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 9 /* Logging support */ 10 PetscLogEvent DMPLEX_Interpolate, PETSCPARTITIONER_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_Preallocate, DMPLEX_ResidualFEM, DMPLEX_JacobianFEM, DMPLEX_InterpolatorFEM, DMPLEX_InjectorFEM, DMPLEX_IntegralFEM, DMPLEX_CreateGmsh; 11 12 PETSC_EXTERN PetscErrorCode VecView_MPI(Vec, PetscViewer); 13 14 /*@ 15 DMPlexRefineSimplexToTensor - Uniformly refines simplicial cells into tensor product cells. 16 3 quadrilaterals per triangle in 2D and 4 hexahedra per tetrahedron in 3D. 17 18 Collective 19 20 Input Parameters: 21 . dm - The DMPlex object 22 23 Output Parameters: 24 . dmRefined - The refined DMPlex object 25 26 Note: Returns NULL if the mesh is already a tensor product mesh. 27 28 Level: intermediate 29 30 .seealso: DMPlexCreate(), DMPlexSetRefinementUniform() 31 @*/ 32 PetscErrorCode DMPlexRefineSimplexToTensor(DM dm, DM *dmRefined) 33 { 34 PetscInt dim, cMax, fMax, cStart, cEnd, coneSize; 35 CellRefiner cellRefiner; 36 PetscBool lop, allnoop, localized; 37 PetscErrorCode ierr; 38 39 PetscFunctionBegin; 40 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 41 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 42 ierr = DMPlexGetHybridBounds(dm,&cMax,&fMax,NULL,NULL);CHKERRQ(ierr); 43 if (cMax >= 0 || fMax >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot handle hybrid meshes yet"); 44 ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr); 45 if (!(cEnd - cStart)) cellRefiner = REFINER_NOOP; 46 else { 47 ierr = DMPlexGetConeSize(dm,cStart,&coneSize);CHKERRQ(ierr); 48 switch (dim) { 49 case 1: 50 cellRefiner = REFINER_NOOP; 51 break; 52 case 2: 53 switch (coneSize) { 54 case 3: 55 cellRefiner = REFINER_SIMPLEX_TO_HEX_2D; 56 break; 57 case 4: 58 cellRefiner = REFINER_NOOP; 59 break; 60 default: SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot handle coneSize %D with dimension %D",coneSize,dim); 61 } 62 break; 63 case 3: 64 switch (coneSize) { 65 case 4: 66 cellRefiner = REFINER_SIMPLEX_TO_HEX_3D; 67 break; 68 case 6: 69 cellRefiner = REFINER_NOOP; 70 break; 71 default: SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot handle coneSize %D with dimension %D",coneSize,dim); 72 } 73 break; 74 default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot handle dimension %D",dim); 75 } 76 } 77 /* return if we don't need to refine */ 78 lop = (cellRefiner == REFINER_NOOP) ? PETSC_TRUE : PETSC_FALSE; 79 ierr = MPIU_Allreduce(&lop,&allnoop,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 80 if (allnoop) { 81 *dmRefined = NULL; 82 PetscFunctionReturn(0); 83 } 84 ierr = DMPlexRefineUniform_Internal(dm, cellRefiner, dmRefined);CHKERRQ(ierr); 85 ierr = DMCopyBoundary(dm, *dmRefined);CHKERRQ(ierr); 86 ierr = DMGetCoordinatesLocalized(dm, &localized);CHKERRQ(ierr); 87 if (localized) { 88 ierr = DMLocalizeCoordinates(*dmRefined);CHKERRQ(ierr); 89 } 90 PetscFunctionReturn(0); 91 } 92 93 PetscErrorCode DMPlexGetFieldType_Internal(DM dm, PetscSection section, PetscInt field, PetscInt *sStart, PetscInt *sEnd, PetscViewerVTKFieldType *ft) 94 { 95 PetscInt dim, pStart, pEnd, vStart, vEnd, cStart, cEnd, cEndInterior, vdof = 0, cdof = 0; 96 PetscErrorCode ierr; 97 98 PetscFunctionBegin; 99 *ft = PETSC_VTK_POINT_FIELD; 100 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 101 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 102 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 103 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 104 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 105 ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); 106 if (field >= 0) { 107 if ((vStart >= pStart) && (vStart < pEnd)) {ierr = PetscSectionGetFieldDof(section, vStart, field, &vdof);CHKERRQ(ierr);} 108 if ((cStart >= pStart) && (cStart < pEnd)) {ierr = PetscSectionGetFieldDof(section, cStart, field, &cdof);CHKERRQ(ierr);} 109 } else { 110 if ((vStart >= pStart) && (vStart < pEnd)) {ierr = PetscSectionGetDof(section, vStart, &vdof);CHKERRQ(ierr);} 111 if ((cStart >= pStart) && (cStart < pEnd)) {ierr = PetscSectionGetDof(section, cStart, &cdof);CHKERRQ(ierr);} 112 } 113 if (vdof) { 114 *sStart = vStart; 115 *sEnd = vEnd; 116 if (vdof == dim) *ft = PETSC_VTK_POINT_VECTOR_FIELD; 117 else *ft = PETSC_VTK_POINT_FIELD; 118 } else if (cdof) { 119 *sStart = cStart; 120 *sEnd = cEnd; 121 if (cdof == dim) *ft = PETSC_VTK_CELL_VECTOR_FIELD; 122 else *ft = PETSC_VTK_CELL_FIELD; 123 } else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Could not classify input Vec for VTK"); 124 PetscFunctionReturn(0); 125 } 126 127 static PetscErrorCode VecView_Plex_Local_Draw(Vec v, PetscViewer viewer) 128 { 129 DM dm; 130 PetscSection s; 131 PetscDraw draw, popup; 132 DM cdm; 133 PetscSection coordSection; 134 Vec coordinates; 135 const PetscScalar *coords, *array; 136 PetscReal bound[4] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL}; 137 PetscReal vbound[2], time; 138 PetscBool isnull, flg; 139 PetscInt dim, Nf, f, Nc, comp, vStart, vEnd, cStart, cEnd, c, N, level, step, w = 0; 140 const char *name; 141 char title[PETSC_MAX_PATH_LEN]; 142 PetscErrorCode ierr; 143 144 PetscFunctionBegin; 145 ierr = PetscViewerDrawGetDraw(viewer, 0, &draw);CHKERRQ(ierr); 146 ierr = PetscDrawIsNull(draw, &isnull);CHKERRQ(ierr); 147 if (isnull) PetscFunctionReturn(0); 148 149 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 150 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 151 if (dim != 2) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Cannot draw meshes of dimension %D. Use PETSCVIEWERGLVIS", dim); 152 ierr = DMGetDefaultSection(dm, &s);CHKERRQ(ierr); 153 ierr = PetscSectionGetNumFields(s, &Nf);CHKERRQ(ierr); 154 ierr = DMGetCoarsenLevel(dm, &level);CHKERRQ(ierr); 155 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 156 ierr = DMGetDefaultSection(cdm, &coordSection);CHKERRQ(ierr); 157 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 158 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 159 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 160 161 ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr); 162 ierr = DMGetOutputSequenceNumber(dm, &step, &time);CHKERRQ(ierr); 163 164 ierr = VecGetLocalSize(coordinates, &N);CHKERRQ(ierr); 165 ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); 166 for (c = 0; c < N; c += dim) { 167 bound[0] = PetscMin(bound[0], PetscRealPart(coords[c])); bound[2] = PetscMax(bound[2], PetscRealPart(coords[c])); 168 bound[1] = PetscMin(bound[1], PetscRealPart(coords[c+1])); bound[3] = PetscMax(bound[3], PetscRealPart(coords[c+1])); 169 } 170 ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); 171 ierr = PetscDrawClear(draw);CHKERRQ(ierr); 172 173 /* Could implement something like DMDASelectFields() */ 174 for (f = 0; f < Nf; ++f) { 175 DM fdm = dm; 176 Vec fv = v; 177 IS fis; 178 char prefix[PETSC_MAX_PATH_LEN]; 179 const char *fname; 180 181 ierr = PetscSectionGetFieldComponents(s, f, &Nc);CHKERRQ(ierr); 182 ierr = PetscSectionGetFieldName(s, f, &fname);CHKERRQ(ierr); 183 184 if (v->hdr.prefix) {ierr = PetscStrcpy(prefix, v->hdr.prefix);CHKERRQ(ierr);} 185 else {prefix[0] = '\0';} 186 if (Nf > 1) { 187 ierr = DMCreateSubDM(dm, 1, &f, &fis, &fdm);CHKERRQ(ierr); 188 ierr = VecGetSubVector(v, fis, &fv);CHKERRQ(ierr); 189 ierr = PetscStrcat(prefix, fname);CHKERRQ(ierr); 190 ierr = PetscStrcat(prefix, "_");CHKERRQ(ierr); 191 } 192 for (comp = 0; comp < Nc; ++comp, ++w) { 193 PetscInt nmax = 2; 194 195 ierr = PetscViewerDrawGetDraw(viewer, w, &draw);CHKERRQ(ierr); 196 if (Nc > 1) {ierr = PetscSNPrintf(title, sizeof(title), "%s:%s_%D Step: %D Time: %.4g", name, fname, comp, step, time);CHKERRQ(ierr);} 197 else {ierr = PetscSNPrintf(title, sizeof(title), "%s:%s Step: %D Time: %.4g", name, fname, step, time);CHKERRQ(ierr);} 198 ierr = PetscDrawSetTitle(draw, title);CHKERRQ(ierr); 199 200 /* TODO Get max and min only for this component */ 201 ierr = PetscOptionsGetRealArray(NULL, prefix, "-vec_view_bounds", vbound, &nmax, &flg);CHKERRQ(ierr); 202 if (!flg) { 203 ierr = VecMin(fv, NULL, &vbound[0]);CHKERRQ(ierr); 204 ierr = VecMax(fv, NULL, &vbound[1]);CHKERRQ(ierr); 205 if (vbound[1] <= vbound[0]) vbound[1] = vbound[0] + 1.0; 206 } 207 ierr = PetscDrawGetPopup(draw, &popup);CHKERRQ(ierr); 208 ierr = PetscDrawScalePopup(popup, vbound[0], vbound[1]);CHKERRQ(ierr); 209 ierr = PetscDrawSetCoordinates(draw, bound[0], bound[1], bound[2], bound[3]);CHKERRQ(ierr); 210 211 ierr = VecGetArrayRead(fv, &array);CHKERRQ(ierr); 212 for (c = cStart; c < cEnd; ++c) { 213 PetscScalar *coords = NULL, *a = NULL; 214 PetscInt numCoords, color[4] = {-1,-1,-1,-1}; 215 216 ierr = DMPlexPointLocalRead(fdm, c, array, &a);CHKERRQ(ierr); 217 if (a) { 218 color[0] = PetscDrawRealToColor(PetscRealPart(a[comp]), vbound[0], vbound[1]); 219 color[1] = color[2] = color[3] = color[0]; 220 } else { 221 PetscScalar *vals = NULL; 222 PetscInt numVals, va; 223 224 ierr = DMPlexVecGetClosure(fdm, NULL, fv, c, &numVals, &vals);CHKERRQ(ierr); 225 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); 226 switch (numVals/Nc) { 227 case 3: /* P1 Triangle */ 228 case 4: /* P1 Quadrangle */ 229 for (va = 0; va < numVals/Nc; ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va*Nc+comp]), vbound[0], vbound[1]); 230 break; 231 case 6: /* P2 Triangle */ 232 case 8: /* P2 Quadrangle */ 233 for (va = 0; va < numVals/(Nc*2); ++va) color[va] = PetscDrawRealToColor(PetscRealPart(vals[va*Nc+comp + numVals/(Nc*2)]), vbound[0], vbound[1]); 234 break; 235 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of values for cell closure %D cannot be handled", numVals/Nc); 236 } 237 ierr = DMPlexVecRestoreClosure(fdm, NULL, fv, c, &numVals, &vals);CHKERRQ(ierr); 238 } 239 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, c, &numCoords, &coords);CHKERRQ(ierr); 240 switch (numCoords) { 241 case 6: 242 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); 243 break; 244 case 8: 245 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); 246 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); 247 break; 248 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %D coordinates", numCoords); 249 } 250 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, &numCoords, &coords);CHKERRQ(ierr); 251 } 252 ierr = VecRestoreArrayRead(fv, &array);CHKERRQ(ierr); 253 ierr = PetscDrawFlush(draw);CHKERRQ(ierr); 254 ierr = PetscDrawPause(draw);CHKERRQ(ierr); 255 ierr = PetscDrawSave(draw);CHKERRQ(ierr); 256 } 257 if (Nf > 1) { 258 ierr = VecRestoreSubVector(v, fis, &fv);CHKERRQ(ierr); 259 ierr = ISDestroy(&fis);CHKERRQ(ierr); 260 ierr = DMDestroy(&fdm);CHKERRQ(ierr); 261 } 262 } 263 PetscFunctionReturn(0); 264 } 265 266 PetscErrorCode VecView_Plex_Local(Vec v, PetscViewer viewer) 267 { 268 DM dm; 269 PetscBool isvtk, ishdf5, isdraw, isseq, isglvis; 270 PetscErrorCode ierr; 271 272 PetscFunctionBegin; 273 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 274 if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 275 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);CHKERRQ(ierr); 276 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 277 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW, &isdraw);CHKERRQ(ierr); 278 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);CHKERRQ(ierr); 279 ierr = PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);CHKERRQ(ierr); 280 if (isvtk || ishdf5 || isglvis) { 281 PetscInt numFields; 282 PetscBool fem = PETSC_FALSE; 283 284 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 285 if (numFields) { 286 PetscObject fe; 287 288 ierr = DMGetField(dm, 0, &fe);CHKERRQ(ierr); 289 if (fe->classid == PETSCFE_CLASSID) fem = PETSC_TRUE; 290 } 291 if (fem) {ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, v, 0.0, NULL, NULL, NULL);CHKERRQ(ierr);} 292 } 293 if (isvtk) { 294 PetscSection section; 295 PetscViewerVTKFieldType ft; 296 PetscInt pStart, pEnd; 297 298 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 299 ierr = DMPlexGetFieldType_Internal(dm, section, PETSC_DETERMINE, &pStart, &pEnd, &ft);CHKERRQ(ierr); 300 ierr = PetscObjectReference((PetscObject) v);CHKERRQ(ierr); /* viewer drops reference */ 301 ierr = PetscViewerVTKAddField(viewer, (PetscObject) dm, DMPlexVTKWriteAll, ft, (PetscObject) v);CHKERRQ(ierr); 302 } else if (ishdf5) { 303 #if defined(PETSC_HAVE_HDF5) 304 ierr = VecView_Plex_Local_HDF5_Internal(v, viewer);CHKERRQ(ierr); 305 #else 306 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 307 #endif 308 } else if (isglvis) { 309 ierr = VecView_GLVis(v, viewer);CHKERRQ(ierr); 310 } else if (isdraw) { 311 ierr = VecView_Plex_Local_Draw(v, viewer);CHKERRQ(ierr); 312 } else { 313 if (isseq) {ierr = VecView_Seq(v, viewer);CHKERRQ(ierr);} 314 else {ierr = VecView_MPI(v, viewer);CHKERRQ(ierr);} 315 } 316 PetscFunctionReturn(0); 317 } 318 319 PetscErrorCode VecView_Plex(Vec v, PetscViewer viewer) 320 { 321 DM dm; 322 PetscReal time = 0.0; 323 PetscBool isvtk, ishdf5, isdraw, isseq, isglvis; 324 PetscErrorCode ierr; 325 326 PetscFunctionBegin; 327 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 328 if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 329 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);CHKERRQ(ierr); 330 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 331 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW, &isdraw);CHKERRQ(ierr); 332 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW, &isdraw);CHKERRQ(ierr); 333 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);CHKERRQ(ierr); 334 ierr = PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);CHKERRQ(ierr); 335 if (isvtk || isglvis) { 336 PetscInt num; 337 Vec locv; 338 const char *name; 339 340 ierr = DMGetLocalVector(dm, &locv);CHKERRQ(ierr); 341 ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr); 342 ierr = PetscObjectSetName((PetscObject) locv, name);CHKERRQ(ierr); 343 ierr = DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv);CHKERRQ(ierr); 344 ierr = DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv);CHKERRQ(ierr); 345 ierr = DMGetOutputSequenceNumber(dm, &num, &time);CHKERRQ(ierr); 346 ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL);CHKERRQ(ierr); 347 ierr = PetscViewerGLVisSetSnapId(viewer, num);CHKERRQ(ierr); 348 ierr = VecView_Plex_Local(locv, viewer);CHKERRQ(ierr); 349 ierr = DMRestoreLocalVector(dm, &locv);CHKERRQ(ierr); 350 } else if (ishdf5) { 351 #if defined(PETSC_HAVE_HDF5) 352 ierr = VecView_Plex_HDF5_Internal(v, viewer);CHKERRQ(ierr); 353 #else 354 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 355 #endif 356 } else if (isdraw) { 357 Vec locv; 358 const char *name; 359 360 ierr = DMGetLocalVector(dm, &locv);CHKERRQ(ierr); 361 ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr); 362 ierr = PetscObjectSetName((PetscObject) locv, name);CHKERRQ(ierr); 363 ierr = DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv);CHKERRQ(ierr); 364 ierr = DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv);CHKERRQ(ierr); 365 ierr = DMGetOutputSequenceNumber(dm, NULL, &time);CHKERRQ(ierr); 366 ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL);CHKERRQ(ierr); 367 ierr = VecView_Plex_Local(locv, viewer);CHKERRQ(ierr); 368 ierr = DMRestoreLocalVector(dm, &locv);CHKERRQ(ierr); 369 } else { 370 if (isseq) {ierr = VecView_Seq(v, viewer);CHKERRQ(ierr);} 371 else {ierr = VecView_MPI(v, viewer);CHKERRQ(ierr);} 372 } 373 PetscFunctionReturn(0); 374 } 375 376 PetscErrorCode VecView_Plex_Native(Vec originalv, PetscViewer viewer) 377 { 378 DM dm; 379 MPI_Comm comm; 380 PetscViewerFormat format; 381 Vec v; 382 PetscBool isvtk, ishdf5; 383 PetscErrorCode ierr; 384 385 PetscFunctionBegin; 386 ierr = VecGetDM(originalv, &dm);CHKERRQ(ierr); 387 ierr = PetscObjectGetComm((PetscObject) originalv, &comm);CHKERRQ(ierr); 388 if (!dm) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 389 ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr); 390 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 391 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);CHKERRQ(ierr); 392 if (format == PETSC_VIEWER_NATIVE) { 393 const char *vecname; 394 PetscInt n, nroots; 395 396 if (dm->sfNatural) { 397 ierr = VecGetLocalSize(originalv, &n);CHKERRQ(ierr); 398 ierr = PetscSFGetGraph(dm->sfNatural, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 399 if (n == nroots) { 400 ierr = DMGetGlobalVector(dm, &v);CHKERRQ(ierr); 401 ierr = DMPlexGlobalToNaturalBegin(dm, originalv, v);CHKERRQ(ierr); 402 ierr = DMPlexGlobalToNaturalEnd(dm, originalv, v);CHKERRQ(ierr); 403 ierr = PetscObjectGetName((PetscObject) originalv, &vecname);CHKERRQ(ierr); 404 ierr = PetscObjectSetName((PetscObject) v, vecname);CHKERRQ(ierr); 405 } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "DM global to natural SF only handles global vectors"); 406 } else SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "DM global to natural SF was not created"); 407 } else { 408 /* we are viewing a natural DMPlex vec. */ 409 v = originalv; 410 } 411 if (ishdf5) { 412 #if defined(PETSC_HAVE_HDF5) 413 ierr = VecView_Plex_HDF5_Native_Internal(v, viewer);CHKERRQ(ierr); 414 #else 415 SETERRQ(comm, PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 416 #endif 417 } else if (isvtk) { 418 SETERRQ(comm, PETSC_ERR_SUP, "VTK format does not support viewing in natural order. Please switch to HDF5."); 419 } else { 420 PetscBool isseq; 421 422 ierr = PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);CHKERRQ(ierr); 423 if (isseq) {ierr = VecView_Seq(v, viewer);CHKERRQ(ierr);} 424 else {ierr = VecView_MPI(v, viewer);CHKERRQ(ierr);} 425 } 426 if (format == PETSC_VIEWER_NATIVE) {ierr = DMRestoreGlobalVector(dm, &v);CHKERRQ(ierr);} 427 PetscFunctionReturn(0); 428 } 429 430 PetscErrorCode VecLoad_Plex_Local(Vec v, PetscViewer viewer) 431 { 432 DM dm; 433 PetscBool ishdf5; 434 PetscErrorCode ierr; 435 436 PetscFunctionBegin; 437 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 438 if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 439 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 440 if (ishdf5) { 441 DM dmBC; 442 Vec gv; 443 const char *name; 444 445 ierr = DMGetOutputDM(dm, &dmBC);CHKERRQ(ierr); 446 ierr = DMGetGlobalVector(dmBC, &gv);CHKERRQ(ierr); 447 ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr); 448 ierr = PetscObjectSetName((PetscObject) gv, name);CHKERRQ(ierr); 449 ierr = VecLoad_Default(gv, viewer);CHKERRQ(ierr); 450 ierr = DMGlobalToLocalBegin(dmBC, gv, INSERT_VALUES, v);CHKERRQ(ierr); 451 ierr = DMGlobalToLocalEnd(dmBC, gv, INSERT_VALUES, v);CHKERRQ(ierr); 452 ierr = DMRestoreGlobalVector(dmBC, &gv);CHKERRQ(ierr); 453 } else { 454 ierr = VecLoad_Default(v, viewer);CHKERRQ(ierr); 455 } 456 PetscFunctionReturn(0); 457 } 458 459 PetscErrorCode VecLoad_Plex(Vec v, PetscViewer viewer) 460 { 461 DM dm; 462 PetscBool ishdf5; 463 PetscErrorCode ierr; 464 465 PetscFunctionBegin; 466 ierr = VecGetDM(v, &dm);CHKERRQ(ierr); 467 if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 468 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 469 if (ishdf5) { 470 #if defined(PETSC_HAVE_HDF5) 471 ierr = VecLoad_Plex_HDF5_Internal(v, viewer);CHKERRQ(ierr); 472 #else 473 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 474 #endif 475 } else { 476 ierr = VecLoad_Default(v, viewer);CHKERRQ(ierr); 477 } 478 PetscFunctionReturn(0); 479 } 480 481 PetscErrorCode VecLoad_Plex_Native(Vec originalv, PetscViewer viewer) 482 { 483 DM dm; 484 PetscViewerFormat format; 485 PetscBool ishdf5; 486 PetscErrorCode ierr; 487 488 PetscFunctionBegin; 489 ierr = VecGetDM(originalv, &dm);CHKERRQ(ierr); 490 if (!dm) SETERRQ(PetscObjectComm((PetscObject) originalv), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM"); 491 ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr); 492 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 493 if (format == PETSC_VIEWER_NATIVE) { 494 if (dm->sfNatural) { 495 if (ishdf5) { 496 #if defined(PETSC_HAVE_HDF5) 497 Vec v; 498 const char *vecname; 499 500 ierr = DMGetGlobalVector(dm, &v);CHKERRQ(ierr); 501 ierr = PetscObjectGetName((PetscObject) originalv, &vecname);CHKERRQ(ierr); 502 ierr = PetscObjectSetName((PetscObject) v, vecname);CHKERRQ(ierr); 503 ierr = VecLoad_Plex_HDF5_Native_Internal(v, viewer);CHKERRQ(ierr); 504 ierr = DMPlexNaturalToGlobalBegin(dm, v, originalv);CHKERRQ(ierr); 505 ierr = DMPlexNaturalToGlobalEnd(dm, v, originalv);CHKERRQ(ierr); 506 ierr = DMRestoreGlobalVector(dm, &v);CHKERRQ(ierr); 507 #else 508 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 509 #endif 510 } else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Reading in natural order is not supported for anything but HDF5."); 511 } 512 } 513 PetscFunctionReturn(0); 514 } 515 516 PETSC_UNUSED static PetscErrorCode DMPlexView_Ascii_Geometry(DM dm, PetscViewer viewer) 517 { 518 PetscSection coordSection; 519 Vec coordinates; 520 DMLabel depthLabel; 521 const char *name[4]; 522 const PetscScalar *a; 523 PetscInt dim, pStart, pEnd, cStart, cEnd, c; 524 PetscErrorCode ierr; 525 526 PetscFunctionBegin; 527 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 528 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 529 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 530 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 531 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 532 ierr = PetscSectionGetChart(coordSection, &pStart, &pEnd);CHKERRQ(ierr); 533 ierr = VecGetArrayRead(coordinates, &a);CHKERRQ(ierr); 534 name[0] = "vertex"; 535 name[1] = "edge"; 536 name[dim-1] = "face"; 537 name[dim] = "cell"; 538 for (c = cStart; c < cEnd; ++c) { 539 PetscInt *closure = NULL; 540 PetscInt closureSize, cl; 541 542 ierr = PetscViewerASCIIPrintf(viewer, "Geometry for cell %D:\n", c);CHKERRQ(ierr); 543 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 544 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 545 for (cl = 0; cl < closureSize*2; cl += 2) { 546 PetscInt point = closure[cl], depth, dof, off, d, p; 547 548 if ((point < pStart) || (point >= pEnd)) continue; 549 ierr = PetscSectionGetDof(coordSection, point, &dof);CHKERRQ(ierr); 550 if (!dof) continue; 551 ierr = DMLabelGetValue(depthLabel, point, &depth);CHKERRQ(ierr); 552 ierr = PetscSectionGetOffset(coordSection, point, &off);CHKERRQ(ierr); 553 ierr = PetscViewerASCIIPrintf(viewer, "%s %D coords:", name[depth], point);CHKERRQ(ierr); 554 for (p = 0; p < dof/dim; ++p) { 555 ierr = PetscViewerASCIIPrintf(viewer, " (");CHKERRQ(ierr); 556 for (d = 0; d < dim; ++d) { 557 if (d > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 558 ierr = PetscViewerASCIIPrintf(viewer, "%g", PetscRealPart(a[off+p*dim+d]));CHKERRQ(ierr); 559 } 560 ierr = PetscViewerASCIIPrintf(viewer, ")");CHKERRQ(ierr); 561 } 562 ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); 563 } 564 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 565 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 566 } 567 ierr = VecRestoreArrayRead(coordinates, &a);CHKERRQ(ierr); 568 PetscFunctionReturn(0); 569 } 570 571 static PetscErrorCode DMPlexView_Ascii(DM dm, PetscViewer viewer) 572 { 573 DM_Plex *mesh = (DM_Plex*) dm->data; 574 DM cdm; 575 DMLabel markers; 576 PetscSection coordSection; 577 Vec coordinates; 578 PetscViewerFormat format; 579 PetscErrorCode ierr; 580 581 PetscFunctionBegin; 582 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 583 ierr = DMGetDefaultSection(cdm, &coordSection);CHKERRQ(ierr); 584 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 585 ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr); 586 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 587 const char *name; 588 PetscInt maxConeSize, maxSupportSize; 589 PetscInt pStart, pEnd, p; 590 PetscMPIInt rank, size; 591 592 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 593 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);CHKERRQ(ierr); 594 ierr = PetscObjectGetName((PetscObject) dm, &name);CHKERRQ(ierr); 595 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 596 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 597 ierr = PetscViewerASCIIPrintf(viewer, "Mesh '%s':\n", name);CHKERRQ(ierr); 598 ierr = PetscViewerASCIIPrintf(viewer, "orientation is missing\n", name);CHKERRQ(ierr); 599 ierr = PetscViewerASCIIPrintf(viewer, "cap --> base:\n", name);CHKERRQ(ierr); 600 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 601 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Max sizes cone: %D support: %D\n", rank,maxConeSize, maxSupportSize);CHKERRQ(ierr); 602 for (p = pStart; p < pEnd; ++p) { 603 PetscInt dof, off, s; 604 605 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 606 ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); 607 for (s = off; s < off+dof; ++s) { 608 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %D ----> %D\n", rank, p, mesh->supports[s]);CHKERRQ(ierr); 609 } 610 } 611 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 612 ierr = PetscViewerASCIIPrintf(viewer, "base <-- cap:\n", name);CHKERRQ(ierr); 613 for (p = pStart; p < pEnd; ++p) { 614 PetscInt dof, off, c; 615 616 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 617 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 618 for (c = off; c < off+dof; ++c) { 619 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "[%d]: %D <---- %D (%D)\n", rank, p, mesh->cones[c], mesh->coneOrientations[c]);CHKERRQ(ierr); 620 } 621 } 622 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 623 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 624 ierr = PetscSectionGetChart(coordSection, &pStart, NULL);CHKERRQ(ierr); 625 if (pStart >= 0) {ierr = PetscSectionVecView(coordSection, coordinates, viewer);CHKERRQ(ierr);} 626 ierr = DMGetLabel(dm, "marker", &markers);CHKERRQ(ierr); 627 ierr = DMLabelView(markers,viewer);CHKERRQ(ierr); 628 if (size > 1) { 629 PetscSF sf; 630 631 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 632 ierr = PetscSFView(sf, viewer);CHKERRQ(ierr); 633 } 634 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 635 } else if (format == PETSC_VIEWER_ASCII_LATEX) { 636 const char *name, *color; 637 const char *defcolors[3] = {"gray", "orange", "green"}; 638 const char *deflcolors[4] = {"blue", "cyan", "red", "magenta"}; 639 PetscReal scale = 2.0; 640 PetscBool useNumbers = PETSC_TRUE, useLabels, useColors; 641 double tcoords[3]; 642 PetscScalar *coords; 643 PetscInt numLabels, l, numColors, numLColors, dim, depth, cStart, cEnd, c, vStart, vEnd, v, eStart = 0, eEnd = 0, e, p; 644 PetscMPIInt rank, size; 645 char **names, **colors, **lcolors; 646 647 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 648 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 649 ierr = DMGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 650 numLabels = PetscMax(numLabels, 10); 651 numColors = 10; 652 numLColors = 10; 653 ierr = PetscCalloc3(numLabels, &names, numColors, &colors, numLColors, &lcolors);CHKERRQ(ierr); 654 ierr = PetscOptionsGetReal(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_scale", &scale, NULL);CHKERRQ(ierr); 655 ierr = PetscOptionsGetBool(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_numbers", &useNumbers, NULL);CHKERRQ(ierr); 656 ierr = PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_labels", names, &numLabels, &useLabels);CHKERRQ(ierr); 657 if (!useLabels) numLabels = 0; 658 ierr = PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_colors", colors, &numColors, &useColors);CHKERRQ(ierr); 659 if (!useColors) { 660 numColors = 3; 661 for (c = 0; c < numColors; ++c) {ierr = PetscStrallocpy(defcolors[c], &colors[c]);CHKERRQ(ierr);} 662 } 663 ierr = PetscOptionsGetStringArray(((PetscObject) viewer)->options,((PetscObject) viewer)->prefix, "-dm_plex_view_lcolors", lcolors, &numLColors, &useColors);CHKERRQ(ierr); 664 if (!useColors) { 665 numLColors = 4; 666 for (c = 0; c < numLColors; ++c) {ierr = PetscStrallocpy(deflcolors[c], &lcolors[c]);CHKERRQ(ierr);} 667 } 668 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 669 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);CHKERRQ(ierr); 670 ierr = PetscObjectGetName((PetscObject) dm, &name);CHKERRQ(ierr); 671 ierr = PetscViewerASCIIPrintf(viewer, "\ 672 \\documentclass[tikz]{standalone}\n\n\ 673 \\usepackage{pgflibraryshapes}\n\ 674 \\usetikzlibrary{backgrounds}\n\ 675 \\usetikzlibrary{arrows}\n\ 676 \\begin{document}\n");CHKERRQ(ierr); 677 if (size > 1) { 678 ierr = PetscViewerASCIIPrintf(viewer, "%s for process ", name);CHKERRQ(ierr); 679 for (p = 0; p < size; ++p) { 680 if (p > 0 && p == size-1) { 681 ierr = PetscViewerASCIIPrintf(viewer, ", and ", colors[p%numColors], p);CHKERRQ(ierr); 682 } else if (p > 0) { 683 ierr = PetscViewerASCIIPrintf(viewer, ", ", colors[p%numColors], p);CHKERRQ(ierr); 684 } 685 ierr = PetscViewerASCIIPrintf(viewer, "{\\textcolor{%s}%D}", colors[p%numColors], p);CHKERRQ(ierr); 686 } 687 ierr = PetscViewerASCIIPrintf(viewer, ".\n\n\n");CHKERRQ(ierr); 688 } 689 ierr = PetscViewerASCIIPrintf(viewer, "\\begin{tikzpicture}[scale = %g,font=\\fontsize{8}{8}\\selectfont]\n", 1.0);CHKERRQ(ierr); 690 /* Plot vertices */ 691 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 692 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 693 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 694 for (v = vStart; v < vEnd; ++v) { 695 PetscInt off, dof, d; 696 PetscBool isLabeled = PETSC_FALSE; 697 698 ierr = PetscSectionGetDof(coordSection, v, &dof);CHKERRQ(ierr); 699 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 700 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "\\path (");CHKERRQ(ierr); 701 if (PetscUnlikely(dof > 3)) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"coordSection vertex %D has dof %D > 3",v,dof); 702 for (d = 0; d < dof; ++d) { 703 tcoords[d] = (double) (scale*PetscRealPart(coords[off+d])); 704 tcoords[d] = PetscAbsReal(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 705 } 706 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 707 if (dim == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;} 708 for (d = 0; d < dof; ++d) { 709 if (d > 0) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, ",");CHKERRQ(ierr);} 710 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "%g", tcoords[d]);CHKERRQ(ierr); 711 } 712 color = colors[rank%numColors]; 713 for (l = 0; l < numLabels; ++l) { 714 PetscInt val; 715 ierr = DMGetLabelValue(dm, names[l], v, &val);CHKERRQ(ierr); 716 if (val >= 0) {color = lcolors[l%numLColors]; isLabeled = PETSC_TRUE; break;} 717 } 718 if (useNumbers) { 719 ierr = PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D};\n", v, rank, color, v);CHKERRQ(ierr); 720 } else { 721 ierr = PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [fill,inner sep=%dpt,shape=circle,color=%s] {};\n", v, rank, !isLabeled ? 1 : 2, color);CHKERRQ(ierr); 722 } 723 } 724 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 725 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 726 /* Plot edges */ 727 if (depth > 1) {ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr);} 728 if (dim < 3 && useNumbers) { 729 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 730 ierr = PetscViewerASCIIPrintf(viewer, "\\path\n");CHKERRQ(ierr); 731 for (e = eStart; e < eEnd; ++e) { 732 const PetscInt *cone; 733 PetscInt coneSize, offA, offB, dof, d; 734 735 ierr = DMPlexGetConeSize(dm, e, &coneSize);CHKERRQ(ierr); 736 if (coneSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Edge %D cone should have two vertices, not %D", e, coneSize); 737 ierr = DMPlexGetCone(dm, e, &cone);CHKERRQ(ierr); 738 ierr = PetscSectionGetDof(coordSection, cone[0], &dof);CHKERRQ(ierr); 739 ierr = PetscSectionGetOffset(coordSection, cone[0], &offA);CHKERRQ(ierr); 740 ierr = PetscSectionGetOffset(coordSection, cone[1], &offB);CHKERRQ(ierr); 741 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "(");CHKERRQ(ierr); 742 for (d = 0; d < dof; ++d) { 743 tcoords[d] = (double) (scale*PetscRealPart(coords[offA+d]+coords[offB+d])); 744 tcoords[d] = PetscAbsReal(tcoords[d]) < 1e-10 ? 