Actual source code: plexfem.c

petsc-master 2019-10-19
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  1:  #include <petsc/private/dmpleximpl.h>
  2:  #include <petscsf.h>

  4:  #include <petsc/private/hashsetij.h>
  5:  #include <petsc/private/petscfeimpl.h>
  6:  #include <petsc/private/petscfvimpl.h>

  8: static PetscErrorCode DMPlexConvertPlex(DM dm, DM *plex, PetscBool copy)
  9: {
 10:   PetscBool      isPlex;

 14:   PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);
 15:   if (isPlex) {
 16:     *plex = dm;
 17:     PetscObjectReference((PetscObject) dm);
 18:   } else {
 19:     PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);
 20:     if (!*plex) {
 21:       DMConvert(dm,DMPLEX,plex);
 22:       PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);
 23:       if (copy) {
 24:         const char *comps[3] = {"A", "dmAux"};
 25:         PetscObject obj;
 26:         PetscInt    i;

 28:         {
 29:           /* Run the subdomain hook (this will copy the DMSNES/DMTS) */
 30:           DMSubDomainHookLink link;
 31:           for (link = dm->subdomainhook; link; link = link->next) {
 32:             if (link->ddhook) {(*link->ddhook)(dm, *plex, link->ctx);}
 33:           }
 34:         }
 35:         for (i = 0; i < 3; i++) {
 36:           PetscObjectQuery((PetscObject) dm, comps[i], &obj);
 37:           PetscObjectCompose((PetscObject) *plex, comps[i], obj);
 38:         }
 39:       }
 40:     } else {
 41:       PetscObjectReference((PetscObject) *plex);
 42:     }
 43:   }
 44:   return(0);
 45: }

 47: static PetscErrorCode PetscContainerUserDestroy_PetscFEGeom (void *ctx)
 48: {
 49:   PetscFEGeom *geom = (PetscFEGeom *) ctx;

 53:   PetscFEGeomDestroy(&geom);
 54:   return(0);
 55: }

 57: static PetscErrorCode DMPlexGetFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom)
 58: {
 59:   char            composeStr[33] = {0};
 60:   PetscObjectId   id;
 61:   PetscContainer  container;
 62:   PetscErrorCode  ierr;

 65:   PetscObjectGetId((PetscObject)quad,&id);
 66:   PetscSNPrintf(composeStr, 32, "DMPlexGetFEGeom_%x\n", id);
 67:   PetscObjectQuery((PetscObject) pointIS, composeStr, (PetscObject *) &container);
 68:   if (container) {
 69:     PetscContainerGetPointer(container, (void **) geom);
 70:   } else {
 71:     DMFieldCreateFEGeom(coordField, pointIS, quad, faceData, geom);
 72:     PetscContainerCreate(PETSC_COMM_SELF,&container);
 73:     PetscContainerSetPointer(container, (void *) *geom);
 74:     PetscContainerSetUserDestroy(container, PetscContainerUserDestroy_PetscFEGeom);
 75:     PetscObjectCompose((PetscObject) pointIS, composeStr, (PetscObject) container);
 76:     PetscContainerDestroy(&container);
 77:   }
 78:   return(0);
 79: }

 81: static PetscErrorCode DMPlexRestoreFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom)
 82: {
 84:   *geom = NULL;
 85:   return(0);
 86: }

 88: /*@
 89:   DMPlexGetScale - Get the scale for the specified fundamental unit

 91:   Not collective

 93:   Input Arguments:
 94: + dm   - the DM
 95: - unit - The SI unit

 97:   Output Argument:
 98: . scale - The value used to scale all quantities with this unit

100:   Level: advanced

102: .seealso: DMPlexSetScale(), PetscUnit
103: @*/
104: PetscErrorCode DMPlexGetScale(DM dm, PetscUnit unit, PetscReal *scale)
105: {
106:   DM_Plex *mesh = (DM_Plex*) dm->data;

111:   *scale = mesh->scale[unit];
112:   return(0);
113: }

115: /*@
116:   DMPlexSetScale - Set the scale for the specified fundamental unit

118:   Not collective

120:   Input Arguments:
121: + dm   - the DM
122: . unit - The SI unit
123: - scale - The value used to scale all quantities with this unit

125:   Level: advanced

127: .seealso: DMPlexGetScale(), PetscUnit
128: @*/
129: PetscErrorCode DMPlexSetScale(DM dm, PetscUnit unit, PetscReal scale)
130: {
131:   DM_Plex *mesh = (DM_Plex*) dm->data;

135:   mesh->scale[unit] = scale;
136:   return(0);
137: }

139: static PetscErrorCode DMPlexProjectRigidBody_Private(PetscInt dim, PetscReal t, const PetscReal X[], PetscInt Nf, PetscScalar *mode, void *ctx)
140: {
141:   const PetscInt eps[3][3][3] = {{{0, 0, 0}, {0, 0, 1}, {0, -1, 0}}, {{0, 0, -1}, {0, 0, 0}, {1, 0, 0}}, {{0, 1, 0}, {-1, 0, 0}, {0, 0, 0}}};
142:   PetscInt *ctxInt  = (PetscInt *) ctx;
143:   PetscInt  dim2    = ctxInt[0];
144:   PetscInt  d       = ctxInt[1];
145:   PetscInt  i, j, k = dim > 2 ? d - dim : d;

148:   if (dim != dim2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Input dimension %D does not match context dimension %D", dim, dim2);
149:   for (i = 0; i < dim; i++) mode[i] = 0.;
150:   if (d < dim) {
151:     mode[d] = 1.; /* Translation along axis d */
152:   } else {
153:     for (i = 0; i < dim; i++) {
154:       for (j = 0; j < dim; j++) {
155:         mode[j] += eps[i][j][k]*X[i]; /* Rotation about axis d */
156:       }
157:     }
158:   }
159:   return(0);
160: }

162: /*@
163:   DMPlexCreateRigidBody - For the default global section, create rigid body modes by function space interpolation

165:   Collective on dm

167:   Input Arguments:
168: . dm - the DM

170:   Output Argument:
171: . sp - the null space

173:   Note: This is necessary to provide a suitable coarse space for algebraic multigrid

175:   Level: advanced

177: .seealso: MatNullSpaceCreate(), PCGAMG
178: @*/
179: PetscErrorCode DMPlexCreateRigidBody(DM dm, MatNullSpace *sp)
180: {
181:   MPI_Comm       comm;
182:   Vec            mode[6];
183:   PetscSection   section, globalSection;
184:   PetscInt       dim, dimEmbed, n, m, mmin, d, i, j;

188:   PetscObjectGetComm((PetscObject)dm,&comm);
189:   DMGetDimension(dm, &dim);
190:   DMGetCoordinateDim(dm, &dimEmbed);
191:   if (dim == 1) {
192:     MatNullSpaceCreate(comm, PETSC_TRUE, 0, NULL, sp);
193:     return(0);
194:   }
195:   DMGetLocalSection(dm, &section);
196:   DMGetGlobalSection(dm, &globalSection);
197:   PetscSectionGetConstrainedStorageSize(globalSection, &n);
198:   m    = (dim*(dim+1))/2;
199:   VecCreate(comm, &mode[0]);
200:   VecSetSizes(mode[0], n, PETSC_DETERMINE);
201:   VecSetUp(mode[0]);
202:   VecGetSize(mode[0], &n);
203:   mmin = PetscMin(m, n);
204:   for (i = 1; i < m; ++i) {VecDuplicate(mode[0], &mode[i]);}
205:   for (d = 0; d < m; d++) {
206:     PetscInt         ctx[2];
207:     PetscErrorCode (*func)(PetscInt, PetscReal, const PetscReal *, PetscInt, PetscScalar *, void *) = DMPlexProjectRigidBody_Private;
208:     void            *voidctx = (void *) (&ctx[0]);

210:     ctx[0] = dimEmbed;
211:     ctx[1] = d;
212:     DMProjectFunction(dm, 0.0, &func, &voidctx, INSERT_VALUES, mode[d]);
213:   }
214:   /* Orthonormalize system */
215:   for (i = 0; i < mmin; ++i) {
216:     PetscScalar dots[6];

218:     VecNormalize(mode[i], NULL);
219:     VecMDot(mode[i], mmin-i-1, mode+i+1, dots+i+1);
220:     for (j = i+1; j < mmin; ++j) {
221:       dots[j] *= -1.0;
222:       VecAXPY(mode[j], dots[j], mode[i]);
223:     }
224:   }
225:   MatNullSpaceCreate(comm, PETSC_FALSE, mmin, mode, sp);
226:   for (i = 0; i < m; ++i) {VecDestroy(&mode[i]);}
227:   return(0);
228: }

230: /*@
231:   DMPlexCreateRigidBodies - For the default global section, create rigid body modes by function space interpolation

233:   Collective on dm

235:   Input Arguments:
236: + dm    - the DM
237: . nb    - The number of bodies
238: . label - The DMLabel marking each domain
239: . nids  - The number of ids per body
240: - ids   - An array of the label ids in sequence for each domain

242:   Output Argument:
243: . sp - the null space

245:   Note: This is necessary to provide a suitable coarse space for algebraic multigrid

247:   Level: advanced

249: .seealso: MatNullSpaceCreate()
250: @*/
251: PetscErrorCode DMPlexCreateRigidBodies(DM dm, PetscInt nb, DMLabel label, const PetscInt nids[], const PetscInt ids[], MatNullSpace *sp)
252: {
253:   MPI_Comm       comm;
254:   PetscSection   section, globalSection;
255:   Vec           *mode;
256:   PetscScalar   *dots;
257:   PetscInt       dim, dimEmbed, n, m, b, d, i, j, off;

261:   PetscObjectGetComm((PetscObject)dm,&comm);
262:   DMGetDimension(dm, &dim);
263:   DMGetCoordinateDim(dm, &dimEmbed);
264:   DMGetLocalSection(dm, &section);
265:   DMGetGlobalSection(dm, &globalSection);
266:   PetscSectionGetConstrainedStorageSize(globalSection, &n);
267:   m    = nb * (dim*(dim+1))/2;
268:   PetscMalloc2(m, &mode, m, &dots);
269:   VecCreate(comm, &mode[0]);
270:   VecSetSizes(mode[0], n, PETSC_DETERMINE);
271:   VecSetUp(mode[0]);
272:   for (i = 1; i < m; ++i) {VecDuplicate(mode[0], &mode[i]);}
273:   for (b = 0, off = 0; b < nb; ++b) {
274:     for (d = 0; d < m/nb; ++d) {
275:       PetscInt         ctx[2];
276:       PetscErrorCode (*func)(PetscInt, PetscReal, const PetscReal *, PetscInt, PetscScalar *, void *) = DMPlexProjectRigidBody_Private;
277:       void            *voidctx = (void *) (&ctx[0]);

279:       ctx[0] = dimEmbed;
280:       ctx[1] = d;
281:       DMProjectFunctionLabel(dm, 0.0, label, nids[b], &ids[off], 0, NULL, &func, &voidctx, INSERT_VALUES, mode[d]);
282:       off   += nids[b];
283:     }
284:   }
285:   /* Orthonormalize system */
286:   for (i = 0; i < m; ++i) {
287:     PetscScalar dots[6];

289:     VecNormalize(mode[i], NULL);
290:     VecMDot(mode[i], m-i-1, mode+i+1, dots+i+1);
291:     for (j = i+1; j < m; ++j) {
292:       dots[j] *= -1.0;
293:       VecAXPY(mode[j], dots[j], mode[i]);
294:     }
295:   }
296:   MatNullSpaceCreate(comm, PETSC_FALSE, m, mode, sp);
297:   for (i = 0; i< m; ++i) {VecDestroy(&mode[i]);}
298:   PetscFree2(mode, dots);
299:   return(0);
300: }

302: /*@
303:   DMPlexSetMaxProjectionHeight - In DMPlexProjectXXXLocal() functions, the projected values of a basis function's dofs
304:   are computed by associating the basis function with one of the mesh points in its transitively-closed support, and
305:   evaluating the dual space basis of that point.  A basis function is associated with the point in its
306:   transitively-closed support whose mesh height is highest (w.r.t. DAG height), but not greater than the maximum
307:   projection height, which is set with this function.  By default, the maximum projection height is zero, which means
308:   that only mesh cells are used to project basis functions.  A height of one, for example, evaluates a cell-interior
309:   basis functions using its cells dual space basis, but all other basis functions with the dual space basis of a face.

311:   Input Parameters:
312: + dm - the DMPlex object
313: - height - the maximum projection height >= 0

315:   Level: advanced

317: .seealso: DMPlexGetMaxProjectionHeight(), DMProjectFunctionLocal(), DMProjectFunctionLabelLocal()
318: @*/
319: PetscErrorCode DMPlexSetMaxProjectionHeight(DM dm, PetscInt height)
320: {
321:   DM_Plex *plex = (DM_Plex *) dm->data;

325:   plex->maxProjectionHeight = height;
326:   return(0);
327: }

329: /*@
330:   DMPlexGetMaxProjectionHeight - Get the maximum height (w.r.t. DAG) of mesh points used to evaluate dual bases in
331:   DMPlexProjectXXXLocal() functions.

333:   Input Parameters:
334: . dm - the DMPlex object

336:   Output Parameters:
337: . height - the maximum projection height

339:   Level: intermediate

341: .seealso: DMPlexSetMaxProjectionHeight(), DMProjectFunctionLocal(), DMProjectFunctionLabelLocal()
342: @*/
343: PetscErrorCode DMPlexGetMaxProjectionHeight(DM dm, PetscInt *height)
344: {
345:   DM_Plex *plex = (DM_Plex *) dm->data;

349:   *height = plex->maxProjectionHeight;
350:   return(0);
351: }

353: typedef struct {
354:   PetscReal    alpha; /* The first Euler angle, and in 2D the only one */
355:   PetscReal    beta;  /* The second Euler angle */
356:   PetscReal    gamma; /* The third Euler angle */
357:   PetscInt     dim;   /* The dimension of R */
358:   PetscScalar *R;     /* The rotation matrix, transforming a vector in the local basis to the global basis */
359:   PetscScalar *RT;    /* The transposed rotation matrix, transforming a vector in the global basis to the local basis */
360: } RotCtx;

362: /*
363:   Note: Following https://en.wikipedia.org/wiki/Euler_angles, we will specify Euler angles by extrinsic rotations, meaning that
364:   we rotate with respect to a fixed initial coordinate system, the local basis (x-y-z). The global basis (X-Y-Z) is reached as follows:
365:   $ The XYZ system rotates about the z axis by alpha. The X axis is now at angle alpha with respect to the x axis.
366:   $ The XYZ system rotates again about the x axis by beta. The Z axis is now at angle beta with respect to the z axis.
367:   $ The XYZ system rotates a third time about the z axis by gamma.
368: */
369: static PetscErrorCode DMPlexBasisTransformSetUp_Rotation_Internal(DM dm, void *ctx)
370: {
371:   RotCtx        *rc  = (RotCtx *) ctx;
372:   PetscInt       dim = rc->dim;
373:   PetscReal      c1, s1, c2, s2, c3, s3;

377:   PetscMalloc2(PetscSqr(dim), &rc->R, PetscSqr(dim), &rc->RT);
378:   switch (dim) {
379:   case 2:
380:     c1 = PetscCosReal(rc->alpha);s1 = PetscSinReal(rc->alpha);
381:     rc->R[0] =  c1;rc->R[1] = s1;
382:     rc->R[2] = -s1;rc->R[3] = c1;
383:     PetscArraycpy(rc->RT, rc->R, PetscSqr(dim));
384:     DMPlex_Transpose2D_Internal(rc->RT);break;
385:     break;
386:   case 3:
387:     c1 = PetscCosReal(rc->alpha);s1 = PetscSinReal(rc->alpha);
388:     c2 = PetscCosReal(rc->beta); s2 = PetscSinReal(rc->beta);
389:     c3 = PetscCosReal(rc->gamma);s3 = PetscSinReal(rc->gamma);
390:     rc->R[0] =  c1*c3 - c2*s1*s3;rc->R[1] =  c3*s1    + c1*c2*s3;rc->R[2] = s2*s3;
391:     rc->R[3] = -c1*s3 - c2*c3*s1;rc->R[4] =  c1*c2*c3 - s1*s3;   rc->R[5] = c3*s2;
392:     rc->R[6] =  s1*s2;           rc->R[7] = -c1*s2;              rc->R[8] = c2;
393:     PetscArraycpy(rc->RT, rc->R, PetscSqr(dim));
394:     DMPlex_Transpose3D_Internal(rc->RT);break;
395:     break;
396:   default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D not supported", dim);
397:   }
398:   return(0);
399: }

401: static PetscErrorCode DMPlexBasisTransformDestroy_Rotation_Internal(DM dm, void *ctx)
402: {
403:   RotCtx        *rc = (RotCtx *) ctx;

407:   PetscFree2(rc->R, rc->RT);
408:   PetscFree(rc);
409:   return(0);
410: }

412: static PetscErrorCode DMPlexBasisTransformGetMatrix_Rotation_Internal(DM dm, const PetscReal x[], PetscBool l2g, const PetscScalar **A, void *ctx)
413: {
414:   RotCtx *rc = (RotCtx *) ctx;

418:   if (l2g) {*A = rc->R;}
419:   else     {*A = rc->RT;}
420:   return(0);
421: }

423: PetscErrorCode DMPlexBasisTransformApplyReal_Internal(DM dm, const PetscReal x[], PetscBool l2g, PetscInt dim, const PetscReal *y, PetscReal *z, void *ctx)
424: {

428:   #if defined(PETSC_USE_COMPLEX)
429:   switch (dim) {
430:     case 2:
431:     {
432:       PetscScalar yt[2], zt[2];

434:       yt[0] = y[0]; yt[1] = y[1];
435:       DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, yt, zt, ctx);
436:       z[0] = PetscRealPart(zt[0]); z[1] = PetscRealPart(zt[1]);
437:     }
438:     break;
439:     case 3:
440:     {
441:       PetscScalar yt[3], zt[3];

443:       yt[0] = y[0]; yt[1] = y[1]; yt[2] = y[2];
444:       DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, yt, zt, ctx);
445:       z[0] = PetscRealPart(zt[0]); z[1] = PetscRealPart(zt[1]); z[2] = PetscRealPart(zt[2]);
446:     }
447:     break;
448:   }
449:   #else
450:   DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, y, z, ctx);
451:   #endif
452:   return(0);
453: }

455: PetscErrorCode DMPlexBasisTransformApply_Internal(DM dm, const PetscReal x[], PetscBool l2g, PetscInt dim, const PetscScalar *y, PetscScalar *z, void *ctx)
456: {
457:   const PetscScalar *A;
458:   PetscErrorCode     ierr;

461:   (*dm->transformGetMatrix)(dm, x, l2g, &A, ctx);
462:   switch (dim) {
463:   case 2: DMPlex_Mult2D_Internal(A, 1, y, z);break;
464:   case 3: DMPlex_Mult3D_Internal(A, 1, y, z);break;
465:   }
466:   return(0);
467: }

469: static PetscErrorCode DMPlexBasisTransformField_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscInt f, PetscBool l2g, PetscScalar *a)
470: {
471:   PetscSection       ts;
472:   const PetscScalar *ta, *tva;
473:   PetscInt           dof;
474:   PetscErrorCode     ierr;

477:   DMGetLocalSection(tdm, &ts);
478:   PetscSectionGetFieldDof(ts, p, f, &dof);
479:   VecGetArrayRead(tv, &ta);
480:   DMPlexPointLocalFieldRead(tdm, p, f, ta, (void *) &tva);
481:   if (l2g) {
482:     switch (dof) {
483:     case 4: DMPlex_Mult2D_Internal(tva, 1, a, a);break;
484:     case 9: DMPlex_Mult3D_Internal(tva, 1, a, a);break;
485:     }
486:   } else {
487:     switch (dof) {
488:     case 4: DMPlex_MultTranspose2D_Internal(tva, 1, a, a);break;
489:     case 9: DMPlex_MultTranspose3D_Internal(tva, 1, a, a);break;
490:     }
491:   }
492:   VecRestoreArrayRead(tv, &ta);
493:   return(0);
494: }

496: static PetscErrorCode DMPlexBasisTransformFieldTensor_Internal(DM dm, DM tdm, Vec tv, PetscInt pf, PetscInt f, PetscInt pg, PetscInt g, PetscBool l2g, PetscInt lda, PetscScalar *a)
497: {
498:   PetscSection       s, ts;
499:   const PetscScalar *ta, *tvaf, *tvag;
500:   PetscInt           fdof, gdof, fpdof, gpdof;
501:   PetscErrorCode     ierr;

504:   DMGetLocalSection(dm, &s);
505:   DMGetLocalSection(tdm, &ts);
506:   PetscSectionGetFieldDof(s, pf, f, &fpdof);
507:   PetscSectionGetFieldDof(s, pg, g, &gpdof);
508:   PetscSectionGetFieldDof(ts, pf, f, &fdof);
509:   PetscSectionGetFieldDof(ts, pg, g, &gdof);
510:   VecGetArrayRead(tv, &ta);
511:   DMPlexPointLocalFieldRead(tdm, pf, f, ta, (void *) &tvaf);
512:   DMPlexPointLocalFieldRead(tdm, pg, g, ta, (void *) &tvag);
513:   if (l2g) {
514:     switch (fdof) {
515:     case 4: DMPlex_MatMult2D_Internal(tvaf, gpdof, lda, a, a);break;
516:     case 9: DMPlex_MatMult3D_Internal(tvaf, gpdof, lda, a, a);break;
517:     }
518:     switch (gdof) {
519:     case 4: DMPlex_MatMultTransposeLeft2D_Internal(tvag, fpdof, lda, a, a);break;
520:     case 9: DMPlex_MatMultTransposeLeft3D_Internal(tvag, fpdof, lda, a, a);break;
521:     }
522:   } else {
523:     switch (fdof) {
524:     case 4: DMPlex_MatMultTranspose2D_Internal(tvaf, gpdof, lda, a, a);break;
525:     case 9: DMPlex_MatMultTranspose3D_Internal(tvaf, gpdof, lda, a, a);break;
526:     }
527:     switch (gdof) {
528:     case 4: DMPlex_MatMultLeft2D_Internal(tvag, fpdof, lda, a, a);break;
529:     case 9: DMPlex_MatMultLeft3D_Internal(tvag, fpdof, lda, a, a);break;
530:     }
531:   }
532:   VecRestoreArrayRead(tv, &ta);
533:   return(0);
534: }

