Actual source code: plexfem.c

petsc-master 2020-11-24
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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 Nc, 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
169: - field - The field number for the rigid body space, or 0 for the default

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

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

176:   Level: advanced

178: .seealso: MatNullSpaceCreate(), PCGAMG
179: @*/
180: PetscErrorCode DMPlexCreateRigidBody(DM dm, PetscInt field, MatNullSpace *sp)
181: {
182:   PetscErrorCode (**func)(PetscInt, PetscReal, const PetscReal *, PetscInt, PetscScalar *, void *);
183:   MPI_Comm          comm;
184:   Vec               mode[6];
185:   PetscSection      section, globalSection;
186:   PetscInt          dim, dimEmbed, Nf, n, m, mmin, d, i, j;
187:   PetscErrorCode    ierr;

190:   PetscObjectGetComm((PetscObject) dm, &comm);
191:   DMGetDimension(dm, &dim);
192:   DMGetCoordinateDim(dm, &dimEmbed);
193:   DMGetNumFields(dm, &Nf);
194:   if (Nf && (field < 0 || field >= Nf)) SETERRQ2(comm, PETSC_ERR_ARG_OUTOFRANGE, "Field %D is not in [0, Nf)", field, Nf);
195:   if (dim == 1 && Nf < 2) {
196:     MatNullSpaceCreate(comm, PETSC_TRUE, 0, NULL, sp);
197:     return(0);
198:   }
199:   DMGetLocalSection(dm, &section);
200:   DMGetGlobalSection(dm, &globalSection);
201:   PetscSectionGetConstrainedStorageSize(globalSection, &n);
202:   PetscCalloc1(Nf, &func);
203:   m    = (dim*(dim+1))/2;
204:   VecCreate(comm, &mode[0]);
205:   VecSetSizes(mode[0], n, PETSC_DETERMINE);
206:   VecSetUp(mode[0]);
207:   VecGetSize(mode[0], &n);
208:   mmin = PetscMin(m, n);
209:   func[field] = DMPlexProjectRigidBody_Private;
210:   for (i = 1; i < m; ++i) {VecDuplicate(mode[0], &mode[i]);}
211:   for (d = 0; d < m; d++) {
212:     PetscInt ctx[2];
213:     void    *voidctx = (void *) (&ctx[0]);

215:     ctx[0] = dimEmbed;
216:     ctx[1] = d;
217:     DMProjectFunction(dm, 0.0, func, &voidctx, INSERT_VALUES, mode[d]);
218:   }
219:   /* Orthonormalize system */
220:   for (i = 0; i < mmin; ++i) {
221:     PetscScalar dots[6];

223:     VecNormalize(mode[i], NULL);
224:     VecMDot(mode[i], mmin-i-1, mode+i+1, dots+i+1);
225:     for (j = i+1; j < mmin; ++j) {
226:       dots[j] *= -1.0;
227:       VecAXPY(mode[j], dots[j], mode[i]);
228:     }
229:   }
230:   MatNullSpaceCreate(comm, PETSC_FALSE, mmin, mode, sp);
231:   for (i = 0; i < m; ++i) {VecDestroy(&mode[i]);}
232:   PetscFree(func);
233:   return(0);
234: }

236: /*@
237:   DMPlexCreateRigidBodies - For the default global section, create rigid body modes by function space interpolation

239:   Collective on dm

241:   Input Arguments:
242: + dm    - the DM
243: . nb    - The number of bodies
244: . label - The DMLabel marking each domain
245: . nids  - The number of ids per body
246: - ids   - An array of the label ids in sequence for each domain

248:   Output Argument:
249: . sp - the null space

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

253:   Level: advanced

255: .seealso: MatNullSpaceCreate()
256: @*/
257: PetscErrorCode DMPlexCreateRigidBodies(DM dm, PetscInt nb, DMLabel label, const PetscInt nids[], const PetscInt ids[], MatNullSpace *sp)
258: {
259:   MPI_Comm       comm;
260:   PetscSection   section, globalSection;
261:   Vec           *mode;
262:   PetscScalar   *dots;
263:   PetscInt       dim, dimEmbed, n, m, b, d, i, j, off;

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

285:       ctx[0] = dimEmbed;
286:       ctx[1] = d;
287:       DMProjectFunctionLabel(dm, 0.0, label, nids[b], &ids[off], 0, NULL, &func, &voidctx, INSERT_VALUES, mode[d]);
288:       off   += nids[b];
289:     }
290:   }
291:   /* Orthonormalize system */
292:   for (i = 0; i < m; ++i) {
293:     PetscScalar dots[6];

295:     VecNormalize(mode[i], NULL);
296:     VecMDot(mode[i], m-i-1, mode+i+1, dots+i+1);
297:     for (j = i+1; j < m; ++j) {
298:       dots[j] *= -1.0;
299:       VecAXPY(mode[j], dots[j], mode[i]);
300:     }
301:   }
302:   MatNullSpaceCreate(comm, PETSC_FALSE, m, mode, sp);
303:   for (i = 0; i< m; ++i) {VecDestroy(&mode[i]);}
304:   PetscFree2(mode, dots);
305:   return(0);
306: }

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

317:   Input Parameters:
318: + dm - the DMPlex object
319: - height - the maximum projection height >= 0

321:   Level: advanced

323: .seealso: DMPlexGetMaxProjectionHeight(), DMProjectFunctionLocal(), DMProjectFunctionLabelLocal()
324: @*/
325: PetscErrorCode DMPlexSetMaxProjectionHeight(DM dm, PetscInt height)
326: {
327:   DM_Plex *plex = (DM_Plex *) dm->data;

331:   plex->maxProjectionHeight = height;
332:   return(0);
333: }

335: /*@
336:   DMPlexGetMaxProjectionHeight - Get the maximum height (w.r.t. DAG) of mesh points used to evaluate dual bases in
337:   DMPlexProjectXXXLocal() functions.

339:   Input Parameters:
340: . dm - the DMPlex object

342:   Output Parameters:
343: . height - the maximum projection height

345:   Level: intermediate

347: .seealso: DMPlexSetMaxProjectionHeight(), DMProjectFunctionLocal(), DMProjectFunctionLabelLocal()
348: @*/
349: PetscErrorCode DMPlexGetMaxProjectionHeight(DM dm, PetscInt *height)
350: {
351:   DM_Plex *plex = (DM_Plex *) dm->data;

355:   *height = plex->maxProjectionHeight;
356:   return(0);
357: }

359: typedef struct {
360:   PetscReal    alpha; /* The first Euler angle, and in 2D the only one */
361:   PetscReal    beta;  /* The second Euler angle */
362:   PetscReal    gamma; /* The third Euler angle */
363:   PetscInt     dim;   /* The dimension of R */
364:   PetscScalar *R;     /* The rotation matrix, transforming a vector in the local basis to the global basis */
365:   PetscScalar *RT;    /* The transposed rotation matrix, transforming a vector in the global basis to the local basis */
366: } RotCtx;

368: /*
369:   Note: Following https://en.wikipedia.org/wiki/Euler_angles, we will specify Euler angles by extrinsic rotations, meaning that
370:   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:
371:   $ The XYZ system rotates about the z axis by alpha. The X axis is now at angle alpha with respect to the x axis.
372:   $ 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.
373:   $ The XYZ system rotates a third time about the z axis by gamma.
374: */
375: static PetscErrorCode DMPlexBasisTransformSetUp_Rotation_Internal(DM dm, void *ctx)
376: {
377:   RotCtx        *rc  = (RotCtx *) ctx;
378:   PetscInt       dim = rc->dim;
379:   PetscReal      c1, s1, c2, s2, c3, s3;

