1 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 3 #include <petsc-private/petscfeimpl.h> 4 #include <petscfv.h> 5 6 #undef __FUNCT__ 7 #define __FUNCT__ "DMPlexGetScale" 8 PetscErrorCode DMPlexGetScale(DM dm, PetscUnit unit, PetscReal *scale) 9 { 10 DM_Plex *mesh = (DM_Plex*) dm->data; 11 12 PetscFunctionBegin; 13 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 14 PetscValidPointer(scale, 3); 15 *scale = mesh->scale[unit]; 16 PetscFunctionReturn(0); 17 } 18 19 #undef __FUNCT__ 20 #define __FUNCT__ "DMPlexSetScale" 21 PetscErrorCode DMPlexSetScale(DM dm, PetscUnit unit, PetscReal scale) 22 { 23 DM_Plex *mesh = (DM_Plex*) dm->data; 24 25 PetscFunctionBegin; 26 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 27 mesh->scale[unit] = scale; 28 PetscFunctionReturn(0); 29 } 30 31 PETSC_STATIC_INLINE PetscInt epsilon(PetscInt i, PetscInt j, PetscInt k) 32 { 33 switch (i) { 34 case 0: 35 switch (j) { 36 case 0: return 0; 37 case 1: 38 switch (k) { 39 case 0: return 0; 40 case 1: return 0; 41 case 2: return 1; 42 } 43 case 2: 44 switch (k) { 45 case 0: return 0; 46 case 1: return -1; 47 case 2: return 0; 48 } 49 } 50 case 1: 51 switch (j) { 52 case 0: 53 switch (k) { 54 case 0: return 0; 55 case 1: return 0; 56 case 2: return -1; 57 } 58 case 1: return 0; 59 case 2: 60 switch (k) { 61 case 0: return 1; 62 case 1: return 0; 63 case 2: return 0; 64 } 65 } 66 case 2: 67 switch (j) { 68 case 0: 69 switch (k) { 70 case 0: return 0; 71 case 1: return 1; 72 case 2: return 0; 73 } 74 case 1: 75 switch (k) { 76 case 0: return -1; 77 case 1: return 0; 78 case 2: return 0; 79 } 80 case 2: return 0; 81 } 82 } 83 return 0; 84 } 85 86 #undef __FUNCT__ 87 #define __FUNCT__ "DMPlexCreateRigidBody" 88 /*@C 89 DMPlexCreateRigidBody - create rigid body modes from coordinates 90 91 Collective on DM 92 93 Input Arguments: 94 + dm - the DM 95 . section - the local section associated with the rigid field, or NULL for the default section 96 - globalSection - the global section associated with the rigid field, or NULL for the default section 97 98 Output Argument: 99 . sp - the null space 100 101 Note: This is necessary to take account of Dirichlet conditions on the displacements 102 103 Level: advanced 104 105 .seealso: MatNullSpaceCreate() 106 @*/ 107 PetscErrorCode DMPlexCreateRigidBody(DM dm, PetscSection section, PetscSection globalSection, MatNullSpace *sp) 108 { 109 MPI_Comm comm; 110 Vec coordinates, localMode, mode[6]; 111 PetscSection coordSection; 112 PetscScalar *coords; 113 PetscInt dim, vStart, vEnd, v, n, m, d, i, j; 114 PetscErrorCode ierr; 115 116 PetscFunctionBegin; 117 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 118 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 119 if (dim == 1) { 120 ierr = MatNullSpaceCreate(comm, PETSC_TRUE, 0, NULL, sp);CHKERRQ(ierr); 121 PetscFunctionReturn(0); 122 } 123 if (!section) {ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);} 124 if (!globalSection) {ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr);} 125 ierr = PetscSectionGetConstrainedStorageSize(globalSection, &n);CHKERRQ(ierr); 126 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 127 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 128 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 129 m = (dim*(dim+1))/2; 130 ierr = VecCreate(comm, &mode[0]);CHKERRQ(ierr); 131 ierr = VecSetSizes(mode[0], n, PETSC_DETERMINE);CHKERRQ(ierr); 132 ierr = VecSetUp(mode[0]);CHKERRQ(ierr); 133 for (i = 1; i < m; ++i) {ierr = VecDuplicate(mode[0], &mode[i]);CHKERRQ(ierr);} 134 /* Assume P1 */ 135 ierr = DMGetLocalVector(dm, &localMode);CHKERRQ(ierr); 136 for (d = 0; d < dim; ++d) { 137 PetscScalar values[3] = {0.0, 0.0, 0.0}; 138 139 values[d] = 1.0; 140 ierr = VecSet(localMode, 0.0);CHKERRQ(ierr); 141 for (v = vStart; v < vEnd; ++v) { 142 ierr = DMPlexVecSetClosure(dm, section, localMode, v, values, INSERT_VALUES);CHKERRQ(ierr); 143 } 144 ierr = DMLocalToGlobalBegin(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 145 ierr = DMLocalToGlobalEnd(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 146 } 147 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 148 for (d = dim; d < dim*(dim+1)/2; ++d) { 149 PetscInt i, j, k = dim > 2 ? d - dim : d; 150 151 ierr = VecSet(localMode, 0.0);CHKERRQ(ierr); 152 for (v = vStart; v < vEnd; ++v) { 153 PetscScalar values[3] = {0.0, 0.0, 0.0}; 154 PetscInt off; 155 156 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 157 for (i = 0; i < dim; ++i) { 158 for (j = 0; j < dim; ++j) { 159 values[j] += epsilon(i, j, k)*PetscRealPart(coords[off+i]); 160 } 161 } 162 ierr = DMPlexVecSetClosure(dm, section, localMode, v, values, INSERT_VALUES);CHKERRQ(ierr); 163 } 164 ierr = DMLocalToGlobalBegin(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 165 ierr = DMLocalToGlobalEnd(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 166 } 167 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 168 ierr = DMRestoreLocalVector(dm, &localMode);CHKERRQ(ierr); 169 for (i = 0; i < dim; ++i) {ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr);} 170 /* Orthonormalize system */ 171 for (i = dim; i < m; ++i) { 172 PetscScalar dots[6]; 173 174 ierr = VecMDot(mode[i], i, mode, dots);CHKERRQ(ierr); 175 for (j = 0; j < i; ++j) dots[j] *= -1.0; 176 ierr = VecMAXPY(mode[i], i, dots, mode);CHKERRQ(ierr); 177 ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr); 178 } 179 ierr = MatNullSpaceCreate(comm, PETSC_FALSE, m, mode, sp);CHKERRQ(ierr); 180 for (i = 0; i< m; ++i) {ierr = VecDestroy(&mode[i]);CHKERRQ(ierr);} 181 PetscFunctionReturn(0); 182 } 183 184 #undef __FUNCT__ 185 #define __FUNCT__ "DMPlexProjectFunctionLabelLocal" 186 PetscErrorCode DMPlexProjectFunctionLabelLocal(DM dm, DMLabel label, PetscInt numIds, const PetscInt ids[], PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, InsertMode mode, Vec localX) 187 { 188 PetscDualSpace *sp; 189 PetscSection section; 190 PetscScalar *values; 191 PetscReal *v0, *J, detJ; 192 PetscBool *fieldActive; 193 PetscInt numFields, numComp, dim, spDim, totDim = 0, numValues, cStart, cEnd, f, d, v, i, comp; 194 PetscErrorCode ierr; 195 196 PetscFunctionBegin; 197 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 198 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 199 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 200 ierr = PetscMalloc3(numFields,&sp,dim,&v0,dim*dim,&J);CHKERRQ(ierr); 201 for (f = 0; f < numFields; ++f) { 202 ierr = PetscFEGetDualSpace(fe[f], &sp[f]);CHKERRQ(ierr); 203 ierr = PetscFEGetNumComponents(fe[f], &numComp);CHKERRQ(ierr); 204 ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr); 205 totDim += spDim*numComp; 206 } 207 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 208 ierr = DMPlexVecGetClosure(dm, section, localX, cStart, &numValues, NULL);CHKERRQ(ierr); 209 if (numValues != totDim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The section cell closure size %d != dual space dimension %d", numValues, totDim); 210 ierr = DMGetWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 211 ierr = DMGetWorkArray(dm, numFields, PETSC_BOOL, &fieldActive);CHKERRQ(ierr); 212 for (f = 0; f < numFields; ++f) fieldActive[f] = funcs[f] ? PETSC_TRUE : PETSC_FALSE; 213 for (i = 0; i < numIds; ++i) { 214 IS pointIS; 215 const PetscInt *points; 216 PetscInt n, p; 217 218 ierr = DMLabelGetStratumIS(label, ids[i], &pointIS);CHKERRQ(ierr); 219 ierr = ISGetLocalSize(pointIS, &n);CHKERRQ(ierr); 220 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 221 for (p = 0; p < n; ++p) { 222 const PetscInt point = points[p]; 223 PetscCellGeometry geom; 224 225 if ((point < cStart) || (point >= cEnd)) continue; 226 ierr = DMPlexComputeCellGeometry(dm, point, v0, J, NULL, &detJ);CHKERRQ(ierr); 227 geom.v0 = v0; 228 geom.J = J; 229 geom.detJ = &detJ; 230 for (f = 0, v = 0; f < numFields; ++f) { 231 void * const ctx = ctxs ? ctxs[f] : NULL; 232 ierr = PetscFEGetNumComponents(fe[f], &numComp);CHKERRQ(ierr); 233 ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr); 234 for (d = 0; d < spDim; ++d) { 235 if (funcs[f]) { 236 ierr = PetscDualSpaceApply(sp[f], d, geom, numComp, funcs[f], ctx, &values[v]);CHKERRQ(ierr); 237 } else { 238 for (comp = 0; comp < numComp; ++comp) values[v+comp] = 0.0; 239 } 240 v += numComp; 241 } 242 } 243 ierr = DMPlexVecSetFieldClosure_Internal(dm, section, localX, fieldActive, point, values, mode);CHKERRQ(ierr); 244 } 245 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 246 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 247 } 248 ierr = DMRestoreWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 249 ierr = DMRestoreWorkArray(dm, numFields, PETSC_BOOL, &fieldActive);CHKERRQ(ierr); 250 ierr = PetscFree3(sp,v0,J);CHKERRQ(ierr); 