal[0] = bs < 0 ? PETSC_MAX_INT : bs; bsLocal[1] = bs; 1440 ierr = PetscGlobalMinMaxInt(PetscObjectComm((PetscObject) dm), bsLocal, bsMinMax);CHKERRQ(ierr); 1441 if (bsMinMax[0] != bsMinMax[1]) {bs = 1;} 1442 else {bs = bsMinMax[0];} 1443 bs = PetscMax(1,bs); 1444 if (isMatIS) { /* Must reduce indices by blocksize */ 1445 PetscInt l; 1446 1447 lsize = lsize/bs; 1448 if (bs > 1) for (l = 0; l < lsize; ++l) ltogidx[l] = ltogidx[l*bs]/bs; 1449 ierr = ISLocalToGlobalMappingCreate(PetscObjectComm((PetscObject)dm), bs, lsize, ltogidx, PETSC_OWN_POINTER, <og);CHKERRQ(ierr); 1450 } 1451 ierr = MatSetLocalToGlobalMapping(*J,ltog,ltog);CHKERRQ(ierr); 1452 if (isMatIS) { 1453 ierr = ISLocalToGlobalMappingDestroy(<og);CHKERRQ(ierr); 1454 } 1455 ierr = PetscCalloc4(localSize/bs, &dnz, localSize/bs, &onz, localSize/bs, &dnzu, localSize/bs, &onzu);CHKERRQ(ierr); 1456 ierr = DMPlexPreallocateOperator(dm, bs, dnz, onz, dnzu, onzu, *J, fillMatrix);CHKERRQ(ierr); 1457 ierr = PetscFree4(dnz, onz, dnzu, onzu);CHKERRQ(ierr); 1458 } 1459 ierr = MatSetDM(*J, dm);CHKERRQ(ierr); 1460 PetscFunctionReturn(0); 1461 } 1462 1463 /*@ 1464 DMPlexGetSubdomainSection - Returns the section associated with the subdomain 1465 1466 Not collective 1467 1468 Input Parameter: 1469 . mesh - The DMPlex 1470 1471 Output Parameters: 1472 . subsection - The subdomain section 1473 1474 Level: developer 1475 1476 .seealso: 1477 @*/ 1478 PetscErrorCode DMPlexGetSubdomainSection(DM dm, PetscSection *subsection) 1479 { 1480 DM_Plex *mesh = (DM_Plex*) dm->data; 1481 PetscErrorCode ierr; 1482 1483 PetscFunctionBegin; 1484 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1485 if (!mesh->subdomainSection) { 1486 PetscSection section; 1487 PetscSF sf; 1488 1489 ierr = PetscSFCreate(PETSC_COMM_SELF,&sf);CHKERRQ(ierr); 1490 ierr = DMGetLocalSection(dm,§ion);CHKERRQ(ierr); 1491 ierr = PetscSectionCreateGlobalSection(section,sf,PETSC_FALSE,PETSC_TRUE,&mesh->subdomainSection);CHKERRQ(ierr); 1492 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1493 } 1494 *subsection = mesh->subdomainSection; 1495 PetscFunctionReturn(0); 1496 } 1497 1498 /*@ 1499 DMPlexGetChart - Return the interval for all mesh points [pStart, pEnd) 1500 1501 Not collective 1502 1503 Input Parameter: 1504 . mesh - The DMPlex 1505 1506 Output Parameters: 1507 + pStart - The first mesh point 1508 - pEnd - The upper bound for mesh points 1509 1510 Level: beginner 1511 1512 .seealso: DMPlexCreate(), DMPlexSetChart() 1513 @*/ 1514 PetscErrorCode DMPlexGetChart(DM dm, PetscInt *pStart, PetscInt *pEnd) 1515 { 1516 DM_Plex *mesh = (DM_Plex*) dm->data; 1517 PetscErrorCode ierr; 1518 1519 PetscFunctionBegin; 1520 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1521 ierr = PetscSectionGetChart(mesh->coneSection, pStart, pEnd);CHKERRQ(ierr); 1522 PetscFunctionReturn(0); 1523 } 1524 1525 /*@ 1526 DMPlexSetChart - Set the interval for all mesh points [pStart, pEnd) 1527 1528 Not collective 1529 1530 Input Parameters: 1531 + mesh - The DMPlex 1532 . pStart - The first mesh point 1533 - pEnd - The upper bound for mesh points 1534 1535 Output Parameters: 1536 1537 Level: beginner 1538 1539 .seealso: DMPlexCreate(), DMPlexGetChart() 1540 @*/ 1541 PetscErrorCode DMPlexSetChart(DM dm, PetscInt pStart, PetscInt pEnd) 1542 { 1543 DM_Plex *mesh = (DM_Plex*) dm->data; 1544 PetscErrorCode ierr; 1545 1546 PetscFunctionBegin; 1547 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1548 ierr = PetscSectionSetChart(mesh->coneSection, pStart, pEnd);CHKERRQ(ierr); 1549 ierr = PetscSectionSetChart(mesh->supportSection, pStart, pEnd);CHKERRQ(ierr); 1550 PetscFunctionReturn(0); 1551 } 1552 1553 /*@ 1554 DMPlexGetConeSize - Return the number of in-edges for this point in the DAG 1555 1556 Not collective 1557 1558 Input Parameters: 1559 + mesh - The DMPlex 1560 - p - The point, which must lie in the chart set with DMPlexSetChart() 1561 1562 Output Parameter: 1563 . size - The cone size for point p 1564 1565 Level: beginner 1566 1567 .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart() 1568 @*/ 1569 PetscErrorCode DMPlexGetConeSize(DM dm, PetscInt p, PetscInt *size) 1570 { 1571 DM_Plex *mesh = (DM_Plex*) dm->data; 1572 PetscErrorCode ierr; 1573 1574 PetscFunctionBegin; 1575 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1576 PetscValidPointer(size, 3); 1577 ierr = PetscSectionGetDof(mesh->coneSection, p, size);CHKERRQ(ierr); 1578 PetscFunctionReturn(0); 1579 } 1580 1581 /*@ 1582 DMPlexSetConeSize - Set the number of in-edges for this point in the DAG 1583 1584 Not collective 1585 1586 Input Parameters: 1587 + mesh - The DMPlex 1588 . p - The point, which must lie in the chart set with DMPlexSetChart() 1589 - size - The cone size for point p 1590 1591 Output Parameter: 1592 1593 Note: 1594 This should be called after DMPlexSetChart(). 1595 1596 Level: beginner 1597 1598 .seealso: DMPlexCreate(), DMPlexGetConeSize(), DMPlexSetChart() 1599 @*/ 1600 PetscErrorCode DMPlexSetConeSize(DM dm, PetscInt p, PetscInt size) 1601 { 1602 DM_Plex *mesh = (DM_Plex*) dm->data; 1603 PetscErrorCode ierr; 1604 1605 PetscFunctionBegin; 1606 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1607 ierr = PetscSectionSetDof(mesh->coneSection, p, size);CHKERRQ(ierr); 1608 1609 mesh->maxConeSize = PetscMax(mesh->maxConeSize, size); 1610 PetscFunctionReturn(0); 1611 } 1612 1613 /*@ 1614 DMPlexAddConeSize - Add the given number of in-edges to this point in the DAG 1615 1616 Not collective 1617 1618 Input Parameters: 1619 + mesh - The DMPlex 1620 . p - The point, which must lie in the chart set with DMPlexSetChart() 1621 - size - The additional cone size for point p 1622 1623 Output Parameter: 1624 1625 Note: 1626 This should be called after DMPlexSetChart(). 1627 1628 Level: beginner 1629 1630 .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexGetConeSize(), DMPlexSetChart() 1631 @*/ 1632 PetscErrorCode DMPlexAddConeSize(DM dm, PetscInt p, PetscInt size) 1633 { 1634 DM_Plex *mesh = (DM_Plex*) dm->data; 1635 PetscInt csize; 1636 PetscErrorCode ierr; 1637 1638 PetscFunctionBegin; 1639 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1640 ierr = PetscSectionAddDof(mesh->coneSection, p, size);CHKERRQ(ierr); 1641 ierr = PetscSectionGetDof(mesh->coneSection, p, &csize);CHKERRQ(ierr); 1642 1643 mesh->maxConeSize = PetscMax(mesh->maxConeSize, csize); 1644 PetscFunctionReturn(0); 1645 } 1646 1647 /*@C 1648 DMPlexGetCone - Return the points on the in-edges for this point in the DAG 1649 1650 Not collective 1651 1652 Input Parameters: 1653 + dm - The DMPlex 1654 - p - The point, which must lie in the chart set with DMPlexSetChart() 1655 1656 Output Parameter: 1657 . cone - An array of points which are on the in-edges for point p 1658 1659 Level: beginner 1660 1661 Fortran Notes: 1662 Since it returns an array, this routine is only available in Fortran 90, and you must 1663 include petsc.h90 in your code. 1664 You must also call DMPlexRestoreCone() after you finish using the returned array. 1665 DMPlexRestoreCone() is not needed/available in C. 1666 1667 .seealso: DMPlexCreate(), DMPlexSetCone(), DMPlexGetConeTuple(), DMPlexSetChart() 1668 @*/ 1669 PetscErrorCode DMPlexGetCone(DM dm, PetscInt p, const PetscInt *cone[]) 1670 { 1671 DM_Plex *mesh = (DM_Plex*) dm->data; 1672 PetscInt off; 1673 PetscErrorCode ierr; 1674 1675 PetscFunctionBegin; 1676 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1677 PetscValidPointer(cone, 3); 1678 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 1679 *cone = &mesh->cones[off]; 1680 PetscFunctionReturn(0); 1681 } 1682 1683 /*@C 1684 DMPlexGetConeTuple - Return the points on the in-edges of several points in the DAG 1685 1686 Not collective 1687 1688 Input Parameters: 1689 + dm - The DMPlex 1690 - p - The IS of points, which must lie in the chart set with DMPlexSetChart() 1691 1692 Output Parameter: 1693 + pConesSection - PetscSection describing the layout of pCones 1694 - pCones - An array of points which are on the in-edges for the point set p 1695 1696 Level: intermediate 1697 1698 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeRecursive(), DMPlexSetChart() 1699 @*/ 1700 PetscErrorCode DMPlexGetConeTuple(DM dm, IS p, PetscSection *pConesSection, IS *pCones) 1701 { 1702 PetscSection cs, newcs; 1703 PetscInt *cones; 1704 PetscInt *newarr=NULL; 1705 PetscInt n; 1706 PetscErrorCode ierr; 1707 1708 PetscFunctionBegin; 1709 ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr); 1710 ierr = DMPlexGetConeSection(dm, &cs);CHKERRQ(ierr); 1711 ierr = PetscSectionExtractDofsFromArray(cs, MPIU_INT, cones, p, &newcs, pCones ? ((void**)&newarr) : NULL);CHKERRQ(ierr); 1712 if (pConesSection) *pConesSection = newcs; 1713 if (pCones) { 1714 ierr = PetscSectionGetStorageSize(newcs, &n);CHKERRQ(ierr); 1715 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)p), n, newarr, PETSC_OWN_POINTER, pCones);CHKERRQ(ierr); 1716 } 1717 PetscFunctionReturn(0); 1718 } 1719 1720 /*@ 1721 DMPlexGetConeRecursiveVertices - Expand each given point into its cone points and do that recursively until we end up just with vertices. 1722 1723 Not collective 1724 1725 Input Parameters: 1726 + dm - The DMPlex 1727 - points - The IS of points, which must lie in the chart set with DMPlexSetChart() 1728 1729 Output Parameter: 1730 . expandedPoints - An array of vertices recursively expanded from input points 1731 1732 Level: advanced 1733 1734 Notes: 1735 Like DMPlexGetConeRecursive but returns only the 0-depth IS (i.e. vertices only) and no sections. 1736 There is no corresponding Restore function, just call ISDestroy() on the returned IS to deallocate. 1737 1738 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeTuple(), DMPlexGetConeRecursive(), DMPlexRestoreConeRecursive(), DMPlexGetDepth() 1739 @*/ 1740 PetscErrorCode DMPlexGetConeRecursiveVertices(DM dm, IS points, IS *expandedPoints) 1741 { 1742 IS *expandedPointsAll; 1743 PetscInt depth; 1744 PetscErrorCode ierr; 1745 1746 PetscFunctionBegin; 1747 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1748 PetscValidHeaderSpecific(points, IS_CLASSID, 2); 1749 PetscValidPointer(expandedPoints, 3); 1750 ierr = DMPlexGetConeRecursive(dm, points, &depth, &expandedPointsAll, NULL);CHKERRQ(ierr); 1751 *expandedPoints = expandedPointsAll[0]; 1752 ierr = PetscObjectReference((PetscObject)expandedPointsAll[0]); 1753 ierr = DMPlexRestoreConeRecursive(dm, points, &depth, &expandedPointsAll, NULL);CHKERRQ(ierr); 1754 PetscFunctionReturn(0); 1755 } 1756 1757 /*@ 1758 DMPlexGetConeRecursive - Expand each given point into its cone points and do that recursively until we end up just with vertices (DAG points of depth 0, i.e. without cones). 1759 1760 Not collective 1761 1762 Input Parameters: 1763 + dm - The DMPlex 1764 - points - The IS of points, which must lie in the chart set with DMPlexSetChart() 1765 1766 Output Parameter: 1767 + depth - (optional) Size of the output arrays, equal to DMPlex depth, returned by DMPlexGetDepth() 1768 . expandedPoints - (optional) An array of index sets with recursively expanded cones 1769 - sections - (optional) An array of sections which describe mappings from points to their cone points 1770 1771 Level: advanced 1772 1773 Notes: 1774 Like DMPlexGetConeTuple() but recursive. 1775 1776 Array expandedPoints has size equal to depth. Each expandedPoints[d] contains DAG points with maximum depth d, recursively cone-wise expanded from the input points. 1777 For example, for d=0 it contains only vertices, for d=1 it can contain vertices and edges, etc. 1778 1779 Array section has size equal to depth. Each PetscSection sections[d] realizes mapping from expandedPoints[d+1] (section points) to expandedPoints[d] (section dofs) as follows: 1780 (1) DAG points in expandedPoints[d+1] with depth d+1 to their cone points in expandedPoints[d]; 1781 (2) DAG points in expandedPoints[d+1] with depth in [0,d] to the same points in expandedPoints[d]. 1782 1783 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeTuple(), DMPlexRestoreConeRecursive(), DMPlexGetConeRecursiveVertices(), DMPlexGetDepth() 1784 @*/ 1785 PetscErrorCode DMPlexGetConeRecursive(DM dm, IS points, PetscInt *depth, IS *expandedPoints[], PetscSection *sections[]) 1786 { 1787 const PetscInt *arr0=NULL, *cone=NULL; 1788 PetscInt *arr=NULL, *newarr=NULL; 1789 PetscInt d, depth_, i, n, newn, cn, co, start, end; 1790 IS *expandedPoints_; 1791 PetscSection *sections_; 1792 PetscErrorCode ierr; 1793 1794 PetscFunctionBegin; 1795 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1796 PetscValidHeaderSpecific(points, IS_CLASSID, 2); 1797 if (depth) PetscValidIntPointer(depth, 3); 1798 if (expandedPoints) PetscValidPointer(expandedPoints, 4); 1799 if (sections) PetscValidPointer(sections, 5); 1800 ierr = ISGetLocalSize(points, &n);CHKERRQ(ierr); 1801 ierr = ISGetIndices(points, &arr0);CHKERRQ(ierr); 1802 ierr = DMPlexGetDepth(dm, &depth_);CHKERRQ(ierr); 1803 ierr = PetscCalloc1(depth_, &expandedPoints_);CHKERRQ(ierr); 1804 ierr = PetscCalloc1(depth_, §ions_);CHKERRQ(ierr); 1805 arr = (PetscInt*) arr0; /* this is ok because first generation of arr is not modified */ 1806 for (d=depth_-1; d>=0; d--) { 1807 ierr = PetscSectionCreate(PETSC_COMM_SELF, §ions_[d]);CHKERRQ(ierr); 1808 ierr = PetscSectionSetChart(sections_[d], 0, n);CHKERRQ(ierr); 1809 for (i=0; i<n; i++) { 1810 ierr = DMPlexGetDepthStratum(dm, d+1, &start, &end);CHKERRQ(ierr); 1811 if (arr[i] >= start && arr[i] < end) { 1812 ierr = DMPlexGetConeSize(dm, arr[i], &cn);CHKERRQ(ierr); 1813 ierr = PetscSectionSetDof(sections_[d], i, cn);CHKERRQ(ierr); 1814 } else { 1815 ierr = PetscSectionSetDof(sections_[d], i, 1);CHKERRQ(ierr); 1816 } 1817 } 1818 ierr = PetscSectionSetUp(sections_[d]);CHKERRQ(ierr); 1819 ierr = PetscSectionGetStorageSize(sections_[d], &newn);CHKERRQ(ierr); 1820 ierr = PetscMalloc1(newn, &newarr);CHKERRQ(ierr); 1821 for (i=0; i<n; i++) { 1822 ierr = PetscSectionGetDof(sections_[d], i, &cn);CHKERRQ(ierr); 1823 ierr = PetscSectionGetOffset(sections_[d], i, &co);CHKERRQ(ierr); 1824 if (cn > 1) { 1825 ierr = DMPlexGetCone(dm, arr[i], &cone);CHKERRQ(ierr); 1826 ierr = PetscMemcpy(&newarr[co], cone, cn*sizeof(PetscInt));CHKERRQ(ierr); 1827 } else { 1828 newarr[co] = arr[i]; 1829 } 1830 } 1831 ierr = ISCreateGeneral(PETSC_COMM_SELF, newn, newarr, PETSC_OWN_POINTER, &expandedPoints_[d]);CHKERRQ(ierr); 1832 arr = newarr; 1833 n = newn; 1834 } 1835 *depth = depth_; 1836 if (expandedPoints) *expandedPoints = expandedPoints_; 1837 else { 1838 for (d=0; d<depth_; d++) {ierr = ISDestroy(&expandedPoints_[d]);CHKERRQ(ierr);} 1839 ierr = PetscFree(expandedPoints_);CHKERRQ(ierr); 1840 } 1841 if (sections) *sections = sections_; 1842 else { 1843 for (d=0; d<depth_; d++) {ierr = PetscSectionDestroy(§ions_[d]);CHKERRQ(ierr);} 1844 ierr = PetscFree(sections_);CHKERRQ(ierr); 1845 } 1846 PetscFunctionReturn(0); 1847 } 1848 1849 /*@ 1850 DMPlexRestoreConeRecursive - Deallocates arrays created by DMPlexGetConeRecursive 1851 1852 Not collective 1853 1854 Input Parameters: 1855 + dm - The DMPlex 1856 - points - The IS of points, which must lie in the chart set with DMPlexSetChart() 1857 1858 Output Parameter: 1859 + depth - (optional) Size of the output arrays, equal to DMPlex depth, returned by DMPlexGetDepth() 1860 . expandedPoints - (optional) An array of recursively expanded cones 1861 - sections - (optional) An array of sections which describe mappings from points to their cone points 1862 1863 Level: advanced 1864 1865 Notes: 1866 See DMPlexGetConeRecursive() for details. 1867 1868 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexGetConeTuple(), DMPlexGetConeRecursive(), DMPlexGetConeRecursiveVertices(), DMPlexGetDepth() 1869 @*/ 1870 PetscErrorCode DMPlexRestoreConeRecursive(DM dm, IS points, PetscInt *depth, IS *expandedPoints[], PetscSection *sections[]) 1871 { 1872 PetscInt d, depth_; 1873 PetscErrorCode ierr; 1874 1875 PetscFunctionBegin; 1876 ierr = DMPlexGetDepth(dm, &depth_);CHKERRQ(ierr); 1877 if (depth && *depth != depth_) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "depth changed since last call to DMPlexGetConeRecursive"); 1878 if (depth) *depth = 0; 1879 if (expandedPoints) { 1880 for (d=0; d<depth_; d++) {ierr = ISDestroy(&((*expandedPoints)[d]));CHKERRQ(ierr);} 1881 ierr = PetscFree(*expandedPoints);CHKERRQ(ierr); 1882 } 1883 if (sections) { 1884 for (d=0; d<depth_; d++) {ierr = PetscSectionDestroy(&((*sections)[d]));CHKERRQ(ierr);} 1885 ierr = PetscFree(*sections);CHKERRQ(ierr); 1886 } 1887 PetscFunctionReturn(0); 1888 } 1889 1890 /*@ 1891 DMPlexSetCone - Set the points on the in-edges for this point in the DAG; that is these are the points that cover the specific point 1892 1893 Not collective 1894 1895 Input Parameters: 1896 + mesh - The DMPlex 1897 . p - The point, which must lie in the chart set with DMPlexSetChart() 1898 - cone - An array of points which are on the in-edges for point p 1899 1900 Output Parameter: 1901 1902 Note: 1903 This should be called after all calls to DMPlexSetConeSize() and DMSetUp(). 1904 1905 Developer Note: Why not call this DMPlexSetCover() 1906 1907 Level: beginner 1908 1909 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp(), DMPlexSetSupport(), DMPlexSetSupportSize() 1910 @*/ 1911 PetscErrorCode DMPlexSetCone(DM dm, PetscInt p, const PetscInt cone[]) 1912 { 1913 DM_Plex *mesh = (DM_Plex*) dm->data; 1914 PetscInt pStart, pEnd; 1915 PetscInt dof, off, c; 1916 PetscErrorCode ierr; 1917 1918 PetscFunctionBegin; 1919 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1920 ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 1921 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 1922 if (dof) PetscValidPointer(cone, 3); 1923 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 1924 if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); 1925 for (c = 0; c < dof; ++c) { 1926 if ((cone[c] < pStart) || (cone[c] >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone point %D is not in the valid range [%D, %D)", cone[c], pStart, pEnd); 1927 mesh->cones[off+c] = cone[c]; 1928 } 1929 PetscFunctionReturn(0); 1930 } 1931 1932 /*@C 1933 DMPlexGetConeOrientation - Return the orientations on the in-edges for this point in the DAG 1934 1935 Not collective 1936 1937 Input Parameters: 1938 + mesh - The DMPlex 1939 - p - The point, which must lie in the chart set with DMPlexSetChart() 1940 1941 Output Parameter: 1942 . coneOrientation - An array of orientations which are on the in-edges for point p. An orientation is an 1943 integer giving the prescription for cone traversal. If it is negative, the cone is 1944 traversed in the opposite direction. Its value 'o', or if negative '-(o+1)', gives 1945 the index of the cone point on which to start. 1946 1947 Level: beginner 1948 1949 Fortran Notes: 1950 Since it returns an array, this routine is only available in Fortran 90, and you must 1951 include petsc.h90 in your code. 1952 You must also call DMPlexRestoreConeOrientation() after you finish using the returned array. 1953 DMPlexRestoreConeOrientation() is not needed/available in C. 1954 1955 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetCone(), DMPlexSetChart() 1956 @*/ 1957 PetscErrorCode DMPlexGetConeOrientation(DM dm, PetscInt p, const PetscInt *coneOrientation[]) 1958 { 1959 DM_Plex *mesh = (DM_Plex*) dm->data; 1960 PetscInt off; 1961 PetscErrorCode ierr; 1962 1963 PetscFunctionBegin; 1964 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1965 #if defined(PETSC_USE_DEBUG) 1966 { 1967 PetscInt dof; 1968 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 1969 if (dof) PetscValidPointer(coneOrientation, 3); 1970 } 1971 #endif 1972 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 1973 1974 *coneOrientation = &mesh->coneOrientations[off]; 1975 PetscFunctionReturn(0); 1976 } 1977 1978 /*@ 1979 DMPlexSetConeOrientation - Set the orientations on the in-edges for this point in the DAG 1980 1981 Not collective 1982 1983 Input Parameters: 1984 + mesh - The DMPlex 1985 . p - The point, which must lie in the chart set with DMPlexSetChart() 1986 - coneOrientation - An array of orientations which are on the in-edges for point p. An orientation is an 1987 integer giving the prescription for cone traversal. If it is negative, the cone is 1988 traversed in the opposite direction. Its value 'o', or if negative '-(o+1)', gives 1989 the index of the cone point on which to start. 1990 1991 Output Parameter: 1992 1993 Note: 1994 This should be called after all calls to DMPlexSetConeSize() and DMSetUp(). 1995 1996 Level: beginner 1997 1998 .seealso: DMPlexCreate(), DMPlexGetConeOrientation(), DMPlexSetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() 1999 @*/ 2000 PetscErrorCode DMPlexSetConeOrientation(DM dm, PetscInt p, const PetscInt coneOrientation[]) 2001 { 2002 DM_Plex *mesh = (DM_Plex*) dm->data; 2003 PetscInt pStart, pEnd; 2004 PetscInt dof, off, c; 2005 PetscErrorCode ierr; 2006 2007 PetscFunctionBegin; 2008 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2009 ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 2010 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 2011 if (dof) PetscValidPointer(coneOrientation, 3); 2012 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 2013 if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); 2014 for (c = 0; c < dof; ++c) { 2015 PetscInt cdof, o = coneOrientation[c]; 2016 2017 ierr = PetscSectionGetDof(mesh->coneSection, mesh->cones[off+c], &cdof);CHKERRQ(ierr); 2018 if (o && ((o < -(cdof+1)) || (o >= cdof))) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone orientation %D is not in the valid range [%D. %D)", o, -(cdof+1), cdof); 2019 mesh->coneOrientations[off+c] = o; 2020 } 2021 PetscFunctionReturn(0); 2022 } 2023 2024 /*@ 2025 DMPlexInsertCone - Insert a point into the in-edges for the point p in the DAG 2026 2027 Not collective 2028 2029 Input Parameters: 2030 + mesh - The DMPlex 2031 . p - The point, which must lie in the chart set with DMPlexSetChart() 2032 . conePos - The local index in the cone where the point should be put 2033 - conePoint - The mesh point to insert 2034 2035 Level: beginner 2036 2037 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() 2038 @*/ 2039 PetscErrorCode DMPlexInsertCone(DM dm, PetscInt p, PetscInt conePos, PetscInt conePoint) 2040 { 2041 DM_Plex *mesh = (DM_Plex*) dm->data; 2042 PetscInt pStart, pEnd; 2043 PetscInt dof, off; 2044 PetscErrorCode ierr; 2045 2046 PetscFunctionBegin; 2047 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2048 ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 2049 if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); 2050 if ((conePoint < pStart) || (conePoint >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone point %D is not in the valid range [%D, %D)", conePoint, pStart, pEnd); 2051 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 2052 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 2053 if ((conePos < 0) || (conePos >= dof)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone position %D of point %D is not in the valid range [0, %D)", conePos, p, dof); 2054 mesh->cones[off+conePos] = conePoint; 2055 PetscFunctionReturn(0); 2056 } 2057 2058 /*@ 2059 DMPlexInsertConeOrientation - Insert a point orientation for the in-edge for the point p in the DAG 2060 2061 Not collective 2062 2063 Input Parameters: 2064 + mesh - The DMPlex 2065 . p - The point, which must lie in the chart set with DMPlexSetChart() 2066 . conePos - The local index in the cone where the point should be put 2067 - coneOrientation - The point orientation to insert 2068 2069 Level: beginner 2070 2071 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() 2072 @*/ 2073 PetscErrorCode DMPlexInsertConeOrientation(DM dm, PetscInt p, PetscInt conePos, PetscInt coneOrientation) 2074 { 2075 DM_Plex *mesh = (DM_Plex*) dm->data; 2076 PetscInt pStart, pEnd; 2077 PetscInt dof, off; 2078 PetscErrorCode ierr; 2079 2080 PetscFunctionBegin; 2081 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2082 ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 2083 if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); 2084 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 2085 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 2086 if ((conePos < 0) || (conePos >= dof)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Cone position %D of point %D is not in the valid range [0, %D)", conePos, p, dof); 2087 mesh->coneOrientations[off+conePos] = coneOrientation; 2088 PetscFunctionReturn(0); 2089 } 2090 2091 /*@ 2092 DMPlexGetSupportSize - Return the number of out-edges for this point in the DAG 2093 2094 Not collective 2095 2096 Input Parameters: 2097 + mesh - The DMPlex 2098 - p - The point, which must lie in the chart set with DMPlexSetChart() 2099 2100 Output Parameter: 2101 . size - The support size for point p 2102 2103 Level: beginner 2104 2105 .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart(), DMPlexGetConeSize() 2106 @*/ 2107 PetscErrorCode DMPlexGetSupportSize(DM dm, PetscInt p, PetscInt *size) 2108 { 2109 DM_Plex *mesh = (DM_Plex*) dm->data; 2110 PetscErrorCode ierr; 2111 2112 PetscFunctionBegin; 2113 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2114 PetscValidPointer(size, 3); 2115 ierr = PetscSectionGetDof(mesh->supportSection, p, size);CHKERRQ(ierr); 2116 PetscFunctionReturn(0); 2117 } 2118 2119 /*@ 2120 DMPlexSetSupportSize - Set the number of out-edges for this point in the DAG 2121 2122 Not collective 2123 2124 Input Parameters: 2125 + mesh - The DMPlex 2126 . p - The point, which must lie in the chart set with DMPlexSetChart() 2127 - size - The support size for point p 2128 2129 Output Parameter: 2130 2131 Note: 2132 This should be called after DMPlexSetChart(). 2133 2134 Level: beginner 2135 2136 .seealso: DMPlexCreate(), DMPlexGetSupportSize(), DMPlexSetChart() 2137 @*/ 2138 PetscErrorCode DMPlexSetSupportSize(DM dm, PetscInt p, PetscInt size) 2139 { 2140 DM_Plex *mesh = (DM_Plex*) dm->data; 2141 PetscErrorCode ierr; 2142 2143 PetscFunctionBegin; 2144 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2145 ierr = PetscSectionSetDof(mesh->supportSection, p, size);CHKERRQ(ierr); 2146 2147 mesh->maxSupportSize = PetscMax(mesh->maxSupportSize, size); 2148 PetscFunctionReturn(0); 2149 } 2150 2151 /*@C 2152 DMPlexGetSupport - Return the points on the out-edges for this point in the DAG 2153 2154 Not collective 2155 2156 Input Parameters: 2157 + mesh - The DMPlex 2158 - p - The point, which must lie in the chart set with DMPlexSetChart() 2159 2160 Output Parameter: 2161 . support - An array of points which are on the out-edges for point p 2162 2163 Level: beginner 2164 2165 Fortran Notes: 2166 Since it returns an array, this routine is only available in Fortran 90, and you must 2167 include petsc.h90 in your code. 2168 You must also call DMPlexRestoreSupport() after you finish using the returned array. 2169 DMPlexRestoreSupport() is not needed/available in C. 2170 2171 .seealso: DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() 2172 @*/ 2173 PetscErrorCode DMPlexGetSupport(DM dm, PetscInt p, const PetscInt *support[]) 2174 { 2175 DM_Plex *mesh = (DM_Plex*) dm->data; 2176 PetscInt off; 2177 PetscErrorCode ierr; 2178 2179 PetscFunctionBegin; 2180 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2181 PetscValidPointer(support, 3); 2182 ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); 2183 *support = &mesh->supports[off]; 2184 PetscFunctionReturn(0); 2185 } 2186 2187 /*@ 2188 DMPlexSetSupport - Set the points on the out-edges for this point in the DAG, that is the list of points that this point covers 2189 2190 Not collective 2191 2192 Input Parameters: 2193 + mesh - The DMPlex 2194 . p - The point, which must lie in the chart set with DMPlexSetChart() 2195 - support - An array of points which are on the out-edges for point p 2196 2197 Output Parameter: 2198 2199 Note: 2200 This should be called after all calls to DMPlexSetSupportSize() and DMSetUp(). 2201 2202 Level: beginner 2203 2204 .seealso: DMPlexSetCone(), DMPlexSetConeSize(), DMPlexCreate(), DMPlexGetSupport(), DMPlexSetChart(), DMPlexSetSupportSize(), DMSetUp() 2205 @*/ 2206 PetscErrorCode DMPlexSetSupport(DM dm, PetscInt p, const PetscInt support[]) 2207 { 2208 DM_Plex *mesh = (DM_Plex*) dm->data; 2209 PetscInt pStart, pEnd; 2210 PetscInt dof, off, c; 2211 PetscErrorCode ierr; 2212 2213 PetscFunctionBegin; 2214 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2215 ierr = PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd);CHKERRQ(ierr); 2216 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 2217 if (dof) PetscValidPointer(support, 3); 2218 ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); 2219 if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); 2220 for (c = 0; c < dof; ++c) { 2221 if ((support[c] < pStart) || (support[c] >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Support point %D is not in the valid range [%D, %D)", support[c], pStart, pEnd); 2222 mesh->supports[off+c] = support[c]; 2223 } 2224 PetscFunctionReturn(0); 2225 } 2226 2227 /*@ 2228 DMPlexInsertSupport - Insert a point into the out-edges for the point p in the DAG 2229 2230 Not collective 2231 2232 Input Parameters: 2233 + mesh - The DMPlex 2234 . p - The point, which must lie in the chart set with DMPlexSetChart() 2235 . supportPos - The local index in the cone where the point should be put 2236 - supportPoint - The mesh point to insert 2237 2238 Level: beginner 2239 2240 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() 2241 @*/ 2242 PetscErrorCode DMPlexInsertSupport(DM dm, PetscInt p, PetscInt supportPos, PetscInt supportPoint) 2243 { 2244 DM_Plex *mesh = (DM_Plex*) dm->data; 2245 PetscInt pStart, pEnd; 2246 PetscInt dof, off; 2247 PetscErrorCode ierr; 2248 2249 PetscFunctionBegin; 2250 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2251 ierr = PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd);CHKERRQ(ierr); 2252 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 2253 ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); 2254 if ((p < pStart) || (p >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D is not in the valid range [%D, %D)", p, pStart, pEnd); 2255 if ((supportPoint < pStart) || (supportPoint >= pEnd)) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Support point %D is not in the valid range [%D, %D)", supportPoint, pStart, pEnd); 2256 if (supportPos >= dof) SETERRQ3(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Support position %D of point %D is not in the valid range [0, %D)", supportPos, p, dof); 2257 mesh->supports[off+supportPos] = supportPoint; 2258 PetscFunctionReturn(0); 2259 } 2260 2261 /*@C 2262 DMPlexGetTransitiveClosure - Return the points on the transitive closure of the in-edges or out-edges for this point in the DAG 2263 2264 Not collective 2265 2266 Input Parameters: 2267 + mesh - The DMPlex 2268 . p - The point, which must lie in the chart set with DMPlexSetChart() 2269 . useCone - PETSC_TRUE for in-edges, otherwise use out-edges 2270 - points - If points is NULL on input, internal storage will be returned, otherwise the provided array is used 2271 2272 Output Parameters: 2273 + numPoints - The number of points in the closure, so points[] is of size 2*numPoints 2274 - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...] 