0.0 : tcoords[d]; 745 } 746 /* Rotate coordinates since PGF makes z point out of the page instead of up */ 747 if (dim == 3) {PetscReal tmp = tcoords[1]; tcoords[1] = tcoords[2]; tcoords[2] = -tmp;} 748 for (d = 0; d < dof; ++d) { 749 if (d > 0) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, ",");CHKERRQ(ierr);} 750 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)tcoords[d]);CHKERRQ(ierr); 751 } 752 color = colors[rank%numColors]; 753 for (l = 0; l < numLabels; ++l) { 754 PetscInt val; 755 ierr = DMGetLabelValue(dm, names[l], v, &val);CHKERRQ(ierr); 756 if (val >= 0) {color = lcolors[l%numLColors]; break;} 757 } 758 ierr = PetscViewerASCIISynchronizedPrintf(viewer, ") node(%D_%d) [draw,shape=circle,color=%s] {%D} --\n", e, rank, color, e);CHKERRQ(ierr); 759 } 760 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 761 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 762 ierr = PetscViewerASCIIPrintf(viewer, "(0,0);\n");CHKERRQ(ierr); 763 } 764 /* Plot cells */ 765 if (dim == 3 || !useNumbers) { 766 for (e = eStart; e < eEnd; ++e) { 767 const PetscInt *cone; 768 769 color = colors[rank%numColors]; 770 for (l = 0; l < numLabels; ++l) { 771 PetscInt val; 772 ierr = DMGetLabelValue(dm, names[l], e, &val);CHKERRQ(ierr); 773 if (val >= 0) {color = lcolors[l%numLColors]; break;} 774 } 775 ierr = DMPlexGetCone(dm, e, &cone);CHKERRQ(ierr); 776 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] (%D_%d) -- (%D_%d);\n", color, cone[0], rank, cone[1], rank);CHKERRQ(ierr); 777 } 778 } else { 779 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 780 for (c = cStart; c < cEnd; ++c) { 781 PetscInt *closure = NULL; 782 PetscInt closureSize, firstPoint = -1; 783 784 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 785 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "\\draw[color=%s] ", colors[rank%numColors]);CHKERRQ(ierr); 786 for (p = 0; p < closureSize*2; p += 2) { 787 const PetscInt point = closure[p]; 788 789 if ((point < vStart) || (point >= vEnd)) continue; 790 if (firstPoint >= 0) {ierr = PetscViewerASCIISynchronizedPrintf(viewer, " -- ");CHKERRQ(ierr);} 791 ierr = PetscViewerASCIISynchronizedPrintf(viewer, "(%D_%d)", point, rank);CHKERRQ(ierr); 792 if (firstPoint < 0) firstPoint = point; 793 } 794 /* Why doesn't this work? ierr = PetscViewerASCIISynchronizedPrintf(viewer, " -- cycle;\n");CHKERRQ(ierr); */ 795 ierr = PetscViewerASCIISynchronizedPrintf(viewer, " -- (%D_%d);\n", firstPoint, rank);CHKERRQ(ierr); 796 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 797 } 798 } 799 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 800 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 801 ierr = PetscViewerASCIIPrintf(viewer, "\\end{tikzpicture}\n");CHKERRQ(ierr); 802 ierr = PetscViewerASCIIPrintf(viewer, "\\end{document}\n", name);CHKERRQ(ierr); 803 for (l = 0; l < numLabels; ++l) {ierr = PetscFree(names[l]);CHKERRQ(ierr);} 804 for (c = 0; c < numColors; ++c) {ierr = PetscFree(colors[c]);CHKERRQ(ierr);} 805 for (c = 0; c < numLColors; ++c) {ierr = PetscFree(lcolors[c]);CHKERRQ(ierr);} 806 ierr = PetscFree3(names, colors, lcolors);CHKERRQ(ierr); 807 } else { 808 MPI_Comm comm; 809 PetscInt *sizes, *hybsizes; 810 PetscInt locDepth, depth, dim, d, pMax[4]; 811 PetscInt pStart, pEnd, p; 812 PetscInt numLabels, l; 813 const char *name; 814 PetscMPIInt size; 815 816 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 817 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 818 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 819 ierr = PetscObjectGetName((PetscObject) dm, &name);CHKERRQ(ierr); 820 if (name) {ierr = PetscViewerASCIIPrintf(viewer, "%s in %D dimensions:\n", name, dim);CHKERRQ(ierr);} 821 else {ierr = PetscViewerASCIIPrintf(viewer, "Mesh in %D dimensions:\n", dim);CHKERRQ(ierr);} 822 ierr = DMPlexGetDepth(dm, &locDepth);CHKERRQ(ierr); 823 ierr = MPIU_Allreduce(&locDepth, &depth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); 824 ierr = DMPlexGetHybridBounds(dm, &pMax[depth], depth > 0 ? &pMax[depth-1] : NULL, &pMax[1], &pMax[0]);CHKERRQ(ierr); 825 ierr = PetscMalloc2(size,&sizes,size,&hybsizes);CHKERRQ(ierr); 826 if (depth == 1) { 827 ierr = DMPlexGetDepthStratum(dm, 0, &pStart, &pEnd);CHKERRQ(ierr); 828 pEnd = pEnd - pStart; 829 ierr = MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 830 ierr = PetscViewerASCIIPrintf(viewer, " %d-cells:", 0);CHKERRQ(ierr); 831 for (p = 0; p < size; ++p) {ierr = PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);CHKERRQ(ierr);} 832 ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); 833 ierr = DMPlexGetHeightStratum(dm, 0, &pStart, &pEnd);CHKERRQ(ierr); 834 pEnd = pEnd - pStart; 835 ierr = MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 836 ierr = PetscViewerASCIIPrintf(viewer, " %D-cells:", dim);CHKERRQ(ierr); 837 for (p = 0; p < size; ++p) {ierr = PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);CHKERRQ(ierr);} 838 ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); 839 } else { 840 PetscMPIInt rank; 841 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 842 for (d = 0; d <= dim; d++) { 843 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 844 pEnd -= pStart; 845 pMax[d] -= pStart; 846 ierr = MPI_Gather(&pEnd, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 847 ierr = MPI_Gather(&pMax[d], 1, MPIU_INT, hybsizes, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 848 ierr = PetscViewerASCIIPrintf(viewer, " %D-cells:", d);CHKERRQ(ierr); 849 for (p = 0; p < size; ++p) { 850 if (!rank) { 851 if (hybsizes[p] >= 0) {ierr = PetscViewerASCIIPrintf(viewer, " %D (%D)", sizes[p], sizes[p] - hybsizes[p]);CHKERRQ(ierr);} 852 else {ierr = PetscViewerASCIIPrintf(viewer, " %D", sizes[p]);CHKERRQ(ierr);} 853 } 854 } 855 ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); 856 } 857 } 858 ierr = PetscFree2(sizes,hybsizes);CHKERRQ(ierr); 859 ierr = DMGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 860 if (numLabels) {ierr = PetscViewerASCIIPrintf(viewer, "Labels:\n");CHKERRQ(ierr);} 861 for (l = 0; l < numLabels; ++l) { 862 DMLabel label; 863 const char *name; 864 IS valueIS; 865 const PetscInt *values; 866 PetscInt numValues, v; 867 868 ierr = DMGetLabelName(dm, l, &name);CHKERRQ(ierr); 869 ierr = DMGetLabel(dm, name, &label);CHKERRQ(ierr); 870 ierr = DMLabelGetNumValues(label, &numValues);CHKERRQ(ierr); 871 ierr = PetscViewerASCIIPrintf(viewer, " %s: %D strata with value/size (", name, numValues);CHKERRQ(ierr); 872 ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr); 873 ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr); 874 ierr = PetscViewerASCIIUseTabs(viewer, PETSC_FALSE);CHKERRQ(ierr); 875 for (v = 0; v < numValues; ++v) { 876 PetscInt size; 877 878 ierr = DMLabelGetStratumSize(label, values[v], &size);CHKERRQ(ierr); 879 if (v > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 880 ierr = PetscViewerASCIIPrintf(viewer, "%D (%D)", values[v], size);CHKERRQ(ierr); 881 } 882 ierr = PetscViewerASCIIPrintf(viewer, ")\n");CHKERRQ(ierr); 883 ierr = PetscViewerASCIIUseTabs(viewer, PETSC_TRUE);CHKERRQ(ierr); 884 ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr); 885 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 886 } 887 ierr = DMGetCoarseDM(dm, &cdm);CHKERRQ(ierr); 888 if (cdm) { 889 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 890 ierr = DMPlexView_Ascii(cdm, viewer);CHKERRQ(ierr); 891 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 892 } 893 } 894 PetscFunctionReturn(0); 895 } 896 897 static PetscErrorCode DMPlexView_Draw(DM dm, PetscViewer viewer) 898 { 899 PetscDraw draw; 900 DM cdm; 901 PetscSection coordSection; 902 Vec coordinates; 903 const PetscScalar *coords; 904 PetscReal xyl[2],xyr[2],bound[4] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL}; 905 PetscBool isnull; 906 PetscInt dim, vStart, vEnd, cStart, cEnd, c, N; 907 PetscErrorCode ierr; 908 909 PetscFunctionBegin; 910 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 911 if (dim != 2) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Cannot draw meshes of dimension %D", dim); 912 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 913 ierr = DMGetDefaultSection(cdm, &coordSection);CHKERRQ(ierr); 914 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 915 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 916 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 917 918 ierr = PetscViewerDrawGetDraw(viewer, 0, &draw);CHKERRQ(ierr); 919 ierr = PetscDrawIsNull(draw, &isnull);CHKERRQ(ierr); 920 if (isnull) PetscFunctionReturn(0); 921 ierr = PetscDrawSetTitle(draw, "Mesh");CHKERRQ(ierr); 922 923 ierr = VecGetLocalSize(coordinates, &N);CHKERRQ(ierr); 924 ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); 925 for (c = 0; c < N; c += dim) { 926 bound[0] = PetscMin(bound[0], PetscRealPart(coords[c])); bound[2] = PetscMax(bound[2], PetscRealPart(coords[c])); 927 bound[1] = PetscMin(bound[1], PetscRealPart(coords[c+1])); bound[3] = PetscMax(bound[3], PetscRealPart(coords[c+1])); 928 } 929 ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); 930 ierr = MPIU_Allreduce(&bound[0],xyl,2,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 931 ierr = MPIU_Allreduce(&bound[2],xyr,2,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 932 ierr = PetscDrawSetCoordinates(draw, xyl[0], xyl[1], xyr[0], xyr[1]);CHKERRQ(ierr); 933 ierr = PetscDrawClear(draw);CHKERRQ(ierr); 934 935 for (c = cStart; c < cEnd; ++c) { 936 PetscScalar *coords = NULL; 937 PetscInt numCoords,coneSize; 938 939 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 940 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, c, &numCoords, &coords);CHKERRQ(ierr); 941 switch (coneSize) { 942 case 3: 943 ierr = PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 944 ierr = PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 945 ierr = PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 946 break; 947 case 4: 948 ierr = PetscDrawLine(draw, PetscRealPart(coords[0]), PetscRealPart(coords[1]), PetscRealPart(coords[2]), PetscRealPart(coords[3]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 949 ierr = PetscDrawLine(draw, PetscRealPart(coords[2]), PetscRealPart(coords[3]), PetscRealPart(coords[4]), PetscRealPart(coords[5]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 950 ierr = PetscDrawLine(draw, PetscRealPart(coords[4]), PetscRealPart(coords[5]), PetscRealPart(coords[6]), PetscRealPart(coords[7]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 951 ierr = PetscDrawLine(draw, PetscRealPart(coords[6]), PetscRealPart(coords[7]), PetscRealPart(coords[0]), PetscRealPart(coords[1]), PETSC_DRAW_BLACK);CHKERRQ(ierr); 952 break; 953 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot draw cells with %D facets", coneSize); 954 } 955 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, &numCoords, &coords);CHKERRQ(ierr); 956 } 957 ierr = PetscDrawFlush(draw);CHKERRQ(ierr); 958 ierr = PetscDrawPause(draw);CHKERRQ(ierr); 959 ierr = PetscDrawSave(draw);CHKERRQ(ierr); 960 PetscFunctionReturn(0); 961 } 962 963 PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer) 964 { 965 PetscBool iascii, ishdf5, isvtk, isdraw, flg, isglvis; 966 PetscErrorCode ierr; 967 968 PetscFunctionBegin; 969 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 970 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 971 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);CHKERRQ(ierr); 972 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERVTK, &isvtk);CHKERRQ(ierr); 973 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 974 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERDRAW, &isdraw);CHKERRQ(ierr); 975 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERGLVIS, &isglvis);CHKERRQ(ierr); 976 if (iascii) { 977 PetscViewerFormat format; 978 ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr); 979 if (format == PETSC_VIEWER_ASCII_GLVIS) { 980 ierr = DMPlexView_GLVis(dm, viewer);CHKERRQ(ierr); 981 } else { 982 ierr = DMPlexView_Ascii(dm, viewer);CHKERRQ(ierr); 983 } 984 } else if (ishdf5) { 985 #if defined(PETSC_HAVE_HDF5) 986 ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_VIZ);CHKERRQ(ierr); 987 ierr = DMPlexView_HDF5_Internal(dm, viewer);CHKERRQ(ierr); 988 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 989 #else 990 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 991 #endif 992 } else if (isvtk) { 993 ierr = DMPlexVTKWriteAll((PetscObject) dm,viewer);CHKERRQ(ierr); 994 } else if (isdraw) { 995 ierr = DMPlexView_Draw(dm, viewer);CHKERRQ(ierr); 996 } else if (isglvis) { 997 ierr = DMPlexView_GLVis(dm, viewer);CHKERRQ(ierr); 998 } 999 /* Optionally view the partition */ 1000 ierr = PetscOptionsHasName(((PetscObject) dm)->options, ((PetscObject) dm)->prefix, "-dm_partition_view", &flg);CHKERRQ(ierr); 1001 if (flg) { 1002 Vec ranks; 1003 ierr = DMPlexCreateRankField(dm, &ranks);CHKERRQ(ierr); 1004 ierr = VecView(ranks, viewer);CHKERRQ(ierr); 1005 ierr = VecDestroy(&ranks);CHKERRQ(ierr); 1006 } 1007 PetscFunctionReturn(0); 1008 } 1009 1010 PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer) 1011 { 1012 PetscBool isbinary, ishdf5; 1013 PetscErrorCode ierr; 1014 1015 PetscFunctionBegin; 1016 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1017 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 1018 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERBINARY, &isbinary);CHKERRQ(ierr); 1019 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5, &ishdf5);CHKERRQ(ierr); 1020 if (isbinary) {SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Do not yet support binary viewers");} 1021 else if (ishdf5) { 1022 #if defined(PETSC_HAVE_HDF5) 1023 ierr = DMPlexLoad_HDF5_Internal(dm, viewer);CHKERRQ(ierr); 1024 #else 1025 SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 1026 #endif 1027 } 1028 PetscFunctionReturn(0); 1029 } 1030 1031 PetscErrorCode DMDestroy_Plex(DM dm) 1032 { 1033 DM_Plex *mesh = (DM_Plex*) dm->data; 1034 PetscErrorCode ierr; 1035 1036 PetscFunctionBegin; 1037 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",NULL);CHKERRQ(ierr); 1038 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C", NULL);CHKERRQ(ierr); 1039 if (--mesh->refct > 0) PetscFunctionReturn(0); 1040 ierr = PetscSectionDestroy(&mesh->coneSection);CHKERRQ(ierr); 1041 ierr = PetscFree(mesh->cones);CHKERRQ(ierr); 1042 ierr = PetscFree(mesh->coneOrientations);CHKERRQ(ierr); 1043 ierr = PetscSectionDestroy(&mesh->supportSection);CHKERRQ(ierr); 1044 ierr = PetscSectionDestroy(&mesh->subdomainSection);CHKERRQ(ierr); 1045 ierr = PetscFree(mesh->supports);CHKERRQ(ierr); 1046 ierr = PetscFree(mesh->facesTmp);CHKERRQ(ierr); 1047 ierr = PetscFree(mesh->tetgenOpts);CHKERRQ(ierr); 1048 ierr = PetscFree(mesh->triangleOpts);CHKERRQ(ierr); 1049 ierr = PetscPartitionerDestroy(&mesh->partitioner);CHKERRQ(ierr); 1050 ierr = DMLabelDestroy(&mesh->subpointMap);CHKERRQ(ierr); 1051 ierr = ISDestroy(&mesh->globalVertexNumbers);CHKERRQ(ierr); 1052 ierr = ISDestroy(&mesh->globalCellNumbers);CHKERRQ(ierr); 1053 ierr = PetscSectionDestroy(&mesh->anchorSection);CHKERRQ(ierr); 1054 ierr = ISDestroy(&mesh->anchorIS);CHKERRQ(ierr); 1055 ierr = PetscSectionDestroy(&mesh->parentSection);CHKERRQ(ierr); 1056 ierr = PetscFree(mesh->parents);CHKERRQ(ierr); 1057 ierr = PetscFree(mesh->childIDs);CHKERRQ(ierr); 1058 ierr = PetscSectionDestroy(&mesh->childSection);CHKERRQ(ierr); 1059 ierr = PetscFree(mesh->children);CHKERRQ(ierr); 1060 ierr = DMDestroy(&mesh->referenceTree);CHKERRQ(ierr); 1061 ierr = PetscGridHashDestroy(&mesh->lbox);CHKERRQ(ierr); 1062 /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */ 1063 ierr = PetscFree(mesh);CHKERRQ(ierr); 1064 PetscFunctionReturn(0); 1065 } 1066 1067 PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J) 1068 { 1069 PetscSection sectionGlobal; 1070 PetscInt bs = -1, mbs; 1071 PetscInt localSize; 1072 PetscBool isShell, isBlock, isSeqBlock, isMPIBlock, isSymBlock, isSymSeqBlock, isSymMPIBlock, isMatIS; 1073 PetscErrorCode ierr; 1074 MatType mtype; 1075 ISLocalToGlobalMapping ltog; 1076 1077 PetscFunctionBegin; 1078 ierr = MatInitializePackage();CHKERRQ(ierr); 1079 mtype = dm->mattype; 1080 ierr = DMGetDefaultGlobalSection(dm, §ionGlobal);CHKERRQ(ierr); 1081 /* ierr = PetscSectionGetStorageSize(sectionGlobal, &localSize);CHKERRQ(ierr); */ 1082 ierr = PetscSectionGetConstrainedStorageSize(sectionGlobal, &localSize);CHKERRQ(ierr); 1083 ierr = MatCreate(PetscObjectComm((PetscObject)dm), J);CHKERRQ(ierr); 1084 ierr = MatSetSizes(*J, localSize, localSize, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 1085 ierr = MatSetType(*J, mtype);CHKERRQ(ierr); 1086 ierr = MatSetFromOptions(*J);CHKERRQ(ierr); 1087 ierr = MatGetBlockSize(*J, &mbs);CHKERRQ(ierr); 1088 if (mbs > 1) bs = mbs; 1089 ierr = PetscStrcmp(mtype, MATSHELL, &isShell);CHKERRQ(ierr); 1090 ierr = PetscStrcmp(mtype, MATBAIJ, &isBlock);CHKERRQ(ierr); 1091 ierr = PetscStrcmp(mtype, MATSEQBAIJ, &isSeqBlock);CHKERRQ(ierr); 1092 ierr = PetscStrcmp(mtype, MATMPIBAIJ, &isMPIBlock);CHKERRQ(ierr); 1093 ierr = PetscStrcmp(mtype, MATSBAIJ, &isSymBlock);CHKERRQ(ierr); 1094 ierr = PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock);CHKERRQ(ierr); 1095 ierr = PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock);CHKERRQ(ierr); 1096 ierr = PetscStrcmp(mtype, MATIS, &isMatIS);CHKERRQ(ierr); 1097 if (!isShell) { 1098 PetscSection subSection; 1099 PetscBool fillMatrix = (PetscBool)(!dm->prealloc_only && !isMatIS); 1100 PetscInt *dnz, *onz, *dnzu, *onzu, bsLocal, bsMax, bsMin, *ltogidx, lsize; 1101 PetscInt pStart, pEnd, p, dof, cdof; 1102 1103 /* Set localtoglobalmapping on the matrix for MatSetValuesLocal() to work (it also creates the local matrices in case of MATIS) */ 1104 if (isMatIS) { /* need a different l2g map than the one computed by DMGetLocalToGlobalMapping */ 1105 PetscSection section; 1106 PetscInt size; 1107 1108 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1109 ierr = PetscSectionGetStorageSize(section, &size);CHKERRQ(ierr); 1110 ierr = PetscMalloc1(size,<ogidx);CHKERRQ(ierr); 1111 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 1112 } else { 1113 ierr = DMGetLocalToGlobalMapping(dm,<og);CHKERRQ(ierr); 1114 } 1115 ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr); 1116 for (p = pStart, lsize = 0; p < pEnd; ++p) { 1117 PetscInt bdof; 1118 1119 ierr = PetscSectionGetDof(sectionGlobal, p, &dof);CHKERRQ(ierr); 1120 ierr = PetscSectionGetConstraintDof(sectionGlobal, p, &cdof);CHKERRQ(ierr); 1121 dof = dof < 0 ? -(dof+1) : dof; 1122 bdof = cdof && (dof-cdof) ? 1 : dof; 1123 if (dof) { 1124 if (bs < 0) {bs = bdof;} 1125 else if (bs != bdof) {bs = 1; if (!isMatIS) break;} 1126 } 1127 if (isMatIS) { 1128 PetscInt loff,c,off; 1129 ierr = PetscSectionGetOffset(subSection, p, &loff);CHKERRQ(ierr); 1130 ierr = PetscSectionGetOffset(sectionGlobal, p, &off);CHKERRQ(ierr); 1131 for (c = 0; c < dof-cdof; ++c, ++lsize) ltogidx[loff+c] = off > -1 ? off+c : -(off+1)+c; 1132 } 1133 } 1134 /* Must have same blocksize on all procs (some might have no points) */ 1135 bsLocal = bs; 1136 ierr = MPIU_Allreduce(&bsLocal, &bsMax, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 1137 bsLocal = bs < 0 ? bsMax : bs; 1138 ierr = MPIU_Allreduce(&bsLocal, &bsMin, 1, MPIU_INT, MPI_MIN, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 1139 if (bsMin != bsMax) {bs = 1;} 1140 else {bs = bsMax;} 1141 bs = bs < 0 ? 1 : bs; 1142 if (isMatIS) { 1143 PetscInt l; 1144 /* Must reduce indices by blocksize */ 1145 if (bs > 1) for (l = 0; l < lsize; ++l) ltogidx[l] /= bs; 1146 ierr = ISLocalToGlobalMappingCreate(PetscObjectComm((PetscObject)dm), bs, lsize, ltogidx, PETSC_OWN_POINTER, <og);CHKERRQ(ierr); 1147 } 1148 ierr = MatSetLocalToGlobalMapping(*J,ltog,ltog);CHKERRQ(ierr); 1149 if (isMatIS) { 1150 ierr = ISLocalToGlobalMappingDestroy(<og);CHKERRQ(ierr); 1151 } 1152 ierr = PetscCalloc4(localSize/bs, &dnz, localSize/bs, &onz, localSize/bs, &dnzu, localSize/bs, &onzu);CHKERRQ(ierr); 1153 ierr = DMPlexPreallocateOperator(dm, bs, dnz, onz, dnzu, onzu, *J, fillMatrix);CHKERRQ(ierr); 1154 ierr = PetscFree4(dnz, onz, dnzu, onzu);CHKERRQ(ierr); 1155 } 1156 ierr = MatSetDM(*J, dm);CHKERRQ(ierr); 1157 PetscFunctionReturn(0); 1158 } 1159 1160 /*@ 1161 DMPlexGetSubdomainSection - Returns the section associated with the subdomain 1162 1163 Not collective 1164 1165 Input Parameter: 1166 . mesh - The DMPlex 1167 1168 Output Parameters: 1169 . subsection - The subdomain section 1170 1171 Level: developer 1172 1173 .seealso: 1174 @*/ 1175 PetscErrorCode DMPlexGetSubdomainSection(DM dm, PetscSection *subsection) 1176 { 1177 DM_Plex *mesh = (DM_Plex*) dm->data; 1178 PetscErrorCode ierr; 1179 1180 PetscFunctionBegin; 1181 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1182 if (!mesh->subdomainSection) { 1183 PetscSection section; 1184 PetscSF sf; 1185 1186 ierr = PetscSFCreate(PETSC_COMM_SELF,&sf);CHKERRQ(ierr); 1187 ierr = DMGetDefaultSection(dm,§ion);CHKERRQ(ierr); 1188 ierr = PetscSectionCreateGlobalSection(section,sf,PETSC_FALSE,PETSC_TRUE,&mesh->subdomainSection);CHKERRQ(ierr); 1189 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1190 } 1191 *subsection = mesh->subdomainSection; 1192 PetscFunctionReturn(0); 1193 } 1194 1195 /*@ 1196 DMPlexGetChart - Return the interval for all mesh points [pStart, pEnd) 1197 1198 Not collective 1199 1200 Input Parameter: 1201 . mesh - The DMPlex 1202 1203 Output Parameters: 1204 + pStart - The first mesh point 1205 - pEnd - The upper bound for mesh points 1206 1207 Level: beginner 1208 1209 .seealso: DMPlexCreate(), DMPlexSetChart() 1210 @*/ 1211 PetscErrorCode DMPlexGetChart(DM dm, PetscInt *pStart, PetscInt *pEnd) 1212 { 1213 DM_Plex *mesh = (DM_Plex*) dm->data; 1214 PetscErrorCode ierr; 1215 1216 PetscFunctionBegin; 1217 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1218 ierr = PetscSectionGetChart(mesh->coneSection, pStart, pEnd);CHKERRQ(ierr); 1219 PetscFunctionReturn(0); 1220 } 1221 1222 /*@ 1223 DMPlexSetChart - Set the interval for all mesh points [pStart, pEnd) 1224 1225 Not collective 1226 1227 Input Parameters: 1228 + mesh - The DMPlex 1229 . pStart - The first mesh point 1230 - pEnd - The upper bound for mesh points 1231 1232 Output Parameters: 1233 1234 Level: beginner 1235 1236 .seealso: DMPlexCreate(), DMPlexGetChart() 1237 @*/ 1238 PetscErrorCode DMPlexSetChart(DM dm, PetscInt pStart, PetscInt pEnd) 1239 { 1240 DM_Plex *mesh = (DM_Plex*) dm->data; 1241 PetscErrorCode ierr; 1242 1243 PetscFunctionBegin; 1244 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1245 ierr = PetscSectionSetChart(mesh->coneSection, pStart, pEnd);CHKERRQ(ierr); 1246 ierr = PetscSectionSetChart(mesh->supportSection, pStart, pEnd);CHKERRQ(ierr); 1247 PetscFunctionReturn(0); 1248 } 1249 1250 /*@ 1251 DMPlexGetConeSize - Return the number of in-edges for this point in the DAG 1252 1253 Not collective 1254 1255 Input Parameters: 1256 + mesh - The DMPlex 1257 - p - The point, which must lie in the chart set with DMPlexSetChart() 1258 1259 Output Parameter: 1260 . size - The cone size for point p 1261 1262 Level: beginner 1263 1264 .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart() 1265 @*/ 1266 PetscErrorCode DMPlexGetConeSize(DM dm, PetscInt p, PetscInt *size) 1267 { 1268 DM_Plex *mesh = (DM_Plex*) dm->data; 1269 PetscErrorCode ierr; 1270 1271 PetscFunctionBegin; 1272 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1273 PetscValidPointer(size, 3); 1274 ierr = PetscSectionGetDof(mesh->coneSection, p, size);CHKERRQ(ierr); 1275 PetscFunctionReturn(0); 1276 } 1277 1278 /*@ 1279 DMPlexSetConeSize - Set the number of in-edges for this point in the DAG 1280 1281 Not collective 1282 1283 Input Parameters: 1284 + mesh - The DMPlex 1285 . p - The point, which must lie in the chart set with DMPlexSetChart() 1286 - size - The cone size for point p 1287 1288 Output Parameter: 1289 1290 Note: 1291 This should be called after DMPlexSetChart(). 1292 1293 Level: beginner 1294 1295 .seealso: DMPlexCreate(), DMPlexGetConeSize(), DMPlexSetChart() 1296 @*/ 1297 PetscErrorCode DMPlexSetConeSize(DM dm, PetscInt p, PetscInt size) 1298 { 1299 DM_Plex *mesh = (DM_Plex*) dm->data; 1300 PetscErrorCode ierr; 1301 1302 PetscFunctionBegin; 1303 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1304 ierr = PetscSectionSetDof(mesh->coneSection, p, size);CHKERRQ(ierr); 1305 1306 mesh->maxConeSize = PetscMax(mesh->maxConeSize, size); 1307 PetscFunctionReturn(0); 1308 } 1309 1310 /*@ 1311 DMPlexAddConeSize - Add the given number of in-edges to this point in the DAG 1312 1313 Not collective 1314 1315 Input Parameters: 1316 + mesh - The DMPlex 1317 . p - The point, which must lie in the chart set with DMPlexSetChart() 1318 - size - The additional cone size for point p 1319 1320 Output Parameter: 1321 1322 Note: 1323 This should be called after DMPlexSetChart(). 1324 1325 Level: beginner 1326 1327 .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexGetConeSize(), DMPlexSetChart() 1328 @*/ 1329 PetscErrorCode DMPlexAddConeSize(DM dm, PetscInt p, PetscInt size) 1330 { 1331 DM_Plex *mesh = (DM_Plex*) dm->data; 1332 PetscInt csize; 1333 PetscErrorCode ierr; 1334 1335 PetscFunctionBegin; 1336 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1337 ierr = PetscSectionAddDof(mesh->coneSection, p, size);CHKERRQ(ierr); 1338 ierr = PetscSectionGetDof(mesh->coneSection, p, &csize);CHKERRQ(ierr); 1339 1340 mesh->maxConeSize = PetscMax(mesh->maxConeSize, csize); 1341 PetscFunctionReturn(0); 1342 } 1343 1344 /*@C 1345 DMPlexGetCone - Return the points on the in-edges for this point in the DAG 1346 1347 Not collective 1348 1349 Input Parameters: 1350 + mesh - The DMPlex 1351 - p - The point, which must lie in the chart set with DMPlexSetChart() 1352 1353 Output Parameter: 1354 . cone - An array of points which are on the in-edges for point p 1355 1356 Level: beginner 1357 1358 Fortran Notes: 1359 Since it returns an array, this routine is only available in Fortran 90, and you must 1360 include petsc.h90 in your code. 1361 1362 You must also call DMPlexRestoreCone() after you finish using the returned array. 1363 1364 .seealso: DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart() 1365 @*/ 1366 PetscErrorCode DMPlexGetCone(DM dm, PetscInt p, const PetscInt *cone[]) 1367 { 1368 DM_Plex *mesh = (DM_Plex*) dm->data; 1369 PetscInt off; 1370 PetscErrorCode ierr; 1371 1372 PetscFunctionBegin; 1373 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1374 PetscValidPointer(cone, 3); 1375 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 1376 *cone = &mesh->cones[off]; 1377 PetscFunctionReturn(0); 1378 } 1379 1380 /*@ 1381 DMPlexSetCone - Set the points on the in-edges for this point in the DAG 1382 1383 Not collective 1384 1385 Input Parameters: 1386 + mesh - The DMPlex 1387 . p - The point, which must lie in the chart set with DMPlexSetChart() 1388 - cone - An array of points which are on the in-edges for point p 1389 1390 Output Parameter: 1391 1392 Note: 1393 This should be called after all calls to DMPlexSetConeSize() and DMSetUp(). 1394 1395 Level: beginner 1396 1397 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() 1398 @*/ 1399 PetscErrorCode DMPlexSetCone(DM dm, PetscInt p, const PetscInt cone[]) 1400 { 1401 DM_Plex *mesh = (DM_Plex*) dm->data; 1402 PetscInt pStart, pEnd; 1403 PetscInt dof, off, c; 1404 PetscErrorCode ierr; 1405 1406 PetscFunctionBegin; 1407 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1408 ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 1409 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 1410 if (dof) PetscValidPointer(cone, 3); 1411 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 1412 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); 1413 for (c = 0; c < dof; ++c) { 1414 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); 1415 mesh->cones[off+c] = cone[c]; 1416 } 1417 PetscFunctionReturn(0); 1418 } 1419 1420 /*@C 1421 DMPlexGetConeOrientation - Return the orientations on the in-edges for this point in the DAG 1422 1423 Not collective 1424 1425 Input Parameters: 1426 + mesh - The DMPlex 1427 - p - The point, which must lie in the chart set with DMPlexSetChart() 1428 1429 Output Parameter: 1430 . coneOrientation - An array of orientations which are on the in-edges for point p. An orientation is an 1431 integer giving the prescription for cone traversal. If it is negative, the cone is 1432 traversed in the opposite direction. Its value 'o', or if negative '-(o+1)', gives 1433 the index of the cone point on which to start. 1434 1435 Level: beginner 1436 1437 Fortran Notes: 1438 Since it returns an array, this routine is only available in Fortran 90, and you must 1439 include petsc.h90 in your code. 1440 1441 You must also call DMPlexRestoreConeOrientation() after you finish using the returned array. 1442 1443 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetCone(), DMPlexSetChart() 1444 @*/ 1445 PetscErrorCode DMPlexGetConeOrientation(DM dm, PetscInt p, const PetscInt *coneOrientation[]) 1446 { 1447 DM_Plex *mesh = (DM_Plex*) dm->data; 1448 PetscInt off; 1449 PetscErrorCode ierr; 1450 1451 PetscFunctionBegin; 1452 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1453 #if defined(PETSC_USE_DEBUG) 1454 { 1455 PetscInt dof; 1456 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 1457 if (dof) PetscValidPointer(coneOrientation, 3); 1458 } 1459 #endif 1460 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 1461 1462 *coneOrientation = &mesh->coneOrientations[off]; 1463 PetscFunctionReturn(0); 1464 } 1465 1466 /*@ 1467 DMPlexSetConeOrientation - Set the orientations on the in-edges for this point in the DAG 1468 1469 Not collective 1470 1471 Input Parameters: 1472 + mesh - The DMPlex 1473 . p - The point, which must lie in the chart set with DMPlexSetChart() 1474 - coneOrientation - An array of orientations which are on the in-edges for point p. An orientation is an 1475 integer giving the prescription for cone traversal. If it is negative, the cone is 1476 traversed in the opposite direction. Its value 'o', or if negative '-(o+1)', gives 1477 the index of the cone point on which to start. 1478 1479 Output Parameter: 1480 1481 Note: 1482 This should be called after all calls to DMPlexSetConeSize() and DMSetUp(). 1483 1484 Level: beginner 1485 1486 .seealso: DMPlexCreate(), DMPlexGetConeOrientation(), DMPlexSetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() 1487 @*/ 1488 PetscErrorCode DMPlexSetConeOrientation(DM dm, PetscInt p, const PetscInt coneOrientation[]) 1489 { 1490 DM_Plex *mesh = (DM_Plex*) dm->data; 1491 PetscInt pStart, pEnd; 1492 PetscInt dof, off, c; 1493 PetscErrorCode ierr; 1494 1495 PetscFunctionBegin; 1496 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1497 ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 1498 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 1499 if (dof) PetscValidPointer(coneOrientation, 3); 1500 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 1501 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); 1502 for (c = 0; c < dof; ++c) { 1503 PetscInt cdof, o = coneOrientation[c]; 1504 1505 ierr = PetscSectionGetDof(mesh->coneSection, mesh->cones[off+c], &cdof);CHKERRQ(ierr); 1506 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); 1507 mesh->coneOrientations[off+c] = o; 1508 } 1509 PetscFunctionReturn(0); 1510 } 1511 1512 /*@ 1513 DMPlexInsertCone - Insert a point into the in-edges for the point p in the DAG 1514 1515 Not collective 1516 1517 Input Parameters: 1518 + mesh - The DMPlex 1519 . p - The point, which must lie in the chart set with DMPlexSetChart() 1520 . conePos - The local index in the cone where the point should be put 1521 - conePoint - The mesh point to insert 1522 1523 Level: beginner 1524 1525 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() 1526 @*/ 1527 PetscErrorCode DMPlexInsertCone(DM dm, PetscInt p, PetscInt conePos, PetscInt conePoint) 1528 { 1529 DM_Plex *mesh = (DM_Plex*) dm->data; 1530 PetscInt pStart, pEnd; 1531 PetscInt dof, off; 1532 PetscErrorCode ierr; 1533 1534 PetscFunctionBegin; 1535 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1536 ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 1537 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); 1538 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); 1539 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 1540 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 1541 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); 1542 mesh->cones[off+conePos] = conePoint; 1543 PetscFunctionReturn(0); 1544 } 1545 1546 /*@ 1547 DMPlexInsertConeOrientation - Insert a point orientation for the in-edge for the point p in the DAG 1548 1549 Not collective 1550 1551 Input Parameters: 1552 + mesh - The DMPlex 1553 . p - The point, which must lie in the chart set with DMPlexSetChart() 1554 . conePos - The local index in the cone where the point should be put 1555 - coneOrientation - The point orientation to insert 1556 1557 Level: beginner 1558 1559 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() 1560 @*/ 1561 PetscErrorCode DMPlexInsertConeOrientation(DM dm, PetscInt p, PetscInt conePos, PetscInt coneOrientation) 1562 { 1563 DM_Plex *mesh = (DM_Plex*) dm->data; 1564 PetscInt pStart, pEnd; 1565 PetscInt dof, off; 1566 PetscErrorCode ierr; 1567 1568 PetscFunctionBegin; 1569 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1570 ierr = PetscSectionGetChart(mesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 1571 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); 1572 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 1573 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 1574 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); 1575 mesh->coneOrientations[off+conePos] = coneOrientation; 1576 PetscFunctionReturn(0); 1577 } 1578 1579 /*@ 1580 DMPlexGetSupportSize - Return the number of out-edges for this point in the DAG 1581 1582 Not collective 1583 1584 Input Parameters: 1585 + mesh - The DMPlex 1586 - p - The point, which must lie in the chart set with DMPlexSetChart() 1587 1588 Output Parameter: 1589 . size - The support size for point p 1590 1591 Level: beginner 1592 1593 .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart(), DMPlexGetConeSize() 1594 @*/ 1595 PetscErrorCode DMPlexGetSupportSize(DM dm, PetscInt p, PetscInt *size) 1596 { 1597 DM_Plex *mesh = (DM_Plex*) dm->data; 1598 PetscErrorCode ierr; 1599 1600 PetscFunctionBegin; 1601 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1602 PetscValidPointer(size, 3); 1603 ierr = PetscSectionGetDof(mesh->supportSection, p, size);CHKERRQ(ierr); 1604 PetscFunctionReturn(0); 1605 } 1606 1607 /*@ 1608 DMPlexSetSupportSize - Set the number of out-edges for this point in the DAG 1609 1610 Not collective 1611 1612 Input Parameters: 1613 + mesh - The DMPlex 1614 . p - The point, which must lie in the chart set with DMPlexSetChart() 1615 - size - The support size for point p 1616 1617 Output Parameter: 1618 1619 Note: 1620 This should be called after DMPlexSetChart(). 1621 1622 Level: beginner 1623 1624 .seealso: DMPlexCreate(), DMPlexGetSupportSize(), DMPlexSetChart() 1625 @*/ 1626 PetscErrorCode DMPlexSetSupportSize(DM dm, PetscInt p, PetscInt size) 1627 { 1628 DM_Plex *mesh = (DM_Plex*) dm->data; 1629 PetscErrorCode ierr; 1630 1631 PetscFunctionBegin; 1632 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1633 ierr = PetscSectionSetDof(mesh->supportSection, p, size);CHKERRQ(ierr); 1634 1635 mesh->maxSupportSize = PetscMax(mesh->maxSupportSize, size); 1636 PetscFunctionReturn(0); 1637 } 1638 1639 /*@C 1640 DMPlexGetSupport - Return the points on the out-edges for this point in the DAG 1641 1642 Not collective 1643 1644 Input Parameters: 1645 + mesh - The DMPlex 1646 - p - The point, which must lie in the chart set with DMPlexSetChart() 1647 1648 Output Parameter: 1649 . support - An array of points which are on the out-edges for point p 1650 1651 Level: beginner 1652 1653 Fortran Notes: 1654 Since it returns an array, this routine is only available in Fortran 90, and you must 1655 include petsc.h90 in your code. 1656 1657 You must also call DMPlexRestoreSupport() after you finish using the returned array. 