251 PetscFunctionReturn(0); 252 } 253 254 #undef __FUNCT__ 255 #define __FUNCT__ "DMPlexProjectFunctionLocal" 256 PetscErrorCode DMPlexProjectFunctionLocal(DM dm, void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, InsertMode mode, Vec localX) 257 { 258 PetscDualSpace *sp; 259 PetscSection section; 260 PetscScalar *values; 261 PetscReal *v0, *J, detJ; 262 PetscInt numFields, numComp, dim, spDim, totDim = 0, numValues, cStart, cEnd, c, f, d, v, comp; 263 PetscErrorCode ierr; 264 265 PetscFunctionBegin; 266 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 267 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 268 ierr = PetscMalloc1(numFields, &sp);CHKERRQ(ierr); 269 for (f = 0; f < numFields; ++f) { 270 PetscFE fe; 271 272 ierr = DMGetField(dm, f, (PetscObject *) &fe);CHKERRQ(ierr); 273 ierr = PetscFEGetDualSpace(fe, &sp[f]);CHKERRQ(ierr); 274 ierr = PetscFEGetNumComponents(fe, &numComp);CHKERRQ(ierr); 275 ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr); 276 totDim += spDim*numComp; 277 } 278 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 279 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 280 ierr = DMPlexVecGetClosure(dm, section, localX, cStart, &numValues, NULL);CHKERRQ(ierr); 281 if (numValues != totDim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The section cell closure size %d != dual space dimension %d", numValues, totDim); 282 ierr = DMGetWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 283 ierr = PetscMalloc2(dim,&v0,dim*dim,&J);CHKERRQ(ierr); 284 for (c = cStart; c < cEnd; ++c) { 285 PetscCellGeometry geom; 286 287 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, NULL, &detJ);CHKERRQ(ierr); 288 geom.v0 = v0; 289 geom.J = J; 290 geom.detJ = &detJ; 291 for (f = 0, v = 0; f < numFields; ++f) { 292 PetscFE fe; 293 void * const ctx = ctxs ? ctxs[f] : NULL; 294 295 ierr = DMGetField(dm, f, (PetscObject *) &fe);CHKERRQ(ierr); 296 ierr = PetscFEGetNumComponents(fe, &numComp);CHKERRQ(ierr); 297 ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr); 298 for (d = 0; d < spDim; ++d) { 299 if (funcs[f]) { 300 ierr = PetscDualSpaceApply(sp[f], d, geom, numComp, funcs[f], ctx, &values[v]);CHKERRQ(ierr); 301 } else { 302 for (comp = 0; comp < numComp; ++comp) values[v+comp] = 0.0; 303 } 304 v += numComp; 305 } 306 } 307 ierr = DMPlexVecSetClosure(dm, section, localX, c, values, mode);CHKERRQ(ierr); 308 } 309 ierr = DMRestoreWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 310 ierr = PetscFree2(v0,J);CHKERRQ(ierr); 311 ierr = PetscFree(sp);CHKERRQ(ierr); 312 PetscFunctionReturn(0); 313 } 314 315 #undef __FUNCT__ 316 #define __FUNCT__ "DMPlexProjectFunction" 317 /*@C 318 DMPlexProjectFunction - This projects the given function into the function space provided. 319 320 Input Parameters: 321 + dm - The DM 322 . funcs - The coordinate functions to evaluate, one per field 323 . ctxs - Optional array of contexts to pass to each coordinate function. ctxs itself may be null. 324 - mode - The insertion mode for values 325 326 Output Parameter: 327 . X - vector 328 329 Level: developer 330 331 .seealso: DMPlexComputeL2Diff() 332 @*/ 333 PetscErrorCode DMPlexProjectFunction(DM dm, void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, InsertMode mode, Vec X) 334 { 335 Vec localX; 336 PetscErrorCode ierr; 337 338 PetscFunctionBegin; 339 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 340 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 341 ierr = DMPlexProjectFunctionLocal(dm, funcs, ctxs, mode, localX);CHKERRQ(ierr); 342 ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr); 343 ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr); 344 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 345 PetscFunctionReturn(0); 346 } 347 348 #undef __FUNCT__ 349 #define __FUNCT__ "DMPlexProjectFieldLocal" 350 PetscErrorCode DMPlexProjectFieldLocal(DM dm, Vec localU, void (**funcs)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal [], PetscScalar []), InsertMode mode, Vec localX) 351 { 352 DM dmAux; 353 PetscProblem prob, probAux; 354 Vec A; 355 PetscSection section; 356 PetscScalar *values, *u, *u_x, *a, *a_x, *coefficients, *coefficientsAux; 357 PetscReal *x, *v0, *J, *invJ, detJ, **basisField, **basisFieldDer, **basisFieldAux, **basisFieldDerAux; 358 PetscInt Nf, cOffset = 0, cOffsetAux = 0, dim, spDim, totDim, totDimAux, numValues, cStart, cEnd, c, f, d, v, comp; 359 PetscErrorCode ierr; 360 361 PetscFunctionBegin; 362 ierr = DMGetProblem(dm, &prob);CHKERRQ(ierr); 363 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 364 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 365 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 366 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 367 ierr = PetscProblemGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 368 ierr = PetscProblemGetTabulation(prob, &basisField, &basisFieldDer);CHKERRQ(ierr); 369 ierr = PetscProblemGetEvaluationArrays(prob, &u, NULL, &u_x);CHKERRQ(ierr); 370 ierr = PetscProblemGetRefCoordArrays(prob, &x, NULL);CHKERRQ(ierr); 371 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 372 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 373 if (dmAux) { 374 ierr = DMGetProblem(dmAux, &probAux);CHKERRQ(ierr); 375 ierr = PetscProblemGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 376 ierr = PetscProblemGetTabulation(prob, &basisFieldAux, &basisFieldDerAux);CHKERRQ(ierr); 377 ierr = PetscProblemGetEvaluationArrays(probAux, &a, NULL, &a_x);CHKERRQ(ierr); 378 } 379 ierr = DMPlexInsertBoundaryValuesFEM(dm, localU);CHKERRQ(ierr); 380 ierr = DMPlexVecGetClosure(dm, section, localX, cStart, &numValues, NULL);CHKERRQ(ierr); 381 if (numValues != totDim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The section cell closure size %d != dual space dimension %d", numValues, totDim); 382 ierr = DMGetWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 383 ierr = PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);CHKERRQ(ierr); 384 for (c = cStart; c < cEnd; ++c) { 385 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); 386 for (f = 0, v = 0; f < Nf; ++f) { 387 PetscFE fe; 388 PetscDualSpace sp; 389 PetscInt Ncf; 390 391 ierr = PetscProblemGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 392 ierr = PetscFEGetDualSpace(fe, &sp);CHKERRQ(ierr); 393 ierr = PetscFEGetNumComponents(fe, &Ncf);CHKERRQ(ierr); 394 ierr = PetscDualSpaceGetDimension(sp, &spDim);CHKERRQ(ierr); 395 for (d = 0; d < spDim; ++d) { 396 PetscQuadrature quad; 397 const PetscReal *points, *weights; 398 PetscInt numPoints, q; 399 400 if (funcs[f]) { 401 ierr = PetscDualSpaceGetFunctional(sp, d, &quad);CHKERRQ(ierr); 402 ierr = PetscQuadratureGetData(quad, NULL, &numPoints, &points, &weights);CHKERRQ(ierr); 403 ierr = PetscFEGetTabulation(fe, numPoints, points, &basisField[f], &basisFieldDer[f], NULL);CHKERRQ(ierr); 404 for (q = 0; q < numPoints; ++q) { 405 CoordinatesRefToReal(dim, dim, v0, J, &points[q*dim], x); 406 ierr = EvaluateFieldJets(prob, PETSC_FALSE, q, invJ, &coefficients[cOffset], NULL, u, u_x, NULL);CHKERRQ(ierr); 407 ierr = EvaluateFieldJets(probAux, PETSC_FALSE, q, invJ, &coefficientsAux[cOffsetAux], NULL, a, a_x, NULL);CHKERRQ(ierr); 408 (*funcs[f])(u, NULL, u_x, a, NULL, a_x, x, &values[v]); 409 } 410 ierr = PetscFERestoreTabulation(fe, numPoints, points, &basisField[f], &basisFieldDer[f], NULL);CHKERRQ(ierr); 411 } else { 412 for (comp = 0; comp < Ncf; ++comp) values[v+comp] = 0.0; 413 } 414 v += Ncf; 415 } 416 } 417 ierr = DMPlexVecSetClosure(dm, section, localX, c, values, mode);CHKERRQ(ierr); 418 cOffset += totDim; 419 cOffsetAux += totDimAux; 420 } 421 ierr = DMRestoreWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 422 ierr = PetscFree3(v0,J,invJ);CHKERRQ(ierr); 423 PetscFunctionReturn(0); 424 } 425 426 #undef __FUNCT__ 427 #define __FUNCT__ "DMPlexProjectField" 428 /*@C 429 DMPlexProjectField - This projects the given function of the fields into the function space provided. 