1 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 3 #include <petscfe.h> 4 5 #undef __FUNCT__ 6 #define __FUNCT__ "DMPlexGetScale" 7 PetscErrorCode DMPlexGetScale(DM dm, PetscUnit unit, PetscReal *scale) 8 { 9 DM_Plex *mesh = (DM_Plex*) dm->data; 10 11 PetscFunctionBegin; 12 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 13 PetscValidPointer(scale, 3); 14 *scale = mesh->scale[unit]; 15 PetscFunctionReturn(0); 16 } 17 18 #undef __FUNCT__ 19 #define __FUNCT__ "DMPlexSetScale" 20 PetscErrorCode DMPlexSetScale(DM dm, PetscUnit unit, PetscReal scale) 21 { 22 DM_Plex *mesh = (DM_Plex*) dm->data; 23 24 PetscFunctionBegin; 25 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 26 mesh->scale[unit] = scale; 27 PetscFunctionReturn(0); 28 } 29 30 PETSC_STATIC_INLINE PetscInt epsilon(PetscInt i, PetscInt j, PetscInt k) 31 { 32 switch (i) { 33 case 0: 34 switch (j) { 35 case 0: return 0; 36 case 1: 37 switch (k) { 38 case 0: return 0; 39 case 1: return 0; 40 case 2: return 1; 41 } 42 case 2: 43 switch (k) { 44 case 0: return 0; 45 case 1: return -1; 46 case 2: return 0; 47 } 48 } 49 case 1: 50 switch (j) { 51 case 0: 52 switch (k) { 53 case 0: return 0; 54 case 1: return 0; 55 case 2: return -1; 56 } 57 case 1: return 0; 58 case 2: 59 switch (k) { 60 case 0: return 1; 61 case 1: return 0; 62 case 2: return 0; 63 } 64 } 65 case 2: 66 switch (j) { 67 case 0: 68 switch (k) { 69 case 0: return 0; 70 case 1: return 1; 71 case 2: return 0; 72 } 73 case 1: 74 switch (k) { 75 case 0: return -1; 76 case 1: return 0; 77 case 2: return 0; 78 } 79 case 2: return 0; 80 } 81 } 82 return 0; 83 } 84 85 #undef __FUNCT__ 86 #define __FUNCT__ "DMPlexCreateRigidBody" 87 /*@C 88 DMPlexCreateRigidBody - create rigid body modes from coordinates 89 90 Collective on DM 91 92 Input Arguments: 93 + dm - the DM 94 . section - the local section associated with the rigid field, or NULL for the default section 95 - globalSection - the global section associated with the rigid field, or NULL for the default section 96 97 Output Argument: 98 . sp - the null space 99 100 Note: This is necessary to take account of Dirichlet conditions on the displacements 101 102 Level: advanced 103 104 .seealso: MatNullSpaceCreate() 105 @*/ 106 PetscErrorCode DMPlexCreateRigidBody(DM dm, PetscSection section, PetscSection globalSection, MatNullSpace *sp) 107 { 108 MPI_Comm comm; 109 Vec coordinates, localMode, mode[6]; 110 PetscSection coordSection; 111 PetscScalar *coords; 112 PetscInt dim, vStart, vEnd, v, n, m, d, i, j; 113 PetscErrorCode ierr; 114 115 PetscFunctionBegin; 116 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 117 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 118 if (dim == 1) { 119 ierr = MatNullSpaceCreate(comm, PETSC_TRUE, 0, NULL, sp);CHKERRQ(ierr); 120 PetscFunctionReturn(0); 121 } 122 if (!section) {ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);} 123 if (!globalSection) {ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr);} 124 ierr = PetscSectionGetConstrainedStorageSize(globalSection, &n);CHKERRQ(ierr); 125 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 126 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 127 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 128 m = (dim*(dim+1))/2; 129 ierr = VecCreate(comm, &mode[0]);CHKERRQ(ierr); 130 ierr = VecSetSizes(mode[0], n, PETSC_DETERMINE);CHKERRQ(ierr); 131 ierr = VecSetUp(mode[0]);CHKERRQ(ierr); 132 for (i = 1; i < m; ++i) {ierr = VecDuplicate(mode[0], &mode[i]);CHKERRQ(ierr);} 133 /* Assume P1 */ 134 ierr = DMGetLocalVector(dm, &localMode);CHKERRQ(ierr); 135 for (d = 0; d < dim; ++d) { 136 PetscScalar values[3] = {0.0, 0.0, 0.0}; 137 138 values[d] = 1.0; 139 ierr = VecSet(localMode, 0.0);CHKERRQ(ierr); 140 for (v = vStart; v < vEnd; ++v) { 141 ierr = DMPlexVecSetClosure(dm, section, localMode, v, values, INSERT_VALUES);CHKERRQ(ierr); 142 } 143 ierr = DMLocalToGlobalBegin(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 144 ierr = DMLocalToGlobalEnd(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 145 } 146 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 147 for (d = dim; d < dim*(dim+1)/2; ++d) { 148 PetscInt i, j, k = dim > 2 ? d - dim : d; 149 150 ierr = VecSet(localMode, 0.0);CHKERRQ(ierr); 151 for (v = vStart; v < vEnd; ++v) { 152 PetscScalar values[3] = {0.0, 0.0, 0.0}; 153 PetscInt off; 154 155 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 156 for (i = 0; i < dim; ++i) { 157 for (j = 0; j < dim; ++j) { 158 values[j] += epsilon(i, j, k)*PetscRealPart(coords[off+i]); 159 } 160 } 161 ierr = DMPlexVecSetClosure(dm, section, localMode, v, values, INSERT_VALUES);CHKERRQ(ierr); 162 } 163 ierr = DMLocalToGlobalBegin(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 164 ierr = DMLocalToGlobalEnd(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr); 165 } 166 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 167 ierr = DMRestoreLocalVector(dm, &localMode);CHKERRQ(ierr); 168 for (i = 0; i < dim; ++i) {ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr);} 169 /* Orthonormalize system */ 170 for (i = dim; i < m; ++i) { 171 PetscScalar dots[6]; 172 173 ierr = VecMDot(mode[i], i, mode, dots);CHKERRQ(ierr); 174 for (j = 0; j < i; ++j) dots[j] *= -1.0; 175 ierr = VecMAXPY(mode[i], i, dots, mode);CHKERRQ(ierr); 176 ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr); 177 } 178 ierr = MatNullSpaceCreate(comm, PETSC_FALSE, m, mode, sp);CHKERRQ(ierr); 179 for (i = 0; i< m; ++i) {ierr = VecDestroy(&mode[i]);CHKERRQ(ierr);} 180 PetscFunctionReturn(0); 181 } 182 183 #undef __FUNCT__ 184 #define __FUNCT__ "DMPlexProjectFunctionLocal" 185 PetscErrorCode DMPlexProjectFunctionLocal(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, InsertMode mode, Vec localX) 186 { 187 PetscDualSpace *sp; 188 PetscSection section; 189 PetscScalar *values; 190 PetscReal *v0, *J, detJ; 191 PetscInt numFields, numComp, dim, spDim, totDim = 0, numValues, cStart, cEnd, c, f, d, v, comp; 192 PetscErrorCode ierr; 193 194 PetscFunctionBegin; 195 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 196 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 197 ierr = PetscMalloc1(numFields, &sp);CHKERRQ(ierr); 198 for (f = 0; f < numFields; ++f) { 199 ierr = PetscFEGetDualSpace(fe[f], &sp[f]);CHKERRQ(ierr); 200 ierr = PetscFEGetNumComponents(fe[f], &numComp);CHKERRQ(ierr); 201 ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr); 202 totDim += spDim*numComp; 203 } 204 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 205 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 206 ierr = DMPlexVecGetClosure(dm, section, localX, cStart, &numValues, NULL);CHKERRQ(ierr); 207 if (numValues != totDim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The section cell closure size %d != dual space dimension %d", numValues, totDim); 208 ierr = DMGetWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 209 ierr = PetscMalloc2(dim,&v0,dim*dim,&J);CHKERRQ(ierr); 210 for (c = cStart; c < cEnd; ++c) { 211 PetscCellGeometry geom; 212 213 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, NULL, &detJ);CHKERRQ(ierr); 214 geom.v0 = v0; 215 geom.J = J; 216 geom.detJ = &detJ; 217 for (f = 0, v = 0; f < numFields; ++f) { 218 void * const ctx = ctxs ? ctxs[f] : NULL; 219 ierr = PetscFEGetNumComponents(fe[f], &numComp);CHKERRQ(ierr); 220 ierr = PetscDualSpaceGetDimension(sp[f], &spDim);CHKERRQ(ierr); 221 for (d = 0; d < spDim; ++d) { 222 if (funcs[f]) { 223 ierr = PetscDualSpaceApply(sp[f], d, geom, numComp, funcs[f], ctx, &values[v]);CHKERRQ(ierr); 224 } else { 225 for (comp = 0; comp < numComp; ++comp) values[v+comp] = 0.0; 226 } 227 v += numComp; 228 } 229 } 230 ierr = DMPlexVecSetClosure(dm, section, localX, c, values, mode);CHKERRQ(ierr); 231 } 232 ierr = DMRestoreWorkArray(dm, numValues, PETSC_SCALAR, &values);CHKERRQ(ierr); 233 ierr = PetscFree2(v0,J);CHKERRQ(ierr); 234 ierr = PetscFree(sp);CHKERRQ(ierr); 235 PetscFunctionReturn(0); 236 } 237 238 #undef __FUNCT__ 239 #define __FUNCT__ "DMPlexProjectFunction" 240 /*@C 241 DMPlexProjectFunction - This projects the given function into the function space provided. 