536: PetscErrorCode DMPlexBasisTransformPoint_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscBool fieldActive[], PetscBool l2g, PetscScalar *a)
537: {
538:   PetscSection    s;
539:   PetscSection    clSection;
540:   IS              clPoints;
541:   const PetscInt *clp;
542:   PetscInt       *points = NULL;
543:   PetscInt        Nf, f, Np, cp, dof, d = 0;
544:   PetscErrorCode  ierr;

547:   DMGetLocalSection(dm, &s);
548:   PetscSectionGetNumFields(s, &Nf);
549:   DMPlexGetCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
550:   for (f = 0; f < Nf; ++f) {
551:     for (cp = 0; cp < Np*2; cp += 2) {
552:       PetscSectionGetFieldDof(s, points[cp], f, &dof);
553:       if (!dof) continue;
554:       if (fieldActive[f]) {DMPlexBasisTransformField_Internal(dm, tdm, tv, points[cp], f, l2g, &a[d]);}
555:       d += dof;
556:     }
557:   }
558:   DMPlexRestoreCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
559:   return(0);
560: }

562: PetscErrorCode DMPlexBasisTransformPointTensor_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscBool l2g, PetscInt lda, PetscScalar *a)
563: {
564:   PetscSection    s;
565:   PetscSection    clSection;
566:   IS              clPoints;
567:   const PetscInt *clp;
568:   PetscInt       *points = NULL;
569:   PetscInt        Nf, f, g, Np, cpf, cpg, fdof, gdof, r, c = 0;
570:   PetscErrorCode  ierr;

573:   DMGetLocalSection(dm, &s);
574:   PetscSectionGetNumFields(s, &Nf);
575:   DMPlexGetCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
576:   for (f = 0, r = 0; f < Nf; ++f) {
577:     for (cpf = 0; cpf < Np*2; cpf += 2) {
578:       PetscSectionGetFieldDof(s, points[cpf], f, &fdof);
579:       for (g = 0, c = 0; g < Nf; ++g) {
580:         for (cpg = 0; cpg < Np*2; cpg += 2) {
581:           PetscSectionGetFieldDof(s, points[cpg], g, &gdof);
582:           DMPlexBasisTransformFieldTensor_Internal(dm, tdm, tv, points[cpf], f, points[cpg], g, l2g, lda, &a[r*lda+c]);
583:           c += gdof;
584:         }
585:       }
586:       if (c != lda) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of columns %D should be %D", c, lda);
587:       r += fdof;
588:     }
589:   }
590:   if (r != lda) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of rows %D should be %D", c, lda);
591:   DMPlexRestoreCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
592:   return(0);
593: }

595: static PetscErrorCode DMPlexBasisTransform_Internal(DM dm, Vec lv, PetscBool l2g)
596: {
597:   DM                 tdm;
598:   Vec                tv;
599:   PetscSection       ts, s;
600:   const PetscScalar *ta;
601:   PetscScalar       *a, *va;
602:   PetscInt           pStart, pEnd, p, Nf, f;
603:   PetscErrorCode     ierr;

606:   DMGetBasisTransformDM_Internal(dm, &tdm);
607:   DMGetBasisTransformVec_Internal(dm, &tv);
608:   DMGetLocalSection(tdm, &ts);
609:   DMGetLocalSection(dm, &s);
610:   PetscSectionGetChart(s, &pStart, &pEnd);
611:   PetscSectionGetNumFields(s, &Nf);
612:   VecGetArray(lv, &a);
613:   VecGetArrayRead(tv, &ta);
614:   for (p = pStart; p < pEnd; ++p) {
615:     for (f = 0; f < Nf; ++f) {
616:       DMPlexPointLocalFieldRef(dm, p, f, a, (void *) &va);
617:       DMPlexBasisTransformField_Internal(dm, tdm, tv, p, f, l2g, va);
618:     }
619:   }
620:   VecRestoreArray(lv, &a);
621:   VecRestoreArrayRead(tv, &ta);
622:   return(0);
623: }

625: /*@
626:   DMPlexGlobalToLocalBasis - Transform the values in the given local vector from the global basis to the local basis

628:   Input Parameters:
629: + dm - The DM
630: - lv - A local vector with values in the global basis

632:   Output Parameters:
633: . lv - A local vector with values in the local basis

635:   Note: This method is only intended to be called inside DMGlobalToLocal(). It is unlikely that a user will have a local vector full of coefficients for the global basis unless they are reimplementing GlobalToLocal.

637:   Level: developer

639: .seealso: DMPlexLocalToGlobalBasis(), DMGetLocalSection()
640: @*/
641: PetscErrorCode DMPlexGlobalToLocalBasis(DM dm, Vec lv)
642: {

648:   DMPlexBasisTransform_Internal(dm, lv, PETSC_FALSE);
649:   return(0);
650: }

652: /*@
653:   DMPlexLocalToGlobalBasis - Transform the values in the given local vector from the local basis to the global basis

655:   Input Parameters:
656: + dm - The DM
657: - lv - A local vector with values in the local basis

659:   Output Parameters:
660: . lv - A local vector with values in the global basis

662:   Note: This method is only intended to be called inside DMGlobalToLocal(). It is unlikely that a user would want a local vector full of coefficients for the global basis unless they are reimplementing GlobalToLocal.

664:   Level: developer

666: .seealso: DMPlexGlobalToLocalBasis(), DMGetLocalSection()
667: @*/
668: PetscErrorCode DMPlexLocalToGlobalBasis(DM dm, Vec lv)
669: {

675:   DMPlexBasisTransform_Internal(dm, lv, PETSC_TRUE);
676:   return(0);
677: }

679: /*@
680:   DMPlexCreateBasisRotation - Create an internal transformation from the global basis, used to specify boundary conditions
681:     and global solutions, to a local basis, appropriate for discretization integrals and assembly.

683:   Input Parameters:
684: + dm    - The DM
685: . alpha - The first Euler angle, and in 2D the only one
686: . beta  - The second Euler angle
687: . gamma - The third Euler angle

689:   Note: Following https://en.wikipedia.org/wiki/Euler_angles, we will specify Euler angles by extrinsic rotations, meaning that
690:   we rotate with respect to a fixed initial coordinate system, the local basis (x-y-z). The global basis (X-Y-Z) is reached as follows:
691:   $ The XYZ system rotates about the z axis by alpha. The X axis is now at angle alpha with respect to the x axis.
692:   $ The XYZ system rotates again about the x axis by beta. The Z axis is now at angle beta with respect to the z axis.
693:   $ The XYZ system rotates a third time about the z axis by gamma.

695:   Level: developer

697: .seealso: DMPlexGlobalToLocalBasis(), DMPlexLocalToGlobalBasis()
698: @*/
699: PetscErrorCode DMPlexCreateBasisRotation(DM dm, PetscReal alpha, PetscReal beta, PetscReal gamma)
700: {
701:   RotCtx        *rc;
702:   PetscInt       cdim;

705:   DMGetCoordinateDim(dm, &cdim);
706:   PetscMalloc1(1, &rc);
707:   dm->transformCtx       = rc;
708:   dm->transformSetUp     = DMPlexBasisTransformSetUp_Rotation_Internal;
709:   dm->transformDestroy   = DMPlexBasisTransformDestroy_Rotation_Internal;
710:   dm->transformGetMatrix = DMPlexBasisTransformGetMatrix_Rotation_Internal;
711:   rc->dim   = cdim;
712:   rc->alpha = alpha;
713:   rc->beta  = beta;
714:   rc->gamma = gamma;
715:   (*dm->transformSetUp)(dm, dm->transformCtx);
716:   DMConstructBasisTransform_Internal(dm);
717:   return(0);
718: }

720: /*@C
721:   DMPlexInsertBoundaryValuesEssential - Insert boundary values into a local vector

723:   Input Parameters:
724: + dm     - The DM, with a PetscDS that matches the problem being constrained
725: . time   - The time
726: . field  - The field to constrain
727: . Nc     - The number of constrained field components, or 0 for all components
728: . comps  - An array of constrained component numbers, or NULL for all components
729: . label  - The DMLabel defining constrained points
730: . numids - The number of DMLabel ids for constrained points
731: . ids    - An array of ids for constrained points
732: . func   - A pointwise function giving boundary values
733: - ctx    - An optional user context for bcFunc

735:   Output Parameter:
736: . locX   - A local vector to receives the boundary values

738:   Level: developer

740: .seealso: DMPlexInsertBoundaryValuesEssentialField(), DMAddBoundary()
741: @*/
742: PetscErrorCode DMPlexInsertBoundaryValuesEssential(DM dm, PetscReal time, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[], PetscErrorCode (*func)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *), void *ctx, Vec locX)
743: {
744:   PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx);
745:   void            **ctxs;
746:   PetscInt          numFields;
747:   PetscErrorCode    ierr;

750:   DMGetNumFields(dm, &numFields);
751:   PetscCalloc2(numFields,&funcs,numFields,&ctxs);
752:   funcs[field] = func;
753:   ctxs[field]  = ctx;
754:   DMProjectFunctionLabelLocal(dm, time, label, numids, ids, Nc, comps, funcs, ctxs, INSERT_BC_VALUES, locX);
755:   PetscFree2(funcs,ctxs);
756:   return(0);
757: }

759: /*@C
760:   DMPlexInsertBoundaryValuesEssentialField - Insert boundary values into a local vector

762:   Input Parameters:
763: + dm     - The DM, with a PetscDS that matches the problem being constrained
764: . time   - The time
765: . locU   - A local vector with the input solution values
766: . field  - The field to constrain
767: . Nc     - The number of constrained field components, or 0 for all components
768: . comps  - An array of constrained component numbers, or NULL for all components
769: . label  - The DMLabel defining constrained points
770: . numids - The number of DMLabel ids for constrained points
771: . ids    - An array of ids for constrained points
772: . func   - A pointwise function giving boundary values
773: - ctx    - An optional user context for bcFunc

775:   Output Parameter:
776: . locX   - A local vector to receives the boundary values

778:   Level: developer

780: .seealso: DMPlexInsertBoundaryValuesEssential(), DMAddBoundary()
781: @*/
782: PetscErrorCode DMPlexInsertBoundaryValuesEssentialField(DM dm, PetscReal time, Vec locU, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[],
783:                                                         void (*func)(PetscInt, PetscInt, PetscInt,
784:                                                                      const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
785:                                                                      const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
786:                                                                      PetscReal, const PetscReal[], PetscInt, const PetscScalar[],
787:                                                                      PetscScalar[]),
788:                                                         void *ctx, Vec locX)
789: {
790:   void (**funcs)(PetscInt, PetscInt, PetscInt,
791:                  const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
792:                  const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
793:                  PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]);
794:   void            **ctxs;
795:   PetscInt          numFields;
796:   PetscErrorCode    ierr;

799:   DMGetNumFields(dm, &numFields);
800:   PetscCalloc2(numFields,&funcs,numFields,&ctxs);
801:   funcs[field] = func;
802:   ctxs[field]  = ctx;
803:   DMProjectFieldLabelLocal(dm, time, label, numids, ids, Nc, comps, locU, funcs, INSERT_BC_VALUES, locX);
804:   PetscFree2(funcs,ctxs);
805:   return(0);
806: }

808: /*@C
809:   DMPlexInsertBoundaryValuesRiemann - Insert boundary values into a local vector

811:   Input Parameters:
812: + dm     - The DM, with a PetscDS that matches the problem being constrained
813: . time   - The time
814: . faceGeometry - A vector with the FVM face geometry information
815: . cellGeometry - A vector with the FVM cell geometry information
816: . Grad         - A vector with the FVM cell gradient information
817: . field  - The field to constrain
818: . Nc     - The number of constrained field components, or 0 for all components
819: . comps  - An array of constrained component numbers, or NULL for all components
820: . label  - The DMLabel defining constrained points
821: . numids - The number of DMLabel ids for constrained points
822: . ids    - An array of ids for constrained points
823: . func   - A pointwise function giving boundary values
824: - ctx    - An optional user context for bcFunc

826:   Output Parameter:
827: . locX   - A local vector to receives the boundary values

829:   Note: This implementation currently ignores the numcomps/comps argument from DMAddBoundary()

831:   Level: developer

833: .seealso: DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialField(), DMAddBoundary()
834: @*/
835: PetscErrorCode DMPlexInsertBoundaryValuesRiemann(DM dm, PetscReal time, Vec faceGeometry, Vec cellGeometry, Vec Grad, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[],
836:                                                  PetscErrorCode (*func)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*), void *ctx, Vec locX)
837: {
838:   PetscDS            prob;
839:   PetscSF            sf;
840:   DM                 dmFace, dmCell, dmGrad;
841:   const PetscScalar *facegeom, *cellgeom = NULL, *grad;
842:   const PetscInt    *leaves;
843:   PetscScalar       *x, *fx;
844:   PetscInt           dim, nleaves, loc, fStart, fEnd, pdim, i;
845:   PetscErrorCode     ierr, ierru = 0;

848:   DMGetPointSF(dm, &sf);
849:   PetscSFGetGraph(sf, NULL, &nleaves, &leaves, NULL);
850:   nleaves = PetscMax(0, nleaves);
851:   DMGetDimension(dm, &dim);
852:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
853:   DMGetDS(dm, &prob);
854:   VecGetDM(faceGeometry, &dmFace);
855:   VecGetArrayRead(faceGeometry, &facegeom);
856:   if (cellGeometry) {
857:     VecGetDM(cellGeometry, &dmCell);
858:     VecGetArrayRead(cellGeometry, &cellgeom);
859:   }
860:   if (Grad) {
861:     PetscFV fv;

863:     PetscDSGetDiscretization(prob, field, (PetscObject *) &fv);
864:     VecGetDM(Grad, &dmGrad);
865:     VecGetArrayRead(Grad, &grad);
866:     PetscFVGetNumComponents(fv, &pdim);
867:     DMGetWorkArray(dm, pdim, MPIU_SCALAR, &fx);
868:   }
869:   VecGetArray(locX, &x);
870:   for (i = 0; i < numids; ++i) {
871:     IS              faceIS;
872:     const PetscInt *faces;
873:     PetscInt        numFaces, f;

875:     DMLabelGetStratumIS(label, ids[i], &faceIS);
876:     if (!faceIS) continue; /* No points with that id on this process */
877:     ISGetLocalSize(faceIS, &numFaces);
878:     ISGetIndices(faceIS, &faces);
879:     for (f = 0; f < numFaces; ++f) {
880:       const PetscInt         face = faces[f], *cells;
881:       PetscFVFaceGeom        *fg;

883:       if ((face < fStart) || (face >= fEnd)) continue; /* Refinement adds non-faces to labels */
884:       PetscFindInt(face, nleaves, (PetscInt *) leaves, &loc);
885:       if (loc >= 0) continue;
886:       DMPlexPointLocalRead(dmFace, face, facegeom, &fg);
887:       DMPlexGetSupport(dm, face, &cells);
888:       if (Grad) {
889:         PetscFVCellGeom       *cg;
890:         PetscScalar           *cx, *cgrad;
891:         PetscScalar           *xG;
892:         PetscReal              dx[3];
893:         PetscInt               d;

895:         DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cg);
896:         DMPlexPointLocalRead(dm, cells[0], x, &cx);
897:         DMPlexPointLocalRead(dmGrad, cells[0], grad, &cgrad);
898:         DMPlexPointLocalFieldRef(dm, cells[1], field, x, &xG);
899:         DMPlex_WaxpyD_Internal(dim, -1, cg->centroid, fg->centroid, dx);
900:         for (d = 0; d < pdim; ++d) fx[d] = cx[d] + DMPlex_DotD_Internal(dim, &cgrad[d*dim], dx);
901:         ierru = (*func)(time, fg->centroid, fg->normal, fx, xG, ctx);
902:         if (ierru) {
903:           ISRestoreIndices(faceIS, &faces);
904:           ISDestroy(&faceIS);
905:           goto cleanup;
906:         }
907:       } else {
908:         PetscScalar       *xI;
909:         PetscScalar       *xG;

911:         DMPlexPointLocalRead(dm, cells[0], x, &xI);
912:         DMPlexPointLocalFieldRef(dm, cells[1], field, x, &xG);
913:         ierru = (*func)(time, fg->centroid, fg->normal, xI, xG, ctx);
914:         if (ierru) {
915:           ISRestoreIndices(faceIS, &faces);
916:           ISDestroy(&faceIS);
917:           goto cleanup;
918:         }
919:       }
920:     }
921:     ISRestoreIndices(faceIS, &faces);
922:     ISDestroy(&faceIS);
923:   }
924:   cleanup:
925:   VecRestoreArray(locX, &x);
926:   if (Grad) {
927:     DMRestoreWorkArray(dm, pdim, MPIU_SCALAR, &fx);
928:     VecRestoreArrayRead(Grad, &grad);
929:   }
930:   if (cellGeometry) {VecRestoreArrayRead(cellGeometry, &cellgeom);}
931:   VecRestoreArrayRead(faceGeometry, &facegeom);
932:   CHKERRQ(ierru);
933:   return(0);
934: }

936: PetscErrorCode DMPlexInsertBoundaryValues_Plex(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM)
937: {
938:   PetscDS        prob;
939:   PetscInt       numBd, b;

943:   DMGetDS(dm, &prob);
944:   PetscDSGetNumBoundary(prob, &numBd);
945:   for (b = 0; b < numBd; ++b) {
946:     DMBoundaryConditionType type;
947:     const char             *name, *labelname;
948:     DMLabel                 label;
949:     PetscInt                field, Nc;
950:     const PetscInt         *comps;
951:     PetscObject             obj;
952:     PetscClassId            id;
953:     void                    (*func)(void);
954:     PetscInt                numids;
955:     const PetscInt         *ids;
956:     void                   *ctx;

958:     DMGetBoundary(dm, b, &type, &name, &labelname, &field, &Nc, &comps, &func, &numids, &ids, &ctx);
959:     if (insertEssential != (type & DM_BC_ESSENTIAL)) continue;
960:     DMGetLabel(dm, labelname, &label);
961:     if (!label) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "Label %s for boundary condition %s does not exist in the DM", labelname, name);
962:     DMGetField(dm, field, NULL, &obj);
963:     PetscObjectGetClassId(obj, &id);
964:     if (id == PETSCFE_CLASSID) {
965:       switch (type) {
966:         /* for FEM, there is no insertion to be done for non-essential boundary conditions */
967:       case DM_BC_ESSENTIAL:
968:         DMPlexLabelAddCells(dm,label);
969:         DMPlexInsertBoundaryValuesEssential(dm, time, field, Nc, comps, label, numids, ids, (PetscErrorCode (*)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *)) func, ctx, locX);
970:         DMPlexLabelClearCells(dm,label);
971:         break;
972:       case DM_BC_ESSENTIAL_FIELD:
973:         DMPlexLabelAddCells(dm,label);
974:         DMPlexInsertBoundaryValuesEssentialField(dm, time, locX, field, Nc, comps, label, numids, ids,
975:                                                         (void (*)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
976:                                                                   const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
977:                                                                   PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[])) func, ctx, locX);
978:         DMPlexLabelClearCells(dm,label);
979:         break;
980:       default: break;
981:       }
982:     } else if (id == PETSCFV_CLASSID) {
983:       if (!faceGeomFVM) continue;
984:       DMPlexInsertBoundaryValuesRiemann(dm, time, faceGeomFVM, cellGeomFVM, gradFVM, field, Nc, comps, label, numids, ids,
985:                                                (PetscErrorCode (*)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*)) func, ctx, locX);
986:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
987:   }
988:   return(0);
989: }

991: /*@
992:   DMPlexInsertBoundaryValues - Puts coefficients which represent boundary values into the local solution vector

994:   Input Parameters:
995: + dm - The DM
996: . insertEssential - Should I insert essential (e.g. Dirichlet) or inessential (e.g. Neumann) boundary conditions
997: . time - The time
998: . faceGeomFVM - Face geometry data for FV discretizations
999: . cellGeomFVM - Cell geometry data for FV discretizations
1000: - gradFVM - Gradient reconstruction data for FV discretizations

1002:   Output Parameters:
1003: . locX - Solution updated with boundary values

1005:   Level: developer

1007: .seealso: DMProjectFunctionLabelLocal()
1008: @*/
1009: PetscErrorCode DMPlexInsertBoundaryValues(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM)
1010: {

1019:   PetscTryMethod(dm,"DMPlexInsertBoundaryValues_C",(DM,PetscBool,Vec,PetscReal,Vec,Vec,Vec),(dm,insertEssential,locX,time,faceGeomFVM,cellGeomFVM,gradFVM));
1020:   return(0);
1021: }

1023: PetscErrorCode DMComputeL2Diff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff)
1024: {
1025:   Vec              localX;
1026:   PetscErrorCode   ierr;

1029:   DMGetLocalVector(dm, &localX);
1030:   DMPlexInsertBoundaryValues(dm, PETSC_TRUE, localX, time, NULL, NULL, NULL);
1031:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
1032:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
1033:   DMPlexComputeL2DiffLocal(dm, time, funcs, ctxs, localX, diff);
1034:   DMRestoreLocalVector(dm, &localX);
1035:   return(0);
1036: }

1038: /*@C
1039:   DMComputeL2DiffLocal - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h.