2275 2276 Note: 2277 If using internal storage (points is NULL on input), each call overwrites the last output. 2278 2279 Fortran Notes: 2280 Since it returns an array, this routine is only available in Fortran 90, and you must 2281 include petsc.h90 in your code. 2282 2283 The numPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2284 2285 Level: beginner 2286 2287 .seealso: DMPlexRestoreTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() 2288 @*/ 2289 PetscErrorCode DMPlexGetTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 2290 { 2291 DM_Plex *mesh = (DM_Plex*) dm->data; 2292 PetscInt *closure, *fifo; 2293 const PetscInt *tmp = NULL, *tmpO = NULL; 2294 PetscInt tmpSize, t; 2295 PetscInt depth = 0, maxSize; 2296 PetscInt closureSize = 2, fifoSize = 0, fifoStart = 0; 2297 PetscErrorCode ierr; 2298 2299 PetscFunctionBegin; 2300 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2301 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2302 /* This is only 1-level */ 2303 if (useCone) { 2304 ierr = DMPlexGetConeSize(dm, p, &tmpSize);CHKERRQ(ierr); 2305 ierr = DMPlexGetCone(dm, p, &tmp);CHKERRQ(ierr); 2306 ierr = DMPlexGetConeOrientation(dm, p, &tmpO);CHKERRQ(ierr); 2307 } else { 2308 ierr = DMPlexGetSupportSize(dm, p, &tmpSize);CHKERRQ(ierr); 2309 ierr = DMPlexGetSupport(dm, p, &tmp);CHKERRQ(ierr); 2310 } 2311 if (depth == 1) { 2312 if (*points) { 2313 closure = *points; 2314 } else { 2315 maxSize = 2*(PetscMax(mesh->maxConeSize, mesh->maxSupportSize)+1); 2316 ierr = DMGetWorkArray(dm, maxSize, MPIU_INT, &closure);CHKERRQ(ierr); 2317 } 2318 closure[0] = p; closure[1] = 0; 2319 for (t = 0; t < tmpSize; ++t, closureSize += 2) { 2320 closure[closureSize] = tmp[t]; 2321 closure[closureSize+1] = tmpO ? tmpO[t] : 0; 2322 } 2323 if (numPoints) *numPoints = closureSize/2; 2324 if (points) *points = closure; 2325 PetscFunctionReturn(0); 2326 } 2327 { 2328 PetscInt c, coneSeries, s,supportSeries; 2329 2330 c = mesh->maxConeSize; 2331 coneSeries = (c > 1) ? ((PetscPowInt(c,depth+1)-1)/(c-1)) : depth+1; 2332 s = mesh->maxSupportSize; 2333 supportSeries = (s > 1) ? ((PetscPowInt(s,depth+1)-1)/(s-1)) : depth+1; 2334 maxSize = 2*PetscMax(coneSeries,supportSeries); 2335 } 2336 ierr = DMGetWorkArray(dm, maxSize, MPIU_INT, &fifo);CHKERRQ(ierr); 2337 if (*points) { 2338 closure = *points; 2339 } else { 2340 ierr = DMGetWorkArray(dm, maxSize, MPIU_INT, &closure);CHKERRQ(ierr); 2341 } 2342 closure[0] = p; closure[1] = 0; 2343 for (t = 0; t < tmpSize; ++t, closureSize += 2, fifoSize += 2) { 2344 const PetscInt cp = tmp[t]; 2345 const PetscInt co = tmpO ? tmpO[t] : 0; 2346 2347 closure[closureSize] = cp; 2348 closure[closureSize+1] = co; 2349 fifo[fifoSize] = cp; 2350 fifo[fifoSize+1] = co; 2351 } 2352 /* Should kick out early when depth is reached, rather than checking all vertices for empty cones */ 2353 while (fifoSize - fifoStart) { 2354 const PetscInt q = fifo[fifoStart]; 2355 const PetscInt o = fifo[fifoStart+1]; 2356 const PetscInt rev = o >= 0 ? 0 : 1; 2357 const PetscInt off = rev ? -(o+1) : o; 2358 2359 if (useCone) { 2360 ierr = DMPlexGetConeSize(dm, q, &tmpSize);CHKERRQ(ierr); 2361 ierr = DMPlexGetCone(dm, q, &tmp);CHKERRQ(ierr); 2362 ierr = DMPlexGetConeOrientation(dm, q, &tmpO);CHKERRQ(ierr); 2363 } else { 2364 ierr = DMPlexGetSupportSize(dm, q, &tmpSize);CHKERRQ(ierr); 2365 ierr = DMPlexGetSupport(dm, q, &tmp);CHKERRQ(ierr); 2366 tmpO = NULL; 2367 } 2368 for (t = 0; t < tmpSize; ++t) { 2369 const PetscInt i = ((rev ? tmpSize-t : t) + off)%tmpSize; 2370 const PetscInt cp = tmp[i]; 2371 /* Must propogate orientation: When we reverse orientation, we both reverse the direction of iteration and start at the other end of the chain. */ 2372 /* HACK: It is worse to get the size here, than to change the interpretation of -(*+1) 2373 const PetscInt co = tmpO ? (rev ? -(tmpO[i]+1) : tmpO[i]) : 0; */ 2374 PetscInt co = tmpO ? tmpO[i] : 0; 2375 PetscInt c; 2376 2377 if (rev) { 2378 PetscInt childSize, coff; 2379 ierr = DMPlexGetConeSize(dm, cp, &childSize);CHKERRQ(ierr); 2380 coff = tmpO[i] < 0 ? -(tmpO[i]+1) : tmpO[i]; 2381 co = childSize ? -(((coff+childSize-1)%childSize)+1) : 0; 2382 } 2383 /* Check for duplicate */ 2384 for (c = 0; c < closureSize; c += 2) { 2385 if (closure[c] == cp) break; 2386 } 2387 if (c == closureSize) { 2388 closure[closureSize] = cp; 2389 closure[closureSize+1] = co; 2390 fifo[fifoSize] = cp; 2391 fifo[fifoSize+1] = co; 2392 closureSize += 2; 2393 fifoSize += 2; 2394 } 2395 } 2396 fifoStart += 2; 2397 } 2398 if (numPoints) *numPoints = closureSize/2; 2399 if (points) *points = closure; 2400 ierr = DMRestoreWorkArray(dm, maxSize, MPIU_INT, &fifo);CHKERRQ(ierr); 2401 PetscFunctionReturn(0); 2402 } 2403 2404 /*@C 2405 DMPlexGetTransitiveClosure_Internal - Return the points on the transitive closure of the in-edges or out-edges for this point in the DAG with a specified initial orientation 2406 2407 Not collective 2408 2409 Input Parameters: 2410 + mesh - The DMPlex 2411 . p - The point, which must lie in the chart set with DMPlexSetChart() 2412 . orientation - The orientation of the point 2413 . useCone - PETSC_TRUE for in-edges, otherwise use out-edges 2414 - points - If points is NULL on input, internal storage will be returned, otherwise the provided array is used 2415 2416 Output Parameters: 2417 + numPoints - The number of points in the closure, so points[] is of size 2*numPoints 2418 - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...] 2419 2420 Note: 2421 If using internal storage (points is NULL on input), each call overwrites the last output. 2422 2423 Fortran Notes: 2424 Since it returns an array, this routine is only available in Fortran 90, and you must 2425 include petsc.h90 in your code. 2426 2427 The numPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2428 2429 Level: beginner 2430 2431 .seealso: DMPlexRestoreTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() 2432 @*/ 2433 PetscErrorCode DMPlexGetTransitiveClosure_Internal(DM dm, PetscInt p, PetscInt ornt, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 2434 { 2435 DM_Plex *mesh = (DM_Plex*) dm->data; 2436 PetscInt *closure, *fifo; 2437 const PetscInt *tmp = NULL, *tmpO = NULL; 2438 PetscInt tmpSize, t; 2439 PetscInt depth = 0, maxSize; 2440 PetscInt closureSize = 2, fifoSize = 0, fifoStart = 0; 2441 PetscErrorCode ierr; 2442 2443 PetscFunctionBegin; 2444 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2445 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2446 /* This is only 1-level */ 2447 if (useCone) { 2448 ierr = DMPlexGetConeSize(dm, p, &tmpSize);CHKERRQ(ierr); 2449 ierr = DMPlexGetCone(dm, p, &tmp);CHKERRQ(ierr); 2450 ierr = DMPlexGetConeOrientation(dm, p, &tmpO);CHKERRQ(ierr); 2451 } else { 2452 ierr = DMPlexGetSupportSize(dm, p, &tmpSize);CHKERRQ(ierr); 2453 ierr = DMPlexGetSupport(dm, p, &tmp);CHKERRQ(ierr); 2454 } 2455 if (depth == 1) { 2456 if (*points) { 2457 closure = *points; 2458 } else { 2459 maxSize = 2*(PetscMax(mesh->maxConeSize, mesh->maxSupportSize)+1); 2460 ierr = DMGetWorkArray(dm, maxSize, MPIU_INT, &closure);CHKERRQ(ierr); 2461 } 2462 closure[0] = p; closure[1] = ornt; 2463 for (t = 0; t < tmpSize; ++t, closureSize += 2) { 2464 const PetscInt i = ornt >= 0 ? (t+ornt)%tmpSize : (-(ornt+1) + tmpSize-t)%tmpSize; 2465 closure[closureSize] = tmp[i]; 2466 closure[closureSize+1] = tmpO ? tmpO[i] : 0; 2467 } 2468 if (numPoints) *numPoints = closureSize/2; 2469 if (points) *points = closure; 2470 PetscFunctionReturn(0); 2471 } 2472 { 2473 PetscInt c, coneSeries, s,supportSeries; 2474 2475 c = mesh->maxConeSize; 2476 coneSeries = (c > 1) ? ((PetscPowInt(c,depth+1)-1)/(c-1)) : depth+1; 2477 s = mesh->maxSupportSize; 2478 supportSeries = (s > 1) ? ((PetscPowInt(s,depth+1)-1)/(s-1)) : depth+1; 2479 maxSize = 2*PetscMax(coneSeries,supportSeries); 2480 } 2481 ierr = DMGetWorkArray(dm, maxSize, MPIU_INT, &fifo);CHKERRQ(ierr); 2482 if (*points) { 2483 closure = *points; 2484 } else { 2485 ierr = DMGetWorkArray(dm, maxSize, MPIU_INT, &closure);CHKERRQ(ierr); 2486 } 2487 closure[0] = p; closure[1] = ornt; 2488 for (t = 0; t < tmpSize; ++t, closureSize += 2, fifoSize += 2) { 2489 const PetscInt i = ornt >= 0 ? (t+ornt)%tmpSize : (-(ornt+1) + tmpSize-t)%tmpSize; 2490 const PetscInt cp = tmp[i]; 2491 PetscInt co = tmpO ? tmpO[i] : 0; 2492 2493 if (ornt < 0) { 2494 PetscInt childSize, coff; 2495 ierr = DMPlexGetConeSize(dm, cp, &childSize);CHKERRQ(ierr); 2496 coff = co < 0 ? -(tmpO[i]+1) : tmpO[i]; 2497 co = childSize ? -(((coff+childSize-1)%childSize)+1) : 0; 2498 } 2499 closure[closureSize] = cp; 2500 closure[closureSize+1] = co; 2501 fifo[fifoSize] = cp; 2502 fifo[fifoSize+1] = co; 2503 } 2504 /* Should kick out early when depth is reached, rather than checking all vertices for empty cones */ 2505 while (fifoSize - fifoStart) { 2506 const PetscInt q = fifo[fifoStart]; 2507 const PetscInt o = fifo[fifoStart+1]; 2508 const PetscInt rev = o >= 0 ? 0 : 1; 2509 const PetscInt off = rev ? -(o+1) : o; 2510 2511 if (useCone) { 2512 ierr = DMPlexGetConeSize(dm, q, &tmpSize);CHKERRQ(ierr); 2513 ierr = DMPlexGetCone(dm, q, &tmp);CHKERRQ(ierr); 2514 ierr = DMPlexGetConeOrientation(dm, q, &tmpO);CHKERRQ(ierr); 2515 } else { 2516 ierr = DMPlexGetSupportSize(dm, q, &tmpSize);CHKERRQ(ierr); 2517 ierr = DMPlexGetSupport(dm, q, &tmp);CHKERRQ(ierr); 2518 tmpO = NULL; 2519 } 2520 for (t = 0; t < tmpSize; ++t) { 2521 const PetscInt i = ((rev ? tmpSize-t : t) + off)%tmpSize; 2522 const PetscInt cp = tmp[i]; 2523 /* Must propogate orientation: When we reverse orientation, we both reverse the direction of iteration and start at the other end of the chain. */ 2524 /* HACK: It is worse to get the size here, than to change the interpretation of -(*+1) 2525 const PetscInt co = tmpO ? (rev ? -(tmpO[i]+1) : tmpO[i]) : 0; */ 2526 PetscInt co = tmpO ? tmpO[i] : 0; 2527 PetscInt c; 2528 2529 if (rev) { 2530 PetscInt childSize, coff; 2531 ierr = DMPlexGetConeSize(dm, cp, &childSize);CHKERRQ(ierr); 2532 coff = tmpO[i] < 0 ? -(tmpO[i]+1) : tmpO[i]; 2533 co = childSize ? -(((coff+childSize-1)%childSize)+1) : 0; 2534 } 2535 /* Check for duplicate */ 2536 for (c = 0; c < closureSize; c += 2) { 2537 if (closure[c] == cp) break; 2538 } 2539 if (c == closureSize) { 2540 closure[closureSize] = cp; 2541 closure[closureSize+1] = co; 2542 fifo[fifoSize] = cp; 2543 fifo[fifoSize+1] = co; 2544 closureSize += 2; 2545 fifoSize += 2; 2546 } 2547 } 2548 fifoStart += 2; 2549 } 2550 if (numPoints) *numPoints = closureSize/2; 2551 if (points) *points = closure; 2552 ierr = DMRestoreWorkArray(dm, maxSize, MPIU_INT, &fifo);CHKERRQ(ierr); 2553 PetscFunctionReturn(0); 2554 } 2555 2556 /*@C 2557 DMPlexRestoreTransitiveClosure - Restore the array of points on the transitive closure of the in-edges or out-edges for this point in the DAG 2558 2559 Not collective 2560 2561 Input Parameters: 2562 + mesh - The DMPlex 2563 . p - The point, which must lie in the chart set with DMPlexSetChart() 2564 . useCone - PETSC_TRUE for in-edges, otherwise use out-edges 2565 . numPoints - The number of points in the closure, so points[] is of size 2*numPoints, zeroed on exit 2566 - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...], zeroed on exit 2567 2568 Note: 2569 If not using internal storage (points is not NULL on input), this call is unnecessary 2570 2571 Fortran Notes: 2572 Since it returns an array, this routine is only available in Fortran 90, and you must 2573 include petsc.h90 in your code. 2574 2575 The numPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2576 2577 Level: beginner 2578 2579 .seealso: DMPlexGetTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() 2580 @*/ 2581 PetscErrorCode DMPlexRestoreTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 2582 { 2583 PetscErrorCode ierr; 2584 2585 PetscFunctionBegin; 2586 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2587 if (numPoints) PetscValidIntPointer(numPoints,4); 2588 if (points) PetscValidPointer(points,5); 2589 ierr = DMRestoreWorkArray(dm, 0, MPIU_INT, points);CHKERRQ(ierr); 2590 if (numPoints) *numPoints = 0; 2591 PetscFunctionReturn(0); 2592 } 2593 2594 /*@ 2595 DMPlexGetMaxSizes - Return the maximum number of in-edges (cone) and out-edges (support) for any point in the DAG 2596 2597 Not collective 2598 2599 Input Parameter: 2600 . mesh - The DMPlex 2601 2602 Output Parameters: 2603 + maxConeSize - The maximum number of in-edges 2604 - maxSupportSize - The maximum number of out-edges 2605 2606 Level: beginner 2607 2608 .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart() 2609 @*/ 2610 PetscErrorCode DMPlexGetMaxSizes(DM dm, PetscInt *maxConeSize, PetscInt *maxSupportSize) 2611 { 2612 DM_Plex *mesh = (DM_Plex*) dm->data; 2613 2614 PetscFunctionBegin; 2615 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2616 if (maxConeSize) *maxConeSize = mesh->maxConeSize; 2617 if (maxSupportSize) *maxSupportSize = mesh->maxSupportSize; 2618 PetscFunctionReturn(0); 2619 } 2620 2621 PetscErrorCode DMSetUp_Plex(DM dm) 2622 { 2623 DM_Plex *mesh = (DM_Plex*) dm->data; 2624 PetscInt size; 2625 PetscErrorCode ierr; 2626 2627 PetscFunctionBegin; 2628 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2629 ierr = PetscSectionSetUp(mesh->coneSection);CHKERRQ(ierr); 2630 ierr = PetscSectionGetStorageSize(mesh->coneSection, &size);CHKERRQ(ierr); 2631 ierr = PetscMalloc1(size, &mesh->cones);CHKERRQ(ierr); 2632 ierr = PetscCalloc1(size, &mesh->coneOrientations);CHKERRQ(ierr); 2633 if (mesh->maxSupportSize) { 2634 ierr = PetscSectionSetUp(mesh->supportSection);CHKERRQ(ierr); 2635 ierr = PetscSectionGetStorageSize(mesh->supportSection, &size);CHKERRQ(ierr); 2636 ierr = PetscMalloc1(size, &mesh->supports);CHKERRQ(ierr); 2637 } 2638 PetscFunctionReturn(0); 2639 } 2640 2641 PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm) 2642 { 2643 PetscErrorCode ierr; 2644 2645 PetscFunctionBegin; 2646 if (subdm) {ierr = DMClone(dm, subdm);CHKERRQ(ierr);} 2647 ierr = DMCreateSectionSubDM(dm, numFields, fields, is, subdm);CHKERRQ(ierr); 2648 if (subdm) {(*subdm)->useNatural = dm->useNatural;} 2649 if (dm->useNatural && dm->sfMigration) { 2650 PetscSF sfMigrationInv,sfNatural; 2651 PetscSection section, sectionSeq; 2652 2653 (*subdm)->sfMigration = dm->sfMigration; 2654 ierr = PetscObjectReference((PetscObject) dm->sfMigration);CHKERRQ(ierr); 2655 ierr = DMGetLocalSection((*subdm), §ion);CHKERRQ(ierr);CHKERRQ(ierr); 2656 ierr = PetscSFCreateInverseSF((*subdm)->sfMigration, &sfMigrationInv);CHKERRQ(ierr); 2657 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) (*subdm)), §ionSeq);CHKERRQ(ierr); 2658 ierr = PetscSFDistributeSection(sfMigrationInv, section, NULL, sectionSeq);CHKERRQ(ierr); 2659 2660 ierr = DMPlexCreateGlobalToNaturalSF(*subdm, sectionSeq, (*subdm)->sfMigration, &sfNatural);CHKERRQ(ierr); 2661 (*subdm)->sfNatural = sfNatural; 2662 ierr = PetscSectionDestroy(§ionSeq);CHKERRQ(ierr); 2663 ierr = PetscSFDestroy(&sfMigrationInv);CHKERRQ(ierr); 2664 } 2665 PetscFunctionReturn(0); 2666 } 2667 2668 PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm) 2669 { 2670 PetscErrorCode ierr; 2671 PetscInt i = 0; 2672 2673 PetscFunctionBegin; 2674 ierr = DMClone(dms[0], superdm);CHKERRQ(ierr); 2675 ierr = DMCreateSectionSuperDM(dms, len, is, superdm);CHKERRQ(ierr); 2676 (*superdm)->useNatural = PETSC_FALSE; 2677 for (i = 0; i < len; i++){ 2678 if (dms[i]->useNatural && dms[i]->sfMigration) { 2679 PetscSF sfMigrationInv,sfNatural; 2680 PetscSection section, sectionSeq; 2681 2682 (*superdm)->sfMigration = dms[i]->sfMigration; 2683 ierr = PetscObjectReference((PetscObject) dms[i]->sfMigration);CHKERRQ(ierr); 2684 (*superdm)->useNatural = PETSC_TRUE; 2685 ierr = DMGetLocalSection((*superdm), §ion);CHKERRQ(ierr); 2686 ierr = PetscSFCreateInverseSF((*superdm)->sfMigration, &sfMigrationInv);CHKERRQ(ierr); 2687 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) (*superdm)), §ionSeq);CHKERRQ(ierr); 2688 ierr = PetscSFDistributeSection(sfMigrationInv, section, NULL, sectionSeq);CHKERRQ(ierr); 2689 2690 ierr = DMPlexCreateGlobalToNaturalSF(*superdm, sectionSeq, (*superdm)->sfMigration, &sfNatural);CHKERRQ(ierr); 2691 (*superdm)->sfNatural = sfNatural; 2692 ierr = PetscSectionDestroy(§ionSeq);CHKERRQ(ierr); 2693 ierr = PetscSFDestroy(&sfMigrationInv);CHKERRQ(ierr); 2694 break; 2695 } 2696 } 2697 PetscFunctionReturn(0); 2698 } 2699 2700 /*@ 2701 DMPlexSymmetrize - Create support (out-edge) information from cone (in-edge) information 2702 2703 Not collective 2704 2705 Input Parameter: 2706 . mesh - The DMPlex 2707 2708 Output Parameter: 2709 2710 Note: 2711 This should be called after all calls to DMPlexSetCone() 2712 2713 Level: beginner 2714 2715 .seealso: DMPlexCreate(), DMPlexSetChart(), DMPlexSetConeSize(), DMPlexSetCone() 2716 @*/ 2717 PetscErrorCode DMPlexSymmetrize(DM dm) 2718 { 2719 DM_Plex *mesh = (DM_Plex*) dm->data; 2720 PetscInt *offsets; 2721 PetscInt supportSize; 2722 PetscInt pStart, pEnd, p; 2723 PetscErrorCode ierr; 2724 2725 PetscFunctionBegin; 2726 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2727 if (mesh->supports) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "Supports were already setup in this DMPlex"); 2728 ierr = PetscLogEventBegin(DMPLEX_Symmetrize,dm,0,0,0);CHKERRQ(ierr); 2729 /* Calculate support sizes */ 2730 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2731 for (p = pStart; p < pEnd; ++p) { 2732 PetscInt dof, off, c; 2733 2734 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 2735 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 2736 for (c = off; c < off+dof; ++c) { 2737 ierr = PetscSectionAddDof(mesh->supportSection, mesh->cones[c], 1);CHKERRQ(ierr); 2738 } 2739 } 2740 for (p = pStart; p < pEnd; ++p) { 2741 PetscInt dof; 2742 2743 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 2744 2745 mesh->maxSupportSize = PetscMax(mesh->maxSupportSize, dof); 2746 } 2747 ierr = PetscSectionSetUp(mesh->supportSection);CHKERRQ(ierr); 2748 /* Calculate supports */ 2749 ierr = PetscSectionGetStorageSize(mesh->supportSection, &supportSize);CHKERRQ(ierr); 2750 ierr = PetscMalloc1(supportSize, &mesh->supports);CHKERRQ(ierr); 2751 ierr = PetscCalloc1(pEnd - pStart, &offsets);CHKERRQ(ierr); 2752 for (p = pStart; p < pEnd; ++p) { 2753 PetscInt dof, off, c; 2754 2755 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 2756 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 2757 for (c = off; c < off+dof; ++c) { 2758 const PetscInt q = mesh->cones[c]; 2759 PetscInt offS; 2760 2761 ierr = PetscSectionGetOffset(mesh->supportSection, q, &offS);CHKERRQ(ierr); 2762 2763 mesh->supports[offS+offsets[q]] = p; 2764 ++offsets[q]; 2765 } 2766 } 2767 ierr = PetscFree(offsets);CHKERRQ(ierr); 2768 ierr = PetscLogEventEnd(DMPLEX_Symmetrize,dm,0,0,0);CHKERRQ(ierr); 2769 PetscFunctionReturn(0); 2770 } 2771 2772 static PetscErrorCode DMPlexCreateDepthStratum(DM dm, DMLabel label, PetscInt depth, PetscInt pStart, PetscInt pEnd) 2773 { 2774 IS stratumIS; 2775 PetscErrorCode ierr; 2776 2777 PetscFunctionBegin; 2778 if (pStart >= pEnd) PetscFunctionReturn(0); 2779 #if defined(PETSC_USE_DEBUG) 2780 { 2781 PetscInt qStart, qEnd, numLevels, level; 2782 PetscBool overlap = PETSC_FALSE; 2783 ierr = DMLabelGetNumValues(label, &numLevels);CHKERRQ(ierr); 2784 for (level = 0; level < numLevels; level++) { 2785 ierr = DMLabelGetStratumBounds(label, level, &qStart, &qEnd);CHKERRQ(ierr); 2786 if ((pStart >= qStart && pStart < qEnd) || (pEnd > qStart && pEnd <= qEnd)) {overlap = PETSC_TRUE; break;} 2787 } 2788 if (overlap) SETERRQ6(PETSC_COMM_SELF, PETSC_ERR_PLIB, "New depth %D range [%D,%D) overlaps with depth %D range [%D,%D)", depth, pStart, pEnd, level, qStart, qEnd); 2789 } 2790 #endif 2791 ierr = ISCreateStride(PETSC_COMM_SELF, pEnd-pStart, pStart, 1, &stratumIS);CHKERRQ(ierr); 2792 ierr = DMLabelSetStratumIS(label, depth, stratumIS);CHKERRQ(ierr); 2793 ierr = ISDestroy(&stratumIS);CHKERRQ(ierr); 2794 PetscFunctionReturn(0); 2795 } 2796 2797 static PetscErrorCode DMPlexCreateDimStratum(DM,DMLabel,DMLabel,PetscInt,PetscInt); 2798 2799 /*@ 2800 DMPlexStratify - The DAG for most topologies is a graded poset (https://en.wikipedia.org/wiki/Graded_poset), and 2801 can be illustrated by a Hasse Diagram (https://en.wikipedia.org/wiki/Hasse_diagram). The strata group all points of the 2802 same grade, and this function calculates the strata. This grade can be seen as the height (or depth) of the point in 2803 the DAG. 2804 2805 Collective on dm 2806 2807 Input Parameter: 2808 . mesh - The DMPlex 2809 2810 Output Parameter: 2811 2812 Notes: 2813 Concretely, DMPlexStratify() creates a new label named "depth" containing the dimension of each element: 0 for vertices, 2814 1 for edges, and so on. The depth label can be accessed through DMPlexGetDepthLabel() or DMPlexGetDepthStratum(), or 2815 manually via DMGetLabel(). The height is defined implicitly by height = maxDimension - depth, and can be accessed 2816 via DMPlexGetHeightStratum(). For example, cells have height 0 and faces have height 1. 2817 2818 DMPlexStratify() should be called after all calls to DMPlexSymmetrize() 2819 2820 Level: beginner 2821 2822 .seealso: DMPlexCreate(), DMPlexSymmetrize() 2823 @*/ 2824 PetscErrorCode DMPlexStratify(DM dm) 2825 { 2826 DM_Plex *mesh = (DM_Plex*) dm->data; 2827 DMLabel label; 2828 PetscInt pStart, pEnd, p; 2829 PetscInt numRoots = 0, numLeaves = 0; 2830 PetscInt cMax, fMax, eMax, vMax; 2831 PetscErrorCode ierr; 2832 2833 PetscFunctionBegin; 2834 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2835 ierr = PetscLogEventBegin(DMPLEX_Stratify,dm,0,0,0);CHKERRQ(ierr); 2836 2837 /* Create depth label */ 2838 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2839 ierr = DMCreateLabel(dm, "depth");CHKERRQ(ierr); 2840 ierr = DMPlexGetDepthLabel(dm, &label);CHKERRQ(ierr); 2841 2842 { 2843 /* Initialize roots and count leaves */ 2844 PetscInt sMin = PETSC_MAX_INT; 2845 PetscInt sMax = PETSC_MIN_INT; 2846 PetscInt coneSize, supportSize; 2847 2848 for (p = pStart; p < pEnd; ++p) { 2849 ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); 2850 ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); 2851 if (!coneSize && supportSize) { 2852 sMin = PetscMin(p, sMin); 2853 sMax = PetscMax(p, sMax); 2854 ++numRoots; 2855 } else if (!supportSize && coneSize) { 2856 ++numLeaves; 2857 } else if (!supportSize && !coneSize) { 2858 /* Isolated points */ 2859 sMin = PetscMin(p, sMin); 2860 sMax = PetscMax(p, sMax); 2861 } 2862 } 2863 ierr = DMPlexCreateDepthStratum(dm, label, 0, sMin, sMax+1);CHKERRQ(ierr); 2864 } 2865 2866 if (numRoots + numLeaves == (pEnd - pStart)) { 2867 PetscInt sMin = PETSC_MAX_INT; 2868 PetscInt sMax = PETSC_MIN_INT; 2869 PetscInt coneSize, supportSize; 2870 2871 for (p = pStart; p < pEnd; ++p) { 2872 ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); 2873 ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); 2874 if (!supportSize && coneSize) { 2875 sMin = PetscMin(p, sMin); 2876 sMax = PetscMax(p, sMax); 2877 } 2878 } 2879 ierr = DMPlexCreateDepthStratum(dm, label, 1, sMin, sMax+1);CHKERRQ(ierr); 2880 } else { 2881 PetscInt level = 0; 2882 PetscInt qStart, qEnd, q; 2883 2884 ierr = DMLabelGetStratumBounds(label, level, &qStart, &qEnd);CHKERRQ(ierr); 2885 while (qEnd > qStart) { 2886 PetscInt sMin = PETSC_MAX_INT; 2887 PetscInt sMax = PETSC_MIN_INT; 2888 2889 for (q = qStart; q < qEnd; ++q) { 2890 const PetscInt *support; 2891 PetscInt supportSize, s; 2892 2893 ierr = DMPlexGetSupportSize(dm, q, &supportSize);CHKERRQ(ierr); 2894 ierr = DMPlexGetSupport(dm, q, &support);CHKERRQ(ierr); 2895 for (s = 0; s < supportSize; ++s) { 2896 sMin = PetscMin(support[s], sMin); 2897 sMax = PetscMax(support[s], sMax); 2898 } 2899 } 2900 ierr = DMLabelGetNumValues(label, &level);CHKERRQ(ierr); 2901 ierr = DMPlexCreateDepthStratum(dm, label, level, sMin, sMax+1);CHKERRQ(ierr); 2902 ierr = DMLabelGetStratumBounds(label, level, &qStart, &qEnd);CHKERRQ(ierr); 2903 } 2904 } 2905 { /* just in case there is an empty process */ 2906 PetscInt numValues, maxValues = 0, v; 2907 2908 ierr = DMLabelGetNumValues(label, &numValues);CHKERRQ(ierr); 2909 ierr = MPI_Allreduce(&numValues,&maxValues,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 2910 for (v = numValues; v < maxValues; v++) { 2911 ierr = DMLabelAddStratum(label, v);CHKERRQ(ierr); 2912 } 2913 } 2914 ierr = PetscObjectStateGet((PetscObject) label, &mesh->depthState);CHKERRQ(ierr); 2915 2916 ierr = DMPlexGetHybridBounds(dm, &cMax, &fMax, &eMax, &vMax);CHKERRQ(ierr); 2917 if (cMax >= 0 || fMax >= 0 || eMax >= 0 || vMax >= 0) { 2918 PetscInt dim; 2919 DMLabel dimLabel; 2920 2921 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2922 ierr = DMCreateLabel(dm, "dim");CHKERRQ(ierr); 2923 ierr = DMGetLabel(dm, "dim", &dimLabel);CHKERRQ(ierr); 2924 if (cMax >= 0) {ierr = DMPlexCreateDimStratum(dm, label, dimLabel, dim, cMax);CHKERRQ(ierr);} 2925 if (fMax >= 0) {ierr = DMPlexCreateDimStratum(dm, label, dimLabel, dim - 1, fMax);CHKERRQ(ierr);} 2926 if (eMax >= 0) {ierr = DMPlexCreateDimStratum(dm, label, dimLabel, 1, eMax);CHKERRQ(ierr);} 2927 if (vMax >= 0) {ierr = DMPlexCreateDimStratum(dm, label, dimLabel, 0, vMax);CHKERRQ(ierr);} 2928 } 2929 ierr = PetscLogEventEnd(DMPLEX_Stratify,dm,0,0,0);CHKERRQ(ierr); 2930 PetscFunctionReturn(0); 2931 } 2932 2933 /*@C 2934 DMPlexGetJoin - Get an array for the join of the set of points 2935 2936 Not Collective 2937 2938 Input Parameters: 2939 + dm - The DMPlex object 2940 . numPoints - The number of input points for the join 2941 - points - The input points 2942 2943 Output Parameters: 2944 + numCoveredPoints - The number of points in the join 2945 - coveredPoints - The points in the join 2946 2947 Level: intermediate 2948 2949 Note: Currently, this is restricted to a single level join 2950 2951 Fortran Notes: 2952 Since it returns an array, this routine is only available in Fortran 90, and you must 2953 include petsc.h90 in your code. 2954 2955 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2956 2957 .seealso: DMPlexRestoreJoin(), DMPlexGetMeet() 2958 @*/ 2959 PetscErrorCode DMPlexGetJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 2960 { 2961 DM_Plex *mesh = (DM_Plex*) dm->data; 2962 PetscInt *join[2]; 2963 PetscInt joinSize, i = 0; 2964 PetscInt dof, off, p, c, m; 2965 PetscErrorCode ierr; 2966 2967 PetscFunctionBegin; 2968 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2969 PetscValidIntPointer(points, 3); 2970 PetscValidIntPointer(numCoveredPoints, 4); 2971 PetscValidPointer(coveredPoints, 5); 2972 ierr = DMGetWorkArray(dm, mesh->maxSupportSize, MPIU_INT, &join[0]);CHKERRQ(ierr); 2973 ierr = DMGetWorkArray(dm, mesh->maxSupportSize, MPIU_INT, &join[1]);CHKERRQ(ierr); 2974 /* Copy in support of first point */ 2975 ierr = PetscSectionGetDof(mesh->supportSection, points[0], &dof);CHKERRQ(ierr); 2976 ierr = PetscSectionGetOffset(mesh->supportSection, points[0], &off);CHKERRQ(ierr); 2977 for (joinSize = 0; joinSize < dof; ++joinSize) { 2978 join[i][joinSize] = mesh->supports[off+joinSize]; 2979 } 2980 /* Check each successive support */ 2981 for (p = 1; p < numPoints; ++p) { 2982 PetscInt newJoinSize = 0; 2983 2984 ierr = PetscSectionGetDof(mesh->supportSection, points[p], &dof);CHKERRQ(ierr); 2985 ierr = PetscSectionGetOffset(mesh->supportSection, points[p], &off);CHKERRQ(ierr); 2986 for (c = 0; c < dof; ++c) { 2987 const PetscInt point = mesh->supports[off+c]; 2988 2989 for (m = 0; m < joinSize; ++m) { 2990 if (point == join[i][m]) { 2991 join[1-i][newJoinSize++] = point; 2992 break; 2993 } 2994 } 2995 } 2996 joinSize = newJoinSize; 2997 i = 1-i; 2998 } 2999 *numCoveredPoints = joinSize; 3000 *coveredPoints = join[i]; 3001 ierr = DMRestoreWorkArray(dm, mesh->maxSupportSize, MPIU_INT, &join[1-i]);CHKERRQ(ierr); 3002 PetscFunctionReturn(0); 3003 } 3004 3005 /*@C 3006 DMPlexRestoreJoin - Restore an array for the join of the set of points 3007 3008 Not Collective 3009 3010 Input Parameters: 3011 + dm - The DMPlex object 3012 . numPoints - The number of input points for the join 3013 - points - The input points 3014 3015 Output Parameters: 3016 + numCoveredPoints - The number of points in the join 3017 - coveredPoints - The points in the join 3018 3019 Fortran Notes: 3020 Since it returns an array, this routine is only available in Fortran 90, and you must 3021 include petsc.h90 in your code. 3022 3023 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 3024 3025 Level: intermediate 3026 3027 .seealso: DMPlexGetJoin(), DMPlexGetFullJoin(), DMPlexGetMeet() 3028 @*/ 3029 PetscErrorCode DMPlexRestoreJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 3030 { 3031 PetscErrorCode ierr; 3032 3033 PetscFunctionBegin; 3034 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3035 if (points) PetscValidIntPointer(points,3); 3036 if (numCoveredPoints) PetscValidIntPointer(numCoveredPoints,4); 3037 PetscValidPointer(coveredPoints, 5); 3038 ierr = DMRestoreWorkArray(dm, 0, MPIU_INT, (void*) coveredPoints);CHKERRQ(ierr); 3039 if (numCoveredPoints) *numCoveredPoints = 0; 3040 PetscFunctionReturn(0); 3041 } 3042 3043 /*@C 3044 DMPlexGetFullJoin - Get an array for the join of the set of points 3045 3046 Not Collective 3047 3048 Input Parameters: 3049 + dm - The DMPlex object 3050 . numPoints - The number of input points for the join 3051 - points - The input points 3052 3053 Output Parameters: 3054 + numCoveredPoints - The number of points in the join 3055 - coveredPoints - The points in the join 3056 3057 Fortran Notes: 3058 Since it returns an array, this routine is only available in Fortran 90, and you must 3059 include petsc.h90 in your code. 3060 3061 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 3062 3063 Level: intermediate 3064 3065 .seealso: DMPlexGetJoin(), DMPlexRestoreJoin(), DMPlexGetMeet() 3066 @*/ 3067 PetscErrorCode DMPlexGetFullJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 3068 { 3069 DM_Plex *mesh = (DM_Plex*) dm->data; 3070 PetscInt *offsets, **closures; 3071 PetscInt *join[2]; 3072 PetscInt depth = 0, maxSize, joinSize = 0, i = 0; 3073 PetscInt p, d, c, m, ms; 3074 PetscErrorCode ierr; 3075 3076 PetscFunctionBegin; 3077 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3078 PetscValidIntPointer(points, 3); 3079 PetscValidIntPointer(numCoveredPoints, 4); 3080 PetscValidPointer(coveredPoints, 5); 3081 3082 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 3083 ierr = PetscCalloc1(numPoints, &closures);CHKERRQ(ierr); 3084 ierr = DMGetWorkArray(dm, numPoints*(depth+2), MPIU_INT, &offsets);CHKERRQ(ierr); 3085 ms = mesh->maxSupportSize; 3086 maxSize = (ms > 1) ? ((PetscPowInt(ms,depth+1)-1)/(ms-1)) : depth + 1; 3087 ierr = DMGetWorkArray(dm, maxSize, MPIU_INT, &join[0]);CHKERRQ(ierr); 3088 ierr = DMGetWorkArray(dm, maxSize, MPIU_INT, &join[1]);CHKERRQ(ierr); 3089 3090 for (p = 0; p < numPoints; ++p) { 3091 PetscInt closureSize; 3092 3093 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &closureSize, &closures[p]);CHKERRQ(ierr); 3094 3095 offsets[p*(depth+2)+0] = 0; 3096 for (d = 0; d < depth+1; ++d) { 3097 PetscInt pStart, pEnd, i; 3098 3099 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 3100 for (i = offsets[p*(depth+2)+d]; i < closureSize; ++i) { 3101 if ((pStart > closures[p][i*2]) || (pEnd <= closures[p][i*2])) { 3102 offsets[p*(depth+2)+d+1] = i; 3103 break; 3104 } 3105 } 3106 if (i == closureSize) offsets[p*(depth+2)+d+1] = i; 3107 } 3108 if (offsets[p*(depth+2)+depth+1] != closureSize) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Total size of closure %D should be %D", offsets[p*(depth+2)+depth+1], closureSize); 3109 } 3110 for (d = 0; d < depth+1; ++d) { 3111 PetscInt dof; 3112 3113 /* Copy in support of first point */ 3114 dof = offsets[d+1] - offsets[d]; 3115 for (joinSize = 0; joinSize < dof; ++joinSize) { 3116 join[i][joinSize] = closures[0][(offsets[d]+joinSize)*2]; 3117 } 3118 /* Check each successive cone */ 3119 for (p = 1; p < numPoints && joinSize; ++p) { 3120 PetscInt newJoinSize = 0; 3121 3122 dof = offsets[p*(depth+2)+d+1] - offsets[p*(depth+2)+d]; 3123 for (c = 0; c < dof; ++c) { 3124 const PetscInt point = closures[p][(offsets[p*(depth+2)+d]+c)*2]; 3125 3126 for (m = 0; m < joinSize; ++m) { 3127 if (point == join[i][m]) { 3128 join[1-i][newJoinSize++] = point; 3129 break; 3130 } 3131 } 3132 } 3133 joinSize = newJoinSize; 3134 i = 1-i; 3135 } 3136 if (joinSize) break; 3137 } 3138 *numCoveredPoints = joinSize; 3139 *coveredPoints = join[i]; 3140 for (p = 0; p < numPoints; ++p) { 3141 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, NULL, &closures[p]);CHKERRQ(ierr); 3142 } 3143 ierr = PetscFree(closures);CHKERRQ(ierr); 3144 ierr = DMRestoreWorkArray(dm, numPoints*(depth+2), MPIU_INT, &offsets);CHKERRQ(ierr); 3145 ierr = DMRestoreWorkArray(dm, mesh->maxSupportSize, MPIU_INT, &join[1-i]);CHKERRQ(ierr); 3146 PetscFunctionReturn(0); 3147 } 3148 3149 /*@C 3150 DMPlexGetMeet - Get an array for the meet of the set of points 3151 3152 Not Collective 3153 3154 Input Parameters: 3155 + dm - The DMPlex object 3156 . numPoints - The number of input points for the meet 3157 - points - The input points 3158 3159 Output Parameters: 3160 + numCoveredPoints - The number of points in the meet 3161 - coveredPoints - The points in the meet 3162 3163 Level: intermediate 3164 3165 Note: Currently, this is restricted to a single level meet 3166 3167 Fortran Notes: 3168 Since it returns an array, this routine is only available in Fortran 90, and you must 3169 include petsc.h90 in your code. 3170 3171 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 3172 3173 .seealso: DMPlexRestoreMeet(), DMPlexGetJoin() 3174 @*/ 3175 PetscErrorCode DMPlexGetMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveringPoints, const PetscInt **coveringPoints) 3176 { 3177 DM_Plex *mesh = (DM_Plex*) dm->data; 3178 PetscInt *meet[2]; 3179 PetscInt meetSize, i = 0; 3180 PetscInt dof, off, p, c, m; 3181 PetscErrorCode ierr; 3182 3183 PetscFunctionBegin; 3184 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3185 PetscValidPointer(points, 2); 3186 PetscValidPointer(numCoveringPoints, 3); 3187 PetscValidPointer(coveringPoints, 4); 3188 ierr = DMGetWorkArray(dm, mesh->maxConeSize, MPIU_INT, &meet[0]);CHKERRQ(ierr); 3189 ierr = DMGetWorkArray(dm, mesh->maxConeSize, MPIU_INT, &meet[1]);CHKERRQ(ierr); 3190 /* Copy in cone of first point */ 3191 ierr = PetscSectionGetDof(mesh->coneSection, points[0], &dof);CHKERRQ(ierr); 3192 ierr = PetscSectionGetOffset(mesh->coneSection, points[0], &off);CHKERRQ(ierr); 3193 for (meetSize = 0; meetSize < dof; ++meetSize) { 3194 meet[i][meetSize] = mesh->cones[off+meetSize]; 3195 } 3196 /* Check each successive cone */ 3197 for (p = 1; p < numPoints; ++p) { 3198 PetscInt newMeetSize = 0; 3199 3200 ierr = PetscSectionGetDof(mesh->coneSection, points[p], &dof);CHKERRQ(ierr); 3201 ierr = PetscSectionGetOffset(mesh->coneSection, points[p], &off);CHKERRQ(ierr); 3202 for (c = 0; c < dof; ++c) { 3203 const PetscInt point = mesh->cones[off+c]; 3204 3205 for (m = 0; m < meetSize; ++m) { 3206 if (point == meet[i][m]) { 3207 meet[1-i][newMeetSize++] = point; 3208 break; 3209 } 3210 } 3211 } 3212 meetSize = newMeetSize; 3213 i = 1-i; 3214 } 3215 *numCoveringPoints = meetSize; 3216 *coveringPoints = meet[i]; 3217 ierr = DMRestoreWorkArray(dm, mesh->maxConeSize, MPIU_INT, &meet[1-i]);CHKERRQ(ierr); 3218 PetscFunctionReturn(0); 3219 } 3220 3221 /*@C 3222 DMPlexRestoreMeet - Restore an array for the meet of the set of points 3223 3224 Not Collective 3225 3226 Input Parameters: 3227 + dm - The DMPlex object 3228 . numPoints - The number of input points for the meet 3229 - points - The input points 3230 3231 Output Parameters: 3232 + numCoveredPoints - The number of points in the meet 3233 - coveredPoints - The points in the meet 3234 3235 Level: intermediate 3236 3237 Fortran Notes: 3238 Since it returns an array, this routine is only available in Fortran 90, and you must 3239 include petsc.h90 in your code. 3240 3241 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 3242 3243 .seealso: DMPlexGetMeet(), DMPlexGetFullMeet(), DMPlexGetJoin() 3244 @*/ 3245 PetscErrorCode DMPlexRestoreMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 3246 { 3247 PetscErrorCode ierr; 3248 3249 PetscFunctionBegin; 3250 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3251 if (points) PetscValidIntPointer(points,3); 3252 if (numCoveredPoints) PetscValidIntPointer(numCoveredPoints,4); 3253 PetscValidPointer(coveredPoints,5); 3254 ierr = DMRestoreWorkArray(dm, 0, MPIU_INT, (void*) coveredPoints);CHKERRQ(ierr); 3255 if (numCoveredPoints) *numCoveredPoints = 0; 3256 PetscFunctionReturn(0); 3257 } 3258 3259 /*@C 3260 DMPlexGetFullMeet - Get an array for the meet of the set of points 3261 3262 Not Collective 3263 3264 Input Parameters: 3265 + dm - The DMPlex object 3266 . numPoints - The number of input points for the meet 3267 - points - The input points 3268 3269 Output Parameters: 3270 + numCoveredPoints - The number of points in the meet 3271 - coveredPoints - The points in the meet 3272 3273 Level: intermediate 3274 3275 Fortran Notes: 3276 Since it returns an array, this routine is only available in Fortran 90, and you must 3277 include petsc.h90 in your code. 3278 3279 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 3280 3281 .seealso: DMPlexGetMeet(), DMPlexRestoreMeet(), DMPlexGetJoin() 3282 @*/ 3283 PetscErrorCode DMPlexGetFullMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 3284 { 3285 DM_Plex *mesh = (DM_Plex*) dm->data; 3286 PetscInt *offsets, **closures; 3287 PetscInt *meet[2]; 3288 PetscInt height = 0, maxSize, meetSize = 0, i = 0; 3289 PetscInt p, h, c, m, mc; 3290 PetscErrorCode ierr; 3291 3292 PetscFunctionBegin; 3293 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3294 PetscValidPointer(points, 2); 3295 PetscValidPointer(numCoveredPoints, 3); 3296 PetscValidPointer(coveredPoints, 4); 3297 3298 ierr = DMPlexGetDepth(dm, &height);CHKERRQ(ierr); 3299 ierr = PetscMalloc1(numPoints, &closures);CHKERRQ(ierr); 3300 ierr = DMGetWorkArray(dm, numPoints*(height+2), MPIU_INT, &offsets);CHKERRQ(ierr); 3301 mc = mesh->maxConeSize; 3302 maxSize = (mc > 1) ? ((PetscPowInt(mc,height+1)-1)/(mc-1)) : height + 1; 3303 ierr = DMGetWorkArray(dm, maxSize, MPIU_INT, &meet[0]);CHKERRQ(ierr); 3304 ierr = DMGetWorkArray(dm, maxSize, MPIU_INT, &meet[1]);CHKERRQ(ierr); 3305 3306 for (p = 0; p < numPoints; ++p) { 3307 PetscInt closureSize; 3308 3309 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closures[p]);CHKERRQ(ierr); 3310 3311 offsets[p*(height+2)+0] = 0; 3312 for (h = 0; h < height+1; ++h) { 3313 PetscInt pStart, pEnd, i; 3314 3315 ierr = DMPlexGetHeightStratum(dm, h, &pStart, &pEnd);CHKERRQ(ierr); 3316 for (i = offsets[p*(height+2)+h]; i < closureSize; ++i) { 3317 if ((pStart > closures[p][i*2]) || (pEnd <= closures[p][i*2])) { 3318 offsets[p*(height+2)+h+1] = i; 3319 break; 3320 } 3321 } 3322 if (i == closureSize) offsets[p*(height+2)+h+1] = i; 3323 } 3324 if (offsets[p*(height+2)+height+1] != closureSize) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Total size of closure %D should be %D", offsets[p*(height+2)+height+1], closureSize); 3325 } 3326 for (h = 0; h < height+1; ++h) { 3327 PetscInt dof; 3328 3329 /* Copy in cone of first point */ 3330 dof = offsets[h+1] - offsets[h]; 3331 for (meetSize = 0; meetSize < dof; ++meetSize) { 3332 meet[i][meetSize] = closures[0][(offsets[h]+meetSize)*2]; 3333 } 3334 /* Check each successive cone */ 3335 for (p = 1; p < numPoints && meetSize; ++p) { 3336 PetscInt newMeetSize = 0; 3337 3338 dof = offsets[p*(height+2)+h+1] - offsets[p*(height+2)+h]; 3339 for (c = 0; c < dof; ++c) { 3340 const PetscInt point = closures[p][(offsets[p*(height+2)+h]+c)*2]; 3341 3342 for (m = 0; m < meetSize; ++m) { 3343 if (point == meet[i][m]) { 3344 meet[1-i][newMeetSize++] = point; 3345 break; 3346 } 3347 } 3348 } 3349 meetSize = newMeetSize; 3350 i = 1-i; 3351 } 3352 if (meetSize) break; 3353 } 3354 *numCoveredPoints = meetSize; 3355 *coveredPoints = meet[i]; 3356 for (p = 0; p < numPoints; ++p) { 3357 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, NULL, &closures[p]);CHKERRQ(ierr); 3358 } 3359 ierr = PetscFree(closures);CHKERRQ(ierr); 3360 ierr = DMRestoreWorkArray(dm, numPoints*(height+2), MPIU_INT, &offsets);CHKERRQ(ierr); 3361 ierr = DMRestoreWorkArray(dm, mesh->maxConeSize, MPIU_INT, &meet[1-i]);CHKERRQ(ierr); 3362 PetscFunctionReturn(0); 3363 } 3364 3365 /*@C 3366 DMPlexEqual - Determine if two DMs have the same topology 3367 3368 Not Collective 3369 3370 Input Parameters: 3371 + dmA - A DMPlex object 3372 - dmB - A DMPlex object 3373 3374 Output Parameters: 3375 . equal - PETSC_TRUE if the topologies are identical 3376 3377 Level: intermediate 3378 3379 Notes: 3380 We are not solving graph isomorphism, so we do not permutation. 3381 3382 .seealso: DMPlexGetCone() 3383 @*/ 3384 PetscErrorCode DMPlexEqual(DM dmA, DM dmB, PetscBool *equal) 3385 { 3386 PetscInt depth, depthB, pStart, pEnd, pStartB, pEndB, p; 3387 PetscErrorCode ierr; 3388 3389 PetscFunctionBegin; 3390 PetscValidHeaderSpecific(dmA, DM_CLASSID, 1); 3391 PetscValidHeaderSpecific(dmB, DM_CLASSID, 2); 3392 PetscValidPointer(equal, 3); 3393 3394 *equal = PETSC_FALSE; 3395 ierr = DMPlexGetDepth(dmA, &depth);CHKERRQ(ierr); 3396 ierr = DMPlexGetDepth(dmB, &depthB);CHKERRQ(ierr); 3397 if (depth != depthB) PetscFunctionReturn(0); 3398 ierr = DMPlexGetChart(dmA, &pStart, &pEnd);CHKERRQ(ierr); 3399 ierr = DMPlexGetChart(dmB, &pStartB, &pEndB);CHKERRQ(ierr); 3400 if ((pStart != pStartB) || (pEnd != pEndB)) PetscFunctionReturn(0); 3401 for (p = pStart; p < pEnd; ++p) { 3402 const PetscInt *cone, *coneB, *ornt, *orntB, *support, *supportB; 3403 PetscInt coneSize, coneSizeB, c, supportSize, supportSizeB, s; 3404 3405 ierr = DMPlexGetConeSize(dmA, p, &coneSize);CHKERRQ(ierr); 3406 ierr = DMPlexGetCone(dmA, p, &cone);CHKERRQ(ierr); 3407 ierr = DMPlexGetConeOrientation(dmA, p, &ornt);CHKERRQ(ierr); 3408 ierr = DMPlexGetConeSize(dmB, p, &coneSizeB);CHKERRQ(ierr); 3409 ierr = DMPlexGetCone(dmB, p, &coneB);CHKERRQ(ierr); 3410 ierr = DMPlexGetConeOrientation(dmB, p, &orntB);CHKERRQ(ierr); 3411 if (coneSize != coneSizeB) PetscFunctionReturn(0); 3412 for (c = 0; c < coneSize; ++c) { 3413 if (cone[c] != coneB[c]) PetscFunctionReturn(0); 3414 if (ornt[c] != orntB[c]) PetscFunctionReturn(0); 3415 } 3416 ierr = DMPlexGetSupportSize(dmA, p, &supportSize);CHKERRQ(ierr); 3417 ierr = DMPlexGetSupport(dmA, p, &support);CHKERRQ(ierr); 3418 ierr = DMPlexGetSupportSize(dmB, p, &supportSizeB);CHKERRQ(ierr); 3419 ierr = DMPlexGetSupport(dmB, p, &supportB);CHKERRQ(ierr); 3420 if (supportSize != supportSizeB) PetscFunctionReturn(0); 3421 for (s = 0; s < supportSize; ++s) { 3422 if (support[s] != supportB[s]) PetscFunctionReturn(0); 3423 } 3424 } 3425 *equal = PETSC_TRUE; 3426 PetscFunctionReturn(0); 3427 } 3428 3429 /*@C 3430 DMPlexGetNumFaceVertices - Returns the number of vertices on a face 3431 3432 Not Collective 3433 3434 Input Parameters: 3435 + dm - The DMPlex 3436 . cellDim - The cell dimension 3437 - numCorners - The number of vertices on a cell 3438 3439 Output Parameters: 3440 . numFaceVertices - The number of vertices on a face 3441 3442 Level: developer 3443 3444 Notes: 3445 Of course this can only work for a restricted set of symmetric shapes 3446 3447 .seealso: DMPlexGetCone() 3448 @*/ 3449 PetscErrorCode DMPlexGetNumFaceVertices(DM dm, PetscInt cellDim, PetscInt numCorners, PetscInt *numFaceVertices) 3450 { 3451 MPI_Comm comm; 3452 PetscErrorCode ierr; 3453 3454 PetscFunctionBegin; 3455 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 3456 PetscValidPointer(numFaceVertices,3); 3457 switch (cellDim) { 3458 case 0: 3459 *numFaceVertices = 0; 3460 break; 3461 case 1: 3462 *numFaceVertices = 1; 3463 break; 3464 case 2: 3465 switch (numCorners) { 3466 case 3: /* triangle */ 3467 *numFaceVertices = 2; /* Edge has 2 vertices */ 3468 break; 3469 case 4: /* quadrilateral */ 3470 *numFaceVertices = 2; /* Edge has 2 vertices */ 3471 break; 3472 case 6: /* quadratic triangle, tri and quad cohesive Lagrange cells */ 3473 *numFaceVertices = 3; /* Edge has 3 vertices */ 3474 break; 3475 case 9: /* quadratic quadrilateral, quadratic quad cohesive Lagrange cells */ 3476 *numFaceVertices = 3; /* Edge has 3 vertices */ 3477 break; 3478 default: 3479 SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %D for dimension %D", numCorners, cellDim); 3480 } 3481 break; 3482 case 3: 3483 switch (numCorners) { 3484 case 4: /* tetradehdron */ 3485 *numFaceVertices = 3; /* Face has 3 vertices */ 3486 break; 3487 case 6: /* tet cohesive cells */ 3488 *numFaceVertices = 4; /* Face has 4 vertices */ 3489 break; 3490 case 8: /* hexahedron */ 3491 *numFaceVertices = 4; /* Face has 4 vertices */ 3492 break; 3493 case 9: /* tet cohesive Lagrange cells */ 3494 *numFaceVertices = 6; /* Face has 6 vertices */ 3495 break; 3496 case 10: /* quadratic tetrahedron */ 3497 *numFaceVertices = 6; /* Face has 6 vertices */ 3498 break; 3499 case 12: /* hex cohesive Lagrange cells */ 3500 *numFaceVertices = 6; /* Face has 6 vertices */ 3501 break; 3502 case 18: /* quadratic tet cohesive Lagrange cells */ 3503 *numFaceVertices = 6; /* Face has 6 vertices */ 3504 break; 3505 case 27: /* quadratic hexahedron, quadratic hex cohesive Lagrange cells */ 3506 *numFaceVertices = 9; /* Face has 9 vertices */ 3507 break; 3508 default: 3509 SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %D for dimension %D", numCorners, cellDim); 3510 } 3511 break; 3512 default: 3513 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid cell dimension %D", cellDim); 3514 } 3515 PetscFunctionReturn(0); 3516 } 3517 3518 /*@ 3519 DMPlexGetDepthLabel - Get the DMLabel recording the depth of each point 3520 3521 Not Collective 3522 3523 Input Parameter: 3524 . dm - The DMPlex object 3525 3526 Output Parameter: 3527 . depthLabel - The DMLabel recording point depth 3528 3529 Level: developer 3530 3531 .seealso: DMPlexGetDepth(), DMPlexGetHeightStratum(), DMPlexGetDepthStratum() 3532 @*/ 3533 PetscErrorCode DMPlexGetDepthLabel(DM dm, DMLabel *depthLabel) 3534 { 3535 PetscErrorCode ierr; 3536 3537 PetscFunctionBegin; 3538 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3539 PetscValidPointer(depthLabel, 2); 3540 if (!dm->depthLabel) {ierr = DMGetLabel(dm, "depth", &dm->depthLabel);CHKERRQ(ierr);} 3541 *depthLabel = dm->depthLabel; 3542 PetscFunctionReturn(0); 3543 } 3544 3545 /*@ 3546 DMPlexGetDepth - Get the depth of the DAG representing this mesh 3547 3548 Not Collective 3549 3550 Input Parameter: 3551 . dm - The DMPlex object 3552 3553 Output Parameter: 3554 . depth - The number of strata (breadth first levels) in the DAG 3555 3556 Level: developer 3557 3558 .seealso: DMPlexGetDepthLabel(), DMPlexGetHeightStratum(), DMPlexGetDepthStratum() 3559 @*/ 3560 PetscErrorCode DMPlexGetDepth(DM dm, PetscInt *depth) 3561 { 3562 DMLabel label; 3563 PetscInt d = 0; 3564 PetscErrorCode ierr; 3565 3566 PetscFunctionBegin; 3567 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3568 PetscValidPointer(depth, 2); 3569 ierr = DMPlexGetDepthLabel(dm, &label);CHKERRQ(ierr); 3570 if (label) {ierr = DMLabelGetNumValues(label, &d);CHKERRQ(ierr);} 3571 *depth = d-1; 3572 PetscFunctionReturn(0); 3573 } 3574 3575 /*@ 3576 DMPlexGetDepthStratum - Get the bounds [start, end) for all points at a certain depth. 3577 3578 Not Collective 3579 3580 Input Parameters: 3581 + dm - The DMPlex object 3582 - stratumValue - The requested depth 3583 3584 Output Parameters: 3585 + start - The first point at this depth 3586 - end - One beyond the last point at this depth 3587 3588 Notes: 3589 Depth indexing is related to topological dimension. Depth stratum 0 contains the lowest topological dimension points, 3590 often "vertices". If the mesh is "interpolated" (see DMPlexInterpolate()), then depth stratum 1 contains the next 3591 higher dimension, e.g., "edges". 3592 3593 Level: developer 3594 3595 .seealso: DMPlexGetHeightStratum(), DMPlexGetDepth() 3596 @*/ 3597 PetscErrorCode DMPlexGetDepthStratum(DM dm, PetscInt stratumValue, PetscInt *start, PetscInt *end) 3598 { 3599 DMLabel label; 3600 PetscInt pStart, pEnd; 3601 PetscErrorCode ierr; 3602 3603 PetscFunctionBegin; 3604 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3605 if (start) {PetscValidPointer(start, 3); *start = 0;} 3606 if (end) {PetscValidPointer(end, 4); *end = 0;} 3607 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 3608 if (pStart == pEnd) PetscFunctionReturn(0); 3609 if (stratumValue < 0) { 3610 if (start) *start = pStart; 3611 if (end) *end = pEnd; 3612 PetscFunctionReturn(0); 3613 } 3614 ierr = DMPlexGetDepthLabel(dm, &label);CHKERRQ(ierr); 3615 if (!label) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "No label named depth was found"); 3616 ierr = DMLabelGetStratumBounds(label, stratumValue, start, end);CHKERRQ(ierr); 3617 PetscFunctionReturn(0); 3618 } 3619 3620 /*@ 3621 DMPlexGetHeightStratum - Get the bounds [start, end) for all points at a certain height. 3622 3623 Not Collective 3624 3625 Input Parameters: 3626 + dm - The DMPlex object 3627 - stratumValue - The requested height 3628 3629 Output Parameters: 3630 + start - The first point at this height 3631 - end - One beyond the last point at this height 3632 3633 Notes: 3634 Height indexing is related to topological codimension. Height stratum 0 contains the highest topological dimension 3635 points, often called "cells" or "elements". If the mesh is "interpolated" (see DMPlexInterpolate()), then height 3636 stratum 1 contains the boundary of these "cells", often called "faces" or "facets". 3637 3638 Level: developer 3639 3640 .seealso: DMPlexGetDepthStratum(), DMPlexGetDepth() 3641 @*/ 3642 PetscErrorCode DMPlexGetHeightStratum(DM dm, PetscInt stratumValue, PetscInt *start, PetscInt *end) 3643 { 3644 DMLabel label; 3645 PetscInt depth, pStart, pEnd; 3646 PetscErrorCode ierr; 3647 3648 PetscFunctionBegin; 3649 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3650 if (start) {PetscValidPointer(start, 3); *start = 0;} 3651 if (end) {PetscValidPointer(end, 4); *end = 0;} 3652 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 3653 if (pStart == pEnd) PetscFunctionReturn(0); 3654 if (stratumValue < 0) { 3655 if (start) *start = pStart; 3656 if (end) *end = pEnd; 3657 PetscFunctionReturn(0); 3658 } 3659 ierr = DMPlexGetDepthLabel(dm, &label);CHKERRQ(ierr); 3660 if (!label) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "No label named depth was found"); 3661 ierr = DMLabelGetNumValues(label, &depth);CHKERRQ(ierr); 3662 ierr = DMLabelGetStratumBounds(label, depth-1-stratumValue, start, end);CHKERRQ(ierr); 3663 PetscFunctionReturn(0); 3664 } 3665 3666 PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm) 3667 { 3668 PetscSection section, s; 3669 Mat m; 3670 PetscInt maxHeight; 3671 PetscErrorCode ierr; 3672 3673 PetscFunctionBegin; 3674 ierr = DMClone(dm, cdm);CHKERRQ(ierr); 3675 ierr = DMPlexGetMaxProjectionHeight(dm, &maxHeight);CHKERRQ(ierr); 3676 ierr = DMPlexSetMaxProjectionHeight(*cdm, maxHeight);CHKERRQ(ierr); 3677 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ion);CHKERRQ(ierr); 3678 ierr = DMSetLocalSection(*cdm, section);CHKERRQ(ierr); 3679 ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr); 3680 ierr = PetscSectionCreate(PETSC_COMM_SELF, &s);CHKERRQ(ierr); 3681 ierr = MatCreate(PETSC_COMM_SELF, &m);CHKERRQ(ierr); 3682 ierr = DMSetDefaultConstraints(*cdm, s, m);CHKERRQ(ierr); 3683 ierr = PetscSectionDestroy(&s);CHKERRQ(ierr); 3684 ierr = MatDestroy(&m);CHKERRQ(ierr); 3685 3686 ierr = DMSetNumFields(*cdm, 1);CHKERRQ(ierr); 3687 ierr = DMCreateDS(*cdm);CHKERRQ(ierr); 3688 PetscFunctionReturn(0); 3689 } 3690 3691 PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field) 3692 { 3693 Vec coordsLocal; 3694 DM coordsDM; 3695 PetscErrorCode ierr; 3696 3697 PetscFunctionBegin; 3698 *field = NULL; 3699 ierr = DMGetCoordinatesLocal(dm,&coordsLocal);CHKERRQ(ierr); 3700 ierr = DMGetCoordinateDM(dm,&coordsDM);CHKERRQ(ierr); 3701 if (coordsLocal && coordsDM) { 3702 ierr = DMFieldCreateDS(coordsDM, 0, coordsLocal, field);CHKERRQ(ierr); 3703 } 3704 PetscFunctionReturn(0); 3705 } 3706 3707 /*@C 3708 DMPlexGetConeSection - Return a section which describes the layout of cone data 3709 3710 Not Collective 3711 3712 Input Parameters: 3713 . dm - The DMPlex object 3714 3715 Output Parameter: 3716 . section - The PetscSection object 3717 3718 Level: developer 3719 3720 .seealso: DMPlexGetSupportSection(), DMPlexGetCones(), DMPlexGetConeOrientations() 3721 @*/ 3722 PetscErrorCode DMPlexGetConeSection(DM dm, PetscSection *section) 3723 { 3724 DM_Plex *mesh = (DM_Plex*) dm->data; 3725 3726 PetscFunctionBegin; 3727 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3728 if (section) *section = mesh->coneSection; 3729 PetscFunctionReturn(0); 3730 } 3731 3732 /*@C 3733 DMPlexGetSupportSection - Return a section which describes the layout of support data 3734 3735 Not Collective 3736 3737 Input Parameters: 3738 . dm - The DMPlex object 3739 3740 Output Parameter: 3741 . section - The PetscSection object 3742 3743 Level: developer 3744 3745 .seealso: DMPlexGetConeSection() 3746 @*/ 3747 PetscErrorCode DMPlexGetSupportSection(DM dm, PetscSection *section) 3748 { 3749 DM_Plex *mesh = (DM_Plex*) dm->data; 3750 3751 PetscFunctionBegin; 3752 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3753 if (section) *section = mesh->supportSection; 3754 PetscFunctionReturn(0); 3755 } 3756 3757 /*@C 3758 DMPlexGetCones - Return cone data 3759 3760 Not Collective 3761 3762 Input Parameters: 3763 . dm - The DMPlex object 3764 3765 Output Parameter: 3766 . cones - The cone for each point 3767 3768 Level: developer 3769 3770 .seealso: DMPlexGetConeSection() 3771 @*/ 3772 PetscErrorCode DMPlexGetCones(DM dm, PetscInt *cones[]) 3773 { 3774 DM_Plex *mesh = (DM_Plex*) dm->data; 3775 3776 PetscFunctionBegin; 3777 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3778 if (cones) *cones = mesh->cones; 3779 PetscFunctionReturn(0); 3780 } 3781 3782 /*@C 3783 DMPlexGetConeOrientations - Return cone orientation data 3784 3785 Not Collective 3786 3787 Input Parameters: 3788 . dm - The DMPlex object 3789 3790 Output Parameter: 3791 . coneOrientations - The cone orientation for each point 3792 3793 Level: developer 3794 3795 .seealso: DMPlexGetConeSection() 3796 @*/ 3797 PetscErrorCode DMPlexGetConeOrientations(DM dm, PetscInt *coneOrientations[]) 3798 { 3799 DM_Plex *mesh = (DM_Plex*) dm->data; 3800 3801 PetscFunctionBegin; 3802 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3803 if (coneOrientations) *coneOrientations = mesh->coneOrientations; 3804 PetscFunctionReturn(0); 3805 } 3806 3807 /******************************** FEM Support **********************************/ 3808 3809 /* 3810 Returns number of components and tensor degree for the field. For interpolated meshes, line should be a point 3811 representing a line in the section. 3812 */ 3813 static PetscErrorCode PetscSectionFieldGetTensorDegree_Private(PetscSection section,PetscInt field,PetscInt line,PetscBool vertexchart,PetscInt *Nc,PetscInt *k) 3814 { 3815 PetscErrorCode ierr; 3816 3817 PetscFunctionBeginHot; 3818 ierr = PetscSectionGetFieldComponents(section, field, Nc);CHKERRQ(ierr); 3819 if (vertexchart) { /* If we only have a vertex chart, we must have degree k=1 */ 3820 *k = 1; 3821 } else { /* Assume the full interpolated mesh is in the chart; lines in particular */ 3822 /* An order k SEM disc has k-1 dofs on an edge */ 3823 ierr = PetscSectionGetFieldDof(section, line, field, k);CHKERRQ(ierr); 3824 *k = *k / *Nc + 1; 3825 } 3826 PetscFunctionReturn(0); 3827 } 3828 3829 /*@ 3830 3831 DMPlexSetClosurePermutationTensor - Create a permutation from the default (BFS) point ordering in the closure, to a 3832 lexicographic ordering over the tensor product cell (i.e., line, quad, hex, etc.), and set this permutation in the 3833 section provided (or the section of the DM). 3834 3835 Input Parameters: 3836 + dm - The DM 3837 . point - Either a cell (highest dim point) or an edge (dim 1 point), or PETSC_DETERMINE 3838 - section - The PetscSection to reorder, or NULL for the default section 3839 3840 Note: The point is used to determine the number of dofs/field on an edge. For SEM, this is related to the polynomial 3841 degree of the basis. 3842 3843 Example: 3844 A typical interpolated single-quad mesh might order points as 3845 .vb 3846 [c0, v1, v2, v3, v4, e5, e6, e7, e8] 3847 3848 v4 -- e6 -- v3 3849 | | 3850 e7 c0 e8 3851 | | 3852 v1 -- e5 -- v2 3853 .ve 3854 3855 (There is no significance to the ordering described here.) The default section for a Q3 quad might typically assign 3856 dofs in the order of points, e.g., 3857 .vb 3858 c0 -> [0,1,2,3] 3859 v1 -> [4] 3860 ... 