242 243 Input Parameters: 244 + dm - The DM 245 . fe - The PetscFE associated with the field 246 . funcs - The coordinate functions to evaluate, one per field 247 . ctxs - Optional array of contexts to pass to each coordinate function. ctxs itself may be null. 248 - mode - The insertion mode for values 249 250 Output Parameter: 251 . X - vector 252 253 Level: developer 254 255 .seealso: DMPlexComputeL2Diff() 256 @*/ 257 PetscErrorCode DMPlexProjectFunction(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, InsertMode mode, Vec X) 258 { 259 Vec localX; 260 PetscErrorCode ierr; 261 262 PetscFunctionBegin; 263 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 264 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 265 ierr = DMPlexProjectFunctionLocal(dm, fe, funcs, ctxs, mode, localX);CHKERRQ(ierr); 266 ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr); 267 ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr); 268 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 269 PetscFunctionReturn(0); 270 } 271 272 #undef __FUNCT__ 273 #define __FUNCT__ "DMPlexComputeL2Diff" 274 /*@C 275 DMPlexComputeL2Diff - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h. 276 277 Input Parameters: 278 + dm - The DM 279 . fe - The PetscFE object for each field 280 . funcs - The functions to evaluate for each field component 281 . ctxs - Optional array of contexts to pass to each function, or NULL. 282 - X - The coefficient vector u_h 283 284 Output Parameter: 285 . diff - The diff ||u - u_h||_2 286 287 Level: developer 288 289 .seealso: DMPlexProjectFunction(), DMPlexComputeL2GradientDiff() 290 @*/ 291 PetscErrorCode DMPlexComputeL2Diff(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff) 292 { 293 const PetscInt debug = 0; 294 PetscSection section; 295 PetscQuadrature quad; 296 Vec localX; 297 PetscScalar *funcVal; 298 PetscReal *coords, *v0, *J, *invJ, detJ; 299 PetscReal localDiff = 0.0; 300 PetscInt dim, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset, comp; 301 PetscErrorCode ierr; 302 303 PetscFunctionBegin; 304 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 305 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 306 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 307 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 308 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 309 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 310 for (field = 0; field < numFields; ++field) { 311 PetscInt Nc; 312 313 ierr = PetscFEGetNumComponents(fe[field], &Nc);CHKERRQ(ierr); 314 numComponents += Nc; 315 } 316 ierr = DMPlexProjectFunctionLocal(dm, fe, funcs, ctxs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); 317 ierr = PetscMalloc5(numComponents,&funcVal,dim,&coords,dim,&v0,dim*dim,&J,dim*dim,&invJ);CHKERRQ(ierr); 318 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 319 ierr = PetscFEGetQuadrature(fe[0], &quad);CHKERRQ(ierr); 320 for (c = cStart; c < cEnd; ++c) { 321 PetscScalar *x = NULL; 322 PetscReal elemDiff = 0.0; 323 324 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); 325 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 326 ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 327 328 for (field = 0, comp = 0, fieldOffset = 0; field < numFields; ++field) { 329 void * const ctx = ctxs ? ctxs[field] : NULL; 330 const PetscReal *quadPoints, *quadWeights; 331 PetscReal *basis; 332 PetscInt numQuadPoints, numBasisFuncs, numBasisComps, q, d, e, fc, f; 333 334 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, &quadPoints, &quadWeights);CHKERRQ(ierr); 335 ierr = PetscFEGetDimension(fe[field], &numBasisFuncs);CHKERRQ(ierr); 336 ierr = PetscFEGetNumComponents(fe[field], &numBasisComps);CHKERRQ(ierr); 337 ierr = PetscFEGetDefaultTabulation(fe[field], &basis, NULL, NULL);CHKERRQ(ierr); 338 if (debug) { 339 char title[1024]; 340 ierr = PetscSNPrintf(title, 1023, "Solution for Field %d", field);CHKERRQ(ierr); 341 ierr = DMPrintCellVector(c, title, numBasisFuncs*numBasisComps, &x[fieldOffset]);CHKERRQ(ierr); 342 } 343 for (q = 0; q < numQuadPoints; ++q) { 344 for (d = 0; d < dim; d++) { 345 coords[d] = v0[d]; 346 for (e = 0; e < dim; e++) { 347 coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0); 348 } 349 } 350 (*funcs[field])(coords, funcVal, ctx); 351 for (fc = 0; fc < numBasisComps; ++fc) { 352 PetscScalar interpolant = 0.0; 353 354 for (f = 0; f < numBasisFuncs; ++f) { 355 const PetscInt fidx = f*numBasisComps+fc; 356 interpolant += x[fieldOffset+fidx]*basis[q*numBasisFuncs*numBasisComps+fidx]; 357 } 358 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);} 359 elemDiff += PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ; 360 } 361 } 362 comp += numBasisComps; 363 fieldOffset += numBasisFuncs*numBasisComps; 364 } 365 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 366 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d diff %g\n", c, elemDiff);CHKERRQ(ierr);} 367 localDiff += elemDiff; 368 } 369 ierr = PetscFree5(funcVal,coords,v0,J,invJ);CHKERRQ(ierr); 370 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 371 ierr = MPI_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 372 *diff = PetscSqrtReal(*diff); 373 PetscFunctionReturn(0); 374 } 375 376 #undef __FUNCT__ 377 #define __FUNCT__ "DMPlexComputeL2GradientDiff" 378 /*@C 379 DMPlexComputeL2GradientDiff - This function computes the L_2 difference between the gradient of a function u and an FEM interpolant solution grad u_h. 380 381 Input Parameters: 382 + dm - The DM 383 . fe - The PetscFE object for each field 384 . funcs - The gradient functions to evaluate for each field component 385 . ctxs - Optional array of contexts to pass to each function, or NULL. 386 . X - The coefficient vector u_h 387 - n - The vector to project along 388 389 Output Parameter: 390 . diff - The diff ||(grad u - grad u_h) . n||_2 391 392 Level: developer 393 394 .seealso: DMPlexProjectFunction(), DMPlexComputeL2Diff() 395 @*/ 396 PetscErrorCode DMPlexComputeL2GradientDiff(DM dm, PetscFE fe[], void (**funcs)(const PetscReal [], const PetscReal [], PetscScalar *, void *), void **ctxs, Vec X, const PetscReal n[], PetscReal *diff) 397 { 398 const PetscInt debug = 0; 399 PetscSection section; 400 PetscQuadrature quad; 401 Vec localX; 402 PetscScalar *funcVal, *interpolantVec; 403 PetscReal *coords, *realSpaceDer, *v0, *J, *invJ, detJ; 404 PetscReal localDiff = 0.0; 405 PetscInt dim, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset, comp; 406 PetscErrorCode ierr; 407 408 PetscFunctionBegin; 409 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 410 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 411 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 412 ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); 413 ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 414 ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr); 415 for (field = 0; field < numFields; ++field) { 416 PetscInt Nc; 417 418 ierr = PetscFEGetNumComponents(fe[field], &Nc);CHKERRQ(ierr); 419 numComponents += Nc; 420 } 421 /* ierr = DMPlexProjectFunctionLocal(dm, fe, funcs, INSERT_BC_VALUES, localX);CHKERRQ(ierr); */ 422 ierr = PetscMalloc7(numComponents,&funcVal,dim,&coords,dim,&realSpaceDer,dim,&v0,dim*dim,&J,dim*dim,&invJ,dim,&interpolantVec);CHKERRQ(ierr); 423 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 424 ierr = PetscFEGetQuadrature(fe[0], &quad);CHKERRQ(ierr); 425 for (c = cStart; c < cEnd; ++c) { 426 PetscScalar *x = NULL; 427 PetscReal elemDiff = 0.0; 428 429 ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); 430 