1041:   Collective on dm

1043:   Input Parameters:
1044: + dm     - The DM
1045: . time   - The time
1046: . funcs  - The functions to evaluate for each field component
1047: . ctxs   - Optional array of contexts to pass to each function, or NULL.
1048: - localX - The coefficient vector u_h, a local vector

1050:   Output Parameter:
1051: . diff - The diff ||u - u_h||_2

1053:   Level: developer

1055: .seealso: DMProjectFunction(), DMComputeL2FieldDiff(), DMComputeL2GradientDiff()
1056: @*/
1057: PetscErrorCode DMPlexComputeL2DiffLocal(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec localX, PetscReal *diff)
1058: {
1059:   const PetscInt   debug = ((DM_Plex*)dm->data)->printL2;
1060:   DM               tdm;
1061:   Vec              tv;
1062:   PetscSection     section;
1063:   PetscQuadrature  quad;
1064:   PetscFEGeom      fegeom;
1065:   PetscScalar     *funcVal, *interpolant;
1066:   PetscReal       *coords, *gcoords;
1067:   PetscReal        localDiff = 0.0;
1068:   const PetscReal *quadWeights;
1069:   PetscInt         dim, coordDim, numFields, numComponents = 0, qNc, Nq, cellHeight, cStart, cEnd, cEndInterior, c, field, fieldOffset;
1070:   PetscBool        transform;
1071:   PetscErrorCode   ierr;

1074:   DMGetDimension(dm, &dim);
1075:   DMGetCoordinateDim(dm, &coordDim);
1076:   fegeom.dimEmbed = coordDim;
1077:   DMGetLocalSection(dm, &section);
1078:   PetscSectionGetNumFields(section, &numFields);
1079:   DMGetBasisTransformDM_Internal(dm, &tdm);
1080:   DMGetBasisTransformVec_Internal(dm, &tv);
1081:   DMHasBasisTransform(dm, &transform);
1082:   for (field = 0; field < numFields; ++field) {
1083:     PetscObject  obj;
1084:     PetscClassId id;
1085:     PetscInt     Nc;

1087:     DMGetField(dm, field, NULL, &obj);
1088:     PetscObjectGetClassId(obj, &id);
1089:     if (id == PETSCFE_CLASSID) {
1090:       PetscFE fe = (PetscFE) obj;

1092:       PetscFEGetQuadrature(fe, &quad);
1093:       PetscFEGetNumComponents(fe, &Nc);
1094:     } else if (id == PETSCFV_CLASSID) {
1095:       PetscFV fv = (PetscFV) obj;

1097:       PetscFVGetQuadrature(fv, &quad);
1098:       PetscFVGetNumComponents(fv, &Nc);
1099:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1100:     numComponents += Nc;
1101:   }
1102:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, NULL, &quadWeights);
1103:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
1104:   PetscMalloc6(numComponents,&funcVal,numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);
1105:   DMPlexGetVTKCellHeight(dm, &cellHeight);
1106:   DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
1107:   DMPlexGetGhostCellStratum(dm, &cEndInterior, NULL);
1108:   cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
1109:   DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);
1110:   cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
1111:   for (c = cStart; c < cEnd; ++c) {
1112:     PetscScalar *x = NULL;
1113:     PetscReal    elemDiff = 0.0;
1114:     PetscInt     qc = 0;

1116:     DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1117:     DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);

1119:     for (field = 0, fieldOffset = 0; field < numFields; ++field) {
1120:       PetscObject  obj;
1121:       PetscClassId id;
1122:       void * const ctx = ctxs ? ctxs[field] : NULL;
1123:       PetscInt     Nb, Nc, q, fc;

1125:       DMGetField(dm, field, NULL, &obj);
1126:       PetscObjectGetClassId(obj, &id);
1127:       if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
1128:       else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
1129:       else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1130:       if (debug) {
1131:         char title[1024];
1132:         PetscSNPrintf(title, 1023, "Solution for Field %D", field);
1133:         DMPrintCellVector(c, title, Nb, &x[fieldOffset]);
1134:       }
1135:       for (q = 0; q < Nq; ++q) {
1136:         PetscFEGeom qgeom;

1138:         qgeom.dimEmbed = fegeom.dimEmbed;
1139:         qgeom.J        = &fegeom.J[q*coordDim*coordDim];
1140:         qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
1141:         qgeom.detJ     = &fegeom.detJ[q];
1142:         if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, point %D", (double)fegeom.detJ[q], c, q);
1143:         if (transform) {
1144:           gcoords = &coords[coordDim*Nq];
1145:           DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);
1146:         } else {
1147:           gcoords = &coords[coordDim*q];
1148:         }
1149:         (*funcs[field])(coordDim, time, gcoords, Nc, funcVal, ctx);
1150:         if (ierr) {
1151:           PetscErrorCode ierr2;
1152:           ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2);
1153:           ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
1154:           ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
1155: 
1156:         }
1157:         if (transform) {DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);}
1158:         if (id == PETSCFE_CLASSID)      {PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);}
1159:         else if (id == PETSCFV_CLASSID) {PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);}
1160:         else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1161:         for (fc = 0; fc < Nc; ++fc) {
1162:           const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
1163:           if (debug) {PetscPrintf(PETSC_COMM_SELF, "    elem %D field %D,%D diff %g\n", c, field, fc, (double)(PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]));}
1164:           elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
1165:         }
1166:       }
1167:       fieldOffset += Nb;
1168:       qc += Nc;
1169:     }
1170:     DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);
1171:     if (debug) {PetscPrintf(PETSC_COMM_SELF, "  elem %D diff %g\n", c, (double)elemDiff);}
1172:     localDiff += elemDiff;
1173:   }
1174:   PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);
1175:   MPIU_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));
1176:   *diff = PetscSqrtReal(*diff);
1177:   return(0);
1178: }

1180: PetscErrorCode DMComputeL2GradientDiff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, const PetscReal n[], PetscReal *diff)
1181: {
1182:   const PetscInt   debug = ((DM_Plex*)dm->data)->printL2;
1183:   DM               tdm;
1184:   PetscSection     section;
1185:   PetscQuadrature  quad;
1186:   Vec              localX, tv;
1187:   PetscScalar     *funcVal, *interpolant;
1188:   const PetscReal *quadWeights;
1189:   PetscFEGeom      fegeom;
1190:   PetscReal       *coords, *gcoords;
1191:   PetscReal        localDiff = 0.0;
1192:   PetscInt         dim, coordDim, qNc = 0, Nq = 0, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset;
1193:   PetscBool        transform;
1194:   PetscErrorCode   ierr;

1197:   DMGetDimension(dm, &dim);
1198:   DMGetCoordinateDim(dm, &coordDim);
1199:   fegeom.dimEmbed = coordDim;
1200:   DMGetLocalSection(dm, &section);
1201:   PetscSectionGetNumFields(section, &numFields);
1202:   DMGetLocalVector(dm, &localX);
1203:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
1204:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
1205:   DMGetBasisTransformDM_Internal(dm, &tdm);
1206:   DMGetBasisTransformVec_Internal(dm, &tv);
1207:   DMHasBasisTransform(dm, &transform);
1208:   for (field = 0; field < numFields; ++field) {
1209:     PetscFE  fe;
1210:     PetscInt Nc;

1212:     DMGetField(dm, field, NULL, (PetscObject *) &fe);
1213:     PetscFEGetQuadrature(fe, &quad);
1214:     PetscFEGetNumComponents(fe, &Nc);
1215:     numComponents += Nc;
1216:   }
1217:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, NULL, &quadWeights);
1218:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
1219:   /* DMProjectFunctionLocal(dm, fe, funcs, INSERT_BC_VALUES, localX); */
1220:   PetscMalloc6(numComponents,&funcVal,coordDim*Nq,&coords,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ,numComponents*coordDim,&interpolant,Nq,&fegeom.detJ);
1221:   DMPlexGetInteriorCellStratum(dm, &cStart, &cEnd);
1222:   for (c = cStart; c < cEnd; ++c) {
1223:     PetscScalar *x = NULL;
1224:     PetscReal    elemDiff = 0.0;
1225:     PetscInt     qc = 0;

1227:     DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1228:     DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);

1230:     for (field = 0, fieldOffset = 0; field < numFields; ++field) {
1231:       PetscFE          fe;
1232:       void * const     ctx = ctxs ? ctxs[field] : NULL;
1233:       PetscInt         Nb, Nc, q, fc;

1235:       DMGetField(dm, field, NULL, (PetscObject *) &fe);
1236:       PetscFEGetDimension(fe, &Nb);
1237:       PetscFEGetNumComponents(fe, &Nc);
1238:       if (debug) {
1239:         char title[1024];
1240:         PetscSNPrintf(title, 1023, "Solution for Field %D", field);
1241:         DMPrintCellVector(c, title, Nb, &x[fieldOffset]);
1242:       }
1243:       for (q = 0; q < Nq; ++q) {
1244:         PetscFEGeom qgeom;

1246:         qgeom.dimEmbed = fegeom.dimEmbed;
1247:         qgeom.J        = &fegeom.J[q*coordDim*coordDim];
1248:         qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
1249:         qgeom.detJ     = &fegeom.detJ[q];
1250:         if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature points %D", (double)fegeom.detJ[q], c, q);
1251:         if (transform) {
1252:           gcoords = &coords[coordDim*Nq];
1253:           DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);
1254:         } else {
1255:           gcoords = &coords[coordDim*q];
1256:         }
1257:         (*funcs[field])(coordDim, time, gcoords, n, Nc, funcVal, ctx);
1258:         if (ierr) {
1259:           PetscErrorCode ierr2;
1260:           ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2);
1261:           ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
1262:           ierr2 = PetscFree6(funcVal,coords,fegeom.J,fegeom.invJ,interpolant,fegeom.detJ);CHKERRQ(ierr2);
1263: 
1264:         }
1265:         if (transform) {DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);}
1266:         PetscFEInterpolateGradient_Static(fe, &x[fieldOffset], &qgeom, q, interpolant);
1267:         /* Overwrite with the dot product if the normal is given */
1268:         if (n) {
1269:           for (fc = 0; fc < Nc; ++fc) {
1270:             PetscScalar sum = 0.0;
1271:             PetscInt    d;
1272:             for (d = 0; d < dim; ++d) sum += interpolant[fc*dim+d]*n[d];
1273:             interpolant[fc] = sum;
1274:           }
1275:         }
1276:         for (fc = 0; fc < Nc; ++fc) {
1277:           const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
1278:           if (debug) {PetscPrintf(PETSC_COMM_SELF, "    elem %D fieldDer %D,%D diff %g\n", c, field, fc, (double)(PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]));}
1279:           elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
1280:         }
1281:       }
1282:       fieldOffset += Nb;
1283:       qc          += Nc;
1284:     }
1285:     DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);
1286:     if (debug) {PetscPrintf(PETSC_COMM_SELF, "  elem %D diff %g\n", c, (double)elemDiff);}
1287:     localDiff += elemDiff;
1288:   }
1289:   PetscFree6(funcVal,coords,fegeom.J,fegeom.invJ,interpolant,fegeom.detJ);
1290:   DMRestoreLocalVector(dm, &localX);
1291:   MPIU_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));
1292:   *diff = PetscSqrtReal(*diff);
1293:   return(0);
1294: }

1296: PetscErrorCode DMComputeL2FieldDiff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff)
1297: {
1298:   const PetscInt   debug = ((DM_Plex*)dm->data)->printL2;
1299:   DM               tdm;
1300:   PetscSection     section;
1301:   PetscQuadrature  quad;
1302:   Vec              localX, tv;
1303:   PetscFEGeom      fegeom;
1304:   PetscScalar     *funcVal, *interpolant;
1305:   PetscReal       *coords, *gcoords;
1306:   PetscReal       *localDiff;
1307:   const PetscReal *quadPoints, *quadWeights;
1308:   PetscInt         dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, c, field, fieldOffset;
1309:   PetscBool        transform;
1310:   PetscErrorCode   ierr;

1313:   DMGetDimension(dm, &dim);
1314:   DMGetCoordinateDim(dm, &coordDim);
1315:   DMGetLocalSection(dm, &section);
1316:   PetscSectionGetNumFields(section, &numFields);
1317:   DMGetLocalVector(dm, &localX);
1318:   VecSet(localX, 0.0);
1319:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
1320:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
1321:   DMProjectFunctionLocal(dm, time, funcs, ctxs, INSERT_BC_VALUES, localX);
1322:   DMGetBasisTransformDM_Internal(dm, &tdm);
1323:   DMGetBasisTransformVec_Internal(dm, &tv);
1324:   DMHasBasisTransform(dm, &transform);
1325:   for (field = 0; field < numFields; ++field) {
1326:     PetscObject  obj;
1327:     PetscClassId id;
1328:     PetscInt     Nc;

1330:     DMGetField(dm, field, NULL, &obj);
1331:     PetscObjectGetClassId(obj, &id);
1332:     if (id == PETSCFE_CLASSID) {
1333:       PetscFE fe = (PetscFE) obj;

1335:       PetscFEGetQuadrature(fe, &quad);
1336:       PetscFEGetNumComponents(fe, &Nc);
1337:     } else if (id == PETSCFV_CLASSID) {
1338:       PetscFV fv = (PetscFV) obj;

1340:       PetscFVGetQuadrature(fv, &quad);
1341:       PetscFVGetNumComponents(fv, &Nc);
1342:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1343:     numComponents += Nc;
1344:   }
1345:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);
1346:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
1347:   PetscCalloc7(numFields,&localDiff,numComponents,&funcVal,numComponents,&interpolant,coordDim*(Nq+1),&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);
1348:   DMPlexGetInteriorCellStratum(dm, &cStart, &cEnd);
1349:   for (c = cStart; c < cEnd; ++c) {
1350:     PetscScalar *x = NULL;
1351:     PetscInt     qc = 0;

1353:     DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1354:     DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);

1356:     for (field = 0, fieldOffset = 0; field < numFields; ++field) {
1357:       PetscObject  obj;
1358:       PetscClassId id;
1359:       void * const ctx = ctxs ? ctxs[field] : NULL;
1360:       PetscInt     Nb, Nc, q, fc;

1362:       PetscReal       elemDiff = 0.0;

1364:       DMGetField(dm, field, NULL, &obj);
1365:       PetscObjectGetClassId(obj, &id);
1366:       if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
1367:       else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
1368:       else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1369:       if (debug) {
1370:         char title[1024];
1371:         PetscSNPrintf(title, 1023, "Solution for Field %D", field);
1372:         DMPrintCellVector(c, title, Nb, &x[fieldOffset]);
1373:       }
1374:       for (q = 0; q < Nq; ++q) {
1375:         PetscFEGeom qgeom;

1377:         qgeom.dimEmbed = fegeom.dimEmbed;
1378:         qgeom.J        = &fegeom.J[q*coordDim*coordDim];
1379:         qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
1380:         qgeom.detJ     = &fegeom.detJ[q];
1381:         if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature point %D", (double)fegeom.detJ[q], c, q);
1382:         if (transform) {
1383:           gcoords = &coords[coordDim*Nq];
1384:           DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);
1385:         } else {
1386:           gcoords = &coords[coordDim*q];
1387:         }
1388:         (*funcs[field])(coordDim, time, gcoords, Nc, funcVal, ctx);
1389:         if (ierr) {
1390:           PetscErrorCode ierr2;
1391:           ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2);
1392:           ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
1393:           ierr2 = PetscFree7(localDiff,funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
1394: 
1395:         }
1396:         if (transform) {DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);}
1397:         if (id == PETSCFE_CLASSID)      {PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);}
1398:         else if (id == PETSCFV_CLASSID) {PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);}
1399:         else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1400:         for (fc = 0; fc < Nc; ++fc) {
1401:           const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
1402:           if (debug) {PetscPrintf(PETSC_COMM_SELF, "    elem %D field %D,%D point %g %g %g diff %g\n", c, field, fc, (double)(coordDim > 0 ? coords[coordDim*q] : 0.), (double)(coordDim > 1 ? coords[coordDim*q+1] : 0.),(double)(coordDim > 2 ? coords[coordDim*q+2] : 0.), (double)(PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]));}
1403:           elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
1404:         }
1405:       }
1406:       fieldOffset += Nb;
1407:       qc          += Nc;
1408:       localDiff[field] += elemDiff;
1409:       if (debug) {PetscPrintf(PETSC_COMM_SELF, "  elem %D field %D cum diff %g\n", c, field, (double)localDiff[field]);}
1410:     }
1411:     DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);
1412:   }
1413:   DMRestoreLocalVector(dm, &localX);
1414:   MPIU_Allreduce(localDiff, diff, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));
1415:   for (field = 0; field < numFields; ++field) diff[field] = PetscSqrtReal(diff[field]);
1416:   PetscFree7(localDiff,funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);
1417:   return(0);
1418: }

1420: /*@C
1421:   DMPlexComputeL2DiffVec - This function computes the cellwise L_2 difference between a function u and an FEM interpolant solution u_h, and stores it in a Vec.

1423:   Collective on dm

1425:   Input Parameters:
1426: + dm    - The DM
1427: . time  - The time
1428: . funcs - The functions to evaluate for each field component: NULL means that component does not contribute to error calculation
1429: . ctxs  - Optional array of contexts to pass to each function, or NULL.
1430: - X     - The coefficient vector u_h

1432:   Output Parameter:
1433: . D - A Vec which holds the difference ||u - u_h||_2 for each cell

1435:   Level: developer

1437: .seealso: DMProjectFunction(), DMComputeL2Diff(), DMPlexComputeL2FieldDiff(), DMComputeL2GradientDiff()
1438: @*/
1439: PetscErrorCode DMPlexComputeL2DiffVec(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, Vec D)
1440: {
1441:   PetscSection     section;
1442:   PetscQuadrature  quad;
1443:   Vec              localX;
1444:   PetscFEGeom      fegeom;
1445:   PetscScalar     *funcVal, *interpolant;
1446:   PetscReal       *coords;
1447:   const PetscReal *quadPoints, *quadWeights;
1448:   PetscInt         dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, c, field, fieldOffset;
1449:   PetscErrorCode   ierr;

1452:   VecSet(D, 0.0);
1453:   DMGetDimension(dm, &dim);
1454:   DMGetCoordinateDim(dm, &coordDim);
1455:   DMGetLocalSection(dm, &section);
1456:   PetscSectionGetNumFields(section, &numFields);
1457:   DMGetLocalVector(dm, &localX);
1458:   DMProjectFunctionLocal(dm, time, funcs, ctxs, INSERT_BC_VALUES, localX);
1459:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
1460:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
1461:   for (field = 0; field < numFields; ++field) {
1462:     PetscObject  obj;
1463:     PetscClassId id;
1464:     PetscInt     Nc;

1466:     DMGetField(dm, field, NULL, &obj);
1467:     PetscObjectGetClassId(obj, &id);
1468:     if (id == PETSCFE_CLASSID) {
1469:       PetscFE fe = (PetscFE) obj;

1471:       PetscFEGetQuadrature(fe, &quad);
1472:       PetscFEGetNumComponents(fe, &Nc);
1473:     } else if (id == PETSCFV_CLASSID) {
1474:       PetscFV fv = (PetscFV) obj;

1476:       PetscFVGetQuadrature(fv, &quad);
1477:       PetscFVGetNumComponents(fv, &Nc);
1478:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1479:     numComponents += Nc;
1480:   }
1481:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);
1482:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
1483:   PetscMalloc6(numComponents,&funcVal,numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);
1484:   DMPlexGetInteriorCellStratum(dm, &cStart, &cEnd);
1485:   for (c = cStart; c < cEnd; ++c) {
1486:     PetscScalar *x = NULL;
1487:     PetscScalar  elemDiff = 0.0;
1488:     PetscInt     qc = 0;

1490:     DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1491:     DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);

1493:     for (field = 0, fieldOffset = 0; field < numFields; ++field) {
1494:       PetscObject  obj;
1495:       PetscClassId id;
1496:       void * const ctx = ctxs ? ctxs[field] : NULL;
1497:       PetscInt     Nb, Nc, q, fc;

1499:       DMGetField(dm, field, NULL, &obj);
1500:       PetscObjectGetClassId(obj, &id);
1501:       if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
1502:       else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
1503:       else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1504:       if (funcs[field]) {
1505:         for (q = 0; q < Nq; ++q) {
1506:           PetscFEGeom qgeom;

1508:           qgeom.dimEmbed = fegeom.dimEmbed;
1509:           qgeom.J        = &fegeom.J[q*coordDim*coordDim];
1510:           qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
1511:           qgeom.detJ     = &fegeom.detJ[q];
1512:           if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature points %D", (double)fegeom.detJ[q], c, q);
1513:           (*funcs[field])(coordDim, time, &coords[q*coordDim], Nc, funcVal, ctx);
1514:           if (ierr) {
1515:             PetscErrorCode ierr2;
1516:             ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2);
1517:             ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
1518:             ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
1519: 
1520:           }
1521:           if (id == PETSCFE_CLASSID)      {PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);}
1522:           else if (id == PETSCFV_CLASSID) {PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);}
1523:           else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1524:           for (fc = 0; fc < Nc; ++fc) {
1525:             const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
1526:             elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
1527:           }
1528:         }
1529:       }
1530:       fieldOffset += Nb;
1531:       qc          += Nc;
1532:     }
1533:     DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);
1534:     VecSetValue(D, c - cStart, elemDiff, INSERT_VALUES);
1535:   }
1536:   PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);
1537:   DMRestoreLocalVector(dm, &localX);
1538:   VecSqrtAbs(D);
1539:   return(0);
1540: }

1542: /*@C
1543:   DMPlexComputeGradientClementInterpolant - This function computes the L2 projection of the cellwise gradient of a function u onto P1, and stores it in a Vec.