3861 e5 -> [8, 9] 3862 .ve 3863 3864 which corresponds to the dofs 3865 .vb 3866 6 10 11 7 3867 13 2 3 15 3868 12 0 1 14 3869 4 8 9 5 3870 .ve 3871 3872 The closure in BFS ordering works through height strata (cells, edges, vertices) to produce the ordering 3873 .vb 3874 0 1 2 3 8 9 14 15 11 10 13 12 4 5 7 6 3875 .ve 3876 3877 After calling DMPlexSetClosurePermutationTensor(), the closure will be ordered lexicographically, 3878 .vb 3879 4 8 9 5 12 0 1 14 13 2 3 15 6 10 11 7 3880 .ve 3881 3882 Level: developer 3883 3884 .seealso: DMGetLocalSection(), PetscSectionSetClosurePermutation(), DMSetGlocalSection() 3885 @*/ 3886 PetscErrorCode DMPlexSetClosurePermutationTensor(DM dm, PetscInt point, PetscSection section) 3887 { 3888 DMLabel label; 3889 PetscInt *perm; 3890 PetscInt dim, depth, eStart, k, Nf, f, Nc, c, i, j, size = 0, offset = 0, foffset = 0; 3891 PetscBool vertexchart; 3892 PetscErrorCode ierr; 3893 3894 PetscFunctionBegin; 3895 if (point < 0) {ierr = DMPlexGetDepthStratum(dm, 1, &point, NULL);CHKERRQ(ierr);} 3896 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3897 ierr = DMPlexGetDepthLabel(dm, &label);CHKERRQ(ierr); 3898 ierr = DMLabelGetValue(label, point, &depth);CHKERRQ(ierr); 3899 if (depth == 1) {eStart = point;} 3900 else if (depth == dim) { 3901 const PetscInt *cone; 3902 3903 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 3904 if (dim == 2) eStart = cone[0]; 3905 else if (dim == 3) { 3906 const PetscInt *cone2; 3907 ierr = DMPlexGetCone(dm, cone[0], &cone2);CHKERRQ(ierr); 3908 eStart = cone2[0]; 3909 } else SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Point %D of depth %D cannot be used to bootstrap spectral ordering for dim %D", point, depth, dim); 3910 } else SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Point %D of depth %D cannot be used to bootstrap spectral ordering for dim %D", point, depth, dim); 3911 if (!section) {ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr);} 3912 { /* Determine whether the chart covers all points or just vertices. */ 3913 PetscInt pStart,pEnd,cStart,cEnd; 3914 ierr = DMPlexGetDepthStratum(dm,0,&pStart,&pEnd);CHKERRQ(ierr); 3915 ierr = PetscSectionGetChart(section,&cStart,&cEnd);CHKERRQ(ierr); 3916 if (pStart == cStart && pEnd == cEnd) vertexchart = PETSC_TRUE; /* Just vertices */ 3917 else vertexchart = PETSC_FALSE; /* Assume all interpolated points are in chart */ 3918 } 3919 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 3920 if (dim < 1) PetscFunctionReturn(0); 3921 for (f = 0; f < Nf; ++f) { 3922 ierr = PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);CHKERRQ(ierr); 3923 size += PetscPowInt(k+1, dim)*Nc; 3924 } 3925 ierr = PetscMalloc1(size, &perm);CHKERRQ(ierr); 3926 for (f = 0; f < Nf; ++f) { 3927 switch (dim) { 3928 case 1: 3929 ierr = PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);CHKERRQ(ierr); 3930 /* 3931 Original ordering is [ edge of length k-1; vtx0; vtx1 ] 3932 We want [ vtx0; edge of length k-1; vtx1 ] 3933 */ 3934 for (c=0; c<Nc; c++,offset++) perm[offset] = (k-1)*Nc + c + foffset; 3935 for (i=0; i<k-1; i++) for (c=0; c<Nc; c++,offset++) perm[offset] = i*Nc + c + foffset; 3936 for (c=0; c<Nc; c++,offset++) perm[offset] = k*Nc + c + foffset; 3937 foffset = offset; 3938 break; 3939 case 2: 3940 /* The original quad closure is oriented clockwise, {f, e_b, e_r, e_t, e_l, v_lb, v_rb, v_tr, v_tl} */ 3941 ierr = PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);CHKERRQ(ierr); 3942 /* The SEM order is 3943 3944 v_lb, {e_b}, v_rb, 3945 e^{(k-1)-i}_l, {f^{i*(k-1)}}, e^i_r, 3946 v_lt, reverse {e_t}, v_rt 3947 */ 3948 { 3949 const PetscInt of = 0; 3950 const PetscInt oeb = of + PetscSqr(k-1); 3951 const PetscInt oer = oeb + (k-1); 3952 const PetscInt oet = oer + (k-1); 3953 const PetscInt oel = oet + (k-1); 3954 const PetscInt ovlb = oel + (k-1); 3955 const PetscInt ovrb = ovlb + 1; 3956 const PetscInt ovrt = ovrb + 1; 3957 const PetscInt ovlt = ovrt + 1; 3958 PetscInt o; 3959 3960 /* bottom */ 3961 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlb*Nc + c + foffset; 3962 for (o = oeb; o < oer; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 3963 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrb*Nc + c + foffset; 3964 /* middle */ 3965 for (i = 0; i < k-1; ++i) { 3966 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oel+(k-2)-i)*Nc + c + foffset; 3967 for (o = of+(k-1)*i; o < of+(k-1)*(i+1); ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 3968 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oer+i)*Nc + c + foffset; 3969 } 3970 /* top */ 3971 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlt*Nc + c + foffset; 3972 for (o = oel-1; o >= oet; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 3973 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrt*Nc + c + foffset; 3974 foffset = offset; 3975 } 3976 break; 3977 case 3: 3978 /* The original hex closure is 3979 3980 {c, 3981 f_b, f_t, f_f, f_b, f_r, f_l, 3982 e_bl, e_bb, e_br, e_bf, e_tf, e_tr, e_tb, e_tl, e_rf, e_lf, e_lb, e_rb, 3983 v_blf, v_blb, v_brb, v_brf, v_tlf, v_trf, v_trb, v_tlb} 3984 */ 3985 ierr = PetscSectionFieldGetTensorDegree_Private(section,f,eStart,vertexchart,&Nc,&k);CHKERRQ(ierr); 3986 /* The SEM order is 3987 Bottom Slice 3988 v_blf, {e^{(k-1)-n}_bf}, v_brf, 3989 e^{i}_bl, f^{n*(k-1)+(k-1)-i}_b, e^{(k-1)-i}_br, 3990 v_blb, {e_bb}, v_brb, 3991 3992 Middle Slice (j) 3993 {e^{(k-1)-j}_lf}, {f^{j*(k-1)+n}_f}, e^j_rf, 3994 f^{i*(k-1)+j}_l, {c^{(j*(k-1) + i)*(k-1)+n}_t}, f^{j*(k-1)+i}_r, 3995 e^j_lb, {f^{j*(k-1)+(k-1)-n}_b}, e^{(k-1)-j}_rb, 3996 3997 Top Slice 3998 v_tlf, {e_tf}, v_trf, 3999 e^{(k-1)-i}_tl, {f^{i*(k-1)}_t}, e^{i}_tr, 4000 v_tlb, {e^{(k-1)-n}_tb}, v_trb, 4001 */ 4002 { 4003 const PetscInt oc = 0; 4004 const PetscInt ofb = oc + PetscSqr(k-1)*(k-1); 4005 const PetscInt oft = ofb + PetscSqr(k-1); 4006 const PetscInt off = oft + PetscSqr(k-1); 4007 const PetscInt ofk = off + PetscSqr(k-1); 4008 const PetscInt ofr = ofk + PetscSqr(k-1); 4009 const PetscInt ofl = ofr + PetscSqr(k-1); 4010 const PetscInt oebl = ofl + PetscSqr(k-1); 4011 const PetscInt oebb = oebl + (k-1); 4012 const PetscInt oebr = oebb + (k-1); 4013 const PetscInt oebf = oebr + (k-1); 4014 const PetscInt oetf = oebf + (k-1); 4015 const PetscInt oetr = oetf + (k-1); 4016 const PetscInt oetb = oetr + (k-1); 4017 const PetscInt oetl = oetb + (k-1); 4018 const PetscInt oerf = oetl + (k-1); 4019 const PetscInt oelf = oerf + (k-1); 4020 const PetscInt oelb = oelf + (k-1); 4021 const PetscInt oerb = oelb + (k-1); 4022 const PetscInt ovblf = oerb + (k-1); 4023 const PetscInt ovblb = ovblf + 1; 4024 const PetscInt ovbrb = ovblb + 1; 4025 const PetscInt ovbrf = ovbrb + 1; 4026 const PetscInt ovtlf = ovbrf + 1; 4027 const PetscInt ovtrf = ovtlf + 1; 4028 const PetscInt ovtrb = ovtrf + 1; 4029 const PetscInt ovtlb = ovtrb + 1; 4030 PetscInt o, n; 4031 4032 /* Bottom Slice */ 4033 /* bottom */ 4034 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblf*Nc + c + foffset; 4035 for (o = oetf-1; o >= oebf; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 4036 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrf*Nc + c + foffset; 4037 /* middle */ 4038 for (i = 0; i < k-1; ++i) { 4039 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebl+i)*Nc + c + foffset; 4040 for (n = 0; n < k-1; ++n) {o = ofb+n*(k-1)+i; for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset;} 4041 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebr+(k-2)-i)*Nc + c + foffset; 4042 } 4043 /* top */ 4044 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblb*Nc + c + foffset; 4045 for (o = oebb; o < oebr; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 4046 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrb*Nc + c + foffset; 4047 4048 /* Middle Slice */ 4049 for (j = 0; j < k-1; ++j) { 4050 /* bottom */ 4051 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelf+(k-2)-j)*Nc + c + foffset; 4052 for (o = off+j*(k-1); o < off+(j+1)*(k-1); ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 4053 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerf+j)*Nc + c + foffset; 4054 /* middle */ 4055 for (i = 0; i < k-1; ++i) { 4056 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofl+i*(k-1)+j)*Nc + c + foffset; 4057 for (n = 0; n < k-1; ++n) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oc+(j*(k-1)+i)*(k-1)+n)*Nc + c + foffset; 4058 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofr+j*(k-1)+i)*Nc + c + foffset; 4059 } 4060 /* top */ 4061 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelb+j)*Nc + c + foffset; 4062 for (o = ofk+j*(k-1)+(k-2); o >= ofk+j*(k-1); --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 4063 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerb+(k-2)-j)*Nc + c + foffset; 4064 } 4065 4066 /* Top Slice */ 4067 /* bottom */ 4068 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlf*Nc + c + foffset; 4069 for (o = oetf; o < oetr; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 4070 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrf*Nc + c + foffset; 4071 /* middle */ 4072 for (i = 0; i < k-1; ++i) { 4073 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetl+(k-2)-i)*Nc + c + foffset; 4074 for (n = 0; n < k-1; ++n) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oft+i*(k-1)+n)*Nc + c + foffset; 4075 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetr+i)*Nc + c + foffset; 4076 } 4077 /* top */ 4078 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlb*Nc + c + foffset; 4079 for (o = oetl-1; o >= oetb; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 4080 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrb*Nc + c + foffset; 4081 4082 foffset = offset; 4083 } 4084 break; 4085 default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No spectral ordering for dimension %D", dim); 4086 } 4087 } 4088 if (offset != size) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Number of permutation entries %D != %D", offset, size); 4089 /* Check permutation */ 4090 { 4091 PetscInt *check; 4092 4093 ierr = PetscMalloc1(size, &check);CHKERRQ(ierr); 4094 for (i = 0; i < size; ++i) {check[i] = -1; if (perm[i] < 0 || perm[i] >= size) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid permutation index p[%D] = %D", i, perm[i]);} 4095 for (i = 0; i < size; ++i) check[perm[i]] = i; 4096 for (i = 0; i < size; ++i) {if (check[i] < 0) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Missing permutation index %D", i);} 4097 ierr = PetscFree(check);CHKERRQ(ierr); 4098 } 4099 ierr = PetscSectionSetClosurePermutation_Internal(section, (PetscObject) dm, size, PETSC_OWN_POINTER, perm);CHKERRQ(ierr); 4100 PetscFunctionReturn(0); 4101 } 4102 4103 PetscErrorCode DMPlexGetPointDualSpaceFEM(DM dm, PetscInt point, PetscInt field, PetscDualSpace *dspace) 4104 { 4105 PetscDS prob; 4106 PetscInt depth, Nf, h; 4107 DMLabel label; 4108 PetscErrorCode ierr; 4109 4110 PetscFunctionBeginHot; 4111 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 4112 Nf = prob->Nf; 4113 label = dm->depthLabel; 4114 *dspace = NULL; 4115 if (field < Nf) { 4116 PetscObject disc = prob->disc[field]; 4117 4118 if (disc->classid == PETSCFE_CLASSID) { 4119 PetscDualSpace dsp; 4120 4121 ierr = PetscFEGetDualSpace((PetscFE)disc,&dsp);CHKERRQ(ierr); 4122 ierr = DMLabelGetNumValues(label,&depth);CHKERRQ(ierr); 4123 ierr = DMLabelGetValue(label,point,&h);CHKERRQ(ierr); 4124 h = depth - 1 - h; 4125 if (h) { 4126 ierr = PetscDualSpaceGetHeightSubspace(dsp,h,dspace);CHKERRQ(ierr); 4127 } else { 4128 *dspace = dsp; 4129 } 4130 } 4131 } 4132 PetscFunctionReturn(0); 4133 } 4134 4135 4136 PETSC_STATIC_INLINE PetscErrorCode DMPlexVecGetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 4137 { 4138 PetscScalar *array, *vArray; 4139 const PetscInt *cone, *coneO; 4140 PetscInt pStart, pEnd, p, numPoints, size = 0, offset = 0; 4141 PetscErrorCode ierr; 4142 4143 PetscFunctionBeginHot; 4144 ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); 4145 ierr = DMPlexGetConeSize(dm, point, &numPoints);CHKERRQ(ierr); 4146 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 4147 ierr = DMPlexGetConeOrientation(dm, point, &coneO);CHKERRQ(ierr); 4148 if (!values || !*values) { 4149 if ((point >= pStart) && (point < pEnd)) { 4150 PetscInt dof; 4151 4152 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4153 size += dof; 4154 } 4155 for (p = 0; p < numPoints; ++p) { 4156 const PetscInt cp = cone[p]; 4157 PetscInt dof; 4158 4159 if ((cp < pStart) || (cp >= pEnd)) continue; 4160 ierr = PetscSectionGetDof(section, cp, &dof);CHKERRQ(ierr); 4161 size += dof; 4162 } 4163 if (!values) { 4164 if (csize) *csize = size; 4165 PetscFunctionReturn(0); 4166 } 4167 ierr = DMGetWorkArray(dm, size, MPIU_SCALAR, &array);CHKERRQ(ierr); 4168 } else { 4169 array = *values; 4170 } 4171 size = 0; 4172 ierr = VecGetArray(v, &vArray);CHKERRQ(ierr); 4173 if ((point >= pStart) && (point < pEnd)) { 4174 PetscInt dof, off, d; 4175 PetscScalar *varr; 4176 4177 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4178 ierr = PetscSectionGetOffset(section, point, &off);CHKERRQ(ierr); 4179 varr = &vArray[off]; 4180 for (d = 0; d < dof; ++d, ++offset) { 4181 array[offset] = varr[d]; 4182 } 4183 size += dof; 4184 } 4185 for (p = 0; p < numPoints; ++p) { 4186 const PetscInt cp = cone[p]; 4187 PetscInt o = coneO[p]; 4188 PetscInt dof, off, d; 4189 PetscScalar *varr; 4190 4191 if ((cp < pStart) || (cp >= pEnd)) continue; 4192 ierr = PetscSectionGetDof(section, cp, &dof);CHKERRQ(ierr); 4193 ierr = PetscSectionGetOffset(section, cp, &off);CHKERRQ(ierr); 4194 varr = &vArray[off]; 4195 if (o >= 0) { 4196 for (d = 0; d < dof; ++d, ++offset) { 4197 array[offset] = varr[d]; 4198 } 4199 } else { 4200 for (d = dof-1; d >= 0; --d, ++offset) { 4201 array[offset] = varr[d]; 4202 } 4203 } 4204 size += dof; 4205 } 4206 ierr = VecRestoreArray(v, &vArray);CHKERRQ(ierr); 4207 if (!*values) { 4208 if (csize) *csize = size; 4209 *values = array; 4210 } else { 4211 if (size > *csize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Size of input array %D < actual size %D", *csize, size); 4212 *csize = size; 4213 } 4214 PetscFunctionReturn(0); 4215 } 4216 4217 PetscErrorCode DMPlexGetCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp) 4218 { 4219 const PetscInt *cla; 4220 PetscInt np, *pts = NULL; 4221 PetscErrorCode ierr; 4222 4223 PetscFunctionBeginHot; 4224 ierr = PetscSectionGetClosureIndex(section, (PetscObject) dm, clSec, clPoints);CHKERRQ(ierr); 4225 if (!*clPoints) { 4226 PetscInt pStart, pEnd, p, q; 4227 4228 ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); 4229 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &np, &pts);CHKERRQ(ierr); 4230 /* Compress out points not in the section */ 4231 for (p = 0, q = 0; p < np; p++) { 4232 PetscInt r = pts[2*p]; 4233 if ((r >= pStart) && (r < pEnd)) { 4234 pts[q*2] = r; 4235 pts[q*2+1] = pts[2*p+1]; 4236 ++q; 4237 } 4238 } 4239 np = q; 4240 cla = NULL; 4241 } else { 4242 PetscInt dof, off; 4243 4244 ierr = PetscSectionGetDof(*clSec, point, &dof);CHKERRQ(ierr); 4245 ierr = PetscSectionGetOffset(*clSec, point, &off);CHKERRQ(ierr); 4246 ierr = ISGetIndices(*clPoints, &cla);CHKERRQ(ierr); 4247 np = dof/2; 4248 pts = (PetscInt *) &cla[off]; 4249 } 4250 *numPoints = np; 4251 *points = pts; 4252 *clp = cla; 4253 4254 PetscFunctionReturn(0); 4255 } 4256 4257 PetscErrorCode DMPlexRestoreCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp) 4258 { 4259 PetscErrorCode ierr; 4260 4261 PetscFunctionBeginHot; 4262 if (!*clPoints) { 4263 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, numPoints, points);CHKERRQ(ierr); 4264 } else { 4265 ierr = ISRestoreIndices(*clPoints, clp);CHKERRQ(ierr); 4266 } 4267 *numPoints = 0; 4268 *points = NULL; 4269 *clSec = NULL; 4270 *clPoints = NULL; 4271 *clp = NULL; 4272 PetscFunctionReturn(0); 4273 } 4274 4275 PETSC_STATIC_INLINE PetscErrorCode DMPlexVecGetClosure_Static(DM dm, PetscSection section, PetscInt numPoints, const PetscInt points[], const PetscInt clperm[], const PetscScalar vArray[], PetscInt *size, PetscScalar array[]) 4276 { 4277 PetscInt offset = 0, p; 4278 const PetscInt **perms = NULL; 4279 const PetscScalar **flips = NULL; 4280 PetscErrorCode ierr; 4281 4282 PetscFunctionBeginHot; 4283 *size = 0; 4284 ierr = PetscSectionGetPointSyms(section,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4285 for (p = 0; p < numPoints; p++) { 4286 const PetscInt point = points[2*p]; 4287 const PetscInt *perm = perms ? perms[p] : NULL; 4288 const PetscScalar *flip = flips ? flips[p] : NULL; 4289 PetscInt dof, off, d; 4290 const PetscScalar *varr; 4291 4292 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4293 ierr = PetscSectionGetOffset(section, point, &off);CHKERRQ(ierr); 4294 varr = &vArray[off]; 4295 if (clperm) { 4296 if (perm) { 4297 for (d = 0; d < dof; d++) array[clperm[offset + perm[d]]] = varr[d]; 4298 } else { 4299 for (d = 0; d < dof; d++) array[clperm[offset + d ]] = varr[d]; 4300 } 4301 if (flip) { 4302 for (d = 0; d < dof; d++) array[clperm[offset + d ]] *= flip[d]; 4303 } 4304 } else { 4305 if (perm) { 4306 for (d = 0; d < dof; d++) array[offset + perm[d]] = varr[d]; 4307 } else { 4308 for (d = 0; d < dof; d++) array[offset + d ] = varr[d]; 4309 } 4310 if (flip) { 4311 for (d = 0; d < dof; d++) array[offset + d ] *= flip[d]; 4312 } 4313 } 4314 offset += dof; 4315 } 4316 ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4317 *size = offset; 4318 PetscFunctionReturn(0); 4319 } 4320 4321 PETSC_STATIC_INLINE PetscErrorCode DMPlexVecGetClosure_Fields_Static(DM dm, PetscSection section, PetscInt numPoints, const PetscInt points[], PetscInt numFields, const PetscInt clperm[], const PetscScalar vArray[], PetscInt *size, PetscScalar array[]) 4322 { 4323 PetscInt offset = 0, f; 4324 PetscErrorCode ierr; 4325 4326 PetscFunctionBeginHot; 4327 *size = 0; 4328 for (f = 0; f < numFields; ++f) { 4329 PetscInt p; 4330 const PetscInt **perms = NULL; 4331 const PetscScalar **flips = NULL; 4332 4333 ierr = PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4334 for (p = 0; p < numPoints; p++) { 4335 const PetscInt point = points[2*p]; 4336 PetscInt fdof, foff, b; 4337 const PetscScalar *varr; 4338 const PetscInt *perm = perms ? perms[p] : NULL; 4339 const PetscScalar *flip = flips ? flips[p] : NULL; 4340 4341 ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); 4342 ierr = PetscSectionGetFieldOffset(section, point, f, &foff);CHKERRQ(ierr); 4343 varr = &vArray[foff]; 4344 if (clperm) { 4345 if (perm) {for (b = 0; b < fdof; b++) {array[clperm[offset + perm[b]]] = varr[b];}} 4346 else {for (b = 0; b < fdof; b++) {array[clperm[offset + b ]] = varr[b];}} 4347 if (flip) {for (b = 0; b < fdof; b++) {array[clperm[offset + b ]] *= flip[b];}} 4348 } else { 4349 if (perm) {for (b = 0; b < fdof; b++) {array[offset + perm[b]] = varr[b];}} 4350 else {for (b = 0; b < fdof; b++) {array[offset + b ] = varr[b];}} 4351 if (flip) {for (b = 0; b < fdof; b++) {array[offset + b ] *= flip[b];}} 4352 } 4353 offset += fdof; 4354 } 4355 ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4356 } 4357 *size = offset; 4358 PetscFunctionReturn(0); 4359 } 4360 4361 /*@C 4362 DMPlexVecGetClosure - Get an array of the values on the closure of 'point' 4363 4364 Not collective 4365 4366 Input Parameters: 4367 + dm - The DM 4368 . section - The section describing the layout in v, or NULL to use the default section 4369 . v - The local vector 4370 . point - The point in the DM 4371 . csize - The size of the input values array, or NULL 4372 - values - An array to use for the values, or NULL to have it allocated automatically 4373 4374 Output Parameters: 4375 + csize - The number of values in the closure 4376 - values - The array of values. If the user provided NULL, it is a borrowed array and should not be freed 4377 4378 $ Note that DMPlexVecGetClosure/DMPlexVecRestoreClosure only allocates the values array if it set to NULL in the 4379 $ calling function. This is because DMPlexVecGetClosure() is typically called in the inner loop of a Vec or Mat 4380 $ assembly function, and a user may already have allocated storage for this operation. 4381 $ 4382 $ A typical use could be 4383 $ 4384 $ values = NULL; 4385 $ ierr = DMPlexVecGetClosure(dm, NULL, v, p, &clSize, &values);CHKERRQ(ierr); 4386 $ for (cl = 0; cl < clSize; ++cl) { 4387 $ <Compute on closure> 4388 $ } 4389 $ ierr = DMPlexVecRestoreClosure(dm, NULL, v, p, &clSize, &values);CHKERRQ(ierr); 4390 $ 4391 $ or 4392 $ 4393 $ PetscMalloc1(clMaxSize, &values); 4394 $ for (p = pStart; p < pEnd; ++p) { 4395 $ clSize = clMaxSize; 4396 $ ierr = DMPlexVecGetClosure(dm, NULL, v, p, &clSize, &values);CHKERRQ(ierr); 4397 $ for (cl = 0; cl < clSize; ++cl) { 4398 $ <Compute on closure> 4399 $ } 4400 $ } 4401 $ PetscFree(values); 4402 4403 Fortran Notes: 4404 Since it returns an array, this routine is only available in Fortran 90, and you must 4405 include petsc.h90 in your code. 4406 4407 The csize argument is not present in the Fortran 90 binding since it is internal to the array. 4408 4409 Level: intermediate 4410 4411 .seealso DMPlexVecRestoreClosure(), DMPlexVecSetClosure(), DMPlexMatSetClosure() 4412 @*/ 4413 PetscErrorCode DMPlexVecGetClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 4414 { 4415 PetscSection clSection; 4416 IS clPoints; 4417 PetscScalar *array; 4418 const PetscScalar *vArray; 4419 PetscInt *points = NULL; 4420 const PetscInt *clp, *perm; 4421 PetscInt depth, numFields, numPoints, size; 4422 PetscErrorCode ierr; 4423 4424 PetscFunctionBeginHot; 4425 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4426 if (!section) {ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr);} 4427 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 4428 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 4429 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 4430 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 4431 if (depth == 1 && numFields < 2) { 4432 ierr = DMPlexVecGetClosure_Depth1_Static(dm, section, v, point, csize, values);CHKERRQ(ierr); 4433 PetscFunctionReturn(0); 4434 } 4435 /* Get points */ 4436 ierr = DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4437 ierr = PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &perm);CHKERRQ(ierr); 4438 /* Get array */ 4439 if (!values || !*values) { 4440 PetscInt asize = 0, dof, p; 4441 4442 for (p = 0; p < numPoints*2; p += 2) { 4443 ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); 4444 asize += dof; 4445 } 4446 if (!values) { 4447 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4448 if (csize) *csize = asize; 4449 PetscFunctionReturn(0); 4450 } 4451 ierr = DMGetWorkArray(dm, asize, MPIU_SCALAR, &array);CHKERRQ(ierr); 4452 } else { 4453 array = *values; 4454 } 4455 ierr = VecGetArrayRead(v, &vArray);CHKERRQ(ierr); 4456 /* Get values */ 4457 if (numFields > 0) {ierr = DMPlexVecGetClosure_Fields_Static(dm, section, numPoints, points, numFields, perm, vArray, &size, array);CHKERRQ(ierr);} 4458 else {ierr = DMPlexVecGetClosure_Static(dm, section, numPoints, points, perm, vArray, &size, array);CHKERRQ(ierr);} 4459 /* Cleanup points */ 4460 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4461 /* Cleanup array */ 4462 ierr = VecRestoreArrayRead(v, &vArray);CHKERRQ(ierr); 4463 if (!*values) { 4464 if (csize) *csize = size; 4465 *values = array; 4466 } else { 4467 if (size > *csize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Size of input array %D < actual size %D", *csize, size); 4468 *csize = size; 4469 } 4470 PetscFunctionReturn(0); 4471 } 4472 4473 /*@C 4474 DMPlexVecRestoreClosure - Restore the array of the values on the closure of 'point' 4475 4476 Not collective 4477 4478 Input Parameters: 4479 + dm - The DM 4480 . section - The section describing the layout in v, or NULL to use the default section 4481 . v - The local vector 4482 . point - The point in the DM 4483 . csize - The number of values in the closure, or NULL 4484 - values - The array of values, which is a borrowed array and should not be freed 4485 4486 Note that the array values are discarded and not copied back into v. In order to copy values back to v, use DMPlexVecSetClosure() 4487 4488 Fortran Notes: 4489 Since it returns an array, this routine is only available in Fortran 90, and you must 4490 include petsc.h90 in your code. 4491 4492 The csize argument is not present in the Fortran 90 binding since it is internal to the array. 4493 4494 Level: intermediate 4495 4496 .seealso DMPlexVecGetClosure(), DMPlexVecSetClosure(), DMPlexMatSetClosure() 4497 @*/ 4498 PetscErrorCode DMPlexVecRestoreClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 4499 { 4500 PetscInt size = 0; 4501 PetscErrorCode ierr; 4502 4503 PetscFunctionBegin; 4504 /* Should work without recalculating size */ 4505 ierr = DMRestoreWorkArray(dm, size, MPIU_SCALAR, (void*) values);CHKERRQ(ierr); 4506 *values = NULL; 4507 PetscFunctionReturn(0); 4508 } 4509 4510 PETSC_STATIC_INLINE void add (PetscScalar *x, PetscScalar y) {*x += y;} 4511 PETSC_STATIC_INLINE void insert(PetscScalar *x, PetscScalar y) {*x = y;} 4512 4513 PETSC_STATIC_INLINE PetscErrorCode updatePoint_private(PetscSection section, PetscInt point, PetscInt dof, void (*fuse)(PetscScalar*, PetscScalar), PetscBool setBC, const PetscInt perm[], const PetscScalar flip[], const PetscInt clperm[], const PetscScalar values[], PetscInt offset, PetscScalar array[]) 4514 { 4515 PetscInt cdof; /* The number of constraints on this point */ 4516 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 4517 PetscScalar *a; 4518 PetscInt off, cind = 0, k; 4519 PetscErrorCode ierr; 4520 4521 PetscFunctionBegin; 4522 ierr = PetscSectionGetConstraintDof(section, point, &cdof);CHKERRQ(ierr); 4523 ierr = PetscSectionGetOffset(section, point, &off);CHKERRQ(ierr); 4524 a = &array[off]; 4525 if (!cdof || setBC) { 4526 if (clperm) { 4527 if (perm) {for (k = 0; k < dof; ++k) {fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.));}} 4528 else {for (k = 0; k < dof; ++k) {fuse(&a[k], values[clperm[offset+ k ]] * (flip ? flip[ k ] : 1.));}} 4529 } else { 4530 if (perm) {for (k = 0; k < dof; ++k) {fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.));}} 4531 else {for (k = 0; k < dof; ++k) {fuse(&a[k], values[offset+ k ] * (flip ? flip[ k ] : 1.));}} 4532 } 4533 } else { 4534 ierr = PetscSectionGetConstraintIndices(section, point, &cdofs);CHKERRQ(ierr); 4535 if (clperm) { 4536 if (perm) {for (k = 0; k < dof; ++k) { 4537 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4538 fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.)); 4539 } 4540 } else { 4541 for (k = 0; k < dof; ++k) { 4542 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4543 fuse(&a[k], values[clperm[offset+ k ]] * (flip ? flip[ k ] : 1.)); 4544 } 4545 } 4546 } else { 4547 if (perm) { 4548 for (k = 0; k < dof; ++k) { 4549 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4550 fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.)); 4551 } 4552 } else { 4553 for (k = 0; k < dof; ++k) { 4554 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4555 fuse(&a[k], values[offset+ k ] * (flip ? flip[ k ] : 1.)); 4556 } 4557 } 4558 } 4559 } 4560 PetscFunctionReturn(0); 4561 } 4562 4563 PETSC_STATIC_INLINE PetscErrorCode updatePointBC_private(PetscSection section, PetscInt point, PetscInt dof, void (*fuse)(PetscScalar*, PetscScalar), const PetscInt perm[], const PetscScalar flip[], const PetscInt clperm[], const PetscScalar values[], PetscInt offset, PetscScalar array[]) 4564 { 4565 PetscInt cdof; /* The number of constraints on this point */ 4566 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 4567 PetscScalar *a; 4568 PetscInt off, cind = 0, k; 4569 PetscErrorCode ierr; 4570 4571 PetscFunctionBegin; 4572 ierr = PetscSectionGetConstraintDof(section, point, &cdof);CHKERRQ(ierr); 4573 ierr = PetscSectionGetOffset(section, point, &off);CHKERRQ(ierr); 4574 a = &array[off]; 4575 if (cdof) { 4576 ierr = PetscSectionGetConstraintIndices(section, point, &cdofs);CHKERRQ(ierr); 4577 if (clperm) { 4578 if (perm) { 4579 for (k = 0; k < dof; ++k) { 4580 if ((cind < cdof) && (k == cdofs[cind])) { 4581 fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.)); 4582 cind++; 4583 } 4584 } 4585 } else { 4586 for (k = 0; k < dof; ++k) { 4587 if ((cind < cdof) && (k == cdofs[cind])) { 4588 fuse(&a[k], values[clperm[offset+ k ]] * (flip ? flip[ k ] : 1.)); 4589 cind++; 4590 } 4591 } 4592 } 4593 } else { 4594 if (perm) { 4595 for (k = 0; k < dof; ++k) { 4596 if ((cind < cdof) && (k == cdofs[cind])) { 4597 fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.)); 4598 cind++; 4599 } 4600 } 4601 } else { 4602 for (k = 0; k < dof; ++k) { 4603 if ((cind < cdof) && (k == cdofs[cind])) { 4604 fuse(&a[k], values[offset+ k ] * (flip ? flip[ k ] : 1.)); 4605 cind++; 4606 } 4607 } 4608 } 4609 } 4610 } 4611 PetscFunctionReturn(0); 4612 } 4613 4614 PETSC_STATIC_INLINE PetscErrorCode updatePointFields_private(PetscSection section, PetscInt point, const PetscInt *perm, const PetscScalar *flip, PetscInt f, void (*fuse)(PetscScalar*, PetscScalar), PetscBool setBC, const PetscInt clperm[], const PetscScalar values[], PetscInt *offset, PetscScalar array[]) 4615 { 4616 PetscScalar *a; 4617 PetscInt fdof, foff, fcdof, foffset = *offset; 4618 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 4619 PetscInt cind = 0, b; 4620 PetscErrorCode ierr; 4621 4622 PetscFunctionBegin; 4623 ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); 4624 ierr = PetscSectionGetFieldConstraintDof(section, point, f, &fcdof);CHKERRQ(ierr); 4625 ierr = PetscSectionGetFieldOffset(section, point, f, &foff);CHKERRQ(ierr); 4626 a = &array[foff]; 4627 if (!fcdof || setBC) { 4628 if (clperm) { 4629 if (perm) {for (b = 0; b < fdof; b++) {fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));}} 4630 else {for (b = 0; b < fdof; b++) {fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.));}} 4631 } else { 4632 if (perm) {for (b = 0; b < fdof; b++) {fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));}} 4633 else {for (b = 0; b < fdof; b++) {fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.));}} 4634 } 4635 } else { 4636 ierr = PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);CHKERRQ(ierr); 4637 if (clperm) { 4638 if (perm) { 4639 for (b = 0; b < fdof; b++) { 4640 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;} 4641 fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.)); 4642 } 4643 } else { 4644 for (b = 0; b < fdof; b++) { 4645 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;} 4646 fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.)); 4647 } 4648 } 4649 } else { 4650 if (perm) { 4651 for (b = 0; b < fdof; b++) { 4652 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;} 4653 fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.)); 4654 } 4655 } else { 4656 for (b = 0; b < fdof; b++) { 4657 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;} 4658 fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.)); 4659 } 4660 } 4661 } 4662 } 4663 *offset += fdof; 4664 PetscFunctionReturn(0); 4665 } 4666 4667 PETSC_STATIC_INLINE PetscErrorCode updatePointFieldsBC_private(PetscSection section, PetscInt point, const PetscInt perm[], const PetscScalar flip[], PetscInt f, PetscInt Ncc, const PetscInt comps[], void (*fuse)(PetscScalar*, PetscScalar), const PetscInt clperm[], const PetscScalar values[], PetscInt *offset, PetscScalar array[]) 4668 { 4669 PetscScalar *a; 4670 PetscInt fdof, foff, fcdof, foffset = *offset; 4671 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 4672 PetscInt cind = 0, ncind = 0, b; 4673 PetscBool ncSet, fcSet; 4674 PetscErrorCode ierr; 4675 4676 PetscFunctionBegin; 4677 ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); 4678 ierr = PetscSectionGetFieldConstraintDof(section, point, f, &fcdof);CHKERRQ(ierr); 4679 ierr = PetscSectionGetFieldOffset(section, point, f, &foff);CHKERRQ(ierr); 4680 a = &array[foff]; 4681 if (fcdof) { 4682 /* We just override fcdof and fcdofs with Ncc and comps */ 4683 ierr = PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);CHKERRQ(ierr); 4684 if (clperm) { 4685 if (perm) { 4686 if (comps) { 4687 for (b = 0; b < fdof; b++) { 4688 ncSet = fcSet = PETSC_FALSE; 4689 if ((ncind < Ncc) && (b == comps[ncind])) {++ncind; ncSet = PETSC_TRUE;} 4690 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; fcSet = PETSC_TRUE;} 4691 if (ncSet && fcSet) {fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));} 4692 } 4693 } else { 4694 for (b = 0; b < fdof; b++) { 4695 if ((cind < fcdof) && (b == fcdofs[cind])) { 4696 fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.)); 4697 ++cind; 4698 } 4699 } 4700 } 4701 } else { 4702 if (comps) { 4703 for (b = 0; b < fdof; b++) { 4704 ncSet = fcSet = PETSC_FALSE; 4705 if ((ncind < Ncc) && (b == comps[ncind])) {++ncind; ncSet = PETSC_TRUE;} 4706 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; fcSet = PETSC_TRUE;} 4707 if (ncSet && fcSet) {fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.));} 4708 } 4709 } else { 4710 for (b = 0; b < fdof; b++) { 4711 if ((cind < fcdof) && (b == fcdofs[cind])) { 4712 fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.)); 4713 ++cind; 4714 } 4715 } 4716 } 4717 } 4718 } else { 4719 if (perm) { 4720 if (comps) { 4721 for (b = 0; b < fdof; b++) { 4722 ncSet = fcSet = PETSC_FALSE; 4723 if ((ncind < Ncc) && (b == comps[ncind])) {++ncind; ncSet = PETSC_TRUE;} 4724 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; fcSet = PETSC_TRUE;} 4725 if (ncSet && fcSet) {fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));} 4726 } 4727 } else { 4728 for (b = 0; b < fdof; b++) { 4729 if ((cind < fcdof) && (b == fcdofs[cind])) { 4730 fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.)); 4731 ++cind; 4732 } 4733 } 4734 } 4735 } else { 4736 if (comps) { 4737 for (b = 0; b < fdof; b++) { 4738 ncSet = fcSet = PETSC_FALSE; 4739 if ((ncind < Ncc) && (b == comps[ncind])) {++ncind; ncSet = PETSC_TRUE;} 4740 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; fcSet = PETSC_TRUE;} 4741 if (ncSet && fcSet) {fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.));} 4742 } 4743 } else { 4744 for (b = 0; b < fdof; b++) { 4745 if ((cind < fcdof) && (b == fcdofs[cind])) { 4746 fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.)); 4747 ++cind; 4748 } 4749 } 4750 } 4751 } 4752 } 4753 } 4754 *offset += fdof; 4755 PetscFunctionReturn(0); 4756 } 4757 4758 PETSC_STATIC_INLINE PetscErrorCode DMPlexVecSetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode) 4759 { 4760 PetscScalar *array; 4761 const PetscInt *cone, *coneO; 4762 PetscInt pStart, pEnd, p, numPoints, off, dof; 4763 PetscErrorCode ierr; 4764 4765 PetscFunctionBeginHot; 4766 ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); 4767 ierr = DMPlexGetConeSize(dm, point, &numPoints);CHKERRQ(ierr); 4768 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 4769 ierr = DMPlexGetConeOrientation(dm, point, &coneO);CHKERRQ(ierr); 4770 ierr = VecGetArray(v, &array);CHKERRQ(ierr); 4771 for (p = 0, off = 0; p <= numPoints; ++p, off += dof) { 4772 const PetscInt cp = !p ? point : cone[p-1]; 4773 const PetscInt o = !p ? 