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 431 ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 432 433 for (field = 0, comp = 0, fieldOffset = 0; field < numFields; ++field) { 434 void * const ctx = ctxs ? ctxs[field] : NULL; 435 const PetscReal *quadPoints, *quadWeights; 436 PetscReal *basisDer; 437 PetscInt numQuadPoints, Nb, Ncomp, q, d, e, fc, f, g; 438 439 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, &quadPoints, &quadWeights);CHKERRQ(ierr); 440 ierr = PetscFEGetDimension(fe[field], &Nb);CHKERRQ(ierr); 441 ierr = PetscFEGetNumComponents(fe[field], &Ncomp);CHKERRQ(ierr); 442 ierr = PetscFEGetDefaultTabulation(fe[field], NULL, &basisDer, NULL);CHKERRQ(ierr); 443 if (debug) { 444 char title[1024]; 445 ierr = PetscSNPrintf(title, 1023, "Solution for Field %d", field);CHKERRQ(ierr); 446 ierr = DMPrintCellVector(c, title, Nb*Ncomp, &x[fieldOffset]);CHKERRQ(ierr); 447 } 448 for (q = 0; q < numQuadPoints; ++q) { 449 for (d = 0; d < dim; d++) { 450 coords[d] = v0[d]; 451 for (e = 0; e < dim; e++) { 452 coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0); 453 } 454 } 455 (*funcs[field])(coords, n, funcVal, ctx); 456 for (fc = 0; fc < Ncomp; ++fc) { 457 PetscScalar interpolant = 0.0; 458 459 for (d = 0; d < dim; ++d) interpolantVec[d] = 0.0; 460 for (f = 0; f < Nb; ++f) { 461 const PetscInt fidx = f*Ncomp+fc; 462 463 for (d = 0; d < dim; ++d) { 464 realSpaceDer[d] = 0.0; 465 for (g = 0; g < dim; ++g) { 466 realSpaceDer[d] += invJ[g*dim+d]*basisDer[(q*Nb*Ncomp+fidx)*dim+g]; 467 } 468 interpolantVec[d] += x[fieldOffset+fidx]*realSpaceDer[d]; 469 } 470 } 471 for (d = 0; d < dim; ++d) interpolant += interpolantVec[d]*n[d]; 472 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);} 473 elemDiff += PetscSqr(PetscRealPart(interpolant - funcVal[fc]))*quadWeights[q]*detJ; 474 } 475 } 476 comp += Ncomp; 477 fieldOffset += Nb*Ncomp; 478 } 479 ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr); 480 if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, " elem %d diff %g\n", c, elemDiff);CHKERRQ(ierr);} 481 localDiff += elemDiff; 482 } 483 ierr = PetscFree7(funcVal,coords,realSpaceDer,v0,J,invJ,interpolantVec);CHKERRQ(ierr); 484 ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); 485 ierr = MPI_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 486 *diff = PetscSqrtReal(*diff); 487 PetscFunctionReturn(0); 488 } 489 490 #undef __FUNCT__ 491 #define __FUNCT__ "DMPlexComputeResidualFEM" 492 /*@ 493 DMPlexComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 494 495 Input Parameters: 496 + dm - The mesh 497 . X - Local input vector 498 - user - The user context 499 500 Output Parameter: 501 . F - Local output vector 502 503 Note: 504 The first member of the user context must be an FEMContext. 505 506 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 507 like a GPU, or vectorize on a multicore machine. 508 509 Level: developer 510 511 .seealso: DMPlexComputeJacobianActionFEM() 512 @*/ 513 PetscErrorCode DMPlexComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 514 { 515 DM_Plex *mesh = (DM_Plex *) dm->data; 516 PetscFEM *fem = (PetscFEM *) user; 517 PetscFE *fe = fem->fe; 518 PetscFE *feAux = fem->feAux; 519 PetscFE *feBd = fem->feBd; 520 const char *name = "Residual"; 521 DM dmAux; 522 Vec A; 523 PetscQuadrature q; 524 PetscCellGeometry geom; 525 PetscSection section, sectionAux; 526 PetscReal *v0, *J, *invJ, *detJ; 527 PetscScalar *elemVec, *u, *a = NULL; 528 PetscInt dim, Nf, NfAux = 0, f, numCells, cStart, cEnd, c; 529 PetscInt cellDof = 0, numComponents = 0; 530 PetscInt cellDofAux = 0, numComponentsAux = 0; 531 PetscErrorCode ierr; 532 533 PetscFunctionBegin; 534 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 535 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 536 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 537 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 538 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 539 numCells = cEnd - cStart; 540 for (f = 0; f < Nf; ++f) { 541 PetscInt Nb, Nc; 542 543 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr); 544 ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr); 545 cellDof += Nb*Nc; 546 numComponents += Nc; 547 } 548 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 549 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 550 if (dmAux) { 551 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 552 ierr = PetscSectionGetNumFields(sectionAux, &NfAux);CHKERRQ(ierr); 553 } 554 for (f = 0; f < NfAux; ++f) { 555 PetscInt Nb, Nc; 556 557 ierr = PetscFEGetDimension(feAux[f], &Nb);CHKERRQ(ierr); 558 ierr = PetscFEGetNumComponents(feAux[f], &Nc);CHKERRQ(ierr); 559 cellDofAux += Nb*Nc; 560 numComponentsAux += Nc; 561 } 562 ierr = DMPlexProjectFunctionLocal(dm, fe, fem->bcFuncs, fem->bcCtxs, INSERT_BC_VALUES, X);CHKERRQ(ierr); 563 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 564 ierr = PetscMalloc6(numCells*cellDof,&u,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*cellDof,&elemVec);CHKERRQ(ierr); 565 if (dmAux) {ierr = PetscMalloc1(numCells*cellDofAux, &a);CHKERRQ(ierr);} 566 for (c = cStart; c < cEnd; ++c) { 567 PetscScalar *x = NULL; 568 PetscInt i; 569 570 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 571 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 572 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 573 for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i]; 574 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 575 if (dmAux) { 576 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 577 for (i = 0; i < cellDofAux; ++i) a[c*cellDofAux+i] = x[i]; 578 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 579 } 580 } 581 for (f = 0; f < Nf; ++f) { 582 void (*f0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->f0Funcs[f]; 583 void (*f1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->f1Funcs[f]; 584 PetscInt numQuadPoints, Nb; 585 /* Conforming batches */ 586 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 587 /* Remainder */ 588 PetscInt Nr, offset; 589 590 ierr = PetscFEGetQuadrature(fe[f], &q);CHKERRQ(ierr); 591 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr); 592 ierr = PetscFEGetTileSizes(fe[f], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 593 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 594 blockSize = Nb*numQuadPoints; 595 batchSize = numBlocks * blockSize; 596 ierr = PetscFESetTileSizes(fe[f], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 597 numChunks = numCells / (numBatches*batchSize); 598 Ne = numChunks*numBatches*batchSize; 599 Nr = numCells % (numBatches*batchSize); 600 offset = numCells - Nr; 601 geom.v0 = v0; 602 geom.J = J; 603 geom.invJ = invJ; 604 geom.detJ = detJ; 605 ierr = PetscFEIntegrateResidual(fe[f], Ne, Nf, fe, f, geom, u, NfAux, feAux, a, f0, f1, elemVec);CHKERRQ(ierr); 606 geom.v0 = &v0[offset*dim]; 607 geom.J = &J[offset*dim*dim]; 608 geom.invJ = &invJ[offset*dim*dim]; 609 geom.detJ = &detJ[offset]; 610 ierr = PetscFEIntegrateResidual(fe[f], Nr, Nf, fe, f, geom, &u[offset*cellDof], NfAux, feAux, &a[offset*cellDofAux], f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr); 611 } 612 for (c = cStart; c < cEnd; ++c) { 613 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, name, cellDof, &elemVec[c*cellDof]);CHKERRQ(ierr);} 614 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*cellDof], ADD_VALUES);CHKERRQ(ierr); 615 } 616 ierr = PetscFree6(u,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr); 617 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 618 if (feBd) { 619 DMLabel label, depth; 620 IS pointIS; 621 const PetscInt *points; 622 PetscInt dep, numPoints, p, numFaces; 623 PetscReal *n; 624 625 ierr = DMPlexGetLabel(dm, "boundary", &label);CHKERRQ(ierr); 626 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 627 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 628 