1545:   Collective on dm

1547:   Input Parameters:
1548: + dm - The DM
1549: - LocX  - The coefficient vector u_h

1551:   Output Parameter:
1552: . locC - A Vec which holds the Clement interpolant of the gradient

1554:   Notes:
1555:     Add citation to (Clement, 1975) and definition of the interpolant
1556:   \nabla u_h(v_i) = \sum_{T_i \in support(v_i)} |T_i| \nabla u_h(T_i) / \sum_{T_i \in support(v_i)} |T_i| where |T_i| is the cell volume

1558:   Level: developer

1560: .seealso: DMProjectFunction(), DMComputeL2Diff(), DMPlexComputeL2FieldDiff(), DMComputeL2GradientDiff()
1561: @*/
1562: PetscErrorCode DMPlexComputeGradientClementInterpolant(DM dm, Vec locX, Vec locC)
1563: {
1564:   DM_Plex         *mesh  = (DM_Plex *) dm->data;
1565:   PetscInt         debug = mesh->printFEM;
1566:   DM               dmC;
1567:   PetscSection     section;
1568:   PetscQuadrature  quad;
1569:   PetscScalar     *interpolant, *gradsum;
1570:   PetscFEGeom      fegeom;
1571:   PetscReal       *coords;
1572:   const PetscReal *quadPoints, *quadWeights;
1573:   PetscInt         dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, vStart, vEnd, v, field, fieldOffset;
1574:   PetscErrorCode   ierr;

1577:   VecGetDM(locC, &dmC);
1578:   VecSet(locC, 0.0);
1579:   DMGetDimension(dm, &dim);
1580:   DMGetCoordinateDim(dm, &coordDim);
1581:   fegeom.dimEmbed = coordDim;
1582:   DMGetLocalSection(dm, &section);
1583:   PetscSectionGetNumFields(section, &numFields);
1584:   for (field = 0; field < numFields; ++field) {
1585:     PetscObject  obj;
1586:     PetscClassId id;
1587:     PetscInt     Nc;

1589:     DMGetField(dm, field, NULL, &obj);
1590:     PetscObjectGetClassId(obj, &id);
1591:     if (id == PETSCFE_CLASSID) {
1592:       PetscFE fe = (PetscFE) obj;

1594:       PetscFEGetQuadrature(fe, &quad);
1595:       PetscFEGetNumComponents(fe, &Nc);
1596:     } else if (id == PETSCFV_CLASSID) {
1597:       PetscFV fv = (PetscFV) obj;

1599:       PetscFVGetQuadrature(fv, &quad);
1600:       PetscFVGetNumComponents(fv, &Nc);
1601:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1602:     numComponents += Nc;
1603:   }
1604:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);
1605:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
1606:   PetscMalloc6(coordDim*numComponents*2,&gradsum,coordDim*numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);
1607:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
1608:   DMPlexGetInteriorCellStratum(dm, &cStart, &cEnd);
1609:   for (v = vStart; v < vEnd; ++v) {
1610:     PetscScalar volsum = 0.0;
1611:     PetscInt   *star = NULL;
1612:     PetscInt    starSize, st, d, fc;

1614:     PetscArrayzero(gradsum, coordDim*numComponents);
1615:     DMPlexGetTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);
1616:     for (st = 0; st < starSize*2; st += 2) {
1617:       const PetscInt cell = star[st];
1618:       PetscScalar   *grad = &gradsum[coordDim*numComponents];
1619:       PetscScalar   *x    = NULL;
1620:       PetscReal      vol  = 0.0;

1622:       if ((cell < cStart) || (cell >= cEnd)) continue;
1623:       DMPlexComputeCellGeometryFEM(dm, cell, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1624:       DMPlexVecGetClosure(dm, NULL, locX, cell, NULL, &x);
1625:       for (field = 0, fieldOffset = 0; field < numFields; ++field) {
1626:         PetscObject  obj;
1627:         PetscClassId id;
1628:         PetscInt     Nb, Nc, q, qc = 0;

1630:         PetscArrayzero(grad, coordDim*numComponents);
1631:         DMGetField(dm, field, NULL, &obj);
1632:         PetscObjectGetClassId(obj, &id);
1633:         if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
1634:         else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
1635:         else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1636:         for (q = 0; q < Nq; ++q) {
1637:           PetscFEGeom qgeom;

1639:           qgeom.dimEmbed = fegeom.dimEmbed;
1640:           qgeom.J        = &fegeom.J[q*coordDim*coordDim];
1641:           qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
1642:           qgeom.detJ     = &fegeom.detJ[q];
1643:           if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %D, quadrature points %D", (double)fegeom.detJ[q], cell, q);
1644:           if (ierr) {
1645:             PetscErrorCode ierr2;
1646:             ierr2 = DMPlexVecRestoreClosure(dm, NULL, locX, cell, NULL, &x);CHKERRQ(ierr2);
1647:             ierr2 = DMPlexRestoreTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr2);
1648:             ierr2 = PetscFree6(gradsum,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
1649: 
1650:           }
1651:           if (id == PETSCFE_CLASSID)      {PetscFEInterpolateGradient_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);}
1652:           else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1653:           for (fc = 0; fc < Nc; ++fc) {
1654:             const PetscReal wt = quadWeights[q*qNc+qc+fc];

1656:             for (d = 0; d < coordDim; ++d) grad[fc*coordDim+d] += interpolant[fc*dim+d]*wt*fegeom.detJ[q];
1657:           }
1658:           vol += quadWeights[q*qNc]*fegeom.detJ[q];
1659:         }
1660:         fieldOffset += Nb;
1661:         qc          += Nc;
1662:       }
1663:       DMPlexVecRestoreClosure(dm, NULL, locX, cell, NULL, &x);
1664:       for (fc = 0; fc < numComponents; ++fc) {
1665:         for (d = 0; d < coordDim; ++d) {
1666:           gradsum[fc*coordDim+d] += grad[fc*coordDim+d];
1667:         }
1668:       }
1669:       volsum += vol;
1670:       if (debug) {
1671:         PetscPrintf(PETSC_COMM_SELF, "Cell %D gradient: [", cell);
1672:         for (fc = 0; fc < numComponents; ++fc) {
1673:           for (d = 0; d < coordDim; ++d) {
1674:             if (fc || d > 0) {PetscPrintf(PETSC_COMM_SELF, ", ");}
1675:             PetscPrintf(PETSC_COMM_SELF, "%g", (double)PetscRealPart(grad[fc*coordDim+d]));
1676:           }
1677:         }
1678:         PetscPrintf(PETSC_COMM_SELF, "]\n");
1679:       }
1680:     }
1681:     for (fc = 0; fc < numComponents; ++fc) {
1682:       for (d = 0; d < coordDim; ++d) gradsum[fc*coordDim+d] /= volsum;
1683:     }
1684:     DMPlexRestoreTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);
1685:     DMPlexVecSetClosure(dmC, NULL, locC, v, gradsum, INSERT_VALUES);
1686:   }
1687:   PetscFree6(gradsum,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);
1688:   return(0);
1689: }

1691: static PetscErrorCode DMPlexComputeIntegral_Internal(DM dm, Vec X, PetscInt cStart, PetscInt cEnd, PetscScalar *cintegral, void *user)
1692: {
1693:   DM                 dmAux = NULL;
1694:   PetscDS            prob,    probAux = NULL;
1695:   PetscSection       section, sectionAux;
1696:   Vec                locX,    locA;
1697:   PetscInt           dim, numCells = cEnd - cStart, c, f;
1698:   PetscBool          useFVM = PETSC_FALSE;
1699:   /* DS */
1700:   PetscInt           Nf,    totDim,    *uOff, *uOff_x, numConstants;
1701:   PetscInt           NfAux, totDimAux, *aOff;
1702:   PetscScalar       *u, *a;
1703:   const PetscScalar *constants;
1704:   /* Geometry */
1705:   PetscFEGeom       *cgeomFEM;
1706:   DM                 dmGrad;
1707:   PetscQuadrature    affineQuad = NULL;
1708:   Vec                cellGeometryFVM = NULL, faceGeometryFVM = NULL, locGrad = NULL;
1709:   PetscFVCellGeom   *cgeomFVM;
1710:   const PetscScalar *lgrad;
1711:   PetscInt           maxDegree;
1712:   DMField            coordField;
1713:   IS                 cellIS;
1714:   PetscErrorCode     ierr;

1717:   DMGetDS(dm, &prob);
1718:   DMGetDimension(dm, &dim);
1719:   DMGetLocalSection(dm, &section);
1720:   PetscSectionGetNumFields(section, &Nf);
1721:   /* Determine which discretizations we have */
1722:   for (f = 0; f < Nf; ++f) {
1723:     PetscObject  obj;
1724:     PetscClassId id;

1726:     PetscDSGetDiscretization(prob, f, &obj);
1727:     PetscObjectGetClassId(obj, &id);
1728:     if (id == PETSCFV_CLASSID) useFVM = PETSC_TRUE;
1729:   }
1730:   /* Get local solution with boundary values */
1731:   DMGetLocalVector(dm, &locX);
1732:   DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locX, 0.0, NULL, NULL, NULL);
1733:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);
1734:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);
1735:   /* Read DS information */
1736:   PetscDSGetTotalDimension(prob, &totDim);
1737:   PetscDSGetComponentOffsets(prob, &uOff);
1738:   PetscDSGetComponentDerivativeOffsets(prob, &uOff_x);
1739:   ISCreateStride(PETSC_COMM_SELF,numCells,cStart,1,&cellIS);
1740:   PetscDSGetConstants(prob, &numConstants, &constants);
1741:   /* Read Auxiliary DS information */
1742:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
1743:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
1744:   if (dmAux) {
1745:     DMGetDS(dmAux, &probAux);
1746:     PetscDSGetNumFields(probAux, &NfAux);
1747:     DMGetLocalSection(dmAux, &sectionAux);
1748:     PetscDSGetTotalDimension(probAux, &totDimAux);
1749:     PetscDSGetComponentOffsets(probAux, &aOff);
1750:   }
1751:   /* Allocate data  arrays */
1752:   PetscCalloc1(numCells*totDim, &u);
1753:   if (dmAux) {PetscMalloc1(numCells*totDimAux, &a);}
1754:   /* Read out geometry */
1755:   DMGetCoordinateField(dm,&coordField);
1756:   DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
1757:   if (maxDegree <= 1) {
1758:     DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);
1759:     if (affineQuad) {
1760:       DMFieldCreateFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&cgeomFEM);
1761:     }
1762:   }
1763:   if (useFVM) {
1764:     PetscFV   fv = NULL;
1765:     Vec       grad;
1766:     PetscInt  fStart, fEnd;
1767:     PetscBool compGrad;

1769:     for (f = 0; f < Nf; ++f) {
1770:       PetscObject  obj;
1771:       PetscClassId id;

1773:       PetscDSGetDiscretization(prob, f, &obj);
1774:       PetscObjectGetClassId(obj, &id);
1775:       if (id == PETSCFV_CLASSID) {fv = (PetscFV) obj; break;}
1776:     }
1777:     PetscFVGetComputeGradients(fv, &compGrad);
1778:     PetscFVSetComputeGradients(fv, PETSC_TRUE);
1779:     DMPlexComputeGeometryFVM(dm, &cellGeometryFVM, &faceGeometryFVM);
1780:     DMPlexComputeGradientFVM(dm, fv, faceGeometryFVM, cellGeometryFVM, &dmGrad);
1781:     PetscFVSetComputeGradients(fv, compGrad);
1782:     VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);
1783:     /* Reconstruct and limit cell gradients */
1784:     DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
1785:     DMGetGlobalVector(dmGrad, &grad);
1786:     DMPlexReconstructGradients_Internal(dm, fv, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);
1787:     /* Communicate gradient values */
1788:     DMGetLocalVector(dmGrad, &locGrad);
1789:     DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);
1790:     DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);
1791:     DMRestoreGlobalVector(dmGrad, &grad);
1792:     /* Handle non-essential (e.g. outflow) boundary values */
1793:     DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, 0.0, faceGeometryFVM, cellGeometryFVM, locGrad);
1794:     VecGetArrayRead(locGrad, &lgrad);
1795:   }
1796:   /* Read out data from inputs */
1797:   for (c = cStart; c < cEnd; ++c) {
1798:     PetscScalar *x = NULL;
1799:     PetscInt     i;

1801:     DMPlexVecGetClosure(dm, section, locX, c, NULL, &x);
1802:     for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i];
1803:     DMPlexVecRestoreClosure(dm, section, locX, c, NULL, &x);
1804:     if (dmAux) {
1805:       DMPlexVecGetClosure(dmAux, sectionAux, locA, c, NULL, &x);
1806:       for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i];
1807:       DMPlexVecRestoreClosure(dmAux, sectionAux, locA, c, NULL, &x);
1808:     }
1809:   }
1810:   /* Do integration for each field */
1811:   for (f = 0; f < Nf; ++f) {
1812:     PetscObject  obj;
1813:     PetscClassId id;
1814:     PetscInt     numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset;

1816:     PetscDSGetDiscretization(prob, f, &obj);
1817:     PetscObjectGetClassId(obj, &id);
1818:     if (id == PETSCFE_CLASSID) {
1819:       PetscFE         fe = (PetscFE) obj;
1820:       PetscQuadrature q;
1821:       PetscFEGeom     *chunkGeom = NULL;
1822:       PetscInt        Nq, Nb;

1824:       PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
1825:       PetscFEGetQuadrature(fe, &q);
1826:       PetscQuadratureGetData(q, NULL, NULL, &Nq, NULL, NULL);
1827:       PetscFEGetDimension(fe, &Nb);
1828:       blockSize = Nb*Nq;
1829:       batchSize = numBlocks * blockSize;
1830:       PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
1831:       numChunks = numCells / (numBatches*batchSize);
1832:       Ne        = numChunks*numBatches*batchSize;
1833:       Nr        = numCells % (numBatches*batchSize);
1834:       offset    = numCells - Nr;
1835:       if (!affineQuad) {
1836:         DMFieldCreateFEGeom(coordField,cellIS,q,PETSC_FALSE,&cgeomFEM);
1837:       }
1838:       PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);
1839:       PetscFEIntegrate(prob, f, Ne, chunkGeom, u, probAux, a, cintegral);
1840:       PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&chunkGeom);
1841:       PetscFEIntegrate(prob, f, Nr, chunkGeom, &u[offset*totDim], probAux, &a[offset*totDimAux], &cintegral[offset*Nf]);
1842:       PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&chunkGeom);
1843:       if (!affineQuad) {
1844:         PetscFEGeomDestroy(&cgeomFEM);
1845:       }
1846:     } else if (id == PETSCFV_CLASSID) {
1847:       PetscInt       foff;
1848:       PetscPointFunc obj_func;
1849:       PetscScalar    lint;

1851:       PetscDSGetObjective(prob, f, &obj_func);
1852:       PetscDSGetFieldOffset(prob, f, &foff);
1853:       if (obj_func) {
1854:         for (c = 0; c < numCells; ++c) {
1855:           PetscScalar *u_x;

1857:           DMPlexPointLocalRead(dmGrad, c, lgrad, &u_x);
1858:           obj_func(dim, Nf, NfAux, uOff, uOff_x, &u[totDim*c+foff], NULL, u_x, aOff, NULL, &a[totDimAux*c], NULL, NULL, 0.0, cgeomFVM[c].centroid, numConstants, constants, &lint);
1859:           cintegral[c*Nf+f] += PetscRealPart(lint)*cgeomFVM[c].volume;
1860:         }
1861:       }
1862:     } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f);
1863:   }
1864:   /* Cleanup data arrays */
1865:   if (useFVM) {
1866:     VecRestoreArrayRead(locGrad, &lgrad);
1867:     VecRestoreArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);
1868:     DMRestoreLocalVector(dmGrad, &locGrad);
1869:     VecDestroy(&faceGeometryFVM);
1870:     VecDestroy(&cellGeometryFVM);
1871:     DMDestroy(&dmGrad);
1872:   }
1873:   if (dmAux) {PetscFree(a);}
1874:   PetscFree(u);
1875:   /* Cleanup */
1876:   if (affineQuad) {
1877:     PetscFEGeomDestroy(&cgeomFEM);
1878:   }
1879:   PetscQuadratureDestroy(&affineQuad);
1880:   ISDestroy(&cellIS);
1881:   DMRestoreLocalVector(dm, &locX);
1882:   return(0);
1883: }

1885: /*@
1886:   DMPlexComputeIntegralFEM - Form the integral over the domain from the global input X using pointwise functions specified by the user

1888:   Input Parameters:
1889: + dm - The mesh
1890: . X  - Global input vector
1891: - user - The user context

1893:   Output Parameter:
1894: . integral - Integral for each field

1896:   Level: developer

1898: .seealso: DMPlexComputeResidualFEM()
1899: @*/
1900: PetscErrorCode DMPlexComputeIntegralFEM(DM dm, Vec X, PetscScalar *integral, void *user)
1901: {
1902:   DM_Plex       *mesh = (DM_Plex *) dm->data;
1903:   PetscScalar   *cintegral, *lintegral;
1904:   PetscInt       Nf, f, cellHeight, cStart, cEnd, cEndInterior[4], cell;

1911:   PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);
1912:   DMGetNumFields(dm, &Nf);
1913:   DMPlexGetVTKCellHeight(dm, &cellHeight);
1914:   DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
1915:   DMPlexGetHybridBounds(dm, &cEndInterior[0], &cEndInterior[1], &cEndInterior[2], &cEndInterior[3]);
1916:   cEnd = cEndInterior[cellHeight] < 0 ? cEnd : cEndInterior[cellHeight];
1917:   /* TODO Introduce a loop over large chunks (right now this is a single chunk) */
1918:   PetscCalloc2(Nf, &lintegral, (cEnd-cStart)*Nf, &cintegral);
1919:   DMPlexComputeIntegral_Internal(dm, X, cStart, cEnd, cintegral, user);
1920:   /* Sum up values */
1921:   for (cell = cStart; cell < cEnd; ++cell) {
1922:     const PetscInt c = cell - cStart;

1924:     if (mesh->printFEM > 1) {DMPrintCellVector(cell, "Cell Integral", Nf, &cintegral[c*Nf]);}
1925:     for (f = 0; f < Nf; ++f) lintegral[f] += cintegral[c*Nf+f];
1926:   }
1927:   MPIU_Allreduce(lintegral, integral, Nf, MPIU_SCALAR, MPIU_SUM, PetscObjectComm((PetscObject) dm));
1928:   if (mesh->printFEM) {
1929:     PetscPrintf(PetscObjectComm((PetscObject) dm), "Integral:");
1930:     for (f = 0; f < Nf; ++f) {PetscPrintf(PetscObjectComm((PetscObject) dm), " %g", (double) PetscRealPart(integral[f]));}
1931:     PetscPrintf(PetscObjectComm((PetscObject) dm), "\n");
1932:   }
1933:   PetscFree2(lintegral, cintegral);
1934:   PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);
1935:   return(0);
1936: }

1938: /*@
1939:   DMPlexComputeCellwiseIntegralFEM - Form the vector of cellwise integrals F from the global input X using pointwise functions specified by the user

1941:   Input Parameters:
1942: + dm - The mesh
1943: . X  - Global input vector
1944: - user - The user context

1946:   Output Parameter:
1947: . integral - Cellwise integrals for each field

1949:   Level: developer

1951: .seealso: DMPlexComputeResidualFEM()
1952: @*/
1953: PetscErrorCode DMPlexComputeCellwiseIntegralFEM(DM dm, Vec X, Vec F, void *user)
1954: {
1955:   DM_Plex       *mesh = (DM_Plex *) dm->data;
1956:   DM             dmF;
1957:   PetscSection   sectionF;
1958:   PetscScalar   *cintegral, *af;
1959:   PetscInt       Nf, f, cellHeight, cStart, cEnd, cEndInterior[4], cell;

1966:   PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);
1967:   DMGetNumFields(dm, &Nf);
1968:   DMPlexGetVTKCellHeight(dm, &cellHeight);
1969:   DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
1970:   DMPlexGetHybridBounds(dm, &cEndInterior[0], &cEndInterior[1], &cEndInterior[2], &cEndInterior[3]);
1971:   cEnd = cEndInterior[cellHeight] < 0 ? cEnd : cEndInterior[cellHeight];
1972:   /* TODO Introduce a loop over large chunks (right now this is a single chunk) */
1973:   PetscCalloc1((cEnd-cStart)*Nf, &cintegral);
1974:   DMPlexComputeIntegral_Internal(dm, X, cStart, cEnd, cintegral, user);
1975:   /* Put values in F*/
1976:   VecGetDM(F, &dmF);
1977:   DMGetLocalSection(dmF, &sectionF);
1978:   VecGetArray(F, &af);
1979:   for (cell = cStart; cell < cEnd; ++cell) {
1980:     const PetscInt c = cell - cStart;
1981:     PetscInt       dof, off;

1983:     if (mesh->printFEM > 1) {DMPrintCellVector(cell, "Cell Integral", Nf, &cintegral[c*Nf]);}
1984:     PetscSectionGetDof(sectionF, cell, &dof);
1985:     PetscSectionGetOffset(sectionF, cell, &off);
1986:     if (dof != Nf) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "The number of cell dofs %D != %D", dof, Nf);
1987:     for (f = 0; f < Nf; ++f) af[off+f] = cintegral[c*Nf+f];
1988:   }
1989:   VecRestoreArray(F, &af);
1990:   PetscFree(cintegral);
1991:   PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);
1992:   return(0);
1993: }

1995: static PetscErrorCode DMPlexComputeBdIntegral_Internal(DM dm, Vec locX, IS pointIS,
1996:                                                        void (*func)(PetscInt, PetscInt, PetscInt,
1997:                                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
1998:                                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
1999:                                                                     PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]),
2000:                                                        PetscScalar *fintegral, void *user)
2001: {
2002:   DM                 plex = NULL, plexA = NULL;
2003:   PetscDS            prob, probAux = NULL;
2004:   PetscSection       section, sectionAux = NULL;
2005:   Vec                locA = NULL;
2006:   DMField            coordField;
2007:   PetscInt           Nf,        totDim,        *uOff, *uOff_x;
2008:   PetscInt           NfAux = 0, totDimAux = 0, *aOff = NULL;
2009:   PetscScalar       *u, *a = NULL;
2010:   const PetscScalar *constants;
2011:   PetscInt           numConstants, f;
2012:   PetscErrorCode     ierr;

2015:   DMGetCoordinateField(dm, &coordField);
2016:   DMConvert(dm, DMPLEX, &plex);
2017:   DMGetDS(dm, &prob);
2018:   DMGetLocalSection(dm, &section);
2019:   PetscSectionGetNumFields(section, &Nf);
2020:   /* Determine which discretizations we have */
2021:   for (f = 0; f < Nf; ++f) {
2022:     PetscObject  obj;
2023:     PetscClassId id;