0 : coneO[p-1]; 4774 4775 if ((cp < pStart) || (cp >= pEnd)) {dof = 0; continue;} 4776 ierr = PetscSectionGetDof(section, cp, &dof);CHKERRQ(ierr); 4777 /* ADD_VALUES */ 4778 { 4779 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 4780 PetscScalar *a; 4781 PetscInt cdof, coff, cind = 0, k; 4782 4783 ierr = PetscSectionGetConstraintDof(section, cp, &cdof);CHKERRQ(ierr); 4784 ierr = PetscSectionGetOffset(section, cp, &coff);CHKERRQ(ierr); 4785 a = &array[coff]; 4786 if (!cdof) { 4787 if (o >= 0) { 4788 for (k = 0; k < dof; ++k) { 4789 a[k] += values[off+k]; 4790 } 4791 } else { 4792 for (k = 0; k < dof; ++k) { 4793 a[k] += values[off+dof-k-1]; 4794 } 4795 } 4796 } else { 4797 ierr = PetscSectionGetConstraintIndices(section, cp, &cdofs);CHKERRQ(ierr); 4798 if (o >= 0) { 4799 for (k = 0; k < dof; ++k) { 4800 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4801 a[k] += values[off+k]; 4802 } 4803 } else { 4804 for (k = 0; k < dof; ++k) { 4805 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4806 a[k] += values[off+dof-k-1]; 4807 } 4808 } 4809 } 4810 } 4811 } 4812 ierr = VecRestoreArray(v, &array);CHKERRQ(ierr); 4813 PetscFunctionReturn(0); 4814 } 4815 4816 /*@C 4817 DMPlexVecSetClosure - Set an array of the values on the closure of 'point' 4818 4819 Not collective 4820 4821 Input Parameters: 4822 + dm - The DM 4823 . section - The section describing the layout in v, or NULL to use the default section 4824 . v - The local vector 4825 . point - The point in the DM 4826 . values - The array of values 4827 - mode - The insert mode. One of INSERT_ALL_VALUES, ADD_ALL_VALUES, INSERT_VALUES, ADD_VALUES, INSERT_BC_VALUES, and ADD_BC_VALUES, 4828 where INSERT_ALL_VALUES and ADD_ALL_VALUES also overwrite boundary conditions. 4829 4830 Fortran Notes: 4831 This routine is only available in Fortran 90, and you must include petsc.h90 in your code. 4832 4833 Level: intermediate 4834 4835 .seealso DMPlexVecGetClosure(), DMPlexMatSetClosure() 4836 @*/ 4837 PetscErrorCode DMPlexVecSetClosure(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode) 4838 { 4839 PetscSection clSection; 4840 IS clPoints; 4841 PetscScalar *array; 4842 PetscInt *points = NULL; 4843 const PetscInt *clp, *clperm; 4844 PetscInt depth, numFields, numPoints, p; 4845 PetscErrorCode ierr; 4846 4847 PetscFunctionBeginHot; 4848 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4849 if (!section) {ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr);} 4850 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 4851 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 4852 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 4853 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 4854 if (depth == 1 && numFields < 2 && mode == ADD_VALUES) { 4855 ierr = DMPlexVecSetClosure_Depth1_Static(dm, section, v, point, values, mode);CHKERRQ(ierr); 4856 PetscFunctionReturn(0); 4857 } 4858 /* Get points */ 4859 ierr = PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &clperm);CHKERRQ(ierr); 4860 ierr = DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4861 /* Get array */ 4862 ierr = VecGetArray(v, &array);CHKERRQ(ierr); 4863 /* Get values */ 4864 if (numFields > 0) { 4865 PetscInt offset = 0, f; 4866 for (f = 0; f < numFields; ++f) { 4867 const PetscInt **perms = NULL; 4868 const PetscScalar **flips = NULL; 4869 4870 ierr = PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4871 switch (mode) { 4872 case INSERT_VALUES: 4873 for (p = 0; p < numPoints; p++) { 4874 const PetscInt point = points[2*p]; 4875 const PetscInt *perm = perms ? perms[p] : NULL; 4876 const PetscScalar *flip = flips ? flips[p] : NULL; 4877 updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, clperm, values, &offset, array); 4878 } break; 4879 case INSERT_ALL_VALUES: 4880 for (p = 0; p < numPoints; p++) { 4881 const PetscInt point = points[2*p]; 4882 const PetscInt *perm = perms ? perms[p] : NULL; 4883 const PetscScalar *flip = flips ? flips[p] : NULL; 4884 updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, clperm, values, &offset, array); 4885 } break; 4886 case INSERT_BC_VALUES: 4887 for (p = 0; p < numPoints; p++) { 4888 const PetscInt point = points[2*p]; 4889 const PetscInt *perm = perms ? perms[p] : NULL; 4890 const PetscScalar *flip = flips ? flips[p] : NULL; 4891 updatePointFieldsBC_private(section, point, perm, flip, f, -1, NULL, insert, clperm, values, &offset, array); 4892 } break; 4893 case ADD_VALUES: 4894 for (p = 0; p < numPoints; p++) { 4895 const PetscInt point = points[2*p]; 4896 const PetscInt *perm = perms ? perms[p] : NULL; 4897 const PetscScalar *flip = flips ? flips[p] : NULL; 4898 updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, clperm, values, &offset, array); 4899 } break; 4900 case ADD_ALL_VALUES: 4901 for (p = 0; p < numPoints; p++) { 4902 const PetscInt point = points[2*p]; 4903 const PetscInt *perm = perms ? perms[p] : NULL; 4904 const PetscScalar *flip = flips ? flips[p] : NULL; 4905 updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, clperm, values, &offset, array); 4906 } break; 4907 case ADD_BC_VALUES: 4908 for (p = 0; p < numPoints; p++) { 4909 const PetscInt point = points[2*p]; 4910 const PetscInt *perm = perms ? perms[p] : NULL; 4911 const PetscScalar *flip = flips ? flips[p] : NULL; 4912 updatePointFieldsBC_private(section, point, perm, flip, f, -1, NULL, add, clperm, values, &offset, array); 4913 } break; 4914 default: 4915 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 4916 } 4917 ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4918 } 4919 } else { 4920 PetscInt dof, off; 4921 const PetscInt **perms = NULL; 4922 const PetscScalar **flips = NULL; 4923 4924 ierr = PetscSectionGetPointSyms(section,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4925 switch (mode) { 4926 case INSERT_VALUES: 4927 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4928 const PetscInt point = points[2*p]; 4929 const PetscInt *perm = perms ? perms[p] : NULL; 4930 const PetscScalar *flip = flips ? flips[p] : NULL; 4931 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4932 updatePoint_private(section, point, dof, insert, PETSC_FALSE, perm, flip, clperm, values, off, array); 4933 } break; 4934 case INSERT_ALL_VALUES: 4935 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4936 const PetscInt point = points[2*p]; 4937 const PetscInt *perm = perms ? perms[p] : NULL; 4938 const PetscScalar *flip = flips ? flips[p] : NULL; 4939 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4940 updatePoint_private(section, point, dof, insert, PETSC_TRUE, perm, flip, clperm, values, off, array); 4941 } break; 4942 case INSERT_BC_VALUES: 4943 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4944 const PetscInt point = points[2*p]; 4945 const PetscInt *perm = perms ? perms[p] : NULL; 4946 const PetscScalar *flip = flips ? flips[p] : NULL; 4947 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4948 updatePointBC_private(section, point, dof, insert, perm, flip, clperm, values, off, array); 4949 } break; 4950 case ADD_VALUES: 4951 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4952 const PetscInt point = points[2*p]; 4953 const PetscInt *perm = perms ? perms[p] : NULL; 4954 const PetscScalar *flip = flips ? flips[p] : NULL; 4955 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4956 updatePoint_private(section, point, dof, add, PETSC_FALSE, perm, flip, clperm, values, off, array); 4957 } break; 4958 case ADD_ALL_VALUES: 4959 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4960 const PetscInt point = points[2*p]; 4961 const PetscInt *perm = perms ? perms[p] : NULL; 4962 const PetscScalar *flip = flips ? flips[p] : NULL; 4963 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4964 updatePoint_private(section, point, dof, add, PETSC_TRUE, perm, flip, clperm, values, off, array); 4965 } break; 4966 case ADD_BC_VALUES: 4967 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4968 const PetscInt point = points[2*p]; 4969 const PetscInt *perm = perms ? perms[p] : NULL; 4970 const PetscScalar *flip = flips ? flips[p] : NULL; 4971 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4972 updatePointBC_private(section, point, dof, add, perm, flip, clperm, values, off, array); 4973 } break; 4974 default: 4975 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 4976 } 4977 ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4978 } 4979 /* Cleanup points */ 4980 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4981 /* Cleanup array */ 4982 ierr = VecRestoreArray(v, &array);CHKERRQ(ierr); 4983 PetscFunctionReturn(0); 4984 } 4985 4986 PetscErrorCode DMPlexVecSetFieldClosure_Internal(DM dm, PetscSection section, Vec v, PetscBool fieldActive[], PetscInt point, PetscInt Ncc, const PetscInt comps[], const PetscScalar values[], InsertMode mode) 4987 { 4988 PetscSection clSection; 4989 IS clPoints; 4990 PetscScalar *array; 4991 PetscInt *points = NULL; 4992 const PetscInt *clp, *clperm; 4993 PetscInt numFields, numPoints, p; 4994 PetscInt offset = 0, f; 4995 PetscErrorCode ierr; 4996 4997 PetscFunctionBeginHot; 4998 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4999 if (!section) {ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr);} 5000 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 5001 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 5002 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 5003 /* Get points */ 5004 ierr = PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &clperm);CHKERRQ(ierr); 5005 ierr = DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5006 /* Get array */ 5007 ierr = VecGetArray(v, &array);CHKERRQ(ierr); 5008 /* Get values */ 5009 for (f = 0; f < numFields; ++f) { 5010 const PetscInt **perms = NULL; 5011 const PetscScalar **flips = NULL; 5012 5013 if (!fieldActive[f]) { 5014 for (p = 0; p < numPoints*2; p += 2) { 5015 PetscInt fdof; 5016 ierr = PetscSectionGetFieldDof(section, points[p], f, &fdof);CHKERRQ(ierr); 5017 offset += fdof; 5018 } 5019 continue; 5020 } 5021 ierr = PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 5022 switch (mode) { 5023 case INSERT_VALUES: 5024 for (p = 0; p < numPoints; p++) { 5025 const PetscInt point = points[2*p]; 5026 const PetscInt *perm = perms ? perms[p] : NULL; 5027 const PetscScalar *flip = flips ? flips[p] : NULL; 5028 updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, clperm, values, &offset, array); 5029 } break; 5030 case INSERT_ALL_VALUES: 5031 for (p = 0; p < numPoints; p++) { 5032 const PetscInt point = points[2*p]; 5033 const PetscInt *perm = perms ? perms[p] : NULL; 5034 const PetscScalar *flip = flips ? flips[p] : NULL; 5035 updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, clperm, values, &offset, array); 5036 } break; 5037 case INSERT_BC_VALUES: 5038 for (p = 0; p < numPoints; p++) { 5039 const PetscInt point = points[2*p]; 5040 const PetscInt *perm = perms ? perms[p] : NULL; 5041 const PetscScalar *flip = flips ? flips[p] : NULL; 5042 updatePointFieldsBC_private(section, point, perm, flip, f, Ncc, comps, insert, clperm, values, &offset, array); 5043 } break; 5044 case ADD_VALUES: 5045 for (p = 0; p < numPoints; p++) { 5046 const PetscInt point = points[2*p]; 5047 const PetscInt *perm = perms ? perms[p] : NULL; 5048 const PetscScalar *flip = flips ? flips[p] : NULL; 5049 updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, clperm, values, &offset, array); 5050 } break; 5051 case ADD_ALL_VALUES: 5052 for (p = 0; p < numPoints; p++) { 5053 const PetscInt point = points[2*p]; 5054 const PetscInt *perm = perms ? perms[p] : NULL; 5055 const PetscScalar *flip = flips ? flips[p] : NULL; 5056 updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, clperm, values, &offset, array); 5057 } break; 5058 default: 5059 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 5060 } 5061 ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 5062 } 5063 /* Cleanup points */ 5064 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5065 /* Cleanup array */ 5066 ierr = VecRestoreArray(v, &array);CHKERRQ(ierr); 5067 PetscFunctionReturn(0); 5068 } 5069 5070 static PetscErrorCode DMPlexPrintMatSetValues(PetscViewer viewer, Mat A, PetscInt point, PetscInt numRIndices, const PetscInt rindices[], PetscInt numCIndices, const PetscInt cindices[], const PetscScalar values[]) 5071 { 5072 PetscMPIInt rank; 5073 PetscInt i, j; 5074 PetscErrorCode ierr; 5075 5076 PetscFunctionBegin; 5077 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);CHKERRQ(ierr); 5078 ierr = PetscViewerASCIIPrintf(viewer, "[%d]mat for point %D\n", rank, point);CHKERRQ(ierr); 5079 for (i = 0; i < numRIndices; i++) {ierr = PetscViewerASCIIPrintf(viewer, "[%d]mat row indices[%D] = %D\n", rank, i, rindices[i]);CHKERRQ(ierr);} 5080 for (i = 0; i < numCIndices; i++) {ierr = PetscViewerASCIIPrintf(viewer, "[%d]mat col indices[%D] = %D\n", rank, i, cindices[i]);CHKERRQ(ierr);} 5081 numCIndices = numCIndices ? numCIndices : numRIndices; 5082 for (i = 0; i < numRIndices; i++) { 5083 ierr = PetscViewerASCIIPrintf(viewer, "[%d]", rank);CHKERRQ(ierr); 5084 for (j = 0; j < numCIndices; j++) { 5085 #if defined(PETSC_USE_COMPLEX) 5086 ierr = PetscViewerASCIIPrintf(viewer, " (%g,%g)", (double)PetscRealPart(values[i*numCIndices+j]), (double)PetscImaginaryPart(values[i*numCIndices+j]));CHKERRQ(ierr); 5087 #else 5088 ierr = PetscViewerASCIIPrintf(viewer, " %g", (double)values[i*numCIndices+j]);CHKERRQ(ierr); 5089 #endif 5090 } 5091 ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); 5092 } 5093 PetscFunctionReturn(0); 5094 } 5095 5096 /* 5097 DMPlexGetIndicesPoint_Internal - Add the indices for dofs on a point to an index array 5098 5099 Input Parameters: 5100 + section - The section for this data layout 5101 . point - The point contributing dofs with these indices 5102 . off - The global offset of this point 5103 . loff - The local offset of each field 5104 . setBC - The flag determining whether to include indices of bounsary values 5105 . perm - A permutation of the dofs on this point, or NULL 5106 - indperm - A permutation of the entire indices array, or NULL 5107 5108 Output Parameter: 5109 . indices - Indices for dofs on this point 5110 5111 Level: developer 5112 5113 Note: The indices could be local or global, depending on the value of 'off'. 5114 */ 5115 PetscErrorCode DMPlexGetIndicesPoint_Internal(PetscSection section, PetscInt point, PetscInt off, PetscInt *loff, PetscBool setBC, const PetscInt perm[], const PetscInt indperm[], PetscInt indices[]) 5116 { 5117 PetscInt dof; /* The number of unknowns on this point */ 5118 PetscInt cdof; /* The number of constraints on this point */ 5119 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 5120 PetscInt cind = 0, k; 5121 PetscErrorCode ierr; 5122 5123 PetscFunctionBegin; 5124 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 5125 ierr = PetscSectionGetConstraintDof(section, point, &cdof);CHKERRQ(ierr); 5126 if (!cdof || setBC) { 5127 for (k = 0; k < dof; ++k) { 5128 const PetscInt preind = perm ? *loff+perm[k] : *loff+k; 5129 const PetscInt ind = indperm ? indperm[preind] : preind; 5130 5131 indices[ind] = off + k; 5132 } 5133 } else { 5134 ierr = PetscSectionGetConstraintIndices(section, point, &cdofs);CHKERRQ(ierr); 5135 for (k = 0; k < dof; ++k) { 5136 const PetscInt preind = perm ? *loff+perm[k] : *loff+k; 5137 const PetscInt ind = indperm ? indperm[preind] : preind; 5138 5139 if ((cind < cdof) && (k == cdofs[cind])) { 5140 /* Insert check for returning constrained indices */ 5141 indices[ind] = -(off+k+1); 5142 ++cind; 5143 } else { 5144 indices[ind] = off+k-cind; 5145 } 5146 } 5147 } 5148 *loff += dof; 5149 PetscFunctionReturn(0); 5150 } 5151 5152 /* 5153 This version only believes the point offset from the globalSection 5154 5155 . off - The global offset of this point 5156 */ 5157 PetscErrorCode DMPlexGetIndicesPointFields_Internal(PetscSection section, PetscInt point, PetscInt off, PetscInt foffs[], PetscBool setBC, const PetscInt ***perms, PetscInt permsoff, const PetscInt indperm[], PetscInt indices[]) 5158 { 5159 PetscInt numFields, foff, f; 5160 PetscErrorCode ierr; 5161 5162 PetscFunctionBegin; 5163 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 5164 for (f = 0, foff = 0; f < numFields; ++f) { 5165 PetscInt fdof, cfdof; 5166 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 5167 PetscInt cind = 0, b; 5168 const PetscInt *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL; 5169 5170 ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); 5171 ierr = PetscSectionGetFieldConstraintDof(section, point, f, &cfdof);CHKERRQ(ierr); 5172 if (!cfdof || setBC) { 5173 for (b = 0; b < fdof; ++b) { 5174 const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b; 5175 const PetscInt ind = indperm ? indperm[preind] : preind; 5176 5177 indices[ind] = off+foff+b; 5178 } 5179 } else { 5180 ierr = PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);CHKERRQ(ierr); 5181 for (b = 0; b < fdof; ++b) { 5182 const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b; 5183 const PetscInt ind = indperm ? indperm[preind] : preind; 5184 5185 if ((cind < cfdof) && (b == fcdofs[cind])) { 5186 indices[ind] = -(off+foff+b+1); 5187 ++cind; 5188 } else { 5189 indices[ind] = off+foff+b-cind; 5190 } 5191 } 5192 } 5193 foff += (setBC ? fdof : (fdof - cfdof)); 5194 foffs[f] += fdof; 5195 } 5196 PetscFunctionReturn(0); 5197 } 5198 5199 /* 5200 This version believes the globalSection offsets for each field, rather than just the point offset 5201 5202 . foffs - The offset into 'indices' for each field, since it is segregated by field 5203 */ 5204 PetscErrorCode DMPlexGetIndicesPointFieldsSplit_Internal(PetscSection section, PetscSection globalSection, PetscInt point, PetscInt foffs[], PetscBool setBC, const PetscInt ***perms, PetscInt permsoff, const PetscInt indperm[], PetscInt indices[]) 5205 { 5206 PetscInt numFields, foff, f; 5207 PetscErrorCode ierr; 5208 5209 PetscFunctionBegin; 5210 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 5211 for (f = 0; f < numFields; ++f) { 5212 PetscInt fdof, cfdof; 5213 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 5214 PetscInt cind = 0, b; 5215 const PetscInt *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL; 5216 5217 ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); 5218 ierr = PetscSectionGetFieldConstraintDof(section, point, f, &cfdof);CHKERRQ(ierr); 5219 ierr = PetscSectionGetFieldOffset(globalSection, point, f, &foff);CHKERRQ(ierr); 5220 if (!cfdof || setBC) { 5221 for (b = 0; b < fdof; ++b) { 5222 const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b; 5223 const PetscInt ind = indperm ? indperm[preind] : preind; 5224 5225 indices[ind] = foff+b; 5226 } 5227 } else { 5228 ierr = PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);CHKERRQ(ierr); 5229 for (b = 0; b < fdof; ++b) { 5230 const PetscInt preind = perm ? foffs[f]+perm[b] : foffs[f]+b; 5231 const PetscInt ind = indperm ? indperm[preind] : preind; 5232 5233 if ((cind < cfdof) && (b == fcdofs[cind])) { 5234 indices[ind] = -(foff+b+1); 5235 ++cind; 5236 } else { 5237 indices[ind] = foff+b-cind; 5238 } 5239 } 5240 } 5241 foffs[f] += fdof; 5242 } 5243 PetscFunctionReturn(0); 5244 } 5245 5246 PetscErrorCode DMPlexAnchorsModifyMat(DM dm, PetscSection section, PetscInt numPoints, PetscInt numIndices, const PetscInt points[], const PetscInt ***perms, const PetscScalar values[], PetscInt *outNumPoints, PetscInt *outNumIndices, PetscInt *outPoints[], PetscScalar *outValues[], PetscInt offsets[], PetscBool multiplyLeft) 5247 { 5248 Mat cMat; 5249 PetscSection aSec, cSec; 5250 IS aIS; 5251 PetscInt aStart = -1, aEnd = -1; 5252 const PetscInt *anchors; 5253 PetscInt numFields, f, p, q, newP = 0; 5254 PetscInt newNumPoints = 0, newNumIndices = 0; 5255 PetscInt *newPoints, *indices, *newIndices; 5256 PetscInt maxAnchor, maxDof; 5257 PetscInt newOffsets[32]; 5258 PetscInt *pointMatOffsets[32]; 5259 PetscInt *newPointOffsets[32]; 5260 PetscScalar *pointMat[32]; 5261 PetscScalar *newValues=NULL,*tmpValues; 5262 PetscBool anyConstrained = PETSC_FALSE; 5263 PetscErrorCode ierr; 5264 5265 PetscFunctionBegin; 5266 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5267 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 5268 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 5269 5270 ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr); 5271 /* if there are point-to-point constraints */ 5272 if (aSec) { 5273 ierr = PetscArrayzero(newOffsets, 32);CHKERRQ(ierr); 5274 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 5275 ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); 5276 /* figure out how many points are going to be in the new element matrix 5277 * (we allow double counting, because it's all just going to be summed 5278 * into the global matrix anyway) */ 5279 for (p = 0; p < 2*numPoints; p+=2) { 5280 PetscInt b = points[p]; 5281 PetscInt bDof = 0, bSecDof; 5282 5283 ierr = PetscSectionGetDof(section,b,&bSecDof);CHKERRQ(ierr); 5284 if (!bSecDof) { 5285 continue; 5286 } 5287 if (b >= aStart && b < aEnd) { 5288 ierr = PetscSectionGetDof(aSec,b,&bDof);CHKERRQ(ierr); 5289 } 5290 if (bDof) { 5291 /* this point is constrained */ 5292 /* it is going to be replaced by its anchors */ 5293 PetscInt bOff, q; 5294 5295 anyConstrained = PETSC_TRUE; 5296 newNumPoints += bDof; 5297 ierr = PetscSectionGetOffset(aSec,b,&bOff);CHKERRQ(ierr); 5298 for (q = 0; q < bDof; q++) { 5299 PetscInt a = anchors[bOff + q]; 5300 PetscInt aDof; 5301 5302 ierr = PetscSectionGetDof(section,a,&aDof);CHKERRQ(ierr); 5303 newNumIndices += aDof; 5304 for (f = 0; f < numFields; ++f) { 5305 PetscInt fDof; 5306 5307 ierr = PetscSectionGetFieldDof(section, a, f, &fDof);CHKERRQ(ierr); 5308 newOffsets[f+1] += fDof; 5309 } 5310 } 5311 } 5312 else { 5313 /* this point is not constrained */ 5314 newNumPoints++; 5315 newNumIndices += bSecDof; 5316 for (f = 0; f < numFields; ++f) { 5317 PetscInt fDof; 5318 5319 ierr = PetscSectionGetFieldDof(section, b, f, &fDof);CHKERRQ(ierr); 5320 newOffsets[f+1] += fDof; 5321 } 5322 } 5323 } 5324 } 5325 if (!anyConstrained) { 5326 if (outNumPoints) *outNumPoints = 0; 5327 if (outNumIndices) *outNumIndices = 0; 5328 if (outPoints) *outPoints = NULL; 5329 if (outValues) *outValues = NULL; 5330 if (aSec) {ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr);} 5331 PetscFunctionReturn(0); 5332 } 5333 5334 if (outNumPoints) *outNumPoints = newNumPoints; 5335 if (outNumIndices) *outNumIndices = newNumIndices; 5336 5337 for (f = 0; f < numFields; ++f) newOffsets[f+1] += newOffsets[f]; 5338 5339 if (!outPoints && !outValues) { 5340 if (offsets) { 5341 for (f = 0; f <= numFields; f++) { 5342 offsets[f] = newOffsets[f]; 5343 } 5344 } 5345 if (aSec) {ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr);} 5346 PetscFunctionReturn(0); 5347 } 5348 5349 if (numFields && newOffsets[numFields] != newNumIndices) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", newOffsets[numFields], newNumIndices); 5350 5351 ierr = DMGetDefaultConstraints(dm, &cSec, &cMat);CHKERRQ(ierr); 5352 5353 /* workspaces */ 5354 if (numFields) { 5355 for (f = 0; f < numFields; f++) { 5356 ierr = DMGetWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[f]);CHKERRQ(ierr); 5357 ierr = DMGetWorkArray(dm,numPoints+1,MPIU_INT,&newPointOffsets[f]);CHKERRQ(ierr); 5358 } 5359 } 5360 else { 5361 ierr = DMGetWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[0]);CHKERRQ(ierr); 5362 ierr = DMGetWorkArray(dm,numPoints,MPIU_INT,&newPointOffsets[0]);CHKERRQ(ierr); 5363 } 5364 5365 /* get workspaces for the point-to-point matrices */ 5366 if (numFields) { 5367 PetscInt totalOffset, totalMatOffset; 5368 5369 for (p = 0; p < numPoints; p++) { 5370 PetscInt b = points[2*p]; 5371 PetscInt bDof = 0, bSecDof; 5372 5373 ierr = PetscSectionGetDof(section,b,&bSecDof);CHKERRQ(ierr); 5374 if (!bSecDof) { 5375 for (f = 0; f < numFields; f++) { 5376 newPointOffsets[f][p + 1] = 0; 5377 pointMatOffsets[f][p + 1] = 0; 5378 } 5379 continue; 5380 } 5381 if (b >= aStart && b < aEnd) { 5382 ierr = PetscSectionGetDof(aSec, b, &bDof);CHKERRQ(ierr); 5383 } 5384 if (bDof) { 5385 for (f = 0; f < numFields; f++) { 5386 PetscInt fDof, q, bOff, allFDof = 0; 5387 5388 ierr = PetscSectionGetFieldDof(section, b, f, &fDof);CHKERRQ(ierr); 5389 ierr = PetscSectionGetOffset(aSec, b, &bOff);CHKERRQ(ierr); 5390 for (q = 0; q < bDof; q++) { 5391 PetscInt a = anchors[bOff + q]; 5392 PetscInt aFDof; 5393 5394 ierr = PetscSectionGetFieldDof(section, a, f, &aFDof);CHKERRQ(ierr); 5395 allFDof += aFDof; 5396 } 5397 newPointOffsets[f][p+1] = allFDof; 5398 pointMatOffsets[f][p+1] = fDof * allFDof; 5399 } 5400 } 5401 else { 5402 for (f = 0; f < numFields; f++) { 5403 PetscInt fDof; 5404 5405 ierr = PetscSectionGetFieldDof(section, b, f, &fDof);CHKERRQ(ierr); 5406 newPointOffsets[f][p+1] = fDof; 5407 pointMatOffsets[f][p+1] = 0; 5408 } 5409 } 5410 } 5411 for (f = 0, totalOffset = 0, totalMatOffset = 0; f < numFields; f++) { 5412 newPointOffsets[f][0] = totalOffset; 5413 pointMatOffsets[f][0] = totalMatOffset; 5414 for (p = 0; p < numPoints; p++) { 5415 newPointOffsets[f][p+1] += newPointOffsets[f][p]; 5416 pointMatOffsets[f][p+1] += pointMatOffsets[f][p]; 5417 } 5418 totalOffset = newPointOffsets[f][numPoints]; 5419 totalMatOffset = pointMatOffsets[f][numPoints]; 5420 ierr = DMGetWorkArray(dm,pointMatOffsets[f][numPoints],MPIU_SCALAR,&pointMat[f]);CHKERRQ(ierr); 5421 } 5422 } 5423 else { 5424 for (p = 0; p < numPoints; p++) { 5425 PetscInt b = points[2*p]; 5426 PetscInt bDof = 0, bSecDof; 5427 5428 ierr = PetscSectionGetDof(section,b,&bSecDof);CHKERRQ(ierr); 5429 if (!bSecDof) { 5430 newPointOffsets[0][p + 1] = 0; 5431 pointMatOffsets[0][p + 1] = 0; 5432 continue; 5433 } 5434 if (b >= aStart && b < aEnd) { 5435 ierr = PetscSectionGetDof(aSec, b, &bDof);CHKERRQ(ierr); 5436 } 5437 if (bDof) { 5438 PetscInt bOff, q, allDof = 0; 5439 5440 ierr = PetscSectionGetOffset(aSec, b, &bOff);CHKERRQ(ierr); 5441 for (q = 0; q < bDof; q++) { 5442 PetscInt a = anchors[bOff + q], aDof; 5443 5444 ierr = PetscSectionGetDof(section, a, &aDof);CHKERRQ(ierr); 5445 allDof += aDof; 5446 } 5447 newPointOffsets[0][p+1] = allDof; 5448 pointMatOffsets[0][p+1] = bSecDof * allDof; 5449 } 5450 else { 5451 newPointOffsets[0][p+1] = bSecDof; 5452 pointMatOffsets[0][p+1] = 0; 5453 } 5454 } 5455 newPointOffsets[0][0] = 0; 5456 pointMatOffsets[0][0] = 0; 5457 for (p = 0; p < numPoints; p++) { 5458 newPointOffsets[0][p+1] += newPointOffsets[0][p]; 5459 pointMatOffsets[0][p+1] += pointMatOffsets[0][p]; 5460 } 5461 ierr = DMGetWorkArray(dm,pointMatOffsets[0][numPoints],MPIU_SCALAR,&pointMat[0]);CHKERRQ(ierr); 5462 } 5463 5464 /* output arrays */ 5465 ierr = DMGetWorkArray(dm,2*newNumPoints,MPIU_INT,&newPoints);CHKERRQ(ierr); 5466 5467 /* get the point-to-point matrices; construct newPoints */ 5468 ierr = PetscSectionGetMaxDof(aSec, &maxAnchor);CHKERRQ(ierr); 5469 ierr = PetscSectionGetMaxDof(section, &maxDof);CHKERRQ(ierr); 5470 ierr = DMGetWorkArray(dm,maxDof,MPIU_INT,&indices);CHKERRQ(ierr); 5471 ierr = DMGetWorkArray(dm,maxAnchor*maxDof,MPIU_INT,&newIndices);CHKERRQ(ierr); 5472 if (numFields) { 5473 for (p = 0, newP = 0; p < numPoints; p++) { 5474 PetscInt b = points[2*p]; 5475 PetscInt o = points[2*p+1]; 5476 PetscInt bDof = 0, bSecDof; 5477 5478 ierr = PetscSectionGetDof(section, b, &bSecDof);CHKERRQ(ierr); 5479 if (!bSecDof) { 5480 continue; 5481 } 5482 if (b >= aStart && b < aEnd) { 5483 ierr = PetscSectionGetDof(aSec, b, &bDof);CHKERRQ(ierr); 5484 } 5485 if (bDof) { 5486 PetscInt fStart[32], fEnd[32], fAnchorStart[32], fAnchorEnd[32], bOff, q; 5487 5488 fStart[0] = 0; 5489 fEnd[0] = 0; 5490 for (f = 0; f < numFields; f++) { 5491 PetscInt fDof; 5492 5493 ierr = PetscSectionGetFieldDof(cSec, b, f, &fDof);CHKERRQ(ierr); 5494 fStart[f+1] = fStart[f] + fDof; 5495 fEnd[f+1] = fStart[f+1]; 5496 } 5497 ierr = PetscSectionGetOffset(cSec, b, &bOff);CHKERRQ(ierr); 5498 ierr = DMPlexGetIndicesPointFields_Internal(cSec, b, bOff, fEnd, PETSC_TRUE, perms, p, NULL, indices);CHKERRQ(ierr); 5499 5500 fAnchorStart[0] = 0; 5501 fAnchorEnd[0] = 0; 5502 for (f = 0; f < numFields; f++) { 5503 PetscInt fDof = newPointOffsets[f][p + 1] - newPointOffsets[f][p]; 5504 5505 fAnchorStart[f+1] = fAnchorStart[f] + fDof; 5506 fAnchorEnd[f+1] = fAnchorStart[f + 1]; 5507 } 5508 ierr = PetscSectionGetOffset(aSec, b, &bOff);CHKERRQ(ierr); 5509 for (q = 0; q < bDof; q++) { 5510 PetscInt a = anchors[bOff + q], aOff; 5511 5512 /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */ 5513 newPoints[2*(newP + q)] = a; 5514 newPoints[2*(newP + q) + 1] = 0; 5515 ierr = PetscSectionGetOffset(section, a, &aOff);CHKERRQ(ierr); 