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 629 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 630 for (f = 0, cellDof = 0, numComponents = 0; f < Nf; ++f) { 631 PetscInt Nb, Nc; 632 633 ierr = PetscFEGetDimension(feBd[f], &Nb);CHKERRQ(ierr); 634 ierr = PetscFEGetNumComponents(feBd[f], &Nc);CHKERRQ(ierr); 635 cellDof += Nb*Nc; 636 numComponents += Nc; 637 } 638 for (p = 0, numFaces = 0; p < numPoints; ++p) { 639 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 640 if (dep == dim-1) ++numFaces; 641 } 642 ierr = PetscMalloc7(numFaces*cellDof,&u,numFaces*dim,&v0,numFaces*dim,&n,numFaces*dim*dim,&J,numFaces*dim*dim,&invJ,numFaces,&detJ,numFaces*cellDof,&elemVec);CHKERRQ(ierr); 643 for (p = 0, f = 0; p < numPoints; ++p) { 644 const PetscInt point = points[p]; 645 PetscScalar *x = NULL; 646 PetscInt i; 647 648 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 649 if (dep != dim-1) continue; 650 ierr = DMPlexComputeCellGeometry(dm, point, &v0[f*dim], &J[f*dim*dim], &invJ[f*dim*dim], &detJ[f]);CHKERRQ(ierr); 651 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, &n[f*dim]); 652 if (detJ[f] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", detJ[f], point); 653 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 654 for (i = 0; i < cellDof; ++i) u[f*cellDof+i] = x[i]; 655 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 656 ++f; 657 } 658 for (f = 0; f < Nf; ++f) { 659 void (*f0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->f0BdFuncs[f]; 660 void (*f1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->f1BdFuncs[f]; 661 PetscInt numQuadPoints, Nb; 662 /* Conforming batches */ 663 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 664 /* Remainder */ 665 PetscInt Nr, offset; 666 667 ierr = PetscFEGetQuadrature(feBd[f], &q);CHKERRQ(ierr); 668 ierr = PetscFEGetDimension(feBd[f], &Nb);CHKERRQ(ierr); 669 ierr = PetscFEGetTileSizes(feBd[f], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 670 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 671 blockSize = Nb*numQuadPoints; 672 batchSize = numBlocks * blockSize; 673 ierr = PetscFESetTileSizes(feBd[f], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 674 numChunks = numFaces / (numBatches*batchSize); 675 Ne = numChunks*numBatches*batchSize; 676 Nr = numFaces % (numBatches*batchSize); 677 offset = numFaces - Nr; 678 geom.v0 = v0; 679 geom.n = n; 680 geom.J = J; 681 geom.invJ = invJ; 682 geom.detJ = detJ; 683 ierr = PetscFEIntegrateBdResidual(feBd[f], Ne, Nf, feBd, f, geom, u, 0, NULL, NULL, f0, f1, elemVec);CHKERRQ(ierr); 684 geom.v0 = &v0[offset*dim]; 685 geom.n = &n[offset*dim]; 686 geom.J = &J[offset*dim*dim]; 687 geom.invJ = &invJ[offset*dim*dim]; 688 geom.detJ = &detJ[offset]; 689 ierr = PetscFEIntegrateBdResidual(feBd[f], Nr, Nf, feBd, f, geom, &u[offset*cellDof], 0, NULL, NULL, f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr); 690 } 691 for (p = 0, f = 0; p < numPoints; ++p) { 692 const PetscInt point = points[p]; 693 694 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 695 if (dep != dim-1) continue; 696 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", cellDof, &elemVec[f*cellDof]);CHKERRQ(ierr);} 697 ierr = DMPlexVecSetClosure(dm, NULL, F, point, &elemVec[f*cellDof], ADD_VALUES);CHKERRQ(ierr); 698 ++f; 699 } 700 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 701 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 702 ierr = PetscFree7(u,v0,n,J,invJ,detJ,elemVec);CHKERRQ(ierr); 703 } 704 if (mesh->printFEM) {ierr = DMPrintLocalVec(dm, name, mesh->printTol, F);CHKERRQ(ierr);} 705 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 706 PetscFunctionReturn(0); 707 } 708 709 #undef __FUNCT__ 710 #define __FUNCT__ "DMPlexComputeIFunctionFEM" 711 /*@ 712 DMPlexComputeIFunctionFEM - Form the local implicit function F from the local input X, X_t using pointwise functions specified by the user 713 714 Input Parameters: 715 + dm - The mesh 716 . X - Local input vector 717 . X_t - Time derivative of the local input vector 718 - user - The user context 719 720 Output Parameter: 721 . F - Local output vector 722 723 Note: 724 The first member of the user context must be an FEMContext. 725 726 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 727 like a GPU, or vectorize on a multicore machine. 728 729 Level: developer 730 731 .seealso: DMPlexComputeResidualFEM() 732 @*/ 733 PetscErrorCode DMPlexComputeIFunctionFEM(DM dm, Vec X, Vec X_t, Vec F, void *user) 734 { 735 DM_Plex *mesh = (DM_Plex *) dm->data; 736 PetscFEM *fem = (PetscFEM *) user; 737 PetscFE *fe = fem->fe; 738 PetscFE *feAux = fem->feAux; 739 PetscFE *feBd = fem->feBd; 740 const char *name = "Residual"; 741 DM dmAux; 742 Vec A; 743 PetscQuadrature q; 744 PetscCellGeometry geom; 745 PetscSection section, sectionAux; 746 PetscReal *v0, *J, *invJ, *detJ; 747 PetscScalar *elemVec, *u, *u_t, *a = NULL; 748 PetscInt dim, Nf, NfAux = 0, f, numCells, cStart, cEnd, c; 749 PetscInt cellDof = 0, numComponents = 0; 750 PetscInt cellDofAux = 0, numComponentsAux = 0; 751 PetscErrorCode ierr; 752 753 PetscFunctionBegin; 754 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 755 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 756 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 757 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 758 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 759 numCells = cEnd - cStart; 760 for (f = 0; f < Nf; ++f) { 761 PetscInt Nb, Nc; 762 763 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr); 764 ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr); 765 cellDof += Nb*Nc; 766 numComponents += Nc; 767 } 768 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 769 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 770 if (dmAux) { 771 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 772 ierr = PetscSectionGetNumFields(sectionAux, &NfAux);CHKERRQ(ierr); 773 } 774 for (f = 0; f < NfAux; ++f) { 775 PetscInt Nb, Nc; 776 777 ierr = PetscFEGetDimension(feAux[f], &Nb);CHKERRQ(ierr); 778 ierr = PetscFEGetNumComponents(feAux[f], &Nc);CHKERRQ(ierr); 779 cellDofAux += Nb*Nc; 780 numComponentsAux += Nc; 781 } 782 ierr = DMPlexProjectFunctionLocal(dm, fe, fem->bcFuncs, fem->bcCtxs, INSERT_BC_VALUES, X);CHKERRQ(ierr); 783 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 784 ierr = PetscMalloc7(numCells*cellDof,&u,numCells*cellDof,&u_t,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*cellDof,&elemVec);CHKERRQ(ierr); 785 if (dmAux) {ierr = PetscMalloc1(numCells*cellDofAux, &a);CHKERRQ(ierr);} 786 for (c = cStart; c < cEnd; ++c) { 787 PetscScalar *x = NULL, *x_t = NULL; 788 PetscInt i; 789 790 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 791 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 792 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 793 for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i]; 794 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 795 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 796 for (i = 0; i < cellDof; ++i) u_t[c*cellDof+i] = x_t[i]; 797 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 798 if (dmAux) { 799 PetscScalar *x_a = NULL; 800 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x_a);CHKERRQ(ierr); 801 for (i = 0; i < cellDofAux; ++i) a[c*cellDofAux+i] = x_a[i]; 802 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x_a);CHKERRQ(ierr); 803 } 804 } 805 for (f = 0; f < Nf; ++f) { 806 void (*f0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->f0IFuncs[f]; 807 void (*f1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->f1IFuncs[f]; 808 PetscInt numQuadPoints, Nb; 809 /* Conforming batches */ 810 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 811 /* Remainder */ 812 PetscInt Nr, offset; 813 814 ierr = PetscFEGetQuadrature(fe[f], &q);CHKERRQ(ierr); 815 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr); 