2025:     PetscDSGetDiscretization(prob, f, &obj);
2026:     PetscObjectGetClassId(obj, &id);
2027:     if (id == PETSCFV_CLASSID) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Not supported for FVM (field %D)", f);
2028:   }
2029:   /* Read DS information */
2030:   PetscDSGetTotalDimension(prob, &totDim);
2031:   PetscDSGetComponentOffsets(prob, &uOff);
2032:   PetscDSGetComponentDerivativeOffsets(prob, &uOff_x);
2033:   PetscDSGetConstants(prob, &numConstants, &constants);
2034:   /* Read Auxiliary DS information */
2035:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
2036:   if (locA) {
2037:     DM dmAux;

2039:     VecGetDM(locA, &dmAux);
2040:     DMConvert(dmAux, DMPLEX, &plexA);
2041:     DMGetDS(dmAux, &probAux);
2042:     PetscDSGetNumFields(probAux, &NfAux);
2043:     DMGetLocalSection(dmAux, &sectionAux);
2044:     PetscDSGetTotalDimension(probAux, &totDimAux);
2045:     PetscDSGetComponentOffsets(probAux, &aOff);
2046:   }
2047:   /* Integrate over points */
2048:   {
2049:     PetscFEGeom    *fgeom, *chunkGeom = NULL;
2050:     PetscInt        maxDegree;
2051:     PetscQuadrature qGeom = NULL;
2052:     const PetscInt *points;
2053:     PetscInt        numFaces, face, Nq, field;
2054:     PetscInt        numChunks, chunkSize, chunk, Nr, offset;

2056:     ISGetLocalSize(pointIS, &numFaces);
2057:     ISGetIndices(pointIS, &points);
2058:     PetscCalloc2(numFaces*totDim, &u, locA ? numFaces*totDimAux : 0, &a);
2059:     DMFieldGetDegree(coordField, pointIS, NULL, &maxDegree);
2060:     for (field = 0; field < Nf; ++field) {
2061:       PetscFE fe;

2063:       PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);
2064:       if (maxDegree <= 1) {DMFieldCreateDefaultQuadrature(coordField, pointIS, &qGeom);}
2065:       if (!qGeom) {
2066:         PetscFEGetFaceQuadrature(fe, &qGeom);
2067:         PetscObjectReference((PetscObject) qGeom);
2068:       }
2069:       PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
2070:       DMPlexGetFEGeom(coordField, pointIS, qGeom, PETSC_TRUE, &fgeom);
2071:       for (face = 0; face < numFaces; ++face) {
2072:         const PetscInt point = points[face], *support, *cone;
2073:         PetscScalar    *x    = NULL;
2074:         PetscInt       i, coneSize, faceLoc;

2076:         DMPlexGetSupport(dm, point, &support);
2077:         DMPlexGetConeSize(dm, support[0], &coneSize);
2078:         DMPlexGetCone(dm, support[0], &cone);
2079:         for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break;
2080:         if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", face, support[0]);
2081:         fgeom->face[face][0] = faceLoc;
2082:         DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);
2083:         for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i];
2084:         DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);
2085:         if (locA) {
2086:           PetscInt subp;
2087:           DMPlexGetSubpoint(plexA, support[0], &subp);
2088:           DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);
2089:           for (i = 0; i < totDimAux; ++i) a[f*totDimAux+i] = x[i];
2090:           DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);
2091:         }
2092:       }
2093:       /* Get blocking */
2094:       {
2095:         PetscQuadrature q;
2096:         PetscInt        numBatches, batchSize, numBlocks, blockSize;
2097:         PetscInt        Nq, Nb;

2099:         PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
2100:         PetscFEGetQuadrature(fe, &q);
2101:         PetscQuadratureGetData(q, NULL, NULL, &Nq, NULL, NULL);
2102:         PetscFEGetDimension(fe, &Nb);
2103:         blockSize = Nb*Nq;
2104:         batchSize = numBlocks * blockSize;
2105:         chunkSize = numBatches*batchSize;
2106:         PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
2107:         numChunks = numFaces / chunkSize;
2108:         Nr        = numFaces % chunkSize;
2109:         offset    = numFaces - Nr;
2110:       }
2111:       /* Do integration for each field */
2112:       for (chunk = 0; chunk < numChunks; ++chunk) {
2113:         PetscFEGeomGetChunk(fgeom, chunk*chunkSize, (chunk+1)*chunkSize, &chunkGeom);
2114:         PetscFEIntegrateBd(prob, field, func, chunkSize, chunkGeom, u, probAux, a, fintegral);
2115:         PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);
2116:       }
2117:       PetscFEGeomGetChunk(fgeom, offset, numFaces, &chunkGeom);
2118:       PetscFEIntegrateBd(prob, field, func, Nr, chunkGeom, &u[offset*totDim], probAux, a ? &a[offset*totDimAux] : NULL, &fintegral[offset*Nf]);
2119:       PetscFEGeomRestoreChunk(fgeom, offset, numFaces, &chunkGeom);
2120:       /* Cleanup data arrays */
2121:       DMPlexRestoreFEGeom(coordField, pointIS, qGeom, PETSC_TRUE, &fgeom);
2122:       PetscQuadratureDestroy(&qGeom);
2123:       PetscFree2(u, a);
2124:       ISRestoreIndices(pointIS, &points);
2125:     }
2126:   }
2127:   if (plex)  {DMDestroy(&plex);}
2128:   if (plexA) {DMDestroy(&plexA);}
2129:   return(0);
2130: }

2132: /*@
2133:   DMPlexComputeBdIntegral - Form the integral over the specified boundary from the global input X using pointwise functions specified by the user

2135:   Input Parameters:
2136: + dm      - The mesh
2137: . X       - Global input vector
2138: . label   - The boundary DMLabel
2139: . numVals - The number of label values to use, or PETSC_DETERMINE for all values
2140: . vals    - The label values to use, or PETSC_NULL for all values
2141: . func    = The function to integrate along the boundary
2142: - user    - The user context

2144:   Output Parameter:
2145: . integral - Integral for each field

2147:   Level: developer

2149: .seealso: DMPlexComputeIntegralFEM(), DMPlexComputeBdResidualFEM()
2150: @*/
2151: PetscErrorCode DMPlexComputeBdIntegral(DM dm, Vec X, DMLabel label, PetscInt numVals, const PetscInt vals[],
2152:                                        void (*func)(PetscInt, PetscInt, PetscInt,
2153:                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
2154:                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
2155:                                                     PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]),
2156:                                        PetscScalar *integral, void *user)
2157: {
2158:   Vec            locX;
2159:   PetscSection   section;
2160:   DMLabel        depthLabel;
2161:   IS             facetIS;
2162:   PetscInt       dim, Nf, f, v;

2171:   PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);
2172:   DMPlexGetDepthLabel(dm, &depthLabel);
2173:   DMGetDimension(dm, &dim);
2174:   DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
2175:   DMGetLocalSection(dm, &section);
2176:   PetscSectionGetNumFields(section, &Nf);
2177:   /* Get local solution with boundary values */
2178:   DMGetLocalVector(dm, &locX);
2179:   DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locX, 0.0, NULL, NULL, NULL);
2180:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);
2181:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);
2182:   /* Loop over label values */
2183:   PetscArrayzero(integral, Nf);
2184:   for (v = 0; v < numVals; ++v) {
2185:     IS           pointIS;
2186:     PetscInt     numFaces, face;
2187:     PetscScalar *fintegral;

2189:     DMLabelGetStratumIS(label, vals[v], &pointIS);
2190:     if (!pointIS) continue; /* No points with that id on this process */
2191:     {
2192:       IS isectIS;

2194:       /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */
2195:       ISIntersect_Caching_Internal(facetIS, pointIS, &isectIS);
2196:       ISDestroy(&pointIS);
2197:       pointIS = isectIS;
2198:     }
2199:     ISGetLocalSize(pointIS, &numFaces);
2200:     PetscCalloc1(numFaces*Nf, &fintegral);
2201:     DMPlexComputeBdIntegral_Internal(dm, locX, pointIS, func, fintegral, user);
2202:     /* Sum point contributions into integral */
2203:     for (f = 0; f < Nf; ++f) for (face = 0; face < numFaces; ++face) integral[f] += fintegral[face*Nf+f];
2204:     PetscFree(fintegral);
2205:     ISDestroy(&pointIS);
2206:   }
2207:   DMRestoreLocalVector(dm, &locX);
2208:   ISDestroy(&facetIS);
2209:   PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);
2210:   return(0);
2211: }

2213: /*@
2214:   DMPlexComputeInterpolatorNested - Form the local portion of the interpolation matrix I from the coarse DM to the uniformly refined DM.

2216:   Input Parameters:
2217: + dmf  - The fine mesh
2218: . dmc  - The coarse mesh
2219: - user - The user context

2221:   Output Parameter:
2222: . In  - The interpolation matrix

2224:   Level: developer

2226: .seealso: DMPlexComputeInterpolatorGeneral(), DMPlexComputeJacobianFEM()
2227: @*/
2228: PetscErrorCode DMPlexComputeInterpolatorNested(DM dmc, DM dmf, Mat In, void *user)
2229: {
2230:   DM_Plex          *mesh  = (DM_Plex *) dmc->data;
2231:   const char       *name  = "Interpolator";
2232:   PetscDS           prob;
2233:   PetscFE          *feRef;
2234:   PetscFV          *fvRef;
2235:   PetscSection      fsection, fglobalSection;
2236:   PetscSection      csection, cglobalSection;
2237:   PetscScalar      *elemMat;
2238:   PetscInt          dim, Nf, f, fieldI, fieldJ, offsetI, offsetJ, cStart, cEnd, c;
2239:   PetscInt          cTotDim, rTotDim = 0;
2240:   PetscErrorCode    ierr;

2243:   PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
2244:   DMGetDimension(dmf, &dim);
2245:   DMGetLocalSection(dmf, &fsection);
2246:   DMGetGlobalSection(dmf, &fglobalSection);
2247:   DMGetLocalSection(dmc, &csection);
2248:   DMGetGlobalSection(dmc, &cglobalSection);
2249:   PetscSectionGetNumFields(fsection, &Nf);
2250:   DMPlexGetInteriorCellStratum(dmc, &cStart, &cEnd);
2251:   DMGetDS(dmf, &prob);
2252:   PetscCalloc2(Nf,&feRef,Nf,&fvRef);
2253:   for (f = 0; f < Nf; ++f) {
2254:     PetscObject  obj;
2255:     PetscClassId id;
2256:     PetscInt     rNb = 0, Nc = 0;

2258:     PetscDSGetDiscretization(prob, f, &obj);
2259:     PetscObjectGetClassId(obj, &id);
2260:     if (id == PETSCFE_CLASSID) {
2261:       PetscFE fe = (PetscFE) obj;

2263:       PetscFERefine(fe, &feRef[f]);
2264:       PetscFEGetDimension(feRef[f], &rNb);
2265:       PetscFEGetNumComponents(fe, &Nc);
2266:     } else if (id == PETSCFV_CLASSID) {
2267:       PetscFV        fv = (PetscFV) obj;
2268:       PetscDualSpace Q;

2270:       PetscFVRefine(fv, &fvRef[f]);
2271:       PetscFVGetDualSpace(fvRef[f], &Q);
2272:       PetscDualSpaceGetDimension(Q, &rNb);
2273:       PetscFVGetNumComponents(fv, &Nc);
2274:     }
2275:     rTotDim += rNb;
2276:   }
2277:   PetscDSGetTotalDimension(prob, &cTotDim);
2278:   PetscMalloc1(rTotDim*cTotDim,&elemMat);
2279:   PetscArrayzero(elemMat, rTotDim*cTotDim);
2280:   for (fieldI = 0, offsetI = 0; fieldI < Nf; ++fieldI) {
2281:     PetscDualSpace   Qref;
2282:     PetscQuadrature  f;
2283:     const PetscReal *qpoints, *qweights;
2284:     PetscReal       *points;
2285:     PetscInt         npoints = 0, Nc, Np, fpdim, i, k, p, d;

2287:     /* Compose points from all dual basis functionals */
2288:     if (feRef[fieldI]) {
2289:       PetscFEGetDualSpace(feRef[fieldI], &Qref);
2290:       PetscFEGetNumComponents(feRef[fieldI], &Nc);
2291:     } else {
2292:       PetscFVGetDualSpace(fvRef[fieldI], &Qref);
2293:       PetscFVGetNumComponents(fvRef[fieldI], &Nc);
2294:     }
2295:     PetscDualSpaceGetDimension(Qref, &fpdim);
2296:     for (i = 0; i < fpdim; ++i) {
2297:       PetscDualSpaceGetFunctional(Qref, i, &f);
2298:       PetscQuadratureGetData(f, NULL, NULL, &Np, NULL, NULL);
2299:       npoints += Np;
2300:     }
2301:     PetscMalloc1(npoints*dim,&points);
2302:     for (i = 0, k = 0; i < fpdim; ++i) {
2303:       PetscDualSpaceGetFunctional(Qref, i, &f);
2304:       PetscQuadratureGetData(f, NULL, NULL, &Np, &qpoints, NULL);
2305:       for (p = 0; p < Np; ++p, ++k) for (d = 0; d < dim; ++d) points[k*dim+d] = qpoints[p*dim+d];
2306:     }

2308:     for (fieldJ = 0, offsetJ = 0; fieldJ < Nf; ++fieldJ) {
2309:       PetscObject  obj;
2310:       PetscClassId id;
2311:       PetscReal   *B;
2312:       PetscInt     NcJ = 0, cpdim = 0, j, qNc;

2314:       PetscDSGetDiscretization(prob, fieldJ, &obj);
2315:       PetscObjectGetClassId(obj, &id);
2316:       if (id == PETSCFE_CLASSID) {
2317:         PetscFE fe = (PetscFE) obj;

2319:         /* Evaluate basis at points */
2320:         PetscFEGetNumComponents(fe, &NcJ);
2321:         PetscFEGetDimension(fe, &cpdim);
2322:         /* For now, fields only interpolate themselves */
2323:         if (fieldI == fieldJ) {
2324:           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);
2325:           PetscFEGetTabulation(fe, npoints, points, &B, NULL, NULL);
2326:           for (i = 0, k = 0; i < fpdim; ++i) {
2327:             PetscDualSpaceGetFunctional(Qref, i, &f);
2328:             PetscQuadratureGetData(f, NULL, &qNc, &Np, NULL, &qweights);
2329:             if (qNc != NcJ) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in quadrature %D does not match coarse field %D", qNc, NcJ);
2330:             for (p = 0; p < Np; ++p, ++k) {
2331:               for (j = 0; j < cpdim; ++j) {
2332:                 /*
2333:                    cTotDim:            Total columns in element interpolation matrix, sum of number of dual basis functionals in each field
2334:                    offsetI, offsetJ:   Offsets into the larger element interpolation matrix for different fields
2335:                    fpdim, i, cpdim, j: Dofs for fine and coarse grids, correspond to dual space basis functionals
2336:                    qNC, Nc, Ncj, c:    Number of components in this field
2337:                    Np, p:              Number of quad points in the fine grid functional i
2338:                    k:                  i*Np + p, overall point number for the interpolation
2339:                 */
2340:                 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i)*cTotDim + offsetJ + j] += B[k*cpdim*NcJ+j*Nc+c]*qweights[p*qNc+c];
2341:               }
2342:             }
2343:           }
2344:           PetscFERestoreTabulation(fe, npoints, points, &B, NULL, NULL);
2345:         }
2346:       } else if (id == PETSCFV_CLASSID) {
2347:         PetscFV        fv = (PetscFV) obj;

2349:         /* Evaluate constant function at points */
2350:         PetscFVGetNumComponents(fv, &NcJ);
2351:         cpdim = 1;
2352:         /* For now, fields only interpolate themselves */
2353:         if (fieldI == fieldJ) {
2354:           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);
2355:           for (i = 0, k = 0; i < fpdim; ++i) {
2356:             PetscDualSpaceGetFunctional(Qref, i, &f);
2357:             PetscQuadratureGetData(f, NULL, &qNc, &Np, NULL, &qweights);
2358:             if (qNc != NcJ) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in quadrature %D does not match coarse field %D", qNc, NcJ);
2359:             for (p = 0; p < Np; ++p, ++k) {
2360:               for (j = 0; j < cpdim; ++j) {
2361:                 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i)*cTotDim + offsetJ + j] += 1.0*qweights[p*qNc+c];
2362:               }
2363:             }
2364:           }
2365:         }
2366:       }
2367:       offsetJ += cpdim;
2368:     }
2369:     offsetI += fpdim;
2370:     PetscFree(points);
2371:   }
2372:   if (mesh->printFEM > 1) {DMPrintCellMatrix(0, name, rTotDim, cTotDim, elemMat);}
2373:   /* Preallocate matrix */
2374:   {
2375:     Mat          preallocator;
2376:     PetscScalar *vals;
2377:     PetscInt    *cellCIndices, *cellFIndices;
2378:     PetscInt     locRows, locCols, cell;

2380:     MatGetLocalSize(In, &locRows, &locCols);
2381:     MatCreate(PetscObjectComm((PetscObject) In), &preallocator);
2382:     MatSetType(preallocator, MATPREALLOCATOR);
2383:     MatSetSizes(preallocator, locRows, locCols, PETSC_DETERMINE, PETSC_DETERMINE);
2384:     MatSetUp(preallocator);
2385:     PetscCalloc3(rTotDim*cTotDim, &vals,cTotDim,&cellCIndices,rTotDim,&cellFIndices);
2386:     for (cell = cStart; cell < cEnd; ++cell) {
2387:       DMPlexMatGetClosureIndicesRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, cell, cellCIndices, cellFIndices);
2388:       MatSetValues(preallocator, rTotDim, cellFIndices, cTotDim, cellCIndices, vals, INSERT_VALUES);
2389:     }
2390:     PetscFree3(vals,cellCIndices,cellFIndices);
2391:     MatAssemblyBegin(preallocator, MAT_FINAL_ASSEMBLY);
2392:     MatAssemblyEnd(preallocator, MAT_FINAL_ASSEMBLY);
2393:     MatPreallocatorPreallocate(preallocator, PETSC_TRUE, In);
2394:     MatDestroy(&preallocator);
2395:   }
2396:   /* Fill matrix */
2397:   MatZeroEntries(In);
2398:   for (c = cStart; c < cEnd; ++c) {
2399:     DMPlexMatSetClosureRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);
2400:   }
2401:   for (f = 0; f < Nf; ++f) {PetscFEDestroy(&feRef[f]);}
2402:   PetscFree2(feRef,fvRef);
2403:   PetscFree(elemMat);
2404:   MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);
2405:   MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);
2406:   if (mesh->printFEM) {
2407:     PetscPrintf(PetscObjectComm((PetscObject)In), "%s:\n", name);
2408:     MatChop(In, 1.0e-10);
2409:     MatView(In, NULL);
2410:   }
2411:   PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
2412:   return(0);
2413: }

2415: PetscErrorCode DMPlexComputeMassMatrixNested(DM dmc, DM dmf, Mat mass, void *user)
2416: {
2417:   SETERRQ(PetscObjectComm((PetscObject) dmc), PETSC_ERR_SUP, "Laziness");
2418: }

2420: /*@
2421:   DMPlexComputeInterpolatorGeneral - Form the local portion of the interpolation matrix I from the coarse DM to a non-nested fine DM.