1658 1659 .seealso: DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() 1660 @*/ 1661 PetscErrorCode DMPlexGetSupport(DM dm, PetscInt p, const PetscInt *support[]) 1662 { 1663 DM_Plex *mesh = (DM_Plex*) dm->data; 1664 PetscInt off; 1665 PetscErrorCode ierr; 1666 1667 PetscFunctionBegin; 1668 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1669 PetscValidPointer(support, 3); 1670 ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); 1671 *support = &mesh->supports[off]; 1672 PetscFunctionReturn(0); 1673 } 1674 1675 /*@ 1676 DMPlexSetSupport - Set the points on the out-edges for this point in the DAG 1677 1678 Not collective 1679 1680 Input Parameters: 1681 + mesh - The DMPlex 1682 . p - The point, which must lie in the chart set with DMPlexSetChart() 1683 - support - An array of points which are on the in-edges for point p 1684 1685 Output Parameter: 1686 1687 Note: 1688 This should be called after all calls to DMPlexSetSupportSize() and DMSetUp(). 1689 1690 Level: beginner 1691 1692 .seealso: DMPlexCreate(), DMPlexGetSupport(), DMPlexSetChart(), DMPlexSetSupportSize(), DMSetUp() 1693 @*/ 1694 PetscErrorCode DMPlexSetSupport(DM dm, PetscInt p, const PetscInt support[]) 1695 { 1696 DM_Plex *mesh = (DM_Plex*) dm->data; 1697 PetscInt pStart, pEnd; 1698 PetscInt dof, off, c; 1699 PetscErrorCode ierr; 1700 1701 PetscFunctionBegin; 1702 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1703 ierr = PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd);CHKERRQ(ierr); 1704 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 1705 if (dof) PetscValidPointer(support, 3); 1706 ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); 1707 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); 1708 for (c = 0; c < dof; ++c) { 1709 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); 1710 mesh->supports[off+c] = support[c]; 1711 } 1712 PetscFunctionReturn(0); 1713 } 1714 1715 /*@ 1716 DMPlexInsertSupport - Insert a point into the out-edges for the point p in the DAG 1717 1718 Not collective 1719 1720 Input Parameters: 1721 + mesh - The DMPlex 1722 . p - The point, which must lie in the chart set with DMPlexSetChart() 1723 . supportPos - The local index in the cone where the point should be put 1724 - supportPoint - The mesh point to insert 1725 1726 Level: beginner 1727 1728 .seealso: DMPlexCreate(), DMPlexGetCone(), DMPlexSetChart(), DMPlexSetConeSize(), DMSetUp() 1729 @*/ 1730 PetscErrorCode DMPlexInsertSupport(DM dm, PetscInt p, PetscInt supportPos, PetscInt supportPoint) 1731 { 1732 DM_Plex *mesh = (DM_Plex*) dm->data; 1733 PetscInt pStart, pEnd; 1734 PetscInt dof, off; 1735 PetscErrorCode ierr; 1736 1737 PetscFunctionBegin; 1738 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1739 ierr = PetscSectionGetChart(mesh->supportSection, &pStart, &pEnd);CHKERRQ(ierr); 1740 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 1741 ierr = PetscSectionGetOffset(mesh->supportSection, p, &off);CHKERRQ(ierr); 1742 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); 1743 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); 1744 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); 1745 mesh->supports[off+supportPos] = supportPoint; 1746 PetscFunctionReturn(0); 1747 } 1748 1749 /*@C 1750 DMPlexGetTransitiveClosure - Return the points on the transitive closure of the in-edges or out-edges for this point in the DAG 1751 1752 Not collective 1753 1754 Input Parameters: 1755 + mesh - The DMPlex 1756 . p - The point, which must lie in the chart set with DMPlexSetChart() 1757 . useCone - PETSC_TRUE for in-edges, otherwise use out-edges 1758 - points - If points is NULL on input, internal storage will be returned, otherwise the provided array is used 1759 1760 Output Parameters: 1761 + numPoints - The number of points in the closure, so points[] is of size 2*numPoints 1762 - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...] 1763 1764 Note: 1765 If using internal storage (points is NULL on input), each call overwrites the last output. 1766 1767 Fortran Notes: 1768 Since it returns an array, this routine is only available in Fortran 90, and you must 1769 include petsc.h90 in your code. 1770 1771 The numPoints argument is not present in the Fortran 90 binding since it is internal to the array. 1772 1773 Level: beginner 1774 1775 .seealso: DMPlexRestoreTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() 1776 @*/ 1777 PetscErrorCode DMPlexGetTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 1778 { 1779 DM_Plex *mesh = (DM_Plex*) dm->data; 1780 PetscInt *closure, *fifo; 1781 const PetscInt *tmp = NULL, *tmpO = NULL; 1782 PetscInt tmpSize, t; 1783 PetscInt depth = 0, maxSize; 1784 PetscInt closureSize = 2, fifoSize = 0, fifoStart = 0; 1785 PetscErrorCode ierr; 1786 1787 PetscFunctionBegin; 1788 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1789 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1790 /* This is only 1-level */ 1791 if (useCone) { 1792 ierr = DMPlexGetConeSize(dm, p, &tmpSize);CHKERRQ(ierr); 1793 ierr = DMPlexGetCone(dm, p, &tmp);CHKERRQ(ierr); 1794 ierr = DMPlexGetConeOrientation(dm, p, &tmpO);CHKERRQ(ierr); 1795 } else { 1796 ierr = DMPlexGetSupportSize(dm, p, &tmpSize);CHKERRQ(ierr); 1797 ierr = DMPlexGetSupport(dm, p, &tmp);CHKERRQ(ierr); 1798 } 1799 if (depth == 1) { 1800 if (*points) { 1801 closure = *points; 1802 } else { 1803 maxSize = 2*(PetscMax(mesh->maxConeSize, mesh->maxSupportSize)+1); 1804 ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &closure);CHKERRQ(ierr); 1805 } 1806 closure[0] = p; closure[1] = 0; 1807 for (t = 0; t < tmpSize; ++t, closureSize += 2) { 1808 closure[closureSize] = tmp[t]; 1809 closure[closureSize+1] = tmpO ? tmpO[t] : 0; 1810 } 1811 if (numPoints) *numPoints = closureSize/2; 1812 if (points) *points = closure; 1813 PetscFunctionReturn(0); 1814 } 1815 { 1816 PetscInt c, coneSeries, s,supportSeries; 1817 1818 c = mesh->maxConeSize; 1819 coneSeries = (c > 1) ? ((PetscPowInt(c,depth+1)-1)/(c-1)) : depth+1; 1820 s = mesh->maxSupportSize; 1821 supportSeries = (s > 1) ? ((PetscPowInt(s,depth+1)-1)/(s-1)) : depth+1; 1822 maxSize = 2*PetscMax(coneSeries,supportSeries); 1823 } 1824 ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &fifo);CHKERRQ(ierr); 1825 if (*points) { 1826 closure = *points; 1827 } else { 1828 ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &closure);CHKERRQ(ierr); 1829 } 1830 closure[0] = p; closure[1] = 0; 1831 for (t = 0; t < tmpSize; ++t, closureSize += 2, fifoSize += 2) { 1832 const PetscInt cp = tmp[t]; 1833 const PetscInt co = tmpO ? tmpO[t] : 0; 1834 1835 closure[closureSize] = cp; 1836 closure[closureSize+1] = co; 1837 fifo[fifoSize] = cp; 1838 fifo[fifoSize+1] = co; 1839 } 1840 /* Should kick out early when depth is reached, rather than checking all vertices for empty cones */ 1841 while (fifoSize - fifoStart) { 1842 const PetscInt q = fifo[fifoStart]; 1843 const PetscInt o = fifo[fifoStart+1]; 1844 const PetscInt rev = o >= 0 ? 0 : 1; 1845 const PetscInt off = rev ? -(o+1) : o; 1846 1847 if (useCone) { 1848 ierr = DMPlexGetConeSize(dm, q, &tmpSize);CHKERRQ(ierr); 1849 ierr = DMPlexGetCone(dm, q, &tmp);CHKERRQ(ierr); 1850 ierr = DMPlexGetConeOrientation(dm, q, &tmpO);CHKERRQ(ierr); 1851 } else { 1852 ierr = DMPlexGetSupportSize(dm, q, &tmpSize);CHKERRQ(ierr); 1853 ierr = DMPlexGetSupport(dm, q, &tmp);CHKERRQ(ierr); 1854 tmpO = NULL; 1855 } 1856 for (t = 0; t < tmpSize; ++t) { 1857 const PetscInt i = ((rev ? tmpSize-t : t) + off)%tmpSize; 1858 const PetscInt cp = tmp[i]; 1859 /* Must propogate orientation: When we reverse orientation, we both reverse the direction of iteration and start at the other end of the chain. */ 1860 /* HACK: It is worse to get the size here, than to change the interpretation of -(*+1) 1861 const PetscInt co = tmpO ? (rev ? -(tmpO[i]+1) : tmpO[i]) : 0; */ 1862 PetscInt co = tmpO ? tmpO[i] : 0; 1863 PetscInt c; 1864 1865 if (rev) { 1866 PetscInt childSize, coff; 1867 ierr = DMPlexGetConeSize(dm, cp, &childSize);CHKERRQ(ierr); 1868 coff = tmpO[i] < 0 ? -(tmpO[i]+1) : tmpO[i]; 1869 co = childSize ? -(((coff+childSize-1)%childSize)+1) : 0; 1870 } 1871 /* Check for duplicate */ 1872 for (c = 0; c < closureSize; c += 2) { 1873 if (closure[c] == cp) break; 1874 } 1875 if (c == closureSize) { 1876 closure[closureSize] = cp; 1877 closure[closureSize+1] = co; 1878 fifo[fifoSize] = cp; 1879 fifo[fifoSize+1] = co; 1880 closureSize += 2; 1881 fifoSize += 2; 1882 } 1883 } 1884 fifoStart += 2; 1885 } 1886 if (numPoints) *numPoints = closureSize/2; 1887 if (points) *points = closure; 1888 ierr = DMRestoreWorkArray(dm, maxSize, PETSC_INT, &fifo);CHKERRQ(ierr); 1889 PetscFunctionReturn(0); 1890 } 1891 1892 /*@C 1893 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 1894 1895 Not collective 1896 1897 Input Parameters: 1898 + mesh - The DMPlex 1899 . p - The point, which must lie in the chart set with DMPlexSetChart() 1900 . orientation - The orientation of the point 1901 . useCone - PETSC_TRUE for in-edges, otherwise use out-edges 1902 - points - If points is NULL on input, internal storage will be returned, otherwise the provided array is used 1903 1904 Output Parameters: 1905 + numPoints - The number of points in the closure, so points[] is of size 2*numPoints 1906 - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...] 1907 1908 Note: 1909 If using internal storage (points is NULL on input), each call overwrites the last output. 1910 1911 Fortran Notes: 1912 Since it returns an array, this routine is only available in Fortran 90, and you must 1913 include petsc.h90 in your code. 1914 1915 The numPoints argument is not present in the Fortran 90 binding since it is internal to the array. 1916 1917 Level: beginner 1918 1919 .seealso: DMPlexRestoreTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() 1920 @*/ 1921 PetscErrorCode DMPlexGetTransitiveClosure_Internal(DM dm, PetscInt p, PetscInt ornt, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 1922 { 1923 DM_Plex *mesh = (DM_Plex*) dm->data; 1924 PetscInt *closure, *fifo; 1925 const PetscInt *tmp = NULL, *tmpO = NULL; 1926 PetscInt tmpSize, t; 1927 PetscInt depth = 0, maxSize; 1928 PetscInt closureSize = 2, fifoSize = 0, fifoStart = 0; 1929 PetscErrorCode ierr; 1930 1931 PetscFunctionBegin; 1932 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1933 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1934 /* This is only 1-level */ 1935 if (useCone) { 1936 ierr = DMPlexGetConeSize(dm, p, &tmpSize);CHKERRQ(ierr); 1937 ierr = DMPlexGetCone(dm, p, &tmp);CHKERRQ(ierr); 1938 ierr = DMPlexGetConeOrientation(dm, p, &tmpO);CHKERRQ(ierr); 1939 } else { 1940 ierr = DMPlexGetSupportSize(dm, p, &tmpSize);CHKERRQ(ierr); 1941 ierr = DMPlexGetSupport(dm, p, &tmp);CHKERRQ(ierr); 1942 } 1943 if (depth == 1) { 1944 if (*points) { 1945 closure = *points; 1946 } else { 1947 maxSize = 2*(PetscMax(mesh->maxConeSize, mesh->maxSupportSize)+1); 1948 ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &closure);CHKERRQ(ierr); 1949 } 1950 closure[0] = p; closure[1] = ornt; 1951 for (t = 0; t < tmpSize; ++t, closureSize += 2) { 1952 const PetscInt i = ornt >= 0 ? (t+ornt)%tmpSize : (-(ornt+1) + tmpSize-t)%tmpSize; 1953 closure[closureSize] = tmp[i]; 1954 closure[closureSize+1] = tmpO ? tmpO[i] : 0; 1955 } 1956 if (numPoints) *numPoints = closureSize/2; 1957 if (points) *points = closure; 1958 PetscFunctionReturn(0); 1959 } 1960 { 1961 PetscInt c, coneSeries, s,supportSeries; 1962 1963 c = mesh->maxConeSize; 1964 coneSeries = (c > 1) ? ((PetscPowInt(c,depth+1)-1)/(c-1)) : depth+1; 1965 s = mesh->maxSupportSize; 1966 supportSeries = (s > 1) ? ((PetscPowInt(s,depth+1)-1)/(s-1)) : depth+1; 1967 maxSize = 2*PetscMax(coneSeries,supportSeries); 1968 } 1969 ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &fifo);CHKERRQ(ierr); 1970 if (*points) { 1971 closure = *points; 1972 } else { 1973 ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &closure);CHKERRQ(ierr); 1974 } 1975 closure[0] = p; closure[1] = ornt; 1976 for (t = 0; t < tmpSize; ++t, closureSize += 2, fifoSize += 2) { 1977 const PetscInt i = ornt >= 0 ? (t+ornt)%tmpSize : (-(ornt+1) + tmpSize-t)%tmpSize; 1978 const PetscInt cp = tmp[i]; 1979 PetscInt co = tmpO ? tmpO[i] : 0; 1980 1981 if (ornt < 0) { 1982 PetscInt childSize, coff; 1983 ierr = DMPlexGetConeSize(dm, cp, &childSize);CHKERRQ(ierr); 1984 coff = co < 0 ? -(tmpO[i]+1) : tmpO[i]; 1985 co = childSize ? -(((coff+childSize-1)%childSize)+1) : 0; 1986 } 1987 closure[closureSize] = cp; 1988 closure[closureSize+1] = co; 1989 fifo[fifoSize] = cp; 1990 fifo[fifoSize+1] = co; 1991 } 1992 /* Should kick out early when depth is reached, rather than checking all vertices for empty cones */ 1993 while (fifoSize - fifoStart) { 1994 const PetscInt q = fifo[fifoStart]; 1995 const PetscInt o = fifo[fifoStart+1]; 1996 const PetscInt rev = o >= 0 ? 0 : 1; 1997 const PetscInt off = rev ? -(o+1) : o; 1998 1999 if (useCone) { 2000 ierr = DMPlexGetConeSize(dm, q, &tmpSize);CHKERRQ(ierr); 2001 ierr = DMPlexGetCone(dm, q, &tmp);CHKERRQ(ierr); 2002 ierr = DMPlexGetConeOrientation(dm, q, &tmpO);CHKERRQ(ierr); 2003 } else { 2004 ierr = DMPlexGetSupportSize(dm, q, &tmpSize);CHKERRQ(ierr); 2005 ierr = DMPlexGetSupport(dm, q, &tmp);CHKERRQ(ierr); 2006 tmpO = NULL; 2007 } 2008 for (t = 0; t < tmpSize; ++t) { 2009 const PetscInt i = ((rev ? tmpSize-t : t) + off)%tmpSize; 2010 const PetscInt cp = tmp[i]; 2011 /* Must propogate orientation: When we reverse orientation, we both reverse the direction of iteration and start at the other end of the chain. */ 2012 /* HACK: It is worse to get the size here, than to change the interpretation of -(*+1) 2013 const PetscInt co = tmpO ? (rev ? -(tmpO[i]+1) : tmpO[i]) : 0; */ 2014 PetscInt co = tmpO ? tmpO[i] : 0; 2015 PetscInt c; 2016 2017 if (rev) { 2018 PetscInt childSize, coff; 2019 ierr = DMPlexGetConeSize(dm, cp, &childSize);CHKERRQ(ierr); 2020 coff = tmpO[i] < 0 ? -(tmpO[i]+1) : tmpO[i]; 2021 co = childSize ? -(((coff+childSize-1)%childSize)+1) : 0; 2022 } 2023 /* Check for duplicate */ 2024 for (c = 0; c < closureSize; c += 2) { 2025 if (closure[c] == cp) break; 2026 } 2027 if (c == closureSize) { 2028 closure[closureSize] = cp; 2029 closure[closureSize+1] = co; 2030 fifo[fifoSize] = cp; 2031 fifo[fifoSize+1] = co; 2032 closureSize += 2; 2033 fifoSize += 2; 2034 } 2035 } 2036 fifoStart += 2; 2037 } 2038 if (numPoints) *numPoints = closureSize/2; 2039 if (points) *points = closure; 2040 ierr = DMRestoreWorkArray(dm, maxSize, PETSC_INT, &fifo);CHKERRQ(ierr); 2041 PetscFunctionReturn(0); 2042 } 2043 2044 /*@C 2045 DMPlexRestoreTransitiveClosure - Restore the array of points on the transitive closure of the in-edges or out-edges for this point in the DAG 2046 2047 Not collective 2048 2049 Input Parameters: 2050 + mesh - The DMPlex 2051 . p - The point, which must lie in the chart set with DMPlexSetChart() 2052 . useCone - PETSC_TRUE for in-edges, otherwise use out-edges 2053 . numPoints - The number of points in the closure, so points[] is of size 2*numPoints, zeroed on exit 2054 - points - The points and point orientations, interleaved as pairs [p0, o0, p1, o1, ...], zeroed on exit 2055 2056 Note: 2057 If not using internal storage (points is not NULL on input), this call is unnecessary 2058 2059 Fortran Notes: 2060 Since it returns an array, this routine is only available in Fortran 90, and you must 2061 include petsc.h90 in your code. 2062 2063 The numPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2064 2065 Level: beginner 2066 2067 .seealso: DMPlexGetTransitiveClosure(), DMPlexCreate(), DMPlexSetCone(), DMPlexSetChart(), DMPlexGetCone() 2068 @*/ 2069 PetscErrorCode DMPlexRestoreTransitiveClosure(DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints, PetscInt *points[]) 2070 { 2071 PetscErrorCode ierr; 2072 2073 PetscFunctionBegin; 2074 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2075 if (numPoints) PetscValidIntPointer(numPoints,4); 2076 if (points) PetscValidPointer(points,5); 2077 ierr = DMRestoreWorkArray(dm, 0, PETSC_INT, points);CHKERRQ(ierr); 2078 if (numPoints) *numPoints = 0; 2079 PetscFunctionReturn(0); 2080 } 2081 2082 /*@ 2083 DMPlexGetMaxSizes - Return the maximum number of in-edges (cone) and out-edges (support) for any point in the DAG 2084 2085 Not collective 2086 2087 Input Parameter: 2088 . mesh - The DMPlex 2089 2090 Output Parameters: 2091 + maxConeSize - The maximum number of in-edges 2092 - maxSupportSize - The maximum number of out-edges 2093 2094 Level: beginner 2095 2096 .seealso: DMPlexCreate(), DMPlexSetConeSize(), DMPlexSetChart() 2097 @*/ 2098 PetscErrorCode DMPlexGetMaxSizes(DM dm, PetscInt *maxConeSize, PetscInt *maxSupportSize) 2099 { 2100 DM_Plex *mesh = (DM_Plex*) dm->data; 2101 2102 PetscFunctionBegin; 2103 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2104 if (maxConeSize) *maxConeSize = mesh->maxConeSize; 2105 if (maxSupportSize) *maxSupportSize = mesh->maxSupportSize; 2106 PetscFunctionReturn(0); 2107 } 2108 2109 PetscErrorCode DMSetUp_Plex(DM dm) 2110 { 2111 DM_Plex *mesh = (DM_Plex*) dm->data; 2112 PetscInt size; 2113 PetscErrorCode ierr; 2114 2115 PetscFunctionBegin; 2116 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2117 ierr = PetscSectionSetUp(mesh->coneSection);CHKERRQ(ierr); 2118 ierr = PetscSectionGetStorageSize(mesh->coneSection, &size);CHKERRQ(ierr); 2119 ierr = PetscMalloc1(size, &mesh->cones);CHKERRQ(ierr); 2120 ierr = PetscCalloc1(size, &mesh->coneOrientations);CHKERRQ(ierr); 2121 if (mesh->maxSupportSize) { 2122 ierr = PetscSectionSetUp(mesh->supportSection);CHKERRQ(ierr); 2123 ierr = PetscSectionGetStorageSize(mesh->supportSection, &size);CHKERRQ(ierr); 2124 ierr = PetscMalloc1(size, &mesh->supports);CHKERRQ(ierr); 2125 } 2126 PetscFunctionReturn(0); 2127 } 2128 2129 PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm) 2130 { 2131 PetscErrorCode ierr; 2132 2133 PetscFunctionBegin; 2134 if (subdm) {ierr = DMClone(dm, subdm);CHKERRQ(ierr);} 2135 ierr = DMCreateSubDM_Section_Private(dm, numFields, fields, is, subdm);CHKERRQ(ierr); 2136 PetscFunctionReturn(0); 2137 } 2138 2139 /*@ 2140 DMPlexSymmetrize - Create support (out-edge) information from cone (in-edge) information 2141 2142 Not collective 2143 2144 Input Parameter: 2145 . mesh - The DMPlex 2146 2147 Output Parameter: 2148 2149 Note: 2150 This should be called after all calls to DMPlexSetCone() 2151 2152 Level: beginner 2153 2154 .seealso: DMPlexCreate(), DMPlexSetChart(), DMPlexSetConeSize(), DMPlexSetCone() 2155 @*/ 2156 PetscErrorCode DMPlexSymmetrize(DM dm) 2157 { 2158 DM_Plex *mesh = (DM_Plex*) dm->data; 2159 PetscInt *offsets; 2160 PetscInt supportSize; 2161 PetscInt pStart, pEnd, p; 2162 PetscErrorCode ierr; 2163 2164 PetscFunctionBegin; 2165 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2166 if (mesh->supports) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONGSTATE, "Supports were already setup in this DMPlex"); 2167 /* Calculate support sizes */ 2168 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2169 for (p = pStart; p < pEnd; ++p) { 2170 PetscInt dof, off, c; 2171 2172 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 2173 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 2174 for (c = off; c < off+dof; ++c) { 2175 ierr = PetscSectionAddDof(mesh->supportSection, mesh->cones[c], 1);CHKERRQ(ierr); 2176 } 2177 } 2178 for (p = pStart; p < pEnd; ++p) { 2179 PetscInt dof; 2180 2181 ierr = PetscSectionGetDof(mesh->supportSection, p, &dof);CHKERRQ(ierr); 2182 2183 mesh->maxSupportSize = PetscMax(mesh->maxSupportSize, dof); 2184 } 2185 ierr = PetscSectionSetUp(mesh->supportSection);CHKERRQ(ierr); 2186 /* Calculate supports */ 2187 ierr = PetscSectionGetStorageSize(mesh->supportSection, &supportSize);CHKERRQ(ierr); 2188 ierr = PetscMalloc1(supportSize, &mesh->supports);CHKERRQ(ierr); 2189 ierr = PetscCalloc1(pEnd - pStart, &offsets);CHKERRQ(ierr); 2190 for (p = pStart; p < pEnd; ++p) { 2191 PetscInt dof, off, c; 2192 2193 ierr = PetscSectionGetDof(mesh->coneSection, p, &dof);CHKERRQ(ierr); 2194 ierr = PetscSectionGetOffset(mesh->coneSection, p, &off);CHKERRQ(ierr); 2195 for (c = off; c < off+dof; ++c) { 2196 const PetscInt q = mesh->cones[c]; 2197 PetscInt offS; 2198 2199 ierr = PetscSectionGetOffset(mesh->supportSection, q, &offS);CHKERRQ(ierr); 2200 2201 mesh->supports[offS+offsets[q]] = p; 2202 ++offsets[q]; 2203 } 2204 } 2205 ierr = PetscFree(offsets);CHKERRQ(ierr); 2206 PetscFunctionReturn(0); 2207 } 2208 2209 /*@ 2210 DMPlexStratify - The DAG for most topologies is a graded poset (http://en.wikipedia.org/wiki/Graded_poset), and 2211 can be illustrated by a Hasse Diagram (a http://en.wikipedia.org/wiki/Hasse_diagram). The strata group all points of the 2212 same grade, and this function calculates the strata. This grade can be seen as the height (or depth) of the point in 2213 the DAG. 2214 2215 Collective on dm 2216 2217 Input Parameter: 2218 . mesh - The DMPlex 2219 2220 Output Parameter: 2221 2222 Notes: 2223 Concretely, DMPlexStratify() creates a new label named "depth" containing the dimension of each element: 0 for vertices, 2224 1 for edges, and so on. The depth label can be accessed through DMPlexGetDepthLabel() or DMPlexGetDepthStratum(), or 2225 manually via DMGetLabel(). The height is defined implicitly by height = maxDimension - depth, and can be accessed 2226 via DMPlexGetHeightStratum(). For example, cells have height 0 and faces have height 1. 2227 2228 DMPlexStratify() should be called after all calls to DMPlexSymmetrize() 2229 2230 Level: beginner 2231 2232 .seealso: DMPlexCreate(), DMPlexSymmetrize() 2233 @*/ 2234 PetscErrorCode DMPlexStratify(DM dm) 2235 { 2236 DM_Plex *mesh = (DM_Plex*) dm->data; 2237 DMLabel label; 2238 PetscInt pStart, pEnd, p; 2239 PetscInt numRoots = 0, numLeaves = 0; 2240 PetscErrorCode ierr; 2241 2242 PetscFunctionBegin; 2243 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2244 ierr = PetscLogEventBegin(DMPLEX_Stratify,dm,0,0,0);CHKERRQ(ierr); 2245 /* Calculate depth */ 2246 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2247 ierr = DMCreateLabel(dm, "depth");CHKERRQ(ierr); 2248 ierr = DMPlexGetDepthLabel(dm, &label);CHKERRQ(ierr); 2249 /* Initialize roots and count leaves */ 2250 for (p = pStart; p < pEnd; ++p) { 2251 PetscInt coneSize, supportSize; 2252 2253 ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); 2254 ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); 2255 if (!coneSize && supportSize) { 2256 ++numRoots; 2257 ierr = DMLabelSetValue(label, p, 0);CHKERRQ(ierr); 2258 } else if (!supportSize && coneSize) { 2259 ++numLeaves; 2260 } else if (!supportSize && !coneSize) { 2261 /* Isolated points */ 2262 ierr = DMLabelSetValue(label, p, 0);CHKERRQ(ierr); 2263 } 2264 } 2265 if (numRoots + numLeaves == (pEnd - pStart)) { 2266 for (p = pStart; p < pEnd; ++p) { 2267 PetscInt coneSize, supportSize; 2268 2269 ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); 2270 ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); 2271 if (!supportSize && coneSize) { 2272 ierr = DMLabelSetValue(label, p, 1);CHKERRQ(ierr); 2273 } 2274 } 2275 } else { 2276 IS pointIS; 2277 PetscInt numPoints = 0, level = 0; 2278 2279 ierr = DMLabelGetStratumIS(label, level, &pointIS);CHKERRQ(ierr); 2280 if (pointIS) {ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr);} 2281 while (numPoints) { 2282 const PetscInt *points; 2283 const PetscInt newLevel = level+1; 2284 2285 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2286 for (p = 0; p < numPoints; ++p) { 2287 const PetscInt point = points[p]; 2288 const PetscInt *support; 2289 PetscInt supportSize, s; 2290 2291 ierr = DMPlexGetSupportSize(dm, point, &supportSize);CHKERRQ(ierr); 2292 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 2293 for (s = 0; s < supportSize; ++s) { 2294 ierr = DMLabelSetValue(label, support[s], newLevel);CHKERRQ(ierr); 2295 } 2296 } 2297 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2298 ++level; 2299 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2300 ierr = DMLabelGetStratumIS(label, level, &pointIS);CHKERRQ(ierr); 2301 if (pointIS) {ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr);} 2302 else {numPoints = 0;} 2303 } 2304 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2305 } 2306 { /* just in case there is an empty process */ 2307 PetscInt numValues, maxValues = 0, v; 2308 2309 ierr = DMLabelGetNumValues(label,&numValues);CHKERRQ(ierr); 2310 for (v = 0; v < numValues; v++) { 2311 IS pointIS; 2312 2313 ierr = DMLabelGetStratumIS(label, v, &pointIS);CHKERRQ(ierr); 2314 if (pointIS) { 2315 PetscInt min, max, numPoints; 2316 PetscInt start; 2317 PetscBool contig; 2318 2319 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 2320 ierr = ISGetMinMax(pointIS, &min, &max);CHKERRQ(ierr); 2321 ierr = ISContiguousLocal(pointIS,min,max+1,&start,&contig);CHKERRQ(ierr); 2322 if (start == 0 && contig) { 2323 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2324 ierr = ISCreateStride(PETSC_COMM_SELF,numPoints,min,1,&pointIS);CHKERRQ(ierr); 2325 ierr = DMLabelSetStratumIS(label, v, pointIS);CHKERRQ(ierr); 2326 } 2327 } 2328 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2329 } 2330 ierr = MPI_Allreduce(&numValues,&maxValues,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 2331 for (v = numValues; v < maxValues; v++) { 2332 DMLabelAddStratum(label,v);CHKERRQ(ierr); 2333 } 2334 } 2335 2336 ierr = DMLabelGetState(label, &mesh->depthState);CHKERRQ(ierr); 2337 ierr = PetscLogEventEnd(DMPLEX_Stratify,dm,0,0,0);CHKERRQ(ierr); 2338 PetscFunctionReturn(0); 2339 } 2340 2341 /*@C 2342 DMPlexGetJoin - Get an array for the join of the set of points 2343 2344 Not Collective 2345 2346 Input Parameters: 2347 + dm - The DMPlex object 2348 . numPoints - The number of input points for the join 2349 - points - The input points 2350 2351 Output Parameters: 2352 + numCoveredPoints - The number of points in the join 2353 - coveredPoints - The points in the join 2354 2355 Level: intermediate 2356 2357 Note: Currently, this is restricted to a single level join 2358 2359 Fortran Notes: 2360 Since it returns an array, this routine is only available in Fortran 90, and you must 2361 include petsc.h90 in your code. 2362 2363 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2364 2365 .keywords: mesh 2366 .seealso: DMPlexRestoreJoin(), DMPlexGetMeet() 2367 @*/ 2368 PetscErrorCode DMPlexGetJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 2369 { 2370 DM_Plex *mesh = (DM_Plex*) dm->data; 2371 PetscInt *join[2]; 2372 PetscInt joinSize, i = 0; 2373 PetscInt dof, off, p, c, m; 2374 PetscErrorCode ierr; 2375 2376 PetscFunctionBegin; 2377 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2378 PetscValidPointer(points, 2); 2379 PetscValidPointer(numCoveredPoints, 3); 2380 PetscValidPointer(coveredPoints, 4); 2381 ierr = DMGetWorkArray(dm, mesh->maxSupportSize, PETSC_INT, &join[0]);CHKERRQ(ierr); 2382 ierr = DMGetWorkArray(dm, mesh->maxSupportSize, PETSC_INT, &join[1]);CHKERRQ(ierr); 2383 /* Copy in support of first point */ 2384 ierr = PetscSectionGetDof(mesh->supportSection, points[0], &dof);CHKERRQ(ierr); 2385 ierr = PetscSectionGetOffset(mesh->supportSection, points[0], &off);CHKERRQ(ierr); 2386 for (joinSize = 0; joinSize < dof; ++joinSize) { 2387 join[i][joinSize] = mesh->supports[off+joinSize]; 2388 } 2389 /* Check each successive support */ 2390 for (p = 1; p < numPoints; ++p) { 2391 PetscInt newJoinSize = 0; 2392 2393 ierr = PetscSectionGetDof(mesh->supportSection, points[p], &dof);CHKERRQ(ierr); 2394 ierr = PetscSectionGetOffset(mesh->supportSection, points[p], &off);CHKERRQ(ierr); 2395 for (c = 0; c < dof; ++c) { 2396 const PetscInt point = mesh->supports[off+c]; 2397 2398 for (m = 0; m < joinSize; ++m) { 2399 if (point == join[i][m]) { 2400 join[1-i][newJoinSize++] = point; 2401 break; 2402 } 2403 } 2404 } 2405 joinSize = newJoinSize; 2406 i = 1-i; 2407 } 2408 *numCoveredPoints = joinSize; 2409 *coveredPoints = join[i]; 2410 ierr = DMRestoreWorkArray(dm, mesh->maxSupportSize, PETSC_INT, &join[1-i]);CHKERRQ(ierr); 2411 PetscFunctionReturn(0); 2412 } 2413 2414 /*@C 2415 DMPlexRestoreJoin - Restore an array for the join of the set of points 2416 2417 Not Collective 2418 2419 Input Parameters: 2420 + dm - The DMPlex object 2421 . numPoints - The number of input points for the join 2422 - points - The input points 2423 2424 Output Parameters: 2425 + numCoveredPoints - The number of points in the join 2426 - coveredPoints - The points in the join 2427 2428 Fortran Notes: 2429 Since it returns an array, this routine is only available in Fortran 90, and you must 2430 include petsc.h90 in your code. 2431 2432 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2433 2434 Level: intermediate 2435 2436 .keywords: mesh 2437 .seealso: DMPlexGetJoin(), DMPlexGetFullJoin(), DMPlexGetMeet() 2438 @*/ 2439 PetscErrorCode DMPlexRestoreJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 2440 { 2441 PetscErrorCode ierr; 2442 2443 PetscFunctionBegin; 2444 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2445 if (points) PetscValidIntPointer(points,3); 2446 if (numCoveredPoints) PetscValidIntPointer(numCoveredPoints,4); 2447 PetscValidPointer(coveredPoints, 5); 2448 ierr = DMRestoreWorkArray(dm, 0, PETSC_INT, (void*) coveredPoints);CHKERRQ(ierr); 2449 if (numCoveredPoints) *numCoveredPoints = 0; 2450 PetscFunctionReturn(0); 2451 } 2452 2453 /*@C 2454 DMPlexGetFullJoin - Get an array for the join of the set of points 2455 2456 Not Collective 2457 2458 Input Parameters: 2459 + dm - The DMPlex object 2460 . numPoints - The number of input points for the join 2461 - points - The input points 2462 2463 Output Parameters: 2464 + numCoveredPoints - The number of points in the join 2465 - coveredPoints - The points in the join 2466 2467 Fortran Notes: 2468 Since it returns an array, this routine is only available in Fortran 90, and you must 2469 include petsc.h90 in your code. 2470 2471 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2472 2473 Level: intermediate 2474 2475 .keywords: mesh 2476 .seealso: DMPlexGetJoin(), DMPlexRestoreJoin(), DMPlexGetMeet() 2477 @*/ 2478 PetscErrorCode DMPlexGetFullJoin(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 2479 { 2480 DM_Plex *mesh = (DM_Plex*) dm->data; 2481 PetscInt *offsets, **closures; 2482 PetscInt *join[2]; 2483 PetscInt depth = 0, maxSize, joinSize = 0, i = 0; 2484 PetscInt p, d, c, m, ms; 2485 PetscErrorCode ierr; 2486 2487 PetscFunctionBegin; 2488 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2489 PetscValidPointer(points, 2); 2490 PetscValidPointer(numCoveredPoints, 3); 2491 PetscValidPointer(coveredPoints, 4); 2492 2493 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2494 ierr = PetscCalloc1(numPoints, &closures);CHKERRQ(ierr); 2495 ierr = DMGetWorkArray(dm, numPoints*(depth+2), PETSC_INT, &offsets);CHKERRQ(ierr); 2496 ms = mesh->maxSupportSize; 2497 maxSize = (ms > 1) ? ((PetscPowInt(ms,depth+1)-1)/(ms-1)) : depth + 1; 2498 ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &join[0]);CHKERRQ(ierr); 2499 ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &join[1]);CHKERRQ(ierr); 2500 2501 for (p = 0; p < numPoints; ++p) { 2502 PetscInt closureSize; 2503 2504 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_FALSE, &closureSize, &closures[p]);CHKERRQ(ierr); 2505 2506 offsets[p*(depth+2)+0] = 0; 2507 for (d = 0; d < depth+1; ++d) { 2508 PetscInt pStart, pEnd, i; 2509 2510 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 2511 for (i = offsets[p*(depth+2)+d]; i < closureSize; ++i) { 2512 if ((pStart > closures[p][i*2]) || (pEnd <= closures[p][i*2])) { 2513 offsets[p*(depth+2)+d+1] = i; 2514 break; 2515 } 2516 } 2517 if (i == closureSize) offsets[p*(depth+2)+d+1] = i; 2518 } 2519 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); 2520 } 2521 for (d = 0; d < depth+1; ++d) { 2522 PetscInt dof; 2523 2524 /* Copy in support of first point */ 2525 dof = offsets[d+1] - offsets[d]; 2526 for (joinSize = 0; joinSize < dof; ++joinSize) { 2527 join[i][joinSize] = closures[0][(offsets[d]+joinSize)*2]; 2528 } 2529 /* Check each successive cone */ 2530 for (p = 1; p < numPoints && joinSize; ++p) { 2531 PetscInt newJoinSize = 0; 2532 2533 dof = offsets[p*(depth+2)+d+1] - offsets[p*(depth+2)+d]; 2534 for (c = 0; c < dof; ++c) { 2535 const PetscInt point = closures[p][(offsets[p*(depth+2)+d]+c)*2]; 2536 2537 for (m = 0; m < joinSize; ++m) { 2538 if (point == join[i][m]) { 2539 join[1-i][newJoinSize++] = point; 2540 break; 2541 } 2542 } 2543 } 2544 joinSize = newJoinSize; 2545 i = 1-i; 2546 } 2547 if (joinSize) break; 2548 } 2549 *numCoveredPoints = joinSize; 2550 *coveredPoints = join[i]; 2551 for (p = 0; p < numPoints; ++p) { 2552 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_FALSE, NULL, &closures[p]);CHKERRQ(ierr); 2553 } 2554 ierr = PetscFree(closures);CHKERRQ(ierr); 2555 ierr = DMRestoreWorkArray(dm, numPoints*(depth+2), PETSC_INT, &offsets);CHKERRQ(ierr); 2556 ierr = DMRestoreWorkArray(dm, mesh->maxSupportSize, PETSC_INT, &join[1-i]);CHKERRQ(ierr); 2557 PetscFunctionReturn(0); 2558 } 2559 2560 /*@C 2561 DMPlexGetMeet - Get an array for the meet of the set of points 2562 2563 Not Collective 2564 2565 Input Parameters: 2566 + dm - The DMPlex object 2567 . numPoints - The number of input points for the meet 2568 - points - The input points 2569 2570 Output Parameters: 2571 + numCoveredPoints - The number of points in the meet 2572 - coveredPoints - The points in the meet 2573 2574 Level: intermediate 2575 2576 Note: Currently, this is restricted to a single level meet 2577 2578 Fortran Notes: 2579 Since it returns an array, this routine is only available in Fortran 90, and you must 2580 include petsc.h90 in your code. 2581 2582 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2583 2584 .keywords: mesh 2585 .seealso: DMPlexRestoreMeet(), DMPlexGetJoin() 2586 @*/ 2587 PetscErrorCode DMPlexGetMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveringPoints, const PetscInt **coveringPoints) 2588 { 2589 DM_Plex *mesh = (DM_Plex*) dm->data; 2590 PetscInt *meet[2]; 2591 PetscInt meetSize, i = 0; 2592 PetscInt dof, off, p, c, m; 2593 PetscErrorCode ierr; 2594 2595 PetscFunctionBegin; 2596 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2597 PetscValidPointer(points, 2); 2598 PetscValidPointer(numCoveringPoints, 3); 2599 PetscValidPointer(coveringPoints, 4); 2600 ierr = DMGetWorkArray(dm, mesh->maxConeSize, PETSC_INT, &meet[0]);CHKERRQ(ierr); 2601 ierr = DMGetWorkArray(dm, mesh->maxConeSize, PETSC_INT, &meet[1]);CHKERRQ(ierr); 2602 /* Copy in cone of first point */ 2603 ierr = PetscSectionGetDof(mesh->coneSection, points[0], &dof);CHKERRQ(ierr); 2604 ierr = PetscSectionGetOffset(mesh->coneSection, points[0], &off);CHKERRQ(ierr); 2605 for (meetSize = 0; meetSize < dof; ++meetSize) { 2606 meet[i][meetSize] = mesh->cones[off+meetSize]; 2607 } 2608 /* Check each successive cone */ 2609 for (p = 1; p < numPoints; ++p) { 2610 PetscInt newMeetSize = 0; 2611 2612 ierr = PetscSectionGetDof(mesh->coneSection, points[p], &dof);CHKERRQ(ierr); 2613 ierr = PetscSectionGetOffset(mesh->coneSection, points[p], &off);CHKERRQ(ierr); 2614 for (c = 0; c < dof; ++c) { 2615 const PetscInt point = mesh->cones[off+c]; 2616 2617 for (m = 0; m < meetSize; ++m) { 2618 if (point == meet[i][m]) { 2619 meet[1-i][newMeetSize++] = point; 2620 break; 2621 } 2622 } 2623 } 2624 meetSize = newMeetSize; 2625 i = 1-i; 2626 } 2627 *numCoveringPoints = meetSize; 2628 *coveringPoints = meet[i]; 2629 ierr = DMRestoreWorkArray(dm, mesh->maxConeSize, PETSC_INT, &meet[1-i]);CHKERRQ(ierr); 2630 PetscFunctionReturn(0); 2631 } 2632 2633 /*@C 2634 DMPlexRestoreMeet - Restore an array for the meet of the set of points 2635 2636 Not Collective 2637 2638 Input Parameters: 2639 + dm - The DMPlex object 2640 . numPoints - The number of input points for the meet 2641 - points - The input points 2642 2643 Output Parameters: 2644 + numCoveredPoints - The number of points in the meet 2645 - coveredPoints - The points in the meet 2646 2647 Level: intermediate 2648 2649 Fortran Notes: 2650 Since it returns an array, this routine is only available in Fortran 90, and you must 2651 include petsc.h90 in your code. 2652 2653 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2654 2655 .keywords: mesh 2656 .seealso: DMPlexGetMeet(), DMPlexGetFullMeet(), DMPlexGetJoin() 2657 @*/ 2658 PetscErrorCode DMPlexRestoreMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 2659 { 2660 PetscErrorCode ierr; 2661 2662 PetscFunctionBegin; 2663 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2664 if (points) PetscValidIntPointer(points,3); 2665 if (numCoveredPoints) PetscValidIntPointer(numCoveredPoints,4); 2666 PetscValidPointer(coveredPoints,5); 2667 ierr = DMRestoreWorkArray(dm, 0, PETSC_INT, (void*) coveredPoints);CHKERRQ(ierr); 2668 if (numCoveredPoints) *numCoveredPoints = 0; 2669 PetscFunctionReturn(0); 2670 } 2671 2672 /*@C 2673 DMPlexGetFullMeet - Get an array for the meet of the set of points 2674 2675 Not Collective 2676 2677 Input Parameters: 2678 + dm - The DMPlex object 2679 . numPoints - The number of input points for the meet 2680 - points - The input points 2681 2682 Output Parameters: 2683 + numCoveredPoints - The number of points in the meet 2684 - coveredPoints - The points in the meet 2685 2686 Level: intermediate 2687 2688 Fortran Notes: 2689 Since it returns an array, this routine is only available in Fortran 90, and you must 2690 include petsc.h90 in your code. 2691 2692 The numCoveredPoints argument is not present in the Fortran 90 binding since it is internal to the array. 