816 ierr = PetscFEGetTileSizes(fe[f], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 817 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 818 blockSize = Nb*numQuadPoints; 819 batchSize = numBlocks * blockSize; 820 ierr = PetscFESetTileSizes(fe[f], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 821 numChunks = numCells / (numBatches*batchSize); 822 Ne = numChunks*numBatches*batchSize; 823 Nr = numCells % (numBatches*batchSize); 824 offset = numCells - Nr; 825 geom.v0 = v0; 826 geom.J = J; 827 geom.invJ = invJ; 828 geom.detJ = detJ; 829 ierr = PetscFEIntegrateIFunction(fe[f], Ne, Nf, fe, f, geom, u, u_t, NfAux, feAux, a, f0, f1, elemVec);CHKERRQ(ierr); 830 geom.v0 = &v0[offset*dim]; 831 geom.J = &J[offset*dim*dim]; 832 geom.invJ = &invJ[offset*dim*dim]; 833 geom.detJ = &detJ[offset]; 834 ierr = PetscFEIntegrateIFunction(fe[f], Nr, Nf, fe, f, geom, &u[offset*cellDof], &u_t[offset*cellDof], NfAux, feAux, &a[offset*cellDofAux], f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr); 835 } 836 for (c = cStart; c < cEnd; ++c) { 837 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, name, cellDof, &elemVec[c*cellDof]);CHKERRQ(ierr);} 838 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*cellDof], ADD_VALUES);CHKERRQ(ierr); 839 } 840 ierr = PetscFree7(u,u_t,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr); 841 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 842 if (feBd) { 843 DMLabel label, depth; 844 IS pointIS; 845 const PetscInt *points; 846 PetscInt dep, numPoints, p, numFaces; 847 PetscReal *n; 848 849 ierr = DMPlexGetLabel(dm, "boundary", &label);CHKERRQ(ierr); 850 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 851 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 852 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 853 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 854 for (f = 0, cellDof = 0, numComponents = 0; f < Nf; ++f) { 855 PetscInt Nb, Nc; 856 857 ierr = PetscFEGetDimension(feBd[f], &Nb);CHKERRQ(ierr); 858 ierr = PetscFEGetNumComponents(feBd[f], &Nc);CHKERRQ(ierr); 859 cellDof += Nb*Nc; 860 numComponents += Nc; 861 } 862 for (p = 0, numFaces = 0; p < numPoints; ++p) { 863 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 864 if (dep == dim-1) ++numFaces; 865 } 866 ierr = PetscMalloc7(numFaces*cellDof,&u,numFaces*dim,&v0,numFaces*dim,&n,numFaces*dim*dim,&J,numFaces*dim*dim,&invJ,numFaces,&detJ,numFaces*cellDof,&elemVec);CHKERRQ(ierr); 867 ierr = PetscMalloc1(numFaces*cellDof,&u_t);CHKERRQ(ierr); 868 for (p = 0, f = 0; p < numPoints; ++p) { 869 const PetscInt point = points[p]; 870 PetscScalar *x = NULL; 871 PetscInt i; 872 873 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 874 if (dep != dim-1) continue; 875 ierr = DMPlexComputeCellGeometry(dm, point, &v0[f*dim], &J[f*dim*dim], &invJ[f*dim*dim], &detJ[f]);CHKERRQ(ierr); 876 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, &n[f*dim]); 877 if (detJ[f] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", detJ[f], point); 878 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 879 for (i = 0; i < cellDof; ++i) u[f*cellDof+i] = x[i]; 880 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 881 ierr = DMPlexVecGetClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 882 for (i = 0; i < cellDof; ++i) u_t[f*cellDof+i] = x[i]; 883 ierr = DMPlexVecRestoreClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 884 ++f; 885 } 886 for (f = 0; f < Nf; ++f) { 887 void (*f0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->f0BdIFuncs[f]; 888 void (*f1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->f1BdIFuncs[f]; 889 PetscInt numQuadPoints, Nb; 890 /* Conforming batches */ 891 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 892 /* Remainder */ 893 PetscInt Nr, offset; 894 895 ierr = PetscFEGetQuadrature(feBd[f], &q);CHKERRQ(ierr); 896 ierr = PetscFEGetDimension(feBd[f], &Nb);CHKERRQ(ierr); 897 ierr = PetscFEGetTileSizes(feBd[f], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 898 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 899 blockSize = Nb*numQuadPoints; 900 batchSize = numBlocks * blockSize; 901 ierr = PetscFESetTileSizes(feBd[f], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 902 numChunks = numFaces / (numBatches*batchSize); 903 Ne = numChunks*numBatches*batchSize; 904 Nr = numFaces % (numBatches*batchSize); 905 offset = numFaces - Nr; 906 geom.v0 = v0; 907 geom.n = n; 908 geom.J = J; 909 geom.invJ = invJ; 910 geom.detJ = detJ; 911 ierr = PetscFEIntegrateBdIFunction(feBd[f], Ne, Nf, feBd, f, geom, u, u_t, 0, NULL, NULL, f0, f1, elemVec);CHKERRQ(ierr); 912 geom.v0 = &v0[offset*dim]; 913 geom.n = &n[offset*dim]; 914 geom.J = &J[offset*dim*dim]; 915 geom.invJ = &invJ[offset*dim*dim]; 916 geom.detJ = &detJ[offset]; 917 ierr = PetscFEIntegrateBdIFunction(feBd[f], Nr, Nf, feBd, f, geom, &u[offset*cellDof], &u_t[offset*cellDof], 0, NULL, NULL, f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr); 918 } 919 for (p = 0, f = 0; p < numPoints; ++p) { 920 const PetscInt point = points[p]; 921 922 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 923 if (dep != dim-1) continue; 924 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", cellDof, &elemVec[f*cellDof]);CHKERRQ(ierr);} 925 ierr = DMPlexVecSetClosure(dm, NULL, F, point, &elemVec[f*cellDof], ADD_VALUES);CHKERRQ(ierr); 926 ++f; 927 } 928 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 929 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 930 ierr = PetscFree7(u,v0,n,J,invJ,detJ,elemVec);CHKERRQ(ierr); 931 ierr = PetscFree(u_t);CHKERRQ(ierr); 932 } 933 if (mesh->printFEM) {ierr = DMPrintLocalVec(dm, name, mesh->printTol, F);CHKERRQ(ierr);} 934 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 935 PetscFunctionReturn(0); 936 } 937 938 #undef __FUNCT__ 939 #define __FUNCT__ "DMPlexComputeJacobianActionFEM" 940 /*@C 941 DMPlexComputeJacobianActionFEM - Form the local action of Jacobian J(u) on the local input X using pointwise functions specified by the user 942 943 Input Parameters: 944 + dm - The mesh 945 . J - The Jacobian shell matrix 946 . X - Local input vector 947 - user - The user context 948 949 Output Parameter: 950 . F - Local output vector 951 952 Note: 953 The first member of the user context must be an FEMContext. 954 955 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 956 like a GPU, or vectorize on a multicore machine. 957 958 Level: developer 959 960 .seealso: DMPlexComputeResidualFEM() 961 @*/ 962 PetscErrorCode DMPlexComputeJacobianActionFEM(DM dm, Mat Jac, Vec X, Vec F, void *user) 963 { 964 DM_Plex *mesh = (DM_Plex *) dm->data; 965 PetscFEM *fem = (PetscFEM *) user; 966 PetscFE *fe = fem->fe; 967 PetscQuadrature quad; 968 PetscCellGeometry geom; 969 PetscSection section; 970 JacActionCtx *jctx; 971 PetscReal *v0, *J, *invJ, *detJ; 972 PetscScalar *elemVec, *u, *a; 973 PetscInt dim, numFields, field, numCells, cStart, cEnd, c; 974 PetscInt cellDof = 0; 975 PetscErrorCode ierr; 976 977 PetscFunctionBegin; 978 /* ierr = PetscLogEventBegin(DMPLEX_JacobianActionFEM,dm,0,0,0);CHKERRQ(ierr); */ 979 ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); 980 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 981 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 982 ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr); 983 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 984 numCells = cEnd - cStart; 985 for (field = 0; field < numFields; ++field) { 986 PetscInt Nb, Nc; 987 988 ierr = PetscFEGetDimension(fe[field], &Nb);CHKERRQ(ierr); 989 ierr = PetscFEGetNumComponents(fe[field], &Nc);CHKERRQ(ierr); 990 cellDof += Nb*Nc; 991 } 992 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 993 ierr = PetscMalloc7(numCells*cellDof,&u,numCells*cellDof,&a,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*cellDof,&elemVec);CHKERRQ(ierr); 994 