5516 ierr = DMPlexGetIndicesPointFields_Internal(section, a, aOff, fAnchorEnd, PETSC_TRUE, NULL, -1, NULL, newIndices);CHKERRQ(ierr); 5517 } 5518 newP += bDof; 5519 5520 if (outValues) { 5521 /* get the point-to-point submatrix */ 5522 for (f = 0; f < numFields; f++) { 5523 ierr = MatGetValues(cMat,fEnd[f]-fStart[f],indices + fStart[f],fAnchorEnd[f] - fAnchorStart[f],newIndices + fAnchorStart[f],pointMat[f] + pointMatOffsets[f][p]);CHKERRQ(ierr); 5524 } 5525 } 5526 } 5527 else { 5528 newPoints[2 * newP] = b; 5529 newPoints[2 * newP + 1] = o; 5530 newP++; 5531 } 5532 } 5533 } else { 5534 for (p = 0; p < numPoints; p++) { 5535 PetscInt b = points[2*p]; 5536 PetscInt o = points[2*p+1]; 5537 PetscInt bDof = 0, bSecDof; 5538 5539 ierr = PetscSectionGetDof(section, b, &bSecDof);CHKERRQ(ierr); 5540 if (!bSecDof) { 5541 continue; 5542 } 5543 if (b >= aStart && b < aEnd) { 5544 ierr = PetscSectionGetDof(aSec, b, &bDof);CHKERRQ(ierr); 5545 } 5546 if (bDof) { 5547 PetscInt bEnd = 0, bAnchorEnd = 0, bOff; 5548 5549 ierr = PetscSectionGetOffset(cSec, b, &bOff);CHKERRQ(ierr); 5550 ierr = DMPlexGetIndicesPoint_Internal(cSec, b, bOff, &bEnd, PETSC_TRUE, (perms && perms[0]) ? perms[0][p] : NULL, NULL, indices);CHKERRQ(ierr); 5551 5552 ierr = PetscSectionGetOffset (aSec, b, &bOff);CHKERRQ(ierr); 5553 for (q = 0; q < bDof; q++) { 5554 PetscInt a = anchors[bOff + q], aOff; 5555 5556 /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */ 5557 5558 newPoints[2*(newP + q)] = a; 5559 newPoints[2*(newP + q) + 1] = 0; 5560 ierr = PetscSectionGetOffset(section, a, &aOff);CHKERRQ(ierr); 5561 ierr = DMPlexGetIndicesPoint_Internal(section, a, aOff, &bAnchorEnd, PETSC_TRUE, NULL, NULL, newIndices);CHKERRQ(ierr); 5562 } 5563 newP += bDof; 5564 5565 /* get the point-to-point submatrix */ 5566 if (outValues) { 5567 ierr = MatGetValues(cMat,bEnd,indices,bAnchorEnd,newIndices,pointMat[0] + pointMatOffsets[0][p]);CHKERRQ(ierr); 5568 } 5569 } 5570 else { 5571 newPoints[2 * newP] = b; 5572 newPoints[2 * newP + 1] = o; 5573 newP++; 5574 } 5575 } 5576 } 5577 5578 if (outValues) { 5579 ierr = DMGetWorkArray(dm,newNumIndices*numIndices,MPIU_SCALAR,&tmpValues);CHKERRQ(ierr); 5580 ierr = PetscArrayzero(tmpValues,newNumIndices*numIndices);CHKERRQ(ierr); 5581 /* multiply constraints on the right */ 5582 if (numFields) { 5583 for (f = 0; f < numFields; f++) { 5584 PetscInt oldOff = offsets[f]; 5585 5586 for (p = 0; p < numPoints; p++) { 5587 PetscInt cStart = newPointOffsets[f][p]; 5588 PetscInt b = points[2 * p]; 5589 PetscInt c, r, k; 5590 PetscInt dof; 5591 5592 ierr = PetscSectionGetFieldDof(section,b,f,&dof);CHKERRQ(ierr); 5593 if (!dof) { 5594 continue; 5595 } 5596 if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) { 5597 PetscInt nCols = newPointOffsets[f][p+1]-cStart; 5598 const PetscScalar *mat = pointMat[f] + pointMatOffsets[f][p]; 5599 5600 for (r = 0; r < numIndices; r++) { 5601 for (c = 0; c < nCols; c++) { 5602 for (k = 0; k < dof; k++) { 5603 tmpValues[r * newNumIndices + cStart + c] += values[r * numIndices + oldOff + k] * mat[k * nCols + c]; 5604 } 5605 } 5606 } 5607 } 5608 else { 5609 /* copy this column as is */ 5610 for (r = 0; r < numIndices; r++) { 5611 for (c = 0; c < dof; c++) { 5612 tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c]; 5613 } 5614 } 5615 } 5616 oldOff += dof; 5617 } 5618 } 5619 } 5620 else { 5621 PetscInt oldOff = 0; 5622 for (p = 0; p < numPoints; p++) { 5623 PetscInt cStart = newPointOffsets[0][p]; 5624 PetscInt b = points[2 * p]; 5625 PetscInt c, r, k; 5626 PetscInt dof; 5627 5628 ierr = PetscSectionGetDof(section,b,&dof);CHKERRQ(ierr); 5629 if (!dof) { 5630 continue; 5631 } 5632 if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) { 5633 PetscInt nCols = newPointOffsets[0][p+1]-cStart; 5634 const PetscScalar *mat = pointMat[0] + pointMatOffsets[0][p]; 5635 5636 for (r = 0; r < numIndices; r++) { 5637 for (c = 0; c < nCols; c++) { 5638 for (k = 0; k < dof; k++) { 5639 tmpValues[r * newNumIndices + cStart + c] += mat[k * nCols + c] * values[r * numIndices + oldOff + k]; 5640 } 5641 } 5642 } 5643 } 5644 else { 5645 /* copy this column as is */ 5646 for (r = 0; r < numIndices; r++) { 5647 for (c = 0; c < dof; c++) { 5648 tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c]; 5649 } 5650 } 5651 } 5652 oldOff += dof; 5653 } 5654 } 5655 5656 if (multiplyLeft) { 5657 ierr = DMGetWorkArray(dm,newNumIndices*newNumIndices,MPIU_SCALAR,&newValues);CHKERRQ(ierr); 5658 ierr = PetscArrayzero(newValues,newNumIndices*newNumIndices);CHKERRQ(ierr); 5659 /* multiply constraints transpose on the left */ 5660 if (numFields) { 5661 for (f = 0; f < numFields; f++) { 5662 PetscInt oldOff = offsets[f]; 5663 5664 for (p = 0; p < numPoints; p++) { 5665 PetscInt rStart = newPointOffsets[f][p]; 5666 PetscInt b = points[2 * p]; 5667 PetscInt c, r, k; 5668 PetscInt dof; 5669 5670 ierr = PetscSectionGetFieldDof(section,b,f,&dof);CHKERRQ(ierr); 5671 if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) { 5672 PetscInt nRows = newPointOffsets[f][p+1]-rStart; 5673 const PetscScalar *PETSC_RESTRICT mat = pointMat[f] + pointMatOffsets[f][p]; 5674 5675 for (r = 0; r < nRows; r++) { 5676 for (c = 0; c < newNumIndices; c++) { 5677 for (k = 0; k < dof; k++) { 5678 newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c]; 5679 } 5680 } 5681 } 5682 } 5683 else { 5684 /* copy this row as is */ 5685 for (r = 0; r < dof; r++) { 5686 for (c = 0; c < newNumIndices; c++) { 5687 newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c]; 5688 } 5689 } 5690 } 5691 oldOff += dof; 5692 } 5693 } 5694 } 5695 else { 5696 PetscInt oldOff = 0; 5697 5698 for (p = 0; p < numPoints; p++) { 5699 PetscInt rStart = newPointOffsets[0][p]; 5700 PetscInt b = points[2 * p]; 5701 PetscInt c, r, k; 5702 PetscInt dof; 5703 5704 ierr = PetscSectionGetDof(section,b,&dof);CHKERRQ(ierr); 5705 if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) { 5706 PetscInt nRows = newPointOffsets[0][p+1]-rStart; 5707 const PetscScalar *PETSC_RESTRICT mat = pointMat[0] + pointMatOffsets[0][p]; 5708 5709 for (r = 0; r < nRows; r++) { 5710 for (c = 0; c < newNumIndices; c++) { 5711 for (k = 0; k < dof; k++) { 5712 newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c]; 5713 } 5714 } 5715 } 5716 } 5717 else { 5718 /* copy this row as is */ 5719 for (r = 0; r < dof; r++) { 5720 for (c = 0; c < newNumIndices; c++) { 5721 newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c]; 5722 } 5723 } 5724 } 5725 oldOff += dof; 5726 } 5727 } 5728 5729 ierr = DMRestoreWorkArray(dm,newNumIndices*numIndices,MPIU_SCALAR,&tmpValues);CHKERRQ(ierr); 5730 } 5731 else { 5732 newValues = tmpValues; 5733 } 5734 } 5735 5736 /* clean up */ 5737 ierr = DMRestoreWorkArray(dm,maxDof,MPIU_INT,&indices);CHKERRQ(ierr); 5738 ierr = DMRestoreWorkArray(dm,maxAnchor*maxDof,MPIU_INT,&newIndices);CHKERRQ(ierr); 5739 5740 if (numFields) { 5741 for (f = 0; f < numFields; f++) { 5742 ierr = DMRestoreWorkArray(dm,pointMatOffsets[f][numPoints],MPIU_SCALAR,&pointMat[f]);CHKERRQ(ierr); 5743 ierr = DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[f]);CHKERRQ(ierr); 5744 ierr = DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&newPointOffsets[f]);CHKERRQ(ierr); 5745 } 5746 } 5747 else { 5748 ierr = DMRestoreWorkArray(dm,pointMatOffsets[0][numPoints],MPIU_SCALAR,&pointMat[0]);CHKERRQ(ierr); 5749 ierr = DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&pointMatOffsets[0]);CHKERRQ(ierr); 5750 ierr = DMRestoreWorkArray(dm,numPoints+1,MPIU_INT,&newPointOffsets[0]);CHKERRQ(ierr); 5751 } 5752 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 5753 5754 /* output */ 5755 if (outPoints) { 5756 *outPoints = newPoints; 5757 } 5758 else { 5759 ierr = DMRestoreWorkArray(dm,2*newNumPoints,MPIU_INT,&newPoints);CHKERRQ(ierr); 5760 } 5761 if (outValues) { 5762 *outValues = newValues; 5763 } 5764 for (f = 0; f <= numFields; f++) { 5765 offsets[f] = newOffsets[f]; 5766 } 5767 PetscFunctionReturn(0); 5768 } 5769 5770 /*@C 5771 DMPlexGetClosureIndices - Get the global indices in a vector v for all points in the closure of the given point 5772 5773 Not collective 5774 5775 Input Parameters: 5776 + dm - The DM 5777 . section - The section describing the layout in v, or NULL to use the default section 5778 . globalSection - The section describing the parallel layout in v, or NULL to use the default section 5779 - point - The mesh point 5780 5781 Output parameters: 5782 + numIndices - The number of indices 5783 . indices - The indices 5784 - outOffsets - Field offset if not NULL 5785 5786 Note: Must call DMPlexRestoreClosureIndices() to free allocated memory 5787 5788 Level: advanced 5789 5790 .seealso DMPlexRestoreClosureIndices(), DMPlexVecGetClosure(), DMPlexMatSetClosure() 5791 @*/ 5792 PetscErrorCode DMPlexGetClosureIndices(DM dm, PetscSection section, PetscSection globalSection, PetscInt point, PetscInt *numIndices, PetscInt **indices, PetscInt *outOffsets) 5793 { 5794 PetscSection clSection; 5795 IS clPoints; 5796 const PetscInt *clp, *clperm; 5797 const PetscInt **perms[32] = {NULL}; 5798 PetscInt *points = NULL, *pointsNew; 5799 PetscInt numPoints, numPointsNew; 5800 PetscInt offsets[32]; 5801 PetscInt Nf, Nind, NindNew, off, globalOff, f, p; 5802 PetscErrorCode ierr; 5803 5804 PetscFunctionBegin; 5805 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5806 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 5807 PetscValidHeaderSpecific(globalSection, PETSC_SECTION_CLASSID, 3); 5808 if (numIndices) PetscValidPointer(numIndices, 4); 5809 PetscValidPointer(indices, 5); 5810 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 5811 if (Nf > 31) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", Nf); 5812 ierr = PetscArrayzero(offsets, 32);CHKERRQ(ierr); 5813 /* Get points in closure */ 5814 ierr = DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5815 ierr = PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &clperm);CHKERRQ(ierr); 5816 /* Get number of indices and indices per field */ 5817 for (p = 0, Nind = 0; p < numPoints*2; p += 2) { 5818 PetscInt dof, fdof; 5819 5820 ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); 5821 for (f = 0; f < Nf; ++f) { 5822 ierr = PetscSectionGetFieldDof(section, points[p], f, &fdof);CHKERRQ(ierr); 5823 offsets[f+1] += fdof; 5824 } 5825 Nind += dof; 5826 } 5827 for (f = 1; f < Nf; ++f) offsets[f+1] += offsets[f]; 5828 if (Nf && offsets[Nf] != Nind) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", offsets[Nf], Nind); 5829 if (!Nf) offsets[1] = Nind; 5830 /* Get dual space symmetries */ 5831 for (f = 0; f < PetscMax(1,Nf); f++) { 5832 if (Nf) {ierr = PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5833 else {ierr = PetscSectionGetPointSyms(section,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5834 } 5835 /* Correct for hanging node constraints */ 5836 { 5837 ierr = DMPlexAnchorsModifyMat(dm, section, numPoints, Nind, points, perms, NULL, &numPointsNew, &NindNew, &pointsNew, NULL, offsets, PETSC_TRUE);CHKERRQ(ierr); 5838 if (numPointsNew) { 5839 for (f = 0; f < PetscMax(1,Nf); f++) { 5840 if (Nf) {ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5841 else {ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5842 } 5843 for (f = 0; f < PetscMax(1,Nf); f++) { 5844 if (Nf) {ierr = PetscSectionGetFieldPointSyms(section,f,numPointsNew,pointsNew,&perms[f],NULL);CHKERRQ(ierr);} 5845 else {ierr = PetscSectionGetPointSyms(section,numPointsNew,pointsNew,&perms[f],NULL);CHKERRQ(ierr);} 5846 } 5847 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5848 numPoints = numPointsNew; 5849 Nind = NindNew; 5850 points = pointsNew; 5851 } 5852 } 5853 /* Calculate indices */ 5854 ierr = DMGetWorkArray(dm, Nind, MPIU_INT, indices);CHKERRQ(ierr); 5855 if (Nf) { 5856 if (outOffsets) { 5857 PetscInt f; 5858 5859 for (f = 0; f <= Nf; f++) { 5860 outOffsets[f] = offsets[f]; 5861 } 5862 } 5863 for (p = 0; p < numPoints; p++) { 5864 ierr = PetscSectionGetOffset(globalSection, points[2*p], &globalOff);CHKERRQ(ierr); 5865 DMPlexGetIndicesPointFields_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, offsets, PETSC_FALSE, perms, p, clperm, *indices); 5866 } 5867 } else { 5868 for (p = 0, off = 0; p < numPoints; p++) { 5869 const PetscInt *perm = perms[0] ? perms[0][p] : NULL; 5870 5871 ierr = PetscSectionGetOffset(globalSection, points[2*p], &globalOff);CHKERRQ(ierr); 5872 DMPlexGetIndicesPoint_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, clperm, *indices); 5873 } 5874 } 5875 /* Cleanup points */ 5876 for (f = 0; f < PetscMax(1,Nf); f++) { 5877 if (Nf) {ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5878 else {ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5879 } 5880 if (numPointsNew) { 5881 ierr = DMRestoreWorkArray(dm, 2*numPointsNew, MPIU_INT, &pointsNew);CHKERRQ(ierr); 5882 } else { 5883 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5884 } 5885 if (numIndices) *numIndices = Nind; 5886 PetscFunctionReturn(0); 5887 } 5888 5889 /*@C 5890 DMPlexRestoreClosureIndices - Restore the indices in a vector v for all points in the closure of the given point 5891 5892 Not collective 5893 5894 Input Parameters: 5895 + dm - The DM 5896 . section - The section describing the layout in v, or NULL to use the default section 5897 . globalSection - The section describing the parallel layout in v, or NULL to use the default section 5898 . point - The mesh point 5899 . numIndices - The number of indices 5900 . indices - The indices 5901 - outOffsets - Field offset if not NULL 5902 5903 Level: advanced 5904 5905 .seealso DMPlexGetClosureIndices(), DMPlexVecGetClosure(), DMPlexMatSetClosure() 5906 @*/ 5907 PetscErrorCode DMPlexRestoreClosureIndices(DM dm, PetscSection section, PetscSection globalSection, PetscInt point, PetscInt *numIndices, PetscInt **indices,PetscInt *outOffsets) 5908 { 5909 PetscErrorCode ierr; 5910 5911 PetscFunctionBegin; 5912 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5913 PetscValidPointer(indices, 5); 5914 ierr = DMRestoreWorkArray(dm, 0, MPIU_INT, indices);CHKERRQ(ierr); 5915 PetscFunctionReturn(0); 5916 } 5917 5918 /*@C 5919 DMPlexMatSetClosure - Set an array of the values on the closure of 'point' 5920 5921 Not collective 5922 5923 Input Parameters: 5924 + dm - The DM 5925 . section - The section describing the layout in v, or NULL to use the default section 5926 . globalSection - The section describing the layout in v, or NULL to use the default global section 5927 . A - The matrix 5928 . point - The point in the DM 5929 . values - The array of values 5930 - mode - The insert mode, where INSERT_ALL_VALUES and ADD_ALL_VALUES also overwrite boundary conditions 5931 5932 Fortran Notes: 5933 This routine is only available in Fortran 90, and you must include petsc.h90 in your code. 5934 5935 Level: intermediate 5936 5937 .seealso DMPlexVecGetClosure(), DMPlexVecSetClosure() 5938 @*/ 5939 PetscErrorCode DMPlexMatSetClosure(DM dm, PetscSection section, PetscSection globalSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 5940 { 5941 DM_Plex *mesh = (DM_Plex*) dm->data; 5942 PetscSection clSection; 5943 IS clPoints; 5944 PetscInt *points = NULL, *newPoints; 5945 const PetscInt *clp, *clperm; 5946 PetscInt *indices; 5947 PetscInt offsets[32]; 5948 const PetscInt **perms[32] = {NULL}; 5949 const PetscScalar **flips[32] = {NULL}; 5950 PetscInt numFields, numPoints, newNumPoints, numIndices, newNumIndices, dof, off, globalOff, p, f; 5951 PetscScalar *valCopy = NULL; 5952 PetscScalar *newValues; 5953 PetscErrorCode ierr; 5954 5955 PetscFunctionBegin; 5956 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5957 if (!section) {ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr);} 5958 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 5959 if (!globalSection) {ierr = DMGetGlobalSection(dm, &globalSection);CHKERRQ(ierr);} 5960 PetscValidHeaderSpecific(globalSection, PETSC_SECTION_CLASSID, 3); 5961 PetscValidHeaderSpecific(A, MAT_CLASSID, 4); 5962 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 5963 if (numFields > 31) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields); 5964 ierr = PetscArrayzero(offsets, 32);CHKERRQ(ierr); 5965 ierr = PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &clperm);CHKERRQ(ierr); 5966 ierr = DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5967 for (p = 0, numIndices = 0; p < numPoints*2; p += 2) { 5968 PetscInt fdof; 5969 5970 ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); 5971 for (f = 0; f < numFields; ++f) { 5972 ierr = PetscSectionGetFieldDof(section, points[p], f, &fdof);CHKERRQ(ierr); 5973 offsets[f+1] += fdof; 5974 } 5975 numIndices += dof; 5976 } 5977 for (f = 1; f < numFields; ++f) offsets[f+1] += offsets[f]; 5978 5979 if (numFields && offsets[numFields] != numIndices) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", offsets[numFields], numIndices); 5980 /* Get symmetries */ 5981 for (f = 0; f < PetscMax(1,numFields); f++) { 5982 if (numFields) {ierr = PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 5983 else {ierr = PetscSectionGetPointSyms(section,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 5984 if (values && flips[f]) { /* may need to apply sign changes to the element matrix */ 5985 PetscInt foffset = offsets[f]; 5986 5987 for (p = 0; p < numPoints; p++) { 5988 PetscInt point = points[2*p], fdof; 5989 const PetscScalar *flip = flips[f] ? flips[f][p] : NULL; 5990 5991 if (!numFields) { 5992 ierr = PetscSectionGetDof(section,point,&fdof);CHKERRQ(ierr); 5993 } else { 5994 ierr = PetscSectionGetFieldDof(section,point,f,&fdof);CHKERRQ(ierr); 5995 } 5996 if (flip) { 5997 PetscInt i, j, k; 5998 5999 if (!valCopy) { 6000 ierr = DMGetWorkArray(dm,numIndices*numIndices,MPIU_SCALAR,&valCopy);CHKERRQ(ierr); 6001 for (j = 0; j < numIndices * numIndices; j++) valCopy[j] = values[j]; 6002 values = valCopy; 6003 } 6004 for (i = 0; i < fdof; i++) { 6005 PetscScalar fval = flip[i]; 6006 6007 for (k = 0; k < numIndices; k++) { 6008 valCopy[numIndices * (foffset + i) + k] *= fval; 6009 valCopy[numIndices * k + (foffset + i)] *= fval; 6010 } 6011 } 6012 } 6013 foffset += fdof; 6014 } 6015 } 6016 } 6017 ierr = DMPlexAnchorsModifyMat(dm,section,numPoints,numIndices,points,perms,values,&newNumPoints,&newNumIndices,&newPoints,&newValues,offsets,PETSC_TRUE);CHKERRQ(ierr); 6018 if (newNumPoints) { 6019 if (valCopy) { 6020 ierr = DMRestoreWorkArray(dm,numIndices*numIndices,MPIU_SCALAR,&valCopy);CHKERRQ(ierr); 6021 } 6022 for (f = 0; f < PetscMax(1,numFields); f++) { 6023 if (numFields) {ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 6024 else {ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 6025 } 6026 for (f = 0; f < PetscMax(1,numFields); f++) { 6027 if (numFields) {ierr = PetscSectionGetFieldPointSyms(section,f,newNumPoints,newPoints,&perms[f],&flips[f]);CHKERRQ(ierr);} 6028 else {ierr = PetscSectionGetPointSyms(section,newNumPoints,newPoints,&perms[f],&flips[f]);CHKERRQ(ierr);} 6029 } 6030 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 6031 numPoints = newNumPoints; 6032 numIndices = newNumIndices; 6033 points = newPoints; 6034 values = newValues; 6035 } 6036 ierr = DMGetWorkArray(dm, numIndices, MPIU_INT, &indices);CHKERRQ(ierr); 6037 if (numFields) { 6038 PetscBool useFieldOffsets; 6039 6040 ierr = PetscSectionGetUseFieldOffsets(globalSection, &useFieldOffsets);CHKERRQ(ierr); 6041 if (useFieldOffsets) { 6042 for (p = 0; p < numPoints; p++) { 6043 DMPlexGetIndicesPointFieldsSplit_Internal(section, globalSection, points[2*p], offsets, PETSC_FALSE, perms, p, clperm, indices); 6044 } 6045 } else { 6046 for (p = 0; p < numPoints; p++) { 6047 ierr = PetscSectionGetOffset(globalSection, points[2*p], &globalOff);CHKERRQ(ierr); 6048 DMPlexGetIndicesPointFields_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, offsets, PETSC_FALSE, perms, p, clperm, indices); 6049 } 6050 } 6051 } else { 6052 for (p = 0, off = 0; p < numPoints; p++) { 6053 const PetscInt *perm = perms[0] ? perms[0][p] : NULL; 6054 ierr = PetscSectionGetOffset(globalSection, points[2*p], &globalOff);CHKERRQ(ierr); 6055 DMPlexGetIndicesPoint_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, clperm, indices); 6056 } 6057 } 6058 if (mesh->printSetValues) {ierr = DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numIndices, indices, 0, NULL, values);CHKERRQ(ierr);} 6059 ierr = MatSetValues(A, numIndices, indices, numIndices, indices, values, mode); 6060 if (mesh->printFEM > 1) { 6061 PetscInt i; 6062 ierr = PetscPrintf(PETSC_COMM_SELF, " Indices:");CHKERRQ(ierr); 6063 for (i = 0; i < numIndices; ++i) {ierr = PetscPrintf(PETSC_COMM_SELF, " %D", indices[i]);CHKERRQ(ierr);} 6064 ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr); 6065 } 6066 if (ierr) { 6067 PetscMPIInt rank; 6068 PetscErrorCode ierr2; 6069 6070 ierr2 = MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);CHKERRQ(ierr2); 6071 ierr2 = (*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank);CHKERRQ(ierr2); 6072 ierr2 = DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numIndices, indices, 0, NULL, values);CHKERRQ(ierr2); 6073 ierr2 = DMRestoreWorkArray(dm, numIndices, MPIU_INT, &indices);CHKERRQ(ierr2); 6074 CHKERRQ(ierr); 6075 } 6076 for (f = 0; f < PetscMax(1,numFields); f++) { 6077 if (numFields) {ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 6078 else {ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 6079 } 6080 if (newNumPoints) { 6081 ierr = DMRestoreWorkArray(dm,newNumIndices*newNumIndices,MPIU_SCALAR,&newValues);CHKERRQ(ierr); 6082 ierr = DMRestoreWorkArray(dm,2*newNumPoints,MPIU_INT,&newPoints);CHKERRQ(ierr); 6083 } 6084 else { 6085 if (valCopy) { 6086 ierr = DMRestoreWorkArray(dm,numIndices*numIndices,MPIU_SCALAR,&valCopy);CHKERRQ(ierr); 6087 } 6088 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 6089 } 6090 ierr = DMRestoreWorkArray(dm, numIndices, MPIU_INT, &indices);CHKERRQ(ierr); 6091 PetscFunctionReturn(0); 6092 } 6093 6094 PetscErrorCode DMPlexMatSetClosureRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 6095 { 6096 DM_Plex *mesh = (DM_Plex*) dmf->data; 6097 PetscInt *fpoints = NULL, *ftotpoints = NULL; 6098 PetscInt *cpoints = NULL; 6099 PetscInt *findices, *cindices; 6100 const PetscInt *fclperm, *cclperm; 6101 PetscInt foffsets[32], coffsets[32]; 6102 CellRefiner cellRefiner; 6103 PetscInt numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f; 6104 PetscErrorCode ierr; 6105 6106 PetscFunctionBegin; 6107 PetscValidHeaderSpecific(dmf, DM_CLASSID, 1); 6108 PetscValidHeaderSpecific(dmc, DM_CLASSID, 4); 6109 if (!fsection) {ierr = DMGetLocalSection(dmf, &fsection);CHKERRQ(ierr);} 6110 PetscValidHeaderSpecific(fsection, PETSC_SECTION_CLASSID, 2); 6111 if (!csection) {ierr = DMGetLocalSection(dmc, &csection);CHKERRQ(ierr);} 6112 PetscValidHeaderSpecific(csection, PETSC_SECTION_CLASSID, 5); 6113 if (!globalFSection) {ierr = DMGetGlobalSection(dmf, &globalFSection);CHKERRQ(ierr);} 6114 PetscValidHeaderSpecific(globalFSection, PETSC_SECTION_CLASSID, 3); 6115 if (!globalCSection) {ierr = DMGetGlobalSection(dmc, &globalCSection);CHKERRQ(ierr);} 6116 PetscValidHeaderSpecific(globalCSection, PETSC_SECTION_CLASSID, 6); 6117 PetscValidHeaderSpecific(A, MAT_CLASSID, 7); 6118 ierr = PetscSectionGetNumFields(fsection, &numFields);CHKERRQ(ierr); 6119 if (numFields > 31) SETERRQ1(PetscObjectComm((PetscObject)dmf), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields); 6120 ierr = PetscArrayzero(foffsets, 32);CHKERRQ(ierr); 6121 ierr = PetscArrayzero(coffsets, 32);CHKERRQ(ierr); 6122 ierr = PetscSectionGetClosureInversePermutation_Internal(fsection, (PetscObject) dmf, NULL, &fclperm);CHKERRQ(ierr); 6123 ierr = PetscSectionGetClosureInversePermutation_Internal(csection, (PetscObject) dmc, NULL, &cclperm);CHKERRQ(ierr); 6124 /* Column indices */ 6125 ierr = DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);CHKERRQ(ierr); 6126 maxFPoints = numCPoints; 6127 /* Compress out points not in the section */ 6128 /* TODO: Squeeze out points with 0 dof as well */ 6129 ierr = PetscSectionGetChart(csection, &pStart, &pEnd);CHKERRQ(ierr); 6130 for (p = 0, q = 0; p < numCPoints*2; p += 2) { 6131 if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) { 6132 cpoints[q*2] = cpoints[p]; 6133 cpoints[q*2+1] = cpoints[p+1]; 6134 ++q; 6135 } 6136 } 6137 numCPoints = q; 6138 for (p = 0, numCIndices = 0; p < numCPoints*2; p += 2) { 6139 PetscInt fdof; 6140 6141 ierr = PetscSectionGetDof(csection, cpoints[p], &dof);CHKERRQ(ierr); 6142 if (!dof) continue; 6143 for (f = 0; f < numFields; ++f) { 6144 ierr = PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof);CHKERRQ(ierr); 6145 coffsets[f+1] += fdof; 6146 } 6147 numCIndices += dof; 6148 } 6149 for (f = 1; f < numFields; ++f) coffsets[f+1] += coffsets[f]; 6150 /* Row indices */ 6151 ierr = DMPlexGetCellRefiner_Internal(dmc, &cellRefiner);CHKERRQ(ierr); 6152 ierr = CellRefinerGetAffineTransforms_Internal(cellRefiner, &numSubcells, NULL, NULL, NULL);CHKERRQ(ierr); 6153 ierr = DMGetWorkArray(dmf, maxFPoints*2*numSubcells, MPIU_INT, &ftotpoints);CHKERRQ(ierr); 6154 for (r = 0, q = 0; r < numSubcells; ++r) { 6155 /* TODO Map from coarse to fine cells */ 6156 ierr = DMPlexGetTransitiveClosure(dmf, point*numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints);CHKERRQ(ierr); 6157 /* Compress out points not in the section */ 6158 ierr = PetscSectionGetChart(fsection, &pStart, &pEnd);CHKERRQ(ierr); 6159 for (p = 0; p < numFPoints*2; p += 2) { 6160 if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) { 6161 ierr = PetscSectionGetDof(fsection, fpoints[p], &dof);CHKERRQ(ierr); 6162 if (!dof) continue; 6163 for (s = 0; s < q; ++s) if (fpoints[p] == ftotpoints[s*2]) break; 6164 if (s < q) continue; 6165 ftotpoints[q*2] = fpoints[p]; 6166 ftotpoints[q*2+1] = fpoints[p+1]; 6167 ++q; 6168 } 6169 } 6170 ierr = DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints);CHKERRQ(ierr); 6171 } 6172 numFPoints = q; 6173 for (p = 0, numFIndices = 0; p < numFPoints*2; p += 2) { 6174 PetscInt fdof; 6175 6176 ierr = PetscSectionGetDof(fsection, ftotpoints[p], &dof);CHKERRQ(ierr); 6177 if (!dof) continue; 6178 for (f = 0; f < numFields; ++f) { 6179 ierr = PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof);CHKERRQ(ierr); 6180 foffsets[f+1] += fdof; 6181 } 6182 numFIndices += dof; 6183 } 6184 for (f = 1; f < numFields; ++f) foffsets[f+1] += foffsets[f]; 6185 6186 if (numFields && foffsets[numFields] != numFIndices) SETERRQ2(PetscObjectComm((PetscObject)dmf), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", foffsets[numFields], numFIndices); 6187 if (numFields && coffsets[numFields] != numCIndices) SETERRQ2(PetscObjectComm((PetscObject)dmc), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", coffsets[numFields], numCIndices); 6188 ierr = DMGetWorkArray(dmf, numFIndices, MPIU_INT, &findices);CHKERRQ(ierr); 6189 ierr = DMGetWorkArray(dmc, numCIndices, MPIU_INT, &cindices);CHKERRQ(ierr); 6190 if (numFields) { 6191 const PetscInt **permsF[32] = {NULL}; 6192 const PetscInt **permsC[32] = {NULL}; 6193 6194 for (f = 0; f < numFields; f++) { 6195 ierr = PetscSectionGetFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);CHKERRQ(ierr); 6196 ierr = PetscSectionGetFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);CHKERRQ(ierr); 6197 } 6198 for (p = 0; p < numFPoints; p++) { 6199 ierr = PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);CHKERRQ(ierr); 6200 ierr = DMPlexGetIndicesPointFields_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, foffsets, PETSC_FALSE, permsF, p, fclperm, findices);CHKERRQ(ierr); 6201 } 6202 for (p = 0; p < numCPoints; p++) { 6203 ierr = PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);CHKERRQ(ierr); 6204 ierr = DMPlexGetIndicesPointFields_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cclperm, cindices);CHKERRQ(ierr); 6205 } 6206 for (f = 0; f < numFields; f++) { 6207 ierr = PetscSectionRestoreFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);CHKERRQ(ierr); 6208 ierr = PetscSectionRestoreFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);CHKERRQ(ierr); 6209 } 6210 } else { 6211 const PetscInt **permsF = NULL; 6212 const PetscInt **permsC = NULL; 6213 6214 ierr = PetscSectionGetPointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);CHKERRQ(ierr); 6215 ierr = PetscSectionGetPointSyms(csection,numCPoints,cpoints,&permsC,NULL);CHKERRQ(ierr); 6216 for (p = 0, off = 0; p < numFPoints; p++) { 6217 const PetscInt *perm = permsF ? permsF[p] : NULL; 6218 6219 ierr = PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);CHKERRQ(ierr); 6220 ierr = DMPlexGetIndicesPoint_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, fclperm, findices);CHKERRQ(ierr); 6221 } 6222 for (p = 0, off = 0; p < numCPoints; p++) { 6223 const PetscInt *perm = permsC ? permsC[p] : NULL; 6224 6225 ierr = PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);CHKERRQ(ierr); 6226 ierr = DMPlexGetIndicesPoint_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, cclperm, cindices);CHKERRQ(ierr); 6227 } 6228 ierr = PetscSectionRestorePointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);CHKERRQ(ierr); 6229 ierr = PetscSectionRestorePointSyms(csection,numCPoints,cpoints,&permsC,NULL);CHKERRQ(ierr); 6230 } 6231 if (mesh->printSetValues) {ierr = DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numFIndices, findices, numCIndices, cindices, values);CHKERRQ(ierr);} 6232 /* TODO: flips */ 6233 ierr = MatSetValues(A, numFIndices, findices, numCIndices, cindices, values, mode); 6234 if (ierr) { 6235 PetscMPIInt rank; 6236 PetscErrorCode ierr2; 6237 6238 ierr2 = MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);CHKERRQ(ierr2); 6239 ierr2 = (*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank);CHKERRQ(ierr2); 6240 ierr2 = DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numFIndices, findices, numCIndices, cindices, values);CHKERRQ(ierr2); 6241 ierr2 = DMRestoreWorkArray(dmf, numFIndices, MPIU_INT, &findices);CHKERRQ(ierr2); 6242 ierr2 = DMRestoreWorkArray(dmc, numCIndices, MPIU_INT, &cindices);CHKERRQ(ierr2); 6243 CHKERRQ(ierr); 6244 } 6245 ierr = DMRestoreWorkArray(dmf, numCPoints*2*4, MPIU_INT, &ftotpoints);CHKERRQ(ierr); 6246 ierr = DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);CHKERRQ(ierr); 6247 ierr = DMRestoreWorkArray(dmf, numFIndices, MPIU_INT, &findices);CHKERRQ(ierr); 6248 ierr = DMRestoreWorkArray(dmc, numCIndices, MPIU_INT, &cindices);CHKERRQ(ierr); 