383:   PetscMalloc2(PetscSqr(dim), &rc->R, PetscSqr(dim), &rc->RT);
384:   switch (dim) {
385:   case 2:
386:     c1 = PetscCosReal(rc->alpha);s1 = PetscSinReal(rc->alpha);
387:     rc->R[0] =  c1;rc->R[1] = s1;
388:     rc->R[2] = -s1;rc->R[3] = c1;
389:     PetscArraycpy(rc->RT, rc->R, PetscSqr(dim));
390:     DMPlex_Transpose2D_Internal(rc->RT);break;
391:     break;
392:   case 3:
393:     c1 = PetscCosReal(rc->alpha);s1 = PetscSinReal(rc->alpha);
394:     c2 = PetscCosReal(rc->beta); s2 = PetscSinReal(rc->beta);
395:     c3 = PetscCosReal(rc->gamma);s3 = PetscSinReal(rc->gamma);
396:     rc->R[0] =  c1*c3 - c2*s1*s3;rc->R[1] =  c3*s1    + c1*c2*s3;rc->R[2] = s2*s3;
397:     rc->R[3] = -c1*s3 - c2*c3*s1;rc->R[4] =  c1*c2*c3 - s1*s3;   rc->R[5] = c3*s2;
398:     rc->R[6] =  s1*s2;           rc->R[7] = -c1*s2;              rc->R[8] = c2;
399:     PetscArraycpy(rc->RT, rc->R, PetscSqr(dim));
400:     DMPlex_Transpose3D_Internal(rc->RT);break;
401:     break;
402:   default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D not supported", dim);
403:   }
404:   return(0);
405: }

407: static PetscErrorCode DMPlexBasisTransformDestroy_Rotation_Internal(DM dm, void *ctx)
408: {
409:   RotCtx        *rc = (RotCtx *) ctx;

413:   PetscFree2(rc->R, rc->RT);
414:   PetscFree(rc);
415:   return(0);
416: }

418: static PetscErrorCode DMPlexBasisTransformGetMatrix_Rotation_Internal(DM dm, const PetscReal x[], PetscBool l2g, const PetscScalar **A, void *ctx)
419: {
420:   RotCtx *rc = (RotCtx *) ctx;

424:   if (l2g) {*A = rc->R;}
425:   else     {*A = rc->RT;}
426:   return(0);
427: }

429: PetscErrorCode DMPlexBasisTransformApplyReal_Internal(DM dm, const PetscReal x[], PetscBool l2g, PetscInt dim, const PetscReal *y, PetscReal *z, void *ctx)
430: {

434:   #if defined(PETSC_USE_COMPLEX)
435:   switch (dim) {
436:     case 2:
437:     {
438:       PetscScalar yt[2], zt[2];

440:       yt[0] = y[0]; yt[1] = y[1];
441:       DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, yt, zt, ctx);
442:       z[0] = PetscRealPart(zt[0]); z[1] = PetscRealPart(zt[1]);
443:     }
444:     break;
445:     case 3:
446:     {
447:       PetscScalar yt[3], zt[3];

449:       yt[0] = y[0]; yt[1] = y[1]; yt[2] = y[2];
450:       DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, yt, zt, ctx);
451:       z[0] = PetscRealPart(zt[0]); z[1] = PetscRealPart(zt[1]); z[2] = PetscRealPart(zt[2]);
452:     }
453:     break;
454:   }
455:   #else
456:   DMPlexBasisTransformApply_Internal(dm, x, l2g, dim, y, z, ctx);
457:   #endif
458:   return(0);
459: }

461: PetscErrorCode DMPlexBasisTransformApply_Internal(DM dm, const PetscReal x[], PetscBool l2g, PetscInt dim, const PetscScalar *y, PetscScalar *z, void *ctx)
462: {
463:   const PetscScalar *A;
464:   PetscErrorCode     ierr;

467:   (*dm->transformGetMatrix)(dm, x, l2g, &A, ctx);
468:   switch (dim) {
469:   case 2: DMPlex_Mult2D_Internal(A, 1, y, z);break;
470:   case 3: DMPlex_Mult3D_Internal(A, 1, y, z);break;
471:   }
472:   return(0);
473: }

475: static PetscErrorCode DMPlexBasisTransformField_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscInt f, PetscBool l2g, PetscScalar *a)
476: {
477:   PetscSection       ts;
478:   const PetscScalar *ta, *tva;
479:   PetscInt           dof;
480:   PetscErrorCode     ierr;

483:   DMGetLocalSection(tdm, &ts);
484:   PetscSectionGetFieldDof(ts, p, f, &dof);
485:   VecGetArrayRead(tv, &ta);
486:   DMPlexPointLocalFieldRead(tdm, p, f, ta, (void *) &tva);
487:   if (l2g) {
488:     switch (dof) {
489:     case 4: DMPlex_Mult2D_Internal(tva, 1, a, a);break;
490:     case 9: DMPlex_Mult3D_Internal(tva, 1, a, a);break;
491:     }
492:   } else {
493:     switch (dof) {
494:     case 4: DMPlex_MultTranspose2D_Internal(tva, 1, a, a);break;
495:     case 9: DMPlex_MultTranspose3D_Internal(tva, 1, a, a);break;
496:     }
497:   }
498:   VecRestoreArrayRead(tv, &ta);
499:   return(0);
500: }

502: static PetscErrorCode DMPlexBasisTransformFieldTensor_Internal(DM dm, DM tdm, Vec tv, PetscInt pf, PetscInt f, PetscInt pg, PetscInt g, PetscBool l2g, PetscInt lda, PetscScalar *a)
503: {
504:   PetscSection       s, ts;
505:   const PetscScalar *ta, *tvaf, *tvag;
506:   PetscInt           fdof, gdof, fpdof, gpdof;
507:   PetscErrorCode     ierr;

510:   DMGetLocalSection(dm, &s);
511:   DMGetLocalSection(tdm, &ts);
512:   PetscSectionGetFieldDof(s, pf, f, &fpdof);
513:   PetscSectionGetFieldDof(s, pg, g, &gpdof);
514:   PetscSectionGetFieldDof(ts, pf, f, &fdof);
515:   PetscSectionGetFieldDof(ts, pg, g, &gdof);
516:   VecGetArrayRead(tv, &ta);
517:   DMPlexPointLocalFieldRead(tdm, pf, f, ta, (void *) &tvaf);
518:   DMPlexPointLocalFieldRead(tdm, pg, g, ta, (void *) &tvag);
519:   if (l2g) {
520:     switch (fdof) {
521:     case 4: DMPlex_MatMult2D_Internal(tvaf, gpdof, lda, a, a);break;
522:     case 9: DMPlex_MatMult3D_Internal(tvaf, gpdof, lda, a, a);break;
523:     }
524:     switch (gdof) {
525:     case 4: DMPlex_MatMultTransposeLeft2D_Internal(tvag, fpdof, lda, a, a);break;
526:     case 9: DMPlex_MatMultTransposeLeft3D_Internal(tvag, fpdof, lda, a, a);break;
527:     }
528:   } else {
529:     switch (fdof) {
530:     case 4: DMPlex_MatMultTranspose2D_Internal(tvaf, gpdof, lda, a, a);break;
531:     case 9: DMPlex_MatMultTranspose3D_Internal(tvaf, gpdof, lda, a, a);break;
532:     }
533:     switch (gdof) {
534:     case 4: DMPlex_MatMultLeft2D_Internal(tvag, fpdof, lda, a, a);break;
535:     case 9: DMPlex_MatMultLeft3D_Internal(tvag, fpdof, lda, a, a);break;
536:     }
537:   }
538:   VecRestoreArrayRead(tv, &ta);
539:   return(0);
540: }