2693 2694 .keywords: mesh 2695 .seealso: DMPlexGetMeet(), DMPlexRestoreMeet(), DMPlexGetJoin() 2696 @*/ 2697 PetscErrorCode DMPlexGetFullMeet(DM dm, PetscInt numPoints, const PetscInt points[], PetscInt *numCoveredPoints, const PetscInt **coveredPoints) 2698 { 2699 DM_Plex *mesh = (DM_Plex*) dm->data; 2700 PetscInt *offsets, **closures; 2701 PetscInt *meet[2]; 2702 PetscInt height = 0, maxSize, meetSize = 0, i = 0; 2703 PetscInt p, h, c, m, mc; 2704 PetscErrorCode ierr; 2705 2706 PetscFunctionBegin; 2707 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2708 PetscValidPointer(points, 2); 2709 PetscValidPointer(numCoveredPoints, 3); 2710 PetscValidPointer(coveredPoints, 4); 2711 2712 ierr = DMPlexGetDepth(dm, &height);CHKERRQ(ierr); 2713 ierr = PetscMalloc1(numPoints, &closures);CHKERRQ(ierr); 2714 ierr = DMGetWorkArray(dm, numPoints*(height+2), PETSC_INT, &offsets);CHKERRQ(ierr); 2715 mc = mesh->maxConeSize; 2716 maxSize = (mc > 1) ? ((PetscPowInt(mc,height+1)-1)/(mc-1)) : height + 1; 2717 ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &meet[0]);CHKERRQ(ierr); 2718 ierr = DMGetWorkArray(dm, maxSize, PETSC_INT, &meet[1]);CHKERRQ(ierr); 2719 2720 for (p = 0; p < numPoints; ++p) { 2721 PetscInt closureSize; 2722 2723 ierr = DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closures[p]);CHKERRQ(ierr); 2724 2725 offsets[p*(height+2)+0] = 0; 2726 for (h = 0; h < height+1; ++h) { 2727 PetscInt pStart, pEnd, i; 2728 2729 ierr = DMPlexGetHeightStratum(dm, h, &pStart, &pEnd);CHKERRQ(ierr); 2730 for (i = offsets[p*(height+2)+h]; i < closureSize; ++i) { 2731 if ((pStart > closures[p][i*2]) || (pEnd <= closures[p][i*2])) { 2732 offsets[p*(height+2)+h+1] = i; 2733 break; 2734 } 2735 } 2736 if (i == closureSize) offsets[p*(height+2)+h+1] = i; 2737 } 2738 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); 2739 } 2740 for (h = 0; h < height+1; ++h) { 2741 PetscInt dof; 2742 2743 /* Copy in cone of first point */ 2744 dof = offsets[h+1] - offsets[h]; 2745 for (meetSize = 0; meetSize < dof; ++meetSize) { 2746 meet[i][meetSize] = closures[0][(offsets[h]+meetSize)*2]; 2747 } 2748 /* Check each successive cone */ 2749 for (p = 1; p < numPoints && meetSize; ++p) { 2750 PetscInt newMeetSize = 0; 2751 2752 dof = offsets[p*(height+2)+h+1] - offsets[p*(height+2)+h]; 2753 for (c = 0; c < dof; ++c) { 2754 const PetscInt point = closures[p][(offsets[p*(height+2)+h]+c)*2]; 2755 2756 for (m = 0; m < meetSize; ++m) { 2757 if (point == meet[i][m]) { 2758 meet[1-i][newMeetSize++] = point; 2759 break; 2760 } 2761 } 2762 } 2763 meetSize = newMeetSize; 2764 i = 1-i; 2765 } 2766 if (meetSize) break; 2767 } 2768 *numCoveredPoints = meetSize; 2769 *coveredPoints = meet[i]; 2770 for (p = 0; p < numPoints; ++p) { 2771 ierr = DMPlexRestoreTransitiveClosure(dm, points[p], PETSC_TRUE, NULL, &closures[p]);CHKERRQ(ierr); 2772 } 2773 ierr = PetscFree(closures);CHKERRQ(ierr); 2774 ierr = DMRestoreWorkArray(dm, numPoints*(height+2), PETSC_INT, &offsets);CHKERRQ(ierr); 2775 ierr = DMRestoreWorkArray(dm, mesh->maxConeSize, PETSC_INT, &meet[1-i]);CHKERRQ(ierr); 2776 PetscFunctionReturn(0); 2777 } 2778 2779 /*@C 2780 DMPlexEqual - Determine if two DMs have the same topology 2781 2782 Not Collective 2783 2784 Input Parameters: 2785 + dmA - A DMPlex object 2786 - dmB - A DMPlex object 2787 2788 Output Parameters: 2789 . equal - PETSC_TRUE if the topologies are identical 2790 2791 Level: intermediate 2792 2793 Notes: 2794 We are not solving graph isomorphism, so we do not permutation. 2795 2796 .keywords: mesh 2797 .seealso: DMPlexGetCone() 2798 @*/ 2799 PetscErrorCode DMPlexEqual(DM dmA, DM dmB, PetscBool *equal) 2800 { 2801 PetscInt depth, depthB, pStart, pEnd, pStartB, pEndB, p; 2802 PetscErrorCode ierr; 2803 2804 PetscFunctionBegin; 2805 PetscValidHeaderSpecific(dmA, DM_CLASSID, 1); 2806 PetscValidHeaderSpecific(dmB, DM_CLASSID, 2); 2807 PetscValidPointer(equal, 3); 2808 2809 *equal = PETSC_FALSE; 2810 ierr = DMPlexGetDepth(dmA, &depth);CHKERRQ(ierr); 2811 ierr = DMPlexGetDepth(dmB, &depthB);CHKERRQ(ierr); 2812 if (depth != depthB) PetscFunctionReturn(0); 2813 ierr = DMPlexGetChart(dmA, &pStart, &pEnd);CHKERRQ(ierr); 2814 ierr = DMPlexGetChart(dmB, &pStartB, &pEndB);CHKERRQ(ierr); 2815 if ((pStart != pStartB) || (pEnd != pEndB)) PetscFunctionReturn(0); 2816 for (p = pStart; p < pEnd; ++p) { 2817 const PetscInt *cone, *coneB, *ornt, *orntB, *support, *supportB; 2818 PetscInt coneSize, coneSizeB, c, supportSize, supportSizeB, s; 2819 2820 ierr = DMPlexGetConeSize(dmA, p, &coneSize);CHKERRQ(ierr); 2821 ierr = DMPlexGetCone(dmA, p, &cone);CHKERRQ(ierr); 2822 ierr = DMPlexGetConeOrientation(dmA, p, &ornt);CHKERRQ(ierr); 2823 ierr = DMPlexGetConeSize(dmB, p, &coneSizeB);CHKERRQ(ierr); 2824 ierr = DMPlexGetCone(dmB, p, &coneB);CHKERRQ(ierr); 2825 ierr = DMPlexGetConeOrientation(dmB, p, &orntB);CHKERRQ(ierr); 2826 if (coneSize != coneSizeB) PetscFunctionReturn(0); 2827 for (c = 0; c < coneSize; ++c) { 2828 if (cone[c] != coneB[c]) PetscFunctionReturn(0); 2829 if (ornt[c] != orntB[c]) PetscFunctionReturn(0); 2830 } 2831 ierr = DMPlexGetSupportSize(dmA, p, &supportSize);CHKERRQ(ierr); 2832 ierr = DMPlexGetSupport(dmA, p, &support);CHKERRQ(ierr); 2833 ierr = DMPlexGetSupportSize(dmB, p, &supportSizeB);CHKERRQ(ierr); 2834 ierr = DMPlexGetSupport(dmB, p, &supportB);CHKERRQ(ierr); 2835 if (supportSize != supportSizeB) PetscFunctionReturn(0); 2836 for (s = 0; s < supportSize; ++s) { 2837 if (support[s] != supportB[s]) PetscFunctionReturn(0); 2838 } 2839 } 2840 *equal = PETSC_TRUE; 2841 PetscFunctionReturn(0); 2842 } 2843 2844 /*@C 2845 DMPlexGetNumFaceVertices - Returns the number of vertices on a face 2846 2847 Not Collective 2848 2849 Input Parameters: 2850 + dm - The DMPlex 2851 . cellDim - The cell dimension 2852 - numCorners - The number of vertices on a cell 2853 2854 Output Parameters: 2855 . numFaceVertices - The number of vertices on a face 2856 2857 Level: developer 2858 2859 Notes: 2860 Of course this can only work for a restricted set of symmetric shapes 2861 2862 .seealso: DMPlexGetCone() 2863 @*/ 2864 PetscErrorCode DMPlexGetNumFaceVertices(DM dm, PetscInt cellDim, PetscInt numCorners, PetscInt *numFaceVertices) 2865 { 2866 MPI_Comm comm; 2867 PetscErrorCode ierr; 2868 2869 PetscFunctionBegin; 2870 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2871 PetscValidPointer(numFaceVertices,3); 2872 switch (cellDim) { 2873 case 0: 2874 *numFaceVertices = 0; 2875 break; 2876 case 1: 2877 *numFaceVertices = 1; 2878 break; 2879 case 2: 2880 switch (numCorners) { 2881 case 3: /* triangle */ 2882 *numFaceVertices = 2; /* Edge has 2 vertices */ 2883 break; 2884 case 4: /* quadrilateral */ 2885 *numFaceVertices = 2; /* Edge has 2 vertices */ 2886 break; 2887 case 6: /* quadratic triangle, tri and quad cohesive Lagrange cells */ 2888 *numFaceVertices = 3; /* Edge has 3 vertices */ 2889 break; 2890 case 9: /* quadratic quadrilateral, quadratic quad cohesive Lagrange cells */ 2891 *numFaceVertices = 3; /* Edge has 3 vertices */ 2892 break; 2893 default: 2894 SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %D for dimension %D", numCorners, cellDim); 2895 } 2896 break; 2897 case 3: 2898 switch (numCorners) { 2899 case 4: /* tetradehdron */ 2900 *numFaceVertices = 3; /* Face has 3 vertices */ 2901 break; 2902 case 6: /* tet cohesive cells */ 2903 *numFaceVertices = 4; /* Face has 4 vertices */ 2904 break; 2905 case 8: /* hexahedron */ 2906 *numFaceVertices = 4; /* Face has 4 vertices */ 2907 break; 2908 case 9: /* tet cohesive Lagrange cells */ 2909 *numFaceVertices = 6; /* Face has 6 vertices */ 2910 break; 2911 case 10: /* quadratic tetrahedron */ 2912 *numFaceVertices = 6; /* Face has 6 vertices */ 2913 break; 2914 case 12: /* hex cohesive Lagrange cells */ 2915 *numFaceVertices = 6; /* Face has 6 vertices */ 2916 break; 2917 case 18: /* quadratic tet cohesive Lagrange cells */ 2918 *numFaceVertices = 6; /* Face has 6 vertices */ 2919 break; 2920 case 27: /* quadratic hexahedron, quadratic hex cohesive Lagrange cells */ 2921 *numFaceVertices = 9; /* Face has 9 vertices */ 2922 break; 2923 default: 2924 SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of face corners %D for dimension %D", numCorners, cellDim); 2925 } 2926 break; 2927 default: 2928 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid cell dimension %D", cellDim); 2929 } 2930 PetscFunctionReturn(0); 2931 } 2932 2933 /*@ 2934 DMPlexGetDepthLabel - Get the DMLabel recording the depth of each point 2935 2936 Not Collective 2937 2938 Input Parameter: 2939 . dm - The DMPlex object 2940 2941 Output Parameter: 2942 . depthLabel - The DMLabel recording point depth 2943 2944 Level: developer 2945 2946 .keywords: mesh, points 2947 .seealso: DMPlexGetDepth(), DMPlexGetHeightStratum(), DMPlexGetDepthStratum() 2948 @*/ 2949 PetscErrorCode DMPlexGetDepthLabel(DM dm, DMLabel *depthLabel) 2950 { 2951 PetscErrorCode ierr; 2952 2953 PetscFunctionBegin; 2954 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2955 PetscValidPointer(depthLabel, 2); 2956 if (!dm->depthLabel) {ierr = DMGetLabel(dm, "depth", &dm->depthLabel);CHKERRQ(ierr);} 2957 *depthLabel = dm->depthLabel; 2958 PetscFunctionReturn(0); 2959 } 2960 2961 /*@ 2962 DMPlexGetDepth - Get the depth of the DAG representing this mesh 2963 2964 Not Collective 2965 2966 Input Parameter: 2967 . dm - The DMPlex object 2968 2969 Output Parameter: 2970 . depth - The number of strata (breadth first levels) in the DAG 2971 2972 Level: developer 2973 2974 .keywords: mesh, points 2975 .seealso: DMPlexGetDepthLabel(), DMPlexGetHeightStratum(), DMPlexGetDepthStratum() 2976 @*/ 2977 PetscErrorCode DMPlexGetDepth(DM dm, PetscInt *depth) 2978 { 2979 DMLabel label; 2980 PetscInt d = 0; 2981 PetscErrorCode ierr; 2982 2983 PetscFunctionBegin; 2984 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2985 PetscValidPointer(depth, 2); 2986 ierr = DMPlexGetDepthLabel(dm, &label);CHKERRQ(ierr); 2987 if (label) {ierr = DMLabelGetNumValues(label, &d);CHKERRQ(ierr);} 2988 *depth = d-1; 2989 PetscFunctionReturn(0); 2990 } 2991 2992 /*@ 2993 DMPlexGetDepthStratum - Get the bounds [start, end) for all points at a certain depth. 2994 2995 Not Collective 2996 2997 Input Parameters: 2998 + dm - The DMPlex object 2999 - stratumValue - The requested depth 3000 3001 Output Parameters: 3002 + start - The first point at this depth 3003 - end - One beyond the last point at this depth 3004 3005 Level: developer 3006 3007 .keywords: mesh, points 3008 .seealso: DMPlexGetHeightStratum(), DMPlexGetDepth() 3009 @*/ 3010 PetscErrorCode DMPlexGetDepthStratum(DM dm, PetscInt stratumValue, PetscInt *start, PetscInt *end) 3011 { 3012 DMLabel label; 3013 PetscInt pStart, pEnd; 3014 PetscErrorCode ierr; 3015 3016 PetscFunctionBegin; 3017 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3018 if (start) {PetscValidPointer(start, 3); *start = 0;} 3019 if (end) {PetscValidPointer(end, 4); *end = 0;} 3020 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 3021 if (pStart == pEnd) PetscFunctionReturn(0); 3022 if (stratumValue < 0) { 3023 if (start) *start = pStart; 3024 if (end) *end = pEnd; 3025 PetscFunctionReturn(0); 3026 } 3027 ierr = DMPlexGetDepthLabel(dm, &label);CHKERRQ(ierr); 3028 if (!label) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "No label named depth was found"); 3029 ierr = DMLabelGetStratumBounds(label, stratumValue, start, end);CHKERRQ(ierr); 3030 PetscFunctionReturn(0); 3031 } 3032 3033 /*@ 3034 DMPlexGetHeightStratum - Get the bounds [start, end) for all points at a certain height. 3035 3036 Not Collective 3037 3038 Input Parameters: 3039 + dm - The DMPlex object 3040 - stratumValue - The requested height 3041 3042 Output Parameters: 3043 + start - The first point at this height 3044 - end - One beyond the last point at this height 3045 3046 Level: developer 3047 3048 .keywords: mesh, points 3049 .seealso: DMPlexGetDepthStratum(), DMPlexGetDepth() 3050 @*/ 3051 PetscErrorCode DMPlexGetHeightStratum(DM dm, PetscInt stratumValue, PetscInt *start, PetscInt *end) 3052 { 3053 DMLabel label; 3054 PetscInt depth, pStart, pEnd; 3055 PetscErrorCode ierr; 3056 3057 PetscFunctionBegin; 3058 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3059 if (start) {PetscValidPointer(start, 3); *start = 0;} 3060 if (end) {PetscValidPointer(end, 4); *end = 0;} 3061 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 3062 if (pStart == pEnd) PetscFunctionReturn(0); 3063 if (stratumValue < 0) { 3064 if (start) *start = pStart; 3065 if (end) *end = pEnd; 3066 PetscFunctionReturn(0); 3067 } 3068 ierr = DMPlexGetDepthLabel(dm, &label);CHKERRQ(ierr); 3069 if (!label) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "No label named depth was found"); 3070 ierr = DMLabelGetNumValues(label, &depth);CHKERRQ(ierr); 3071 ierr = DMLabelGetStratumBounds(label, depth-1-stratumValue, start, end);CHKERRQ(ierr); 3072 PetscFunctionReturn(0); 3073 } 3074 3075 /* Set the number of dof on each point and separate by fields */ 3076 static PetscErrorCode DMPlexCreateSectionInitial(DM dm, PetscInt dim, PetscInt numFields,const PetscInt numComp[],const PetscInt numDof[], PetscSection *section) 3077 { 3078 PetscInt *pMax; 3079 PetscInt depth, pStart = 0, pEnd = 0; 3080 PetscInt Nf, p, d, dep, f; 3081 PetscBool *isFE; 3082 PetscErrorCode ierr; 3083 3084 PetscFunctionBegin; 3085 ierr = PetscMalloc1(numFields, &isFE);CHKERRQ(ierr); 3086 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 3087 for (f = 0; f < numFields; ++f) { 3088 PetscObject obj; 3089 PetscClassId id; 3090 3091 isFE[f] = PETSC_FALSE; 3092 if (f >= Nf) continue; 3093 ierr = DMGetField(dm, f, &obj);CHKERRQ(ierr); 3094 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 3095 if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} 3096 else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} 3097 } 3098 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), section);CHKERRQ(ierr); 3099 if (numFields > 0) { 3100 ierr = PetscSectionSetNumFields(*section, numFields);CHKERRQ(ierr); 3101 if (numComp) { 3102 for (f = 0; f < numFields; ++f) { 3103 ierr = PetscSectionSetFieldComponents(*section, f, numComp[f]);CHKERRQ(ierr); 3104 if (isFE[f]) { 3105 PetscFE fe; 3106 PetscDualSpace dspace; 3107 const PetscInt ***perms; 3108 const PetscScalar ***flips; 3109 const PetscInt *numDof; 3110 3111 ierr = DMGetField(dm,f,(PetscObject *) &fe);CHKERRQ(ierr); 3112 ierr = PetscFEGetDualSpace(fe,&dspace);CHKERRQ(ierr); 3113 ierr = PetscDualSpaceGetSymmetries(dspace,&perms,&flips);CHKERRQ(ierr); 3114 ierr = PetscDualSpaceGetNumDof(dspace,&numDof);CHKERRQ(ierr); 3115 if (perms || flips) { 3116 DM K; 3117 DMLabel depthLabel; 3118 PetscInt depth, h; 3119 PetscSectionSym sym; 3120 3121 ierr = PetscDualSpaceGetDM(dspace,&K);CHKERRQ(ierr); 3122 ierr = DMPlexGetDepthLabel(dm,&depthLabel);CHKERRQ(ierr); 3123 ierr = DMPlexGetDepth(dm,&depth);CHKERRQ(ierr); 3124 ierr = PetscSectionSymCreateLabel(PetscObjectComm((PetscObject)*section),depthLabel,&sym);CHKERRQ(ierr); 3125 for (h = 0; h <= depth; h++) { 3126 PetscDualSpace hspace; 3127 PetscInt kStart, kEnd; 3128 PetscInt kConeSize; 3129 const PetscInt **perms0 = NULL; 3130 const PetscScalar **flips0 = NULL; 3131 3132 ierr = PetscDualSpaceGetHeightSubspace(dspace,h,&hspace);CHKERRQ(ierr); 3133 ierr = DMPlexGetHeightStratum(K,h,&kStart,&kEnd);CHKERRQ(ierr); 3134 if (!hspace) continue; 3135 ierr = PetscDualSpaceGetSymmetries(hspace,&perms,&flips);CHKERRQ(ierr); 3136 if (perms) perms0 = perms[0]; 3137 if (flips) flips0 = flips[0]; 3138 if (!(perms0 || flips0)) continue; 3139 ierr = DMPlexGetConeSize(K,kStart,&kConeSize);CHKERRQ(ierr); 3140 ierr = PetscSectionSymLabelSetStratum(sym,depth - h,numDof[depth - h],-kConeSize,kConeSize,PETSC_USE_POINTER,perms0 ? &perms0[-kConeSize] : NULL,flips0 ? &flips0[-kConeSize] : NULL);CHKERRQ(ierr); 3141 } 3142 ierr = PetscSectionSetFieldSym(*section,f,sym);CHKERRQ(ierr); 3143 ierr = PetscSectionSymDestroy(&sym);CHKERRQ(ierr); 3144 } 3145 } 3146 } 3147 } 3148 } 3149 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 3150 ierr = PetscSectionSetChart(*section, pStart, pEnd);CHKERRQ(ierr); 3151 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 3152 ierr = PetscMalloc1(depth+1,&pMax);CHKERRQ(ierr); 3153 ierr = DMPlexGetHybridBounds(dm, depth >= 0 ? &pMax[depth] : NULL, depth>1 ? &pMax[depth-1] : NULL, depth>2 ? &pMax[1] : NULL, &pMax[0]);CHKERRQ(ierr); 3154 for (dep = 0; dep <= depth; ++dep) { 3155 d = dim == depth ? dep : (!dep ? 0 : dim); 3156 ierr = DMPlexGetDepthStratum(dm, dep, &pStart, &pEnd);CHKERRQ(ierr); 3157 pMax[dep] = pMax[dep] < 0 ? pEnd : pMax[dep]; 3158 for (p = pStart; p < pEnd; ++p) { 3159 PetscInt tot = 0; 3160 3161 for (f = 0; f < numFields; ++f) { 3162 if (isFE[f] && p >= pMax[dep]) continue; 3163 ierr = PetscSectionSetFieldDof(*section, p, f, numDof[f*(dim+1)+d]);CHKERRQ(ierr); 3164 tot += numDof[f*(dim+1)+d]; 3165 } 3166 ierr = PetscSectionSetDof(*section, p, tot);CHKERRQ(ierr); 3167 } 3168 } 3169 ierr = PetscFree(pMax);CHKERRQ(ierr); 3170 ierr = PetscFree(isFE);CHKERRQ(ierr); 3171 PetscFunctionReturn(0); 3172 } 3173 3174 /* Set the number of dof on each point and separate by fields 3175 If bcComps is NULL or the IS is NULL, constrain every dof on the point 3176 */ 3177 static PetscErrorCode DMPlexCreateSectionBCDof(DM dm, PetscInt numBC, const PetscInt bcField[], const IS bcComps[], const IS bcPoints[], PetscSection section) 3178 { 3179 PetscInt numFields; 3180 PetscInt bc; 3181 PetscSection aSec; 3182 PetscErrorCode ierr; 3183 3184 PetscFunctionBegin; 3185 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 3186 for (bc = 0; bc < numBC; ++bc) { 3187 PetscInt field = 0; 3188 const PetscInt *comp; 3189 const PetscInt *idx; 3190 PetscInt Nc = -1, n, i; 3191 3192 if (numFields) field = bcField[bc]; 3193 if (bcComps && bcComps[bc]) {ierr = ISGetLocalSize(bcComps[bc], &Nc);CHKERRQ(ierr);} 3194 if (bcComps && bcComps[bc]) {ierr = ISGetIndices(bcComps[bc], &comp);CHKERRQ(ierr);} 3195 ierr = ISGetLocalSize(bcPoints[bc], &n);CHKERRQ(ierr); 3196 ierr = ISGetIndices(bcPoints[bc], &idx);CHKERRQ(ierr); 3197 for (i = 0; i < n; ++i) { 3198 const PetscInt p = idx[i]; 3199 PetscInt numConst; 3200 3201 if (numFields) { 3202 ierr = PetscSectionGetFieldDof(section, p, field, &numConst);CHKERRQ(ierr); 3203 } else { 3204 ierr = PetscSectionGetDof(section, p, &numConst);CHKERRQ(ierr); 3205 } 3206 /* If Nc < 0, constrain every dof on the point */ 3207 if (Nc > 0) numConst = PetscMin(numConst, Nc); 3208 if (numFields) {ierr = PetscSectionAddFieldConstraintDof(section, p, field, numConst);CHKERRQ(ierr);} 3209 ierr = PetscSectionAddConstraintDof(section, p, numConst);CHKERRQ(ierr); 3210 } 3211 ierr = ISRestoreIndices(bcPoints[bc], &idx);CHKERRQ(ierr); 3212 if (bcComps && bcComps[bc]) {ierr = ISRestoreIndices(bcComps[bc], &comp);CHKERRQ(ierr);} 3213 } 3214 ierr = DMPlexGetAnchors(dm, &aSec, NULL);CHKERRQ(ierr); 3215 if (aSec) { 3216 PetscInt aStart, aEnd, a; 3217 3218 ierr = PetscSectionGetChart(aSec, &aStart, &aEnd);CHKERRQ(ierr); 3219 for (a = aStart; a < aEnd; a++) { 3220 PetscInt dof, f; 3221 3222 ierr = PetscSectionGetDof(aSec, a, &dof);CHKERRQ(ierr); 3223 if (dof) { 3224 /* if there are point-to-point constraints, then all dofs are constrained */ 3225 ierr = PetscSectionGetDof(section, a, &dof);CHKERRQ(ierr); 3226 ierr = PetscSectionSetConstraintDof(section, a, dof);CHKERRQ(ierr); 3227 for (f = 0; f < numFields; f++) { 3228 ierr = PetscSectionGetFieldDof(section, a, f, &dof);CHKERRQ(ierr); 3229 ierr = PetscSectionSetFieldConstraintDof(section, a, f, dof);CHKERRQ(ierr); 3230 } 3231 } 3232 } 3233 } 3234 PetscFunctionReturn(0); 3235 } 3236 3237 /* Set the constrained field indices on each point 3238 If bcComps is NULL or the IS is NULL, constrain every dof on the point 3239 */ 3240 static PetscErrorCode DMPlexCreateSectionBCIndicesField(DM dm, PetscInt numBC,const PetscInt bcField[], const IS bcComps[], const IS bcPoints[], PetscSection section) 3241 { 3242 PetscSection aSec; 3243 PetscInt *indices; 3244 PetscInt numFields, cdof, maxDof = 0, pStart, pEnd, p, bc, f, d; 3245 PetscErrorCode ierr; 3246 3247 PetscFunctionBegin; 3248 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 3249 if (!numFields) PetscFunctionReturn(0); 3250 /* Initialize all field indices to -1 */ 3251 ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); 3252 for (p = pStart; p < pEnd; ++p) {ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr); maxDof = PetscMax(maxDof, cdof);} 3253 ierr = PetscMalloc1(maxDof, &indices);CHKERRQ(ierr); 3254 for (d = 0; d < maxDof; ++d) indices[d] = -1; 3255 for (p = pStart; p < pEnd; ++p) for (f = 0; f < numFields; ++f) {ierr = PetscSectionSetFieldConstraintIndices(section, p, f, indices);CHKERRQ(ierr);} 3256 /* Handle BC constraints */ 3257 for (bc = 0; bc < numBC; ++bc) { 3258 const PetscInt field = bcField[bc]; 3259 const PetscInt *comp, *idx; 3260 PetscInt Nc = -1, n, i; 3261 3262 if (bcComps && bcComps[bc]) {ierr = ISGetLocalSize(bcComps[bc], &Nc);CHKERRQ(ierr);} 3263 if (bcComps && bcComps[bc]) {ierr = ISGetIndices(bcComps[bc], &comp);CHKERRQ(ierr);} 3264 ierr = ISGetLocalSize(bcPoints[bc], &n);CHKERRQ(ierr); 3265 ierr = ISGetIndices(bcPoints[bc], &idx);CHKERRQ(ierr); 3266 for (i = 0; i < n; ++i) { 3267 const PetscInt p = idx[i]; 3268 const PetscInt *find; 3269 PetscInt fdof, fcdof, c; 3270 3271 ierr = PetscSectionGetFieldDof(section, p, field, &fdof);CHKERRQ(ierr); 3272 if (!fdof) continue; 3273 if (Nc < 0) { 3274 for (d = 0; d < fdof; ++d) indices[d] = d; 3275 fcdof = fdof; 3276 } else { 3277 ierr = PetscSectionGetFieldConstraintDof(section, p, field, &fcdof);CHKERRQ(ierr); 3278 ierr = PetscSectionGetFieldConstraintIndices(section, p, field, &find);CHKERRQ(ierr); 3279 for (d = 0; d < fcdof; ++d) {if (find[d] < 0) break; indices[d] = find[d];} 3280 for (c = 0; c < Nc; ++c) indices[d++] = comp[c]; 3281 ierr = PetscSortRemoveDupsInt(&d, indices);CHKERRQ(ierr); 3282 for (c = d; c < fcdof; ++c) indices[c] = -1; 3283 fcdof = d; 3284 } 3285 ierr = PetscSectionSetFieldConstraintDof(section, p, field, fcdof);CHKERRQ(ierr); 3286 ierr = PetscSectionSetFieldConstraintIndices(section, p, field, indices);CHKERRQ(ierr); 3287 } 3288 if (bcComps && bcComps[bc]) {ierr = ISRestoreIndices(bcComps[bc], &comp);CHKERRQ(ierr);} 3289 ierr = ISRestoreIndices(bcPoints[bc], &idx);CHKERRQ(ierr); 3290 } 3291 /* Handle anchors */ 3292 ierr = DMPlexGetAnchors(dm, &aSec, NULL);CHKERRQ(ierr); 3293 if (aSec) { 3294 PetscInt aStart, aEnd, a; 3295 3296 for (d = 0; d < maxDof; ++d) indices[d] = d; 3297 ierr = PetscSectionGetChart(aSec, &aStart, &aEnd);CHKERRQ(ierr); 3298 for (a = aStart; a < aEnd; a++) { 3299 PetscInt dof, f; 3300 3301 ierr = PetscSectionGetDof(aSec, a, &dof);CHKERRQ(ierr); 3302 if (dof) { 3303 /* if there are point-to-point constraints, then all dofs are constrained */ 3304 for (f = 0; f < numFields; f++) { 3305 ierr = PetscSectionSetFieldConstraintIndices(section, a, f, indices);CHKERRQ(ierr); 3306 } 3307 } 3308 } 3309 } 3310 ierr = PetscFree(indices);CHKERRQ(ierr); 3311 PetscFunctionReturn(0); 3312 } 3313 3314 /* Set the constrained indices on each point */ 3315 static PetscErrorCode DMPlexCreateSectionBCIndices(DM dm, PetscSection section) 3316 { 3317 PetscInt *indices; 3318 PetscInt numFields, maxDof, pStart, pEnd, p, f, d; 3319 PetscErrorCode ierr; 3320 3321 PetscFunctionBegin; 3322 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 3323 ierr = PetscSectionGetMaxDof(section, &maxDof);CHKERRQ(ierr); 3324 ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); 3325 ierr = PetscMalloc1(maxDof, &indices);CHKERRQ(ierr); 3326 for (d = 0; d < maxDof; ++d) indices[d] = -1; 3327 for (p = pStart; p < pEnd; ++p) { 3328 PetscInt cdof, d; 3329 3330 ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr); 3331 if (cdof) { 3332 if (numFields) { 3333 PetscInt numConst = 0, foff = 0; 3334 3335 for (f = 0; f < numFields; ++f) { 3336 const PetscInt *find; 3337 PetscInt fcdof, fdof; 3338 3339 ierr = PetscSectionGetFieldDof(section, p, f, &fdof);CHKERRQ(ierr); 3340 ierr = PetscSectionGetFieldConstraintDof(section, p, f, &fcdof);CHKERRQ(ierr); 3341 /* Change constraint numbering from field component to local dof number */ 3342 ierr = PetscSectionGetFieldConstraintIndices(section, p, f, &find);CHKERRQ(ierr); 3343 for (d = 0; d < fcdof; ++d) indices[numConst+d] = find[d] + foff; 3344 numConst += fcdof; 3345 foff += fdof; 3346 } 3347 if (cdof != numConst) {ierr = PetscSectionSetConstraintDof(section, p, numConst);CHKERRQ(ierr);} 3348 } else { 3349 for (d = 0; d < cdof; ++d) indices[d] = d; 3350 } 3351 ierr = PetscSectionSetConstraintIndices(section, p, indices);CHKERRQ(ierr); 3352 } 3353 } 3354 ierr = PetscFree(indices);CHKERRQ(ierr); 3355 PetscFunctionReturn(0); 3356 } 3357 3358 /*@C 3359 DMPlexCreateSection - Create a PetscSection based upon the dof layout specification provided. 