for (c = cStart; c < cEnd; ++c) { 995 PetscScalar *x = NULL; 996 PetscInt i; 997 998 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 999 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 1000 ierr = DMPlexVecGetClosure(dm, NULL, jctx->u, c, NULL, &x);CHKERRQ(ierr); 1001 for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i]; 1002 ierr = DMPlexVecRestoreClosure(dm, NULL, jctx->u, c, NULL, &x);CHKERRQ(ierr); 1003 ierr = DMPlexVecGetClosure(dm, NULL, X, c, NULL, &x);CHKERRQ(ierr); 1004 for (i = 0; i < cellDof; ++i) a[c*cellDof+i] = x[i]; 1005 ierr = DMPlexVecRestoreClosure(dm, NULL, X, c, NULL, &x);CHKERRQ(ierr); 1006 } 1007 for (field = 0; field < numFields; ++field) { 1008 PetscInt numQuadPoints, Nb; 1009 /* Conforming batches */ 1010 PetscInt numBlocks = 1; 1011 PetscInt numBatches = 1; 1012 PetscInt numChunks, Ne, blockSize, batchSize; 1013 /* Remainder */ 1014 PetscInt Nr, offset; 1015 1016 ierr = PetscFEGetQuadrature(fe[field], &quad);CHKERRQ(ierr); 1017 ierr = PetscFEGetDimension(fe[field], &Nb);CHKERRQ(ierr); 1018 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1019 blockSize = Nb*numQuadPoints; 1020 batchSize = numBlocks * blockSize; 1021 numChunks = numCells / (numBatches*batchSize); 1022 Ne = numChunks*numBatches*batchSize; 1023 Nr = numCells % (numBatches*batchSize); 1024 offset = numCells - Nr; 1025 geom.v0 = v0; 1026 geom.J = J; 1027 geom.invJ = invJ; 1028 geom.detJ = detJ; 1029 ierr = PetscFEIntegrateJacobianAction(fe[field], Ne, numFields, fe, field, geom, u, a, fem->g0Funcs, fem->g1Funcs, fem->g2Funcs, fem->g3Funcs, elemVec);CHKERRQ(ierr); 1030 geom.v0 = &v0[offset*dim]; 1031 geom.J = &J[offset*dim*dim]; 1032 geom.invJ = &invJ[offset*dim*dim]; 1033 geom.detJ = &detJ[offset]; 1034 ierr = PetscFEIntegrateJacobianAction(fe[field], Nr, numFields, fe, field, geom, &u[offset*cellDof], &a[offset*cellDof], 1035 fem->g0Funcs, fem->g1Funcs, fem->g2Funcs, fem->g3Funcs, &elemVec[offset*cellDof]);CHKERRQ(ierr); 1036 } 1037 for (c = cStart; c < cEnd; ++c) { 1038 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, "Jacobian Action", cellDof, &elemVec[c*cellDof]);CHKERRQ(ierr);} 1039 ierr = DMPlexVecSetClosure(dm, NULL, F, c, &elemVec[c*cellDof], ADD_VALUES);CHKERRQ(ierr); 1040 } 1041 ierr = PetscFree7(u,a,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr); 1042 if (mesh->printFEM) { 1043 PetscMPIInt rank, numProcs; 1044 PetscInt p; 1045 1046 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 1047 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &numProcs);CHKERRQ(ierr); 1048 ierr = PetscPrintf(PetscObjectComm((PetscObject)dm), "Jacobian Action:\n");CHKERRQ(ierr); 1049 for (p = 0; p < numProcs; ++p) { 1050 if (p == rank) {ierr = VecView(F, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);} 1051 ierr = PetscBarrier((PetscObject) dm);CHKERRQ(ierr); 1052 } 1053 } 1054 /* ierr = PetscLogEventEnd(DMPLEX_JacobianActionFEM,dm,0,0,0);CHKERRQ(ierr); */ 1055 PetscFunctionReturn(0); 1056 } 1057 1058 #undef __FUNCT__ 1059 #define __FUNCT__ "DMPlexComputeJacobianFEM" 1060 /*@ 1061 DMPlexComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 1062 1063 Input Parameters: 1064 + dm - The mesh 1065 . X - Local input vector 1066 - user - The user context 1067 1068 Output Parameter: 1069 . Jac - Jacobian matrix 1070 1071 Note: 1072 The first member of the user context must be an FEMContext. 1073 1074 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 1075 like a GPU, or vectorize on a multicore machine. 1076 1077 Level: developer 1078 1079 .seealso: FormFunctionLocal() 1080 @*/ 1081 PetscErrorCode DMPlexComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 1082 { 1083 DM_Plex *mesh = (DM_Plex *) dm->data; 1084 PetscFEM *fem = (PetscFEM *) user; 1085 PetscFE *fe = fem->fe; 1086 PetscFE *feAux = fem->feAux; 1087 const char *name = "Jacobian"; 1088 DM dmAux; 1089 Vec A; 1090 PetscQuadrature quad; 1091 PetscCellGeometry geom; 1092 PetscSection section, globalSection, sectionAux; 1093 PetscReal *v0, *J, *invJ, *detJ; 1094 PetscScalar *elemMat, *u, *a; 1095 PetscInt dim, Nf, NfAux = 0, f, fieldI, fieldJ, numCells, cStart, cEnd, c; 1096 PetscInt cellDof = 0, numComponents = 0; 1097 PetscInt cellDofAux = 0, numComponentsAux = 0; 1098 PetscBool isShell; 1099 PetscErrorCode ierr; 1100 1101 PetscFunctionBegin; 1102 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 1103 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1104 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1105 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 1106 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1107 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1108 numCells = cEnd - cStart; 1109 for (f = 0; f < Nf; ++f) { 1110 PetscInt Nb, Nc; 1111 1112 ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr); 1113 ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr); 1114 cellDof += Nb*Nc; 1115 numComponents += Nc; 1116 } 1117 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1118 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1119 if (dmAux) { 1120 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1121 ierr = PetscSectionGetNumFields(sectionAux, &NfAux);CHKERRQ(ierr); 1122 } 1123 for (f = 0; f < NfAux; ++f) { 1124 PetscInt Nb, Nc; 1125 1126 ierr = PetscFEGetDimension(feAux[f], &Nb);CHKERRQ(ierr); 1127 ierr = PetscFEGetNumComponents(feAux[f], &Nc);CHKERRQ(ierr); 1128 cellDofAux += Nb*Nc; 1129 numComponentsAux += Nc; 1130 } 1131 ierr = DMPlexProjectFunctionLocal(dm, fe, fem->bcFuncs, fem->bcCtxs, INSERT_BC_VALUES, X);CHKERRQ(ierr); 1132 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 1133 ierr = PetscMalloc6(numCells*cellDof,&u,numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*cellDof*cellDof,&elemMat);CHKERRQ(ierr); 1134 if (dmAux) {ierr = PetscMalloc1(numCells*cellDofAux, &a);CHKERRQ(ierr);} 1135 for (c = cStart; c < cEnd; ++c) { 1136 PetscScalar *x = NULL; 1137 PetscInt i; 1138 1139 ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 1140 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 1141 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1142 for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i]; 1143 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1144 if (dmAux) { 1145 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1146 for (i = 0; i < cellDofAux; ++i) a[c*cellDofAux+i] = x[i]; 1147 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1148 } 1149 } 1150 ierr = PetscMemzero(elemMat, numCells*cellDof*cellDof * sizeof(PetscScalar));CHKERRQ(ierr); 1151 for (fieldI = 0; fieldI < Nf; ++fieldI) { 1152 PetscInt numQuadPoints, Nb; 1153 /* Conforming batches */ 1154 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1155 /* Remainder */ 1156 PetscInt Nr, offset; 1157 1158 ierr = PetscFEGetQuadrature(fe[fieldI], &quad);CHKERRQ(ierr); 1159 ierr = PetscFEGetDimension(fe[fieldI], &Nb);CHKERRQ(ierr); 1160 ierr = PetscFEGetTileSizes(fe[fieldI], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1161 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1162 blockSize = Nb*numQuadPoints; 1163 batchSize = numBlocks * blockSize; 1164 ierr = PetscFESetTileSizes(fe[fieldI], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1165 numChunks = numCells / (numBatches*batchSize); 1166 Ne = numChunks*numBatches*batchSize; 1167 Nr = numCells % (numBatches*batchSize); 1168 offset = numCells - Nr; 1169 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1170 void (*g0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g0Funcs[fieldI*Nf+fieldJ]; 1171 void (*g1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g1Funcs[fieldI*Nf+fieldJ]; 1172 void (*g2)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g2Funcs[fieldI*Nf+fieldJ]; 1173 void (*g3)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g3Funcs[fieldI*Nf+fieldJ]; 1174 1175 geom.v0 = v0; 1176 geom.J = J; 1177 