2423:   Input Parameters:
2424: + dmf  - The fine mesh
2425: . dmc  - The coarse mesh
2426: - user - The user context

2428:   Output Parameter:
2429: . In  - The interpolation matrix

2431:   Level: developer

2433: .seealso: DMPlexComputeInterpolatorNested(), DMPlexComputeJacobianFEM()
2434: @*/
2435: PetscErrorCode DMPlexComputeInterpolatorGeneral(DM dmc, DM dmf, Mat In, void *user)
2436: {
2437:   DM_Plex       *mesh = (DM_Plex *) dmf->data;
2438:   const char    *name = "Interpolator";
2439:   PetscDS        prob;
2440:   PetscSection   fsection, csection, globalFSection, globalCSection;
2441:   PetscHSetIJ    ht;
2442:   PetscLayout    rLayout;
2443:   PetscInt      *dnz, *onz;
2444:   PetscInt       locRows, rStart, rEnd;
2445:   PetscReal     *x, *v0, *J, *invJ, detJ;
2446:   PetscReal     *v0c, *Jc, *invJc, detJc;
2447:   PetscScalar   *elemMat;
2448:   PetscInt       dim, Nf, field, totDim, cStart, cEnd, cell, ccell;

2452:   PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
2453:   DMGetCoordinateDim(dmc, &dim);
2454:   DMGetDS(dmc, &prob);
2455:   PetscDSGetWorkspace(prob, &x, NULL, NULL, NULL, NULL);
2456:   PetscDSGetNumFields(prob, &Nf);
2457:   PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);
2458:   PetscMalloc3(dim,&v0c,dim*dim,&Jc,dim*dim,&invJc);
2459:   DMGetLocalSection(dmf, &fsection);
2460:   DMGetGlobalSection(dmf, &globalFSection);
2461:   DMGetLocalSection(dmc, &csection);
2462:   DMGetGlobalSection(dmc, &globalCSection);
2463:   DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);
2464:   PetscDSGetTotalDimension(prob, &totDim);
2465:   PetscMalloc1(totDim, &elemMat);

2467:   MatGetLocalSize(In, &locRows, NULL);
2468:   PetscLayoutCreate(PetscObjectComm((PetscObject) In), &rLayout);
2469:   PetscLayoutSetLocalSize(rLayout, locRows);
2470:   PetscLayoutSetBlockSize(rLayout, 1);
2471:   PetscLayoutSetUp(rLayout);
2472:   PetscLayoutGetRange(rLayout, &rStart, &rEnd);
2473:   PetscLayoutDestroy(&rLayout);
2474:   PetscCalloc2(locRows,&dnz,locRows,&onz);
2475:   PetscHSetIJCreate(&ht);
2476:   for (field = 0; field < Nf; ++field) {
2477:     PetscObject      obj;
2478:     PetscClassId     id;
2479:     PetscDualSpace   Q = NULL;
2480:     PetscQuadrature  f;
2481:     const PetscReal *qpoints;
2482:     PetscInt         Nc, Np, fpdim, i, d;

2484:     PetscDSGetDiscretization(prob, field, &obj);
2485:     PetscObjectGetClassId(obj, &id);
2486:     if (id == PETSCFE_CLASSID) {
2487:       PetscFE fe = (PetscFE) obj;

2489:       PetscFEGetDualSpace(fe, &Q);
2490:       PetscFEGetNumComponents(fe, &Nc);
2491:     } else if (id == PETSCFV_CLASSID) {
2492:       PetscFV fv = (PetscFV) obj;

2494:       PetscFVGetDualSpace(fv, &Q);
2495:       Nc   = 1;
2496:     }
2497:     PetscDualSpaceGetDimension(Q, &fpdim);
2498:     /* For each fine grid cell */
2499:     for (cell = cStart; cell < cEnd; ++cell) {
2500:       PetscInt *findices,   *cindices;
2501:       PetscInt  numFIndices, numCIndices;

2503:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, &numFIndices, &findices, NULL);
2504:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
2505:       if (numFIndices != fpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of fine indices %D != %D dual basis vecs", numFIndices, fpdim);
2506:       for (i = 0; i < fpdim; ++i) {
2507:         Vec             pointVec;
2508:         PetscScalar    *pV;
2509:         PetscSF         coarseCellSF = NULL;
2510:         const PetscSFNode *coarseCells;
2511:         PetscInt        numCoarseCells, q, c;

2513:         /* Get points from the dual basis functional quadrature */
2514:         PetscDualSpaceGetFunctional(Q, i, &f);
2515:         PetscQuadratureGetData(f, NULL, NULL, &Np, &qpoints, NULL);
2516:         VecCreateSeq(PETSC_COMM_SELF, Np*dim, &pointVec);
2517:         VecSetBlockSize(pointVec, dim);
2518:         VecGetArray(pointVec, &pV);
2519:         for (q = 0; q < Np; ++q) {
2520:           const PetscReal xi0[3] = {-1., -1., -1.};

2522:           /* Transform point to real space */
2523:           CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
2524:           for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
2525:         }
2526:         VecRestoreArray(pointVec, &pV);
2527:         /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
2528:         /* OPT: Pack all quad points from fine cell */
2529:         DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
2530:         PetscSFViewFromOptions(coarseCellSF, NULL, "-interp_sf_view");
2531:         /* Update preallocation info */
2532:         PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
2533:         if (numCoarseCells != Np) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
2534:         {
2535:           PetscHashIJKey key;
2536:           PetscBool      missing;

2538:           key.i = findices[i];
2539:           if (key.i >= 0) {
2540:             /* Get indices for coarse elements */
2541:             for (ccell = 0; ccell < numCoarseCells; ++ccell) {
2542:               DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, &numCIndices, &cindices, NULL);
2543:               for (c = 0; c < numCIndices; ++c) {
2544:                 key.j = cindices[c];
2545:                 if (key.j < 0) continue;
2546:                 PetscHSetIJQueryAdd(ht, key, &missing);
2547:                 if (missing) {
2548:                   if ((key.j >= rStart) && (key.j < rEnd)) ++dnz[key.i-rStart];
2549:                   else                                     ++onz[key.i-rStart];
2550:                 }
2551:               }
2552:               DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, &numCIndices, &cindices, NULL);
2553:             }
2554:           }
2555:         }
2556:         PetscSFDestroy(&coarseCellSF);
2557:         VecDestroy(&pointVec);
2558:       }
2559:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, &numFIndices, &findices, NULL);
2560:     }
2561:   }
2562:   PetscHSetIJDestroy(&ht);
2563:   MatXAIJSetPreallocation(In, 1, dnz, onz, NULL, NULL);
2564:   MatSetOption(In, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
2565:   PetscFree2(dnz,onz);
2566:   for (field = 0; field < Nf; ++field) {
2567:     PetscObject      obj;
2568:     PetscClassId     id;
2569:     PetscDualSpace   Q = NULL;
2570:     PetscQuadrature  f;
2571:     const PetscReal *qpoints, *qweights;
2572:     PetscInt         Nc, qNc, Np, fpdim, i, d;

2574:     PetscDSGetDiscretization(prob, field, &obj);
2575:     PetscObjectGetClassId(obj, &id);
2576:     if (id == PETSCFE_CLASSID) {
2577:       PetscFE fe = (PetscFE) obj;

2579:       PetscFEGetDualSpace(fe, &Q);
2580:       PetscFEGetNumComponents(fe, &Nc);
2581:     } else if (id == PETSCFV_CLASSID) {
2582:       PetscFV fv = (PetscFV) obj;

2584:       PetscFVGetDualSpace(fv, &Q);
2585:       Nc   = 1;
2586:     } else SETERRQ1(PetscObjectComm((PetscObject)dmc),PETSC_ERR_ARG_WRONG,"Unknown discretization type for field %D",field);
2587:     PetscDualSpaceGetDimension(Q, &fpdim);
2588:     /* For each fine grid cell */
2589:     for (cell = cStart; cell < cEnd; ++cell) {
2590:       PetscInt *findices,   *cindices;
2591:       PetscInt  numFIndices, numCIndices;

2593:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, &numFIndices, &findices, NULL);
2594:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
2595:       if (numFIndices != fpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of fine indices %D != %D dual basis vecs", numFIndices, fpdim);
2596:       for (i = 0; i < fpdim; ++i) {
2597:         Vec             pointVec;
2598:         PetscScalar    *pV;
2599:         PetscSF         coarseCellSF = NULL;
2600:         const PetscSFNode *coarseCells;
2601:         PetscInt        numCoarseCells, cpdim, q, c, j;

2603:         /* Get points from the dual basis functional quadrature */
2604:         PetscDualSpaceGetFunctional(Q, i, &f);
2605:         PetscQuadratureGetData(f, NULL, &qNc, &Np, &qpoints, &qweights);
2606:         if (qNc != Nc) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in quadrature %D does not match coarse field %D", qNc, Nc);
2607:         VecCreateSeq(PETSC_COMM_SELF, Np*dim, &pointVec);
2608:         VecSetBlockSize(pointVec, dim);
2609:         VecGetArray(pointVec, &pV);
2610:         for (q = 0; q < Np; ++q) {
2611:           const PetscReal xi0[3] = {-1., -1., -1.};

2613:           /* Transform point to real space */
2614:           CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
2615:           for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
2616:         }
2617:         VecRestoreArray(pointVec, &pV);
2618:         /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
2619:         /* OPT: Read this out from preallocation information */
2620:         DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
2621:         /* Update preallocation info */
2622:         PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
2623:         if (numCoarseCells != Np) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
2624:         VecGetArray(pointVec, &pV);
2625:         for (ccell = 0; ccell < numCoarseCells; ++ccell) {
2626:           PetscReal pVReal[3];
2627:           const PetscReal xi0[3] = {-1., -1., -1.};

2629:           DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, &numCIndices, &cindices, NULL);
2630:           /* Transform points from real space to coarse reference space */
2631:           DMPlexComputeCellGeometryFEM(dmc, coarseCells[ccell].index, NULL, v0c, Jc, invJc, &detJc);
2632:           for (d = 0; d < dim; ++d) pVReal[d] = PetscRealPart(pV[ccell*dim+d]);
2633:           CoordinatesRealToRef(dim, dim, xi0, v0c, invJc, pVReal, x);

2635:           if (id == PETSCFE_CLASSID) {
2636:             PetscFE    fe = (PetscFE) obj;
2637:             PetscReal *B;

2639:             /* Evaluate coarse basis on contained point */
2640:             PetscFEGetDimension(fe, &cpdim);
2641:             PetscFEGetTabulation(fe, 1, x, &B, NULL, NULL);
2642:             PetscArrayzero(elemMat, cpdim);
2643:             /* Get elemMat entries by multiplying by weight */
2644:             for (j = 0; j < cpdim; ++j) {
2645:               for (c = 0; c < Nc; ++c) elemMat[j] += B[j*Nc + c]*qweights[ccell*qNc + c];
2646:             }
2647:             PetscFERestoreTabulation(fe, 1, x, &B, NULL, NULL);
2648:           } else {
2649:             cpdim = 1;
2650:             for (j = 0; j < cpdim; ++j) {
2651:               for (c = 0; c < Nc; ++c) elemMat[j] += 1.0*qweights[ccell*qNc + c];
2652:             }
2653:           }
2654:           /* Update interpolator */
2655:           if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
2656:           if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim);
2657:           MatSetValues(In, 1, &findices[i], numCIndices, cindices, elemMat, INSERT_VALUES);
2658:           DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, &numCIndices, &cindices, NULL);
2659:         }
2660:         VecRestoreArray(pointVec, &pV);
2661:         PetscSFDestroy(&coarseCellSF);
2662:         VecDestroy(&pointVec);
2663:       }
2664:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, &numFIndices, &findices, NULL);
2665:     }
2666:   }
2667:   PetscFree3(v0,J,invJ);
2668:   PetscFree3(v0c,Jc,invJc);
2669:   PetscFree(elemMat);
2670:   MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);
2671:   MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);
2672:   PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
2673:   return(0);
2674: }

2676: /*@
2677:   DMPlexComputeMassMatrixGeneral - Form the local portion of the mass matrix M from the coarse DM to a non-nested fine DM.

2679:   Input Parameters:
2680: + dmf  - The fine mesh
2681: . dmc  - The coarse mesh
2682: - user - The user context

2684:   Output Parameter:
2685: . mass  - The mass matrix

2687:   Level: developer

2689: .seealso: DMPlexComputeMassMatrixNested(), DMPlexComputeInterpolatorNested(), DMPlexComputeInterpolatorGeneral(), DMPlexComputeJacobianFEM()
2690: @*/
2691: PetscErrorCode DMPlexComputeMassMatrixGeneral(DM dmc, DM dmf, Mat mass, void *user)
2692: {
2693:   DM_Plex       *mesh = (DM_Plex *) dmf->data;
2694:   const char    *name = "Mass Matrix";
2695:   PetscDS        prob;
2696:   PetscSection   fsection, csection, globalFSection, globalCSection;
2697:   PetscHSetIJ    ht;
2698:   PetscLayout    rLayout;
2699:   PetscInt      *dnz, *onz;
2700:   PetscInt       locRows, rStart, rEnd;
2701:   PetscReal     *x, *v0, *J, *invJ, detJ;
2702:   PetscReal     *v0c, *Jc, *invJc, detJc;
2703:   PetscScalar   *elemMat;
2704:   PetscInt       dim, Nf, field, totDim, cStart, cEnd, cell, ccell;

2708:   DMGetCoordinateDim(dmc, &dim);
2709:   DMGetDS(dmc, &prob);
2710:   PetscDSGetWorkspace(prob, &x, NULL, NULL, NULL, NULL);
2711:   PetscDSGetNumFields(prob, &Nf);
2712:   PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);
2713:   PetscMalloc3(dim,&v0c,dim*dim,&Jc,dim*dim,&invJc);
2714:   DMGetLocalSection(dmf, &fsection);
2715:   DMGetGlobalSection(dmf, &globalFSection);
2716:   DMGetLocalSection(dmc, &csection);
2717:   DMGetGlobalSection(dmc, &globalCSection);
2718:   DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);
2719:   PetscDSGetTotalDimension(prob, &totDim);
2720:   PetscMalloc1(totDim, &elemMat);

2722:   MatGetLocalSize(mass, &locRows, NULL);
2723:   PetscLayoutCreate(PetscObjectComm((PetscObject) mass), &rLayout);
2724:   PetscLayoutSetLocalSize(rLayout, locRows);
2725:   PetscLayoutSetBlockSize(rLayout, 1);
2726:   PetscLayoutSetUp(rLayout);
2727:   PetscLayoutGetRange(rLayout, &rStart, &rEnd);
2728:   PetscLayoutDestroy(&rLayout);
2729:   PetscCalloc2(locRows,&dnz,locRows,&onz);
2730:   PetscHSetIJCreate(&ht);
2731:   for (field = 0; field < Nf; ++field) {
2732:     PetscObject      obj;
2733:     PetscClassId     id;
2734:     PetscQuadrature  quad;
2735:     const PetscReal *qpoints;
2736:     PetscInt         Nq, Nc, i, d;

2738:     PetscDSGetDiscretization(prob, field, &obj);
2739:     PetscObjectGetClassId(obj, &id);
2740:     if (id == PETSCFE_CLASSID) {PetscFEGetQuadrature((PetscFE) obj, &quad);}
2741:     else                       {PetscFVGetQuadrature((PetscFV) obj, &quad);}
2742:     PetscQuadratureGetData(quad, NULL, &Nc, &Nq, &qpoints, NULL);
2743:     /* For each fine grid cell */
2744:     for (cell = cStart; cell < cEnd; ++cell) {
2745:       Vec                pointVec;
2746:       PetscScalar       *pV;
2747:       PetscSF            coarseCellSF = NULL;
2748:       const PetscSFNode *coarseCells;
2749:       PetscInt           numCoarseCells, q, c;
2750:       PetscInt          *findices,   *cindices;
2751:       PetscInt           numFIndices, numCIndices;

2753:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, &numFIndices, &findices, NULL);
2754:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
2755:       /* Get points from the quadrature */
2756:       VecCreateSeq(PETSC_COMM_SELF, Nq*dim, &pointVec);
2757:       VecSetBlockSize(pointVec, dim);
2758:       VecGetArray(pointVec, &pV);
2759:       for (q = 0; q < Nq; ++q) {
2760:         const PetscReal xi0[3] = {-1., -1., -1.};

2762:         /* Transform point to real space */
2763:         CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
2764:         for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
2765:       }
2766:       VecRestoreArray(pointVec, &pV);
2767:       /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
2768:       DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
2769:       PetscSFViewFromOptions(coarseCellSF, NULL, "-interp_sf_view");
2770:       /* Update preallocation info */
2771:       PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
2772:       if (numCoarseCells != Nq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
2773:       {
2774:         PetscHashIJKey key;
2775:         PetscBool      missing;

2777:         for (i = 0; i < numFIndices; ++i) {
2778:           key.i = findices[i];
2779:           if (key.i >= 0) {
2780:             /* Get indices for coarse elements */
2781:             for (ccell = 0; ccell < numCoarseCells; ++ccell) {
2782:               DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, &numCIndices, &cindices, NULL);
2783:               for (c = 0; c < numCIndices; ++c) {
2784:                 key.j = cindices[c];
2785:                 if (key.j < 0) continue;
2786:                 PetscHSetIJQueryAdd(ht, key, &missing);
2787:                 if (missing) {
2788:                   if ((key.j >= rStart) && (key.j < rEnd)) ++dnz[key.i-rStart];
2789:                   else                                     ++onz[key.i-rStart];
2790:                 }
2791:               }
2792:               DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, &numCIndices, &cindices, NULL);
2793:             }
2794:           }
2795:         }
2796:       }
2797:       PetscSFDestroy(&coarseCellSF);
2798:       VecDestroy(&pointVec);
2799:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, &numFIndices, &findices, NULL);
2800:     }
2801:   }
2802:   PetscHSetIJDestroy(&ht);
2803:   MatXAIJSetPreallocation(mass, 1, dnz, onz, NULL, NULL);
2804:   MatSetOption(mass, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
2805:   PetscFree2(dnz,onz);
2806:   for (field = 0; field < Nf; ++field) {
2807:     PetscObject      obj;
2808:     PetscClassId     id;
2809:     PetscQuadrature  quad;
2810:     PetscReal       *Bfine;
2811:     const PetscReal *qpoints, *qweights;
2812:     PetscInt         Nq, Nc, i, d;

2814:     PetscDSGetDiscretization(prob, field, &obj);
2815:     PetscObjectGetClassId(obj, &id);
2816:     if (id == PETSCFE_CLASSID) {PetscFEGetQuadrature((PetscFE) obj, &quad);PetscFEGetDefaultTabulation((PetscFE) obj, &Bfine, NULL, NULL);}
2817:     else                       {PetscFVGetQuadrature((PetscFV) obj, &quad);}
2818:     PetscQuadratureGetData(quad, NULL, &Nc, &Nq, &qpoints, &qweights);
2819:     /* For each fine grid cell */
2820:     for (cell = cStart; cell < cEnd; ++cell) {
2821:       Vec                pointVec;
2822:       PetscScalar       *pV;
2823:       PetscSF            coarseCellSF = NULL;
2824:       const PetscSFNode *coarseCells;
2825:       PetscInt           numCoarseCells, cpdim, q, c, j;
2826:       PetscInt          *findices,   *cindices;
2827:       PetscInt           numFIndices, numCIndices;

2829:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, &numFIndices, &findices, NULL);
2830:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
2831:       /* Get points from the quadrature */
2832:       VecCreateSeq(PETSC_COMM_SELF, Nq*dim, &pointVec);
2833:       VecSetBlockSize(pointVec, dim);
2834:       VecGetArray(pointVec, &pV);
2835:       for (q = 0; q < Nq; ++q) {
2836:         const PetscReal xi0[3] = {-1., -1., -1.};

2838:         /* Transform point to real space */
2839:         CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
2840:         for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
2841:       }
2842:       VecRestoreArray(pointVec, &pV);
2843:       /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
2844:       DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
2845:       /* Update matrix */
2846:       PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
2847:       if (numCoarseCells != Nq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
2848:       VecGetArray(pointVec, &pV);
2849:       for (ccell = 0; ccell < numCoarseCells; ++ccell) {
2850:         PetscReal pVReal[3];
2851:         const PetscReal xi0[3] = {-1., -1., -1.};


2854:         DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, &numCIndices, &cindices, NULL);
2855:         /* Transform points from real space to coarse reference space */
2856:         DMPlexComputeCellGeometryFEM(dmc, coarseCells[ccell].index, NULL, v0c, Jc, invJc, &detJc);
2857:         for (d = 0; d < dim; ++d) pVReal[d] = PetscRealPart(pV[ccell*dim+d]);
2858:         CoordinatesRealToRef(dim, dim, xi0, v0c, invJc, pVReal, x);

2860:         if (id == PETSCFE_CLASSID) {
2861:           PetscFE    fe = (PetscFE) obj;
2862:           PetscReal *B;

2864:           /* Evaluate coarse basis on contained point */
2865:           PetscFEGetDimension(fe, &cpdim);
2866:           PetscFEGetTabulation(fe, 1, x, &B, NULL, NULL);
2867:           /* Get elemMat entries by multiplying by weight */
2868:           for (i = 0; i < numFIndices; ++i) {
2869:             PetscArrayzero(elemMat, cpdim);
2870:             for (j = 0; j < cpdim; ++j) {
2871:               for (c = 0; c < Nc; ++c) elemMat[j] += B[j*Nc + c]*Bfine[(ccell*numFIndices + i)*Nc + c]*qweights[ccell*Nc + c]*detJ;
2872:             }
2873:             /* Update interpolator */
2874:             if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
2875:             if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim);
2876:             MatSetValues(mass, 1, &findices[i], numCIndices, cindices, elemMat, ADD_VALUES);
2877:           }
2878:           PetscFERestoreTabulation(fe, 1, x, &B, NULL, NULL);
2879:         } else {
2880:           cpdim = 1;
2881:           for (i = 0; i < numFIndices; ++i) {
2882:             PetscArrayzero(elemMat, cpdim);
2883:             for (j = 0; j < cpdim; ++j) {
2884:               for (c = 0; c < Nc; ++c) elemMat[j] += 1.0*1.0*qweights[ccell*Nc + c]*detJ;
2885:             }
2886:             /* Update interpolator */
2887:             if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
2888:             PetscPrintf(PETSC_COMM_SELF, "Nq: %D %D Nf: %D %D Nc: %D %D\n", ccell, Nq, i, numFIndices, j, numCIndices);
2889:             if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim);
2890:             MatSetValues(mass, 1, &findices[i], numCIndices, cindices, elemMat, ADD_VALUES);
2891:           }
2892:         }
2893:         DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, &numCIndices, &cindices, NULL);
2894:       }
2895:       VecRestoreArray(pointVec, &pV);
2896:       PetscSFDestroy(&coarseCellSF);
2897:       VecDestroy(&pointVec);
2898:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, &numFIndices, &findices, NULL);
2899:     }
2900:   }
2901:   PetscFree3(v0,J,invJ);
2902:   PetscFree3(v0c,Jc,invJc);
2903:   PetscFree(elemMat);
2904:   MatAssemblyBegin(mass, MAT_FINAL_ASSEMBLY);
2905:   MatAssemblyEnd(mass, MAT_FINAL_ASSEMBLY);
2906:   return(0);
2907: }

2909: /*@
2910:   DMPlexComputeInjectorFEM - Compute a mapping from coarse unknowns to fine unknowns

2912:   Input Parameters:
2913: + dmc  - The coarse mesh
2914: - dmf  - The fine mesh
2915: - user - The user context

2917:   Output Parameter:
2918: . sc   - The mapping

2920:   Level: developer

2922: .seealso: DMPlexComputeInterpolatorNested(), DMPlexComputeJacobianFEM()
2923: @*/
2924: PetscErrorCode DMPlexComputeInjectorFEM(DM dmc, DM dmf, VecScatter *sc, void *user)
2925: {
2926:   PetscDS        prob;
2927:   PetscFE       *feRef;
2928:   PetscFV       *fvRef;
2929:   Vec            fv, cv;
2930:   IS             fis, cis;
2931:   PetscSection   fsection, fglobalSection, csection, cglobalSection;
2932:   PetscInt      *cmap, *cellCIndices, *cellFIndices, *cindices, *findices;
2933:   PetscInt       cTotDim, fTotDim = 0, Nf, f, field, cStart, cEnd, c, dim, d, startC, endC, offsetC, offsetF, m;
2934:   PetscBool     *needAvg;