3360 3361 Not Collective 3362 3363 Input Parameters: 3364 + dm - The DMPlex object 3365 . dim - The spatial dimension of the problem 3366 . numFields - The number of fields in the problem 3367 . numComp - An array of size numFields that holds the number of components for each field 3368 . numDof - An array of size numFields*(dim+1) which holds the number of dof for each field on a mesh piece of dimension d 3369 . numBC - The number of boundary conditions 3370 . bcField - An array of size numBC giving the field number for each boundry condition 3371 . bcComps - [Optional] An array of size numBC giving an IS holding the field components to which each boundary condition applies 3372 . bcPoints - An array of size numBC giving an IS holding the Plex points to which each boundary condition applies 3373 - perm - Optional permutation of the chart, or NULL 3374 3375 Output Parameter: 3376 . section - The PetscSection object 3377 3378 Notes: numDof[f*(dim+1)+d] gives the number of dof for field f on points of dimension d. For instance, numDof[1] is the 3379 number of dof for field 0 on each edge. 3380 3381 The chart permutation is the same one set using PetscSectionSetPermutation() 3382 3383 Level: developer 3384 3385 Fortran Notes: 3386 A Fortran 90 version is available as DMPlexCreateSectionF90() 3387 3388 .keywords: mesh, elements 3389 .seealso: DMPlexCreate(), PetscSectionCreate(), PetscSectionSetPermutation() 3390 @*/ 3391 PetscErrorCode DMPlexCreateSection(DM dm, PetscInt dim, PetscInt numFields,const PetscInt numComp[],const PetscInt numDof[], PetscInt numBC,const PetscInt bcField[], const IS bcComps[], const IS bcPoints[], IS perm, PetscSection *section) 3392 { 3393 PetscSection aSec; 3394 PetscErrorCode ierr; 3395 3396 PetscFunctionBegin; 3397 ierr = DMPlexCreateSectionInitial(dm, dim, numFields, numComp, numDof, section);CHKERRQ(ierr); 3398 ierr = DMPlexCreateSectionBCDof(dm, numBC, bcField, bcComps, bcPoints, *section);CHKERRQ(ierr); 3399 if (perm) {ierr = PetscSectionSetPermutation(*section, perm);CHKERRQ(ierr);} 3400 ierr = PetscSectionSetUp(*section);CHKERRQ(ierr); 3401 ierr = DMPlexGetAnchors(dm,&aSec,NULL);CHKERRQ(ierr); 3402 if (numBC || aSec) { 3403 ierr = DMPlexCreateSectionBCIndicesField(dm, numBC, bcField, bcComps, bcPoints, *section);CHKERRQ(ierr); 3404 ierr = DMPlexCreateSectionBCIndices(dm, *section);CHKERRQ(ierr); 3405 } 3406 ierr = PetscSectionViewFromOptions(*section,NULL,"-section_view");CHKERRQ(ierr); 3407 PetscFunctionReturn(0); 3408 } 3409 3410 PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm) 3411 { 3412 PetscSection section, s; 3413 Mat m; 3414 PetscInt maxHeight; 3415 PetscErrorCode ierr; 3416 3417 PetscFunctionBegin; 3418 ierr = DMClone(dm, cdm);CHKERRQ(ierr); 3419 ierr = DMPlexGetMaxProjectionHeight(dm, &maxHeight);CHKERRQ(ierr); 3420 ierr = DMPlexSetMaxProjectionHeight(*cdm, maxHeight);CHKERRQ(ierr); 3421 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ion);CHKERRQ(ierr); 3422 ierr = DMSetDefaultSection(*cdm, section);CHKERRQ(ierr); 3423 ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr); 3424 ierr = PetscSectionCreate(PETSC_COMM_SELF, &s);CHKERRQ(ierr); 3425 ierr = MatCreate(PETSC_COMM_SELF, &m);CHKERRQ(ierr); 3426 ierr = DMSetDefaultConstraints(*cdm, s, m);CHKERRQ(ierr); 3427 ierr = PetscSectionDestroy(&s);CHKERRQ(ierr); 3428 ierr = MatDestroy(&m);CHKERRQ(ierr); 3429 PetscFunctionReturn(0); 3430 } 3431 3432 /*@C 3433 DMPlexGetConeSection - Return a section which describes the layout of cone data 3434 3435 Not Collective 3436 3437 Input Parameters: 3438 . dm - The DMPlex object 3439 3440 Output Parameter: 3441 . section - The PetscSection object 3442 3443 Level: developer 3444 3445 .seealso: DMPlexGetSupportSection(), DMPlexGetCones(), DMPlexGetConeOrientations() 3446 @*/ 3447 PetscErrorCode DMPlexGetConeSection(DM dm, PetscSection *section) 3448 { 3449 DM_Plex *mesh = (DM_Plex*) dm->data; 3450 3451 PetscFunctionBegin; 3452 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3453 if (section) *section = mesh->coneSection; 3454 PetscFunctionReturn(0); 3455 } 3456 3457 /*@C 3458 DMPlexGetSupportSection - Return a section which describes the layout of support data 3459 3460 Not Collective 3461 3462 Input Parameters: 3463 . dm - The DMPlex object 3464 3465 Output Parameter: 3466 . section - The PetscSection object 3467 3468 Level: developer 3469 3470 .seealso: DMPlexGetConeSection() 3471 @*/ 3472 PetscErrorCode DMPlexGetSupportSection(DM dm, PetscSection *section) 3473 { 3474 DM_Plex *mesh = (DM_Plex*) dm->data; 3475 3476 PetscFunctionBegin; 3477 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3478 if (section) *section = mesh->supportSection; 3479 PetscFunctionReturn(0); 3480 } 3481 3482 /*@C 3483 DMPlexGetCones - Return cone data 3484 3485 Not Collective 3486 3487 Input Parameters: 3488 . dm - The DMPlex object 3489 3490 Output Parameter: 3491 . cones - The cone for each point 3492 3493 Level: developer 3494 3495 .seealso: DMPlexGetConeSection() 3496 @*/ 3497 PetscErrorCode DMPlexGetCones(DM dm, PetscInt *cones[]) 3498 { 3499 DM_Plex *mesh = (DM_Plex*) dm->data; 3500 3501 PetscFunctionBegin; 3502 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3503 if (cones) *cones = mesh->cones; 3504 PetscFunctionReturn(0); 3505 } 3506 3507 /*@C 3508 DMPlexGetConeOrientations - Return cone orientation data 3509 3510 Not Collective 3511 3512 Input Parameters: 3513 . dm - The DMPlex object 3514 3515 Output Parameter: 3516 . coneOrientations - The cone orientation for each point 3517 3518 Level: developer 3519 3520 .seealso: DMPlexGetConeSection() 3521 @*/ 3522 PetscErrorCode DMPlexGetConeOrientations(DM dm, PetscInt *coneOrientations[]) 3523 { 3524 DM_Plex *mesh = (DM_Plex*) dm->data; 3525 3526 PetscFunctionBegin; 3527 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 3528 if (coneOrientations) *coneOrientations = mesh->coneOrientations; 3529 PetscFunctionReturn(0); 3530 } 3531 3532 /******************************** FEM Support **********************************/ 3533 3534 PetscErrorCode DMPlexCreateSpectralClosurePermutation(DM dm, PetscSection section) 3535 { 3536 PetscInt *perm; 3537 PetscInt dim, eStart, k, Nf, f, Nc, c, i, j, size = 0, offset = 0, foffset = 0; 3538 PetscErrorCode ierr; 3539 3540 PetscFunctionBegin; 3541 if (!section) {ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);} 3542 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3543 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 3544 if (dim <= 1) PetscFunctionReturn(0); 3545 for (f = 0; f < Nf; ++f) { 3546 /* An order k SEM disc has k-1 dofs on an edge */ 3547 ierr = DMPlexGetDepthStratum(dm, 1, &eStart, NULL);CHKERRQ(ierr); 3548 ierr = PetscSectionGetFieldDof(section, eStart, f, &k);CHKERRQ(ierr); 3549 ierr = PetscSectionGetFieldComponents(section, f, &Nc);CHKERRQ(ierr); 3550 k = k/Nc + 1; 3551 size += PetscPowInt(k+1, dim)*Nc; 3552 } 3553 ierr = PetscMalloc1(size, &perm);CHKERRQ(ierr); 3554 for (f = 0; f < Nf; ++f) { 3555 switch (dim) { 3556 case 2: 3557 /* The original quad closure is oriented clockwise, {f, e_b, e_r, e_t, e_l, v_lb, v_rb, v_tr, v_tl} */ 3558 ierr = DMPlexGetDepthStratum(dm, 1, &eStart, NULL);CHKERRQ(ierr); 3559 ierr = PetscSectionGetFieldDof(section, eStart, f, &k);CHKERRQ(ierr); 3560 ierr = PetscSectionGetFieldComponents(section, f, &Nc);CHKERRQ(ierr); 3561 k = k/Nc + 1; 3562 /* The SEM order is 3563 3564 v_lb, {e_b}, v_rb, 3565 e^{(k-1)-i}_l, {f^{i*(k-1)}}, e^i_r, 3566 v_lt, reverse {e_t}, v_rt 3567 */ 3568 { 3569 const PetscInt of = 0; 3570 const PetscInt oeb = of + PetscSqr(k-1); 3571 const PetscInt oer = oeb + (k-1); 3572 const PetscInt oet = oer + (k-1); 3573 const PetscInt oel = oet + (k-1); 3574 const PetscInt ovlb = oel + (k-1); 3575 const PetscInt ovrb = ovlb + 1; 3576 const PetscInt ovrt = ovrb + 1; 3577 const PetscInt ovlt = ovrt + 1; 3578 PetscInt o; 3579 3580 /* bottom */ 3581 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlb*Nc + c + foffset; 3582 for (o = oeb; o < oer; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 3583 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrb*Nc + c + foffset; 3584 /* middle */ 3585 for (i = 0; i < k-1; ++i) { 3586 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oel+(k-2)-i)*Nc + c + foffset; 3587 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; 3588 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oer+i)*Nc + c + foffset; 3589 } 3590 /* top */ 3591 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovlt*Nc + c + foffset; 3592 for (o = oel-1; o >= oet; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 3593 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovrt*Nc + c + foffset; 3594 foffset = offset; 3595 } 3596 break; 3597 case 3: 3598 /* The original hex closure is 3599 3600 {c, 3601 f_b, f_t, f_f, f_b, f_r, f_l, 3602 e_bl, e_bb, e_br, e_bf, e_tf, e_tr, e_tb, e_tl, e_rf, e_lf, e_lb, e_rb, 3603 v_blf, v_blb, v_brb, v_brf, v_tlf, v_trf, v_trb, v_tlb} 3604 */ 3605 ierr = DMPlexGetDepthStratum(dm, 1, &eStart, NULL);CHKERRQ(ierr); 3606 ierr = PetscSectionGetFieldDof(section, eStart, f, &k);CHKERRQ(ierr); 3607 ierr = PetscSectionGetFieldComponents(section, f, &Nc);CHKERRQ(ierr); 3608 k = k/Nc + 1; 3609 /* The SEM order is 3610 Bottom Slice 3611 v_blf, {e^{(k-1)-n}_bf}, v_brf, 3612 e^{i}_bl, f^{n*(k-1)+(k-1)-i}_b, e^{(k-1)-i}_br, 3613 v_blb, {e_bb}, v_brb, 3614 3615 Middle Slice (j) 3616 {e^{(k-1)-j}_lf}, {f^{j*(k-1)+n}_f}, e^j_rf, 3617 f^{i*(k-1)+j}_l, {c^{(j*(k-1) + i)*(k-1)+n}_t}, f^{j*(k-1)+i}_r, 3618 e^j_lb, {f^{j*(k-1)+(k-1)-n}_b}, e^{(k-1)-j}_rb, 3619 3620 Top Slice 3621 v_tlf, {e_tf}, v_trf, 3622 e^{(k-1)-i}_tl, {f^{i*(k-1)}_t}, e^{i}_tr, 3623 v_tlb, {e^{(k-1)-n}_tb}, v_trb, 3624 */ 3625 { 3626 const PetscInt oc = 0; 3627 const PetscInt ofb = oc + PetscSqr(k-1)*(k-1); 3628 const PetscInt oft = ofb + PetscSqr(k-1); 3629 const PetscInt off = oft + PetscSqr(k-1); 3630 const PetscInt ofk = off + PetscSqr(k-1); 3631 const PetscInt ofr = ofk + PetscSqr(k-1); 3632 const PetscInt ofl = ofr + PetscSqr(k-1); 3633 const PetscInt oebl = ofl + PetscSqr(k-1); 3634 const PetscInt oebb = oebl + (k-1); 3635 const PetscInt oebr = oebb + (k-1); 3636 const PetscInt oebf = oebr + (k-1); 3637 const PetscInt oetf = oebf + (k-1); 3638 const PetscInt oetr = oetf + (k-1); 3639 const PetscInt oetb = oetr + (k-1); 3640 const PetscInt oetl = oetb + (k-1); 3641 const PetscInt oerf = oetl + (k-1); 3642 const PetscInt oelf = oerf + (k-1); 3643 const PetscInt oelb = oelf + (k-1); 3644 const PetscInt oerb = oelb + (k-1); 3645 const PetscInt ovblf = oerb + (k-1); 3646 const PetscInt ovblb = ovblf + 1; 3647 const PetscInt ovbrb = ovblb + 1; 3648 const PetscInt ovbrf = ovbrb + 1; 3649 const PetscInt ovtlf = ovbrf + 1; 3650 const PetscInt ovtrf = ovtlf + 1; 3651 const PetscInt ovtrb = ovtrf + 1; 3652 const PetscInt ovtlb = ovtrb + 1; 3653 PetscInt o, n; 3654 3655 /* Bottom Slice */ 3656 /* bottom */ 3657 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblf*Nc + c + foffset; 3658 for (o = oetf-1; o >= oebf; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 3659 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrf*Nc + c + foffset; 3660 /* middle */ 3661 for (i = 0; i < k-1; ++i) { 3662 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebl+i)*Nc + c + foffset; 3663 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;} 3664 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oebr+(k-2)-i)*Nc + c + foffset; 3665 } 3666 /* top */ 3667 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovblb*Nc + c + foffset; 3668 for (o = oebb; o < oebr; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 3669 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovbrb*Nc + c + foffset; 3670 3671 /* Middle Slice */ 3672 for (j = 0; j < k-1; ++j) { 3673 /* bottom */ 3674 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelf+(k-2)-j)*Nc + c + foffset; 3675 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; 3676 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerf+j)*Nc + c + foffset; 3677 /* middle */ 3678 for (i = 0; i < k-1; ++i) { 3679 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofl+i*(k-1)+j)*Nc + c + foffset; 3680 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; 3681 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (ofr+j*(k-1)+i)*Nc + c + foffset; 3682 } 3683 /* top */ 3684 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oelb+j)*Nc + c + foffset; 3685 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; 3686 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oerb+(k-2)-j)*Nc + c + foffset; 3687 } 3688 3689 /* Top Slice */ 3690 /* bottom */ 3691 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlf*Nc + c + foffset; 3692 for (o = oetf; o < oetr; ++o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 3693 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrf*Nc + c + foffset; 3694 /* middle */ 3695 for (i = 0; i < k-1; ++i) { 3696 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetl+(k-2)-i)*Nc + c + foffset; 3697 for (n = 0; n < k-1; ++n) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oft+i*(k-1)+n)*Nc + c + foffset; 3698 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = (oetr+i)*Nc + c + foffset; 3699 } 3700 /* top */ 3701 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtlb*Nc + c + foffset; 3702 for (o = oetl-1; o >= oetb; --o) for (c = 0; c < Nc; ++c, ++offset) perm[offset] = o*Nc + c + foffset; 3703 for (c = 0; c < Nc; ++c, ++offset) perm[offset] = ovtrb*Nc + c + foffset; 3704 3705 foffset = offset; 3706 } 3707 break; 3708 default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No spectral ordering for dimension %D", dim); 3709 } 3710 } 3711 if (offset != size) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Number of permutation entries %D != %D", offset, size); 3712 /* Check permutation */ 3713 { 3714 PetscInt *check; 3715 3716 ierr = PetscMalloc1(size, &check);CHKERRQ(ierr); 3717 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]);} 3718 for (i = 0; i < size; ++i) check[perm[i]] = i; 3719 for (i = 0; i < size; ++i) {if (check[i] < 0) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Missing permutation index %D", i);} 3720 ierr = PetscFree(check);CHKERRQ(ierr); 3721 } 3722 ierr = PetscSectionSetClosurePermutation_Internal(section, (PetscObject) dm, size, PETSC_OWN_POINTER, perm);CHKERRQ(ierr); 3723 PetscFunctionReturn(0); 3724 } 3725 3726 PetscErrorCode DMPlexGetPointDualSpaceFEM(DM dm, PetscInt point, PetscInt field, PetscDualSpace *dspace) 3727 { 3728 PetscDS prob; 3729 PetscInt depth, Nf, h; 3730 DMLabel label; 3731 PetscErrorCode ierr; 3732 3733 PetscFunctionBeginHot; 3734 prob = dm->prob; 3735 Nf = prob->Nf; 3736 label = dm->depthLabel; 3737 *dspace = NULL; 3738 if (field < Nf) { 3739 PetscObject disc = prob->disc[field]; 3740 3741 if (disc->classid == PETSCFE_CLASSID) { 3742 PetscDualSpace dsp; 3743 3744 ierr = PetscFEGetDualSpace((PetscFE)disc,&dsp);CHKERRQ(ierr); 3745 ierr = DMLabelGetNumValues(label,&depth);CHKERRQ(ierr); 3746 ierr = DMLabelGetValue(label,point,&h);CHKERRQ(ierr); 3747 h = depth - 1 - h; 3748 if (h) { 3749 ierr = PetscDualSpaceGetHeightSubspace(dsp,h,dspace);CHKERRQ(ierr); 3750 } else { 3751 *dspace = dsp; 3752 } 3753 } 3754 } 3755 PetscFunctionReturn(0); 3756 } 3757 3758 3759 PETSC_STATIC_INLINE PetscErrorCode DMPlexVecGetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 3760 { 3761 PetscScalar *array, *vArray; 3762 const PetscInt *cone, *coneO; 3763 PetscInt pStart, pEnd, p, numPoints, size = 0, offset = 0; 3764 PetscErrorCode ierr; 3765 3766 PetscFunctionBeginHot; 3767 ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); 3768 ierr = DMPlexGetConeSize(dm, point, &numPoints);CHKERRQ(ierr); 3769 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 3770 ierr = DMPlexGetConeOrientation(dm, point, &coneO);CHKERRQ(ierr); 3771 if (!values || !*values) { 3772 if ((point >= pStart) && (point < pEnd)) { 3773 PetscInt dof; 3774 3775 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 3776 size += dof; 3777 } 3778 for (p = 0; p < numPoints; ++p) { 3779 const PetscInt cp = cone[p]; 3780 PetscInt dof; 3781 3782 if ((cp < pStart) || (cp >= pEnd)) continue; 3783 ierr = PetscSectionGetDof(section, cp, &dof);CHKERRQ(ierr); 3784 size += dof; 3785 } 3786 if (!values) { 3787 if (csize) *csize = size; 3788 PetscFunctionReturn(0); 3789 } 3790 ierr = DMGetWorkArray(dm, size, PETSC_SCALAR, &array);CHKERRQ(ierr); 3791 } else { 3792 array = *values; 3793 } 3794 size = 0; 3795 ierr = VecGetArray(v, &vArray);CHKERRQ(ierr); 3796 if ((point >= pStart) && (point < pEnd)) { 3797 PetscInt dof, off, d; 3798 PetscScalar *varr; 3799 3800 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 3801 ierr = PetscSectionGetOffset(section, point, &off);CHKERRQ(ierr); 3802 varr = &vArray[off]; 3803 for (d = 0; d < dof; ++d, ++offset) { 3804 array[offset] = varr[d]; 3805 } 3806 size += dof; 3807 } 3808 for (p = 0; p < numPoints; ++p) { 3809 const PetscInt cp = cone[p]; 3810 PetscInt o = coneO[p]; 3811 PetscInt dof, off, d; 3812 PetscScalar *varr; 3813 3814 if ((cp < pStart) || (cp >= pEnd)) continue; 3815 ierr = PetscSectionGetDof(section, cp, &dof);CHKERRQ(ierr); 3816 ierr = PetscSectionGetOffset(section, cp, &off);CHKERRQ(ierr); 3817 varr = &vArray[off]; 3818 if (o >= 0) { 3819 for (d = 0; d < dof; ++d, ++offset) { 3820 array[offset] = varr[d]; 3821 } 3822 } else { 3823 for (d = dof-1; d >= 0; --d, ++offset) { 3824 array[offset] = varr[d]; 3825 } 3826 } 3827 size += dof; 3828 } 3829 ierr = VecRestoreArray(v, &vArray);CHKERRQ(ierr); 3830 if (!*values) { 3831 if (csize) *csize = size; 3832 *values = array; 3833 } else { 3834 if (size > *csize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Size of input array %D < actual size %D", *csize, size); 3835 *csize = size; 3836 } 3837 PetscFunctionReturn(0); 3838 } 3839 3840 static PetscErrorCode DMPlexGetCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp) 3841 { 3842 const PetscInt *cla; 3843 PetscInt np, *pts = NULL; 3844 PetscErrorCode ierr; 3845 3846 PetscFunctionBeginHot; 3847 ierr = PetscSectionGetClosureIndex(section, (PetscObject) dm, clSec, clPoints);CHKERRQ(ierr); 3848 if (!*clPoints) { 3849 PetscInt pStart, pEnd, p, q; 3850 3851 ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); 3852 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_TRUE, &np, &pts);CHKERRQ(ierr); 3853 /* Compress out points not in the section */ 3854 for (p = 0, q = 0; p < np; p++) { 3855 PetscInt r = pts[2*p]; 3856 if ((r >= pStart) && (r < pEnd)) { 3857 pts[q*2] = r; 3858 pts[q*2+1] = pts[2*p+1]; 3859 ++q; 3860 } 3861 } 3862 np = q; 3863 cla = NULL; 3864 } else { 3865 PetscInt dof, off; 3866 3867 ierr = PetscSectionGetDof(*clSec, point, &dof);CHKERRQ(ierr); 3868 ierr = PetscSectionGetOffset(*clSec, point, &off);CHKERRQ(ierr); 3869 ierr = ISGetIndices(*clPoints, &cla);CHKERRQ(ierr); 3870 np = dof/2; 3871 pts = (PetscInt *) &cla[off]; 3872 } 3873 *numPoints = np; 3874 *points = pts; 3875 *clp = cla; 3876 3877 PetscFunctionReturn(0); 3878 } 3879 3880 static PetscErrorCode DMPlexRestoreCompressedClosure(DM dm, PetscSection section, PetscInt point, PetscInt *numPoints, PetscInt **points, PetscSection *clSec, IS *clPoints, const PetscInt **clp) 3881 { 3882 PetscErrorCode ierr; 3883 3884 PetscFunctionBeginHot; 3885 if (!*clPoints) { 3886 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_TRUE, numPoints, points);CHKERRQ(ierr); 3887 } else { 3888 ierr = ISRestoreIndices(*clPoints, clp);CHKERRQ(ierr); 3889 } 3890 *numPoints = 0; 3891 *points = NULL; 3892 *clSec = NULL; 3893 *clPoints = NULL; 3894 *clp = NULL; 3895 PetscFunctionReturn(0); 3896 } 3897 3898 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[]) 3899 { 3900 PetscInt offset = 0, p; 3901 const PetscInt **perms = NULL; 3902 const PetscScalar **flips = NULL; 3903 PetscErrorCode ierr; 3904 3905 PetscFunctionBeginHot; 3906 *size = 0; 3907 ierr = PetscSectionGetPointSyms(section,numPoints,points,&perms,&flips);CHKERRQ(ierr); 3908 for (p = 0; p < numPoints; p++) { 3909 const PetscInt point = points[2*p]; 3910 const PetscInt *perm = perms ? perms[p] : NULL; 3911 const PetscScalar *flip = flips ? flips[p] : NULL; 3912 PetscInt dof, off, d; 3913 const PetscScalar *varr; 3914 3915 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 3916 ierr = PetscSectionGetOffset(section, point, &off);CHKERRQ(ierr); 3917 varr = &vArray[off]; 3918 if (clperm) { 3919 if (perm) { 3920 for (d = 0; d < dof; d++) array[clperm[offset + perm[d]]] = varr[d]; 3921 } else { 3922 for (d = 0; d < dof; d++) array[clperm[offset + d ]] = varr[d]; 3923 } 3924 if (flip) { 3925 for (d = 0; d < dof; d++) array[clperm[offset + d ]] *= flip[d]; 3926 } 3927 } else { 3928 if (perm) { 3929 for (d = 0; d < dof; d++) array[offset + perm[d]] = varr[d]; 3930 } else { 3931 for (d = 0; d < dof; d++) array[offset + d ] = varr[d]; 3932 } 3933 if (flip) { 3934 for (d = 0; d < dof; d++) array[offset + d ] *= flip[d]; 3935 } 3936 } 3937 offset += dof; 3938 } 3939 ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms,&flips);CHKERRQ(ierr); 3940 *size = offset; 3941 PetscFunctionReturn(0); 3942 } 3943 3944 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[]) 3945 { 3946 PetscInt offset = 0, f; 3947 PetscErrorCode ierr; 3948 3949 PetscFunctionBeginHot; 3950 *size = 0; 3951 for (f = 0; f < numFields; ++f) { 3952 PetscInt p; 3953 const PetscInt **perms = NULL; 3954 const PetscScalar **flips = NULL; 3955 3956 ierr = PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 3957 for (p = 0; p < numPoints; p++) { 3958 const PetscInt point = points[2*p]; 3959 PetscInt fdof, foff, b; 3960 const PetscScalar *varr; 3961 const PetscInt *perm = perms ? perms[p] : NULL; 3962 const PetscScalar *flip = flips ? flips[p] : NULL; 3963 3964 ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); 3965 ierr = PetscSectionGetFieldOffset(section, point, f, &foff);CHKERRQ(ierr); 3966 varr = &vArray[foff]; 3967 if (clperm) { 3968 if (perm) {for (b = 0; b < fdof; b++) {array[clperm[offset + perm[b]]] = varr[b];}} 3969 else {for (b = 0; b < fdof; b++) {array[clperm[offset + b ]] = varr[b];}} 3970 if (flip) {for (b = 0; b < fdof; b++) {array[clperm[offset + b ]] *= flip[b];}} 3971 } else { 3972 if (perm) {for (b = 0; b < fdof; b++) {array[offset + perm[b]] = varr[b];}} 3973 else {for (b = 0; b < fdof; b++) {array[offset + b ] = varr[b];}} 3974 if (flip) {for (b = 0; b < fdof; b++) {array[offset + b ] *= flip[b];}} 3975 } 3976 offset += fdof; 3977 } 3978 ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 3979 } 3980 *size = offset; 3981 PetscFunctionReturn(0); 3982 } 3983 3984 /*@C 3985 DMPlexVecGetClosure - Get an array of the values on the closure of 'point' 3986 3987 Not collective 3988 3989 Input Parameters: 3990 + dm - The DM 3991 . section - The section describing the layout in v, or NULL to use the default section 3992 . v - The local vector 3993 - point - The point in the DM 3994 3995 Output Parameters: 3996 + csize - The number of values in the closure, or NULL 3997 - values - The array of values, which is a borrowed array and should not be freed 3998 3999 Fortran Notes: 4000 Since it returns an array, this routine is only available in Fortran 90, and you must 4001 include petsc.h90 in your code. 4002 4003 The csize argument is not present in the Fortran 90 binding since it is internal to the array. 4004 4005 Level: intermediate 4006 4007 .seealso DMPlexVecRestoreClosure(), DMPlexVecSetClosure(), DMPlexMatSetClosure() 4008 @*/ 4009 PetscErrorCode DMPlexVecGetClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 4010 { 4011 PetscSection clSection; 4012 IS clPoints; 4013 PetscScalar *array; 4014 const PetscScalar *vArray; 4015 PetscInt *points = NULL; 4016 const PetscInt *clp, *perm; 4017 PetscInt depth, numFields, numPoints, size; 4018 PetscErrorCode ierr; 4019 4020 PetscFunctionBeginHot; 4021 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4022 if (!section) {ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);} 4023 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 4024 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 4025 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 4026 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 4027 if (depth == 1 && numFields < 2) { 4028 ierr = DMPlexVecGetClosure_Depth1_Static(dm, section, v, point, csize, values);CHKERRQ(ierr); 4029 PetscFunctionReturn(0); 4030 } 4031 /* Get points */ 4032 ierr = DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4033 ierr = PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &perm);CHKERRQ(ierr); 4034 /* Get array */ 4035 if (!values || !*values) { 4036 PetscInt asize = 0, dof, p; 4037 4038 for (p = 0; p < numPoints*2; p += 2) { 4039 ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); 4040 asize += dof; 4041 } 4042 if (!values) { 4043 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4044 if (csize) *csize = asize; 4045 PetscFunctionReturn(0); 4046 } 4047 ierr = DMGetWorkArray(dm, asize, PETSC_SCALAR, &array);CHKERRQ(ierr); 4048 } else { 4049 array = *values; 4050 } 4051 ierr = VecGetArrayRead(v, &vArray);CHKERRQ(ierr); 4052 /* Get values */ 4053 if (numFields > 0) {ierr = DMPlexVecGetClosure_Fields_Static(dm, section, numPoints, points, numFields, perm, vArray, &size, array);CHKERRQ(ierr);} 4054 else {ierr = DMPlexVecGetClosure_Static(dm, section, numPoints, points, perm, vArray, &size, array);CHKERRQ(ierr);} 4055 /* Cleanup points */ 4056 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4057 /* Cleanup array */ 4058 ierr = VecRestoreArrayRead(v, &vArray);CHKERRQ(ierr); 4059 if (!*values) { 4060 if (csize) *csize = size; 4061 *values = array; 4062 } else { 4063 if (size > *csize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Size of input array %D < actual size %D", *csize, size); 4064 *csize = size; 4065 } 4066 PetscFunctionReturn(0); 4067 } 4068 4069 /*@C 4070 DMPlexVecRestoreClosure - Restore the array of the values on the closure of 'point' 4071 4072 Not collective 4073 4074 Input Parameters: 4075 + dm - The DM 4076 . section - The section describing the layout in v, or NULL to use the default section 4077 . v - The local vector 4078 . point - The point in the DM 4079 . csize - The number of values in the closure, or NULL 4080 - values - The array of values, which is a borrowed array and should not be freed 4081 4082 Fortran Notes: 4083 Since it returns an array, this routine is only available in Fortran 90, and you must 4084 include petsc.h90 in your code. 4085 4086 The csize argument is not present in the Fortran 90 binding since it is internal to the array. 4087 4088 Level: intermediate 4089 4090 .seealso DMPlexVecGetClosure(), DMPlexVecSetClosure(), DMPlexMatSetClosure() 4091 @*/ 4092 PetscErrorCode DMPlexVecRestoreClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, PetscScalar *values[]) 4093 { 4094 PetscInt size = 0; 4095 PetscErrorCode ierr; 4096 4097 PetscFunctionBegin; 4098 /* Should work without recalculating size */ 4099 ierr = DMRestoreWorkArray(dm, size, PETSC_SCALAR, (void*) values);CHKERRQ(ierr); 4100 PetscFunctionReturn(0); 4101 } 4102 4103 PETSC_STATIC_INLINE void add (PetscScalar *x, PetscScalar y) {*x += y;} 4104 PETSC_STATIC_INLINE void insert(PetscScalar *x, PetscScalar y) {*x = y;} 4105 4106 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[]) 4107 { 4108 PetscInt cdof; /* The number of constraints on this point */ 4109 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 4110 PetscScalar *a; 4111 PetscInt off, cind = 0, k; 4112 PetscErrorCode ierr; 4113 4114 PetscFunctionBegin; 4115 ierr = PetscSectionGetConstraintDof(section, point, &cdof);CHKERRQ(ierr); 4116 ierr = PetscSectionGetOffset(section, point, &off);CHKERRQ(ierr); 4117 a = &array[off]; 4118 if (!cdof || setBC) { 4119 if (clperm) { 4120 if (perm) {for (k = 0; k < dof; ++k) {fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.));}} 4121 else {for (k = 0; k < dof; ++k) {fuse(&a[k], values[clperm[offset+ k ]] * (flip ? flip[ k ] : 1.));}} 4122 } else { 4123 if (perm) {for (k = 0; k < dof; ++k) {fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.));}} 4124 else {for (k = 0; k < dof; ++k) {fuse(&a[k], values[offset+ k ] * (flip ? flip[ k ] : 1.));}} 4125 } 4126 } else { 4127 ierr = PetscSectionGetConstraintIndices(section, point, &cdofs);CHKERRQ(ierr); 4128 if (clperm) { 4129 if (perm) {for (k = 0; k < dof; ++k) { 4130 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4131 fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.)); 4132 } 4133 } else { 4134 for (k = 0; k < dof; ++k) { 4135 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4136 fuse(&a[k], values[clperm[offset+ k ]] * (flip ? flip[ k ] : 1.)); 4137 } 4138 } 4139 } else { 4140 if (perm) { 4141 for (k = 0; k < dof; ++k) { 4142 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4143 fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.)); 4144 } 4145 } else { 4146 for (k = 0; k < dof; ++k) { 4147 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4148 fuse(&a[k], values[offset+ k ] * (flip ? flip[ k ] : 1.)); 4149 } 4150 } 4151 } 4152 } 4153 PetscFunctionReturn(0); 4154 } 4155 4156 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[]) 4157 { 4158 PetscInt cdof; /* The number of constraints on this point */ 4159 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 4160 PetscScalar *a; 4161 PetscInt off, cind = 0, k; 4162 PetscErrorCode ierr; 4163 4164 PetscFunctionBegin; 4165 ierr = PetscSectionGetConstraintDof(section, point, &cdof);CHKERRQ(ierr); 4166 ierr = PetscSectionGetOffset(section, point, &off);CHKERRQ(ierr); 4167 a = &array[off]; 4168 if (cdof) { 4169 ierr = PetscSectionGetConstraintIndices(section, point, &cdofs);CHKERRQ(ierr); 4170 if (clperm) { 4171 if (perm) { 4172 for (k = 0; k < dof; ++k) { 4173 if ((cind < cdof) && (k == cdofs[cind])) { 4174 fuse(&a[k], values[clperm[offset+perm[k]]] * (flip ? flip[perm[k]] : 1.)); 4175 cind++; 4176 } 4177 } 4178 } else { 4179 for (k = 0; k < dof; ++k) { 4180 if ((cind < cdof) && (k == cdofs[cind])) { 4181 fuse(&a[k], values[clperm[offset+ k ]] * (flip ? flip[ k ] : 1.)); 4182 cind++; 4183 } 4184 } 4185 } 4186 } else { 4187 if (perm) { 4188 for (k = 0; k < dof; ++k) { 4189 if ((cind < cdof) && (k == cdofs[cind])) { 4190 fuse(&a[k], values[offset+perm[k]] * (flip ? flip[perm[k]] : 1.)); 4191 cind++; 4192 } 4193 } 4194 } else { 4195 for (k = 0; k < dof; ++k) { 4196 if ((cind < cdof) && (k == cdofs[cind])) { 4197 fuse(&a[k], values[offset+ k ] * (flip ? flip[ k ] : 1.)); 4198 cind++; 4199 } 4200 } 4201 } 4202 } 4203 } 4204 PetscFunctionReturn(0); 4205 } 4206 4207 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[]) 4208 { 4209 PetscScalar *a; 4210 PetscInt fdof, foff, fcdof, foffset = *offset; 4211 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 4212 PetscInt cind = 0, b; 4213 PetscErrorCode ierr; 4214 4215 PetscFunctionBegin; 4216 ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); 4217 ierr = PetscSectionGetFieldConstraintDof(section, point, f, &fcdof);CHKERRQ(ierr); 4218 ierr = PetscSectionGetFieldOffset(section, point, f, &foff);CHKERRQ(ierr); 4219 a = &array[foff]; 4220 if (!fcdof || setBC) { 4221 if (clperm) { 4222 if (perm) {for (b = 0; b < fdof; b++) {fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.));}} 4223 else {for (b = 0; b < fdof; b++) {fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.));}} 4224 } else { 4225 if (perm) {for (b = 0; b < fdof; b++) {fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.));}} 4226 else {for (b = 0; b < fdof; b++) {fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.));}} 4227 } 4228 } else { 4229 ierr = PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);CHKERRQ(ierr); 4230 if (clperm) { 4231 if (perm) { 4232 for (b = 0; b < fdof; b++) { 4233 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;} 4234 fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.)); 4235 } 4236 } else { 4237 for (b = 0; b < fdof; b++) { 4238 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;} 4239 fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.)); 4240 } 4241 } 4242 } else { 4243 if (perm) { 4244 for (b = 0; b < fdof; b++) { 4245 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;} 4246 fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.)); 4247 } 4248 } else { 4249 for (b = 0; b < fdof; b++) { 4250 if ((cind < fcdof) && (b == fcdofs[cind])) {++cind; continue;} 4251 fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.)); 4252 } 4253 } 4254 } 4255 } 4256 *offset += fdof; 4257 PetscFunctionReturn(0); 4258 } 4259 4260 PETSC_STATIC_INLINE PetscErrorCode updatePointFieldsBC_private(PetscSection section, PetscInt point, const PetscInt perm[], const PetscScalar flip[], PetscInt f, void (*fuse)(PetscScalar*, PetscScalar), const PetscInt clperm[], const PetscScalar values[], PetscInt *offset, PetscScalar array[]) 4261 { 4262 PetscScalar *a; 4263 PetscInt fdof, foff, fcdof, foffset = *offset; 4264 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 4265 PetscInt cind = 0, b; 4266 PetscErrorCode ierr; 4267 4268 PetscFunctionBegin; 4269 ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); 4270 ierr = PetscSectionGetFieldConstraintDof(section, point, f, &fcdof);CHKERRQ(ierr); 4271 ierr = PetscSectionGetFieldOffset(section, point, f, &foff);CHKERRQ(ierr); 4272 a = &array[foff]; 4273 if (fcdof) { 4274 ierr = PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);CHKERRQ(ierr); 4275 if (clperm) { 4276 if (perm) { 4277 for (b = 0; b < fdof; b++) { 4278 if ((cind < fcdof) && (b == fcdofs[cind])) { 4279 fuse(&a[b], values[clperm[foffset+perm[b]]] * (flip ? flip[perm[b]] : 1.)); 4280 ++cind; 4281 } 4282 } 4283 } else { 4284 for (b = 0; b < fdof; b++) { 4285 if ((cind < fcdof) && (b == fcdofs[cind])) { 4286 fuse(&a[b], values[clperm[foffset+ b ]] * (flip ? flip[ b ] : 1.)); 4287 ++cind; 4288 } 4289 } 4290 } 4291 } else { 4292 if (perm) { 4293 for (b = 0; b < fdof; b++) { 4294 if ((cind < fcdof) && (b == fcdofs[cind])) { 4295 fuse(&a[b], values[foffset+perm[b]] * (flip ? flip[perm[b]] : 1.)); 4296 ++cind; 4297 } 4298 } 4299 } else { 4300 for (b = 0; b < fdof; b++) { 4301 if ((cind < fcdof) && (b == fcdofs[cind])) { 4302 fuse(&a[b], values[foffset+ b ] * (flip ? flip[ b ] : 1.)); 4303 ++cind; 4304 } 4305 } 4306 } 4307 } 4308 } 4309 *offset += fdof; 4310 PetscFunctionReturn(0); 4311 } 4312 4313 PETSC_STATIC_INLINE PetscErrorCode DMPlexVecSetClosure_Depth1_Static(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode) 4314 { 4315 PetscScalar *array; 4316 const PetscInt *cone, *coneO; 4317 PetscInt pStart, pEnd, p, numPoints, off, dof; 4318 PetscErrorCode ierr; 4319 4320 PetscFunctionBeginHot; 4321 ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr); 4322 ierr = DMPlexGetConeSize(dm, point, &numPoints);CHKERRQ(ierr); 4323 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 4324 ierr = DMPlexGetConeOrientation(dm, point, &coneO);CHKERRQ(ierr); 4325 ierr = VecGetArray(v, &array);CHKERRQ(ierr); 4326 for (p = 0, off = 0; p <= numPoints; ++p, off += dof) { 4327 const PetscInt cp = !p ? point : cone[p-1]; 4328 const PetscInt o = !p ? 