geom.invJ = invJ; 1178 geom.detJ = detJ; 1179 ierr = PetscFEIntegrateJacobian(fe[fieldI], Ne, Nf, fe, fieldI, fieldJ, geom, u, NfAux, feAux, a, g0, g1, g2, g3, elemMat);CHKERRQ(ierr); 1180 geom.v0 = &v0[offset*dim]; 1181 geom.J = &J[offset*dim*dim]; 1182 geom.invJ = &invJ[offset*dim*dim]; 1183 geom.detJ = &detJ[offset]; 1184 ierr = PetscFEIntegrateJacobian(fe[fieldI], Nr, Nf, fe, fieldI, fieldJ, geom, &u[offset*cellDof], NfAux, feAux, &a[offset*cellDofAux], g0, g1, g2, g3, &elemMat[offset*cellDof*cellDof]);CHKERRQ(ierr); 1185 } 1186 } 1187 for (c = cStart; c < cEnd; ++c) { 1188 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, cellDof, cellDof, &elemMat[c*cellDof*cellDof]);CHKERRQ(ierr);} 1189 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMat[c*cellDof*cellDof], ADD_VALUES);CHKERRQ(ierr); 1190 } 1191 ierr = PetscFree6(u,v0,J,invJ,detJ,elemMat);CHKERRQ(ierr); 1192 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 1193 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1194 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1195 if (mesh->printFEM) { 1196 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 1197 ierr = MatChop(JacP, 1.0e-10);CHKERRQ(ierr); 1198 ierr = MatView(JacP, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1199 } 1200 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 1201 ierr = PetscObjectTypeCompare((PetscObject) Jac, MATSHELL, &isShell);CHKERRQ(ierr); 1202 if (isShell) { 1203 JacActionCtx *jctx; 1204 1205 ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); 1206 ierr = VecCopy(X, jctx->u);CHKERRQ(ierr); 1207 } 1208 PetscFunctionReturn(0); 1209 } 1210 1211 #if 0 1212 1213 static void g0_identity_1d_static(const PetscScalar u[], const PetscScalar gradU[], const PetscScalar a[], const PetscScalar gradA[], const PetscReal x[], PetscScalar g3[]) 1214 { 1215 g3[0] = 1.0; 1216 } 1217 1218 static void g0_identity_2d_static(const PetscScalar u[], const PetscScalar gradU[], const PetscScalar a[], const PetscScalar gradA[], const PetscReal x[], PetscScalar g3[]) 1219 { 1220 g3[0] = g3[3] = 1.0; 1221 } 1222 1223 static void g0_identity_3d_static(const PetscScalar u[], const PetscScalar gradU[], const PetscScalar a[], const PetscScalar gradA[], const PetscReal x[], PetscScalar g3[]) 1224 { 1225 g3[0] = g3[4] = g3[8] = 1.0; 1226 } 1227 1228 #undef __FUNCT__ 1229 #define __FUNCT__ "DMPlexComputeInterpolatorFEMBroken" 1230 PetscErrorCode DMPlexComputeInterpolatorFEMBroken(DM dmc, DM dmf, Mat I, void *user) 1231 { 1232 DM_Plex *mesh = (DM_Plex *) dmc->data; 1233 PetscFEM *fem = (PetscFEM *) user; 1234 PetscFE *fe = fem->fe; 1235 const char *name = "Interpolator"; 1236 PetscFE *feRef; 1237 PetscQuadrature quad, quadOld; 1238 PetscCellGeometry geom; 1239 PetscSection fsection, fglobalSection; 1240 PetscSection csection, cglobalSection; 1241 PetscReal *v0, *J, *invJ, *detJ; 1242 PetscScalar *elemMat; 1243 PetscInt dim, Nf, f, fieldI, fieldJ, numCells, cStart, cEnd, c; 1244 PetscInt rCellDof = 0, cCellDof = 0, numComponents = 0; 1245 PetscErrorCode ierr; 1246 1247 PetscFunctionBegin; 1248 #if 0 1249 ierr = PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 1250 #endif 1251 ierr = DMPlexGetDimension(dmf, &dim);CHKERRQ(ierr); 1252 ierr = DMGetDefaultSection(dmf, &fsection);CHKERRQ(ierr); 1253 ierr = DMGetDefaultGlobalSection(dmf, &fglobalSection);CHKERRQ(ierr); 1254 ierr = DMGetDefaultSection(dmc, &csection);CHKERRQ(ierr); 1255 ierr = DMGetDefaultGlobalSection(dmc, &cglobalSection);CHKERRQ(ierr); 1256 ierr = PetscSectionGetNumFields(fsection, &Nf);CHKERRQ(ierr); 1257 ierr = DMPlexGetHeightStratum(dmc, 0, &cStart, &cEnd);CHKERRQ(ierr); 1258 numCells = cEnd - cStart; 1259 ierr = PetscMalloc1(Nf,&feRef);CHKERRQ(ierr); 1260 for (fieldI = 0; fieldI < Nf; ++fieldI) { 1261 ierr = PetscFERefine(fe[fieldI], &feRef[fieldI]);CHKERRQ(ierr); 1262 } 1263 for (f = 0; f < Nf; ++f) { 1264 PetscInt rNb, cNb, Nc; 1265 1266 ierr = PetscFEGetDimension(feRef[f], &rNb);CHKERRQ(ierr); 1267 ierr = PetscFEGetDimension(fe[f], &cNb);CHKERRQ(ierr); 1268 ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr); 1269 numComponents += Nc; 1270 rCellDof += rNb*Nc; 1271 cCellDof += cNb*Nc; 1272 } 1273 ierr = MatZeroEntries(I);CHKERRQ(ierr); 1274 ierr = PetscMalloc5(numCells*dim,&v0,numCells*dim*dim,&J,numCells*dim*dim,&invJ,numCells,&detJ,numCells*rCellDof*cCellDof,&elemMat);CHKERRQ(ierr); 1275 for (c = cStart; c < cEnd; ++c) { 1276 ierr = DMPlexComputeCellGeometry(dmc, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr); 1277 if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c); 1278 } 1279 ierr = PetscMemzero(elemMat, numCells*rCellDof*cCellDof * sizeof(PetscScalar));CHKERRQ(ierr); 1280 for (fieldI = 0; fieldI < Nf; ++fieldI) { 1281 PetscInt numQuadPoints, Nb; 1282 /* Conforming batches */ 1283 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1284 /* Remainder */ 1285 PetscInt Nr, offset; 1286 1287 /* Make new fine FE which refines the ref cell and the quadrature rule */ 1288 ierr = PetscFEGetQuadrature(feRef[fieldI], &quad);CHKERRQ(ierr); 1289 ierr = PetscFEGetDimension(feRef[fieldI], &Nb);CHKERRQ(ierr); 1290 ierr = PetscFEGetTileSizes(feRef[fieldI], NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1291 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1292 blockSize = Nb*numQuadPoints; 1293 batchSize = numBlocks * blockSize; 1294 ierr = PetscFESetTileSizes(feRef[fieldI], blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1295 numChunks = numCells / (numBatches*batchSize); 1296 Ne = numChunks*numBatches*batchSize; 1297 Nr = numCells % (numBatches*batchSize); 1298 offset = numCells - Nr; 1299 1300 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 1301 /* void (*g0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g0Funcs[fieldI*Nf+fieldJ]; */ 1302 void (*g0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = g0_identity_2d_static; 1303 1304 /* Replace quadrature in coarse FE with refined quadrature */ 1305 ierr = PetscFEGetQuadrature(fe[fieldJ], &quadOld);CHKERRQ(ierr); 1306 ierr = PetscObjectReference((PetscObject) quadOld);CHKERRQ(ierr); 1307 ierr = PetscFESetQuadrature(fe[fieldJ], quad);CHKERRQ(ierr); 1308 geom.v0 = v0; 1309 geom.J = J; 1310 geom.invJ = invJ; 1311 geom.detJ = detJ; 1312 ierr = PetscFEIntegrateInterpolator_Basic(feRef[fieldI], Ne, Nf, feRef, fieldI, fe, fieldJ, geom, g0, elemMat);CHKERRQ(ierr); 1313 geom.v0 = &v0[offset*dim]; 1314 geom.J = &J[offset*dim*dim]; 1315 geom.invJ = &invJ[offset*dim*dim]; 1316 geom.detJ = &detJ[offset]; 1317 ierr = PetscFEIntegrateInterpolator_Basic(feRef[fieldI], Nr, Nf, feRef, fieldI, fe, fieldJ, geom, g0, &elemMat[offset*rCellDof*cCellDof]);CHKERRQ(ierr); 1318 ierr = PetscFESetQuadrature(fe[fieldJ], quadOld);CHKERRQ(ierr); 1319 } 1320 } 1321 for (c = cStart; c < cEnd; ++c) { 1322 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, rCellDof, cCellDof, &elemMat[c*rCellDof*cCellDof]);CHKERRQ(ierr);} 1323 ierr = DMPlexMatSetClosureRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, I, c, &elemMat[c*rCellDof*cCellDof], ADD_VALUES);CHKERRQ(ierr); 1324 } 1325 ierr = PetscFree5(v0,J,invJ,detJ,elemMat);CHKERRQ(ierr); 1326 ierr = PetscFree(feRef);CHKERRQ(ierr); 1327 ierr = MatAssemblyBegin(I, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1328 ierr = MatAssemblyEnd(I, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1329 if (mesh->printFEM) { 1330 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 1331 ierr = MatChop(I, 1.0e-10);CHKERRQ(ierr); 1332 ierr = MatView(I, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1333 } 1334 #if 0 1335 ierr = PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 1336 #endif 1337 PetscFunctionReturn(0); 1338 } 1339 #endif 1340 1341 #undef __FUNCT__ 1342 #define __FUNCT__ "DMPlexComputeInterpolatorFEM" 1343 /*@ 1344 DMPlexComputeInterpolatorFEM - Form the local portion of the interpolation matrix I from the coarse DM to the uniformly refined DM. 1345 1346 Input Parameters: 1347 + dmf - The fine mesh 1348 . dmc - The coarse mesh 1349 - user - The user context 1350 1351 Output Parameter: 1352 . In - The interpolation matrix 1353 1354 Note: 1355 The first member of the user context must be an FEMContext. 