2938:   PetscLogEventBegin(DMPLEX_InjectorFEM,dmc,dmf,0,0);
2939:   DMGetDimension(dmf, &dim);
2940:   DMGetLocalSection(dmf, &fsection);
2941:   DMGetGlobalSection(dmf, &fglobalSection);
2942:   DMGetLocalSection(dmc, &csection);
2943:   DMGetGlobalSection(dmc, &cglobalSection);
2944:   PetscSectionGetNumFields(fsection, &Nf);
2945:   DMPlexGetInteriorCellStratum(dmc, &cStart, &cEnd);
2946:   DMGetDS(dmc, &prob);
2947:   PetscCalloc3(Nf,&feRef,Nf,&fvRef,Nf,&needAvg);
2948:   for (f = 0; f < Nf; ++f) {
2949:     PetscObject  obj;
2950:     PetscClassId id;
2951:     PetscInt     fNb = 0, Nc = 0;

2953:     PetscDSGetDiscretization(prob, f, &obj);
2954:     PetscObjectGetClassId(obj, &id);
2955:     if (id == PETSCFE_CLASSID) {
2956:       PetscFE    fe = (PetscFE) obj;
2957:       PetscSpace sp;
2958:       PetscInt   maxDegree;

2960:       PetscFERefine(fe, &feRef[f]);
2961:       PetscFEGetDimension(feRef[f], &fNb);
2962:       PetscFEGetNumComponents(fe, &Nc);
2963:       PetscFEGetBasisSpace(fe, &sp);
2964:       PetscSpaceGetDegree(sp, NULL, &maxDegree);
2965:       if (!maxDegree) needAvg[f] = PETSC_TRUE;
2966:     } else if (id == PETSCFV_CLASSID) {
2967:       PetscFV        fv = (PetscFV) obj;
2968:       PetscDualSpace Q;

2970:       PetscFVRefine(fv, &fvRef[f]);
2971:       PetscFVGetDualSpace(fvRef[f], &Q);
2972:       PetscDualSpaceGetDimension(Q, &fNb);
2973:       PetscFVGetNumComponents(fv, &Nc);
2974:       needAvg[f] = PETSC_TRUE;
2975:     }
2976:     fTotDim += fNb;
2977:   }
2978:   PetscDSGetTotalDimension(prob, &cTotDim);
2979:   PetscMalloc1(cTotDim,&cmap);
2980:   for (field = 0, offsetC = 0, offsetF = 0; field < Nf; ++field) {
2981:     PetscFE        feC;
2982:     PetscFV        fvC;
2983:     PetscDualSpace QF, QC;
2984:     PetscInt       order = -1, NcF, NcC, fpdim, cpdim;

2986:     if (feRef[field]) {
2987:       PetscDSGetDiscretization(prob, field, (PetscObject *) &feC);
2988:       PetscFEGetNumComponents(feC, &NcC);
2989:       PetscFEGetNumComponents(feRef[field], &NcF);
2990:       PetscFEGetDualSpace(feRef[field], &QF);
2991:       PetscDualSpaceGetOrder(QF, &order);
2992:       PetscDualSpaceGetDimension(QF, &fpdim);
2993:       PetscFEGetDualSpace(feC, &QC);
2994:       PetscDualSpaceGetDimension(QC, &cpdim);
2995:     } else {
2996:       PetscDSGetDiscretization(prob, field, (PetscObject *) &fvC);
2997:       PetscFVGetNumComponents(fvC, &NcC);
2998:       PetscFVGetNumComponents(fvRef[field], &NcF);
2999:       PetscFVGetDualSpace(fvRef[field], &QF);
3000:       PetscDualSpaceGetDimension(QF, &fpdim);
3001:       PetscFVGetDualSpace(fvC, &QC);
3002:       PetscDualSpaceGetDimension(QC, &cpdim);
3003:     }
3004:     if (NcF != NcC) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of components in fine space field %D does not match coarse field %D", NcF, NcC);
3005:     for (c = 0; c < cpdim; ++c) {
3006:       PetscQuadrature  cfunc;
3007:       const PetscReal *cqpoints, *cqweights;
3008:       PetscInt         NqcC, NpC;
3009:       PetscBool        found = PETSC_FALSE;

3011:       PetscDualSpaceGetFunctional(QC, c, &cfunc);
3012:       PetscQuadratureGetData(cfunc, NULL, &NqcC, &NpC, &cqpoints, &cqweights);
3013:       if (NqcC != NcC) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of quadrature components %D must match number of field components %D", NqcC, NcC);
3014:       if (NpC != 1 && feRef[field]) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Do not know how to do injection for moments");
3015:       for (f = 0; f < fpdim; ++f) {
3016:         PetscQuadrature  ffunc;
3017:         const PetscReal *fqpoints, *fqweights;
3018:         PetscReal        sum = 0.0;
3019:         PetscInt         NqcF, NpF;

3021:         PetscDualSpaceGetFunctional(QF, f, &ffunc);
3022:         PetscQuadratureGetData(ffunc, NULL, &NqcF, &NpF, &fqpoints, &fqweights);
3023:         if (NqcF != NcF) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of quadrature components %D must match number of field components %D", NqcF, NcF);
3024:         if (NpC != NpF) continue;
3025:         for (d = 0; d < dim; ++d) sum += PetscAbsReal(cqpoints[d] - fqpoints[d]);
3026:         if (sum > 1.0e-9) continue;
3027:         for (d = 0; d < NcC; ++d) sum += PetscAbsReal(cqweights[d]*fqweights[d]);
3028:         if (sum < 1.0e-9) continue;
3029:         cmap[offsetC+c] = offsetF+f;
3030:         found = PETSC_TRUE;
3031:         break;
3032:       }
3033:       if (!found) {
3034:         /* TODO We really want the average here, but some asshole put VecScatter in the interface */
3035:         if (fvRef[field] || (feRef[field] && order == 0)) {
3036:           cmap[offsetC+c] = offsetF+0;
3037:         } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate matching functional for injection");
3038:       }
3039:     }
3040:     offsetC += cpdim;
3041:     offsetF += fpdim;
3042:   }
3043:   for (f = 0; f < Nf; ++f) {PetscFEDestroy(&feRef[f]);PetscFVDestroy(&fvRef[f]);}
3044:   PetscFree3(feRef,fvRef,needAvg);

3046:   DMGetGlobalVector(dmf, &fv);
3047:   DMGetGlobalVector(dmc, &cv);
3048:   VecGetOwnershipRange(cv, &startC, &endC);
3049:   PetscSectionGetConstrainedStorageSize(cglobalSection, &m);
3050:   PetscMalloc2(cTotDim,&cellCIndices,fTotDim,&cellFIndices);
3051:   PetscMalloc1(m,&cindices);
3052:   PetscMalloc1(m,&findices);
3053:   for (d = 0; d < m; ++d) cindices[d] = findices[d] = -1;
3054:   for (c = cStart; c < cEnd; ++c) {
3055:     DMPlexMatGetClosureIndicesRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, c, cellCIndices, cellFIndices);
3056:     for (d = 0; d < cTotDim; ++d) {
3057:       if ((cellCIndices[d] < startC) || (cellCIndices[d] >= endC)) continue;
3058:       if ((findices[cellCIndices[d]-startC] >= 0) && (findices[cellCIndices[d]-startC] != cellFIndices[cmap[d]])) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Coarse dof %D maps to both %D and %D", cindices[cellCIndices[d]-startC], findices[cellCIndices[d]-startC], cellFIndices[cmap[d]]);
3059:       cindices[cellCIndices[d]-startC] = cellCIndices[d];
3060:       findices[cellCIndices[d]-startC] = cellFIndices[cmap[d]];
3061:     }
3062:   }
3063:   PetscFree(cmap);
3064:   PetscFree2(cellCIndices,cellFIndices);

3066:   ISCreateGeneral(PETSC_COMM_SELF, m, cindices, PETSC_OWN_POINTER, &cis);
3067:   ISCreateGeneral(PETSC_COMM_SELF, m, findices, PETSC_OWN_POINTER, &fis);
3068:   VecScatterCreate(cv, cis, fv, fis, sc);
3069:   ISDestroy(&cis);
3070:   ISDestroy(&fis);
3071:   DMRestoreGlobalVector(dmf, &fv);
3072:   DMRestoreGlobalVector(dmc, &cv);
3073:   PetscLogEventEnd(DMPLEX_InjectorFEM,dmc,dmf,0,0);
3074:   return(0);
3075: }

3077: /*@C
3078:   DMPlexGetCellFields - Retrieve the field values values for a chunk of cells

3080:   Input Parameters:
3081: + dm     - The DM
3082: . cellIS - The cells to include
3083: . locX   - A local vector with the solution fields
3084: . locX_t - A local vector with solution field time derivatives, or NULL
3085: - locA   - A local vector with auxiliary fields, or NULL

3087:   Output Parameters:
3088: + u   - The field coefficients
3089: . u_t - The fields derivative coefficients
3090: - a   - The auxiliary field coefficients

3092:   Level: developer

3094: .seealso: DMPlexGetFaceFields()
3095: @*/
3096: PetscErrorCode DMPlexGetCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a)
3097: {
3098:   DM              plex, plexA = NULL;
3099:   PetscSection    section, sectionAux;
3100:   PetscDS         prob;
3101:   const PetscInt *cells;
3102:   PetscInt        cStart, cEnd, numCells, totDim, totDimAux, c;
3103:   PetscErrorCode  ierr;

3113:   DMPlexConvertPlex(dm, &plex, PETSC_FALSE);
3114:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
3115:   DMGetLocalSection(dm, &section);
3116:   DMGetCellDS(dm, cStart, &prob);
3117:   PetscDSGetTotalDimension(prob, &totDim);
3118:   if (locA) {
3119:     DM      dmAux;
3120:     PetscDS probAux;

3122:     VecGetDM(locA, &dmAux);
3123:     DMPlexConvertPlex(dmAux, &plexA, PETSC_FALSE);
3124:     DMGetLocalSection(dmAux, &sectionAux);
3125:     DMGetDS(dmAux, &probAux);
3126:     PetscDSGetTotalDimension(probAux, &totDimAux);
3127:   }
3128:   numCells = cEnd - cStart;
3129:   DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u);
3130:   if (locX_t) {DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u_t);} else {*u_t = NULL;}
3131:   if (locA)   {DMGetWorkArray(dm, numCells*totDimAux, MPIU_SCALAR, a);} else {*a = NULL;}
3132:   for (c = cStart; c < cEnd; ++c) {
3133:     const PetscInt cell = cells ? cells[c] : c;
3134:     const PetscInt cind = c - cStart;
3135:     PetscScalar   *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a;
3136:     PetscInt       i;

3138:     DMPlexVecGetClosure(plex, section, locX, cell, NULL, &x);
3139:     for (i = 0; i < totDim; ++i) ul[cind*totDim+i] = x[i];
3140:     DMPlexVecRestoreClosure(plex, section, locX, cell, NULL, &x);
3141:     if (locX_t) {
3142:       DMPlexVecGetClosure(plex, section, locX_t, cell, NULL, &x_t);
3143:       for (i = 0; i < totDim; ++i) ul_t[cind*totDim+i] = x_t[i];
3144:       DMPlexVecRestoreClosure(plex, section, locX_t, cell, NULL, &x_t);
3145:     }
3146:     if (locA) {
3147:       PetscInt subcell;
3148:       DMPlexGetAuxiliaryPoint(plex, plexA, cell, &subcell);
3149:       DMPlexVecGetClosure(plexA, sectionAux, locA, subcell, NULL, &x);
3150:       for (i = 0; i < totDimAux; ++i) al[cind*totDimAux+i] = x[i];
3151:       DMPlexVecRestoreClosure(plexA, sectionAux, locA, subcell, NULL, &x);
3152:     }
3153:   }
3154:   DMDestroy(&plex);
3155:   if (locA) {DMDestroy(&plexA);}
3156:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
3157:   return(0);
3158: }

3160: /*@C
3161:   DMPlexRestoreCellFields - Restore the field values values for a chunk of cells

3163:   Input Parameters:
3164: + dm     - The DM
3165: . cellIS - The cells to include
3166: . locX   - A local vector with the solution fields
3167: . locX_t - A local vector with solution field time derivatives, or NULL
3168: - locA   - A local vector with auxiliary fields, or NULL

3170:   Output Parameters:
3171: + u   - The field coefficients
3172: . u_t - The fields derivative coefficients
3173: - a   - The auxiliary field coefficients

3175:   Level: developer

3177: .seealso: DMPlexGetFaceFields()
3178: @*/
3179: PetscErrorCode DMPlexRestoreCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a)
3180: {

3184:   DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u);
3185:   if (locX_t) {DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u_t);}
3186:   if (locA)   {DMRestoreWorkArray(dm, 0, MPIU_SCALAR, a);}
3187:   return(0);
3188: }

3190: /*@C
3191:   DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces

3193:   Input Parameters:
3194: + dm     - The DM
3195: . fStart - The first face to include
3196: . fEnd   - The first face to exclude
3197: . locX   - A local vector with the solution fields
3198: . locX_t - A local vector with solution field time derivatives, or NULL
3199: . faceGeometry - A local vector with face geometry
3200: . cellGeometry - A local vector with cell geometry
3201: - locaGrad - A local vector with field gradients, or NULL

3203:   Output Parameters:
3204: + Nface - The number of faces with field values
3205: . uL - The field values at the left side of the face
3206: - uR - The field values at the right side of the face

3208:   Level: developer

3210: .seealso: DMPlexGetCellFields()
3211: @*/
3212: PetscErrorCode DMPlexGetFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscInt *Nface, PetscScalar **uL, PetscScalar **uR)
3213: {
3214:   DM                 dmFace, dmCell, dmGrad = NULL;
3215:   PetscSection       section;
3216:   PetscDS            prob;
3217:   DMLabel            ghostLabel;
3218:   const PetscScalar *facegeom, *cellgeom, *x, *lgrad;
3219:   PetscBool         *isFE;
3220:   PetscInt           dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face;
3221:   PetscErrorCode     ierr;

3232:   DMGetDimension(dm, &dim);
3233:   DMGetDS(dm, &prob);
3234:   DMGetLocalSection(dm, &section);
3235:   PetscDSGetNumFields(prob, &Nf);
3236:   PetscDSGetTotalComponents(prob, &Nc);
3237:   PetscMalloc1(Nf, &isFE);
3238:   for (f = 0; f < Nf; ++f) {
3239:     PetscObject  obj;
3240:     PetscClassId id;

3242:     PetscDSGetDiscretization(prob, f, &obj);
3243:     PetscObjectGetClassId(obj, &id);
3244:     if (id == PETSCFE_CLASSID)      {isFE[f] = PETSC_TRUE;}
3245:     else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;}
3246:     else                            {isFE[f] = PETSC_FALSE;}
3247:   }
3248:   DMGetLabel(dm, "ghost", &ghostLabel);
3249:   VecGetArrayRead(locX, &x);
3250:   VecGetDM(faceGeometry, &dmFace);
3251:   VecGetArrayRead(faceGeometry, &facegeom);
3252:   VecGetDM(cellGeometry, &dmCell);
3253:   VecGetArrayRead(cellGeometry, &cellgeom);
3254:   if (locGrad) {
3255:     VecGetDM(locGrad, &dmGrad);
3256:     VecGetArrayRead(locGrad, &lgrad);
3257:   }
3258:   DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uL);
3259:   DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uR);
3260:   /* Right now just eat the extra work for FE (could make a cell loop) */
3261:   for (face = fStart, iface = 0; face < fEnd; ++face) {
3262:     const PetscInt        *cells;
3263:     PetscFVFaceGeom       *fg;
3264:     PetscFVCellGeom       *cgL, *cgR;
3265:     PetscScalar           *xL, *xR, *gL, *gR;
3266:     PetscScalar           *uLl = *uL, *uRl = *uR;
3267:     PetscInt               ghost, nsupp, nchild;

3269:     DMLabelGetValue(ghostLabel, face, &ghost);
3270:     DMPlexGetSupportSize(dm, face, &nsupp);
3271:     DMPlexGetTreeChildren(dm, face, &nchild, NULL);
3272:     if (ghost >= 0 || nsupp > 2 || nchild > 0) continue;
3273:     DMPlexPointLocalRead(dmFace, face, facegeom, &fg);
3274:     DMPlexGetSupport(dm, face, &cells);
3275:     DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);
3276:     DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);
3277:     for (f = 0; f < Nf; ++f) {
3278:       PetscInt off;

3280:       PetscDSGetComponentOffset(prob, f, &off);
3281:       if (isFE[f]) {
3282:         const PetscInt *cone;
3283:         PetscInt        comp, coneSizeL, coneSizeR, faceLocL, faceLocR, ldof, rdof, d;

3285:         xL = xR = NULL;
3286:         PetscSectionGetFieldComponents(section, f, &comp);
3287:         DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);
3288:         DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);
3289:         DMPlexGetCone(dm, cells[0], &cone);
3290:         DMPlexGetConeSize(dm, cells[0], &coneSizeL);
3291:         for (faceLocL = 0; faceLocL < coneSizeL; ++faceLocL) if (cone[faceLocL] == face) break;
3292:         DMPlexGetCone(dm, cells[1], &cone);
3293:         DMPlexGetConeSize(dm, cells[1], &coneSizeR);
3294:         for (faceLocR = 0; faceLocR < coneSizeR; ++faceLocR) if (cone[faceLocR] == face) break;
3295:         if (faceLocL == coneSizeL && faceLocR == coneSizeR) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of cell %D or cell %D", face, cells[0], cells[1]);
3296:         /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */
3297:         /* TODO: this is a hack that might not be right for nonconforming */
3298:         if (faceLocL < coneSizeL) {
3299:           PetscFEEvaluateFaceFields_Internal(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);
3300:           if (rdof == ldof && faceLocR < coneSizeR) {PetscFEEvaluateFaceFields_Internal(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);}
3301:           else              {for(d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];}
3302:         }
3303:         else {
3304:           PetscFEEvaluateFaceFields_Internal(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);
3305:           PetscSectionGetFieldComponents(section, f, &comp);
3306:           for(d = 0; d < comp; ++d) uLl[iface*Nc+off+d] = uRl[iface*Nc+off+d];
3307:         }
3308:         DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);
3309:         DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);
3310:       } else {
3311:         PetscFV  fv;
3312:         PetscInt numComp, c;

3314:         PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);
3315:         PetscFVGetNumComponents(fv, &numComp);
3316:         DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);
3317:         DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);
3318:         if (dmGrad) {
3319:           PetscReal dxL[3], dxR[3];

3321:           DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);
3322:           DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);
3323:           DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL);
3324:           DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR);
3325:           for (c = 0; c < numComp; ++c) {
3326:             uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL);
3327:             uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR);
3328:           }
3329:         } else {
3330:           for (c = 0; c < numComp; ++c) {
3331:             uLl[iface*Nc+off+c] = xL[c];
3332:             uRl[iface*Nc+off+c] = xR[c];
3333:           }
3334:         }
3335:       }
3336:     }
3337:     ++iface;
3338:   }
3339:   *Nface = iface;
3340:   VecRestoreArrayRead(locX, &x);
3341:   VecRestoreArrayRead(faceGeometry, &facegeom);
3342:   VecRestoreArrayRead(cellGeometry, &cellgeom);
3343:   if (locGrad) {
3344:     VecRestoreArrayRead(locGrad, &lgrad);
3345:   }
3346:   PetscFree(isFE);
3347:   return(0);
3348: }

3350: /*@C
3351:   DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces

3353:   Input Parameters:
3354: + dm     - The DM
3355: . fStart - The first face to include
3356: . fEnd   - The first face to exclude
3357: . locX   - A local vector with the solution fields
3358: . locX_t - A local vector with solution field time derivatives, or NULL
3359: . faceGeometry - A local vector with face geometry
3360: . cellGeometry - A local vector with cell geometry
3361: - locaGrad - A local vector with field gradients, or NULL

3363:   Output Parameters:
3364: + Nface - The number of faces with field values
3365: . uL - The field values at the left side of the face
3366: - uR - The field values at the right side of the face

3368:   Level: developer

3370: .seealso: DMPlexGetFaceFields()
3371: @*/
3372: PetscErrorCode DMPlexRestoreFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscInt *Nface, PetscScalar **uL, PetscScalar **uR)
3373: {

3377:   DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uL);
3378:   DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uR);
3379:   return(0);
3380: }

3382: /*@C
3383:   DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces

3385:   Input Parameters:
3386: + dm     - The DM
3387: . fStart - The first face to include
3388: . fEnd   - The first face to exclude
3389: . faceGeometry - A local vector with face geometry
3390: - cellGeometry - A local vector with cell geometry

3392:   Output Parameters:
3393: + Nface - The number of faces with field values
3394: . fgeom - The extract the face centroid and normal
3395: - vol   - The cell volume

3397:   Level: developer

3399: .seealso: DMPlexGetCellFields()
3400: @*/
3401: PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol)
3402: {
3403:   DM                 dmFace, dmCell;
3404:   DMLabel            ghostLabel;
3405:   const PetscScalar *facegeom, *cellgeom;
3406:   PetscInt           dim, numFaces = fEnd - fStart, iface, face;
3407:   PetscErrorCode     ierr;

3415:   DMGetDimension(dm, &dim);
3416:   DMGetLabel(dm, "ghost", &ghostLabel);
3417:   VecGetDM(faceGeometry, &dmFace);
3418:   VecGetArrayRead(faceGeometry, &facegeom);
3419:   VecGetDM(cellGeometry, &dmCell);
3420:   VecGetArrayRead(cellGeometry, &cellgeom);
3421:   PetscMalloc1(numFaces, fgeom);
3422:   DMGetWorkArray(dm, numFaces*2, MPIU_SCALAR, vol);
3423:   for (face = fStart, iface = 0; face < fEnd; ++face) {
3424:     const PetscInt        *cells;
3425:     PetscFVFaceGeom       *fg;
3426:     PetscFVCellGeom       *cgL, *cgR;
3427:     PetscFVFaceGeom       *fgeoml = *fgeom;
3428:     PetscReal             *voll   = *vol;
3429:     PetscInt               ghost, d, nchild, nsupp;