430 431 Input Parameters: 432 + dm - The DM 433 . U - The input field vector 434 . funcs - The functions to evaluate, one per field 435 - mode - The insertion mode for values 436 437 Output Parameter: 438 . X - The output vector 439 440 Level: developer 441 442 .seealso: DMPlexProjectFunction(), DMPlexComputeL2Diff() 443 @*/ 444 PetscErrorCode DMPlexProjectField(DM dm, Vec U, void (**funcs)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal [], PetscScalar []), InsertMode mode, Vec X) 445 { 446 Vec localX, localU; 447 PetscErrorCode ierr; 448 449 PetscFunctionBegin; 450 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 451 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 452 ierr = DMGetLocalVector(dm, &localU);CHKERRQ(ierr); 453 ierr = DMGlobalToLocalBegin(dm, U, INSERT_VALUES, localU);CHKERRQ(ierr); 454 ierr = DMGlobalToLocalEnd(dm, U, INSERT_VALUES, localU);CHKERRQ(ierr); 455 ierr = DMPlexProjectFieldLocal(dm, localU, funcs, mode, localX);CHKERRQ(ierr); 456 ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr); 457 ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr); 458 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 459 ierr = DMRestoreLocalVector(dm, &localU);CHKERRQ(ierr); 460 PetscFunctionReturn(0); 461 } 462 463 #undef __FUNCT__ 464 #define __FUNCT__ "DMPlexInsertBoundaryValuesFEM" 465 PetscErrorCode DMPlexInsertBoundaryValuesFEM(DM dm, Vec localX) 466 { 467 void (**funcs)(const PetscReal x[], PetscScalar *u, void *ctx); 468 void **ctxs; 469 PetscFE *fe; 470 PetscInt numFields, f, numBd, b; 471 PetscErrorCode ierr; 472 473 PetscFunctionBegin; 474 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 475 PetscValidHeaderSpecific(localX, VEC_CLASSID, 2); 476 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 477 ierr = PetscMalloc3(numFields,&fe,numFields,&funcs,numFields,&ctxs);CHKERRQ(ierr); 478 for (f = 0; f < numFields; ++f) {ierr = DMGetField(dm, f, (PetscObject *) &fe[f]);CHKERRQ(ierr);} 479 /* OPT: Could attempt to do multiple BCs at once */ 480 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 481 for (b = 0; b < numBd; ++b) { 482 DMLabel label; 483 const PetscInt *ids; 484 const char *labelname; 485 PetscInt numids, field; 486 PetscBool isEssential; 487 void (*func)(); 488 void *ctx; 489 490 ierr = DMPlexGetBoundary(dm, b, &isEssential, NULL, &labelname, &field, &func, &numids, &ids, &ctx);CHKERRQ(ierr); 491 ierr = DMPlexGetLabel(dm, labelname, &label);CHKERRQ(ierr); 492 for (f = 0; f < numFields; ++f) { 493 funcs[f] = field == f ? (void (*)(const PetscReal[], PetscScalar *, void *)) func : NULL; 494 ctxs[f] = field == f ? ctx : NULL; 495 } 496 ierr = DMPlexProjectFunctionLabelLocal(dm, label, numids, ids, fe, funcs, ctxs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); 497 } 498 ierr = PetscFree3(fe,funcs,ctxs);CHKERRQ(ierr); 499 PetscFunctionReturn(0); 500 } 501 502 #undef __FUNCT__ 503 #define __FUNCT__ "DMPlexComputeL2Diff" 504 /*@C 505 DMPlexComputeL2Diff - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h. 506 507 Input Parameters: 508 + dm - The DM 509 . funcs - The functions to evaluate for each field component 510 . ctxs - Optional array of contexts to pass to each function, or NULL. 511 - X - The coefficient vector u_h 512 513 Output Parameter: 514 . diff - The diff ||u - u_h||_2 515 516 Level: developer 517 518 .seealso: DMPlexProjectFunction(), DMPlexComputeL2GradientDiff() 519 @*/ 520 PetscErrorCode DMPlexComputeL2Diff(DM dm, void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff) 521 { 522 const PetscInt debug = 0; 523 PetscSection section; 524 PetscQuadrature quad; 525 Vec localX; 526 PetscScalar *funcVal; 527 PetscReal *coords, *v0, *J, *invJ, detJ; 528 PetscReal localDiff = 0.0; 529 PetscInt dim, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset, comp; 530 PetscErrorCode ierr; 531 532 PetscFunctionBegin; 533 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 534 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 535 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 536 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 537 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 538 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 539 for (field = 0; field < numFields; ++field) { 540 PetscFE fe; 541 PetscInt Nc; 542 543 ierr = DMGetField(dm, field, (PetscObject *) &fe);CHKERRQ(ierr); 544 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 545 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 546 numComponents += Nc; 547 } 548 ierr = DMPlexProjectFunctionLocal(dm, funcs, ctxs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); 549 ierr = PetscMalloc5(numComponents,&funcVal,dim,&coords,dim,&v0,dim*dim,&J,dim*dim,&invJ);CHKERRQ(ierr); 550 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 551 for (c = cStart; c < cEnd; ++c) { 552 PetscScalar *x = NULL; 553 PetscReal elemDiff = 0.0; 554 555 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); 556 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 557 ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 558 559 for (field = 0, comp = 0, fieldOffset = 0; field < numFields; ++field) { 560 PetscFE fe; 561 void * const ctx = ctxs ? ctxs[field] : NULL; 562 const PetscReal *quadPoints, *quadWeights; 563 PetscReal *basis; 564 PetscInt numQuadPoints, numBasisFuncs, numBasisComps, q, d, e, fc, f; 565 566 ierr = DMGetField(dm, field, (PetscObject *) &fe);CHKERRQ(ierr); 567 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, &quadPoints, &quadWeights);CHKERRQ(ierr); 568 ierr = PetscFEGetDimension(fe, &numBasisFuncs);CHKERRQ(ierr); 569 ierr = PetscFEGetNumComponents(fe, &numBasisComps);CHKERRQ(ierr); 570 ierr = PetscFEGetDefaultTabulation(fe, &basis, NULL, NULL);CHKERRQ(ierr); 571 if (debug) { 572 char title[1024]; 573 ierr = PetscSNPrintf(title, 1023, "Solution for Field %d", field);CHKERRQ(ierr); 574 ierr = DMPrintCellVector(c, title, numBasisFuncs*numBasisComps, &x[fieldOffset]);CHKERRQ(ierr); 575 } 576 for (q = 0; q < numQuadPoints; ++q) { 577 for (d = 0; d < dim; d++) { 578 coords[d] = v0[d]; 579 for (e = 0; e < dim; e++) { 580 coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0); 581 } 582 } 583 (*funcs[field])(coords, funcVal, ctx); 584 for (fc = 0; fc < numBasisComps; ++fc) { 585 PetscScalar interpolant = 0.0; 586 587 for (f = 0; f < numBasisFuncs; ++f) { 588 const PetscInt fidx = f*numBasisComps+fc; 589 interpolant += x[fieldOffset+fidx]*basis[q*numBasisFuncs*numBasisComps+fidx]; 590 } 591 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d field %d diff %g\n", c, field, PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ);CHKERRQ(ierr);} 592 elemDiff += PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ; 593 } 594 } 595 comp += numBasisComps; 596 fieldOffset += numBasisFuncs*numBasisComps; 597 } 598 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 599 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d diff %g\n", c, elemDiff);CHKERRQ(ierr);} 600 localDiff += elemDiff; 601 } 602 ierr = PetscFree5(funcVal,coords,v0,J,invJ);CHKERRQ(ierr); 603 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 604 ierr = MPI_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 605 *diff = PetscSqrtReal(*diff); 606 PetscFunctionReturn(0); 607 } 608 609 #undef __FUNCT__ 610 #define __FUNCT__ "DMPlexComputeL2GradientDiff" 611 /*@C 612 DMPlexComputeL2GradientDiff - This function computes the L_2 difference between the gradient of a function u and an FEM interpolant solution grad u_h. 613 614 Input Parameters: 615 + dm - The DM 616 . funcs - The gradient functions to evaluate for each field component 617 . ctxs - Optional array of contexts to pass to each function, or NULL. 618 . X - The coefficient vector u_h 619 - n - The vector to project along 620 621 Output Parameter: 622 . diff - The diff ||(grad u - grad u_h) . n||_2 623 624 Level: developer 625 626 .seealso: DMPlexProjectFunction(), DMPlexComputeL2Diff() 627 @*/ 628 PetscErrorCode DMPlexComputeL2GradientDiff(DM dm, void (**funcs)(const PetscReal [], const PetscReal [], PetscScalar *, void *), void **ctxs, Vec X, const PetscReal n[], PetscReal *diff) 629 { 630 const PetscInt debug = 0; 631 PetscSection section; 632 PetscQuadrature quad; 633 Vec localX; 634 PetscScalar *funcVal, *interpolantVec; 635 PetscReal *coords, *realSpaceDer, *v0, *J, *invJ, detJ; 636 PetscReal localDiff = 0.0; 637 PetscInt dim, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset, comp; 638 PetscErrorCode ierr; 639 640 PetscFunctionBegin; 641 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 642 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 643 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 644 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 645 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 646 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 647 for (field = 0; field < numFields; ++field) { 648 PetscFE fe; 649 PetscInt Nc; 650 651 ierr = DMGetField(dm, field, (PetscObject *) &fe);CHKERRQ(ierr); 652 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 653 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 654 numComponents += Nc; 655 } 656 /* ierr = DMPlexProjectFunctionLocal(dm, fe, funcs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); */ 657 ierr = PetscMalloc7(numComponents,&funcVal,dim,&coords,dim,&realSpaceDer,dim,&v0,dim*dim,&J,dim*dim,&invJ,dim,&interpolantVec);CHKERRQ(ierr); 658 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 659 for (c = cStart; c < cEnd; ++c) { 660 PetscScalar *x = NULL; 661 PetscReal elemDiff = 0.0; 662 663 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); 664 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 665 ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 666 667 for (field = 0, comp = 0, fieldOffset = 0; field < numFields; ++field) { 668 PetscFE fe; 669 void * const ctx = ctxs ? ctxs[field] : NULL; 670 const PetscReal *quadPoints, *quadWeights; 671 PetscReal *basisDer; 672 PetscInt numQuadPoints, Nb, Ncomp, q, d, e, fc, f, g; 673 674 ierr = DMGetField(dm, field, (PetscObject *) &fe);CHKERRQ(ierr); 675 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, &quadPoints, &quadWeights);CHKERRQ(ierr); 676 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 677 ierr = PetscFEGetNumComponents(fe, &Ncomp);CHKERRQ(ierr); 678 ierr = PetscFEGetDefaultTabulation(fe, NULL, &basisDer, NULL);CHKERRQ(ierr); 679 if (debug) { 680 char title[1024]; 681 ierr = PetscSNPrintf(title, 1023, "Solution for Field %d", field);CHKERRQ(ierr); 682 ierr = DMPrintCellVector(c, title, Nb*Ncomp, &x[fieldOffset]);CHKERRQ(ierr); 683 } 684 for (q = 0; q < numQuadPoints; ++q) { 685 for (d = 0; d < dim; d++) { 686 coords[d] = v0[d]; 687 for (e = 0; e < dim; e++) { 688 coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0); 689 } 690 } 691 (*funcs[field])(coords, n, funcVal, ctx); 692 for (fc = 0; fc < Ncomp; ++fc) { 693 PetscScalar interpolant = 0.0; 694 695 for (d = 0; d < dim; ++d) interpolantVec[d] = 0.0; 696 for (f = 0; f < Nb; ++f) { 697 const PetscInt fidx = f*Ncomp+fc; 698 699 for (d = 0; d < dim; ++d) { 700 realSpaceDer[d] = 0.0; 701 for (g = 0; g < dim; ++g) { 702 realSpaceDer[d] += invJ[g*dim+d]*basisDer[(q*Nb*Ncomp+fidx)*dim+g]; 703 } 704 interpolantVec[d] += x[fieldOffset+fidx]*realSpaceDer[d]; 705 } 706 } 707 for (d = 0; d < dim; ++d) interpolant += interpolantVec[d]*n[d]; 708 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d fieldDer %d diff %g\n", c, field, PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ);CHKERRQ(ierr);} 709 elemDiff += PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ; 710 } 711 } 712 comp += Ncomp; 713 fieldOffset += Nb*Ncomp; 714 } 715 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 716 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d diff %g\n", c, elemDiff);CHKERRQ(ierr);} 717 localDiff += elemDiff; 718 } 719 ierr = PetscFree7(funcVal,coords,realSpaceDer,v0,J,invJ,interpolantVec);CHKERRQ(ierr); 720 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 721 ierr = MPI_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 722 *diff = PetscSqrtReal(*diff); 723 PetscFunctionReturn(0); 724 } 725 726 #undef __FUNCT__ 727 #define __FUNCT__ "DMPlexComputeL2FieldDiff" 728 PetscErrorCode DMPlexComputeL2FieldDiff(DM dm, void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, Vec X, PetscReal diff[]) 729 { 730 const PetscInt debug = 0; 731 PetscSection section; 732 PetscQuadrature quad; 733 Vec localX; 734 PetscScalar *funcVal; 735 PetscReal *coords, *v0, *J, *invJ, detJ; 736 PetscReal *localDiff; 737 PetscInt dim, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset, comp; 738 PetscErrorCode ierr; 739 740 PetscFunctionBegin; 741 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 742 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 743 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 744 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 745 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 746 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 747 for (field = 0; field < numFields; ++field) { 748 PetscFE fe; 749 PetscInt Nc; 750 751 ierr = DMGetField(dm, field, (PetscObject *) &fe);CHKERRQ(ierr); 752 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 753 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 754 numComponents += Nc; 755 } 756 ierr = DMPlexProjectFunctionLocal(dm, funcs, ctxs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); 757 ierr = PetscCalloc6(numFields,&localDiff,numComponents,&funcVal,dim,&coords,dim,&v0,dim*dim,&J,dim*dim,&invJ);CHKERRQ(ierr); 758 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 759 for (c = cStart; c < cEnd; ++c) { 760 PetscScalar *x = NULL; 761 762 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); 763 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 764 ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 765 766 for (field = 0, comp = 0, fieldOffset = 0; field < numFields; ++field) { 767 PetscFE fe; 768 void * const ctx = ctxs ? ctxs[field] : NULL; 769 const PetscReal *quadPoints, *quadWeights; 770 PetscReal *basis, elemDiff = 0.0; 771 PetscInt numQuadPoints, numBasisFuncs, numBasisComps, q, d, e, fc, f; 772 773 ierr = DMGetField(dm, field, (PetscObject *) &fe);CHKERRQ(ierr); 774 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, &quadPoints, &quadWeights);CHKERRQ(ierr); 775 ierr = PetscFEGetDimension(fe, &numBasisFuncs);CHKERRQ(ierr); 776 ierr = PetscFEGetNumComponents(fe, &numBasisComps);CHKERRQ(ierr); 777 ierr = PetscFEGetDefaultTabulation(fe, &basis, NULL, NULL);CHKERRQ(ierr); 778 if (debug) { 779 char title[1024]; 780 ierr = PetscSNPrintf(title, 1023, "Solution for Field %d", field);CHKERRQ(ierr); 781 ierr = DMPrintCellVector(c, title, numBasisFuncs*numBasisComps, &x[fieldOffset]);CHKERRQ(ierr); 782 } 783 for (q = 0; q < numQuadPoints; ++q) { 784 for (d = 0; d < dim; d++) { 785 coords[d] = v0[d]; 786 for (e = 0; e < dim; e++) { 787 coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0); 788 } 789 } 790 (*funcs[field])(coords, funcVal, ctx); 791 for (fc = 0; fc < numBasisComps; ++fc) { 792 PetscScalar interpolant = 0.0; 793 794 for (f = 0; f < numBasisFuncs; ++f) { 795 const PetscInt fidx = f*numBasisComps+fc; 796 interpolant += x[fieldOffset+fidx]*basis[q*numBasisFuncs*numBasisComps+fidx]; 797 } 798 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d field %d diff %g\n", c, field, PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ);CHKERRQ(ierr);} 799 elemDiff += PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ; 800 } 801 } 802 comp += numBasisComps; 803 fieldOffset += numBasisFuncs*numBasisComps; 804 localDiff[field] += elemDiff; 805 } 806 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 807 } 808 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 809 ierr = MPI_Allreduce(localDiff, diff, numFields, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 810 for (field = 0; field < numFields; ++field) diff[field] = PetscSqrtReal(diff[field]); 811 ierr = PetscFree6(localDiff,funcVal,coords,v0,J,invJ);CHKERRQ(ierr); 812 PetscFunctionReturn(0); 813 } 814 815 #undef __FUNCT__ 816 #define __FUNCT__ "DMPlexComputeIntegralFEM" 817 /*@ 818 DMPlexComputeIntegralFEM - Form the local integral F from the local input X using pointwise functions specified by the user 819 820 Input Parameters: 821 + dm - The mesh 822 . X - Local input vector 823 - user - The user context 824 825 Output Parameter: 826 . integral - Local integral for each field 827 828 Level: developer 829 830 .seealso: DMPlexComputeResidualFEM() 831 @*/ 832 PetscErrorCode DMPlexComputeIntegralFEM(DM dm, Vec X, PetscReal *integral, void *user) 833 { 834 DM_Plex *mesh = (DM_Plex *) dm->data; 835 DM dmAux; 836 Vec localX, A; 837 PetscProblem prob, probAux = NULL; 838 PetscQuadrature q; 839 PetscCellGeometry geom; 840 PetscSection section, sectionAux; 841 PetscReal *v0, *J, *invJ, *detJ; 842 PetscScalar *u, *a = NULL; 843 PetscInt dim, Nf, f, numCells, cStart, cEnd, c; 844 PetscInt totDim, totDimAux; 845 PetscErrorCode ierr; 846 847 PetscFunctionBegin; 848 /*ierr = PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr);*/ 849 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 850 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 851 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 852 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 853 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 854 ierr = DMGetProblem(dm, &prob);CHKERRQ(ierr); 855 ierr = PetscProblemGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 856 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 857 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 858 numCells = cEnd - cStart; 859 for (f = 0; f < Nf; ++f) {integral[f] = 0.0;} 860 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 861 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 862 if (dmAux) { 863 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 864 ierr = DMGetProblem(dmAux, &probAux);CHKERRQ(ierr); 865 ierr = PetscProblemGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 866 } 867 ierr = DMPlexInsertBoundaryValuesFEM(dm, localX);CHKERRQ(ierr); 868 ierr = PetscMalloc5(numCells*totDim,&u,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ);CHKERRQ(ierr); 869 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 870 for (c = cStart; c < cEnd; ++c) { 871 PetscScalar *x = NULL; 872 PetscInt i; 873 874 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 875 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 876 ierr = DMPlexVecGetClosure(dm, section, localX, c, NULL, &x);CHKERRQ(ierr); 877 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 878 ierr = DMPlexVecRestoreClosure(dm, section, localX, c, NULL, &x);CHKERRQ(ierr); 879 if (dmAux) { 880 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 881 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 882 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 883 } 884 } 885 for (f = 0; f < Nf; ++f) { 886 PetscFE fe; 887 PetscInt numQuadPoints, Nb; 888 /* Conforming batches */ 889 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 890 /* Remainder */ 891 PetscInt Nr, offset; 892 893 ierr = PetscProblemGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 894 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 895 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 896 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 897 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 898 blockSize = Nb*numQuadPoints; 899 batchSize = numBlocks * blockSize; 900 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 901 numChunks = numCells / (numBatches*batchSize); 902 Ne = numChunks*numBatches*batchSize; 903 Nr = numCells % (numBatches*batchSize); 904 offset = numCells - Nr; 905 geom.v0 = v0; 906 geom.J = J; 907 geom.invJ = invJ; 908 geom.detJ = detJ; 909 ierr = PetscFEIntegrate(fe, prob, f, Ne, geom, u, probAux, a, integral);CHKERRQ(ierr); 910 geom.v0 = &v0[offset*dim]; 911 geom.J = &J[offset*dim*dim]; 912 geom.invJ = &invJ[offset*dim*dim]; 913 geom.detJ = &detJ[offset]; 914 ierr = PetscFEIntegrate(fe, prob, f, Nr, geom, &u[offset*totDim], probAux, &a[offset*totDimAux], integral);CHKERRQ(ierr); 915 } 916 ierr = PetscFree5(u,v0,J,invJ,detJ);CHKERRQ(ierr); 917 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 918 if (mesh->printFEM) { 919 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Local integral:");CHKERRQ(ierr); 920 for (f = 0; f < Nf; ++f) {ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), " %g", integral[f]);CHKERRQ(ierr);} 921 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "\n");CHKERRQ(ierr); 922 } 923 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 924 /* TODO: Allreduce for integral */ 925 /*ierr = PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);CHKERRQ(ierr);*/ 926 PetscFunctionReturn(0); 927 } 928 929 #undef __FUNCT__ 930 #define __FUNCT__ "DMPlexComputeResidualFEM_Internal" 931 PetscErrorCode DMPlexComputeResidualFEM_Internal(DM dm, Vec X, Vec X_t, Vec F, void *user) 932 { 933 DM_Plex *mesh = (DM_Plex *) dm->data; 934 const char *name = "Residual"; 935 DM dmAux; 936 DMLabel depth; 937 Vec A; 938 PetscProblem prob, probAux = NULL; 939 PetscQuadrature q; 940 PetscCellGeometry geom; 941 PetscSection section, sectionAux; 942 PetscReal *v0, *J, *invJ, *detJ; 943 PetscScalar *elemVec, *u, *u_t, *a = NULL; 944 PetscInt dim, Nf, f, numCells, cStart, cEnd, c, numBd, bd; 945 PetscInt totDim, totDimBd, totDimAux; 946 PetscErrorCode ierr; 947 948 PetscFunctionBegin; 949 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 950 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 951 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 952 ierr = DMGetProblem(dm, &prob);CHKERRQ(ierr); 953 ierr = PetscProblemGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 954 ierr = PetscProblemGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 955 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 956 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 957 numCells = cEnd - cStart; 958 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 959 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 960 if (dmAux) { 961 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 962 ierr = DMGetProblem(dmAux, &probAux);CHKERRQ(ierr); 963 ierr = PetscProblemGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 964 } 965 ierr = DMPlexInsertBoundaryValuesFEM(dm, X);CHKERRQ(ierr); 966 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 967 ierr = PetscMalloc7(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*totDim,&elemVec);CHKERRQ(ierr); 968 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 969 for (c = cStart; c < cEnd; ++c) { 970 PetscScalar *x = NULL, *x_t = NULL; 971 PetscInt i; 972 973 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 974 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 975 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 976 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 977 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 978 if (X_t) { 979 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 980 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 981 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 982 } 983 if (dmAux) { 984 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 985 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 986 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 987 } 988 } 989 for (f = 0; f < Nf; ++f) { 990 PetscFE fe; 991 PetscInt numQuadPoints, Nb; 992 /* Conforming batches */ 993 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 994 /* Remainder */ 995 PetscInt Nr, offset; 996 997 ierr = PetscProblemGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 998 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 999 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1000 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1001 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1002 blockSize = Nb*numQuadPoints; 1003 batchSize = numBlocks * blockSize; 1004 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1005 numChunks = numCells / (numBatches*batchSize); 1006 Ne = numChunks*numBatches*batchSize; 1007 Nr = numCells % (numBatches*batchSize); 1008 offset = numCells - Nr; 1009 geom.v0 = v0; 1010 geom.J = J; 1011 geom.invJ = invJ; 1012 geom.detJ = detJ; 1013 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, geom, u, u_t, probAux, a, elemVec);CHKERRQ(ierr); 1014 geom.v0 = &v0[offset*dim]; 1015 geom.J = &J[offset*dim*dim]; 1016 geom.invJ = &invJ[offset*dim*dim]; 1017 geom.detJ = &detJ[offset]; 1018 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, geom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemVec[offset*totDim]);CHKERRQ(ierr); 1019 } 1020 for (c = cStart; c < cEnd; ++c) { 1021 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, name, totDim, &elemVec[c*totDim]);CHKERRQ(ierr);} 1022 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*totDim], ADD_VALUES);CHKERRQ(ierr); 1023 } 1024 ierr = PetscFree7(u,u_t,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr); 1025 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 1026 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1027 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1028 for (bd = 0; bd < numBd; ++bd) { 1029 const char *bdLabel; 1030 DMLabel label; 1031 IS pointIS; 1032 const PetscInt *points; 1033 const PetscInt *values; 1034 PetscReal *n; 1035 PetscInt field, numValues, numPoints, p, dep, numFaces; 1036 PetscBool isEssential; 1037 1038 ierr = DMPlexGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1039 if (isEssential) continue; 1040 if (numValues != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Bug me and I will fix this"); 1041 ierr = DMPlexGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1042 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 1043 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 1044 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1045 for (p = 0, numFaces = 0; p < numPoints; ++p) { 1046 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1047 if (dep == dim-1) ++numFaces; 1048 } 1049 ierr = PetscMalloc7(numFaces*totDimBd,&u,numFaces*dim,&v0,numFaces*dim,&n,numFaces*dim*dim,&J,numFaces*dim*dim,&invJ,numFaces,&detJ,numFaces*totDimBd,&elemVec);CHKERRQ(ierr); 1050 if (X_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 1051 for (p = 0, f = 0; p < numPoints; ++p) { 1052 const PetscInt point = points[p]; 1053 PetscScalar *x = NULL; 1054 PetscInt i; 1055 1056 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1057 if (dep != dim-1) continue; 1058 ierr = DMPlexComputeCellGeometry(dm, point, &v0[f*dim], &J[f*dim*dim], &invJ[f*dim*dim], &detJ[f]);CHKERRQ(ierr); 1059 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, &n[f*dim]); 1060 if (detJ[f] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", detJ[f], point); 1061 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 1062 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 1063 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 1064 if (X_t) { 1065 ierr = DMPlexVecGetClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 1066 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 1067 ierr = DMPlexVecRestoreClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 1068 } 1069 ++f; 1070 } 1071 for (f = 0; f < Nf; ++f) { 1072 PetscFE fe; 1073 PetscInt numQuadPoints, Nb; 1074 /* Conforming batches */ 1075 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1076 /* Remainder */ 1077 PetscInt Nr, offset; 1078 1079 ierr = PetscProblemGetBdDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1080 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1081 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1082 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1083 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1084 blockSize = Nb*numQuadPoints; 1085 batchSize = numBlocks * blockSize; 1086 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1087 numChunks = numFaces / (numBatches*batchSize); 1088 Ne = numChunks*numBatches*batchSize; 1089 Nr = numFaces % (numBatches*batchSize); 1090 offset = numFaces - Nr; 1091 geom.v0 = v0; 1092 geom.n = n; 1093 geom.J = J; 1094 geom.invJ = invJ; 1095 geom.detJ = detJ; 1096 ierr = PetscFEIntegrateBdResidual(fe, prob, f, Ne, geom, u, u_t, NULL, NULL, elemVec);CHKERRQ(ierr); 1097 geom.v0 = &v0[offset*dim]; 1098 geom.n = &n[offset*dim]; 1099 geom.J = &J[offset*dim*dim]; 1100 geom.invJ = &invJ[offset*dim*dim]; 1101 geom.detJ = &detJ[offset]; 1102 ierr = PetscFEIntegrateBdResidual(fe, prob, f, Nr, geom, &u[offset*totDimBd], u_t ? &u_t[offset*totDimBd] : NULL, NULL, NULL, &elemVec[offset*totDimBd]);CHKERRQ(ierr); 1103 } 1104 for (p = 0, f = 0; p < numPoints; ++p) { 1105 const PetscInt point = points[p]; 1106 1107 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 1108 if (dep != dim-1) continue; 1109 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDimBd, &elemVec[f*totDimBd]);CHKERRQ(ierr);} 1110 ierr = DMPlexVecSetClosure(dm, NULL, F, point, &elemVec[f*totDimBd], ADD_VALUES);CHKERRQ(ierr); 1111 ++f; 1112 } 1113 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1114 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1115 ierr = PetscFree7(u,v0,n,J,invJ,detJ,elemVec);CHKERRQ(ierr); 1116 if (X_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 1117 } 1118 if (mesh->printFEM) {ierr = DMPrintLocalVec(dm, name, mesh->printTol, F);CHKERRQ(ierr);} 1119 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1120 PetscFunctionReturn(0); 1121 } 1122 1123 #undef __FUNCT__ 1124 #define __FUNCT__ "DMPlexSNESComputeResidualFEM" 1125 /*@ 1126 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 1127 1128 Input Parameters: 1129 + dm - The mesh 1130 . X - Local solution 1131 - user - The user context 1132 1133 Output Parameter: 1134 . F - Local output vector 1135 1136 Level: developer 1137 1138 .seealso: DMPlexComputeJacobianActionFEM() 1139 @*/ 1140 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 1141 { 1142 PetscErrorCode ierr; 1143 1144 PetscFunctionBegin; 1145 ierr = DMPlexComputeResidualFEM_Internal(dm, X, NULL, F, user);CHKERRQ(ierr); 1146 PetscFunctionReturn(0); 1147 } 1148 1149 #undef __FUNCT__ 1150 #define __FUNCT__ "DMPlexTSComputeIFunctionFEM" 1151 /*@ 1152 DMPlexTSComputeIFunctionFEM - Form the local residual F from the local input X using pointwise functions specified by the user 1153 1154 Input Parameters: 1155 + dm - The mesh 1156 . t - The time 1157 . X - Local solution 1158 . X_t - Local solution time derivative, or NULL 1159 - user - The user context 1160 1161 Output Parameter: 1162 . F - Local output vector 1163 1164 Level: developer 1165 1166 .seealso: DMPlexComputeJacobianActionFEM() 1167 @*/ 1168 PetscErrorCode DMPlexTSComputeIFunctionFEM(DM dm, PetscReal time, Vec X, Vec X_t, Vec F, void *user) 1169 { 1170 PetscErrorCode ierr; 1171 1172 PetscFunctionBegin; 1173 ierr = DMPlexComputeResidualFEM_Internal(dm, X, X_t, F, user);CHKERRQ(ierr); 1174 PetscFunctionReturn(0); 1175 } 1176 1177 #undef __FUNCT__ 1178 #define __FUNCT__ "DMPlexComputeJacobianFEM_Internal" 1179 PetscErrorCode DMPlexComputeJacobianFEM_Internal(DM dm, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 1180 { 1181 DM_Plex *mesh = (DM_Plex *) dm->data; 1182 const char *name = "Jacobian"; 1183 DM dmAux; 1184 DMLabel depth; 1185 Vec A; 1186 PetscProblem prob, probAux = NULL; 1187 PetscQuadrature quad; 1188 PetscCellGeometry geom; 1189 PetscSection section, globalSection, sectionAux; 1190 PetscReal *v0, *J, *invJ, *detJ; 1191 PetscScalar *elemMat, *u, *u_t, *a = NULL; 1192 PetscInt dim, Nf, f, fieldI, fieldJ, numCells, cStart, cEnd, c; 1193 PetscInt totDim, totDimBd, totDimAux, numBd, bd; 1194 PetscBool isShell; 1195 PetscErrorCode ierr; 1196 1197 PetscFunctionBegin; 1198 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 1199 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1200 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1201 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1202 ierr = DMGetProblem(dm, &prob);CHKERRQ(ierr); 1203 ierr = PetscProblemGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1204 ierr = PetscProblemGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 1205 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1206 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1207 numCells = cEnd - cStart; 1208 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1209 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1210 if (dmAux) { 1211 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1212 ierr = DMGetProblem(dmAux, &probAux);CHKERRQ(ierr); 1213 ierr = PetscProblemGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1214 } 1215 ierr = DMPlexInsertBoundaryValuesFEM(dm, X);CHKERRQ(ierr); 1216 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 1217 ierr = PetscMalloc7(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*totDim*totDim,&elemMat);CHKERRQ(ierr); 1218 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1219 for (c = cStart; c < cEnd; ++c) { 1220 PetscScalar *x = NULL, *x_t = NULL; 1221 PetscInt i; 1222 1223 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 1224 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 1225 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1226 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 1227 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1228 if (X_t) { 1229 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1230 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 1231 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1232 } 1233 if (dmAux) { 1234 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1235 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 1236 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1237 } 1238 } 1239 ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1240 for (fieldI = 0; fieldI < Nf; ++fieldI) { 1241 PetscFE fe; 1242 PetscInt numQuadPoints, Nb; 1243 /* Conforming batches */ 1244 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1245 /* Remainder */ 1246 PetscInt Nr, offset; 1247 1248 ierr = PetscProblemGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1249 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1250 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1251 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1252 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1253 blockSize = Nb*numQuadPoints; 1254 batchSize = numBlocks * blockSize; 1255 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1256 numChunks = numCells / (numBatches*batchSize); 1257 Ne = numChunks*numBatches*batchSize; 1258 Nr = numCells % (numBatches*batchSize); 1259 offset = numCells - Nr; 1260 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1261 geom.v0 = v0; 1262 geom.J = J; 1263 geom.invJ = invJ; 1264 geom.detJ = detJ; 1265 ierr = PetscFEIntegrateJacobian(fe, prob, fieldI, fieldJ, Ne, geom, u, u_t, probAux, a, elemMat);CHKERRQ(ierr); 1266 geom.v0 = &v0[offset*dim]; 1267 geom.J = &J[offset*dim*dim]; 1268 geom.invJ = &invJ[offset*dim*dim]; 1269 geom.detJ = &detJ[offset]; 1270 ierr = PetscFEIntegrateJacobian(fe, prob, fieldI, fieldJ, Nr, geom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 1271 } 1272 } 1273 for (c = cStart; c < cEnd; ++c) { 1274 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[c*totDim*totDim]);CHKERRQ(ierr);} 1275 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMat[c*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 1276 } 1277 ierr = PetscFree7(u,u_t,v0,J,invJ,detJ,elemMat);CHKERRQ(ierr); 1278 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 1279 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1280 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1281 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1282 ierr = DMPlexGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1283 for (bd = 0; bd < numBd; ++bd) { 1284 const char *bdLabel; 1285 DMLabel label; 1286 IS pointIS; 1287 const PetscInt *points; 1288 const PetscInt *values; 1289 PetscReal *n; 1290 PetscInt field, numValues, numPoints, p, dep, numFaces; 1291 PetscBool isEssential; 1292 1293 ierr = DMPlexGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1294 if (isEssential) continue; 1295 if (numValues != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Bug me and I will fix this"); 1296 ierr = DMPlexGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1297 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 1298 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 1299 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1300 for (p = 0, numFaces = 0; p < numPoints; ++p) { 1301 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1302 if (dep == dim-1) ++numFaces; 1303 } 1304 ierr = PetscMalloc7(numFaces*totDimBd,&u,numFaces*dim,&v0,numFaces*dim,&n,numFaces*dim*dim,&J,numFaces*dim*dim,&invJ,numFaces,&detJ,numFaces*totDimBd*totDimBd,&elemMat);CHKERRQ(ierr); 1305 if (X_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 1306 for (p = 0, f = 0; p < numPoints; ++p) { 1307 const PetscInt point = points[p]; 1308 PetscScalar *x = NULL; 1309 PetscInt i; 1310 1311 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1312 if (dep != dim-1) continue; 1313 ierr = DMPlexComputeCellGeometry(dm, point, &v0[f*dim], &J[f*dim*dim], &invJ[f*dim*dim], &detJ[f]);CHKERRQ(ierr); 1314 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, &n[f*dim]); 1315 if (detJ[f] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", detJ[f], point); 1316 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 1317 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 1318 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 1319 if (X_t) { 1320 ierr = DMPlexVecGetClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 1321 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 1322 ierr = DMPlexVecRestoreClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 1323 } 1324 ++f; 1325 } 1326 ierr = PetscMemzero(elemMat, numFaces*totDimBd*totDimBd * sizeof(PetscScalar));CHKERRQ(ierr); 1327 for (fieldI = 0; fieldI < Nf; ++fieldI) { 1328 PetscFE fe; 1329 PetscInt numQuadPoints, Nb; 1330 /* Conforming batches */ 1331 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1332 /* Remainder */ 1333 PetscInt Nr, offset; 1334 1335 ierr = PetscProblemGetBdDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 1336 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1337 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1338 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1339 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1340 blockSize = Nb*numQuadPoints; 1341 batchSize = numBlocks * blockSize; 1342 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1343 numChunks = numFaces / (numBatches*batchSize); 1344 Ne = numChunks*numBatches*batchSize; 1345 Nr = numFaces % (numBatches*batchSize); 1346 offset = numFaces - Nr; 1347 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1348 geom.v0 = v0; 1349 geom.n = n; 1350 geom.J = J; 1351 geom.invJ = invJ; 1352 geom.detJ = detJ; 1353 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Ne, geom, u, u_t, NULL, NULL, elemMat);CHKERRQ(ierr); 1354 geom.v0 = &v0[offset*dim]; 1355 geom.n = &n[offset*dim]; 1356 geom.J = &J[offset*dim*dim]; 1357 geom.invJ = &invJ[offset*dim*dim]; 1358 geom.detJ = &detJ[offset]; 1359 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Nr, geom, &u[offset*totDimBd], u_t ? &u_t[offset*totDimBd] : NULL, NULL, NULL, &elemMat[offset*totDimBd*totDimBd]);CHKERRQ(ierr); 1360 } 1361 } 1362 for (p = 0, f = 0; p < numPoints; ++p) { 1363 const PetscInt point = points[p]; 1364 1365 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 1366 if (dep != dim-1) continue; 1367 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDimBd, totDimBd, &elemMat[f*totDimBd*totDimBd]);CHKERRQ(ierr);} 1368 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, point, &elemMat[f*totDimBd*totDimBd], ADD_VALUES);CHKERRQ(ierr); 1369 ++f; 1370 } 1371 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1372 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1373 ierr = PetscFree7(u,v0,n,J,invJ,detJ,elemMat);CHKERRQ(ierr); 1374 if (X_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 1375 } 1376 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1377 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1378 if (mesh->printFEM) { 1379 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 1380 ierr = MatChop(JacP, 1.0e-10);CHKERRQ(ierr); 1381 ierr = MatView(JacP, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1382 } 1383 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 1384 ierr = PetscObjectTypeCompare((PetscObject) Jac, MATSHELL, &isShell);CHKERRQ(ierr); 1385 if (isShell) { 1386 JacActionCtx *jctx; 1387 1388 ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); 1389 ierr = VecCopy(X, jctx->u);CHKERRQ(ierr); 1390 } 1391 PetscFunctionReturn(0); 1392 } 1393 1394 #undef __FUNCT__ 1395 #define __FUNCT__ "DMPlexSNESComputeJacobianFEM" 1396 /*@ 1397 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 1398 1399 Input Parameters: 1400 + dm - The mesh 1401 . X - Local input vector 1402 - user - The user context 1403 1404 Output Parameter: 1405 . Jac - Jacobian matrix 1406 1407 Note: 1408 The first member of the user context must be an FEMContext. 1409 1410 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 1411 like a GPU, or vectorize on a multicore machine. 1412 1413 Level: developer 1414 1415 .seealso: FormFunctionLocal() 1416 @*/ 1417 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 1418 { 1419 PetscErrorCode ierr; 1420 1421 PetscFunctionBegin; 1422 ierr = DMPlexComputeJacobianFEM_Internal(dm, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 1423 PetscFunctionReturn(0); 1424 } 1425 1426 #undef __FUNCT__ 1427 #define __FUNCT__ "DMPlexComputeInterpolatorFEM" 1428 /*@ 1429 DMPlexComputeInterpolatorFEM - Form the local portion of the interpolation matrix I from the coarse DM to the uniformly refined DM. 1430 1431 Input Parameters: 1432 + dmf - The fine mesh 1433 . dmc - The coarse mesh 1434 - user - The user context 1435 1436 Output Parameter: 1437 . In - The interpolation matrix 1438 1439 Note: 1440 The first member of the user context must be an FEMContext. 1441 1442 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 1443 like a GPU, or vectorize on a multicore machine. 1444 1445 Level: developer 1446 1447 .seealso: DMPlexComputeJacobianFEM() 1448 @*/ 1449 PetscErrorCode DMPlexComputeInterpolatorFEM(DM dmc, DM dmf, Mat In, void *user) 1450 { 1451 DM_Plex *mesh = (DM_Plex *) dmc->data; 1452 const char *name = "Interpolator"; 1453 PetscProblem prob; 1454 PetscFE *feRef; 1455 PetscSection fsection, fglobalSection; 1456 PetscSection csection, cglobalSection; 1457 PetscScalar *elemMat; 1458 PetscInt dim, Nf, f, fieldI, fieldJ, offsetI, offsetJ, cStart, cEnd, c; 1459 PetscInt cTotDim, rTotDim = 0; 1460 PetscErrorCode ierr; 1461 1462 PetscFunctionBegin; 1463 #if 0 1464 ierr = PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 1465 #endif 1466 ierr = DMPlexGetDimension(dmf, &dim);CHKERRQ(ierr); 1467 ierr = DMGetDefaultSection(dmf, &fsection);CHKERRQ(ierr); 1468 ierr = DMGetDefaultGlobalSection(dmf, &fglobalSection);CHKERRQ(ierr); 1469 ierr = DMGetDefaultSection(dmc, &csection);CHKERRQ(ierr); 1470 ierr = DMGetDefaultGlobalSection(dmc, &cglobalSection);CHKERRQ(ierr); 1471 ierr = PetscSectionGetNumFields(fsection, &Nf);CHKERRQ(ierr); 1472 ierr = DMPlexGetHeightStratum(dmc, 0, &cStart, &cEnd);CHKERRQ(ierr); 1473 ierr = DMGetProblem(dmf, &prob);CHKERRQ(ierr); 1474 ierr = PetscMalloc1(Nf,&feRef);CHKERRQ(ierr); 1475 for (f = 0; f < Nf; ++f) { 1476 PetscFE fe; 1477 PetscInt rNb, Nc; 1478 1479 ierr = PetscProblemGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1480 ierr = PetscFERefine(fe, &feRef[f]);CHKERRQ(ierr); 1481 ierr = PetscFEGetDimension(feRef[f], &rNb);CHKERRQ(ierr); 1482 ierr = PetscFEGetNumComponents(fe, &Nc);CHKERRQ(ierr); 1483 rTotDim += rNb*Nc; 1484 } 1485 ierr = PetscProblemGetTotalDimension(prob, &cTotDim);CHKERRQ(ierr); 1486 ierr = MatZeroEntries(In);CHKERRQ(ierr); 1487 ierr = PetscMalloc1(rTotDim*cTotDim,&elemMat);CHKERRQ(ierr); 1488 ierr = PetscMemzero(elemMat, rTotDim*cTotDim * sizeof(PetscScalar));CHKERRQ(ierr); 1489 for (fieldI = 0, offsetI = 0; fieldI < Nf; ++fieldI) { 1490 PetscDualSpace Qref; 1491 PetscQuadrature f; 1492 const PetscReal *qpoints, *qweights; 1493 PetscReal *points; 1494 PetscInt npoints = 0, Nc, Np, fpdim, i, k, p, d; 1495 1496 /* Compose points from all dual basis functionals */ 1497 ierr = PetscFEGetDualSpace(feRef[fieldI], &Qref);CHKERRQ(ierr); 1498 ierr = PetscFEGetNumComponents(feRef[fieldI], &Nc);CHKERRQ(ierr); 1499 ierr = PetscDualSpaceGetDimension(Qref, &fpdim);CHKERRQ(ierr); 1500 for (i = 0; i < fpdim; ++i) { 1501 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 1502 ierr = PetscQuadratureGetData(f, NULL, &Np, NULL, NULL);CHKERRQ(ierr); 1503 npoints += Np; 1504 } 1505 ierr = PetscMalloc1(npoints*dim,&points);CHKERRQ(ierr); 1506 for (i = 0, k = 0; i < fpdim; ++i) { 1507 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 1508 ierr = PetscQuadratureGetData(f, NULL, &Np, &qpoints, NULL);CHKERRQ(ierr); 1509 for (p = 0; p < Np; ++p, ++k) for (d = 0; d < dim; ++d) points[k*dim+d] = qpoints[p*dim+d]; 1510 } 1511 1512 for (fieldJ = 0, offsetJ = 0; fieldJ < Nf; ++fieldJ) { 1513 PetscFE fe; 1514 PetscReal *B; 1515 PetscInt NcJ, cpdim, j; 1516 1517 /* Evaluate basis at points */ 1518 ierr = PetscProblemGetDiscretization(prob, fieldJ, (PetscObject *) &fe);CHKERRQ(ierr); 1519 ierr = PetscFEGetNumComponents(fe, &NcJ);CHKERRQ(ierr); 1520 if (Nc != NcJ) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in fine space field %d does not match coarse field %d", Nc, NcJ); 1521 ierr = PetscFEGetDimension(fe, &cpdim);CHKERRQ(ierr); 1522 /* For now, fields only interpolate themselves */ 1523 if (fieldI == fieldJ) { 1524 ierr = PetscFEGetTabulation(fe, npoints, points, &B, NULL, NULL);CHKERRQ(ierr); 1525 for (i = 0, k = 0; i < fpdim; ++i) { 1526 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 1527 ierr = PetscQuadratureGetData(f, NULL, &Np, NULL, &qweights);CHKERRQ(ierr); 1528 for (p = 0; p < Np; ++p, ++k) { 1529 for (j = 0; j < cpdim; ++j) { 1530 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i*Nc + c)*cTotDim + offsetJ + j*NcJ + c] += B[k*cpdim*NcJ+j*Nc+c]*qweights[p]; 1531 } 1532 } 1533 } 1534 ierr = PetscFERestoreTabulation(fe, npoints, points, &B, NULL, NULL);CHKERRQ(ierr);CHKERRQ(ierr); 1535 } 1536 offsetJ += cpdim*NcJ; 1537 } 1538 offsetI += fpdim*Nc; 1539 ierr = PetscFree(points);CHKERRQ(ierr); 1540 } 1541 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(0, name, rTotDim, cTotDim, elemMat);CHKERRQ(ierr);} 1542 for (c = cStart; c < cEnd; ++c) { 1543 ierr = DMPlexMatSetClosureRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);CHKERRQ(ierr); 1544 } 1545 for (f = 0; f < Nf; ++f) {ierr = PetscFEDestroy(&feRef[f]);CHKERRQ(ierr);} 1546 ierr = PetscFree(feRef);CHKERRQ(ierr); 1547 ierr = PetscFree(elemMat);CHKERRQ(ierr); 1548 ierr = MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1549 ierr = MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1550 if (mesh->printFEM) { 1551 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 1552 ierr = MatChop(In, 1.0e-10);CHKERRQ(ierr); 1553 ierr = MatView(In, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1554 } 1555 #if 0 1556 ierr = PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 1557 #endif 1558 PetscFunctionReturn(0); 1559 } 1560 1561 #undef __FUNCT__ 1562 #define __FUNCT__ "BoundaryDuplicate" 1563 static PetscErrorCode BoundaryDuplicate(DMBoundary bd, DMBoundary *boundary) 1564 { 1565 DMBoundary b = bd, b2, bold = NULL; 1566 PetscErrorCode ierr; 1567 1568 PetscFunctionBegin; 1569 *boundary = NULL; 1570 for (; b; b = b->next, bold = b2) { 1571 ierr = PetscNew(&b2);CHKERRQ(ierr); 1572 ierr = PetscStrallocpy(b->name, (char **) &b2->name);CHKERRQ(ierr); 1573 ierr = PetscStrallocpy(b->labelname, (char **) &b2->labelname);CHKERRQ(ierr); 1574 ierr = PetscMalloc1(b->numids, &b2->ids);CHKERRQ(ierr); 1575 ierr = PetscMemcpy(b2->ids, b->ids, b->numids*sizeof(PetscInt));CHKERRQ(ierr); 1576 b2->label = NULL; 1577 b2->essential = b->essential; 1578 b2->field = b->field; 1579 b2->func = b->func; 1580 b2->numids = b->numids; 1581 b2->ctx = b->ctx; 1582 b2->next = NULL; 1583 if (!*boundary) *boundary = b2; 1584 if (bold) bold->next = b2; 1585 } 1586 PetscFunctionReturn(0); 1587 } 1588 1589 #undef __FUNCT__ 1590 #define __FUNCT__ "DMPlexCopyBoundary" 1591 PetscErrorCode DMPlexCopyBoundary(DM dm, DM dmNew) 1592 { 1593 DM_Plex *mesh = (DM_Plex *) dm->data; 1594 DM_Plex *meshNew = (DM_Plex *) dmNew->data; 1595 DMBoundary b; 1596 PetscErrorCode ierr; 1597 1598 PetscFunctionBegin; 1599 ierr = BoundaryDuplicate(mesh->boundary, &meshNew->boundary);CHKERRQ(ierr); 1600 for (b = meshNew->boundary; b; b = b->next) { 1601 if (b->labelname) { 1602 ierr = DMPlexGetLabel(dmNew, b->labelname, &b->label);CHKERRQ(ierr); 1603 if (!b->label) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Label %s does not exist in this DM", b->labelname); 1604 } 1605 } 1606 PetscFunctionReturn(0); 1607 } 1608 1609 #undef __FUNCT__ 1610 #define __FUNCT__ "DMPlexAddBoundary" 1611 /* The ids can be overridden by the command line option -bc_<boundary name> */ 1612 PetscErrorCode DMPlexAddBoundary(DM dm, PetscBool isEssential, const char name[], const char labelname[], PetscInt field, void (*bcFunc)(), PetscInt numids, const PetscInt *ids, void *ctx) 1613 { 1614 DM_Plex *mesh = (DM_Plex *) dm->data; 1615 DMBoundary b; 1616 PetscErrorCode ierr; 1617 1618 PetscFunctionBegin; 1619 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1620 ierr = PetscNew(&b);CHKERRQ(ierr); 1621 ierr = PetscStrallocpy(name, (char **) &b->name);CHKERRQ(ierr); 1622 ierr = PetscStrallocpy(labelname, (char **) &b->labelname);CHKERRQ(ierr); 1623 ierr = PetscMalloc1(numids, &b->ids);CHKERRQ(ierr); 1624 ierr = PetscMemcpy(b->ids, ids, numids*sizeof(PetscInt));CHKERRQ(ierr); 1625 if (b->labelname) { 1626 ierr = DMPlexGetLabel(dm, b->labelname, &b->label);CHKERRQ(ierr); 1627 if (!b->label) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Label %s does not exist in this DM", b->labelname); 1628 } 1629 b->essential = isEssential; 1630 b->field = field; 1631 b->func = bcFunc; 1632 b->numids = numids; 1633 b->ctx = ctx; 1634 b->next = mesh->boundary; 1635 mesh->boundary = b; 1636 PetscFunctionReturn(0); 1637 } 1638 1639 #undef __FUNCT__ 1640 #define __FUNCT__ "DMPlexGetNumBoundary" 1641 PetscErrorCode DMPlexGetNumBoundary(DM dm, PetscInt *numBd) 1642 { 1643 DM_Plex *mesh = (DM_Plex *) dm->data; 1644 DMBoundary b = mesh->boundary; 1645 1646 PetscFunctionBegin; 1647 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1648 PetscValidPointer(numBd, 2); 1649 *numBd = 0; 1650 while (b) {++(*numBd); b = b->next;} 1651 PetscFunctionReturn(0); 1652 } 1653 1654 #undef __FUNCT__ 1655 #define __FUNCT__ "DMPlexGetBoundary" 1656 PetscErrorCode DMPlexGetBoundary(DM dm, PetscInt bd, PetscBool *isEssential, const char **name, const char **labelname, PetscInt *field, void (**func)(), PetscInt *numids, const PetscInt **ids, void **ctx) 1657 { 1658 DM_Plex *mesh = (DM_Plex *) dm->data; 1659 DMBoundary b = mesh->boundary; 1660 PetscInt n = 0; 1661 1662 PetscFunctionBegin; 1663 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1664 while (b) { 1665 if (n == bd) break; 1666 b = b->next; 1667 ++n; 1668 } 1669 if (n != bd) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Boundary %d is not in [0, %d)", bd, n); 1670 if (isEssential) { 1671 PetscValidPointer(isEssential, 3); 1672 *isEssential = b->essential; 1673 } 1674 if (name) { 1675 PetscValidPointer(name, 4); 1676 *name = b->name; 1677 } 1678 if (labelname) { 1679 PetscValidPointer(labelname, 5); 1680 *labelname = b->labelname; 1681 } 1682 if (field) { 1683 PetscValidPointer(field, 6); 1684 *field = b->field; 1685 } 1686 if (func) { 1687 PetscValidPointer(func, 7); 1688 *func = b->func; 1689 } 1690 if (numids) { 1691 PetscValidPointer(numids, 8); 1692 *numids = b->numids; 1693 } 1694 if (ids) { 1695 PetscValidPointer(ids, 9); 1696 *ids = b->ids; 1697 } 1698 if (ctx) { 1699 PetscValidPointer(ctx, 10); 1700 *ctx = b->ctx; 1701 } 1702 PetscFunctionReturn(0); 1703 } 1704 1705 #undef __FUNCT__ 1706 #define __FUNCT__ "DMPlexIsBoundaryPoint" 1707 PetscErrorCode DMPlexIsBoundaryPoint(DM dm, PetscInt point, PetscBool *isBd) 1708 { 1709 DM_Plex *mesh = (DM_Plex *) dm->data; 1710 DMBoundary b = mesh->boundary; 1711 PetscErrorCode ierr; 1712 1713 PetscFunctionBegin; 1714 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1715 PetscValidPointer(isBd, 3); 1716 *isBd = PETSC_FALSE; 1717 while (b && !(*isBd)) { 1718 if (b->label) { 1719 PetscInt i; 1720 1721 for (i = 0; i < b->numids && !(*isBd); ++i) { 1722 ierr = DMLabelStratumHasPoint(b->label, b->ids[i], point, isBd);CHKERRQ(ierr); 1723 } 1724 } 1725 b = b->next; 1726 } 1727 PetscFunctionReturn(0); 1728 } 1729