1356 1357 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 1358 like a GPU, or vectorize on a multicore machine. 1359 1360 Level: developer 1361 1362 .seealso: DMPlexComputeJacobianFEM() 1363 @*/ 1364 PetscErrorCode DMPlexComputeInterpolatorFEM(DM dmc, DM dmf, Mat In, void *user) 1365 { 1366 DM_Plex *mesh = (DM_Plex *) dmc->data; 1367 PetscFEM *fem = (PetscFEM *) user; 1368 PetscFE *fe = fem->fe; 1369 const char *name = "Interpolator"; 1370 PetscFE *feRef; 1371 PetscSection fsection, fglobalSection; 1372 PetscSection csection, cglobalSection; 1373 PetscScalar *elemMat; 1374 PetscInt dim, Nf, f, fieldI, fieldJ, offsetI, offsetJ, cStart, cEnd, c; 1375 PetscInt rCellDof = 0, cCellDof = 0; 1376 PetscErrorCode ierr; 1377 1378 PetscFunctionBegin; 1379 #if 0 1380 ierr = PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 1381 #endif 1382 ierr = DMPlexGetDimension(dmf, &dim);CHKERRQ(ierr); 1383 ierr = DMGetDefaultSection(dmf, &fsection);CHKERRQ(ierr); 1384 ierr = DMGetDefaultGlobalSection(dmf, &fglobalSection);CHKERRQ(ierr); 1385 ierr = DMGetDefaultSection(dmc, &csection);CHKERRQ(ierr); 1386 ierr = DMGetDefaultGlobalSection(dmc, &cglobalSection);CHKERRQ(ierr); 1387 ierr = PetscSectionGetNumFields(fsection, &Nf);CHKERRQ(ierr); 1388 ierr = DMPlexGetHeightStratum(dmc, 0, &cStart, &cEnd);CHKERRQ(ierr); 1389 ierr = PetscMalloc1(Nf,&feRef);CHKERRQ(ierr); 1390 for (f = 0; f < Nf; ++f) { 1391 PetscInt rNb, cNb, Nc; 1392 1393 ierr = PetscFERefine(fe[f], &feRef[f]);CHKERRQ(ierr); 1394 ierr = PetscFEGetDimension(feRef[f], &rNb);CHKERRQ(ierr); 1395 ierr = PetscFEGetDimension(fe[f], &cNb);CHKERRQ(ierr); 1396 ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr); 1397 rCellDof += rNb*Nc; 1398 cCellDof += cNb*Nc; 1399 } 1400 ierr = MatZeroEntries(In);CHKERRQ(ierr); 1401 ierr = PetscMalloc1(rCellDof*cCellDof,&elemMat);CHKERRQ(ierr); 1402 ierr = PetscMemzero(elemMat, rCellDof*cCellDof * sizeof(PetscScalar));CHKERRQ(ierr); 1403 for (fieldI = 0, offsetI = 0; fieldI < Nf; ++fieldI) { 1404 PetscDualSpace Qref; 1405 PetscQuadrature f; 1406 const PetscReal *qpoints, *qweights; 1407 PetscReal *points; 1408 PetscInt npoints = 0, Nc, Np, fpdim, i, k, p, d; 1409 1410 /* Compose points from all dual basis functionals */ 1411 ierr = PetscFEGetNumComponents(fe[fieldI], &Nc);CHKERRQ(ierr); 1412 ierr = PetscFEGetDualSpace(feRef[fieldI], &Qref);CHKERRQ(ierr); 1413 ierr = PetscDualSpaceGetDimension(Qref, &fpdim);CHKERRQ(ierr); 1414 for (i = 0; i < fpdim; ++i) { 1415 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 1416 ierr = PetscQuadratureGetData(f, NULL, &Np, NULL, NULL);CHKERRQ(ierr); 1417 npoints += Np; 1418 } 1419 ierr = PetscMalloc1(npoints*dim,&points);CHKERRQ(ierr); 1420 for (i = 0, k = 0; i < fpdim; ++i) { 1421 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 1422 ierr = PetscQuadratureGetData(f, NULL, &Np, &qpoints, NULL);CHKERRQ(ierr); 1423 for (p = 0; p < Np; ++p, ++k) for (d = 0; d < dim; ++d) points[k*dim+d] = qpoints[p*dim+d]; 1424 } 1425 1426 for (fieldJ = 0, offsetJ = 0; fieldJ < Nf; ++fieldJ) { 1427 PetscReal *B; 1428 PetscInt NcJ, cpdim, j; 1429 1430 /* Evaluate basis at points */ 1431 ierr = PetscFEGetNumComponents(fe[fieldJ], &NcJ);CHKERRQ(ierr); 1432 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); 1433 ierr = PetscFEGetDimension(fe[fieldJ], &cpdim);CHKERRQ(ierr); 1434 /* For now, fields only interpolate themselves */ 1435 if (fieldI == fieldJ) { 1436 ierr = PetscFEGetTabulation(fe[fieldJ], npoints, points, &B, NULL, NULL);CHKERRQ(ierr); 1437 for (i = 0, k = 0; i < fpdim; ++i) { 1438 ierr = PetscDualSpaceGetFunctional(Qref, i, &f);CHKERRQ(ierr); 1439 ierr = PetscQuadratureGetData(f, NULL, &Np, NULL, &qweights);CHKERRQ(ierr); 1440 for (p = 0; p < Np; ++p, ++k) { 1441 for (j = 0; j < cpdim; ++j) { 1442 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i*Nc + c)*cCellDof + offsetJ + j*NcJ + c] += B[k*cpdim*NcJ+j*Nc+c]*qweights[p]; 1443 } 1444 } 1445 } 1446 ierr = PetscFERestoreTabulation(fe[fieldJ], npoints, points, &B, NULL, NULL);CHKERRQ(ierr);CHKERRQ(ierr); 1447 } 1448 offsetJ += cpdim*NcJ; 1449 } 1450 offsetI += fpdim*Nc; 1451 ierr = PetscFree(points);CHKERRQ(ierr); 1452 } 1453 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(0, name, rCellDof, cCellDof, elemMat);CHKERRQ(ierr);} 1454 for (c = cStart; c < cEnd; ++c) { 1455 ierr = DMPlexMatSetClosureRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);CHKERRQ(ierr); 1456 } 1457 for (f = 0; f < Nf; ++f) {ierr = PetscFEDestroy(&feRef[f]);CHKERRQ(ierr);} 1458 ierr = PetscFree(feRef);CHKERRQ(ierr); 1459 ierr = PetscFree(elemMat);CHKERRQ(ierr); 1460 ierr = MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1461 ierr = MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1462 if (mesh->printFEM) { 1463 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 1464 ierr = MatChop(In, 1.0e-10);CHKERRQ(ierr); 1465 ierr = MatView(In, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1466 } 1467 #if 0 1468 ierr = PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);CHKERRQ(ierr); 1469 #endif 1470 PetscFunctionReturn(0); 1471 } 1472 1473 #undef __FUNCT__ 1474 #define __FUNCT__ "DMPlexAddBoundary" 1475 /* The ids can be overridden by the command line option -bc_<boundary name> */ 1476 PetscErrorCode DMPlexAddBoundary(DM dm, PetscBool isEssential, const char name[], PetscInt field, void (*bcFunc)(), PetscInt numids, const PetscInt *ids, void *ctx) 1477 { 1478 DM_Plex *mesh = (DM_Plex *) dm->data; 1479 DMBoundary b; 1480 PetscErrorCode ierr; 1481 1482 PetscFunctionBegin; 1483 ierr = PetscNew(&b);CHKERRQ(ierr); 1484 ierr = PetscStrallocpy(name, (char **) &b->name);CHKERRQ(ierr); 1485 ierr = PetscMalloc1(numids, &b->ids);CHKERRQ(ierr); 1486 ierr = PetscMemcpy(b->ids, ids, numids*sizeof(PetscInt));CHKERRQ(ierr); 1487 b->essential = isEssential; 1488 b->field = field; 1489 b->func = bcFunc; 1490 b->numids = numids; 1491 b->ctx = ctx; 1492 b->next = mesh->boundary; 1493 mesh->boundary = b; 1494 PetscFunctionReturn(0); 1495 } 1496 1497 #undef __FUNCT__ 1498 #define __FUNCT__ "DMPlexGetNumBoundary" 1499 PetscErrorCode DMPlexGetNumBoundary(DM dm, PetscInt *numBd) 1500 { 1501 DM_Plex *mesh = (DM_Plex *) dm->data; 1502 DMBoundary b = mesh->boundary; 1503 1504 PetscFunctionBegin; 1505 *numBd = 0; 1506 while (b) {++(*numBd); b = b->next;} 1507 PetscFunctionReturn(0); 1508 } 1509 1510 #undef __FUNCT__ 1511 #define __FUNCT__ "DMPlexGetBoundary" 1512 PetscErrorCode DMPlexGetBoundary(DM dm, PetscInt bd, PetscBool *isEssential, const char **name, PetscInt *field, void (**func)(), PetscInt *numids, const PetscInt **ids, void **ctx) 1513 { 1514 DM_Plex *mesh = (DM_Plex *) dm->data; 1515 DMBoundary b = mesh->boundary; 1516 PetscInt n = 0; 1517 1518 PetscFunctionBegin; 1519 while (b) { 1520 if (n == bd) break; 1521 b = b->next; 1522 ++n; 1523 } 1524 if (n != bd) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Boundary %d is not in [0, %d)", bd, n); 1525 if (isEssential) { 1526 PetscValidPointer(isEssential, 3); 1527 *isEssential = b->essential; 1528 } 1529 if (name) { 1530 PetscValidPointer(name, 4); 1531 *name = b->name; 1532 } 1533 if (field) { 1534 PetscValidPointer(field, 5); 1535 *field = b->field; 1536 } 1537 if (func) { 1538 PetscValidPointer(func, 6); 1539 *func = b->func; 1540 } 1541 if (numids) { 1542 PetscValidPointer(numids, 7); 1543 *numids = b->numids; 1544 } 1545 if (ids) { 1546 PetscValidPointer(ids, 8); 1547 *ids = b->ids; 1548 } 1549 if (ctx) { 1550 PetscValidPointer(ctx, 9); 1551 *ctx = b->ctx; 1552 } 1553 PetscFunctionReturn(0); 1554 } 1555