3431:     DMLabelGetValue(ghostLabel, face, &ghost);
3432:     DMPlexGetSupportSize(dm, face, &nsupp);
3433:     DMPlexGetTreeChildren(dm, face, &nchild, NULL);
3434:     if (ghost >= 0 || nsupp > 2 || nchild > 0) continue;
3435:     DMPlexPointLocalRead(dmFace, face, facegeom, &fg);
3436:     DMPlexGetSupport(dm, face, &cells);
3437:     DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);
3438:     DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);
3439:     for (d = 0; d < dim; ++d) {
3440:       fgeoml[iface].centroid[d] = fg->centroid[d];
3441:       fgeoml[iface].normal[d]   = fg->normal[d];
3442:     }
3443:     voll[iface*2+0] = cgL->volume;
3444:     voll[iface*2+1] = cgR->volume;
3445:     ++iface;
3446:   }
3447:   *Nface = iface;
3448:   VecRestoreArrayRead(faceGeometry, &facegeom);
3449:   VecRestoreArrayRead(cellGeometry, &cellgeom);
3450:   return(0);
3451: }

3453: /*@C
3454:   DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces

3456:   Input Parameters:
3457: + dm     - The DM
3458: . fStart - The first face to include
3459: . fEnd   - The first face to exclude
3460: . faceGeometry - A local vector with face geometry
3461: - cellGeometry - A local vector with cell geometry

3463:   Output Parameters:
3464: + Nface - The number of faces with field values
3465: . fgeom - The extract the face centroid and normal
3466: - vol   - The cell volume

3468:   Level: developer

3470: .seealso: DMPlexGetFaceFields()
3471: @*/
3472: PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol)
3473: {

3477:   PetscFree(*fgeom);
3478:   DMRestoreWorkArray(dm, 0, MPIU_REAL, vol);
3479:   return(0);
3480: }

3482: PetscErrorCode DMSNESGetFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom)
3483: {
3484:   char            composeStr[33] = {0};
3485:   PetscObjectId   id;
3486:   PetscContainer  container;
3487:   PetscErrorCode  ierr;

3490:   PetscObjectGetId((PetscObject)quad,&id);
3491:   PetscSNPrintf(composeStr, 32, "DMSNESGetFEGeom_%x\n", id);
3492:   PetscObjectQuery((PetscObject) pointIS, composeStr, (PetscObject *) &container);
3493:   if (container) {
3494:     PetscContainerGetPointer(container, (void **) geom);
3495:   } else {
3496:     DMFieldCreateFEGeom(coordField, pointIS, quad, faceData, geom);
3497:     PetscContainerCreate(PETSC_COMM_SELF,&container);
3498:     PetscContainerSetPointer(container, (void *) *geom);
3499:     PetscContainerSetUserDestroy(container, PetscContainerUserDestroy_PetscFEGeom);
3500:     PetscObjectCompose((PetscObject) pointIS, composeStr, (PetscObject) container);
3501:     PetscContainerDestroy(&container);
3502:   }
3503:   return(0);
3504: }

3506: PetscErrorCode DMSNESRestoreFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom)
3507: {
3509:   *geom = NULL;
3510:   return(0);
3511: }

3513: PetscErrorCode DMPlexComputeResidual_Patch_Internal(DM dm, PetscSection section, IS cellIS, PetscReal t, Vec locX, Vec locX_t, Vec locF, void *user)
3514: {
3515:   DM_Plex         *mesh       = (DM_Plex *) dm->data;
3516:   const char      *name       = "Residual";
3517:   DM               dmAux      = NULL;
3518:   DMLabel          ghostLabel = NULL;
3519:   PetscDS          prob       = NULL;
3520:   PetscDS          probAux    = NULL;
3521:   PetscBool        useFEM     = PETSC_FALSE;
3522:   PetscBool        isImplicit = (locX_t || t == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE;
3523:   DMField          coordField = NULL;
3524:   Vec              locA;
3525:   PetscScalar     *u = NULL, *u_t, *a, *uL = NULL, *uR = NULL;
3526:   IS               chunkIS;
3527:   const PetscInt  *cells;
3528:   PetscInt         cStart, cEnd, numCells;
3529:   PetscInt         Nf, f, totDim, totDimAux, numChunks, cellChunkSize, chunk, fStart, fEnd;
3530:   PetscInt         maxDegree = PETSC_MAX_INT;
3531:   PetscQuadrature  affineQuad = NULL, *quads = NULL;
3532:   PetscFEGeom     *affineGeom = NULL, **geoms = NULL;
3533:   PetscErrorCode   ierr;

3536:   PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);
3537:   /* FEM+FVM */
3538:   /* 1: Get sizes from dm and dmAux */
3539:   DMGetLabel(dm, "ghost", &ghostLabel);
3540:   DMGetDS(dm, &prob);
3541:   PetscDSGetNumFields(prob, &Nf);
3542:   PetscDSGetTotalDimension(prob, &totDim);
3543:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
3544:   if (locA) {
3545:     VecGetDM(locA, &dmAux);
3546:     DMGetDS(dmAux, &probAux);
3547:     PetscDSGetTotalDimension(probAux, &totDimAux);
3548:   }
3549:   /* 2: Get geometric data */
3550:   for (f = 0; f < Nf; ++f) {
3551:     PetscObject  obj;
3552:     PetscClassId id;
3553:     PetscBool    fimp;

3555:     PetscDSGetImplicit(prob, f, &fimp);
3556:     if (isImplicit != fimp) continue;
3557:     PetscDSGetDiscretization(prob, f, &obj);
3558:     PetscObjectGetClassId(obj, &id);
3559:     if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;}
3560:     if (id == PETSCFV_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Use of FVM with PCPATCH not yet implemented");
3561:   }
3562:   if (useFEM) {
3563:     DMGetCoordinateField(dm, &coordField);
3564:     DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
3565:     if (maxDegree <= 1) {
3566:       DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);
3567:       if (affineQuad) {
3568:         DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
3569:       }
3570:     } else {
3571:       PetscCalloc2(Nf,&quads,Nf,&geoms);
3572:       for (f = 0; f < Nf; ++f) {
3573:         PetscObject  obj;
3574:         PetscClassId id;
3575:         PetscBool    fimp;

3577:         PetscDSGetImplicit(prob, f, &fimp);
3578:         if (isImplicit != fimp) continue;
3579:         PetscDSGetDiscretization(prob, f, &obj);
3580:         PetscObjectGetClassId(obj, &id);
3581:         if (id == PETSCFE_CLASSID) {
3582:           PetscFE fe = (PetscFE) obj;

3584:           PetscFEGetQuadrature(fe, &quads[f]);
3585:           PetscObjectReference((PetscObject)quads[f]);
3586:           DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
3587:         }
3588:       }
3589:     }
3590:   }
3591:   /* Loop over chunks */
3592:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
3593:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
3594:   if (useFEM) {ISCreate(PETSC_COMM_SELF, &chunkIS);}
3595:   numCells      = cEnd - cStart;
3596:   numChunks     = 1;
3597:   cellChunkSize = numCells/numChunks;
3598:   numChunks     = PetscMin(1,numCells);
3599:   for (chunk = 0; chunk < numChunks; ++chunk) {
3600:     PetscScalar     *elemVec, *fluxL = NULL, *fluxR = NULL;
3601:     PetscReal       *vol = NULL;
3602:     PetscFVFaceGeom *fgeom = NULL;
3603:     PetscInt         cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c;
3604:     PetscInt         numFaces = 0;

3606:     /* Extract field coefficients */
3607:     if (useFEM) {
3608:       ISGetPointSubrange(chunkIS, cS, cE, cells);
3609:       DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
3610:       DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
3611:       PetscArrayzero(elemVec, numCells*totDim);
3612:     }
3613:     /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */
3614:     /* Loop over fields */
3615:     for (f = 0; f < Nf; ++f) {
3616:       PetscObject  obj;
3617:       PetscClassId id;
3618:       PetscBool    fimp;
3619:       PetscInt     numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset;

3621:       PetscDSGetImplicit(prob, f, &fimp);
3622:       if (isImplicit != fimp) continue;
3623:       PetscDSGetDiscretization(prob, f, &obj);
3624:       PetscObjectGetClassId(obj, &id);
3625:       if (id == PETSCFE_CLASSID) {
3626:         PetscFE         fe = (PetscFE) obj;
3627:         PetscFEGeom    *geom = affineGeom ? affineGeom : geoms[f];
3628:         PetscFEGeom    *chunkGeom = NULL;
3629:         PetscQuadrature quad = affineQuad ? affineQuad : quads[f];
3630:         PetscInt        Nq, Nb;

3632:         PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
3633:         PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);
3634:         PetscFEGetDimension(fe, &Nb);
3635:         blockSize = Nb;
3636:         batchSize = numBlocks * blockSize;
3637:         PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
3638:         numChunks = numCells / (numBatches*batchSize);
3639:         Ne        = numChunks*numBatches*batchSize;
3640:         Nr        = numCells % (numBatches*batchSize);
3641:         offset    = numCells - Nr;
3642:         /* Integrate FE residual to get elemVec (need fields at quadrature points) */
3643:         /*   For FV, I think we use a P0 basis and the cell coefficients (for subdivided cells, we can tweak the basis tabulation to be the indicator function) */
3644:         PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
3645:         PetscFEIntegrateResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);
3646:         PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);
3647:         PetscFEIntegrateResidual(prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);
3648:         PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);
3649:       } else if (id == PETSCFV_CLASSID) {
3650:         PetscFV fv = (PetscFV) obj;

3652:         Ne = numFaces;
3653:         /* Riemann solve over faces (need fields at face centroids) */
3654:         /*   We need to evaluate FE fields at those coordinates */
3655:         PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);
3656:       } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f);
3657:     }
3658:     /* Loop over domain */
3659:     if (useFEM) {
3660:       /* Add elemVec to locX */
3661:       for (c = cS; c < cE; ++c) {
3662:         const PetscInt cell = cells ? cells[c] : c;
3663:         const PetscInt cind = c - cStart;

3665:         if (mesh->printFEM > 1) {DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);}
3666:         if (ghostLabel) {
3667:           PetscInt ghostVal;

3669:           DMLabelGetValue(ghostLabel,cell,&ghostVal);
3670:           if (ghostVal > 0) continue;
3671:         }
3672:         DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);
3673:       }
3674:     }
3675:     /* Handle time derivative */
3676:     if (locX_t) {
3677:       PetscScalar *x_t, *fa;

3679:       VecGetArray(locF, &fa);
3680:       VecGetArray(locX_t, &x_t);
3681:       for (f = 0; f < Nf; ++f) {
3682:         PetscFV      fv;
3683:         PetscObject  obj;
3684:         PetscClassId id;
3685:         PetscInt     pdim, d;

3687:         PetscDSGetDiscretization(prob, f, &obj);
3688:         PetscObjectGetClassId(obj, &id);
3689:         if (id != PETSCFV_CLASSID) continue;
3690:         fv   = (PetscFV) obj;
3691:         PetscFVGetNumComponents(fv, &pdim);
3692:         for (c = cS; c < cE; ++c) {
3693:           const PetscInt cell = cells ? cells[c] : c;
3694:           PetscScalar   *u_t, *r;

3696:           if (ghostLabel) {
3697:             PetscInt ghostVal;

3699:             DMLabelGetValue(ghostLabel, cell, &ghostVal);
3700:             if (ghostVal > 0) continue;
3701:           }
3702:           DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);
3703:           DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);
3704:           for (d = 0; d < pdim; ++d) r[d] += u_t[d];
3705:         }
3706:       }
3707:       VecRestoreArray(locX_t, &x_t);
3708:       VecRestoreArray(locF, &fa);
3709:     }
3710:     if (useFEM) {
3711:       DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
3712:       DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
3713:     }
3714:   }
3715:   if (useFEM) {ISDestroy(&chunkIS);}
3716:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
3717:   /* TODO Could include boundary residual here (see DMPlexComputeResidual_Internal) */
3718:   if (useFEM) {
3719:     if (maxDegree <= 1) {
3720:       DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
3721:       PetscQuadratureDestroy(&affineQuad);
3722:     } else {
3723:       for (f = 0; f < Nf; ++f) {
3724:         DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
3725:         PetscQuadratureDestroy(&quads[f]);
3726:       }
3727:       PetscFree2(quads,geoms);
3728:     }
3729:   }
3730:   PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);
3731:   return(0);
3732: }

3734: /*
3735:   We always assemble JacP, and if the matrix is different from Jac and two different sets of point functions are provided, we also assemble Jac

3737:   X   - The local solution vector
3738:   X_t - The local solution time derviative vector, or NULL
3739: */
3740: PetscErrorCode DMPlexComputeJacobian_Patch_Internal(DM dm, PetscSection section, PetscSection globalSection, IS cellIS,
3741:                                                     PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP, void *ctx)
3742: {
3743:   DM_Plex         *mesh  = (DM_Plex *) dm->data;
3744:   const char      *name = "Jacobian", *nameP = "JacobianPre";
3745:   DM               dmAux = NULL;
3746:   PetscDS          prob,   probAux = NULL;
3747:   PetscSection     sectionAux = NULL;
3748:   Vec              A;
3749:   DMField          coordField;
3750:   PetscFEGeom     *cgeomFEM;
3751:   PetscQuadrature  qGeom = NULL;
3752:   Mat              J = Jac, JP = JacP;
3753:   PetscScalar     *work, *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL, *elemMatP = NULL, *elemMatD = NULL;
3754:   PetscBool        hasJac, hasPrec, hasDyn, assembleJac, isMatIS, isMatISP, *isFE, hasFV = PETSC_FALSE;
3755:   const PetscInt  *cells;
3756:   PetscInt         Nf, fieldI, fieldJ, maxDegree, numCells, cStart, cEnd, numChunks, chunkSize, chunk, totDim, totDimAux = 0, sz, wsz, off = 0, offCell = 0;
3757:   PetscErrorCode   ierr;

3760:   CHKMEMQ;
3761:   ISGetLocalSize(cellIS, &numCells);
3762:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
3763:   PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);
3764:   DMGetDS(dm, &prob);
3765:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
3766:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
3767:   if (dmAux) {
3768:     DMGetLocalSection(dmAux, &sectionAux);
3769:     DMGetDS(dmAux, &probAux);
3770:   }
3771:   /* Get flags */
3772:   PetscDSGetNumFields(prob, &Nf);
3773:   DMGetWorkArray(dm, Nf, MPIU_BOOL, &isFE);
3774:   for (fieldI = 0; fieldI < Nf; ++fieldI) {
3775:     PetscObject  disc;
3776:     PetscClassId id;
3777:     PetscDSGetDiscretization(prob, fieldI, &disc);
3778:     PetscObjectGetClassId(disc, &id);
3779:     if (id == PETSCFE_CLASSID)      {isFE[fieldI] = PETSC_TRUE;}
3780:     else if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; isFE[fieldI] = PETSC_FALSE;}
3781:   }
3782:   PetscDSHasJacobian(prob, &hasJac);
3783:   PetscDSHasJacobianPreconditioner(prob, &hasPrec);
3784:   PetscDSHasDynamicJacobian(prob, &hasDyn);
3785:   assembleJac = hasJac && hasPrec && (Jac != JacP) ? PETSC_TRUE : PETSC_FALSE;
3786:   hasDyn      = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE;
3787:   PetscObjectTypeCompare((PetscObject) Jac,  MATIS, &isMatIS);
3788:   PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
3789:   /* Setup input data and temp arrays (should be DMGetWorkArray) */
3790:   if (isMatISP || isMatISP) {DMPlexGetSubdomainSection(dm, &globalSection);}
3791:   if (isMatIS)  {MatISGetLocalMat(Jac,  &J);}
3792:   if (isMatISP) {MatISGetLocalMat(JacP, &JP);}
3793:   if (hasFV)    {MatSetOption(JP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);} /* No allocated space for FV stuff, so ignore the zero entries */
3794:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
3795:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
3796:   PetscDSGetTotalDimension(prob, &totDim);
3797:   if (probAux) {PetscDSGetTotalDimension(probAux, &totDimAux);}
3798:   CHKMEMQ;
3799:   /* Compute batch sizes */
3800:   if (isFE[0]) {
3801:     PetscFE         fe;
3802:     PetscQuadrature q;
3803:     PetscInt        numQuadPoints, numBatches, batchSize, numBlocks, blockSize, Nb;

3805:     PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);
3806:     PetscFEGetQuadrature(fe, &q);
3807:     PetscQuadratureGetData(q, NULL, NULL, &numQuadPoints, NULL, NULL);
3808:     PetscFEGetDimension(fe, &Nb);
3809:     PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
3810:     blockSize = Nb*numQuadPoints;
3811:     batchSize = numBlocks  * blockSize;
3812:     chunkSize = numBatches * batchSize;
3813:     numChunks = numCells / chunkSize + numCells % chunkSize;
3814:     PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
3815:   } else {
3816:     chunkSize = numCells;
3817:     numChunks = 1;
3818:   }
3819:   /* Get work space */
3820:   wsz  = (((X?1:0) + (X_t?1:0) + (dmAux?1:0))*totDim + ((hasJac?1:0) + (hasPrec?1:0) + (hasDyn?1:0))*totDim*totDim)*chunkSize;
3821:   DMGetWorkArray(dm, wsz, MPIU_SCALAR, &work);
3822:   PetscArrayzero(work, wsz);
3823:   off      = 0;
3824:   u        = X       ? (sz = chunkSize*totDim,        off += sz, work+off-sz) : NULL;
3825:   u_t      = X_t     ? (sz = chunkSize*totDim,        off += sz, work+off-sz) : NULL;
3826:   a        = dmAux   ? (sz = chunkSize*totDimAux,     off += sz, work+off-sz) : NULL;
3827:   elemMat  = hasJac  ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL;
3828:   elemMatP = hasPrec ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL;
3829:   elemMatD = hasDyn  ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL;
3830:   if (off != wsz) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Error is workspace size %D should be %D", off, wsz);
3831:   /* Setup geometry */
3832:   DMGetCoordinateField(dm, &coordField);
3833:   DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);
3834:   if (maxDegree <= 1) {DMFieldCreateDefaultQuadrature(coordField, cellIS, &qGeom);}
3835:   if (!qGeom) {
3836:     PetscFE fe;

3838:     PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);
3839:     PetscFEGetQuadrature(fe, &qGeom);
3840:     PetscObjectReference((PetscObject) qGeom);
3841:   }
3842:   DMSNESGetFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);
3843:   /* Compute volume integrals */
3844:   if (assembleJac) {MatZeroEntries(J);}
3845:   MatZeroEntries(JP);
3846:   for (chunk = 0; chunk < numChunks; ++chunk, offCell += chunkSize) {
3847:     const PetscInt   Ncell = PetscMin(chunkSize, numCells - offCell);
3848:     PetscInt         c;

3850:     /* Extract values */
3851:     for (c = 0; c < Ncell; ++c) {
3852:       const PetscInt cell = cells ? cells[c+offCell] : c+offCell;
3853:       PetscScalar   *x = NULL,  *x_t = NULL;
3854:       PetscInt       i;

3856:       if (X) {
3857:         DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);
3858:         for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i];
3859:         DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);
3860:       }
3861:       if (X_t) {
3862:         DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);
3863:         for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i];
3864:         DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);
3865:       }
3866:       if (dmAux) {
3867:         DMPlexVecGetClosure(dmAux, sectionAux, A, cell, NULL, &x);
3868:         for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i];
3869:         DMPlexVecRestoreClosure(dmAux, sectionAux, A, cell, NULL, &x);
3870:       }
3871:     }
3872:     CHKMEMQ;
3873:     for (fieldI = 0; fieldI < Nf; ++fieldI) {
3874:       PetscFE fe;
3875:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
3876:       for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
3877:         if (hasJac)  {PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN,     fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMat);}
3878:         if (hasPrec) {PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatP);}
3879:         if (hasDyn)  {PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatD);}
3880:       }
3881:       /* For finite volume, add the identity */
3882:       if (!isFE[fieldI]) {
3883:         PetscFV  fv;
3884:         PetscInt eOffset = 0, Nc, fc, foff;

3886:         PetscDSGetFieldOffset(prob, fieldI, &foff);
3887:         PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);
3888:         PetscFVGetNumComponents(fv, &Nc);
3889:         for (c = 0; c < chunkSize; ++c, eOffset += totDim*totDim) {
3890:           for (fc = 0; fc < Nc; ++fc) {
3891:             const PetscInt i = foff + fc;
3892:             if (hasJac)  {elemMat [eOffset+i*totDim+i] = 1.0;}
3893:             if (hasPrec) {elemMatP[eOffset+i*totDim+i] = 1.0;}
3894:           }
3895:         }
3896:       }
3897:     }
3898:     CHKMEMQ;
3899:     /*   Add contribution from X_t */
3900:     if (hasDyn) {for (c = 0; c < chunkSize*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];}
3901:     /* Insert values into matrix */
3902:     for (c = 0; c < Ncell; ++c) {
3903:       const PetscInt cell = cells ? cells[c+offCell] : c+offCell;
3904:       if (mesh->printFEM > 1) {
3905:         if (hasJac)  {DMPrintCellMatrix(cell, name,  totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);}
3906:         if (hasPrec) {DMPrintCellMatrix(cell, nameP, totDim, totDim, &elemMatP[(c-cStart)*totDim*totDim]);}
3907:       }
3908:       if (assembleJac) {DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);}
3909:       DMPlexMatSetClosure(dm, section, globalSection, JP, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);
3910:     }
3911:     CHKMEMQ;
3912:   }
3913:   /* Cleanup */
3914:   DMSNESRestoreFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);
3915:   PetscQuadratureDestroy(&qGeom);
3916:   if (hasFV) {MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);}
3917:   DMRestoreWorkArray(dm, Nf, MPIU_BOOL, &isFE);
3918:   DMRestoreWorkArray(dm, ((1 + (X_t?1:0) + (dmAux?1:0))*totDim + ((hasJac?1:0) + (hasPrec?1:0) + (hasDyn?1:0))*totDim*totDim)*chunkSize, MPIU_SCALAR, &work);
3919:   /* Compute boundary integrals */
3920:   /* DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, ctx); */
3921:   /* Assemble matrix */
3922:   if (assembleJac) {MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);}
3923:   MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);
3924:   PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);
3925:   CHKMEMQ;
3926:   return(0);
3927: }