542: PetscErrorCode DMPlexBasisTransformPoint_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscBool fieldActive[], PetscBool l2g, PetscScalar *a)
543: {
544:   PetscSection    s;
545:   PetscSection    clSection;
546:   IS              clPoints;
547:   const PetscInt *clp;
548:   PetscInt       *points = NULL;
549:   PetscInt        Nf, f, Np, cp, dof, d = 0;
550:   PetscErrorCode  ierr;

553:   DMGetLocalSection(dm, &s);
554:   PetscSectionGetNumFields(s, &Nf);
555:   DMPlexGetCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
556:   for (f = 0; f < Nf; ++f) {
557:     for (cp = 0; cp < Np*2; cp += 2) {
558:       PetscSectionGetFieldDof(s, points[cp], f, &dof);
559:       if (!dof) continue;
560:       if (fieldActive[f]) {DMPlexBasisTransformField_Internal(dm, tdm, tv, points[cp], f, l2g, &a[d]);}
561:       d += dof;
562:     }
563:   }
564:   DMPlexRestoreCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
565:   return(0);
566: }

568: PetscErrorCode DMPlexBasisTransformPointTensor_Internal(DM dm, DM tdm, Vec tv, PetscInt p, PetscBool l2g, PetscInt lda, PetscScalar *a)
569: {
570:   PetscSection    s;
571:   PetscSection    clSection;
572:   IS              clPoints;
573:   const PetscInt *clp;
574:   PetscInt       *points = NULL;
575:   PetscInt        Nf, f, g, Np, cpf, cpg, fdof, gdof, r, c = 0;
576:   PetscErrorCode  ierr;

579:   DMGetLocalSection(dm, &s);
580:   PetscSectionGetNumFields(s, &Nf);
581:   DMPlexGetCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
582:   for (f = 0, r = 0; f < Nf; ++f) {
583:     for (cpf = 0; cpf < Np*2; cpf += 2) {
584:       PetscSectionGetFieldDof(s, points[cpf], f, &fdof);
585:       for (g = 0, c = 0; g < Nf; ++g) {
586:         for (cpg = 0; cpg < Np*2; cpg += 2) {
587:           PetscSectionGetFieldDof(s, points[cpg], g, &gdof);
588:           DMPlexBasisTransformFieldTensor_Internal(dm, tdm, tv, points[cpf], f, points[cpg], g, l2g, lda, &a[r*lda+c]);
589:           c += gdof;
590:         }
591:       }
592:       if (c != lda) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of columns %D should be %D", c, lda);
593:       r += fdof;
594:     }
595:   }
596:   if (r != lda) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of rows %D should be %D", c, lda);
597:   DMPlexRestoreCompressedClosure(dm, s, p, &Np, &points, &clSection, &clPoints, &clp);
598:   return(0);
599: }

601: static PetscErrorCode DMPlexBasisTransform_Internal(DM dm, Vec lv, PetscBool l2g)
602: {
603:   DM                 tdm;
604:   Vec                tv;
605:   PetscSection       ts, s;
606:   const PetscScalar *ta;
607:   PetscScalar       *a, *va;
608:   PetscInt           pStart, pEnd, p, Nf, f;
609:   PetscErrorCode     ierr;

612:   DMGetBasisTransformDM_Internal(dm, &tdm);
613:   DMGetBasisTransformVec_Internal(dm, &tv);
614:   DMGetLocalSection(tdm, &ts);
615:   DMGetLocalSection(dm, &s);
616:   PetscSectionGetChart(s, &pStart, &pEnd);
617:   PetscSectionGetNumFields(s, &Nf);
618:   VecGetArray(lv, &a);
619:   VecGetArrayRead(tv, &ta);
620:   for (p = pStart; p < pEnd; ++p) {
621:     for (f = 0; f < Nf; ++f) {
622:       DMPlexPointLocalFieldRef(dm, p, f, a, (void *) &va);
623:       DMPlexBasisTransformField_Internal(dm, tdm, tv, p, f, l2g, va);
624:     }
625:   }
626:   VecRestoreArray(lv, &a);
627:   VecRestoreArrayRead(tv, &ta);
628:   return(0);
629: }

631: /*@
632:   DMPlexGlobalToLocalBasis - Transform the values in the given local vector from the global basis to the local basis

634:   Input Parameters:
635: + dm - The DM
636: - lv - A local vector with values in the global basis

638:   Output Parameters:
639: . lv - A local vector with values in the local basis

641:   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.

643:   Level: developer

645: .seealso: DMPlexLocalToGlobalBasis(), DMGetLocalSection(), DMPlexCreateBasisRotation()
646: @*/
647: PetscErrorCode DMPlexGlobalToLocalBasis(DM dm, Vec lv)
648: {

654:   DMPlexBasisTransform_Internal(dm, lv, PETSC_FALSE);
655:   return(0);
656: }

658: /*@
659:   DMPlexLocalToGlobalBasis - Transform the values in the given local vector from the local basis to the global basis

661:   Input Parameters:
662: + dm - The DM
663: - lv - A local vector with values in the local basis

665:   Output Parameters:
666: . lv - A local vector with values in the global basis

668:   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.

670:   Level: developer

672: .seealso: DMPlexGlobalToLocalBasis(), DMGetLocalSection(), DMPlexCreateBasisRotation()
673: @*/
674: PetscErrorCode DMPlexLocalToGlobalBasis(DM dm, Vec lv)
675: {

681:   DMPlexBasisTransform_Internal(dm, lv, PETSC_TRUE);
682:   return(0);
683: }

685: /*@
686:   DMPlexCreateBasisRotation - Create an internal transformation from the global basis, used to specify boundary conditions
687:     and global solutions, to a local basis, appropriate for discretization integrals and assembly.

689:   Input Parameters:
690: + dm    - The DM
691: . alpha - The first Euler angle, and in 2D the only one
692: . beta  - The second Euler angle
693: - gamma - The third Euler angle

695:   Note: Following https://en.wikipedia.org/wiki/Euler_angles, we will specify Euler angles by extrinsic rotations, meaning that
696:   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:
697:   $ The XYZ system rotates about the z axis by alpha. The X axis is now at angle alpha with respect to the x axis.
698:   $ 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.
699:   $ The XYZ system rotates a third time about the z axis by gamma.