6249 PetscFunctionReturn(0); 6250 } 6251 6252 PetscErrorCode DMPlexMatGetClosureIndicesRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, PetscInt point, PetscInt cindices[], PetscInt findices[]) 6253 { 6254 PetscInt *fpoints = NULL, *ftotpoints = NULL; 6255 PetscInt *cpoints = NULL; 6256 PetscInt foffsets[32], coffsets[32]; 6257 const PetscInt *fclperm, *cclperm; 6258 CellRefiner cellRefiner; 6259 PetscInt numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f; 6260 PetscErrorCode ierr; 6261 6262 PetscFunctionBegin; 6263 PetscValidHeaderSpecific(dmf, DM_CLASSID, 1); 6264 PetscValidHeaderSpecific(dmc, DM_CLASSID, 4); 6265 if (!fsection) {ierr = DMGetLocalSection(dmf, &fsection);CHKERRQ(ierr);} 6266 PetscValidHeaderSpecific(fsection, PETSC_SECTION_CLASSID, 2); 6267 if (!csection) {ierr = DMGetLocalSection(dmc, &csection);CHKERRQ(ierr);} 6268 PetscValidHeaderSpecific(csection, PETSC_SECTION_CLASSID, 5); 6269 if (!globalFSection) {ierr = DMGetGlobalSection(dmf, &globalFSection);CHKERRQ(ierr);} 6270 PetscValidHeaderSpecific(globalFSection, PETSC_SECTION_CLASSID, 3); 6271 if (!globalCSection) {ierr = DMGetGlobalSection(dmc, &globalCSection);CHKERRQ(ierr);} 6272 PetscValidHeaderSpecific(globalCSection, PETSC_SECTION_CLASSID, 6); 6273 ierr = PetscSectionGetNumFields(fsection, &numFields);CHKERRQ(ierr); 6274 if (numFields > 31) SETERRQ1(PetscObjectComm((PetscObject)dmf), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields); 6275 ierr = PetscArrayzero(foffsets, 32);CHKERRQ(ierr); 6276 ierr = PetscArrayzero(coffsets, 32);CHKERRQ(ierr); 6277 ierr = PetscSectionGetClosureInversePermutation_Internal(fsection, (PetscObject) dmf, NULL, &fclperm);CHKERRQ(ierr); 6278 ierr = PetscSectionGetClosureInversePermutation_Internal(csection, (PetscObject) dmc, NULL, &cclperm);CHKERRQ(ierr); 6279 /* Column indices */ 6280 ierr = DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);CHKERRQ(ierr); 6281 maxFPoints = numCPoints; 6282 /* Compress out points not in the section */ 6283 /* TODO: Squeeze out points with 0 dof as well */ 6284 ierr = PetscSectionGetChart(csection, &pStart, &pEnd);CHKERRQ(ierr); 6285 for (p = 0, q = 0; p < numCPoints*2; p += 2) { 6286 if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) { 6287 cpoints[q*2] = cpoints[p]; 6288 cpoints[q*2+1] = cpoints[p+1]; 6289 ++q; 6290 } 6291 } 6292 numCPoints = q; 6293 for (p = 0, numCIndices = 0; p < numCPoints*2; p += 2) { 6294 PetscInt fdof; 6295 6296 ierr = PetscSectionGetDof(csection, cpoints[p], &dof);CHKERRQ(ierr); 6297 if (!dof) continue; 6298 for (f = 0; f < numFields; ++f) { 6299 ierr = PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof);CHKERRQ(ierr); 6300 coffsets[f+1] += fdof; 6301 } 6302 numCIndices += dof; 6303 } 6304 for (f = 1; f < numFields; ++f) coffsets[f+1] += coffsets[f]; 6305 /* Row indices */ 6306 ierr = DMPlexGetCellRefiner_Internal(dmc, &cellRefiner);CHKERRQ(ierr); 6307 ierr = CellRefinerGetAffineTransforms_Internal(cellRefiner, &numSubcells, NULL, NULL, NULL);CHKERRQ(ierr); 6308 ierr = DMGetWorkArray(dmf, maxFPoints*2*numSubcells, MPIU_INT, &ftotpoints);CHKERRQ(ierr); 6309 for (r = 0, q = 0; r < numSubcells; ++r) { 6310 /* TODO Map from coarse to fine cells */ 6311 ierr = DMPlexGetTransitiveClosure(dmf, point*numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints);CHKERRQ(ierr); 6312 /* Compress out points not in the section */ 6313 ierr = PetscSectionGetChart(fsection, &pStart, &pEnd);CHKERRQ(ierr); 6314 for (p = 0; p < numFPoints*2; p += 2) { 6315 if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) { 6316 ierr = PetscSectionGetDof(fsection, fpoints[p], &dof);CHKERRQ(ierr); 6317 if (!dof) continue; 6318 for (s = 0; s < q; ++s) if (fpoints[p] == ftotpoints[s*2]) break; 6319 if (s < q) continue; 6320 ftotpoints[q*2] = fpoints[p]; 6321 ftotpoints[q*2+1] = fpoints[p+1]; 6322 ++q; 6323 } 6324 } 6325 ierr = DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints);CHKERRQ(ierr); 6326 } 6327 numFPoints = q; 6328 for (p = 0, numFIndices = 0; p < numFPoints*2; p += 2) { 6329 PetscInt fdof; 6330 6331 ierr = PetscSectionGetDof(fsection, ftotpoints[p], &dof);CHKERRQ(ierr); 6332 if (!dof) continue; 6333 for (f = 0; f < numFields; ++f) { 6334 ierr = PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof);CHKERRQ(ierr); 6335 foffsets[f+1] += fdof; 6336 } 6337 numFIndices += dof; 6338 } 6339 for (f = 1; f < numFields; ++f) foffsets[f+1] += foffsets[f]; 6340 6341 if (numFields && foffsets[numFields] != numFIndices) SETERRQ2(PetscObjectComm((PetscObject)dmf), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", foffsets[numFields], numFIndices); 6342 if (numFields && coffsets[numFields] != numCIndices) SETERRQ2(PetscObjectComm((PetscObject)dmc), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", coffsets[numFields], numCIndices); 6343 if (numFields) { 6344 const PetscInt **permsF[32] = {NULL}; 6345 const PetscInt **permsC[32] = {NULL}; 6346 6347 for (f = 0; f < numFields; f++) { 6348 ierr = PetscSectionGetFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);CHKERRQ(ierr); 6349 ierr = PetscSectionGetFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);CHKERRQ(ierr); 6350 } 6351 for (p = 0; p < numFPoints; p++) { 6352 ierr = PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);CHKERRQ(ierr); 6353 DMPlexGetIndicesPointFields_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, foffsets, PETSC_FALSE, permsF, p, fclperm, findices); 6354 } 6355 for (p = 0; p < numCPoints; p++) { 6356 ierr = PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);CHKERRQ(ierr); 6357 DMPlexGetIndicesPointFields_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cclperm, cindices); 6358 } 6359 for (f = 0; f < numFields; f++) { 6360 ierr = PetscSectionRestoreFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);CHKERRQ(ierr); 6361 ierr = PetscSectionRestoreFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);CHKERRQ(ierr); 6362 } 6363 } else { 6364 const PetscInt **permsF = NULL; 6365 const PetscInt **permsC = NULL; 6366 6367 ierr = PetscSectionGetPointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);CHKERRQ(ierr); 6368 ierr = PetscSectionGetPointSyms(csection,numCPoints,cpoints,&permsC,NULL);CHKERRQ(ierr); 6369 for (p = 0, off = 0; p < numFPoints; p++) { 6370 const PetscInt *perm = permsF ? permsF[p] : NULL; 6371 6372 ierr = PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);CHKERRQ(ierr); 6373 DMPlexGetIndicesPoint_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, fclperm, findices); 6374 } 6375 for (p = 0, off = 0; p < numCPoints; p++) { 6376 const PetscInt *perm = permsC ? permsC[p] : NULL; 6377 6378 ierr = PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);CHKERRQ(ierr); 6379 DMPlexGetIndicesPoint_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, cclperm, cindices); 6380 } 6381 ierr = PetscSectionRestorePointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);CHKERRQ(ierr); 6382 ierr = PetscSectionRestorePointSyms(csection,numCPoints,cpoints,&permsC,NULL);CHKERRQ(ierr); 6383 } 6384 ierr = DMRestoreWorkArray(dmf, numCPoints*2*4, MPIU_INT, &ftotpoints);CHKERRQ(ierr); 6385 ierr = DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);CHKERRQ(ierr); 6386 PetscFunctionReturn(0); 6387 } 6388 6389 /*@ 6390 DMPlexGetHybridBounds - Get the first mesh point of each dimension which is a hybrid 6391 6392 Input Parameter: 6393 . dm - The DMPlex object 6394 6395 Output Parameters: 6396 + cMax - The first hybrid cell 6397 . fMax - The first hybrid face 6398 . eMax - The first hybrid edge 6399 - vMax - The first hybrid vertex 6400 6401 Level: developer 6402 6403 .seealso DMPlexCreateHybridMesh(), DMPlexSetHybridBounds() 6404 @*/ 6405 PetscErrorCode DMPlexGetHybridBounds(DM dm, PetscInt *cMax, PetscInt *fMax, PetscInt *eMax, PetscInt *vMax) 6406 { 6407 DM_Plex *mesh = (DM_Plex*) dm->data; 6408 PetscInt dim; 6409 PetscErrorCode ierr; 6410 6411 PetscFunctionBegin; 6412 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6413 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 6414 if (dim < 0) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "DM dimension not yet set"); 6415 if (cMax) *cMax = mesh->hybridPointMax[dim]; 6416 if (fMax) *fMax = mesh->hybridPointMax[PetscMax(dim-1,0)]; 6417 if (eMax) *eMax = mesh->hybridPointMax[1]; 6418 if (vMax) *vMax = mesh->hybridPointMax[0]; 6419 PetscFunctionReturn(0); 6420 } 6421 6422 static PetscErrorCode DMPlexCreateDimStratum(DM dm, DMLabel depthLabel, DMLabel dimLabel, PetscInt d, PetscInt dMax) 6423 { 6424 IS is, his; 6425 PetscInt first = 0, stride; 6426 PetscBool isStride; 6427 PetscErrorCode ierr; 6428 6429 PetscFunctionBegin; 6430 ierr = DMLabelGetStratumIS(depthLabel, d, &is);CHKERRQ(ierr); 6431 ierr = PetscObjectTypeCompare((PetscObject) is, ISSTRIDE, &isStride);CHKERRQ(ierr); 6432 if (isStride) { 6433 ierr = ISStrideGetInfo(is, &first, &stride);CHKERRQ(ierr); 6434 } 6435 if (is && (!isStride || stride != 1)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "DM is not stratified: depth %D IS is not contiguous", d); 6436 ierr = ISCreateStride(PETSC_COMM_SELF, (dMax - first), first, 1, &his);CHKERRQ(ierr); 6437 ierr = DMLabelSetStratumIS(dimLabel, d, his);CHKERRQ(ierr); 6438 ierr = ISDestroy(&his);CHKERRQ(ierr); 6439 ierr = ISDestroy(&is);CHKERRQ(ierr); 6440 PetscFunctionReturn(0); 6441 } 6442 6443 /*@ 6444 DMPlexSetHybridBounds - Set the first mesh point of each dimension which is a hybrid 6445 6446 Input Parameters: 6447 + dm - The DMPlex object 6448 . cMax - The first hybrid cell 6449 . fMax - The first hybrid face 6450 . eMax - The first hybrid edge 6451 - vMax - The first hybrid vertex 6452 6453 Level: developer 6454 6455 .seealso DMPlexCreateHybridMesh(), DMPlexGetHybridBounds() 6456 @*/ 6457 PetscErrorCode DMPlexSetHybridBounds(DM dm, PetscInt cMax, PetscInt fMax, PetscInt eMax, PetscInt vMax) 6458 { 6459 DM_Plex *mesh = (DM_Plex*) dm->data; 6460 PetscInt dim; 6461 PetscErrorCode ierr; 6462 6463 PetscFunctionBegin; 6464 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6465 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 6466 if (dim < 0) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "DM dimension not yet set"); 6467 if (cMax >= 0) mesh->hybridPointMax[dim] = cMax; 6468 if (fMax >= 0) mesh->hybridPointMax[PetscMax(dim-1,0)] = fMax; 6469 if (eMax >= 0) mesh->hybridPointMax[1] = eMax; 6470 if (vMax >= 0) mesh->hybridPointMax[0] = vMax; 6471 PetscFunctionReturn(0); 6472 } 6473 6474 /*@C 6475 DMPlexGetVTKCellHeight - Returns the height in the DAG used to determine which points are cells (normally 0) 6476 6477 Input Parameter: 6478 . dm - The DMPlex object 6479 6480 Output Parameter: 6481 . cellHeight - The height of a cell 6482 6483 Level: developer 6484 6485 .seealso DMPlexSetVTKCellHeight() 6486 @*/ 6487 PetscErrorCode DMPlexGetVTKCellHeight(DM dm, PetscInt *cellHeight) 6488 { 6489 DM_Plex *mesh = (DM_Plex*) dm->data; 6490 6491 PetscFunctionBegin; 6492 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6493 PetscValidPointer(cellHeight, 2); 6494 *cellHeight = mesh->vtkCellHeight; 6495 PetscFunctionReturn(0); 6496 } 6497 6498 /*@C 6499 DMPlexSetVTKCellHeight - Sets the height in the DAG used to determine which points are cells (normally 0) 6500 6501 Input Parameters: 6502 + dm - The DMPlex object 6503 - cellHeight - The height of a cell 6504 6505 Level: developer 6506 6507 .seealso DMPlexGetVTKCellHeight() 6508 @*/ 6509 PetscErrorCode DMPlexSetVTKCellHeight(DM dm, PetscInt cellHeight) 6510 { 6511 DM_Plex *mesh = (DM_Plex*) dm->data; 6512 6513 PetscFunctionBegin; 6514 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6515 mesh->vtkCellHeight = cellHeight; 6516 PetscFunctionReturn(0); 6517 } 6518 6519 /* We can easily have a form that takes an IS instead */ 6520 PetscErrorCode DMPlexCreateNumbering_Internal(DM dm, PetscInt pStart, PetscInt pEnd, PetscInt shift, PetscInt *globalSize, PetscSF sf, IS *numbering) 6521 { 6522 PetscSection section, globalSection; 6523 PetscInt *numbers, p; 6524 PetscErrorCode ierr; 6525 6526 PetscFunctionBegin; 6527 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ion);CHKERRQ(ierr); 6528 ierr = PetscSectionSetChart(section, pStart, pEnd);CHKERRQ(ierr); 6529 for (p = pStart; p < pEnd; ++p) { 6530 ierr = PetscSectionSetDof(section, p, 1);CHKERRQ(ierr); 6531 } 6532 ierr = PetscSectionSetUp(section);CHKERRQ(ierr); 6533 ierr = PetscSectionCreateGlobalSection(section, sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr); 6534 ierr = PetscMalloc1(pEnd - pStart, &numbers);CHKERRQ(ierr); 6535 for (p = pStart; p < pEnd; ++p) { 6536 ierr = PetscSectionGetOffset(globalSection, p, &numbers[p-pStart]);CHKERRQ(ierr); 6537 if (numbers[p-pStart] < 0) numbers[p-pStart] -= shift; 6538 else numbers[p-pStart] += shift; 6539 } 6540 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) dm), pEnd - pStart, numbers, PETSC_OWN_POINTER, numbering);CHKERRQ(ierr); 6541 if (globalSize) { 6542 PetscLayout layout; 6543 ierr = PetscSectionGetPointLayout(PetscObjectComm((PetscObject) dm), globalSection, &layout);CHKERRQ(ierr); 6544 ierr = PetscLayoutGetSize(layout, globalSize);CHKERRQ(ierr); 6545 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 6546 } 6547 ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr); 6548 ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr); 6549 PetscFunctionReturn(0); 6550 } 6551 6552 PetscErrorCode DMPlexCreateCellNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalCellNumbers) 6553 { 6554 PetscInt cellHeight, cStart, cEnd, cMax; 6555 PetscErrorCode ierr; 6556 6557 PetscFunctionBegin; 6558 ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); 6559 ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); 6560 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 6561 if (cMax >= 0 && !includeHybrid) cEnd = PetscMin(cEnd, cMax); 6562 ierr = DMPlexCreateNumbering_Internal(dm, cStart, cEnd, 0, NULL, dm->sf, globalCellNumbers);CHKERRQ(ierr); 6563 PetscFunctionReturn(0); 6564 } 6565 6566 /*@ 6567 DMPlexGetCellNumbering - Get a global cell numbering for all cells on this process 6568 6569 Input Parameter: 6570 . dm - The DMPlex object 6571 6572 Output Parameter: 6573 . globalCellNumbers - Global cell numbers for all cells on this process 6574 6575 Level: developer 6576 6577 .seealso DMPlexGetVertexNumbering() 6578 @*/ 6579 PetscErrorCode DMPlexGetCellNumbering(DM dm, IS *globalCellNumbers) 6580 { 6581 DM_Plex *mesh = (DM_Plex*) dm->data; 6582 PetscErrorCode ierr; 6583 6584 PetscFunctionBegin; 6585 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6586 if (!mesh->globalCellNumbers) {ierr = DMPlexCreateCellNumbering_Internal(dm, PETSC_FALSE, &mesh->globalCellNumbers);CHKERRQ(ierr);} 6587 *globalCellNumbers = mesh->globalCellNumbers; 6588 PetscFunctionReturn(0); 6589 } 6590 6591 PetscErrorCode DMPlexCreateVertexNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalVertexNumbers) 6592 { 6593 PetscInt vStart, vEnd, vMax; 6594 PetscErrorCode ierr; 6595 6596 PetscFunctionBegin; 6597 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6598 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 6599 ierr = DMPlexGetHybridBounds(dm, NULL, NULL, NULL, &vMax);CHKERRQ(ierr); 6600 if (vMax >= 0 && !includeHybrid) vEnd = PetscMin(vEnd, vMax); 6601 ierr = DMPlexCreateNumbering_Internal(dm, vStart, vEnd, 0, NULL, dm->sf, globalVertexNumbers);CHKERRQ(ierr); 6602 PetscFunctionReturn(0); 6603 } 6604 6605 /*@ 6606 DMPlexGetVertexNumbering - Get a global certex numbering for all vertices on this process 6607 6608 Input Parameter: 6609 . dm - The DMPlex object 6610 6611 Output Parameter: 6612 . globalVertexNumbers - Global vertex numbers for all vertices on this process 6613 6614 Level: developer 6615 6616 .seealso DMPlexGetCellNumbering() 6617 @*/ 6618 PetscErrorCode DMPlexGetVertexNumbering(DM dm, IS *globalVertexNumbers) 6619 { 6620 DM_Plex *mesh = (DM_Plex*) dm->data; 6621 PetscErrorCode ierr; 6622 6623 PetscFunctionBegin; 6624 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6625 if (!mesh->globalVertexNumbers) {ierr = DMPlexCreateVertexNumbering_Internal(dm, PETSC_FALSE, &mesh->globalVertexNumbers);CHKERRQ(ierr);} 6626 *globalVertexNumbers = mesh->globalVertexNumbers; 6627 PetscFunctionReturn(0); 6628 } 6629 6630 /*@ 6631 DMPlexCreatePointNumbering - Create a global numbering for all points on this process 6632 6633 Input Parameter: 6634 . dm - The DMPlex object 6635 6636 Output Parameter: 6637 . globalPointNumbers - Global numbers for all points on this process 6638 6639 Level: developer 6640 6641 .seealso DMPlexGetCellNumbering() 6642 @*/ 6643 PetscErrorCode DMPlexCreatePointNumbering(DM dm, IS *globalPointNumbers) 6644 { 6645 IS nums[4]; 6646 PetscInt depths[4], gdepths[4], starts[4]; 6647 PetscInt depth, d, shift = 0; 6648 PetscErrorCode ierr; 6649 6650 PetscFunctionBegin; 6651 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6652 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 6653 /* For unstratified meshes use dim instead of depth */ 6654 if (depth < 0) {ierr = DMGetDimension(dm, &depth);CHKERRQ(ierr);} 6655 for (d = 0; d <= depth; ++d) { 6656 PetscInt end; 6657 6658 depths[d] = depth-d; 6659 ierr = DMPlexGetDepthStratum(dm, depths[d], &starts[d], &end);CHKERRQ(ierr); 6660 if (!(starts[d]-end)) { starts[d] = depths[d] = -1; } 6661 } 6662 ierr = PetscSortIntWithArray(depth+1, starts, depths);CHKERRQ(ierr); 6663 ierr = MPIU_Allreduce(depths, gdepths, depth+1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 6664 for (d = 0; d <= depth; ++d) { 6665 if (starts[d] >= 0 && depths[d] != gdepths[d]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Expected depth %D, found %D",depths[d],gdepths[d]); 6666 } 6667 for (d = 0; d <= depth; ++d) { 6668 PetscInt pStart, pEnd, gsize; 6669 6670 ierr = DMPlexGetDepthStratum(dm, gdepths[d], &pStart, &pEnd);CHKERRQ(ierr); 6671 ierr = DMPlexCreateNumbering_Internal(dm, pStart, pEnd, shift, &gsize, dm->sf, &nums[d]);CHKERRQ(ierr); 6672 shift += gsize; 6673 } 6674 ierr = ISConcatenate(PetscObjectComm((PetscObject) dm), depth+1, nums, globalPointNumbers);CHKERRQ(ierr); 6675 for (d = 0; d <= depth; ++d) {ierr = ISDestroy(&nums[d]);CHKERRQ(ierr);} 6676 PetscFunctionReturn(0); 6677 } 6678 6679 6680 /*@ 6681 DMPlexCreateRankField - Create a cell field whose value is the rank of the owner 6682 6683 Input Parameter: 6684 . dm - The DMPlex object 6685 6686 Output Parameter: 6687 . ranks - The rank field 6688 6689 Options Database Keys: 6690 . -dm_partition_view - Adds the rank field into the DM output from -dm_view using the same viewer 6691 6692 Level: intermediate 6693 6694 .seealso: DMView() 6695 @*/ 6696 PetscErrorCode DMPlexCreateRankField(DM dm, Vec *ranks) 6697 { 6698 DM rdm; 6699 PetscFE fe; 6700 PetscScalar *r; 6701 PetscMPIInt rank; 6702 PetscInt dim, cStart, cEnd, c; 6703 PetscErrorCode ierr; 6704 6705 PetscFunctionBeginUser; 6706 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6707 PetscValidPointer(ranks, 2); 6708 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 6709 ierr = DMClone(dm, &rdm);CHKERRQ(ierr); 6710 ierr = DMGetDimension(rdm, &dim);CHKERRQ(ierr); 6711 ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) rdm), dim, 1, PETSC_TRUE, "PETSc___rank_", -1, &fe);CHKERRQ(ierr); 6712 ierr = PetscObjectSetName((PetscObject) fe, "rank");CHKERRQ(ierr); 6713 ierr = DMSetField(rdm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr); 6714 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 6715 ierr = DMCreateDS(rdm);CHKERRQ(ierr); 6716 ierr = DMPlexGetHeightStratum(rdm, 0, &cStart, &cEnd);CHKERRQ(ierr); 6717 ierr = DMCreateGlobalVector(rdm, ranks);CHKERRQ(ierr); 6718 ierr = PetscObjectSetName((PetscObject) *ranks, "partition");CHKERRQ(ierr); 6719 ierr = VecGetArray(*ranks, &r);CHKERRQ(ierr); 6720 for (c = cStart; c < cEnd; ++c) { 6721 PetscScalar *lr; 6722 6723 ierr = DMPlexPointGlobalRef(rdm, c, r, &lr);CHKERRQ(ierr); 6724 *lr = rank; 6725 } 6726 ierr = VecRestoreArray(*ranks, &r);CHKERRQ(ierr); 6727 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 6728 PetscFunctionReturn(0); 6729 } 6730 6731 /*@ 6732 DMPlexCreateLabelField - Create a cell field whose value is the label value for that cell 6733 6734 Input Parameters: 6735 + dm - The DMPlex 6736 - label - The DMLabel 6737 6738 Output Parameter: 6739 . val - The label value field 6740 6741 Options Database Keys: 6742 . -dm_label_view - Adds the label value field into the DM output from -dm_view using the same viewer 6743 6744 Level: intermediate 6745 6746 .seealso: DMView() 6747 @*/ 6748 PetscErrorCode DMPlexCreateLabelField(DM dm, DMLabel label, Vec *val) 6749 { 6750 DM rdm; 6751 PetscFE fe; 6752 PetscScalar *v; 6753 PetscInt dim, cStart, cEnd, c; 6754 PetscErrorCode ierr; 6755 6756 PetscFunctionBeginUser; 6757 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6758 PetscValidPointer(label, 2); 6759 PetscValidPointer(val, 3); 6760 ierr = DMClone(dm, &rdm);CHKERRQ(ierr); 6761 ierr = DMGetDimension(rdm, &dim);CHKERRQ(ierr); 6762 ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) rdm), dim, 1, PETSC_TRUE, "PETSc___label_value_", -1, &fe);CHKERRQ(ierr); 6763 ierr = PetscObjectSetName((PetscObject) fe, "label_value");CHKERRQ(ierr); 6764 ierr = DMSetField(rdm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr); 6765 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 6766 ierr = DMCreateDS(rdm);CHKERRQ(ierr); 6767 ierr = DMPlexGetHeightStratum(rdm, 0, &cStart, &cEnd);CHKERRQ(ierr); 6768 ierr = DMCreateGlobalVector(rdm, val);CHKERRQ(ierr); 6769 ierr = PetscObjectSetName((PetscObject) *val, "label_value");CHKERRQ(ierr); 6770 ierr = VecGetArray(*val, &v);CHKERRQ(ierr); 6771 for (c = cStart; c < cEnd; ++c) { 6772 PetscScalar *lv; 6773 PetscInt cval; 6774 6775 ierr = DMPlexPointGlobalRef(rdm, c, v, &lv);CHKERRQ(ierr); 6776 ierr = DMLabelGetValue(label, c, &cval);CHKERRQ(ierr); 6777 *lv = cval; 6778 } 6779 ierr = VecRestoreArray(*val, &v);CHKERRQ(ierr); 6780 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 6781 PetscFunctionReturn(0); 6782 } 6783 6784 /*@ 6785 DMPlexCheckSymmetry - Check that the adjacency information in the mesh is symmetric. 6786 6787 Input Parameter: 6788 . dm - The DMPlex object 6789 6790 Note: This is a useful diagnostic when creating meshes programmatically. 6791 6792 Level: developer 6793 6794 .seealso: DMCreate(), DMPlexCheckSkeleton(), DMPlexCheckFaces() 6795 @*/ 6796 PetscErrorCode DMPlexCheckSymmetry(DM dm) 6797 { 6798 PetscSection coneSection, supportSection; 6799 const PetscInt *cone, *support; 6800 PetscInt coneSize, c, supportSize, s; 6801 PetscInt pStart, pEnd, p, pp, csize, ssize; 6802 PetscBool storagecheck = PETSC_TRUE; 6803 PetscErrorCode ierr; 6804 6805 PetscFunctionBegin; 6806 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6807 ierr = DMPlexGetConeSection(dm, &coneSection);CHKERRQ(ierr); 6808 ierr = DMPlexGetSupportSection(dm, &supportSection);CHKERRQ(ierr); 6809 /* Check that point p is found in the support of its cone points, and vice versa */ 6810 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 6811 for (p = pStart; p < pEnd; ++p) { 6812 ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); 6813 ierr = DMPlexGetCone(dm, p, &cone);CHKERRQ(ierr); 6814 for (c = 0; c < coneSize; ++c) { 6815 PetscBool dup = PETSC_FALSE; 6816 PetscInt d; 6817 for (d = c-1; d >= 0; --d) { 6818 if (cone[c] == cone[d]) {dup = PETSC_TRUE; break;} 6819 } 6820 ierr = DMPlexGetSupportSize(dm, cone[c], &supportSize);CHKERRQ(ierr); 6821 ierr = DMPlexGetSupport(dm, cone[c], &support);CHKERRQ(ierr); 6822 for (s = 0; s < supportSize; ++s) { 6823 if (support[s] == p) break; 6824 } 6825 if ((s >= supportSize) || (dup && (support[s+1] != p))) { 6826 ierr = PetscPrintf(PETSC_COMM_SELF, "p: %D cone: ", p);CHKERRQ(ierr); 6827 for (s = 0; s < coneSize; ++s) { 6828 ierr = PetscPrintf(PETSC_COMM_SELF, "%D, ", cone[s]);CHKERRQ(ierr); 6829 } 6830 ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr); 6831 ierr = PetscPrintf(PETSC_COMM_SELF, "p: %D support: ", cone[c]);CHKERRQ(ierr); 6832 for (s = 0; s < supportSize; ++s) { 6833 ierr = PetscPrintf(PETSC_COMM_SELF, "%D, ", support[s]);CHKERRQ(ierr); 6834 } 6835 ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr); 6836 if (dup) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not repeatedly found in support of repeated cone point %D", p, cone[c]); 6837 else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not found in support of cone point %D", p, cone[c]); 6838 } 6839 } 6840 ierr = DMPlexGetTreeParent(dm, p, &pp, NULL);CHKERRQ(ierr); 6841 if (p != pp) { storagecheck = PETSC_FALSE; continue; } 6842 ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); 6843 ierr = DMPlexGetSupport(dm, p, &support);CHKERRQ(ierr); 6844 for (s = 0; s < supportSize; ++s) { 6845 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 6846 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 6847 for (c = 0; c < coneSize; ++c) { 6848 ierr = DMPlexGetTreeParent(dm, cone[c], &pp, NULL);CHKERRQ(ierr); 6849 if (cone[c] != pp) { c = 0; break; } 6850 if (cone[c] == p) break; 6851 } 6852 if (c >= coneSize) { 6853 ierr = PetscPrintf(PETSC_COMM_SELF, "p: %D support: ", p);CHKERRQ(ierr); 6854 for (c = 0; c < supportSize; ++c) { 6855 ierr = PetscPrintf(PETSC_COMM_SELF, "%D, ", support[c]);CHKERRQ(ierr); 6856 } 6857 ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr); 6858 ierr = PetscPrintf(PETSC_COMM_SELF, "p: %D cone: ", support[s]);CHKERRQ(ierr); 6859 for (c = 0; c < coneSize; ++c) { 6860 ierr = PetscPrintf(PETSC_COMM_SELF, "%D, ", cone[c]);CHKERRQ(ierr); 6861 } 6862 ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr); 6863 SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not found in cone of support point %D", p, support[s]); 6864 } 6865 } 6866 } 6867 if (storagecheck) { 6868 ierr = PetscSectionGetStorageSize(coneSection, &csize);CHKERRQ(ierr); 6869 ierr = PetscSectionGetStorageSize(supportSection, &ssize);CHKERRQ(ierr); 6870 if (csize != ssize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Total cone size %D != Total support size %D", csize, ssize); 6871 } 6872 PetscFunctionReturn(0); 6873 } 6874 6875 /*@ 6876 DMPlexCheckSkeleton - Check that each cell has the correct number of vertices 6877 6878 Input Parameters: 6879 + dm - The DMPlex object 6880 - cellHeight - Normally 0 6881 6882 Note: This is a useful diagnostic when creating meshes programmatically. 6883 Currently applicable only to homogeneous simplex or tensor meshes. 6884 6885 Level: developer 6886 6887 .seealso: DMCreate(), DMPlexCheckSymmetry(), DMPlexCheckFaces() 6888 @*/ 6889 PetscErrorCode DMPlexCheckSkeleton(DM dm, PetscInt cellHeight) 6890 { 6891 PetscInt dim, numCorners, numHybridCorners, vStart, vEnd, cStart, cEnd, cMax, c; 6892 PetscBool isSimplex = PETSC_FALSE; 6893 PetscErrorCode ierr; 6894 6895 PetscFunctionBegin; 6896 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6897 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 6898 ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); 6899 if (cStart < cEnd) { 6900 ierr = DMPlexGetConeSize(dm, cStart, &c);CHKERRQ(ierr); 6901 isSimplex = c == dim+1 ? PETSC_TRUE : PETSC_FALSE; 6902 } 6903 switch (dim) { 6904 case 1: numCorners = isSimplex ? 2 : 2; numHybridCorners = isSimplex ? 2 : 2; break; 6905 case 2: numCorners = isSimplex ? 3 : 4; numHybridCorners = isSimplex ? 4 : 4; break; 6906 case 3: numCorners = isSimplex ? 4 : 8; numHybridCorners = isSimplex ? 6 : 8; break; 6907 default: 6908 SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot handle meshes of dimension %D", dim); 6909 } 6910 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 6911 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 6912 cMax = cMax >= 0 ? cMax : cEnd; 6913 for (c = cStart; c < cMax; ++c) { 6914 PetscInt *closure = NULL, closureSize, cl, coneSize = 0; 6915 6916 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6917 for (cl = 0; cl < closureSize*2; cl += 2) { 6918 const PetscInt p = closure[cl]; 6919 if ((p >= vStart) && (p < vEnd)) ++coneSize; 6920 } 6921 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6922 if (coneSize != numCorners) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %D has %D vertices != %D", c, coneSize, numCorners); 6923 } 6924 for (c = cMax; c < cEnd; ++c) { 6925 PetscInt *closure = NULL, closureSize, cl, coneSize = 0; 6926 6927 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6928 for (cl = 0; cl < closureSize*2; cl += 2) { 6929 const PetscInt p = closure[cl]; 6930 if ((p >= vStart) && (p < vEnd)) ++coneSize; 6931 } 6932 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6933 if (coneSize > numHybridCorners) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Hybrid cell %D has %D vertices > %D", c, coneSize, numHybridCorners); 6934 } 6935 PetscFunctionReturn(0); 6936 } 6937 6938 /*@ 6939 DMPlexCheckFaces - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type 6940 6941 Input Parameters: 6942 + dm - The DMPlex object 6943 - cellHeight - Normally 0 6944 6945 Note: This is a useful diagnostic when creating meshes programmatically. 