0 : coneO[p-1]; 4329 4330 if ((cp < pStart) || (cp >= pEnd)) {dof = 0; continue;} 4331 ierr = PetscSectionGetDof(section, cp, &dof);CHKERRQ(ierr); 4332 /* ADD_VALUES */ 4333 { 4334 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 4335 PetscScalar *a; 4336 PetscInt cdof, coff, cind = 0, k; 4337 4338 ierr = PetscSectionGetConstraintDof(section, cp, &cdof);CHKERRQ(ierr); 4339 ierr = PetscSectionGetOffset(section, cp, &coff);CHKERRQ(ierr); 4340 a = &array[coff]; 4341 if (!cdof) { 4342 if (o >= 0) { 4343 for (k = 0; k < dof; ++k) { 4344 a[k] += values[off+k]; 4345 } 4346 } else { 4347 for (k = 0; k < dof; ++k) { 4348 a[k] += values[off+dof-k-1]; 4349 } 4350 } 4351 } else { 4352 ierr = PetscSectionGetConstraintIndices(section, cp, &cdofs);CHKERRQ(ierr); 4353 if (o >= 0) { 4354 for (k = 0; k < dof; ++k) { 4355 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4356 a[k] += values[off+k]; 4357 } 4358 } else { 4359 for (k = 0; k < dof; ++k) { 4360 if ((cind < cdof) && (k == cdofs[cind])) {++cind; continue;} 4361 a[k] += values[off+dof-k-1]; 4362 } 4363 } 4364 } 4365 } 4366 } 4367 ierr = VecRestoreArray(v, &array);CHKERRQ(ierr); 4368 PetscFunctionReturn(0); 4369 } 4370 4371 /*@C 4372 DMPlexVecSetClosure - Set an array of the values on the closure of 'point' 4373 4374 Not collective 4375 4376 Input Parameters: 4377 + dm - The DM 4378 . section - The section describing the layout in v, or NULL to use the default section 4379 . v - The local vector 4380 . point - The point in the DM 4381 . values - The array of values 4382 - mode - The insert mode, where INSERT_ALL_VALUES and ADD_ALL_VALUES also overwrite boundary conditions 4383 4384 Fortran Notes: 4385 This routine is only available in Fortran 90, and you must include petsc.h90 in your code. 4386 4387 Level: intermediate 4388 4389 .seealso DMPlexVecGetClosure(), DMPlexMatSetClosure() 4390 @*/ 4391 PetscErrorCode DMPlexVecSetClosure(DM dm, PetscSection section, Vec v, PetscInt point, const PetscScalar values[], InsertMode mode) 4392 { 4393 PetscSection clSection; 4394 IS clPoints; 4395 PetscScalar *array; 4396 PetscInt *points = NULL; 4397 const PetscInt *clp, *clperm; 4398 PetscInt depth, numFields, numPoints, p; 4399 PetscErrorCode ierr; 4400 4401 PetscFunctionBeginHot; 4402 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4403 if (!section) {ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);} 4404 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 4405 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 4406 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 4407 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 4408 if (depth == 1 && numFields < 2 && mode == ADD_VALUES) { 4409 ierr = DMPlexVecSetClosure_Depth1_Static(dm, section, v, point, values, mode);CHKERRQ(ierr); 4410 PetscFunctionReturn(0); 4411 } 4412 /* Get points */ 4413 ierr = PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &clperm);CHKERRQ(ierr); 4414 ierr = DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4415 /* Get array */ 4416 ierr = VecGetArray(v, &array);CHKERRQ(ierr); 4417 /* Get values */ 4418 if (numFields > 0) { 4419 PetscInt offset = 0, f; 4420 for (f = 0; f < numFields; ++f) { 4421 const PetscInt **perms = NULL; 4422 const PetscScalar **flips = NULL; 4423 4424 ierr = PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4425 switch (mode) { 4426 case INSERT_VALUES: 4427 for (p = 0; p < numPoints; p++) { 4428 const PetscInt point = points[2*p]; 4429 const PetscInt *perm = perms ? perms[p] : NULL; 4430 const PetscScalar *flip = flips ? flips[p] : NULL; 4431 updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, clperm, values, &offset, array); 4432 } break; 4433 case INSERT_ALL_VALUES: 4434 for (p = 0; p < numPoints; p++) { 4435 const PetscInt point = points[2*p]; 4436 const PetscInt *perm = perms ? perms[p] : NULL; 4437 const PetscScalar *flip = flips ? flips[p] : NULL; 4438 updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, clperm, values, &offset, array); 4439 } break; 4440 case INSERT_BC_VALUES: 4441 for (p = 0; p < numPoints; p++) { 4442 const PetscInt point = points[2*p]; 4443 const PetscInt *perm = perms ? perms[p] : NULL; 4444 const PetscScalar *flip = flips ? flips[p] : NULL; 4445 updatePointFieldsBC_private(section, point, perm, flip, f, insert, clperm, values, &offset, array); 4446 } break; 4447 case ADD_VALUES: 4448 for (p = 0; p < numPoints; p++) { 4449 const PetscInt point = points[2*p]; 4450 const PetscInt *perm = perms ? perms[p] : NULL; 4451 const PetscScalar *flip = flips ? flips[p] : NULL; 4452 updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, clperm, values, &offset, array); 4453 } break; 4454 case ADD_ALL_VALUES: 4455 for (p = 0; p < numPoints; p++) { 4456 const PetscInt point = points[2*p]; 4457 const PetscInt *perm = perms ? perms[p] : NULL; 4458 const PetscScalar *flip = flips ? flips[p] : NULL; 4459 updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, clperm, values, &offset, array); 4460 } break; 4461 case ADD_BC_VALUES: 4462 for (p = 0; p < numPoints; p++) { 4463 const PetscInt point = points[2*p]; 4464 const PetscInt *perm = perms ? perms[p] : NULL; 4465 const PetscScalar *flip = flips ? flips[p] : NULL; 4466 updatePointFieldsBC_private(section, point, perm, flip, f, add, clperm, values, &offset, array); 4467 } break; 4468 default: 4469 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 4470 } 4471 ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4472 } 4473 } else { 4474 PetscInt dof, off; 4475 const PetscInt **perms = NULL; 4476 const PetscScalar **flips = NULL; 4477 4478 ierr = PetscSectionGetPointSyms(section,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4479 switch (mode) { 4480 case INSERT_VALUES: 4481 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4482 const PetscInt point = points[2*p]; 4483 const PetscInt *perm = perms ? perms[p] : NULL; 4484 const PetscScalar *flip = flips ? flips[p] : NULL; 4485 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4486 updatePoint_private(section, point, dof, insert, PETSC_FALSE, perm, flip, clperm, values, off, array); 4487 } break; 4488 case INSERT_ALL_VALUES: 4489 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4490 const PetscInt point = points[2*p]; 4491 const PetscInt *perm = perms ? perms[p] : NULL; 4492 const PetscScalar *flip = flips ? flips[p] : NULL; 4493 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4494 updatePoint_private(section, point, dof, insert, PETSC_TRUE, perm, flip, clperm, values, off, array); 4495 } break; 4496 case INSERT_BC_VALUES: 4497 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4498 const PetscInt point = points[2*p]; 4499 const PetscInt *perm = perms ? perms[p] : NULL; 4500 const PetscScalar *flip = flips ? flips[p] : NULL; 4501 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4502 updatePointBC_private(section, point, dof, insert, perm, flip, clperm, values, off, array); 4503 } break; 4504 case ADD_VALUES: 4505 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4506 const PetscInt point = points[2*p]; 4507 const PetscInt *perm = perms ? perms[p] : NULL; 4508 const PetscScalar *flip = flips ? flips[p] : NULL; 4509 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4510 updatePoint_private(section, point, dof, add, PETSC_FALSE, perm, flip, clperm, values, off, array); 4511 } break; 4512 case ADD_ALL_VALUES: 4513 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4514 const PetscInt point = points[2*p]; 4515 const PetscInt *perm = perms ? perms[p] : NULL; 4516 const PetscScalar *flip = flips ? flips[p] : NULL; 4517 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4518 updatePoint_private(section, point, dof, add, PETSC_TRUE, perm, flip, clperm, values, off, array); 4519 } break; 4520 case ADD_BC_VALUES: 4521 for (p = 0, off = 0; p < numPoints; p++, off += dof) { 4522 const PetscInt point = points[2*p]; 4523 const PetscInt *perm = perms ? perms[p] : NULL; 4524 const PetscScalar *flip = flips ? flips[p] : NULL; 4525 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4526 updatePointBC_private(section, point, dof, add, perm, flip, clperm, values, off, array); 4527 } break; 4528 default: 4529 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 4530 } 4531 ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4532 } 4533 /* Cleanup points */ 4534 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4535 /* Cleanup array */ 4536 ierr = VecRestoreArray(v, &array);CHKERRQ(ierr); 4537 PetscFunctionReturn(0); 4538 } 4539 4540 PetscErrorCode DMPlexVecSetFieldClosure_Internal(DM dm, PetscSection section, Vec v, PetscBool fieldActive[], PetscInt point, const PetscScalar values[], InsertMode mode) 4541 { 4542 PetscSection clSection; 4543 IS clPoints; 4544 PetscScalar *array; 4545 PetscInt *points = NULL; 4546 const PetscInt *clp, *clperm; 4547 PetscInt numFields, numPoints, p; 4548 PetscInt offset = 0, f; 4549 PetscErrorCode ierr; 4550 4551 PetscFunctionBeginHot; 4552 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4553 if (!section) {ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);} 4554 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 4555 PetscValidHeaderSpecific(v, VEC_CLASSID, 3); 4556 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 4557 /* Get points */ 4558 ierr = PetscSectionGetClosureInversePermutation_Internal(section, (PetscObject) dm, NULL, &clperm);CHKERRQ(ierr); 4559 ierr = DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4560 /* Get array */ 4561 ierr = VecGetArray(v, &array);CHKERRQ(ierr); 4562 /* Get values */ 4563 for (f = 0; f < numFields; ++f) { 4564 const PetscInt **perms = NULL; 4565 const PetscScalar **flips = NULL; 4566 4567 if (!fieldActive[f]) { 4568 for (p = 0; p < numPoints*2; p += 2) { 4569 PetscInt fdof; 4570 ierr = PetscSectionGetFieldDof(section, points[p], f, &fdof);CHKERRQ(ierr); 4571 offset += fdof; 4572 } 4573 continue; 4574 } 4575 ierr = PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4576 switch (mode) { 4577 case INSERT_VALUES: 4578 for (p = 0; p < numPoints; p++) { 4579 const PetscInt point = points[2*p]; 4580 const PetscInt *perm = perms ? perms[p] : NULL; 4581 const PetscScalar *flip = flips ? flips[p] : NULL; 4582 updatePointFields_private(section, point, perm, flip, f, insert, PETSC_FALSE, clperm, values, &offset, array); 4583 } break; 4584 case INSERT_ALL_VALUES: 4585 for (p = 0; p < numPoints; p++) { 4586 const PetscInt point = points[2*p]; 4587 const PetscInt *perm = perms ? perms[p] : NULL; 4588 const PetscScalar *flip = flips ? flips[p] : NULL; 4589 updatePointFields_private(section, point, perm, flip, f, insert, PETSC_TRUE, clperm, values, &offset, array); 4590 } break; 4591 case INSERT_BC_VALUES: 4592 for (p = 0; p < numPoints; p++) { 4593 const PetscInt point = points[2*p]; 4594 const PetscInt *perm = perms ? perms[p] : NULL; 4595 const PetscScalar *flip = flips ? flips[p] : NULL; 4596 updatePointFieldsBC_private(section, point, perm, flip, f, insert, clperm, values, &offset, array); 4597 } break; 4598 case ADD_VALUES: 4599 for (p = 0; p < numPoints; p++) { 4600 const PetscInt point = points[2*p]; 4601 const PetscInt *perm = perms ? perms[p] : NULL; 4602 const PetscScalar *flip = flips ? flips[p] : NULL; 4603 updatePointFields_private(section, point, perm, flip, f, add, PETSC_FALSE, clperm, values, &offset, array); 4604 } break; 4605 case ADD_ALL_VALUES: 4606 for (p = 0; p < numPoints; p++) { 4607 const PetscInt point = points[2*p]; 4608 const PetscInt *perm = perms ? perms[p] : NULL; 4609 const PetscScalar *flip = flips ? flips[p] : NULL; 4610 updatePointFields_private(section, point, perm, flip, f, add, PETSC_TRUE, clperm, values, &offset, array); 4611 } break; 4612 default: 4613 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Invalid insert mode %d", mode); 4614 } 4615 ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms,&flips);CHKERRQ(ierr); 4616 } 4617 /* Cleanup points */ 4618 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 4619 /* Cleanup array */ 4620 ierr = VecRestoreArray(v, &array);CHKERRQ(ierr); 4621 PetscFunctionReturn(0); 4622 } 4623 4624 static PetscErrorCode DMPlexPrintMatSetValues(PetscViewer viewer, Mat A, PetscInt point, PetscInt numRIndices, const PetscInt rindices[], PetscInt numCIndices, const PetscInt cindices[], const PetscScalar values[]) 4625 { 4626 PetscMPIInt rank; 4627 PetscInt i, j; 4628 PetscErrorCode ierr; 4629 4630 PetscFunctionBegin; 4631 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);CHKERRQ(ierr); 4632 ierr = PetscViewerASCIIPrintf(viewer, "[%d]mat for point %D\n", rank, point);CHKERRQ(ierr); 4633 for (i = 0; i < numRIndices; i++) {ierr = PetscViewerASCIIPrintf(viewer, "[%d]mat row indices[%D] = %D\n", rank, i, rindices[i]);CHKERRQ(ierr);} 4634 for (i = 0; i < numCIndices; i++) {ierr = PetscViewerASCIIPrintf(viewer, "[%d]mat col indices[%D] = %D\n", rank, i, cindices[i]);CHKERRQ(ierr);} 4635 numCIndices = numCIndices ? numCIndices : numRIndices; 4636 for (i = 0; i < numRIndices; i++) { 4637 ierr = PetscViewerASCIIPrintf(viewer, "[%d]", rank);CHKERRQ(ierr); 4638 for (j = 0; j < numCIndices; j++) { 4639 #if defined(PETSC_USE_COMPLEX) 4640 ierr = PetscViewerASCIIPrintf(viewer, " (%g,%g)", (double)PetscRealPart(values[i*numCIndices+j]), (double)PetscImaginaryPart(values[i*numCIndices+j]));CHKERRQ(ierr); 4641 #else 4642 ierr = PetscViewerASCIIPrintf(viewer, " %g", (double)values[i*numCIndices+j]);CHKERRQ(ierr); 4643 #endif 4644 } 4645 ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr); 4646 } 4647 PetscFunctionReturn(0); 4648 } 4649 4650 /* . off - The global offset of this point */ 4651 PetscErrorCode DMPlexGetIndicesPoint_Internal(PetscSection section, PetscInt point, PetscInt off, PetscInt *loff, PetscBool setBC, const PetscInt perm[], PetscInt indices[]) 4652 { 4653 PetscInt dof; /* The number of unknowns on this point */ 4654 PetscInt cdof; /* The number of constraints on this point */ 4655 const PetscInt *cdofs; /* The indices of the constrained dofs on this point */ 4656 PetscInt cind = 0, k; 4657 PetscErrorCode ierr; 4658 4659 PetscFunctionBegin; 4660 ierr = PetscSectionGetDof(section, point, &dof);CHKERRQ(ierr); 4661 ierr = PetscSectionGetConstraintDof(section, point, &cdof);CHKERRQ(ierr); 4662 if (!cdof || setBC) { 4663 if (perm) { 4664 for (k = 0; k < dof; k++) indices[*loff+perm[k]] = off + k; 4665 } else { 4666 for (k = 0; k < dof; k++) indices[*loff+k] = off + k; 4667 } 4668 } else { 4669 ierr = PetscSectionGetConstraintIndices(section, point, &cdofs);CHKERRQ(ierr); 4670 if (perm) { 4671 for (k = 0; k < dof; ++k) { 4672 if ((cind < cdof) && (k == cdofs[cind])) { 4673 /* Insert check for returning constrained indices */ 4674 indices[*loff+perm[k]] = -(off+k+1); 4675 ++cind; 4676 } else { 4677 indices[*loff+perm[k]] = off+k-cind; 4678 } 4679 } 4680 } else { 4681 for (k = 0; k < dof; ++k) { 4682 if ((cind < cdof) && (k == cdofs[cind])) { 4683 /* Insert check for returning constrained indices */ 4684 indices[*loff+k] = -(off+k+1); 4685 ++cind; 4686 } else { 4687 indices[*loff+k] = off+k-cind; 4688 } 4689 } 4690 } 4691 } 4692 *loff += dof; 4693 PetscFunctionReturn(0); 4694 } 4695 4696 /* . off - The global offset of this point */ 4697 PetscErrorCode DMPlexGetIndicesPointFields_Internal(PetscSection section, PetscInt point, PetscInt off, PetscInt foffs[], PetscBool setBC, const PetscInt ***perms, PetscInt permsoff, PetscInt indices[]) 4698 { 4699 PetscInt numFields, foff, f; 4700 PetscErrorCode ierr; 4701 4702 PetscFunctionBegin; 4703 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 4704 for (f = 0, foff = 0; f < numFields; ++f) { 4705 PetscInt fdof, cfdof; 4706 const PetscInt *fcdofs; /* The indices of the constrained dofs for field f on this point */ 4707 PetscInt cind = 0, b; 4708 const PetscInt *perm = (perms && perms[f]) ? perms[f][permsoff] : NULL; 4709 4710 ierr = PetscSectionGetFieldDof(section, point, f, &fdof);CHKERRQ(ierr); 4711 ierr = PetscSectionGetFieldConstraintDof(section, point, f, &cfdof);CHKERRQ(ierr); 4712 if (!cfdof || setBC) { 4713 if (perm) {for (b = 0; b < fdof; b++) {indices[foffs[f]+perm[b]] = off+foff+b;}} 4714 else {for (b = 0; b < fdof; b++) {indices[foffs[f]+ b ] = off+foff+b;}} 4715 } else { 4716 ierr = PetscSectionGetFieldConstraintIndices(section, point, f, &fcdofs);CHKERRQ(ierr); 4717 if (perm) { 4718 for (b = 0; b < fdof; b++) { 4719 if ((cind < cfdof) && (b == fcdofs[cind])) { 4720 indices[foffs[f]+perm[b]] = -(off+foff+b+1); 4721 ++cind; 4722 } else { 4723 indices[foffs[f]+perm[b]] = off+foff+b-cind; 4724 } 4725 } 4726 } else { 4727 for (b = 0; b < fdof; b++) { 4728 if ((cind < cfdof) && (b == fcdofs[cind])) { 4729 indices[foffs[f]+b] = -(off+foff+b+1); 4730 ++cind; 4731 } else { 4732 indices[foffs[f]+b] = off+foff+b-cind; 4733 } 4734 } 4735 } 4736 } 4737 foff += (setBC ? fdof : (fdof - cfdof)); 4738 foffs[f] += fdof; 4739 } 4740 PetscFunctionReturn(0); 4741 } 4742 4743 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) 4744 { 4745 Mat cMat; 4746 PetscSection aSec, cSec; 4747 IS aIS; 4748 PetscInt aStart = -1, aEnd = -1; 4749 const PetscInt *anchors; 4750 PetscInt numFields, f, p, q, newP = 0; 4751 PetscInt newNumPoints = 0, newNumIndices = 0; 4752 PetscInt *newPoints, *indices, *newIndices; 4753 PetscInt maxAnchor, maxDof; 4754 PetscInt newOffsets[32]; 4755 PetscInt *pointMatOffsets[32]; 4756 PetscInt *newPointOffsets[32]; 4757 PetscScalar *pointMat[32]; 4758 PetscScalar *newValues=NULL,*tmpValues; 4759 PetscBool anyConstrained = PETSC_FALSE; 4760 PetscErrorCode ierr; 4761 4762 PetscFunctionBegin; 4763 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 4764 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 4765 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 4766 4767 ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr); 4768 /* if there are point-to-point constraints */ 4769 if (aSec) { 4770 ierr = PetscMemzero(newOffsets, 32 * sizeof(PetscInt));CHKERRQ(ierr); 4771 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 4772 ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); 4773 /* figure out how many points are going to be in the new element matrix 4774 * (we allow double counting, because it's all just going to be summed 4775 * into the global matrix anyway) */ 4776 for (p = 0; p < 2*numPoints; p+=2) { 4777 PetscInt b = points[p]; 4778 PetscInt bDof = 0, bSecDof; 4779 4780 ierr = PetscSectionGetDof(section,b,&bSecDof);CHKERRQ(ierr); 4781 if (!bSecDof) { 4782 continue; 4783 } 4784 if (b >= aStart && b < aEnd) { 4785 ierr = PetscSectionGetDof(aSec,b,&bDof);CHKERRQ(ierr); 4786 } 4787 if (bDof) { 4788 /* this point is constrained */ 4789 /* it is going to be replaced by its anchors */ 4790 PetscInt bOff, q; 4791 4792 anyConstrained = PETSC_TRUE; 4793 newNumPoints += bDof; 4794 ierr = PetscSectionGetOffset(aSec,b,&bOff);CHKERRQ(ierr); 4795 for (q = 0; q < bDof; q++) { 4796 PetscInt a = anchors[bOff + q]; 4797 PetscInt aDof; 4798 4799 ierr = PetscSectionGetDof(section,a,&aDof);CHKERRQ(ierr); 4800 newNumIndices += aDof; 4801 for (f = 0; f < numFields; ++f) { 4802 PetscInt fDof; 4803 4804 ierr = PetscSectionGetFieldDof(section, a, f, &fDof);CHKERRQ(ierr); 4805 newOffsets[f+1] += fDof; 4806 } 4807 } 4808 } 4809 else { 4810 /* this point is not constrained */ 4811 newNumPoints++; 4812 newNumIndices += bSecDof; 4813 for (f = 0; f < numFields; ++f) { 4814 PetscInt fDof; 4815 4816 ierr = PetscSectionGetFieldDof(section, b, f, &fDof);CHKERRQ(ierr); 4817 newOffsets[f+1] += fDof; 4818 } 4819 } 4820 } 4821 } 4822 if (!anyConstrained) { 4823 if (outNumPoints) *outNumPoints = 0; 4824 if (outNumIndices) *outNumIndices = 0; 4825 if (outPoints) *outPoints = NULL; 4826 if (outValues) *outValues = NULL; 4827 if (aSec) {ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr);} 4828 PetscFunctionReturn(0); 4829 } 4830 4831 if (outNumPoints) *outNumPoints = newNumPoints; 4832 if (outNumIndices) *outNumIndices = newNumIndices; 4833 4834 for (f = 0; f < numFields; ++f) newOffsets[f+1] += newOffsets[f]; 4835 4836 if (!outPoints && !outValues) { 4837 if (offsets) { 4838 for (f = 0; f <= numFields; f++) { 4839 offsets[f] = newOffsets[f]; 4840 } 4841 } 4842 if (aSec) {ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr);} 4843 PetscFunctionReturn(0); 4844 } 4845 4846 if (numFields && newOffsets[numFields] != newNumIndices) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", newOffsets[numFields], newNumIndices); 4847 4848 ierr = DMGetDefaultConstraints(dm, &cSec, &cMat);CHKERRQ(ierr); 4849 4850 /* workspaces */ 4851 if (numFields) { 4852 for (f = 0; f < numFields; f++) { 4853 ierr = DMGetWorkArray(dm,numPoints+1,PETSC_INT,&pointMatOffsets[f]);CHKERRQ(ierr); 4854 ierr = DMGetWorkArray(dm,numPoints+1,PETSC_INT,&newPointOffsets[f]);CHKERRQ(ierr); 4855 } 4856 } 4857 else { 4858 ierr = DMGetWorkArray(dm,numPoints+1,PETSC_INT,&pointMatOffsets[0]);CHKERRQ(ierr); 4859 ierr = DMGetWorkArray(dm,numPoints,PETSC_INT,&newPointOffsets[0]);CHKERRQ(ierr); 4860 } 4861 4862 /* get workspaces for the point-to-point matrices */ 4863 if (numFields) { 4864 PetscInt totalOffset, totalMatOffset; 4865 4866 for (p = 0; p < numPoints; p++) { 4867 PetscInt b = points[2*p]; 4868 PetscInt bDof = 0, bSecDof; 4869 4870 ierr = PetscSectionGetDof(section,b,&bSecDof);CHKERRQ(ierr); 4871 if (!bSecDof) { 4872 for (f = 0; f < numFields; f++) { 4873 newPointOffsets[f][p + 1] = 0; 4874 pointMatOffsets[f][p + 1] = 0; 4875 } 4876 continue; 4877 } 4878 if (b >= aStart && b < aEnd) { 4879 ierr = PetscSectionGetDof(aSec, b, &bDof);CHKERRQ(ierr); 4880 } 4881 if (bDof) { 4882 for (f = 0; f < numFields; f++) { 4883 PetscInt fDof, q, bOff, allFDof = 0; 4884 4885 ierr = PetscSectionGetFieldDof(section, b, f, &fDof);CHKERRQ(ierr); 4886 ierr = PetscSectionGetOffset(aSec, b, &bOff);CHKERRQ(ierr); 4887 for (q = 0; q < bDof; q++) { 4888 PetscInt a = anchors[bOff + q]; 4889 PetscInt aFDof; 4890 4891 ierr = PetscSectionGetFieldDof(section, a, f, &aFDof);CHKERRQ(ierr); 4892 allFDof += aFDof; 4893 } 4894 newPointOffsets[f][p+1] = allFDof; 4895 pointMatOffsets[f][p+1] = fDof * allFDof; 4896 } 4897 } 4898 else { 4899 for (f = 0; f < numFields; f++) { 4900 PetscInt fDof; 4901 4902 ierr = PetscSectionGetFieldDof(section, b, f, &fDof);CHKERRQ(ierr); 4903 newPointOffsets[f][p+1] = fDof; 4904 pointMatOffsets[f][p+1] = 0; 4905 } 4906 } 4907 } 4908 for (f = 0, totalOffset = 0, totalMatOffset = 0; f < numFields; f++) { 4909 newPointOffsets[f][0] = totalOffset; 4910 pointMatOffsets[f][0] = totalMatOffset; 4911 for (p = 0; p < numPoints; p++) { 4912 newPointOffsets[f][p+1] += newPointOffsets[f][p]; 4913 pointMatOffsets[f][p+1] += pointMatOffsets[f][p]; 4914 } 4915 totalOffset = newPointOffsets[f][numPoints]; 4916 totalMatOffset = pointMatOffsets[f][numPoints]; 4917 ierr = DMGetWorkArray(dm,pointMatOffsets[f][numPoints],PETSC_SCALAR,&pointMat[f]);CHKERRQ(ierr); 4918 } 4919 } 4920 else { 4921 for (p = 0; p < numPoints; p++) { 4922 PetscInt b = points[2*p]; 4923 PetscInt bDof = 0, bSecDof; 4924 4925 ierr = PetscSectionGetDof(section,b,&bSecDof);CHKERRQ(ierr); 4926 if (!bSecDof) { 4927 newPointOffsets[0][p + 1] = 0; 4928 pointMatOffsets[0][p + 1] = 0; 4929 continue; 4930 } 4931 if (b >= aStart && b < aEnd) { 4932 ierr = PetscSectionGetDof(aSec, b, &bDof);CHKERRQ(ierr); 4933 } 4934 if (bDof) { 4935 PetscInt bOff, q, allDof = 0; 4936 4937 ierr = PetscSectionGetOffset(aSec, b, &bOff);CHKERRQ(ierr); 4938 for (q = 0; q < bDof; q++) { 4939 PetscInt a = anchors[bOff + q], aDof; 4940 4941 ierr = PetscSectionGetDof(section, a, &aDof);CHKERRQ(ierr); 4942 allDof += aDof; 4943 } 4944 newPointOffsets[0][p+1] = allDof; 4945 pointMatOffsets[0][p+1] = bSecDof * allDof; 4946 } 4947 else { 4948 newPointOffsets[0][p+1] = bSecDof; 4949 pointMatOffsets[0][p+1] = 0; 4950 } 4951 } 4952 newPointOffsets[0][0] = 0; 4953 pointMatOffsets[0][0] = 0; 4954 for (p = 0; p < numPoints; p++) { 4955 newPointOffsets[0][p+1] += newPointOffsets[0][p]; 4956 pointMatOffsets[0][p+1] += pointMatOffsets[0][p]; 4957 } 4958 ierr = DMGetWorkArray(dm,pointMatOffsets[0][numPoints],PETSC_SCALAR,&pointMat[0]);CHKERRQ(ierr); 4959 } 4960 4961 /* output arrays */ 4962 ierr = DMGetWorkArray(dm,2*newNumPoints,PETSC_INT,&newPoints);CHKERRQ(ierr); 4963 4964 /* get the point-to-point matrices; construct newPoints */ 4965 ierr = PetscSectionGetMaxDof(aSec, &maxAnchor);CHKERRQ(ierr); 4966 ierr = PetscSectionGetMaxDof(section, &maxDof);CHKERRQ(ierr); 4967 ierr = DMGetWorkArray(dm,maxDof,PETSC_INT,&indices);CHKERRQ(ierr); 4968 ierr = DMGetWorkArray(dm,maxAnchor*maxDof,PETSC_INT,&newIndices);CHKERRQ(ierr); 4969 if (numFields) { 4970 for (p = 0, newP = 0; p < numPoints; p++) { 4971 PetscInt b = points[2*p]; 4972 PetscInt o = points[2*p+1]; 4973 PetscInt bDof = 0, bSecDof; 4974 4975 ierr = PetscSectionGetDof(section, b, &bSecDof);CHKERRQ(ierr); 4976 if (!bSecDof) { 4977 continue; 4978 } 4979 if (b >= aStart && b < aEnd) { 4980 ierr = PetscSectionGetDof(aSec, b, &bDof);CHKERRQ(ierr); 4981 } 4982 if (bDof) { 4983 PetscInt fStart[32], fEnd[32], fAnchorStart[32], fAnchorEnd[32], bOff, q; 4984 4985 fStart[0] = 0; 4986 fEnd[0] = 0; 4987 for (f = 0; f < numFields; f++) { 4988 PetscInt fDof; 4989 4990 ierr = PetscSectionGetFieldDof(cSec, b, f, &fDof);CHKERRQ(ierr); 4991 fStart[f+1] = fStart[f] + fDof; 4992 fEnd[f+1] = fStart[f+1]; 4993 } 4994 ierr = PetscSectionGetOffset(cSec, b, &bOff);CHKERRQ(ierr); 4995 ierr = DMPlexGetIndicesPointFields_Internal(cSec, b, bOff, fEnd, PETSC_TRUE, perms, p, indices);CHKERRQ(ierr); 4996 4997 fAnchorStart[0] = 0; 4998 fAnchorEnd[0] = 0; 4999 for (f = 0; f < numFields; f++) { 5000 PetscInt fDof = newPointOffsets[f][p + 1] - newPointOffsets[f][p]; 5001 5002 fAnchorStart[f+1] = fAnchorStart[f] + fDof; 5003 fAnchorEnd[f+1] = fAnchorStart[f + 1]; 5004 } 5005 ierr = PetscSectionGetOffset(aSec, b, &bOff);CHKERRQ(ierr); 5006 for (q = 0; q < bDof; q++) { 5007 PetscInt a = anchors[bOff + q], aOff; 5008 5009 /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */ 5010 newPoints[2*(newP + q)] = a; 5011 newPoints[2*(newP + q) + 1] = 0; 5012 ierr = PetscSectionGetOffset(section, a, &aOff);CHKERRQ(ierr); 5013 ierr = DMPlexGetIndicesPointFields_Internal(section, a, aOff, fAnchorEnd, PETSC_TRUE, NULL, -1, newIndices);CHKERRQ(ierr); 5014 } 5015 newP += bDof; 5016 5017 if (outValues) { 5018 /* get the point-to-point submatrix */ 5019 for (f = 0; f < numFields; f++) { 5020 ierr = MatGetValues(cMat,fEnd[f]-fStart[f],indices + fStart[f],fAnchorEnd[f] - fAnchorStart[f],newIndices + fAnchorStart[f],pointMat[f] + pointMatOffsets[f][p]);CHKERRQ(ierr); 5021 } 5022 } 5023 } 5024 else { 5025 newPoints[2 * newP] = b; 5026 newPoints[2 * newP + 1] = o; 5027 newP++; 5028 } 5029 } 5030 } else { 5031 for (p = 0; p < numPoints; p++) { 5032 PetscInt b = points[2*p]; 5033 PetscInt o = points[2*p+1]; 5034 PetscInt bDof = 0, bSecDof; 5035 5036 ierr = PetscSectionGetDof(section, b, &bSecDof);CHKERRQ(ierr); 5037 if (!bSecDof) { 5038 continue; 5039 } 5040 if (b >= aStart && b < aEnd) { 5041 ierr = PetscSectionGetDof(aSec, b, &bDof);CHKERRQ(ierr); 5042 } 5043 if (bDof) { 5044 PetscInt bEnd = 0, bAnchorEnd = 0, bOff; 5045 5046 ierr = PetscSectionGetOffset(cSec, b, &bOff);CHKERRQ(ierr); 5047 ierr = DMPlexGetIndicesPoint_Internal(cSec, b, bOff, &bEnd, PETSC_TRUE, (perms && perms[0]) ? perms[0][p] : NULL, indices);CHKERRQ(ierr); 5048 5049 ierr = PetscSectionGetOffset (aSec, b, &bOff);CHKERRQ(ierr); 5050 for (q = 0; q < bDof; q++) { 5051 PetscInt a = anchors[bOff + q], aOff; 5052 5053 /* we take the orientation of ap into account in the order that we constructed the indices above: the newly added points have no orientation */ 5054 5055 newPoints[2*(newP + q)] = a; 5056 newPoints[2*(newP + q) + 1] = 0; 5057 ierr = PetscSectionGetOffset(section, a, &aOff);CHKERRQ(ierr); 5058 ierr = DMPlexGetIndicesPoint_Internal(section, a, aOff, &bAnchorEnd, PETSC_TRUE, NULL, newIndices);CHKERRQ(ierr); 5059 } 5060 newP += bDof; 5061 5062 /* get the point-to-point submatrix */ 5063 if (outValues) { 5064 ierr = MatGetValues(cMat,bEnd,indices,bAnchorEnd,newIndices,pointMat[0] + pointMatOffsets[0][p]);CHKERRQ(ierr); 5065 } 5066 } 5067 else { 5068 newPoints[2 * newP] = b; 5069 newPoints[2 * newP + 1] = o; 5070 newP++; 5071 } 5072 } 5073 } 5074 5075 if (outValues) { 5076 ierr = DMGetWorkArray(dm,newNumIndices*numIndices,PETSC_SCALAR,&tmpValues);CHKERRQ(ierr); 5077 ierr = PetscMemzero(tmpValues,newNumIndices*numIndices*sizeof(*tmpValues));CHKERRQ(ierr); 5078 /* multiply constraints on the right */ 5079 if (numFields) { 5080 for (f = 0; f < numFields; f++) { 5081 PetscInt oldOff = offsets[f]; 5082 5083 for (p = 0; p < numPoints; p++) { 5084 PetscInt cStart = newPointOffsets[f][p]; 5085 PetscInt b = points[2 * p]; 5086 PetscInt c, r, k; 5087 PetscInt dof; 5088 5089 ierr = PetscSectionGetFieldDof(section,b,f,&dof);CHKERRQ(ierr); 5090 if (!dof) { 5091 continue; 5092 } 5093 if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) { 5094 PetscInt nCols = newPointOffsets[f][p+1]-cStart; 5095 const PetscScalar *mat = pointMat[f] + pointMatOffsets[f][p]; 5096 5097 for (r = 0; r < numIndices; r++) { 5098 for (c = 0; c < nCols; c++) { 5099 for (k = 0; k < dof; k++) { 5100 tmpValues[r * newNumIndices + cStart + c] += values[r * numIndices + oldOff + k] * mat[k * nCols + c]; 5101 } 5102 } 5103 } 5104 } 5105 else { 5106 /* copy this column as is */ 5107 for (r = 0; r < numIndices; r++) { 5108 for (c = 0; c < dof; c++) { 5109 tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c]; 5110 } 5111 } 5112 } 5113 oldOff += dof; 5114 } 5115 } 5116 } 5117 else { 5118 PetscInt oldOff = 0; 5119 for (p = 0; p < numPoints; p++) { 5120 PetscInt cStart = newPointOffsets[0][p]; 5121 PetscInt b = points[2 * p]; 5122 PetscInt c, r, k; 5123 PetscInt dof; 5124 5125 ierr = PetscSectionGetDof(section,b,&dof);CHKERRQ(ierr); 5126 if (!dof) { 5127 continue; 5128 } 5129 if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) { 5130 PetscInt nCols = newPointOffsets[0][p+1]-cStart; 5131 const PetscScalar *mat = pointMat[0] + pointMatOffsets[0][p]; 5132 5133 for (r = 0; r < numIndices; r++) { 5134 for (c = 0; c < nCols; c++) { 5135 for (k = 0; k < dof; k++) { 5136 tmpValues[r * newNumIndices + cStart + c] += mat[k * nCols + c] * values[r * numIndices + oldOff + k]; 5137 } 5138 } 5139 } 5140 } 5141 else { 5142 /* copy this column as is */ 5143 for (r = 0; r < numIndices; r++) { 5144 for (c = 0; c < dof; c++) { 5145 tmpValues[r * newNumIndices + cStart + c] = values[r * numIndices + oldOff + c]; 5146 } 5147 } 5148 } 5149 oldOff += dof; 5150 } 5151 } 5152 5153 if (multiplyLeft) { 5154 ierr = DMGetWorkArray(dm,newNumIndices*newNumIndices,PETSC_SCALAR,&newValues);CHKERRQ(ierr); 5155 ierr = PetscMemzero(newValues,newNumIndices*newNumIndices*sizeof(*newValues));CHKERRQ(ierr); 5156 /* multiply constraints transpose on the left */ 5157 if (numFields) { 5158 for (f = 0; f < numFields; f++) { 5159 PetscInt oldOff = offsets[f]; 5160 5161 for (p = 0; p < numPoints; p++) { 5162 PetscInt rStart = newPointOffsets[f][p]; 5163 PetscInt b = points[2 * p]; 5164 PetscInt c, r, k; 5165 PetscInt dof; 5166 5167 ierr = PetscSectionGetFieldDof(section,b,f,&dof);CHKERRQ(ierr); 5168 if (pointMatOffsets[f][p] < pointMatOffsets[f][p + 1]) { 5169 PetscInt nRows = newPointOffsets[f][p+1]-rStart; 5170 const PetscScalar *PETSC_RESTRICT mat = pointMat[f] + pointMatOffsets[f][p]; 5171 5172 for (r = 0; r < nRows; r++) { 5173 for (c = 0; c < newNumIndices; c++) { 5174 for (k = 0; k < dof; k++) { 5175 newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c]; 5176 } 5177 } 5178 } 5179 } 5180 else { 5181 /* copy this row as is */ 5182 for (r = 0; r < dof; r++) { 5183 for (c = 0; c < newNumIndices; c++) { 5184 newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c]; 5185 } 5186 } 5187 } 5188 oldOff += dof; 5189 } 5190 } 5191 } 5192 else { 5193 PetscInt oldOff = 0; 5194 5195 for (p = 0; p < numPoints; p++) { 5196 PetscInt rStart = newPointOffsets[0][p]; 5197 PetscInt b = points[2 * p]; 5198 PetscInt c, r, k; 5199 PetscInt dof; 5200 5201 ierr = PetscSectionGetDof(section,b,&dof);CHKERRQ(ierr); 5202 if (pointMatOffsets[0][p] < pointMatOffsets[0][p + 1]) { 5203 PetscInt nRows = newPointOffsets[0][p+1]-rStart; 5204 const PetscScalar *PETSC_RESTRICT mat = pointMat[0] + pointMatOffsets[0][p]; 5205 5206 for (r = 0; r < nRows; r++) { 5207 for (c = 0; c < newNumIndices; c++) { 5208 for (k = 0; k < dof; k++) { 5209 newValues[(rStart + r) * newNumIndices + c] += mat[k * nRows + r] * tmpValues[(oldOff + k) * newNumIndices + c]; 5210 } 5211 } 5212 } 5213 } 5214 else { 5215 /* copy this row as is */ 5216 for (r = 0; r < dof; r++) { 5217 for (c = 0; c < newNumIndices; c++) { 5218 newValues[(rStart + r) * newNumIndices + c] = tmpValues[(oldOff + r) * newNumIndices + c]; 5219 } 5220 } 5221 } 5222 oldOff += dof; 5223 } 5224 } 5225 5226 ierr = DMRestoreWorkArray(dm,newNumIndices*numIndices,PETSC_SCALAR,&tmpValues);CHKERRQ(ierr); 5227 } 5228 else { 5229 newValues = tmpValues; 5230 } 5231 } 5232 5233 /* clean up */ 5234 ierr = DMRestoreWorkArray(dm,maxDof,PETSC_INT,&indices);CHKERRQ(ierr); 5235 ierr = DMRestoreWorkArray(dm,maxAnchor*maxDof,PETSC_INT,&newIndices);CHKERRQ(ierr); 5236 5237 if (numFields) { 5238 for (f = 0; f < numFields; f++) { 5239 ierr = DMRestoreWorkArray(dm,pointMatOffsets[f][numPoints],PETSC_SCALAR,&pointMat[f]);CHKERRQ(ierr); 5240 ierr = DMRestoreWorkArray(dm,numPoints+1,PETSC_INT,&pointMatOffsets[f]);CHKERRQ(ierr); 5241 ierr = DMRestoreWorkArray(dm,numPoints+1,PETSC_INT,&newPointOffsets[f]);CHKERRQ(ierr); 5242 } 5243 } 5244 else { 5245 ierr = DMRestoreWorkArray(dm,pointMatOffsets[0][numPoints],PETSC_SCALAR,&pointMat[0]);CHKERRQ(ierr); 5246 ierr = DMRestoreWorkArray(dm,numPoints+1,PETSC_INT,&pointMatOffsets[0]);CHKERRQ(ierr); 5247 ierr = DMRestoreWorkArray(dm,numPoints+1,PETSC_INT,&newPointOffsets[0]);CHKERRQ(ierr); 5248 } 5249 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 5250 5251 /* output */ 5252 if (outPoints) { 5253 *outPoints = newPoints; 5254 } 5255 else { 5256 ierr = DMRestoreWorkArray(dm,2*newNumPoints,PETSC_INT,&newPoints);CHKERRQ(ierr); 5257 } 5258 if (outValues) { 5259 *outValues = newValues; 5260 } 5261 for (f = 0; f <= numFields; f++) { 5262 offsets[f] = newOffsets[f]; 5263 } 5264 PetscFunctionReturn(0); 5265 } 5266 5267 /*@C 5268 DMPlexGetClosureIndices - Get the global indices in a vector v for all points in the closure of the given point 5269 5270 Not collective 5271 5272 Input Parameters: 5273 + dm - The DM 5274 . section - The section describing the layout in v, or NULL to use the default section 5275 . globalSection - The section describing the parallel layout in v, or NULL to use the default section 5276 - point - The mesh point 5277 5278 Output parameters: 5279 + numIndices - The number of indices 5280 . indices - The indices 5281 - outOffsets - Field offset if not NULL 5282 5283 Note: Must call DMPlexRestoreClosureIndices() to free allocated memory 5284 5285 Level: advanced 5286 5287 .seealso DMPlexRestoreClosureIndices(), DMPlexVecGetClosure(), DMPlexMatSetClosure() 5288 @*/ 5289 PetscErrorCode DMPlexGetClosureIndices(DM dm, PetscSection section, PetscSection globalSection, PetscInt point, PetscInt *numIndices, PetscInt **indices, PetscInt *outOffsets) 5290 { 5291 PetscSection clSection; 5292 IS clPoints; 5293 const PetscInt *clp; 5294 const PetscInt **perms[32] = {NULL}; 5295 PetscInt *points = NULL, *pointsNew; 5296 PetscInt numPoints, numPointsNew; 5297 PetscInt offsets[32]; 5298 PetscInt Nf, Nind, NindNew, off, globalOff, f, p; 5299 PetscErrorCode ierr; 5300 5301 PetscFunctionBegin; 5302 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5303 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 5304 PetscValidHeaderSpecific(globalSection, PETSC_SECTION_CLASSID, 3); 5305 if (numIndices) PetscValidPointer(numIndices, 4); 5306 PetscValidPointer(indices, 5); 5307 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 5308 if (Nf > 31) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", Nf); 5309 ierr = PetscMemzero(offsets, 32 * sizeof(PetscInt));CHKERRQ(ierr); 5310 /* Get points in closure */ 5311 ierr = DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5312 /* Get number of indices and indices per field */ 5313 for (p = 0, Nind = 0; p < numPoints*2; p += 2) { 5314 PetscInt dof, fdof; 5315 5316 ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); 5317 for (f = 0; f < Nf; ++f) { 5318 ierr = PetscSectionGetFieldDof(section, points[p], f, &fdof);CHKERRQ(ierr); 5319 offsets[f+1] += fdof; 5320 } 5321 Nind += dof; 5322 } 5323 for (f = 1; f < Nf; ++f) offsets[f+1] += offsets[f]; 5324 if (Nf && offsets[Nf] != Nind) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", offsets[Nf], Nind); 5325 if (!Nf) offsets[1] = Nind; 5326 /* Get dual space symmetries */ 5327 for (f = 0; f < PetscMax(1,Nf); f++) { 5328 if (Nf) {ierr = PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5329 else {ierr = PetscSectionGetPointSyms(section,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5330 } 5331 /* Correct for hanging node constraints */ 5332 { 5333 ierr = DMPlexAnchorsModifyMat(dm, section, numPoints, Nind, points, perms, NULL, &numPointsNew, &NindNew, &pointsNew, NULL, offsets, PETSC_TRUE);CHKERRQ(ierr); 5334 if (numPointsNew) { 5335 for (f = 0; f < PetscMax(1,Nf); f++) { 5336 if (Nf) {ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5337 else {ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5338 } 5339 for (f = 0; f < PetscMax(1,Nf); f++) { 5340 if (Nf) {ierr = PetscSectionGetFieldPointSyms(section,f,numPointsNew,pointsNew,&perms[f],NULL);CHKERRQ(ierr);} 5341 else {ierr = PetscSectionGetPointSyms(section,numPointsNew,pointsNew,&perms[f],NULL);CHKERRQ(ierr);} 5342 } 5343 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5344 numPoints = numPointsNew; 5345 Nind = NindNew; 5346 points = pointsNew; 5347 } 5348 } 5349 /* Calculate indices */ 5350 ierr = DMGetWorkArray(dm, Nind, PETSC_INT, indices);CHKERRQ(ierr); 5351 if (Nf) { 5352 if (outOffsets) { 5353 PetscInt f; 5354 5355 for (f = 0; f <= Nf; f++) { 5356 outOffsets[f] = offsets[f]; 5357 } 5358 } 5359 for (p = 0; p < numPoints; p++) { 5360 ierr = PetscSectionGetOffset(globalSection, points[2*p], &globalOff);CHKERRQ(ierr); 5361 DMPlexGetIndicesPointFields_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, offsets, PETSC_FALSE, perms, p, *indices); 5362 } 5363 } else { 5364 for (p = 0, off = 0; p < numPoints; p++) { 5365 const PetscInt *perm = perms[0] ? perms[0][p] : NULL; 5366 5367 ierr = PetscSectionGetOffset(globalSection, points[2*p], &globalOff);CHKERRQ(ierr); 5368 DMPlexGetIndicesPoint_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, *indices); 5369 } 5370 } 5371 /* Cleanup points */ 5372 for (f = 0; f < PetscMax(1,Nf); f++) { 5373 if (Nf) {ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5374 else {ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],NULL);CHKERRQ(ierr);} 5375 } 5376 if (numPointsNew) { 5377 ierr = DMRestoreWorkArray(dm, 2*numPointsNew, PETSC_INT, &pointsNew);CHKERRQ(ierr); 5378 } else { 5379 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5380 } 5381 if (numIndices) *numIndices = Nind; 5382 PetscFunctionReturn(0); 5383 } 5384 5385 /*@C 5386 DMPlexRestoreClosureIndices - Restore the indices in a vector v for all points in the closure of the given point 5387 5388 Not collective 5389 5390 Input Parameters: 5391 + dm - The DM 5392 . section - The section describing the layout in v, or NULL to use the default section 5393 . globalSection - The section describing the parallel layout in v, or NULL to use the default section 5394 . point - The mesh point 5395 . numIndices - The number of indices 5396 . indices - The indices 5397 - outOffsets - Field offset if not NULL 5398 5399 Level: advanced 5400 5401 .seealso DMPlexGetClosureIndices(), DMPlexVecGetClosure(), DMPlexMatSetClosure() 5402 @*/ 5403 PetscErrorCode DMPlexRestoreClosureIndices(DM dm, PetscSection section, PetscSection globalSection, PetscInt point, PetscInt *numIndices, PetscInt **indices,PetscInt *outOffsets) 5404 { 5405 PetscErrorCode ierr; 5406 5407 PetscFunctionBegin; 5408 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5409 PetscValidPointer(indices, 5); 5410 ierr = DMRestoreWorkArray(dm, 0, PETSC_INT, indices);CHKERRQ(ierr); 5411 PetscFunctionReturn(0); 5412 } 5413 5414 /*@C 5415 DMPlexMatSetClosure - Set an array of the values on the closure of 'point' 5416 5417 Not collective 5418 5419 Input Parameters: 5420 + dm - The DM 5421 . section - The section describing the layout in v, or NULL to use the default section 5422 . globalSection - The section describing the layout in v, or NULL to use the default global section 5423 . A - The matrix 5424 . point - The point in the DM 5425 . values - The array of values 5426 - mode - The insert mode, where INSERT_ALL_VALUES and ADD_ALL_VALUES also overwrite boundary conditions 5427 5428 Fortran Notes: 5429 This routine is only available in Fortran 90, and you must include petsc.h90 in your code. 5430 5431 Level: intermediate 5432 5433 .seealso DMPlexVecGetClosure(), DMPlexVecSetClosure() 5434 @*/ 5435 PetscErrorCode DMPlexMatSetClosure(DM dm, PetscSection section, PetscSection globalSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 5436 { 5437 DM_Plex *mesh = (DM_Plex*) dm->data; 5438 PetscSection clSection; 5439 IS clPoints; 5440 PetscInt *points = NULL, *newPoints; 5441 const PetscInt *clp; 5442 PetscInt *indices; 5443 PetscInt offsets[32]; 5444 const PetscInt **perms[32] = {NULL}; 5445 const PetscScalar **flips[32] = {NULL}; 5446 PetscInt numFields, numPoints, newNumPoints, numIndices, newNumIndices, dof, off, globalOff, p, f; 5447 PetscScalar *valCopy = NULL; 5448 PetscScalar *newValues; 5449 PetscErrorCode ierr; 5450 5451 PetscFunctionBegin; 5452 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5453 if (!section) {ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);} 5454 PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 2); 5455 if (!globalSection) {ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr);} 5456 PetscValidHeaderSpecific(globalSection, PETSC_SECTION_CLASSID, 3); 5457 PetscValidHeaderSpecific(A, MAT_CLASSID, 4); 5458 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 5459 if (numFields > 31) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields); 5460 ierr = PetscMemzero(offsets, 32 * sizeof(PetscInt));CHKERRQ(ierr); 5461 ierr = DMPlexGetCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5462 for (p = 0, numIndices = 0; p < numPoints*2; p += 2) { 5463 PetscInt fdof; 5464 5465 ierr = PetscSectionGetDof(section, points[p], &dof);CHKERRQ(ierr); 5466 for (f = 0; f < numFields; ++f) { 5467 ierr = PetscSectionGetFieldDof(section, points[p], f, &fdof);CHKERRQ(ierr); 5468 offsets[f+1] += fdof; 5469 } 5470 numIndices += dof; 5471 } 5472 for (f = 1; f < numFields; ++f) offsets[f+1] += offsets[f]; 5473 5474 if (numFields && offsets[numFields] != numIndices) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", offsets[numFields], numIndices); 5475 /* Get symmetries */ 5476 for (f = 0; f < PetscMax(1,numFields); f++) { 5477 if (numFields) {ierr = PetscSectionGetFieldPointSyms(section,f,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 5478 else {ierr = PetscSectionGetPointSyms(section,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 5479 if (values && flips[f]) { /* may need to apply sign changes to the element matrix */ 5480 PetscInt foffset = offsets[f]; 5481 5482 for (p = 0; p < numPoints; p++) { 5483 PetscInt point = points[2*p], fdof; 5484 const PetscScalar *flip = flips[f] ? flips[f][p] : NULL; 5485 5486 if (!numFields) { 5487 ierr = PetscSectionGetDof(section,point,&fdof);CHKERRQ(ierr); 5488 } else { 5489 ierr = PetscSectionGetFieldDof(section,point,f,&fdof);CHKERRQ(ierr); 5490 } 5491 if (flip) { 5492 PetscInt i, j, k; 5493 5494 if (!valCopy) { 5495 ierr = DMGetWorkArray(dm,numIndices*numIndices,PETSC_SCALAR,&valCopy);CHKERRQ(ierr); 5496 for (j = 0; j < numIndices * numIndices; j++) valCopy[j] = values[j]; 5497 values = valCopy; 5498 } 5499 for (i = 0; i < fdof; i++) { 5500 PetscScalar fval = flip[i]; 5501 5502 for (k = 0; k < numIndices; k++) { 5503 valCopy[numIndices * (foffset + i) + k] *= fval; 5504 valCopy[numIndices * k + (foffset + i)] *= fval; 5505 } 5506 } 5507 } 5508 foffset += fdof; 5509 } 5510 } 5511 } 5512 ierr = DMPlexAnchorsModifyMat(dm,section,numPoints,numIndices,points,perms,values,&newNumPoints,&newNumIndices,&newPoints,&newValues,offsets,PETSC_TRUE);CHKERRQ(ierr); 5513 if (newNumPoints) { 5514 if (valCopy) { 5515 ierr = DMRestoreWorkArray(dm,numIndices*numIndices,PETSC_SCALAR,&valCopy);CHKERRQ(ierr); 5516 } 5517 for (f = 0; f < PetscMax(1,numFields); f++) { 5518 if (numFields) {ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 5519 else {ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 5520 } 5521 for (f = 0; f < PetscMax(1,numFields); f++) { 5522 if (numFields) {ierr = PetscSectionGetFieldPointSyms(section,f,newNumPoints,newPoints,&perms[f],&flips[f]);CHKERRQ(ierr);} 5523 else {ierr = PetscSectionGetPointSyms(section,newNumPoints,newPoints,&perms[f],&flips[f]);CHKERRQ(ierr);} 5524 } 5525 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5526 numPoints = newNumPoints; 5527 numIndices = newNumIndices; 5528 points = newPoints; 5529 values = newValues; 5530 } 5531 ierr = DMGetWorkArray(dm, numIndices, PETSC_INT, &indices);CHKERRQ(ierr); 5532 if (numFields) { 5533 for (p = 0; p < numPoints; p++) { 5534 ierr = PetscSectionGetOffset(globalSection, points[2*p], &globalOff);CHKERRQ(ierr); 5535 DMPlexGetIndicesPointFields_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, offsets, PETSC_FALSE, perms, p, indices); 5536 } 5537 } else { 5538 for (p = 0, off = 0; p < numPoints; p++) { 5539 const PetscInt *perm = perms[0] ? perms[0][p] : NULL; 5540 ierr = PetscSectionGetOffset(globalSection, points[2*p], &globalOff);CHKERRQ(ierr); 5541 DMPlexGetIndicesPoint_Internal(section, points[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, indices); 5542 } 5543 } 5544 if (mesh->printSetValues) {ierr = DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numIndices, indices, 0, NULL, values);CHKERRQ(ierr);} 5545 ierr = MatSetValues(A, numIndices, indices, numIndices, indices, values, mode); 5546 if (mesh->printFEM > 1) { 5547 PetscInt i; 5548 ierr = PetscPrintf(PETSC_COMM_SELF, " Indices:");CHKERRQ(ierr); 5549 for (i = 0; i < numIndices; ++i) {ierr = PetscPrintf(PETSC_COMM_SELF, " %D", indices[i]);CHKERRQ(ierr);} 5550 ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr); 5551 } 5552 if (ierr) { 5553 PetscMPIInt rank; 5554 PetscErrorCode ierr2; 5555 5556 ierr2 = MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);CHKERRQ(ierr2); 5557 ierr2 = (*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank);CHKERRQ(ierr2); 5558 ierr2 = DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numIndices, indices, 0, NULL, values);CHKERRQ(ierr2); 5559 ierr2 = DMRestoreWorkArray(dm, numIndices, PETSC_INT, &indices);CHKERRQ(ierr2); 5560 CHKERRQ(ierr); 5561 } 5562 for (f = 0; f < PetscMax(1,numFields); f++) { 5563 if (numFields) {ierr = PetscSectionRestoreFieldPointSyms(section,f,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 5564 else {ierr = PetscSectionRestorePointSyms(section,numPoints,points,&perms[f],&flips[f]);CHKERRQ(ierr);} 5565 } 5566 if (newNumPoints) { 5567 ierr = DMRestoreWorkArray(dm,newNumIndices*newNumIndices,PETSC_SCALAR,&newValues);CHKERRQ(ierr); 5568 ierr = DMRestoreWorkArray(dm,2*newNumPoints,PETSC_INT,&newPoints);CHKERRQ(ierr); 5569 } 5570 else { 5571 if (valCopy) { 5572 ierr = DMRestoreWorkArray(dm,numIndices*numIndices,PETSC_SCALAR,&valCopy);CHKERRQ(ierr); 5573 } 5574 ierr = DMPlexRestoreCompressedClosure(dm,section,point,&numPoints,&points,&clSection,&clPoints,&clp);CHKERRQ(ierr); 5575 } 5576 ierr = DMRestoreWorkArray(dm, numIndices, PETSC_INT, &indices);CHKERRQ(ierr); 5577 PetscFunctionReturn(0); 5578 } 5579 5580 PetscErrorCode DMPlexMatSetClosureRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, Mat A, PetscInt point, const PetscScalar values[], InsertMode mode) 5581 { 5582 DM_Plex *mesh = (DM_Plex*) dmf->data; 5583 PetscInt *fpoints = NULL, *ftotpoints = NULL; 5584 PetscInt *cpoints = NULL; 5585 PetscInt *findices, *cindices; 5586 PetscInt foffsets[32], coffsets[32]; 5587 CellRefiner cellRefiner; 5588 PetscInt numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f; 5589 PetscErrorCode ierr; 5590 5591 PetscFunctionBegin; 5592 PetscValidHeaderSpecific(dmf, DM_CLASSID, 1); 5593 PetscValidHeaderSpecific(dmc, DM_CLASSID, 4); 5594 if (!fsection) {ierr = DMGetDefaultSection(dmf, &fsection);CHKERRQ(ierr);} 5595 PetscValidHeaderSpecific(fsection, PETSC_SECTION_CLASSID, 2); 5596 if (!csection) {ierr = DMGetDefaultSection(dmc, &csection);CHKERRQ(ierr);} 5597 PetscValidHeaderSpecific(csection, PETSC_SECTION_CLASSID, 5); 5598 if (!globalFSection) {ierr = DMGetDefaultGlobalSection(dmf, &globalFSection);CHKERRQ(ierr);} 5599 PetscValidHeaderSpecific(globalFSection, PETSC_SECTION_CLASSID, 3); 5600 if (!globalCSection) {ierr = DMGetDefaultGlobalSection(dmc, &globalCSection);CHKERRQ(ierr);} 5601 PetscValidHeaderSpecific(globalCSection, PETSC_SECTION_CLASSID, 6); 5602 PetscValidHeaderSpecific(A, MAT_CLASSID, 7); 5603 ierr = PetscSectionGetNumFields(fsection, &numFields);CHKERRQ(ierr); 5604 if (numFields > 31) SETERRQ1(PetscObjectComm((PetscObject)dmf), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields); 5605 ierr = PetscMemzero(foffsets, 32 * sizeof(PetscInt));CHKERRQ(ierr); 5606 ierr = PetscMemzero(coffsets, 32 * sizeof(PetscInt));CHKERRQ(ierr); 5607 /* Column indices */ 5608 ierr = DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);CHKERRQ(ierr); 5609 maxFPoints = numCPoints; 5610 /* Compress out points not in the section */ 5611 /* TODO: Squeeze out points with 0 dof as well */ 5612 ierr = PetscSectionGetChart(csection, &pStart, &pEnd);CHKERRQ(ierr); 5613 for (p = 0, q = 0; p < numCPoints*2; p += 2) { 5614 if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) { 5615 cpoints[q*2] = cpoints[p]; 5616 cpoints[q*2+1] = cpoints[p+1]; 5617 ++q; 5618 } 5619 } 5620 numCPoints = q; 5621 for (p = 0, numCIndices = 0; p < numCPoints*2; p += 2) { 5622 PetscInt fdof; 5623 5624 ierr = PetscSectionGetDof(csection, cpoints[p], &dof);CHKERRQ(ierr); 5625 if (!dof) continue; 5626 for (f = 0; f < numFields; ++f) { 5627 ierr = PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof);CHKERRQ(ierr); 5628 coffsets[f+1] += fdof; 5629 } 5630 numCIndices += dof; 5631 } 5632 for (f = 1; f < numFields; ++f) coffsets[f+1] += coffsets[f]; 5633 /* Row indices */ 5634 ierr = DMPlexGetCellRefiner_Internal(dmc, &cellRefiner);CHKERRQ(ierr); 5635 ierr = CellRefinerGetAffineTransforms_Internal(cellRefiner, &numSubcells, NULL, NULL, NULL);CHKERRQ(ierr); 5636 ierr = DMGetWorkArray(dmf, maxFPoints*2*numSubcells, PETSC_INT, &ftotpoints);CHKERRQ(ierr); 5637 for (r = 0, q = 0; r < numSubcells; ++r) { 5638 /* TODO Map from coarse to fine cells */ 5639 ierr = DMPlexGetTransitiveClosure(dmf, point*numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints);CHKERRQ(ierr); 5640 /* Compress out points not in the section */ 5641 ierr = PetscSectionGetChart(fsection, &pStart, &pEnd);CHKERRQ(ierr); 5642 for (p = 0; p < numFPoints*2; p += 2) { 5643 if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) { 5644 ierr = PetscSectionGetDof(fsection, fpoints[p], &dof);CHKERRQ(ierr); 5645 if (!dof) continue; 5646 for (s = 0; s < q; ++s) if (fpoints[p] == ftotpoints[s*2]) break; 5647 if (s < q) continue; 5648 ftotpoints[q*2] = fpoints[p]; 5649 ftotpoints[q*2+1] = fpoints[p+1]; 5650 ++q; 5651 } 5652 } 5653 ierr = DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints);CHKERRQ(ierr); 5654 } 5655 numFPoints = q; 5656 for (p = 0, numFIndices = 0; p < numFPoints*2; p += 2) { 5657 PetscInt fdof; 5658 5659 ierr = PetscSectionGetDof(fsection, ftotpoints[p], &dof);CHKERRQ(ierr); 5660 if (!dof) continue; 5661 for (f = 0; f < numFields; ++f) { 5662 ierr = PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof);CHKERRQ(ierr); 5663 foffsets[f+1] += fdof; 5664 } 5665 numFIndices += dof; 5666 } 5667 for (f = 1; f < numFields; ++f) foffsets[f+1] += foffsets[f]; 5668 5669 if (numFields && foffsets[numFields] != numFIndices) SETERRQ2(PetscObjectComm((PetscObject)dmf), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", foffsets[numFields], numFIndices); 5670 if (numFields && coffsets[numFields] != numCIndices) SETERRQ2(PetscObjectComm((PetscObject)dmc), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", coffsets[numFields], numCIndices); 5671 ierr = DMGetWorkArray(dmf, numFIndices, PETSC_INT, &findices);CHKERRQ(ierr); 5672 ierr = DMGetWorkArray(dmc, numCIndices, PETSC_INT, &cindices);CHKERRQ(ierr); 5673 if (numFields) { 5674 const PetscInt **permsF[32] = {NULL}; 5675 const PetscInt **permsC[32] = {NULL}; 5676 5677 for (f = 0; f < numFields; f++) { 5678 ierr = PetscSectionGetFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);CHKERRQ(ierr); 5679 ierr = PetscSectionGetFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);CHKERRQ(ierr); 5680 } 5681 for (p = 0; p < numFPoints; p++) { 5682 ierr = PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);CHKERRQ(ierr); 5683 DMPlexGetIndicesPointFields_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, foffsets, PETSC_FALSE, permsF, p, findices); 5684 } 5685 for (p = 0; p < numCPoints; p++) { 5686 ierr = PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);CHKERRQ(ierr); 5687 DMPlexGetIndicesPointFields_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cindices); 5688 } 5689 for (f = 0; f < numFields; f++) { 5690 ierr = PetscSectionRestoreFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);CHKERRQ(ierr); 5691 ierr = PetscSectionRestoreFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);CHKERRQ(ierr); 5692 } 5693 } else { 5694 const PetscInt **permsF = NULL; 5695 const PetscInt **permsC = NULL; 5696 5697 ierr = PetscSectionGetPointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);CHKERRQ(ierr); 5698 ierr = PetscSectionGetPointSyms(csection,numCPoints,cpoints,&permsC,NULL);CHKERRQ(ierr); 5699 for (p = 0, off = 0; p < numFPoints; p++) { 5700 const PetscInt *perm = permsF ? permsF[p] : NULL; 5701 5702 ierr = PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);CHKERRQ(ierr); 5703 ierr = DMPlexGetIndicesPoint_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, findices);CHKERRQ(ierr); 5704 } 5705 for (p = 0, off = 0; p < numCPoints; p++) { 5706 const PetscInt *perm = permsC ? permsC[p] : NULL; 5707 5708 ierr = PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);CHKERRQ(ierr); 5709 ierr = DMPlexGetIndicesPoint_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, cindices);CHKERRQ(ierr); 5710 } 5711 ierr = PetscSectionRestorePointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);CHKERRQ(ierr); 5712 ierr = PetscSectionRestorePointSyms(csection,numCPoints,cpoints,&permsC,NULL);CHKERRQ(ierr); 5713 } 5714 if (mesh->printSetValues) {ierr = DMPlexPrintMatSetValues(PETSC_VIEWER_STDOUT_SELF, A, point, numFIndices, findices, numCIndices, cindices, values);CHKERRQ(ierr);} 5715 /* TODO: flips */ 5716 ierr = MatSetValues(A, numFIndices, findices, numCIndices, cindices, values, mode); 5717 if (ierr) { 5718 PetscMPIInt rank; 5719 PetscErrorCode ierr2; 5720 5721 ierr2 = MPI_Comm_rank(PetscObjectComm((PetscObject)A), &rank);CHKERRQ(ierr2); 5722 ierr2 = (*PetscErrorPrintf)("[%d]ERROR in DMPlexMatSetClosure\n", rank);CHKERRQ(ierr2); 5723 ierr2 = DMPlexPrintMatSetValues(PETSC_VIEWER_STDERR_SELF, A, point, numFIndices, findices, numCIndices, cindices, values);CHKERRQ(ierr2); 5724 ierr2 = DMRestoreWorkArray(dmf, numFIndices, PETSC_INT, &findices);CHKERRQ(ierr2); 5725 ierr2 = DMRestoreWorkArray(dmc, numCIndices, PETSC_INT, &cindices);CHKERRQ(ierr2); 5726 CHKERRQ(ierr); 5727 } 5728 ierr = DMRestoreWorkArray(dmf, numCPoints*2*4, PETSC_INT, &ftotpoints);CHKERRQ(ierr); 5729 ierr = DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);CHKERRQ(ierr); 5730 ierr = DMRestoreWorkArray(dmf, numFIndices, PETSC_INT, &findices);CHKERRQ(ierr); 5731 ierr = DMRestoreWorkArray(dmc, numCIndices, PETSC_INT, &cindices);CHKERRQ(ierr); 5732 PetscFunctionReturn(0); 5733 } 5734 5735 PetscErrorCode DMPlexMatGetClosureIndicesRefined(DM dmf, PetscSection fsection, PetscSection globalFSection, DM dmc, PetscSection csection, PetscSection globalCSection, PetscInt point, PetscInt cindices[], PetscInt findices[]) 5736 { 5737 PetscInt *fpoints = NULL, *ftotpoints = NULL; 5738 PetscInt *cpoints = NULL; 5739 PetscInt foffsets[32], coffsets[32]; 5740 CellRefiner cellRefiner; 5741 PetscInt numFields, numSubcells, maxFPoints, numFPoints, numCPoints, numFIndices, numCIndices, dof, off, globalOff, pStart, pEnd, p, q, r, s, f; 5742 PetscErrorCode ierr; 5743 5744 PetscFunctionBegin; 5745 PetscValidHeaderSpecific(dmf, DM_CLASSID, 1); 5746 PetscValidHeaderSpecific(dmc, DM_CLASSID, 4); 5747 if (!fsection) {ierr = DMGetDefaultSection(dmf, &fsection);CHKERRQ(ierr);} 5748 PetscValidHeaderSpecific(fsection, PETSC_SECTION_CLASSID, 2); 5749 if (!csection) {ierr = DMGetDefaultSection(dmc, &csection);CHKERRQ(ierr);} 5750 PetscValidHeaderSpecific(csection, PETSC_SECTION_CLASSID, 5); 5751 if (!globalFSection) {ierr = DMGetDefaultGlobalSection(dmf, &globalFSection);CHKERRQ(ierr);} 5752 PetscValidHeaderSpecific(globalFSection, PETSC_SECTION_CLASSID, 3); 5753 if (!globalCSection) {ierr = DMGetDefaultGlobalSection(dmc, &globalCSection);CHKERRQ(ierr);} 5754 PetscValidHeaderSpecific(globalCSection, PETSC_SECTION_CLASSID, 6); 5755 ierr = PetscSectionGetNumFields(fsection, &numFields);CHKERRQ(ierr); 5756 if (numFields > 31) SETERRQ1(PetscObjectComm((PetscObject)dmf), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields %D limited to 31", numFields); 5757 ierr = PetscMemzero(foffsets, 32 * sizeof(PetscInt));CHKERRQ(ierr); 5758 ierr = PetscMemzero(coffsets, 32 * sizeof(PetscInt));CHKERRQ(ierr); 5759 /* Column indices */ 5760 ierr = DMPlexGetTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);CHKERRQ(ierr); 5761 maxFPoints = numCPoints; 5762 /* Compress out points not in the section */ 5763 /* TODO: Squeeze out points with 0 dof as well */ 5764 ierr = PetscSectionGetChart(csection, &pStart, &pEnd);CHKERRQ(ierr); 5765 for (p = 0, q = 0; p < numCPoints*2; p += 2) { 5766 if ((cpoints[p] >= pStart) && (cpoints[p] < pEnd)) { 5767 cpoints[q*2] = cpoints[p]; 5768 cpoints[q*2+1] = cpoints[p+1]; 5769 ++q; 5770 } 5771 } 5772 numCPoints = q; 5773 for (p = 0, numCIndices = 0; p < numCPoints*2; p += 2) { 5774 PetscInt fdof; 5775 5776 ierr = PetscSectionGetDof(csection, cpoints[p], &dof);CHKERRQ(ierr); 5777 if (!dof) continue; 5778 for (f = 0; f < numFields; ++f) { 5779 ierr = PetscSectionGetFieldDof(csection, cpoints[p], f, &fdof);CHKERRQ(ierr); 5780 coffsets[f+1] += fdof; 5781 } 5782 numCIndices += dof; 5783 } 5784 for (f = 1; f < numFields; ++f) coffsets[f+1] += coffsets[f]; 5785 /* Row indices */ 5786 ierr = DMPlexGetCellRefiner_Internal(dmc, &cellRefiner);CHKERRQ(ierr); 5787 ierr = CellRefinerGetAffineTransforms_Internal(cellRefiner, &numSubcells, NULL, NULL, NULL);CHKERRQ(ierr); 5788 ierr = DMGetWorkArray(dmf, maxFPoints*2*numSubcells, PETSC_INT, &ftotpoints);CHKERRQ(ierr); 5789 for (r = 0, q = 0; r < numSubcells; ++r) { 5790 /* TODO Map from coarse to fine cells */ 5791 ierr = DMPlexGetTransitiveClosure(dmf, point*numSubcells + r, PETSC_TRUE, &numFPoints, &fpoints);CHKERRQ(ierr); 5792 /* Compress out points not in the section */ 5793 ierr = PetscSectionGetChart(fsection, &pStart, &pEnd);CHKERRQ(ierr); 5794 for (p = 0; p < numFPoints*2; p += 2) { 5795 if ((fpoints[p] >= pStart) && (fpoints[p] < pEnd)) { 5796 ierr = PetscSectionGetDof(fsection, fpoints[p], &dof);CHKERRQ(ierr); 5797 if (!dof) continue; 5798 for (s = 0; s < q; ++s) if (fpoints[p] == ftotpoints[s*2]) break; 5799 if (s < q) continue; 5800 ftotpoints[q*2] = fpoints[p]; 5801 ftotpoints[q*2+1] = fpoints[p+1]; 5802 ++q; 5803 } 5804 } 5805 ierr = DMPlexRestoreTransitiveClosure(dmf, point, PETSC_TRUE, &numFPoints, &fpoints);CHKERRQ(ierr); 5806 } 5807 numFPoints = q; 5808 for (p = 0, numFIndices = 0; p < numFPoints*2; p += 2) { 5809 PetscInt fdof; 5810 5811 ierr = PetscSectionGetDof(fsection, ftotpoints[p], &dof);CHKERRQ(ierr); 5812 if (!dof) continue; 5813 for (f = 0; f < numFields; ++f) { 5814 ierr = PetscSectionGetFieldDof(fsection, ftotpoints[p], f, &fdof);CHKERRQ(ierr); 5815 foffsets[f+1] += fdof; 5816 } 5817 numFIndices += dof; 5818 } 5819 for (f = 1; f < numFields; ++f) foffsets[f+1] += foffsets[f]; 5820 5821 if (numFields && foffsets[numFields] != numFIndices) SETERRQ2(PetscObjectComm((PetscObject)dmf), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", foffsets[numFields], numFIndices); 5822 if (numFields && coffsets[numFields] != numCIndices) SETERRQ2(PetscObjectComm((PetscObject)dmc), PETSC_ERR_PLIB, "Invalid size for closure %D should be %D", coffsets[numFields], numCIndices); 5823 if (numFields) { 5824 const PetscInt **permsF[32] = {NULL}; 5825 const PetscInt **permsC[32] = {NULL}; 5826 5827 for (f = 0; f < numFields; f++) { 5828 ierr = PetscSectionGetFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);CHKERRQ(ierr); 5829 ierr = PetscSectionGetFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);CHKERRQ(ierr); 5830 } 5831 for (p = 0; p < numFPoints; p++) { 5832 ierr = PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);CHKERRQ(ierr); 5833 DMPlexGetIndicesPointFields_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, foffsets, PETSC_FALSE, permsF, p, findices); 5834 } 5835 for (p = 0; p < numCPoints; p++) { 5836 ierr = PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);CHKERRQ(ierr); 5837 DMPlexGetIndicesPointFields_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, coffsets, PETSC_FALSE, permsC, p, cindices); 5838 } 5839 for (f = 0; f < numFields; f++) { 5840 ierr = PetscSectionRestoreFieldPointSyms(fsection,f,numFPoints,ftotpoints,&permsF[f],NULL);CHKERRQ(ierr); 5841 ierr = PetscSectionRestoreFieldPointSyms(csection,f,numCPoints,cpoints,&permsC[f],NULL);CHKERRQ(ierr); 5842 } 5843 } else { 5844 const PetscInt **permsF = NULL; 5845 const PetscInt **permsC = NULL; 5846 5847 ierr = PetscSectionGetPointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);CHKERRQ(ierr); 5848 ierr = PetscSectionGetPointSyms(csection,numCPoints,cpoints,&permsC,NULL);CHKERRQ(ierr); 5849 for (p = 0, off = 0; p < numFPoints; p++) { 5850 const PetscInt *perm = permsF ? permsF[p] : NULL; 5851 5852 ierr = PetscSectionGetOffset(globalFSection, ftotpoints[2*p], &globalOff);CHKERRQ(ierr); 5853 DMPlexGetIndicesPoint_Internal(fsection, ftotpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, findices); 5854 } 5855 for (p = 0, off = 0; p < numCPoints; p++) { 5856 const PetscInt *perm = permsC ? permsC[p] : NULL; 5857 5858 ierr = PetscSectionGetOffset(globalCSection, cpoints[2*p], &globalOff);CHKERRQ(ierr); 5859 DMPlexGetIndicesPoint_Internal(csection, cpoints[2*p], globalOff < 0 ? -(globalOff+1) : globalOff, &off, PETSC_FALSE, perm, cindices); 5860 } 5861 ierr = PetscSectionRestorePointSyms(fsection,numFPoints,ftotpoints,&permsF,NULL);CHKERRQ(ierr); 5862 ierr = PetscSectionRestorePointSyms(csection,numCPoints,cpoints,&permsC,NULL);CHKERRQ(ierr); 5863 } 5864 ierr = DMRestoreWorkArray(dmf, numCPoints*2*4, PETSC_INT, &ftotpoints);CHKERRQ(ierr); 5865 ierr = DMPlexRestoreTransitiveClosure(dmc, point, PETSC_TRUE, &numCPoints, &cpoints);CHKERRQ(ierr); 5866 PetscFunctionReturn(0); 5867 } 5868 5869 /*@ 5870 DMPlexGetHybridBounds - Get the first mesh point of each dimension which is a hybrid 5871 5872 Input Parameter: 5873 . dm - The DMPlex object 5874 5875 Output Parameters: 5876 + cMax - The first hybrid cell 5877 . fMax - The first hybrid face 5878 . eMax - The first hybrid edge 5879 - vMax - The first hybrid vertex 5880 5881 Level: developer 5882 5883 .seealso DMPlexCreateHybridMesh(), DMPlexSetHybridBounds() 5884 @*/ 5885 PetscErrorCode DMPlexGetHybridBounds(DM dm, PetscInt *cMax, PetscInt *fMax, PetscInt *eMax, PetscInt *vMax) 5886 { 5887 DM_Plex *mesh = (DM_Plex*) dm->data; 5888 PetscInt dim; 5889 PetscErrorCode ierr; 5890 5891 PetscFunctionBegin; 5892 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5893 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 5894 if (cMax) *cMax = mesh->hybridPointMax[dim]; 5895 if (fMax) *fMax = mesh->hybridPointMax[dim-1]; 5896 if (eMax) *eMax = mesh->hybridPointMax[1]; 5897 if (vMax) *vMax = mesh->hybridPointMax[0]; 5898 PetscFunctionReturn(0); 5899 } 5900 5901 /*@ 5902 DMPlexSetHybridBounds - Set the first mesh point of each dimension which is a hybrid 5903 5904 Input Parameters: 5905 . dm - The DMPlex object 5906 . cMax - The first hybrid cell 5907 . fMax - The first hybrid face 5908 . eMax - The first hybrid edge 5909 - vMax - The first hybrid vertex 5910 5911 Level: developer 5912 5913 .seealso DMPlexCreateHybridMesh(), DMPlexGetHybridBounds() 5914 @*/ 5915 PetscErrorCode DMPlexSetHybridBounds(DM dm, PetscInt cMax, PetscInt fMax, PetscInt eMax, PetscInt vMax) 5916 { 5917 DM_Plex *mesh = (DM_Plex*) dm->data; 5918 PetscInt dim; 5919 PetscErrorCode ierr; 5920 5921 PetscFunctionBegin; 5922 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5923 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 5924 if (cMax >= 0) mesh->hybridPointMax[dim] = cMax; 5925 if (fMax >= 0) mesh->hybridPointMax[dim-1] = fMax; 5926 if (eMax >= 0) mesh->hybridPointMax[1] = eMax; 5927 if (vMax >= 0) mesh->hybridPointMax[0] = vMax; 5928 PetscFunctionReturn(0); 5929 } 5930 5931 /*@C 5932 DMPlexGetVTKCellHeight - Returns the height in the DAG used to determine which points are cells (normally 0) 5933 5934 Input Parameter: 5935 . dm - The DMPlex object 5936 5937 Output Parameter: 5938 . cellHeight - The height of a cell 5939 5940 Level: developer 5941 5942 .seealso DMPlexSetVTKCellHeight() 5943 @*/ 5944 PetscErrorCode DMPlexGetVTKCellHeight(DM dm, PetscInt *cellHeight) 5945 { 5946 DM_Plex *mesh = (DM_Plex*) dm->data; 5947 5948 PetscFunctionBegin; 5949 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5950 PetscValidPointer(cellHeight, 2); 5951 *cellHeight = mesh->vtkCellHeight; 5952 PetscFunctionReturn(0); 5953 } 5954 5955 /*@C 5956 DMPlexSetVTKCellHeight - Sets the height in the DAG used to determine which points are cells (normally 0) 5957 5958 Input Parameters: 5959 + dm - The DMPlex object 5960 - cellHeight - The height of a cell 5961 5962 Level: developer 5963 5964 .seealso DMPlexGetVTKCellHeight() 5965 @*/ 5966 PetscErrorCode DMPlexSetVTKCellHeight(DM dm, PetscInt cellHeight) 5967 { 5968 DM_Plex *mesh = (DM_Plex*) dm->data; 5969 5970 PetscFunctionBegin; 5971 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 5972 mesh->vtkCellHeight = cellHeight; 5973 PetscFunctionReturn(0); 5974 } 5975 5976 /* We can easily have a form that takes an IS instead */ 5977 static PetscErrorCode DMPlexCreateNumbering_Private(DM dm, PetscInt pStart, PetscInt pEnd, PetscInt shift, PetscInt *globalSize, PetscSF sf, IS *numbering) 5978 { 5979 PetscSection section, globalSection; 5980 PetscInt *numbers, p; 5981 PetscErrorCode ierr; 5982 5983 PetscFunctionBegin; 5984 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ion);CHKERRQ(ierr); 5985 ierr = PetscSectionSetChart(section, pStart, pEnd);CHKERRQ(ierr); 5986 for (p = pStart; p < pEnd; ++p) { 5987 ierr = PetscSectionSetDof(section, p, 1);CHKERRQ(ierr); 5988 } 5989 ierr = PetscSectionSetUp(section);CHKERRQ(ierr); 5990 ierr = PetscSectionCreateGlobalSection(section, sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr); 5991 ierr = PetscMalloc1(pEnd - pStart, &numbers);CHKERRQ(ierr); 5992 for (p = pStart; p < pEnd; ++p) { 5993 ierr = PetscSectionGetOffset(globalSection, p, &numbers[p-pStart]);CHKERRQ(ierr); 5994 if (numbers[p-pStart] < 0) numbers[p-pStart] -= shift; 5995 else numbers[p-pStart] += shift; 5996 } 5997 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) dm), pEnd - pStart, numbers, PETSC_OWN_POINTER, numbering);CHKERRQ(ierr); 5998 if (globalSize) { 5999 PetscLayout layout; 6000 ierr = PetscSectionGetPointLayout(PetscObjectComm((PetscObject) dm), globalSection, &layout);CHKERRQ(ierr); 6001 ierr = PetscLayoutGetSize(layout, globalSize);CHKERRQ(ierr); 6002 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 6003 } 6004 ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr); 6005 ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr); 6006 PetscFunctionReturn(0); 6007 } 6008 6009 PetscErrorCode DMPlexCreateCellNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalCellNumbers) 6010 { 6011 PetscInt cellHeight, cStart, cEnd, cMax; 6012 PetscErrorCode ierr; 6013 6014 PetscFunctionBegin; 6015 ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr); 6016 ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); 6017 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 6018 if (cMax >= 0 && !includeHybrid) cEnd = PetscMin(cEnd, cMax); 6019 ierr = DMPlexCreateNumbering_Private(dm, cStart, cEnd, 0, NULL, dm->sf, globalCellNumbers);CHKERRQ(ierr); 6020 PetscFunctionReturn(0); 6021 } 6022 6023 /*@C 6024 DMPlexGetCellNumbering - Get a global cell numbering for all cells on this process 6025 6026 Input Parameter: 6027 . dm - The DMPlex object 6028 6029 Output Parameter: 6030 . globalCellNumbers - Global cell numbers for all cells on this process 6031 6032 Level: developer 6033 6034 .seealso DMPlexGetVertexNumbering() 6035 @*/ 6036 PetscErrorCode DMPlexGetCellNumbering(DM dm, IS *globalCellNumbers) 6037 { 6038 DM_Plex *mesh = (DM_Plex*) dm->data; 6039 PetscErrorCode ierr; 6040 6041 PetscFunctionBegin; 6042 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6043 if (!mesh->globalCellNumbers) {ierr = DMPlexCreateCellNumbering_Internal(dm, PETSC_FALSE, &mesh->globalCellNumbers);CHKERRQ(ierr);} 6044 *globalCellNumbers = mesh->globalCellNumbers; 6045 PetscFunctionReturn(0); 6046 } 6047 6048 PetscErrorCode DMPlexCreateVertexNumbering_Internal(DM dm, PetscBool includeHybrid, IS *globalVertexNumbers) 6049 { 6050 PetscInt vStart, vEnd, vMax; 6051 PetscErrorCode ierr; 6052 6053 PetscFunctionBegin; 6054 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6055 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 6056 ierr = DMPlexGetHybridBounds(dm, NULL, NULL, NULL, &vMax);CHKERRQ(ierr); 6057 if (vMax >= 0 && !includeHybrid) vEnd = PetscMin(vEnd, vMax); 6058 ierr = DMPlexCreateNumbering_Private(dm, vStart, vEnd, 0, NULL, dm->sf, globalVertexNumbers);CHKERRQ(ierr); 6059 PetscFunctionReturn(0); 6060 } 6061 6062 /*@C 6063 DMPlexGetVertexNumbering - Get a global certex numbering for all vertices on this process 6064 6065 Input Parameter: 6066 . dm - The DMPlex object 6067 6068 Output Parameter: 6069 . globalVertexNumbers - Global vertex numbers for all vertices on this process 6070 6071 Level: developer 6072 6073 .seealso DMPlexGetCellNumbering() 6074 @*/ 6075 PetscErrorCode DMPlexGetVertexNumbering(DM dm, IS *globalVertexNumbers) 6076 { 6077 DM_Plex *mesh = (DM_Plex*) dm->data; 6078 PetscErrorCode ierr; 6079 6080 PetscFunctionBegin; 6081 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6082 if (!mesh->globalVertexNumbers) {ierr = DMPlexCreateVertexNumbering_Internal(dm, PETSC_FALSE, &mesh->globalVertexNumbers);CHKERRQ(ierr);} 6083 *globalVertexNumbers = mesh->globalVertexNumbers; 6084 PetscFunctionReturn(0); 6085 } 6086 6087 /*@C 6088 DMPlexCreatePointNumbering - Create a global numbering for all points on this process 6089 6090 Input Parameter: 6091 . dm - The DMPlex object 6092 6093 Output Parameter: 6094 . globalPointNumbers - Global numbers for all points on this process 6095 6096 Level: developer 6097 6098 .seealso DMPlexGetCellNumbering() 6099 @*/ 6100 PetscErrorCode DMPlexCreatePointNumbering(DM dm, IS *globalPointNumbers) 6101 { 6102 IS nums[4]; 6103 PetscInt depths[4]; 6104 PetscInt depth, d, shift = 0; 6105 PetscErrorCode ierr; 6106 6107 PetscFunctionBegin; 6108 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6109 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 6110 /* For unstratified meshes use dim instead of depth */ 6111 if (depth < 0) {ierr = DMGetDimension(dm, &depth);CHKERRQ(ierr);} 6112 depths[0] = depth; depths[1] = 0; 6113 for (d = 2; d <= depth; ++d) depths[d] = depth-d+1; 6114 for (d = 0; d <= depth; ++d) { 6115 PetscInt pStart, pEnd, gsize; 6116 6117 ierr = DMPlexGetDepthStratum(dm, depths[d], &pStart, &pEnd);CHKERRQ(ierr); 6118 ierr = DMPlexCreateNumbering_Private(dm, pStart, pEnd, shift, &gsize, dm->sf, &nums[d]);CHKERRQ(ierr); 6119 shift += gsize; 6120 } 6121 ierr = ISConcatenate(PetscObjectComm((PetscObject) dm), depth+1, nums, globalPointNumbers);CHKERRQ(ierr); 6122 for (d = 0; d <= depth; ++d) {ierr = ISDestroy(&nums[d]);CHKERRQ(ierr);} 6123 PetscFunctionReturn(0); 6124 } 6125 6126 6127 /*@ 6128 DMPlexCreateRankField - Create a cell field whose value is the rank of the owner 6129 6130 Input Parameter: 6131 . dm - The DMPlex object 6132 6133 Output Parameter: 6134 . ranks - The rank field 6135 6136 Options Database Keys: 6137 . -dm_partition_view - Adds the rank field into the DM output from -dm_view using the same viewer 6138 6139 Level: intermediate 6140 6141 .seealso: DMView() 6142 @*/ 6143 PetscErrorCode DMPlexCreateRankField(DM dm, Vec *ranks) 6144 { 6145 DM rdm; 6146 PetscDS prob; 6147 PetscFE fe; 6148 PetscScalar *r; 6149 PetscMPIInt rank; 6150 PetscInt dim, cStart, cEnd, c; 6151 PetscErrorCode ierr; 6152 6153 PetscFunctionBeginUser; 6154 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 6155 ierr = DMClone(dm, &rdm);CHKERRQ(ierr); 6156 ierr = DMGetDimension(rdm, &dim);CHKERRQ(ierr); 6157 ierr = PetscFECreateDefault(rdm, dim, 1, PETSC_TRUE, NULL, -1, &fe);CHKERRQ(ierr); 6158 ierr = PetscObjectSetName((PetscObject) fe, "rank");CHKERRQ(ierr); 6159 ierr = DMGetDS(rdm, &prob);CHKERRQ(ierr); 6160 ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr); 6161 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 6162 ierr = DMPlexGetHeightStratum(rdm, 0, &cStart, &cEnd);CHKERRQ(ierr); 6163 ierr = DMCreateGlobalVector(rdm, ranks);CHKERRQ(ierr); 6164 ierr = PetscObjectSetName((PetscObject) *ranks, "partition");CHKERRQ(ierr); 6165 ierr = VecGetArray(*ranks, &r);CHKERRQ(ierr); 6166 for (c = cStart; c < cEnd; ++c) { 6167 PetscScalar *lr; 6168 6169 ierr = DMPlexPointGlobalRef(rdm, c, r, &lr);CHKERRQ(ierr); 6170 *lr = rank; 6171 } 6172 ierr = VecRestoreArray(*ranks, &r);CHKERRQ(ierr); 6173 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 6174 PetscFunctionReturn(0); 6175 } 6176 6177 /*@ 6178 DMPlexCheckSymmetry - Check that the adjacency information in the mesh is symmetric. 