701:   Level: developer

703: .seealso: DMPlexGlobalToLocalBasis(), DMPlexLocalToGlobalBasis()
704: @*/
705: PetscErrorCode DMPlexCreateBasisRotation(DM dm, PetscReal alpha, PetscReal beta, PetscReal gamma)
706: {
707:   RotCtx        *rc;
708:   PetscInt       cdim;

711:   DMGetCoordinateDim(dm, &cdim);
712:   PetscMalloc1(1, &rc);
713:   dm->transformCtx       = rc;
714:   dm->transformSetUp     = DMPlexBasisTransformSetUp_Rotation_Internal;
715:   dm->transformDestroy   = DMPlexBasisTransformDestroy_Rotation_Internal;
716:   dm->transformGetMatrix = DMPlexBasisTransformGetMatrix_Rotation_Internal;
717:   rc->dim   = cdim;
718:   rc->alpha = alpha;
719:   rc->beta  = beta;
720:   rc->gamma = gamma;
721:   (*dm->transformSetUp)(dm, dm->transformCtx);
722:   DMConstructBasisTransform_Internal(dm);
723:   return(0);
724: }

726: /*@C
727:   DMPlexInsertBoundaryValuesEssential - Insert boundary values into a local vector using a function of the coordinates

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

741:   Output Parameter:
742: . locX   - A local vector to receives the boundary values

744:   Level: developer

746: .seealso: DMPlexInsertBoundaryValuesEssentialField(), DMPlexInsertBoundaryValuesEssentialBdField(), DMAddBoundary()
747: @*/
748: 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)
749: {
750:   PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx);
751:   void            **ctxs;
752:   PetscInt          numFields;
753:   PetscErrorCode    ierr;

756:   DMGetNumFields(dm, &numFields);
757:   PetscCalloc2(numFields,&funcs,numFields,&ctxs);
758:   funcs[field] = func;
759:   ctxs[field]  = ctx;
760:   DMProjectFunctionLabelLocal(dm, time, label, numids, ids, Nc, comps, funcs, ctxs, INSERT_BC_VALUES, locX);
761:   PetscFree2(funcs,ctxs);
762:   return(0);
763: }

765: /*@C
766:   DMPlexInsertBoundaryValuesEssentialField - Insert boundary values into a local vector using a function of the coordinates and field data

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

781:   Output Parameter:
782: . locX   - A local vector to receives the boundary values

784:   Level: developer

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

805:   DMGetNumFields(dm, &numFields);
806:   PetscCalloc2(numFields,&funcs,numFields,&ctxs);
807:   funcs[field] = func;
808:   ctxs[field]  = ctx;
809:   DMProjectFieldLabelLocal(dm, time, label, numids, ids, Nc, comps, locU, funcs, INSERT_BC_VALUES, locX);
810:   PetscFree2(funcs,ctxs);
811:   return(0);
812: }

814: /*@C
815:   DMPlexInsertBoundaryValuesEssentialBdField - Insert boundary values into a local vector using a function of the coodinates and boundary field data

817:   Collective on dm

819:   Input Parameters:
820: + dm     - The DM, with a PetscDS that matches the problem being constrained
821: . time   - The time
822: . locU   - A local vector with the input solution values
823: . field  - The field to constrain
824: . Nc     - The number of constrained field components, or 0 for all components
825: . comps  - An array of constrained component numbers, or NULL for all components
826: . label  - The DMLabel defining constrained points
827: . numids - The number of DMLabel ids for constrained points
828: . ids    - An array of ids for constrained points
829: . func   - A pointwise function giving boundary values, the calling sequence is given in DMProjectBdFieldLabelLocal()
830: - ctx    - An optional user context for bcFunc

832:   Output Parameter:
833: . locX   - A local vector to receive the boundary values

835:   Level: developer

837: .seealso: DMProjectBdFieldLabelLocal(), DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialField(), DMAddBoundary()
838: @*/
839: PetscErrorCode DMPlexInsertBoundaryValuesEssentialBdField(DM dm, PetscReal time, Vec locU, PetscInt field, PetscInt Nc, const PetscInt comps[], DMLabel label, PetscInt numids, const PetscInt ids[],
840:                                                           void (*func)(PetscInt, PetscInt, PetscInt,
841:                                                                        const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
842:                                                                        const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
843:                                                                        PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[],
844:                                                                        PetscScalar[]),
845:                                                           void *ctx, Vec locX)
846: {
847:   void (**funcs)(PetscInt, PetscInt, PetscInt,
848:                  const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
849:                  const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
850:                  PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]);
851:   void            **ctxs;
852:   PetscInt          numFields;
853:   PetscErrorCode    ierr;

856:   DMGetNumFields(dm, &numFields);
857:   PetscCalloc2(numFields,&funcs,numFields,&ctxs);
858:   funcs[field] = func;
859:   ctxs[field]  = ctx;
860:   DMProjectBdFieldLabelLocal(dm, time, label, numids, ids, Nc, comps, locU, funcs, INSERT_BC_VALUES, locX);
861:   PetscFree2(funcs,ctxs);
862:   return(0);
863: }

865: /*@C
866:   DMPlexInsertBoundaryValuesRiemann - Insert boundary values into a local vector

868:   Input Parameters:
869: + dm     - The DM, with a PetscDS that matches the problem being constrained
870: . time   - The time
871: . faceGeometry - A vector with the FVM face geometry information
872: . cellGeometry - A vector with the FVM cell geometry information
873: . Grad         - A vector with the FVM cell gradient information
874: . field  - The field to constrain
875: . Nc     - The number of constrained field components, or 0 for all components
876: . comps  - An array of constrained component numbers, or NULL for all components
877: . label  - The DMLabel defining constrained points
878: . numids - The number of DMLabel ids for constrained points
879: . ids    - An array of ids for constrained points
880: . func   - A pointwise function giving boundary values
881: - ctx    - An optional user context for bcFunc

883:   Output Parameter:
884: . locX   - A local vector to receives the boundary values

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

888:   Level: developer

890: .seealso: DMPlexInsertBoundaryValuesEssential(), DMPlexInsertBoundaryValuesEssentialField(), DMAddBoundary()
891: @*/
892: 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[],
893:                                                  PetscErrorCode (*func)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*), void *ctx, Vec locX)
894: {
895:   PetscDS            prob;
896:   PetscSF            sf;
897:   DM                 dmFace, dmCell, dmGrad;
898:   const PetscScalar *facegeom, *cellgeom = NULL, *grad;
899:   const PetscInt    *leaves;
900:   PetscScalar       *x, *fx;
901:   PetscInt           dim, nleaves, loc, fStart, fEnd, pdim, i;
902:   PetscErrorCode     ierr, ierru = 0;

905:   DMGetPointSF(dm, &sf);
906:   PetscSFGetGraph(sf, NULL, &nleaves, &leaves, NULL);
907:   nleaves = PetscMax(0, nleaves);
908:   DMGetDimension(dm, &dim);
909:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
910:   DMGetDS(dm, &prob);
911:   VecGetDM(faceGeometry, &dmFace);
912:   VecGetArrayRead(faceGeometry, &facegeom);
913:   if (cellGeometry) {
914:     VecGetDM(cellGeometry, &dmCell);
915:     VecGetArrayRead(cellGeometry, &cellgeom);
916:   }
917:   if (Grad) {
918:     PetscFV fv;

920:     PetscDSGetDiscretization(prob, field, (PetscObject *) &fv);
921:     VecGetDM(Grad, &dmGrad);
922:     VecGetArrayRead(Grad, &grad);
923:     PetscFVGetNumComponents(fv, &pdim);
924:     DMGetWorkArray(dm, pdim, MPIU_SCALAR, &fx);
925:   }
926:   VecGetArray(locX, &x);
927:   for (i = 0; i < numids; ++i) {
928:     IS              faceIS;
929:     const PetscInt *faces;
930:     PetscInt        numFaces, f;

932:     DMLabelGetStratumIS(label, ids[i], &faceIS);
933:     if (!faceIS) continue; /* No points with that id on this process */
934:     ISGetLocalSize(faceIS, &numFaces);
935:     ISGetIndices(faceIS, &faces);
936:     for (f = 0; f < numFaces; ++f) {
937:       const PetscInt         face = faces[f], *cells;
938:       PetscFVFaceGeom        *fg;