6946 6947 Level: developer 6948 6949 .seealso: DMCreate(), DMPlexCheckSymmetry(), DMPlexCheckSkeleton() 6950 @*/ 6951 PetscErrorCode DMPlexCheckFaces(DM dm, PetscInt cellHeight) 6952 { 6953 PetscInt pMax[4]; 6954 PetscInt dim, depth, vStart, vEnd, cStart, cEnd, c, h; 6955 PetscErrorCode ierr; 6956 6957 PetscFunctionBegin; 6958 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6959 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 6960 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 6961 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 6962 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], &pMax[dim-1], &pMax[1], &pMax[0]);CHKERRQ(ierr); 6963 for (h = cellHeight; h < PetscMin(depth, dim); ++h) { 6964 ierr = DMPlexGetHeightStratum(dm, h, &cStart, &cEnd);CHKERRQ(ierr); 6965 for (c = cStart; c < cEnd; ++c) { 6966 const PetscInt *cone, *ornt, *faces; 6967 PetscInt numFaces, faceSize, coneSize,f; 6968 PetscInt *closure = NULL, closureSize, cl, numCorners = 0; 6969 6970 if (pMax[dim-h] >= 0 && c >= pMax[dim-h]) continue; 6971 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 6972 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 6973 ierr = DMPlexGetConeOrientation(dm, c, &ornt);CHKERRQ(ierr); 6974 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6975 for (cl = 0; cl < closureSize*2; cl += 2) { 6976 const PetscInt p = closure[cl]; 6977 if ((p >= vStart) && (p < vEnd)) closure[numCorners++] = p; 6978 } 6979 ierr = DMPlexGetRawFaces_Internal(dm, dim-h, numCorners, closure, &numFaces, &faceSize, &faces);CHKERRQ(ierr); 6980 if (coneSize != numFaces) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %D has %D faces but should have %D", c, coneSize, numFaces); 6981 for (f = 0; f < numFaces; ++f) { 6982 PetscInt *fclosure = NULL, fclosureSize, cl, fnumCorners = 0, v; 6983 6984 ierr = DMPlexGetTransitiveClosure_Internal(dm, cone[f], ornt[f], PETSC_TRUE, &fclosureSize, &fclosure);CHKERRQ(ierr); 6985 for (cl = 0; cl < fclosureSize*2; cl += 2) { 6986 const PetscInt p = fclosure[cl]; 6987 if ((p >= vStart) && (p < vEnd)) fclosure[fnumCorners++] = p; 6988 } 6989 if (fnumCorners != faceSize) SETERRQ5(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D (%D) of cell %D has %D vertices but should have %D", cone[f], f, c, fnumCorners, faceSize); 6990 for (v = 0; v < fnumCorners; ++v) { 6991 if (fclosure[v] != faces[f*faceSize+v]) SETERRQ6(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %D (%d) of cell %D vertex %D, %D != %D", cone[f], f, c, v, fclosure[v], faces[f*faceSize+v]); 6992 } 6993 ierr = DMPlexRestoreTransitiveClosure(dm, cone[f], PETSC_TRUE, &fclosureSize, &fclosure);CHKERRQ(ierr); 6994 } 6995 ierr = DMPlexRestoreFaces_Internal(dm, dim, c, &numFaces, &faceSize, &faces);CHKERRQ(ierr); 6996 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6997 } 6998 } 6999 PetscFunctionReturn(0); 7000 } 7001 7002 /*@ 7003 DMPlexCheckGeometry - Check the geometry of mesh cells 7004 7005 Input Parameter: 7006 . dm - The DMPlex object 7007 7008 Note: This is a useful diagnostic when creating meshes programmatically. 7009 7010 Level: developer 7011 7012 .seealso: DMCreate(), DMCheckSymmetry(), DMCheckSkeleton(), DMCheckFaces() 7013 @*/ 7014 PetscErrorCode DMPlexCheckGeometry(DM dm) 7015 { 7016 PetscReal detJ, J[9], refVol = 1.0; 7017 PetscReal vol; 7018 PetscInt dim, depth, d, cStart, cEnd, c, cMax; 7019 PetscErrorCode ierr; 7020 7021 PetscFunctionBegin; 7022 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 7023 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 7024 for (d = 0; d < dim; ++d) refVol *= 2.0; 7025 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 7026 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 7027 cMax = cMax < 0 ? cEnd : cMax; 7028 for (c = cStart; c < cMax; ++c) { 7029 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, NULL, J, NULL, &detJ);CHKERRQ(ierr); 7030 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %D is inverted, |J| = %g", c, (double) detJ); 7031 ierr = PetscInfo2(dm, "Cell %D FEM Volume %g\n", c, (double) detJ*refVol);CHKERRQ(ierr); 7032 if (depth > 1) { 7033 ierr = DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);CHKERRQ(ierr); 7034 if (vol <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %d is inverted, vol = %g", c, (double) vol); 7035 ierr = PetscInfo2(dm, "Cell %D FVM Volume %g\n", c, (double) vol);CHKERRQ(ierr); 7036 } 7037 } 7038 PetscFunctionReturn(0); 7039 } 7040 7041 static PetscErrorCode DMPlexAreAllConePointsInArray_Private(DM dm, PetscInt p, PetscInt npoints, const PetscInt *points, PetscInt *missingPoint) 7042 { 7043 PetscInt i,l,n; 7044 const PetscInt *cone; 7045 PetscErrorCode ierr; 7046 7047 PetscFunctionBegin; 7048 *missingPoint = -1; 7049 ierr = DMPlexGetConeSize(dm, p, &n);CHKERRQ(ierr); 7050 ierr = DMPlexGetCone(dm, p, &cone);CHKERRQ(ierr); 7051 for (i=0; i<n; i++) { 7052 ierr = PetscFindInt(cone[i], npoints, points, &l);CHKERRQ(ierr); 7053 if (l < 0) { 7054 *missingPoint = cone[i]; 7055 break; 7056 } 7057 } 7058 PetscFunctionReturn(0); 7059 } 7060 7061 /*@ 7062 DMPlexCheckPointSF - Check that several sufficient conditions are met for the point SF of this plex. 7063 7064 Input Parameters: 7065 . dm - The DMPlex object 7066 7067 Note: This is mainly intended for debugging/testing purposes. 7068 7069 Level: developer 7070 7071 .seealso: DMGetPointSF(), DMPlexCheckSymmetry(), DMPlexCheckSkeleton(), DMPlexCheckFaces() 7072 @*/ 7073 PetscErrorCode DMPlexCheckPointSF(DM dm) 7074 { 7075 PetscSF sf; 7076 PetscInt d,depth,i,nleaves,p,plo,phi,missingPoint; 7077 const PetscInt *locals; 7078 PetscErrorCode ierr; 7079 7080 PetscFunctionBegin; 7081 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7082 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 7083 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 7084 ierr = PetscSFGetGraph(sf, NULL, &nleaves, &locals, NULL);CHKERRQ(ierr); 7085 7086 /* 1) check there are no faces in 2D, cells in 3D, in interface */ 7087 ierr = DMPlexGetVTKCellHeight(dm, &d);CHKERRQ(ierr); 7088 ierr = DMPlexGetHeightStratum(dm, d, &plo, &phi);CHKERRQ(ierr); 7089 for (i=0; i<nleaves; i++) { 7090 p = locals[i]; 7091 if (p >= plo && p < phi) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "point SF contains %d which is a cell",p); 7092 } 7093 7094 /* 2) if some point is in interface, then all its cone points must be also in interface */ 7095 for (i=0; i<nleaves; i++) { 7096 p = locals[i]; 7097 ierr = DMPlexAreAllConePointsInArray_Private(dm, p, nleaves, locals, &missingPoint);CHKERRQ(ierr); 7098 if (missingPoint >= 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "point SF contains %d but not %d from its cone",p,missingPoint); 7099 } 7100 PetscFunctionReturn(0); 7101 } 7102 7103 typedef struct cell_stats 7104 { 7105 PetscReal min, max, sum, squaresum; 7106 PetscInt count; 7107 } cell_stats_t; 7108 7109 static void cell_stats_reduce(void *a, void *b, int * len, MPI_Datatype *datatype) 7110 { 7111 PetscInt i, N = *len; 7112 7113 for (i = 0; i < N; i++) { 7114 cell_stats_t *A = (cell_stats_t *) a; 7115 cell_stats_t *B = (cell_stats_t *) b; 7116 7117 B->min = PetscMin(A->min,B->min); 7118 B->max = PetscMax(A->max,B->max); 7119 B->sum += A->sum; 7120 B->squaresum += A->squaresum; 7121 B->count += A->count; 7122 } 7123 } 7124 7125 /*@ 7126 DMPlexCheckCellShape - Checks the Jacobian of the mapping and computes some minimal statistics. 7127 7128 Input Parameters: 7129 + dm - The DMPlex object 7130 - output - If true, statistics will be displayed on stdout 7131 7132 Note: This is mainly intended for debugging/testing purposes. 7133 7134 Level: developer 7135 7136 .seealso: DMPlexCheckSymmetry(), DMPlexCheckSkeleton(), DMPlexCheckFaces() 7137 @*/ 7138 PetscErrorCode DMPlexCheckCellShape(DM dm, PetscBool output) 7139 { 7140 PetscMPIInt rank,size; 7141 PetscInt dim, c, cStart, cEnd, cMax, count = 0; 7142 cell_stats_t stats, globalStats; 7143 PetscReal *J, *invJ, min = 0, max = 0, mean = 0, stdev = 0; 7144 MPI_Comm comm = PetscObjectComm((PetscObject)dm); 7145 DM dmCoarse; 7146 PetscErrorCode ierr; 7147 7148 PetscFunctionBegin; 7149 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7150 stats.min = PETSC_MAX_REAL; 7151 stats.max = PETSC_MIN_REAL; 7152 stats.sum = stats.squaresum = 0.; 7153 stats.count = 0; 7154 7155 ierr = DMGetCoordinateDim(dm,&dim);CHKERRQ(ierr); 7156 ierr = PetscMalloc2(dim * dim, &J, dim * dim, &invJ);CHKERRQ(ierr); 7157 ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr); 7158 ierr = DMPlexGetHybridBounds(dm,&cMax,NULL,NULL,NULL);CHKERRQ(ierr); 7159 cMax = cMax < 0 ? cEnd : cMax; 7160 for (c = cStart; c < cMax; c++) { 7161 PetscInt i; 7162 PetscReal frobJ = 0., frobInvJ = 0., cond2, cond, detJ; 7163 7164 ierr = DMPlexComputeCellGeometryAffineFEM(dm,c,NULL,J,invJ,&detJ);CHKERRQ(ierr); 7165 if (detJ < 0.0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh cell %D is inverted", c); 7166 for (i = 0; i < dim * dim; i++) { 7167 frobJ += J[i] * J[i]; 7168 frobInvJ += invJ[i] * invJ[i]; 7169 } 7170 cond2 = frobJ * frobInvJ; 7171 cond = PetscSqrtReal(cond2); 7172 7173 stats.min = PetscMin(stats.min,cond); 7174 stats.max = PetscMax(stats.max,cond); 7175 stats.sum += cond; 7176 stats.squaresum += cond2; 7177 stats.count++; 7178 } 7179 7180 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 7181 if (size > 1) { 7182 PetscMPIInt blockLengths[2] = {4,1}; 7183 MPI_Aint blockOffsets[2] = {offsetof(cell_stats_t,min),offsetof(cell_stats_t,count)}; 7184 MPI_Datatype blockTypes[2] = {MPIU_REAL,MPIU_INT}, statType; 7185 MPI_Op statReduce; 7186 7187 ierr = MPI_Type_create_struct(2,blockLengths,blockOffsets,blockTypes,&statType);CHKERRQ(ierr); 7188 ierr = MPI_Type_commit(&statType);CHKERRQ(ierr); 7189 ierr = MPI_Op_create(cell_stats_reduce, PETSC_TRUE, &statReduce);CHKERRQ(ierr); 7190 ierr = MPI_Reduce(&stats,&globalStats,1,statType,statReduce,0,comm);CHKERRQ(ierr); 7191 ierr = MPI_Op_free(&statReduce);CHKERRQ(ierr); 7192 ierr = MPI_Type_free(&statType);CHKERRQ(ierr); 7193 } else { 7194 ierr = PetscArraycpy(&globalStats,&stats,1);CHKERRQ(ierr); 7195 } 7196 7197 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 7198 if (!rank) { 7199 count = globalStats.count; 7200 min = globalStats.min; 7201 max = globalStats.max; 7202 mean = globalStats.sum / globalStats.count; 7203 stdev = globalStats.count > 1 ? PetscSqrtReal(PetscMax((globalStats.squaresum - globalStats.count * mean * mean) / (globalStats.count - 1),0)) : 0.0; 7204 } 7205 7206 if (output) { 7207 ierr = PetscPrintf(comm,"Mesh with %D cells, shape condition numbers: min = %g, max = %g, mean = %g, stddev = %g\n", count, (double) min, (double) max, (double) mean, (double) stdev);CHKERRQ(ierr); 7208 } 7209 ierr = PetscFree2(J,invJ);CHKERRQ(ierr); 7210 7211 ierr = DMGetCoarseDM(dm,&dmCoarse);CHKERRQ(ierr); 7212 if (dmCoarse) { 7213 PetscBool isplex; 7214 7215 ierr = PetscObjectTypeCompare((PetscObject)dmCoarse,DMPLEX,&isplex);CHKERRQ(ierr); 7216 if (isplex) { 7217 ierr = DMPlexCheckCellShape(dmCoarse,output);CHKERRQ(ierr); 7218 } 7219 } 7220 PetscFunctionReturn(0); 7221 } 7222 7223 /* Pointwise interpolation 7224 Just code FEM for now 7225 u^f = I u^c 7226 sum_k u^f_k phi^f_k = I sum_j u^c_j phi^c_j 7227 u^f_i = sum_j psi^f_i I phi^c_j u^c_j 7228 I_{ij} = psi^f_i phi^c_j 7229 */ 7230 PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling) 7231 { 7232 PetscSection gsc, gsf; 7233 PetscInt m, n; 7234 void *ctx; 7235 DM cdm; 7236 PetscBool regular, ismatis; 7237 PetscErrorCode ierr; 7238 7239 PetscFunctionBegin; 7240 ierr = DMGetGlobalSection(dmFine, &gsf);CHKERRQ(ierr); 7241 ierr = PetscSectionGetConstrainedStorageSize(gsf, &m);CHKERRQ(ierr); 7242 ierr = DMGetGlobalSection(dmCoarse, &gsc);CHKERRQ(ierr); 7243 ierr = PetscSectionGetConstrainedStorageSize(gsc, &n);CHKERRQ(ierr); 7244 7245 ierr = PetscStrcmp(dmCoarse->mattype, MATIS, &ismatis);CHKERRQ(ierr); 7246 ierr = MatCreate(PetscObjectComm((PetscObject) dmCoarse), interpolation);CHKERRQ(ierr); 7247 ierr = MatSetSizes(*interpolation, m, n, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 7248 ierr = MatSetType(*interpolation, ismatis ? MATAIJ : dmCoarse->mattype);CHKERRQ(ierr); 7249 ierr = DMGetApplicationContext(dmFine, &ctx);CHKERRQ(ierr); 7250 7251 ierr = DMGetCoarseDM(dmFine, &cdm);CHKERRQ(ierr); 7252 ierr = DMPlexGetRegularRefinement(dmFine, ®ular);CHKERRQ(ierr); 7253 if (regular && cdm == dmCoarse) {ierr = DMPlexComputeInterpolatorNested(dmCoarse, dmFine, *interpolation, ctx);CHKERRQ(ierr);} 7254 else {ierr = DMPlexComputeInterpolatorGeneral(dmCoarse, dmFine, *interpolation, ctx);CHKERRQ(ierr);} 7255 ierr = MatViewFromOptions(*interpolation, NULL, "-interp_mat_view");CHKERRQ(ierr); 7256 if (scaling) { 7257 /* Use naive scaling */ 7258 ierr = DMCreateInterpolationScale(dmCoarse, dmFine, *interpolation, scaling);CHKERRQ(ierr); 7259 } 7260 PetscFunctionReturn(0); 7261 } 7262 7263 PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat) 7264 { 7265 PetscErrorCode ierr; 7266 VecScatter ctx; 7267 7268 PetscFunctionBegin; 7269 ierr = DMPlexComputeInjectorFEM(dmCoarse, dmFine, &ctx, NULL);CHKERRQ(ierr); 7270 ierr = MatCreateScatter(PetscObjectComm((PetscObject)ctx), ctx, mat);CHKERRQ(ierr); 7271 ierr = VecScatterDestroy(&ctx);CHKERRQ(ierr); 7272 PetscFunctionReturn(0); 7273 } 7274 7275 PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mass) 7276 { 7277 PetscSection gsc, gsf; 7278 PetscInt m, n; 7279 void *ctx; 7280 DM cdm; 7281 PetscBool regular; 7282 PetscErrorCode ierr; 7283 7284 PetscFunctionBegin; 7285 ierr = DMGetGlobalSection(dmFine, &gsf);CHKERRQ(ierr); 7286 ierr = PetscSectionGetConstrainedStorageSize(gsf, &m);CHKERRQ(ierr); 7287 ierr = DMGetGlobalSection(dmCoarse, &gsc);CHKERRQ(ierr); 7288 ierr = PetscSectionGetConstrainedStorageSize(gsc, &n);CHKERRQ(ierr); 7289 7290 ierr = MatCreate(PetscObjectComm((PetscObject) dmCoarse), mass);CHKERRQ(ierr); 7291 ierr = MatSetSizes(*mass, m, n, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 7292 ierr = MatSetType(*mass, dmCoarse->mattype);CHKERRQ(ierr); 7293 ierr = DMGetApplicationContext(dmFine, &ctx);CHKERRQ(ierr); 7294 7295 ierr = DMGetCoarseDM(dmFine, &cdm);CHKERRQ(ierr); 7296 ierr = DMPlexGetRegularRefinement(dmFine, ®ular);CHKERRQ(ierr); 7297 if (regular && cdm == dmCoarse) {ierr = DMPlexComputeMassMatrixNested(dmCoarse, dmFine, *mass, ctx);CHKERRQ(ierr);} 7298 else {ierr = DMPlexComputeMassMatrixGeneral(dmCoarse, dmFine, *mass, ctx);CHKERRQ(ierr);} 7299 ierr = MatViewFromOptions(*mass, NULL, "-mass_mat_view");CHKERRQ(ierr); 7300 PetscFunctionReturn(0); 7301 } 7302 7303 /*@ 7304 DMPlexGetRegularRefinement - Get the flag indicating that this mesh was obtained by regular refinement from its coarse mesh 7305 7306 Input Parameter: 7307 . dm - The DMPlex object 7308 7309 Output Parameter: 7310 . regular - The flag 7311 7312 Level: intermediate 7313 7314 .seealso: DMPlexSetRegularRefinement() 7315 @*/ 7316 PetscErrorCode DMPlexGetRegularRefinement(DM dm, PetscBool *regular) 7317 { 7318 PetscFunctionBegin; 7319 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7320 PetscValidPointer(regular, 2); 7321 *regular = ((DM_Plex *) dm->data)->regularRefinement; 7322 PetscFunctionReturn(0); 7323 } 7324 7325 /*@ 7326 DMPlexSetRegularRefinement - Set the flag indicating that this mesh was obtained by regular refinement from its coarse mesh 7327 7328 Input Parameters: 7329 + dm - The DMPlex object 7330 - regular - The flag 7331 7332 Level: intermediate 7333 7334 .seealso: DMPlexGetRegularRefinement() 7335 @*/ 7336 PetscErrorCode DMPlexSetRegularRefinement(DM dm, PetscBool regular) 7337 { 7338 PetscFunctionBegin; 7339 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7340 ((DM_Plex *) dm->data)->regularRefinement = regular; 7341 PetscFunctionReturn(0); 7342 } 7343 7344 /* anchors */ 7345 /*@ 7346 DMPlexGetAnchors - Get the layout of the anchor (point-to-point) constraints. Typically, the user will not have to 7347 call DMPlexGetAnchors() directly: if there are anchors, then DMPlexGetAnchors() is called during DMGetConstraints(). 7348 7349 not collective 7350 7351 Input Parameters: 7352 . dm - The DMPlex object 7353 7354 Output Parameters: 7355 + anchorSection - If not NULL, set to the section describing which points anchor the constrained points. 7356 - anchorIS - If not NULL, set to the list of anchors indexed by anchorSection 7357 7358 7359 Level: intermediate 7360 7361 .seealso: DMPlexSetAnchors(), DMGetConstraints(), DMSetConstraints() 7362 @*/ 7363 PetscErrorCode DMPlexGetAnchors(DM dm, PetscSection *anchorSection, IS *anchorIS) 7364 { 7365 DM_Plex *plex = (DM_Plex *)dm->data; 7366 PetscErrorCode ierr; 7367 7368 PetscFunctionBegin; 7369 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7370 if (!plex->anchorSection && !plex->anchorIS && plex->createanchors) {ierr = (*plex->createanchors)(dm);CHKERRQ(ierr);} 7371 if (anchorSection) *anchorSection = plex->anchorSection; 7372 if (anchorIS) *anchorIS = plex->anchorIS; 7373 PetscFunctionReturn(0); 7374 } 7375 7376 /*@ 7377 DMPlexSetAnchors - Set the layout of the local anchor (point-to-point) constraints. Unlike boundary conditions, 7378 when a point's degrees of freedom in a section are constrained to an outside value, the anchor constraints set a 7379 point's degrees of freedom to be a linear combination of other points' degrees of freedom. 7380 7381 After specifying the layout of constraints with DMPlexSetAnchors(), one specifies the constraints by calling 7382 DMGetConstraints() and filling in the entries in the constraint matrix. 7383 7384 collective on dm 7385 7386 Input Parameters: 7387 + dm - The DMPlex object 7388 . anchorSection - The section that describes the mapping from constrained points to the anchor points listed in anchorIS. Must have a local communicator (PETSC_COMM_SELF or derivative). 7389 - anchorIS - The list of all anchor points. Must have a local communicator (PETSC_COMM_SELF or derivative). 7390 7391 The reference counts of anchorSection and anchorIS are incremented. 7392 7393 Level: intermediate 7394 7395 .seealso: DMPlexGetAnchors(), DMGetConstraints(), DMSetConstraints() 7396 @*/ 7397 PetscErrorCode DMPlexSetAnchors(DM dm, PetscSection anchorSection, IS anchorIS) 7398 { 7399 DM_Plex *plex = (DM_Plex *)dm->data; 7400 PetscMPIInt result; 7401 PetscErrorCode ierr; 7402 7403 PetscFunctionBegin; 7404 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7405 if (anchorSection) { 7406 PetscValidHeaderSpecific(anchorSection,PETSC_SECTION_CLASSID,2); 7407 ierr = MPI_Comm_compare(PETSC_COMM_SELF,PetscObjectComm((PetscObject)anchorSection),&result);CHKERRQ(ierr); 7408 if (result != MPI_CONGRUENT && result != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMECOMM,"anchor section must have local communicator"); 7409 } 7410 if (anchorIS) { 7411 PetscValidHeaderSpecific(anchorIS,IS_CLASSID,3); 7412 ierr = MPI_Comm_compare(PETSC_COMM_SELF,PetscObjectComm((PetscObject)anchorIS),&result);CHKERRQ(ierr); 7413 if (result != MPI_CONGRUENT && result != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMECOMM,"anchor IS must have local communicator"); 7414 } 7415 7416 ierr = PetscObjectReference((PetscObject)anchorSection);CHKERRQ(ierr); 7417 ierr = PetscSectionDestroy(&plex->anchorSection);CHKERRQ(ierr); 7418 plex->anchorSection = anchorSection; 7419 7420 ierr = PetscObjectReference((PetscObject)anchorIS);CHKERRQ(ierr); 7421 ierr = ISDestroy(&plex->anchorIS);CHKERRQ(ierr); 7422 plex->anchorIS = anchorIS; 7423 7424 #if defined(PETSC_USE_DEBUG) 7425 if (anchorIS && anchorSection) { 7426 PetscInt size, a, pStart, pEnd; 7427 const PetscInt *anchors; 7428 7429 ierr = PetscSectionGetChart(anchorSection,&pStart,&pEnd);CHKERRQ(ierr); 7430 ierr = ISGetLocalSize(anchorIS,&size);CHKERRQ(ierr); 7431 ierr = ISGetIndices(anchorIS,&anchors);CHKERRQ(ierr); 7432 for (a = 0; a < size; a++) { 7433 PetscInt p; 7434 7435 p = anchors[a]; 7436 if (p >= pStart && p < pEnd) { 7437 PetscInt dof; 7438 7439 ierr = PetscSectionGetDof(anchorSection,p,&dof);CHKERRQ(ierr); 7440 if (dof) { 7441 PetscErrorCode ierr2; 7442 7443 ierr2 = ISRestoreIndices(anchorIS,&anchors);CHKERRQ(ierr2); 7444 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Point %D cannot be constrained and an anchor",p); 7445 } 7446 } 7447 } 7448 ierr = ISRestoreIndices(anchorIS,&anchors);CHKERRQ(ierr); 7449 } 7450 #endif 7451 /* reset the generic constraints */ 7452 ierr = DMSetDefaultConstraints(dm,NULL,NULL);CHKERRQ(ierr); 7453 PetscFunctionReturn(0); 7454 } 7455 7456 static PetscErrorCode DMPlexCreateConstraintSection_Anchors(DM dm, PetscSection section, PetscSection *cSec) 7457 { 7458 PetscSection anchorSection; 7459 PetscInt pStart, pEnd, sStart, sEnd, p, dof, numFields, f; 7460 PetscErrorCode ierr; 7461 7462 PetscFunctionBegin; 7463 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7464 ierr = DMPlexGetAnchors(dm,&anchorSection,NULL);CHKERRQ(ierr); 7465 ierr = PetscSectionCreate(PETSC_COMM_SELF,cSec);CHKERRQ(ierr); 7466 ierr = PetscSectionGetNumFields(section,&numFields);CHKERRQ(ierr); 7467 if (numFields) { 7468 PetscInt f; 7469 ierr = PetscSectionSetNumFields(*cSec,numFields);CHKERRQ(ierr); 7470 7471 for (f = 0; f < numFields; f++) { 7472 PetscInt numComp; 7473 7474 ierr = PetscSectionGetFieldComponents(section,f,&numComp);CHKERRQ(ierr); 7475 ierr = PetscSectionSetFieldComponents(*cSec,f,numComp);CHKERRQ(ierr); 7476 } 7477 } 7478 ierr = PetscSectionGetChart(anchorSection,&pStart,&pEnd);CHKERRQ(ierr); 7479 ierr = PetscSectionGetChart(section,&sStart,&sEnd);CHKERRQ(ierr); 7480 pStart = PetscMax(pStart,sStart); 7481 pEnd = PetscMin(pEnd,sEnd); 7482 pEnd = PetscMax(pStart,pEnd); 7483 ierr = PetscSectionSetChart(*cSec,pStart,pEnd);CHKERRQ(ierr); 7484 for (p = pStart; p < pEnd; p++) { 7485 ierr = PetscSectionGetDof(anchorSection,p,&dof);CHKERRQ(ierr); 7486 if (dof) { 7487 ierr = PetscSectionGetDof(section,p,&dof);CHKERRQ(ierr); 7488 ierr = PetscSectionSetDof(*cSec,p,dof);CHKERRQ(ierr); 7489 for (f = 0; f < numFields; f++) { 7490 ierr = PetscSectionGetFieldDof(section,p,f,&dof);CHKERRQ(ierr); 7491 ierr = PetscSectionSetFieldDof(*cSec,p,f,dof);CHKERRQ(ierr); 7492 } 7493 } 7494 } 7495 ierr = PetscSectionSetUp(*cSec);CHKERRQ(ierr); 7496 PetscFunctionReturn(0); 7497 } 7498 7499 static PetscErrorCode DMPlexCreateConstraintMatrix_Anchors(DM dm, PetscSection section, PetscSection cSec, Mat *cMat) 7500 { 7501 PetscSection aSec; 7502 PetscInt pStart, pEnd, p, dof, aDof, aOff, off, nnz, annz, m, n, q, a, offset, *i, *j; 7503 const PetscInt *anchors; 7504 PetscInt numFields, f; 7505 IS aIS; 7506 PetscErrorCode ierr; 7507 7508 PetscFunctionBegin; 7509 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7510 ierr = PetscSectionGetStorageSize(cSec, &m);CHKERRQ(ierr); 7511 ierr = PetscSectionGetStorageSize(section, &n);CHKERRQ(ierr); 7512 ierr = MatCreate(PETSC_COMM_SELF,cMat);CHKERRQ(ierr); 7513 ierr = MatSetSizes(*cMat,m,n,m,n);CHKERRQ(ierr); 7514 ierr = MatSetType(*cMat,MATSEQAIJ);CHKERRQ(ierr); 7515 ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr); 7516 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 7517 /* cSec will be a subset of aSec and section */ 7518 ierr = PetscSectionGetChart(cSec,&pStart,&pEnd);CHKERRQ(ierr); 7519 ierr = PetscMalloc1(m+1,&i);CHKERRQ(ierr); 7520 i[0] = 0; 7521 ierr = PetscSectionGetNumFields(section,&numFields);CHKERRQ(ierr); 7522 for (p = pStart; p < pEnd; p++) { 7523 PetscInt rDof, rOff, r; 7524 7525 ierr = PetscSectionGetDof(aSec,p,&rDof);CHKERRQ(ierr); 7526 if (!rDof) continue; 7527 ierr = PetscSectionGetOffset(aSec,p,&rOff);CHKERRQ(ierr); 7528 if (numFields) { 7529 for (f = 0; f < numFields; f++) { 7530 annz = 0; 7531 for (r = 0; r < rDof; r++) { 7532 a = anchors[rOff + r]; 7533 ierr = PetscSectionGetFieldDof(section,a,f,&aDof);CHKERRQ(ierr); 7534 annz += aDof; 7535 } 7536 ierr = PetscSectionGetFieldDof(cSec,p,f,&dof);CHKERRQ(ierr); 7537 ierr = PetscSectionGetFieldOffset(cSec,p,f,&off);CHKERRQ(ierr); 7538 for (q = 0; q < dof; q++) { 7539 i[off + q + 1] = i[off + q] + annz; 7540 } 7541 } 7542 } 7543 else { 7544 annz = 0; 7545 for (q = 0; q < dof; q++) { 7546 a = anchors[off + q]; 7547 ierr = PetscSectionGetDof(section,a,&aDof);CHKERRQ(ierr); 7548 annz += aDof; 7549 } 7550 ierr = PetscSectionGetDof(cSec,p,&dof);CHKERRQ(ierr); 7551 ierr = PetscSectionGetOffset(cSec,p,&off);CHKERRQ(ierr); 7552 for (q = 0; q < dof; q++) { 7553 i[off + q + 1] = i[off + q] + annz; 7554 } 7555 } 7556 } 7557 nnz = i[m]; 7558 ierr = PetscMalloc1(nnz,&j);CHKERRQ(ierr); 7559 offset = 0; 7560 for (p = pStart; p < pEnd; p++) { 7561 if (numFields) { 7562 for (f = 0; f < numFields; f++) { 7563 ierr = PetscSectionGetFieldDof(cSec,p,f,&dof);CHKERRQ(ierr); 7564 for (q = 0; q < dof; q++) { 7565 PetscInt rDof, rOff, r; 7566 ierr = PetscSectionGetDof(aSec,p,&rDof);CHKERRQ(ierr); 7567 ierr = PetscSectionGetOffset(aSec,p,&rOff);CHKERRQ(ierr); 7568 for (r = 0; r < rDof; r++) { 7569 PetscInt s; 7570 7571 a = anchors[rOff + r]; 7572 ierr = PetscSectionGetFieldDof(section,a,f,&aDof);CHKERRQ(ierr); 7573 ierr = PetscSectionGetFieldOffset(section,a,f,&aOff);CHKERRQ(ierr); 7574 for (s = 0; s < aDof; s++) { 7575 j[offset++] = aOff + s; 7576 } 7577 } 7578 } 7579 } 7580 } 7581 else { 7582 ierr = PetscSectionGetDof(cSec,p,&dof);CHKERRQ(ierr); 7583 for (q = 0; q < dof; q++) { 7584 PetscInt rDof, rOff, r; 7585 ierr = PetscSectionGetDof(aSec,p,&rDof);CHKERRQ(ierr); 7586 ierr = PetscSectionGetOffset(aSec,p,&rOff);CHKERRQ(ierr); 7587 for (r = 0; r < rDof; r++) { 7588 PetscInt s; 7589 7590 a = anchors[rOff + r]; 7591 ierr = PetscSectionGetDof(section,a,&aDof);CHKERRQ(ierr); 7592 ierr = PetscSectionGetOffset(section,a,&aOff);CHKERRQ(ierr); 7593 for (s = 0; s < aDof; s++) { 7594 j[offset++] = aOff + s; 7595 } 7596 } 7597 } 7598 } 7599 } 7600 ierr = MatSeqAIJSetPreallocationCSR(*cMat,i,j,NULL);CHKERRQ(ierr); 7601 ierr = PetscFree(i);CHKERRQ(ierr); 7602 ierr = PetscFree(j);CHKERRQ(ierr); 7603 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 7604 PetscFunctionReturn(0); 7605 } 7606 7607 PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm) 7608 { 7609 DM_Plex *plex = (DM_Plex *)dm->data; 7610 PetscSection anchorSection, section, cSec; 7611 Mat cMat; 7612 PetscErrorCode ierr; 7613 7614 PetscFunctionBegin; 7615 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 7616 ierr = DMPlexGetAnchors(dm,&anchorSection,NULL);CHKERRQ(ierr); 7617 if (anchorSection) { 7618 PetscInt Nf; 7619 7620 ierr = DMGetLocalSection(dm,§ion);CHKERRQ(ierr); 7621 ierr = DMPlexCreateConstraintSection_Anchors(dm,section,&cSec);CHKERRQ(ierr); 7622 ierr = DMPlexCreateConstraintMatrix_Anchors(dm,section,cSec,&cMat);CHKERRQ(ierr); 7623 ierr = DMGetNumFields(dm,&Nf);CHKERRQ(ierr); 7624 if (Nf && plex->computeanchormatrix) {ierr = (*plex->computeanchormatrix)(dm,section,cSec,cMat);CHKERRQ(ierr);} 7625 ierr = DMSetDefaultConstraints(dm,cSec,cMat);CHKERRQ(ierr); 7626 ierr = PetscSectionDestroy(&cSec);CHKERRQ(ierr); 7627 ierr = MatDestroy(&cMat);CHKERRQ(ierr); 7628 } 7629 PetscFunctionReturn(0); 7630 } 7631 7632 PetscErrorCode DMCreateSubDomainDM_Plex(DM dm, DMLabel label, PetscInt value, IS *is, DM *subdm) 7633 { 7634 IS subis; 7635 PetscSection section, subsection; 7636 PetscErrorCode ierr; 7637 7638 PetscFunctionBegin; 7639 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 7640 if (!section) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Must set default section for DM before splitting subdomain"); 7641 if (!subdm) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Must set output subDM for splitting subdomain"); 7642 /* Create subdomain */ 7643 ierr = DMPlexFilter(dm, label, value, subdm);CHKERRQ(ierr); 7644 /* Create submodel */ 7645 ierr = DMPlexCreateSubpointIS(*subdm, &subis);CHKERRQ(ierr); 7646 ierr = PetscSectionCreateSubmeshSection(section, subis, &subsection);CHKERRQ(ierr); 7647 ierr = ISDestroy(&subis);CHKERRQ(ierr); 7648 ierr = DMSetLocalSection(*subdm, subsection);CHKERRQ(ierr); 7649 ierr = PetscSectionDestroy(&subsection);CHKERRQ(ierr); 7650 ierr = DMCopyDisc(dm, *subdm);CHKERRQ(ierr); 7651 /* Create map from submodel to global model */ 7652 if (is) { 7653 PetscSection sectionGlobal, subsectionGlobal; 7654 IS spIS; 7655 const PetscInt *spmap; 7656 PetscInt *subIndices; 7657 PetscInt subSize = 0, subOff = 0, pStart, pEnd, p; 7658 PetscInt Nf, f, bs = -1, bsLocal[2], bsMinMax[2]; 7659 7660 ierr = DMPlexCreateSubpointIS(*subdm, &spIS);CHKERRQ(ierr); 7661 ierr = ISGetIndices(spIS, &spmap);CHKERRQ(ierr); 7662 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 7663 ierr = DMGetGlobalSection(dm, §ionGlobal);CHKERRQ(ierr); 7664 ierr = DMGetGlobalSection(*subdm, &subsectionGlobal);CHKERRQ(ierr); 7665 ierr = PetscSectionGetChart(subsection, &pStart, &pEnd);CHKERRQ(ierr); 7666 for (p = pStart; p < pEnd; ++p) { 7667 PetscInt gdof, pSubSize = 0; 7668 7669 ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr); 7670 if (gdof > 0) { 7671 for (f = 0; f < Nf; ++f) { 7672 PetscInt fdof, fcdof; 7673 7674 ierr = PetscSectionGetFieldDof(subsection, p, f, &fdof);CHKERRQ(ierr); 7675 ierr = PetscSectionGetFieldConstraintDof(subsection, p, f, &fcdof);CHKERRQ(ierr); 7676 pSubSize += fdof-fcdof; 7677 } 7678 subSize += pSubSize; 7679 if (pSubSize) { 7680 if (bs < 0) { 7681 bs = pSubSize; 7682 } else if (bs != pSubSize) { 7683 /* Layout does not admit a pointwise block size */ 7684 bs = 1; 7685 } 7686 } 7687 } 7688 } 7689 /* Must have same blocksize on all procs (some might have no points) */ 7690 bsLocal[0] = bs < 0 ? PETSC_MAX_INT : bs; bsLocal[1] = bs; 7691 ierr = PetscGlobalMinMaxInt(PetscObjectComm((PetscObject) dm), bsLocal, bsMinMax);CHKERRQ(ierr); 7692 if (bsMinMax[0] != bsMinMax[1]) {bs = 1;} 7693 else {bs = bsMinMax[0];} 7694 ierr = PetscMalloc1(subSize, &subIndices);CHKERRQ(ierr); 7695 for (p = pStart; p < pEnd; ++p) { 7696 PetscInt gdof, goff; 7697 7698 ierr = PetscSectionGetDof(subsectionGlobal, p, &gdof);CHKERRQ(ierr); 7699 if (gdof > 0) { 7700 const PetscInt point = spmap[p]; 7701 7702 ierr = PetscSectionGetOffset(sectionGlobal, point, &goff);CHKERRQ(ierr); 7703 for (f = 0; f < Nf; ++f) { 7704 PetscInt fdof, fcdof, fc, f2, poff = 0; 7705 7706 /* Can get rid of this loop by storing field information in the global section */ 7707 for (f2 = 0; f2 < f; ++f2) { 7708 ierr = PetscSectionGetFieldDof(section, p, f2, &fdof);CHKERRQ(ierr); 7709 ierr = PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof);CHKERRQ(ierr); 7710 poff += fdof-fcdof; 7711 } 7712 ierr = PetscSectionGetFieldDof(section, p, f, &fdof);CHKERRQ(ierr); 7713 ierr = PetscSectionGetFieldConstraintDof(section, p, f, &fcdof);CHKERRQ(ierr); 7714 for (fc = 0; fc < fdof-fcdof; ++fc, ++subOff) { 7715 subIndices[subOff] = goff+poff+fc; 7716 } 7717 } 7718 } 7719 } 7720 ierr = ISRestoreIndices(spIS, &spmap);CHKERRQ(ierr); 7721 ierr = ISDestroy(&spIS);CHKERRQ(ierr); 7722 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is);CHKERRQ(ierr); 7723 if (bs > 1) { 7724 /* We need to check that the block size does not come from non-contiguous fields */ 7725 PetscInt i, j, set = 1; 7726 for (i = 0; i < subSize; i += bs) { 7727 for (j = 0; j < bs; ++j) { 7728 if (subIndices[i+j] != subIndices[i]+j) {set = 0; break;} 7729 } 7730 } 7731 if (set) {ierr = ISSetBlockSize(*is, bs);CHKERRQ(ierr);} 7732 } 7733 /* Attach nullspace */ 7734 for (f = 0; f < Nf; ++f) { 7735 (*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[f]; 7736 if ((*subdm)->nullspaceConstructors[f]) break; 7737 } 7738 if (f < Nf) { 7739 MatNullSpace nullSpace; 7740 7741 ierr = (*(*subdm)->nullspaceConstructors[f])(*subdm, f, &nullSpace);CHKERRQ(ierr); 7742 ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) nullSpace);CHKERRQ(ierr); 7743 ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); 7744 } 7745 } 7746 PetscFunctionReturn(0); 7747 } 7748