6179 6180 Input Parameter: 6181 . dm - The DMPlex object 6182 6183 Note: This is a useful diagnostic when creating meshes programmatically. 6184 6185 Level: developer 6186 6187 .seealso: DMCreate(), DMCheckSkeleton(), DMCheckFaces() 6188 @*/ 6189 PetscErrorCode DMPlexCheckSymmetry(DM dm) 6190 { 6191 PetscSection coneSection, supportSection; 6192 const PetscInt *cone, *support; 6193 PetscInt coneSize, c, supportSize, s; 6194 PetscInt pStart, pEnd, p, csize, ssize; 6195 PetscErrorCode ierr; 6196 6197 PetscFunctionBegin; 6198 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6199 ierr = DMPlexGetConeSection(dm, &coneSection);CHKERRQ(ierr); 6200 ierr = DMPlexGetSupportSection(dm, &supportSection);CHKERRQ(ierr); 6201 /* Check that point p is found in the support of its cone points, and vice versa */ 6202 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 6203 for (p = pStart; p < pEnd; ++p) { 6204 ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); 6205 ierr = DMPlexGetCone(dm, p, &cone);CHKERRQ(ierr); 6206 for (c = 0; c < coneSize; ++c) { 6207 PetscBool dup = PETSC_FALSE; 6208 PetscInt d; 6209 for (d = c-1; d >= 0; --d) { 6210 if (cone[c] == cone[d]) {dup = PETSC_TRUE; break;} 6211 } 6212 ierr = DMPlexGetSupportSize(dm, cone[c], &supportSize);CHKERRQ(ierr); 6213 ierr = DMPlexGetSupport(dm, cone[c], &support);CHKERRQ(ierr); 6214 for (s = 0; s < supportSize; ++s) { 6215 if (support[s] == p) break; 6216 } 6217 if ((s >= supportSize) || (dup && (support[s+1] != p))) { 6218 ierr = PetscPrintf(PETSC_COMM_SELF, "p: %D cone: ", p);CHKERRQ(ierr); 6219 for (s = 0; s < coneSize; ++s) { 6220 ierr = PetscPrintf(PETSC_COMM_SELF, "%D, ", cone[s]);CHKERRQ(ierr); 6221 } 6222 ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr); 6223 ierr = PetscPrintf(PETSC_COMM_SELF, "p: %D support: ", cone[c]);CHKERRQ(ierr); 6224 for (s = 0; s < supportSize; ++s) { 6225 ierr = PetscPrintf(PETSC_COMM_SELF, "%D, ", support[s]);CHKERRQ(ierr); 6226 } 6227 ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr); 6228 if (dup) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not repeatedly found in support of repeated cone point %D", p, cone[c]); 6229 else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not found in support of cone point %D", p, cone[c]); 6230 } 6231 } 6232 ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); 6233 ierr = DMPlexGetSupport(dm, p, &support);CHKERRQ(ierr); 6234 for (s = 0; s < supportSize; ++s) { 6235 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 6236 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 6237 for (c = 0; c < coneSize; ++c) { 6238 if (cone[c] == p) break; 6239 } 6240 if (c >= coneSize) { 6241 ierr = PetscPrintf(PETSC_COMM_SELF, "p: %D support: ", p);CHKERRQ(ierr); 6242 for (c = 0; c < supportSize; ++c) { 6243 ierr = PetscPrintf(PETSC_COMM_SELF, "%D, ", support[c]);CHKERRQ(ierr); 6244 } 6245 ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr); 6246 ierr = PetscPrintf(PETSC_COMM_SELF, "p: %D cone: ", support[s]);CHKERRQ(ierr); 6247 for (c = 0; c < coneSize; ++c) { 6248 ierr = PetscPrintf(PETSC_COMM_SELF, "%D, ", cone[c]);CHKERRQ(ierr); 6249 } 6250 ierr = PetscPrintf(PETSC_COMM_SELF, "\n");CHKERRQ(ierr); 6251 SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Point %D not found in cone of support point %D", p, support[s]); 6252 } 6253 } 6254 } 6255 ierr = PetscSectionGetStorageSize(coneSection, &csize);CHKERRQ(ierr); 6256 ierr = PetscSectionGetStorageSize(supportSection, &ssize);CHKERRQ(ierr); 6257 if (csize != ssize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Total cone size %D != Total support size %D", csize, ssize); 6258 PetscFunctionReturn(0); 6259 } 6260 6261 /*@ 6262 DMPlexCheckSkeleton - Check that each cell has the correct number of vertices 6263 6264 Input Parameters: 6265 + dm - The DMPlex object 6266 . isSimplex - Are the cells simplices or tensor products 6267 - cellHeight - Normally 0 6268 6269 Note: This is a useful diagnostic when creating meshes programmatically. 6270 6271 Level: developer 6272 6273 .seealso: DMCreate(), DMCheckSymmetry(), DMCheckFaces() 6274 @*/ 6275 PetscErrorCode DMPlexCheckSkeleton(DM dm, PetscBool isSimplex, PetscInt cellHeight) 6276 { 6277 PetscInt dim, numCorners, numHybridCorners, vStart, vEnd, cStart, cEnd, cMax, c; 6278 PetscErrorCode ierr; 6279 6280 PetscFunctionBegin; 6281 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6282 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 6283 switch (dim) { 6284 case 1: numCorners = isSimplex ? 2 : 2; numHybridCorners = isSimplex ? 2 : 2; break; 6285 case 2: numCorners = isSimplex ? 3 : 4; numHybridCorners = isSimplex ? 4 : 4; break; 6286 case 3: numCorners = isSimplex ? 4 : 8; numHybridCorners = isSimplex ? 6 : 8; break; 6287 default: 6288 SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Cannot handle meshes of dimension %D", dim); 6289 } 6290 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 6291 ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr); 6292 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 6293 cMax = cMax >= 0 ? cMax : cEnd; 6294 for (c = cStart; c < cMax; ++c) { 6295 PetscInt *closure = NULL, closureSize, cl, coneSize = 0; 6296 6297 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6298 for (cl = 0; cl < closureSize*2; cl += 2) { 6299 const PetscInt p = closure[cl]; 6300 if ((p >= vStart) && (p < vEnd)) ++coneSize; 6301 } 6302 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6303 if (coneSize != numCorners) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %D has %D vertices != %D", c, coneSize, numCorners); 6304 } 6305 for (c = cMax; c < cEnd; ++c) { 6306 PetscInt *closure = NULL, closureSize, cl, coneSize = 0; 6307 6308 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6309 for (cl = 0; cl < closureSize*2; cl += 2) { 6310 const PetscInt p = closure[cl]; 6311 if ((p >= vStart) && (p < vEnd)) ++coneSize; 6312 } 6313 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6314 if (coneSize > numHybridCorners) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Hybrid cell %D has %D vertices > %D", c, coneSize, numHybridCorners); 6315 } 6316 PetscFunctionReturn(0); 6317 } 6318 6319 /*@ 6320 DMPlexCheckFaces - Check that the faces of each cell give a vertex order this is consistent with what we expect from the cell type 6321 6322 Input Parameters: 6323 + dm - The DMPlex object 6324 . isSimplex - Are the cells simplices or tensor products 6325 - cellHeight - Normally 0 6326 6327 Note: This is a useful diagnostic when creating meshes programmatically. 6328 6329 Level: developer 6330 6331 .seealso: DMCreate(), DMCheckSymmetry(), DMCheckSkeleton() 6332 @*/ 6333 PetscErrorCode DMPlexCheckFaces(DM dm, PetscBool isSimplex, PetscInt cellHeight) 6334 { 6335 PetscInt pMax[4]; 6336 PetscInt dim, vStart, vEnd, cStart, cEnd, c, h; 6337 PetscErrorCode ierr; 6338 6339 PetscFunctionBegin; 6340 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6341 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 6342 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 6343 ierr = DMPlexGetHybridBounds(dm, &pMax[dim], &pMax[dim-1], &pMax[1], &pMax[0]);CHKERRQ(ierr); 6344 for (h = cellHeight; h < dim; ++h) { 6345 ierr = DMPlexGetHeightStratum(dm, h, &cStart, &cEnd);CHKERRQ(ierr); 6346 for (c = cStart; c < cEnd; ++c) { 6347 const PetscInt *cone, *ornt, *faces; 6348 PetscInt numFaces, faceSize, coneSize,f; 6349 PetscInt *closure = NULL, closureSize, cl, numCorners = 0; 6350 6351 if (pMax[dim-h] >= 0 && c >= pMax[dim-h]) continue; 6352 ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); 6353 ierr = DMPlexGetCone(dm, c, &cone);CHKERRQ(ierr); 6354 ierr = DMPlexGetConeOrientation(dm, c, &ornt);CHKERRQ(ierr); 6355 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6356 for (cl = 0; cl < closureSize*2; cl += 2) { 6357 const PetscInt p = closure[cl]; 6358 if ((p >= vStart) && (p < vEnd)) closure[numCorners++] = p; 6359 } 6360 ierr = DMPlexGetRawFaces_Internal(dm, dim-h, numCorners, closure, &numFaces, &faceSize, &faces);CHKERRQ(ierr); 6361 if (coneSize != numFaces) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cell %D has %D faces but should have %D", c, coneSize, numFaces); 6362 for (f = 0; f < numFaces; ++f) { 6363 PetscInt *fclosure = NULL, fclosureSize, cl, fnumCorners = 0, v; 6364 6365 ierr = DMPlexGetTransitiveClosure_Internal(dm, cone[f], ornt[f], PETSC_TRUE, &fclosureSize, &fclosure);CHKERRQ(ierr); 6366 for (cl = 0; cl < fclosureSize*2; cl += 2) { 6367 const PetscInt p = fclosure[cl]; 6368 if ((p >= vStart) && (p < vEnd)) fclosure[fnumCorners++] = p; 6369 } 6370 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); 6371 for (v = 0; v < fnumCorners; ++v) { 6372 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]); 6373 } 6374 ierr = DMPlexRestoreTransitiveClosure(dm, cone[f], PETSC_TRUE, &fclosureSize, &fclosure);CHKERRQ(ierr); 6375 } 6376 ierr = DMPlexRestoreFaces_Internal(dm, dim, c, &numFaces, &faceSize, &faces);CHKERRQ(ierr); 6377 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 6378 } 6379 } 6380 PetscFunctionReturn(0); 6381 } 6382 6383 /* Pointwise interpolation 6384 Just code FEM for now 6385 u^f = I u^c 6386 sum_k u^f_k phi^f_k = I sum_j u^c_j phi^c_j 6387 u^f_i = sum_j psi^f_i I phi^c_j u^c_j 6388 I_{ij} = psi^f_i phi^c_j 6389 */ 6390 PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling) 6391 { 6392 PetscSection gsc, gsf; 6393 PetscInt m, n; 6394 void *ctx; 6395 DM cdm; 6396 PetscBool regular; 6397 PetscErrorCode ierr; 6398 6399 PetscFunctionBegin; 6400 ierr = DMGetDefaultGlobalSection(dmFine, &gsf);CHKERRQ(ierr); 6401 ierr = PetscSectionGetConstrainedStorageSize(gsf, &m);CHKERRQ(ierr); 6402 ierr = DMGetDefaultGlobalSection(dmCoarse, &gsc);CHKERRQ(ierr); 6403 ierr = PetscSectionGetConstrainedStorageSize(gsc, &n);CHKERRQ(ierr); 6404 6405 ierr = MatCreate(PetscObjectComm((PetscObject) dmCoarse), interpolation);CHKERRQ(ierr); 6406 ierr = MatSetSizes(*interpolation, m, n, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 6407 ierr = MatSetType(*interpolation, dmCoarse->mattype);CHKERRQ(ierr); 6408 ierr = DMGetApplicationContext(dmFine, &ctx);CHKERRQ(ierr); 6409 6410 ierr = DMGetCoarseDM(dmFine, &cdm);CHKERRQ(ierr); 6411 ierr = DMPlexGetRegularRefinement(dmFine, ®ular);CHKERRQ(ierr); 6412 if (regular && cdm == dmCoarse) {ierr = DMPlexComputeInterpolatorNested(dmCoarse, dmFine, *interpolation, ctx);CHKERRQ(ierr);} 6413 else {ierr = DMPlexComputeInterpolatorGeneral(dmCoarse, dmFine, *interpolation, ctx);CHKERRQ(ierr);} 6414 ierr = MatViewFromOptions(*interpolation, NULL, "-interp_mat_view");CHKERRQ(ierr); 6415 /* Use naive scaling */ 6416 ierr = DMCreateInterpolationScale(dmCoarse, dmFine, *interpolation, scaling);CHKERRQ(ierr); 6417 PetscFunctionReturn(0); 6418 } 6419 6420 PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat) 6421 { 6422 PetscErrorCode ierr; 6423 VecScatter ctx; 6424 6425 PetscFunctionBegin; 6426 ierr = DMPlexComputeInjectorFEM(dmCoarse, dmFine, &ctx, NULL);CHKERRQ(ierr); 6427 ierr = MatCreateScatter(PetscObjectComm((PetscObject)ctx), ctx, mat);CHKERRQ(ierr); 6428 ierr = VecScatterDestroy(&ctx);CHKERRQ(ierr); 6429 PetscFunctionReturn(0); 6430 } 6431 6432 PetscErrorCode DMCreateDefaultSection_Plex(DM dm) 6433 { 6434 PetscSection section; 6435 IS *bcPoints, *bcComps; 6436 PetscBool *isFE; 6437 PetscInt *bcFields, *numComp, *numDof; 6438 PetscInt depth, dim, numBd, numBC = 0, numFields, bd, bc = 0, f; 6439 PetscInt cStart, cEnd, cEndInterior; 6440 PetscErrorCode ierr; 6441 6442 PetscFunctionBegin; 6443 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 6444 if (!numFields) PetscFunctionReturn(0); 6445 /* FE and FV boundary conditions are handled slightly differently */ 6446 ierr = PetscMalloc1(numFields, &isFE);CHKERRQ(ierr); 6447 for (f = 0; f < numFields; ++f) { 6448 PetscObject obj; 6449 PetscClassId id; 6450 6451 ierr = DMGetField(dm, f, &obj);CHKERRQ(ierr); 6452 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 6453 if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} 6454 else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} 6455 else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f); 6456 } 6457 /* Allocate boundary point storage for FEM boundaries */ 6458 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 6459 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 6460 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 6461 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 6462 ierr = PetscDSGetNumBoundary(dm->prob, &numBd);CHKERRQ(ierr); 6463 for (bd = 0; bd < numBd; ++bd) { 6464 PetscInt field; 6465 DMBoundaryConditionType type; 6466 const char *labelName; 6467 DMLabel label; 6468 6469 ierr = PetscDSGetBoundary(dm->prob, bd, &type, NULL, &labelName, &field, NULL, NULL, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 6470 ierr = DMGetLabel(dm,labelName,&label);CHKERRQ(ierr); 6471 if (label && isFE[field] && (type & DM_BC_ESSENTIAL)) ++numBC; 6472 } 6473 /* Add ghost cell boundaries for FVM */ 6474 for (f = 0; f < numFields; ++f) if (!isFE[f] && cEndInterior >= 0) ++numBC; 6475 ierr = PetscCalloc3(numBC,&bcFields,numBC,&bcPoints,numBC,&bcComps);CHKERRQ(ierr); 6476 /* Constrain ghost cells for FV */ 6477 for (f = 0; f < numFields; ++f) { 6478 PetscInt *newidx, c; 6479 6480 if (isFE[f] || cEndInterior < 0) continue; 6481 ierr = PetscMalloc1(cEnd-cEndInterior,&newidx);CHKERRQ(ierr); 6482 for (c = cEndInterior; c < cEnd; ++c) newidx[c-cEndInterior] = c; 6483 bcFields[bc] = f; 6484 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) dm), cEnd-cEndInterior, newidx, PETSC_OWN_POINTER, &bcPoints[bc++]);CHKERRQ(ierr); 6485 } 6486 /* Handle FEM Dirichlet boundaries */ 6487 for (bd = 0; bd < numBd; ++bd) { 6488 const char *bdLabel; 6489 DMLabel label; 6490 const PetscInt *comps; 6491 const PetscInt *values; 6492 PetscInt bd2, field, numComps, numValues; 6493 DMBoundaryConditionType type; 6494 PetscBool duplicate = PETSC_FALSE; 6495 6496 ierr = PetscDSGetBoundary(dm->prob, bd, &type, NULL, &bdLabel, &field, &numComps, &comps, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 6497 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 6498 if (!isFE[field] || !label) continue; 6499 /* Only want to modify label once */ 6500 for (bd2 = 0; bd2 < bd; ++bd2) { 6501 const char *bdname; 6502 ierr = PetscDSGetBoundary(dm->prob, bd2, NULL, NULL, &bdname, NULL, NULL, NULL, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 6503 ierr = PetscStrcmp(bdname, bdLabel, &duplicate);CHKERRQ(ierr); 6504 if (duplicate) break; 6505 } 6506 if (!duplicate && (isFE[field])) { 6507 /* don't complete cells, which are just present to give orientation to the boundary */ 6508 ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr); 6509 } 6510 /* Filter out cells, if you actually want to constrain cells you need to do things by hand right now */ 6511 if (type & DM_BC_ESSENTIAL) { 6512 PetscInt *newidx; 6513 PetscInt n, newn = 0, p, v; 6514 6515 bcFields[bc] = field; 6516 if (numComps) {ierr = ISCreateGeneral(PetscObjectComm((PetscObject) dm), numComps, comps, PETSC_COPY_VALUES, &bcComps[bc]);CHKERRQ(ierr);} 6517 for (v = 0; v < numValues; ++v) { 6518 IS tmp; 6519 const PetscInt *idx; 6520 6521 ierr = DMGetStratumIS(dm, bdLabel, values[v], &tmp);CHKERRQ(ierr); 6522 if (!tmp) continue; 6523 ierr = ISGetLocalSize(tmp, &n);CHKERRQ(ierr); 6524 ierr = ISGetIndices(tmp, &idx);CHKERRQ(ierr); 6525 if (isFE[field]) { 6526 for (p = 0; p < n; ++p) if ((idx[p] < cStart) || (idx[p] >= cEnd)) ++newn; 6527 } else { 6528 for (p = 0; p < n; ++p) if ((idx[p] >= cStart) || (idx[p] < cEnd)) ++newn; 6529 } 6530 ierr = ISRestoreIndices(tmp, &idx);CHKERRQ(ierr); 6531 ierr = ISDestroy(&tmp);CHKERRQ(ierr); 6532 } 6533 ierr = PetscMalloc1(newn,&newidx);CHKERRQ(ierr); 6534 newn = 0; 6535 for (v = 0; v < numValues; ++v) { 6536 IS tmp; 6537 const PetscInt *idx; 6538 6539 ierr = DMGetStratumIS(dm, bdLabel, values[v], &tmp);CHKERRQ(ierr); 6540 if (!tmp) continue; 6541 ierr = ISGetLocalSize(tmp, &n);CHKERRQ(ierr); 6542 ierr = ISGetIndices(tmp, &idx);CHKERRQ(ierr); 6543 if (isFE[field]) { 6544 for (p = 0; p < n; ++p) if ((idx[p] < cStart) || (idx[p] >= cEnd)) newidx[newn++] = idx[p]; 6545 } else { 6546 for (p = 0; p < n; ++p) if ((idx[p] >= cStart) || (idx[p] < cEnd)) newidx[newn++] = idx[p]; 6547 } 6548 ierr = ISRestoreIndices(tmp, &idx);CHKERRQ(ierr); 6549 ierr = ISDestroy(&tmp);CHKERRQ(ierr); 6550 } 6551 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) dm), newn, newidx, PETSC_OWN_POINTER, &bcPoints[bc++]);CHKERRQ(ierr); 6552 } 6553 } 6554 /* Handle discretization */ 6555 ierr = PetscCalloc2(numFields,&numComp,numFields*(dim+1),&numDof);CHKERRQ(ierr); 6556 for (f = 0; f < numFields; ++f) { 6557 PetscObject obj; 6558 6559 ierr = DMGetField(dm, f, &obj);CHKERRQ(ierr); 6560 if (isFE[f]) { 6561 PetscFE fe = (PetscFE) obj; 6562 const PetscInt *numFieldDof; 6563 PetscInt d; 6564 6565 ierr = PetscFEGetNumComponents(fe, &numComp[f]);CHKERRQ(ierr); 6566 ierr = PetscFEGetNumDof(fe, &numFieldDof);CHKERRQ(ierr); 6567 for (d = 0; d < dim+1; ++d) numDof[f*(dim+1)+d] = numFieldDof[d]; 6568 } else { 6569 PetscFV fv = (PetscFV) obj; 6570 6571 ierr = PetscFVGetNumComponents(fv, &numComp[f]);CHKERRQ(ierr); 6572 numDof[f*(dim+1)+dim] = numComp[f]; 6573 } 6574 } 6575 for (f = 0; f < numFields; ++f) { 6576 PetscInt d; 6577 for (d = 1; d < dim; ++d) { 6578 if ((numDof[f*(dim+1)+d] > 0) && (depth < dim)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Mesh must be interpolated when unknowns are specified on edges or faces."); 6579 } 6580 } 6581 ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBC, bcFields, bcComps, bcPoints, NULL, §ion);CHKERRQ(ierr); 6582 for (f = 0; f < numFields; ++f) { 6583 PetscFE fe; 6584 const char *name; 6585 6586 ierr = DMGetField(dm, f, (PetscObject *) &fe);CHKERRQ(ierr); 6587 ierr = PetscObjectGetName((PetscObject) fe, &name);CHKERRQ(ierr); 6588 ierr = PetscSectionSetFieldName(section, f, name);CHKERRQ(ierr); 6589 } 6590 ierr = DMSetDefaultSection(dm, section);CHKERRQ(ierr); 6591 ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr); 6592 for (bc = 0; bc < numBC; ++bc) {ierr = ISDestroy(&bcPoints[bc]);CHKERRQ(ierr);ierr = ISDestroy(&bcComps[bc]);CHKERRQ(ierr);} 6593 ierr = PetscFree3(bcFields,bcPoints,bcComps);CHKERRQ(ierr); 6594 ierr = PetscFree2(numComp,numDof);CHKERRQ(ierr); 6595 ierr = PetscFree(isFE);CHKERRQ(ierr); 6596 PetscFunctionReturn(0); 6597 } 6598 6599 /*@ 6600 DMPlexGetRegularRefinement - Get the flag indicating that this mesh was obtained by regular refinement from its coarse mesh 6601 6602 Input Parameter: 6603 . dm - The DMPlex object 6604 6605 Output Parameter: 6606 . regular - The flag 6607 6608 Level: intermediate 6609 6610 .seealso: DMPlexSetRegularRefinement() 6611 @*/ 6612 PetscErrorCode DMPlexGetRegularRefinement(DM dm, PetscBool *regular) 6613 { 6614 PetscFunctionBegin; 6615 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6616 PetscValidPointer(regular, 2); 6617 *regular = ((DM_Plex *) dm->data)->regularRefinement; 6618 PetscFunctionReturn(0); 6619 } 6620 6621 /*@ 6622 DMPlexSetRegularRefinement - Set the flag indicating that this mesh was obtained by regular refinement from its coarse mesh 6623 6624 Input Parameters: 6625 + dm - The DMPlex object 6626 - regular - The flag 6627 6628 Level: intermediate 6629 6630 .seealso: DMPlexGetRegularRefinement() 6631 @*/ 6632 PetscErrorCode DMPlexSetRegularRefinement(DM dm, PetscBool regular) 6633 { 6634 PetscFunctionBegin; 6635 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6636 ((DM_Plex *) dm->data)->regularRefinement = regular; 6637 PetscFunctionReturn(0); 6638 } 6639 6640 /* anchors */ 6641 /*@ 6642 DMPlexGetAnchors - Get the layout of the anchor (point-to-point) constraints. Typically, the user will not have to 6643 call DMPlexGetAnchors() directly: if there are anchors, then DMPlexGetAnchors() is called during DMGetConstraints(). 6644 6645 not collective 6646 6647 Input Parameters: 6648 . dm - The DMPlex object 6649 6650 Output Parameters: 6651 + anchorSection - If not NULL, set to the section describing which points anchor the constrained points. 6652 - anchorIS - If not NULL, set to the list of anchors indexed by anchorSection 6653 6654 6655 Level: intermediate 6656 6657 .seealso: DMPlexSetAnchors(), DMGetConstraints(), DMSetConstraints() 6658 @*/ 6659 PetscErrorCode DMPlexGetAnchors(DM dm, PetscSection *anchorSection, IS *anchorIS) 6660 { 6661 DM_Plex *plex = (DM_Plex *)dm->data; 6662 PetscErrorCode ierr; 6663 6664 PetscFunctionBegin; 6665 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6666 if (!plex->anchorSection && !plex->anchorIS && plex->createanchors) {ierr = (*plex->createanchors)(dm);CHKERRQ(ierr);} 6667 if (anchorSection) *anchorSection = plex->anchorSection; 6668 if (anchorIS) *anchorIS = plex->anchorIS; 6669 PetscFunctionReturn(0); 6670 } 6671 6672 /*@ 6673 DMPlexSetAnchors - Set the layout of the local anchor (point-to-point) constraints. Unlike boundary conditions, 6674 when a point's degrees of freedom in a section are constrained to an outside value, the anchor constraints set a 6675 point's degrees of freedom to be a linear combination of other points' degrees of freedom. 6676 6677 After specifying the layout of constraints with DMPlexSetAnchors(), one specifies the constraints by calling 6678 DMGetConstraints() and filling in the entries in the constraint matrix. 6679 6680 collective on dm 6681 6682 Input Parameters: 6683 + dm - The DMPlex object 6684 . 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). 6685 - anchorIS - The list of all anchor points. Must have a local communicator (PETSC_COMM_SELF or derivative). 6686 6687 The reference counts of anchorSection and anchorIS are incremented. 6688 6689 Level: intermediate 6690 6691 .seealso: DMPlexGetAnchors(), DMGetConstraints(), DMSetConstraints() 6692 @*/ 6693 PetscErrorCode DMPlexSetAnchors(DM dm, PetscSection anchorSection, IS anchorIS) 6694 { 6695 DM_Plex *plex = (DM_Plex *)dm->data; 6696 PetscMPIInt result; 6697 PetscErrorCode ierr; 6698 6699 PetscFunctionBegin; 6700 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6701 if (anchorSection) { 6702 PetscValidHeaderSpecific(anchorSection,PETSC_SECTION_CLASSID,2); 6703 ierr = MPI_Comm_compare(PETSC_COMM_SELF,PetscObjectComm((PetscObject)anchorSection),&result);CHKERRQ(ierr); 6704 if (result != MPI_CONGRUENT && result != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMECOMM,"anchor section must have local communicator"); 6705 } 6706 if (anchorIS) { 6707 PetscValidHeaderSpecific(anchorIS,IS_CLASSID,3); 6708 ierr = MPI_Comm_compare(PETSC_COMM_SELF,PetscObjectComm((PetscObject)anchorIS),&result);CHKERRQ(ierr); 6709 if (result != MPI_CONGRUENT && result != MPI_IDENT) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMECOMM,"anchor IS must have local communicator"); 6710 } 6711 6712 ierr = PetscObjectReference((PetscObject)anchorSection);CHKERRQ(ierr); 6713 ierr = PetscSectionDestroy(&plex->anchorSection);CHKERRQ(ierr); 6714 plex->anchorSection = anchorSection; 6715 6716 ierr = PetscObjectReference((PetscObject)anchorIS);CHKERRQ(ierr); 6717 ierr = ISDestroy(&plex->anchorIS);CHKERRQ(ierr); 6718 plex->anchorIS = anchorIS; 6719 6720 #if defined(PETSC_USE_DEBUG) 6721 if (anchorIS && anchorSection) { 6722 PetscInt size, a, pStart, pEnd; 6723 const PetscInt *anchors; 6724 6725 ierr = PetscSectionGetChart(anchorSection,&pStart,&pEnd);CHKERRQ(ierr); 6726 ierr = ISGetLocalSize(anchorIS,&size);CHKERRQ(ierr); 6727 ierr = ISGetIndices(anchorIS,&anchors);CHKERRQ(ierr); 6728 for (a = 0; a < size; a++) { 6729 PetscInt p; 6730 6731 p = anchors[a]; 6732 if (p >= pStart && p < pEnd) { 6733 PetscInt dof; 6734 6735 ierr = PetscSectionGetDof(anchorSection,p,&dof);CHKERRQ(ierr); 6736 if (dof) { 6737 PetscErrorCode ierr2; 6738 6739 ierr2 = ISRestoreIndices(anchorIS,&anchors);CHKERRQ(ierr2); 6740 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Point %D cannot be constrained and an anchor",p); 6741 } 6742 } 6743 } 6744 ierr = ISRestoreIndices(anchorIS,&anchors);CHKERRQ(ierr); 6745 } 6746 #endif 6747 /* reset the generic constraints */ 6748 ierr = DMSetDefaultConstraints(dm,NULL,NULL);CHKERRQ(ierr); 6749 PetscFunctionReturn(0); 6750 } 6751 6752 static PetscErrorCode DMPlexCreateConstraintSection_Anchors(DM dm, PetscSection section, PetscSection *cSec) 6753 { 6754 PetscSection anchorSection; 6755 PetscInt pStart, pEnd, sStart, sEnd, p, dof, numFields, f; 6756 PetscErrorCode ierr; 6757 6758 PetscFunctionBegin; 6759 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6760 ierr = DMPlexGetAnchors(dm,&anchorSection,NULL);CHKERRQ(ierr); 6761 ierr = PetscSectionCreate(PETSC_COMM_SELF,cSec);CHKERRQ(ierr); 6762 ierr = PetscSectionGetNumFields(section,&numFields);CHKERRQ(ierr); 6763 if (numFields) { 6764 PetscInt f; 6765 ierr = PetscSectionSetNumFields(*cSec,numFields);CHKERRQ(ierr); 6766 6767 for (f = 0; f < numFields; f++) { 6768 PetscInt numComp; 6769 6770 ierr = PetscSectionGetFieldComponents(section,f,&numComp);CHKERRQ(ierr); 6771 ierr = PetscSectionSetFieldComponents(*cSec,f,numComp);CHKERRQ(ierr); 6772 } 6773 } 6774 ierr = PetscSectionGetChart(anchorSection,&pStart,&pEnd);CHKERRQ(ierr); 6775 ierr = PetscSectionGetChart(section,&sStart,&sEnd);CHKERRQ(ierr); 6776 pStart = PetscMax(pStart,sStart); 6777 pEnd = PetscMin(pEnd,sEnd); 6778 pEnd = PetscMax(pStart,pEnd); 6779 ierr = PetscSectionSetChart(*cSec,pStart,pEnd);CHKERRQ(ierr); 6780 for (p = pStart; p < pEnd; p++) { 6781 ierr = PetscSectionGetDof(anchorSection,p,&dof);CHKERRQ(ierr); 6782 if (dof) { 6783 ierr = PetscSectionGetDof(section,p,&dof);CHKERRQ(ierr); 6784 ierr = PetscSectionSetDof(*cSec,p,dof);CHKERRQ(ierr); 6785 for (f = 0; f < numFields; f++) { 6786 ierr = PetscSectionGetFieldDof(section,p,f,&dof);CHKERRQ(ierr); 6787 ierr = PetscSectionSetFieldDof(*cSec,p,f,dof);CHKERRQ(ierr); 6788 } 6789 } 6790 } 6791 ierr = PetscSectionSetUp(*cSec);CHKERRQ(ierr); 6792 PetscFunctionReturn(0); 6793 } 6794 6795 static PetscErrorCode DMPlexCreateConstraintMatrix_Anchors(DM dm, PetscSection section, PetscSection cSec, Mat *cMat) 6796 { 6797 PetscSection aSec; 6798 PetscInt pStart, pEnd, p, dof, aDof, aOff, off, nnz, annz, m, n, q, a, offset, *i, *j; 6799 const PetscInt *anchors; 6800 PetscInt numFields, f; 6801 IS aIS; 6802 PetscErrorCode ierr; 6803 6804 PetscFunctionBegin; 6805 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6806 ierr = PetscSectionGetStorageSize(cSec, &m);CHKERRQ(ierr); 6807 ierr = PetscSectionGetStorageSize(section, &n);CHKERRQ(ierr); 6808 ierr = MatCreate(PETSC_COMM_SELF,cMat);CHKERRQ(ierr); 6809 ierr = MatSetSizes(*cMat,m,n,m,n);CHKERRQ(ierr); 6810 ierr = MatSetType(*cMat,MATSEQAIJ);CHKERRQ(ierr); 6811 ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr); 6812 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 6813 /* cSec will be a subset of aSec and section */ 6814 ierr = PetscSectionGetChart(cSec,&pStart,&pEnd);CHKERRQ(ierr); 6815 ierr = PetscMalloc1(m+1,&i);CHKERRQ(ierr); 6816 i[0] = 0; 6817 ierr = PetscSectionGetNumFields(section,&numFields);CHKERRQ(ierr); 6818 for (p = pStart; p < pEnd; p++) { 6819 PetscInt rDof, rOff, r; 6820 6821 ierr = PetscSectionGetDof(aSec,p,&rDof);CHKERRQ(ierr); 6822 if (!rDof) continue; 6823 ierr = PetscSectionGetOffset(aSec,p,&rOff);CHKERRQ(ierr); 6824 if (numFields) { 6825 for (f = 0; f < numFields; f++) { 6826 annz = 0; 6827 for (r = 0; r < rDof; r++) { 6828 a = anchors[rOff + r]; 6829 ierr = PetscSectionGetFieldDof(section,a,f,&aDof);CHKERRQ(ierr); 6830 annz += aDof; 6831 } 6832 ierr = PetscSectionGetFieldDof(cSec,p,f,&dof);CHKERRQ(ierr); 6833 ierr = PetscSectionGetFieldOffset(cSec,p,f,&off);CHKERRQ(ierr); 6834 for (q = 0; q < dof; q++) { 6835 i[off + q + 1] = i[off + q] + annz; 6836 } 6837 } 6838 } 6839 else { 6840 annz = 0; 6841 for (q = 0; q < dof; q++) { 6842 a = anchors[off + q]; 6843 ierr = PetscSectionGetDof(section,a,&aDof);CHKERRQ(ierr); 6844 annz += aDof; 6845 } 6846 ierr = PetscSectionGetDof(cSec,p,&dof);CHKERRQ(ierr); 6847 ierr = PetscSectionGetOffset(cSec,p,&off);CHKERRQ(ierr); 6848 for (q = 0; q < dof; q++) { 6849 i[off + q + 1] = i[off + q] + annz; 6850 } 6851 } 6852 } 6853 nnz = i[m]; 6854 ierr = PetscMalloc1(nnz,&j);CHKERRQ(ierr); 6855 offset = 0; 6856 for (p = pStart; p < pEnd; p++) { 6857 if (numFields) { 6858 for (f = 0; f < numFields; f++) { 6859 ierr = PetscSectionGetFieldDof(cSec,p,f,&dof);CHKERRQ(ierr); 6860 for (q = 0; q < dof; q++) { 6861 PetscInt rDof, rOff, r; 6862 ierr = PetscSectionGetDof(aSec,p,&rDof);CHKERRQ(ierr); 6863 ierr = PetscSectionGetOffset(aSec,p,&rOff);CHKERRQ(ierr); 6864 for (r = 0; r < rDof; r++) { 6865 PetscInt s; 6866 6867 a = anchors[rOff + r]; 6868 ierr = PetscSectionGetFieldDof(section,a,f,&aDof);CHKERRQ(ierr); 6869 ierr = PetscSectionGetFieldOffset(section,a,f,&aOff);CHKERRQ(ierr); 6870 for (s = 0; s < aDof; s++) { 6871 j[offset++] = aOff + s; 6872 } 6873 } 6874 } 6875 } 6876 } 6877 else { 6878 ierr = PetscSectionGetDof(cSec,p,&dof);CHKERRQ(ierr); 6879 for (q = 0; q < dof; q++) { 6880 PetscInt rDof, rOff, r; 6881 ierr = PetscSectionGetDof(aSec,p,&rDof);CHKERRQ(ierr); 6882 ierr = PetscSectionGetOffset(aSec,p,&rOff);CHKERRQ(ierr); 6883 for (r = 0; r < rDof; r++) { 6884 PetscInt s; 6885 6886 a = anchors[rOff + r]; 6887 ierr = PetscSectionGetDof(section,a,&aDof);CHKERRQ(ierr); 6888 ierr = PetscSectionGetOffset(section,a,&aOff);CHKERRQ(ierr); 6889 for (s = 0; s < aDof; s++) { 6890 j[offset++] = aOff + s; 6891 } 6892 } 6893 } 6894 } 6895 } 6896 ierr = MatSeqAIJSetPreallocationCSR(*cMat,i,j,NULL);CHKERRQ(ierr); 6897 ierr = PetscFree(i);CHKERRQ(ierr); 6898 ierr = PetscFree(j);CHKERRQ(ierr); 6899 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 6900 PetscFunctionReturn(0); 6901 } 6902 6903 PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm) 6904 { 6905 DM_Plex *plex = (DM_Plex *)dm->data; 6906 PetscSection anchorSection, section, cSec; 6907 Mat cMat; 6908 PetscErrorCode ierr; 6909 6910 PetscFunctionBegin; 6911 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 6912 ierr = DMPlexGetAnchors(dm,&anchorSection,NULL);CHKERRQ(ierr); 6913 if (anchorSection) { 6914 PetscDS ds; 6915 PetscInt nf; 6916 6917 ierr = DMGetDefaultSection(dm,§ion);CHKERRQ(ierr); 6918 ierr = DMPlexCreateConstraintSection_Anchors(dm,section,&cSec);CHKERRQ(ierr); 6919 ierr = DMPlexCreateConstraintMatrix_Anchors(dm,section,cSec,&cMat);CHKERRQ(ierr); 6920 ierr = DMGetDS(dm,&ds);CHKERRQ(ierr); 6921 ierr = PetscDSGetNumFields(ds,&nf);CHKERRQ(ierr); 6922 if (nf && plex->computeanchormatrix) {ierr = (*plex->computeanchormatrix)(dm,section,cSec,cMat);CHKERRQ(ierr);} 6923 ierr = DMSetDefaultConstraints(dm,cSec,cMat);CHKERRQ(ierr); 6924 ierr = PetscSectionDestroy(&cSec);CHKERRQ(ierr); 6925 ierr = MatDestroy(&cMat);CHKERRQ(ierr); 6926 } 6927 PetscFunctionReturn(0); 6928 } 6929