940:       if ((face < fStart) || (face >= fEnd)) continue; /* Refinement adds non-faces to labels */
941:       PetscFindInt(face, nleaves, (PetscInt *) leaves, &loc);
942:       if (loc >= 0) continue;
943:       DMPlexPointLocalRead(dmFace, face, facegeom, &fg);
944:       DMPlexGetSupport(dm, face, &cells);
945:       if (Grad) {
946:         PetscFVCellGeom       *cg;
947:         PetscScalar           *cx, *cgrad;
948:         PetscScalar           *xG;
949:         PetscReal              dx[3];
950:         PetscInt               d;

952:         DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cg);
953:         DMPlexPointLocalRead(dm, cells[0], x, &cx);
954:         DMPlexPointLocalRead(dmGrad, cells[0], grad, &cgrad);
955:         DMPlexPointLocalFieldRef(dm, cells[1], field, x, &xG);
956:         DMPlex_WaxpyD_Internal(dim, -1, cg->centroid, fg->centroid, dx);
957:         for (d = 0; d < pdim; ++d) fx[d] = cx[d] + DMPlex_DotD_Internal(dim, &cgrad[d*dim], dx);
958:         ierru = (*func)(time, fg->centroid, fg->normal, fx, xG, ctx);
959:         if (ierru) {
960:           ISRestoreIndices(faceIS, &faces);
961:           ISDestroy(&faceIS);
962:           goto cleanup;
963:         }
964:       } else {
965:         PetscScalar       *xI;
966:         PetscScalar       *xG;

968:         DMPlexPointLocalRead(dm, cells[0], x, &xI);
969:         DMPlexPointLocalFieldRef(dm, cells[1], field, x, &xG);
970:         ierru = (*func)(time, fg->centroid, fg->normal, xI, xG, ctx);
971:         if (ierru) {
972:           ISRestoreIndices(faceIS, &faces);
973:           ISDestroy(&faceIS);
974:           goto cleanup;
975:         }
976:       }
977:     }
978:     ISRestoreIndices(faceIS, &faces);
979:     ISDestroy(&faceIS);
980:   }
981:   cleanup:
982:   VecRestoreArray(locX, &x);
983:   if (Grad) {
984:     DMRestoreWorkArray(dm, pdim, MPIU_SCALAR, &fx);
985:     VecRestoreArrayRead(Grad, &grad);
986:   }
987:   if (cellGeometry) {VecRestoreArrayRead(cellGeometry, &cellgeom);}
988:   VecRestoreArrayRead(faceGeometry, &facegeom);
989:   CHKERRQ(ierru);
990:   return(0);
991: }

993: static PetscErrorCode zero(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nc, PetscScalar *u, void *ctx)
994: {
995:   PetscInt c;
996:   for (c = 0; c < Nc; ++c) u[c] = 0.0;
997:   return 0;
998: }

1000: PetscErrorCode DMPlexInsertBoundaryValues_Plex(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM)
1001: {
1002:   PetscObject    isZero;
1003:   PetscDS        prob;
1004:   PetscInt       numBd, b;

1008:   DMGetDS(dm, &prob);
1009:   PetscDSGetNumBoundary(prob, &numBd);
1010:   PetscObjectQuery((PetscObject) locX, "__Vec_bc_zero__", &isZero);
1011:   for (b = 0; b < numBd; ++b) {
1012:     DMBoundaryConditionType type;
1013:     const char             *name, *labelname;
1014:     DMLabel                 label;
1015:     PetscInt                field, Nc;
1016:     const PetscInt         *comps;
1017:     PetscObject             obj;
1018:     PetscClassId            id;
1019:     void                    (*func)(void);
1020:     PetscInt                numids;
1021:     const PetscInt         *ids;
1022:     void                   *ctx;

1024:     DMGetBoundary(dm, b, &type, &name, &labelname, &field, &Nc, &comps, &func, NULL, &numids, &ids, &ctx);
1025:     if (insertEssential != (type & DM_BC_ESSENTIAL)) continue;
1026:     DMGetLabel(dm, labelname, &label);
1027:     if (!label) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "Label %s for boundary condition %s does not exist in the DM", labelname, name);
1028:     DMGetField(dm, field, NULL, &obj);
1029:     PetscObjectGetClassId(obj, &id);
1030:     if (id == PETSCFE_CLASSID) {
1031:       switch (type) {
1032:         /* for FEM, there is no insertion to be done for non-essential boundary conditions */
1033:       case DM_BC_ESSENTIAL:
1034:         if (isZero) func = (void (*)(void)) zero;
1035:         DMPlexLabelAddCells(dm,label);
1036:         DMPlexInsertBoundaryValuesEssential(dm, time, field, Nc, comps, label, numids, ids, (PetscErrorCode (*)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *)) func, ctx, locX);
1037:         DMPlexLabelClearCells(dm,label);
1038:         break;
1039:       case DM_BC_ESSENTIAL_FIELD:
1040:         DMPlexLabelAddCells(dm,label);
1041:         DMPlexInsertBoundaryValuesEssentialField(dm, time, locX, field, Nc, comps, label, numids, ids,
1042:                                                         (void (*)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
1043:                                                                   const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
1044:                                                                   PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[])) func, ctx, locX);
1045:         DMPlexLabelClearCells(dm,label);
1046:         break;
1047:       default: break;
1048:       }
1049:     } else if (id == PETSCFV_CLASSID) {
1050:       if (!faceGeomFVM) continue;
1051:       DMPlexInsertBoundaryValuesRiemann(dm, time, faceGeomFVM, cellGeomFVM, gradFVM, field, Nc, comps, label, numids, ids,
1052:                                                (PetscErrorCode (*)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*)) func, ctx, locX);
1053:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1054:   }
1055:   return(0);
1056: }

1058: PetscErrorCode DMPlexInsertTimeDerivativeBoundaryValues_Plex(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM)
1059: {
1060:   PetscObject    isZero;
1061:   PetscDS        prob;
1062:   PetscInt       numBd, b;

1066:   if (!locX) return(0);
1067:   DMGetDS(dm, &prob);
1068:   PetscDSGetNumBoundary(prob, &numBd);
1069:   PetscObjectQuery((PetscObject) locX, "__Vec_bc_zero__", &isZero);
1070:   for (b = 0; b < numBd; ++b) {
1071:     DMBoundaryConditionType type;
1072:     const char             *name, *labelname;
1073:     DMLabel                 label;
1074:     PetscInt                field, Nc;
1075:     const PetscInt         *comps;
1076:     PetscObject             obj;
1077:     PetscClassId            id;
1078:     void                    (*func_t)(void);
1079:     PetscInt                numids;
1080:     const PetscInt         *ids;
1081:     void                   *ctx;

1083:     DMGetBoundary(dm, b, &type, &name, &labelname, &field, &Nc, &comps, NULL, &func_t, &numids, &ids, &ctx);
1084:     if (!func_t) continue;
1085:     if (insertEssential != (type & DM_BC_ESSENTIAL)) continue;
1086:     DMGetLabel(dm, labelname, &label);
1087:     if (!label) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "Label %s for boundary condition %s does not exist in the DM", labelname, name);
1088:     DMGetField(dm, field, NULL, &obj);
1089:     PetscObjectGetClassId(obj, &id);
1090:     if (id == PETSCFE_CLASSID) {
1091:       switch (type) {
1092:         /* for FEM, there is no insertion to be done for non-essential boundary conditions */
1093:       case DM_BC_ESSENTIAL:
1094:         if (isZero) func_t = (void (*)(void)) zero;
1095:         DMPlexLabelAddCells(dm,label);
1096:         DMPlexInsertBoundaryValuesEssential(dm, time, field, Nc, comps, label, numids, ids, (PetscErrorCode (*)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *)) func_t, ctx, locX);
1097:         DMPlexLabelClearCells(dm,label);
1098:         break;
1099:       case DM_BC_ESSENTIAL_FIELD:
1100:         DMPlexLabelAddCells(dm,label);
1101:         DMPlexInsertBoundaryValuesEssentialField(dm, time, locX, field, Nc, comps, label, numids, ids,
1102:                                                         (void (*)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
1103:                                                                   const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
1104:                                                                   PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[])) func_t, ctx, locX);
1105:         DMPlexLabelClearCells(dm,label);
1106:         break;
1107:       default: break;
1108:       }
1109:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1110:   }
1111:   return(0);
1112: }

1114: /*@
1115:   DMPlexInsertBoundaryValues - Puts coefficients which represent boundary values into the local solution vector

1117:   Input Parameters:
1118: + dm - The DM
1119: . insertEssential - Should I insert essential (e.g. Dirichlet) or inessential (e.g. Neumann) boundary conditions
1120: . time - The time
1121: . faceGeomFVM - Face geometry data for FV discretizations
1122: . cellGeomFVM - Cell geometry data for FV discretizations
1123: - gradFVM - Gradient reconstruction data for FV discretizations

1125:   Output Parameters:
1126: . locX - Solution updated with boundary values

1128:   Level: developer

1130: .seealso: DMProjectFunctionLabelLocal()
1131: @*/
1132: PetscErrorCode DMPlexInsertBoundaryValues(DM dm, PetscBool insertEssential, Vec locX, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM)
1133: {

1142:   PetscTryMethod(dm,"DMPlexInsertBoundaryValues_C",(DM,PetscBool,Vec,PetscReal,Vec,Vec,Vec),(dm,insertEssential,locX,time,faceGeomFVM,cellGeomFVM,gradFVM));
1143:   return(0);
1144: }

1146: /*@
1147:   DMPlexInsertTimeDerivativeBoundaryValues - Puts coefficients which represent boundary values of the time derviative into the local solution vector

1149:   Input Parameters:
1150: + dm - The DM
1151: . insertEssential - Should I insert essential (e.g. Dirichlet) or inessential (e.g. Neumann) boundary conditions
1152: . time - The time
1153: . faceGeomFVM - Face geometry data for FV discretizations
1154: . cellGeomFVM - Cell geometry data for FV discretizations
1155: - gradFVM - Gradient reconstruction data for FV discretizations

1157:   Output Parameters:
1158: . locX_t - Solution updated with boundary values

1160:   Level: developer

1162: .seealso: DMProjectFunctionLabelLocal()
1163: @*/
1164: PetscErrorCode DMPlexInsertTimeDerivativeBoundaryValues(DM dm, PetscBool insertEssential, Vec locX_t, PetscReal time, Vec faceGeomFVM, Vec cellGeomFVM, Vec gradFVM)
1165: {

1174:   PetscTryMethod(dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",(DM,PetscBool,Vec,PetscReal,Vec,Vec,Vec),(dm,insertEssential,locX_t,time,faceGeomFVM,cellGeomFVM,gradFVM));
1175:   return(0);
1176: }

1178: PetscErrorCode DMComputeL2Diff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff)
1179: {
1180:   Vec              localX;
1181:   PetscErrorCode   ierr;

1184:   DMGetLocalVector(dm, &localX);
1185:   DMPlexInsertBoundaryValues(dm, PETSC_TRUE, localX, time, NULL, NULL, NULL);
1186:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
1187:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
1188:   DMPlexComputeL2DiffLocal(dm, time, funcs, ctxs, localX, diff);
1189:   DMRestoreLocalVector(dm, &localX);
1190:   return(0);
1191: }

1193: /*@C
1194:   DMComputeL2DiffLocal - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h.

1196:   Collective on dm

1198:   Input Parameters:
1199: + dm     - The DM
1200: . time   - The time
1201: . funcs  - The functions to evaluate for each field component
1202: . ctxs   - Optional array of contexts to pass to each function, or NULL.
1203: - localX - The coefficient vector u_h, a local vector

1205:   Output Parameter:
1206: . diff - The diff ||u - u_h||_2

1208:   Level: developer

1210: .seealso: DMProjectFunction(), DMComputeL2FieldDiff(), DMComputeL2GradientDiff()
1211: @*/
1212: PetscErrorCode DMPlexComputeL2DiffLocal(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec localX, PetscReal *diff)
1213: {
1214:   const PetscInt   debug = ((DM_Plex*)dm->data)->printL2;
1215:   DM               tdm;
1216:   Vec              tv;
1217:   PetscSection     section;
1218:   PetscQuadrature  quad;
1219:   PetscFEGeom      fegeom;
1220:   PetscScalar     *funcVal, *interpolant;
1221:   PetscReal       *coords, *gcoords;
1222:   PetscReal        localDiff = 0.0;
1223:   const PetscReal *quadWeights;
1224:   PetscInt         dim, coordDim, numFields, numComponents = 0, qNc, Nq, cellHeight, cStart, cEnd, c, field, fieldOffset;
1225:   PetscBool        transform;
1226:   PetscErrorCode   ierr;

1229:   DMGetDimension(dm, &dim);
1230:   DMGetCoordinateDim(dm, &coordDim);
1231:   fegeom.dimEmbed = coordDim;
1232:   DMGetLocalSection(dm, &section);
1233:   PetscSectionGetNumFields(section, &numFields);
1234:   DMGetBasisTransformDM_Internal(dm, &tdm);
1235:   DMGetBasisTransformVec_Internal(dm, &tv);
1236:   DMHasBasisTransform(dm, &transform);
1237:   for (field = 0; field < numFields; ++field) {
1238:     PetscObject  obj;
1239:     PetscClassId id;
1240:     PetscInt     Nc;

1242:     DMGetField(dm, field, NULL, &obj);
1243:     PetscObjectGetClassId(obj, &id);
1244:     if (id == PETSCFE_CLASSID) {
1245:       PetscFE fe = (PetscFE) obj;

1247:       PetscFEGetQuadrature(fe, &quad);
1248:       PetscFEGetNumComponents(fe, &Nc);
1249:     } else if (id == PETSCFV_CLASSID) {
1250:       PetscFV fv = (PetscFV) obj;

1252:       PetscFVGetQuadrature(fv, &quad);
1253:       PetscFVGetNumComponents(fv, &Nc);
1254:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1255:     numComponents += Nc;
1256:   }
1257:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, NULL, &quadWeights);
1258:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
1259:   PetscMalloc6(numComponents,&funcVal,numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);
1260:   DMPlexGetVTKCellHeight(dm, &cellHeight);
1261:   DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);
1262:   for (c = cStart; c < cEnd; ++c) {
1263:     PetscScalar *x = NULL;
1264:     PetscReal    elemDiff = 0.0;
1265:     PetscInt     qc = 0;

1267:     DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1268:     DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);

1270:     for (field = 0, fieldOffset = 0; field < numFields; ++field) {
1271:       PetscObject  obj;
1272:       PetscClassId id;
1273:       void * const ctx = ctxs ? ctxs[field] : NULL;
1274:       PetscInt     Nb, Nc, q, fc;

1276:       DMGetField(dm, field, NULL, &obj);
1277:       PetscObjectGetClassId(obj, &id);
1278:       if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
1279:       else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
1280:       else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1281:       if (debug) {
1282:         char title[1024];
1283:         PetscSNPrintf(title, 1023, "Solution for Field %D", field);
1284:         DMPrintCellVector(c, title, Nb, &x[fieldOffset]);
1285:       }
1286:       for (q = 0; q < Nq; ++q) {
1287:         PetscFEGeom qgeom;

1289:         qgeom.dimEmbed = fegeom.dimEmbed;
1290:         qgeom.J        = &fegeom.J[q*coordDim*coordDim];
1291:         qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
1292:         qgeom.detJ     = &fegeom.detJ[q];
1293:         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);
1294:         if (transform) {
1295:           gcoords = &coords[coordDim*Nq];
1296:           DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);
1297:         } else {
1298:           gcoords = &coords[coordDim*q];
1299:         }
1300:         (*funcs[field])(coordDim, time, gcoords, Nc, funcVal, ctx);
1301:         if (ierr) {
1302:           PetscErrorCode ierr2;
1303:           ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2);
1304:           ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
1305:           ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
1306:           
1307:         }
1308:         if (transform) {DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);}
1309:         if (id == PETSCFE_CLASSID)      {PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);}
1310:         else if (id == PETSCFV_CLASSID) {PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);}
1311:         else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1312:         for (fc = 0; fc < Nc; ++fc) {
1313:           const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
1314:           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]));}
1315:           elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
1316:         }
1317:       }
1318:       fieldOffset += Nb;
1319:       qc += Nc;
1320:     }
1321:     DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);
1322:     if (debug) {PetscPrintf(PETSC_COMM_SELF, "  elem %D diff %g\n", c, (double)elemDiff);}
1323:     localDiff += elemDiff;
1324:   }
1325:   PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);
1326:   MPIU_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));
1327:   *diff = PetscSqrtReal(*diff);
1328:   return(0);
1329: }

1331: 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)
1332: {
1333:   const PetscInt   debug = ((DM_Plex*)dm->data)->printL2;
1334:   DM               tdm;
1335:   PetscSection     section;
1336:   PetscQuadrature  quad;
1337:   Vec              localX, tv;
1338:   PetscScalar     *funcVal, *interpolant;
1339:   const PetscReal *quadWeights;
1340:   PetscFEGeom      fegeom;
1341:   PetscReal       *coords, *gcoords;
1342:   PetscReal        localDiff = 0.0;
1343:   PetscInt         dim, coordDim, qNc = 0, Nq = 0, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset;
1344:   PetscBool        transform;
1345:   PetscErrorCode   ierr;

1348:   DMGetDimension(dm, &dim);
1349:   DMGetCoordinateDim(dm, &coordDim);
1350:   fegeom.dimEmbed = coordDim;
1351:   DMGetLocalSection(dm, &section);
1352:   PetscSectionGetNumFields(section, &numFields);
1353:   DMGetLocalVector(dm, &localX);
1354:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
1355:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
1356:   DMGetBasisTransformDM_Internal(dm, &tdm);
1357:   DMGetBasisTransformVec_Internal(dm, &tv);
1358:   DMHasBasisTransform(dm, &transform);
1359:   for (field = 0; field < numFields; ++field) {
1360:     PetscFE  fe;
1361:     PetscInt Nc;

1363:     DMGetField(dm, field, NULL, (PetscObject *) &fe);
1364:     PetscFEGetQuadrature(fe, &quad);
1365:     PetscFEGetNumComponents(fe, &Nc);
1366:     numComponents += Nc;
1367:   }
1368:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, NULL, &quadWeights);
1369:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
1370:   /* DMProjectFunctionLocal(dm, fe, funcs, INSERT_BC_VALUES, localX); */
1371:   PetscMalloc6(numComponents,&funcVal,coordDim*Nq,&coords,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ,numComponents*coordDim,&interpolant,Nq,&fegeom.detJ);
1372:   DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);
1373:   for (c = cStart; c < cEnd; ++c) {
1374:     PetscScalar *x = NULL;
1375:     PetscReal    elemDiff = 0.0;
1376:     PetscInt     qc = 0;

1378:     DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1379:     DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);

1381:     for (field = 0, fieldOffset = 0; field < numFields; ++field) {
1382:       PetscFE          fe;
1383:       void * const     ctx = ctxs ? ctxs[field] : NULL;
1384:       PetscInt         Nb, Nc, q, fc;

1386:       DMGetField(dm, field, NULL, (PetscObject *) &fe);
1387:       PetscFEGetDimension(fe, &Nb);
1388:       PetscFEGetNumComponents(fe, &Nc);
1389:       if (debug) {
1390:         char title[1024];
1391:         PetscSNPrintf(title, 1023, "Solution for Field %D", field);
1392:         DMPrintCellVector(c, title, Nb, &x[fieldOffset]);
1393:       }
1394:       for (q = 0; q < Nq; ++q) {
1395:         PetscFEGeom qgeom;

1397:         qgeom.dimEmbed = fegeom.dimEmbed;
1398:         qgeom.J        = &fegeom.J[q*coordDim*coordDim];
1399:         qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
1400:         qgeom.detJ     = &fegeom.detJ[q];
1401:         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);
1402:         if (transform) {
1403:           gcoords = &coords[coordDim*Nq];
1404:           DMPlexBasisTransformApplyReal_Internal(dm, &coords[coordDim*q], PETSC_TRUE, coordDim, &coords[coordDim*q], gcoords, dm->transformCtx);
1405:         } else {
1406:           gcoords = &coords[coordDim*q];
1407:         }
1408:         (*funcs[field])(coordDim, time, gcoords, n, Nc, funcVal, ctx);
1409:         if (ierr) {
1410:           PetscErrorCode ierr2;
1411:           ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2);
1412:           ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
1413:           ierr2 = PetscFree6(funcVal,coords,fegeom.J,fegeom.invJ,interpolant,fegeom.detJ);CHKERRQ(ierr2);
1414:           
1415:         }
1416:         if (transform) {DMPlexBasisTransformApply_Internal(dm, &coords[coordDim*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);}
1417:         PetscFEInterpolateGradient_Static(fe, &x[fieldOffset], &qgeom, q, interpolant);
1418:         /* Overwrite with the dot product if the normal is given */
1419:         if (n) {
1420:           for (fc = 0; fc < Nc; ++fc) {
1421:             PetscScalar sum = 0.0;
1422:             PetscInt    d;
1423:             for (d = 0; d < dim; ++d) sum += interpolant[fc*dim+d]*n[d];
1424:             interpolant[fc] = sum;
1425:           }
1426:         }
1427:         for (fc = 0; fc < Nc; ++fc) {
1428:           const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
1429:           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]));}
1430:           elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
1431:         }
1432:       }
1433:       fieldOffset += Nb;
1434:       qc          += Nc;
1435:     }
1436:     DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);
1437:     if (debug) {PetscPrintf(PETSC_COMM_SELF, "  elem %D diff %g\n", c, (double)elemDiff);}
1438:     localDiff += elemDiff;
1439:   }
1440:   PetscFree6(funcVal,coords,fegeom.J,fegeom.invJ,interpolant,fegeom.detJ);
1441:   DMRestoreLocalVector(dm, &localX);
1442:   MPIU_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));
1443:   *diff = PetscSqrtReal(*diff);
1444:   return(0);
1445: }

1447: PetscErrorCode DMComputeL2FieldDiff_Plex(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, PetscReal *diff)
1448: {
1449:   const PetscInt   debug = ((DM_Plex*)dm->data)->printL2;
1450:   DM               tdm;
1451:   DMLabel          depthLabel;
1452:   PetscSection     section;
1453:   Vec              localX, tv;
1454:   PetscReal       *localDiff;
1455:   PetscInt         dim, depth, dE, Nf, f, Nds, s;
1456:   PetscBool        transform;
1457:   PetscErrorCode   ierr;

1460:   DMGetDimension(dm, &dim);
1461:   DMGetCoordinateDim(dm, &dE);
1462:   DMGetLocalSection(dm, &section);
1463:   DMGetLocalVector(dm, &localX);
1464:   DMGetBasisTransformDM_Internal(dm, &tdm);
1465:   DMGetBasisTransformVec_Internal(dm, &tv);
1466:   DMHasBasisTransform(dm, &transform);
1467:   DMGetNumFields(dm, &Nf);
1468:   DMPlexGetDepthLabel(dm, &depthLabel);
1469:   DMLabelGetNumValues(depthLabel, &depth);

1471:   VecSet(localX, 0.0);
1472:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
1473:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
1474:   DMProjectFunctionLocal(dm, time, funcs, ctxs, INSERT_BC_VALUES, localX);
1475:   DMGetNumDS(dm, &Nds);
1476:   PetscCalloc1(Nf, &localDiff);
1477:   for (s = 0; s < Nds; ++s) {
1478:     PetscDS          ds;
1479:     DMLabel          label;
1480:     IS               fieldIS, pointIS;
1481:     const PetscInt  *fields, *points = NULL;
1482:     PetscQuadrature  quad;
1483:     const PetscReal *quadPoints, *quadWeights;
1484:     PetscFEGeom      fegeom;
1485:     PetscReal       *coords, *gcoords;
1486:     PetscScalar     *funcVal, *interpolant;
1487:     PetscBool        isHybrid;
1488:     PetscInt         qNc, Nq, totNc, cStart = 0, cEnd, c, dsNf;

1490:     DMGetRegionNumDS(dm, s, &label, &fieldIS, &ds);
1491:     ISGetIndices(fieldIS, &fields);
1492:     PetscDSGetHybrid(ds, &isHybrid);
1493:     PetscDSGetNumFields(ds, &dsNf);
1494:     PetscDSGetTotalComponents(ds, &totNc);
1495:     PetscDSGetQuadrature(ds, &quad);
1496:     PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);
1497:     if ((qNc != 1) && (qNc != totNc)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, totNc);
1498:     PetscCalloc6(totNc, &funcVal, totNc, &interpolant, dE*(Nq+1), &coords,Nq, &fegeom.detJ, dE*dE*Nq, &fegeom.J, dE*dE*Nq, &fegeom.invJ);
1499:     if (!label) {
1500:       DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);
1501:     } else {
1502:       DMLabelGetStratumIS(label, 1, &pointIS);
1503:       ISGetLocalSize(pointIS, &cEnd);
1504:       ISGetIndices(pointIS, &points);
1505:     }
1506:     for (c = cStart; c < cEnd; ++c) {
1507:       const PetscInt cell = points ? points[c] : c;
1508:       PetscScalar   *x    = NULL;
1509:       PetscInt       qc   = 0, fOff = 0, dep, fStart = isHybrid ? dsNf-1 : 0;

1511:       DMLabelGetValue(depthLabel, cell, &dep);
1512:       if (dep != depth-1) continue;
1513:       if (isHybrid) {
1514:         const PetscInt *cone;

1516:         DMPlexGetCone(dm, cell, &cone);
1517:         DMPlexComputeCellGeometryFEM(dm, cone[0], quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1518:       } else {
1519:         DMPlexComputeCellGeometryFEM(dm, cell, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1520:       }
1521:       DMPlexVecGetClosure(dm, NULL, localX, cell, NULL, &x);
1522:       for (f = fStart; f < dsNf; ++f) {
1523:         PetscObject  obj;
1524:         PetscClassId id;
1525:         void * const ctx = ctxs ? ctxs[fields[f]] : NULL;
1526:         PetscInt     Nb, Nc, q, fc;
1527:         PetscReal    elemDiff = 0.0;

1529:         PetscDSGetDiscretization(ds, f, &obj);
1530:         PetscObjectGetClassId(obj, &id);
1531:         if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
1532:         else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
1533:         else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", fields[f]);
1534:         if (debug) {
1535:           char title[1024];
1536:           PetscSNPrintf(title, 1023, "Solution for Field %D", fields[f]);
1537:           DMPrintCellVector(cell, title, Nb, &x[fOff]);
1538:         }
1539:         for (q = 0; q < Nq; ++q) {
1540:           PetscFEGeom qgeom;

1542:           qgeom.dimEmbed = fegeom.dimEmbed;
1543:           qgeom.J        = &fegeom.J[q*dE*dE];
1544:           qgeom.invJ     = &fegeom.invJ[q*dE*dE];
1545:           qgeom.detJ     = &fegeom.detJ[q];
1546:           if (fegeom.detJ[q] <= 0.0) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for cell %D, quadrature point %D", (double)fegeom.detJ[q], cell, q);
1547:           if (transform) {
1548:             gcoords = &coords[dE*Nq];
1549:             DMPlexBasisTransformApplyReal_Internal(dm, &coords[dE*q], PETSC_TRUE, dE, &coords[dE*q], gcoords, dm->transformCtx);
1550:           } else {
1551:             gcoords = &coords[dE*q];
1552:           }
1553:           (*funcs[fields[f]])(dE, time, gcoords, Nc, funcVal, ctx);
1554:           if (ierr) {
1555:             PetscErrorCode ierr2;
1556:             ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, cell, NULL, &x);CHKERRQ(ierr2);
1557:             ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
1558:             ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
1559:             
1560:           }
1561:           if (transform) {DMPlexBasisTransformApply_Internal(dm, &coords[dE*q], PETSC_FALSE, Nc, funcVal, funcVal, dm->transformCtx);}
1562:           /* Call once for each face, except for lagrange field */
1563:           if (id == PETSCFE_CLASSID)      {PetscFEInterpolate_Static((PetscFE) obj, &x[fOff], &qgeom, q, interpolant);}
1564:           else if (id == PETSCFV_CLASSID) {PetscFVInterpolate_Static((PetscFV) obj, &x[fOff], q, interpolant);}
1565:           else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", fields[f]);
1566:           for (fc = 0; fc < Nc; ++fc) {
1567:             const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
1568:             if (debug) {PetscPrintf(PETSC_COMM_SELF, "    cell %D field %D,%D point %g %g %g diff %g\n", cell, fields[f], fc, (double)(dE > 0 ? coords[dE*q] : 0.), (double)(dE > 1 ? coords[dE*q+1] : 0.),(double)(dE > 2 ? coords[dE*q+2] : 0.), (double)(PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q]));}
1569:             elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
1570:           }
1571:         }
1572:         fOff += Nb;
1573:         qc   += Nc;
1574:         localDiff[fields[f]] += elemDiff;
1575:         if (debug) {PetscPrintf(PETSC_COMM_SELF, "  cell %D field %D cum diff %g\n", cell, fields[f], (double)localDiff[fields[f]]);}
1576:       }
1577:       DMPlexVecRestoreClosure(dm, NULL, localX, cell, NULL, &x);
1578:     }
1579:     if (label) {
1580:       ISRestoreIndices(pointIS, &points);
1581:       ISDestroy(&pointIS);
1582:     }
1583:     ISRestoreIndices(fieldIS, &fields);
1584:     PetscFree6(funcVal, interpolant, coords, fegeom.detJ, fegeom.J, fegeom.invJ);
1585:   }
1586:   DMRestoreLocalVector(dm, &localX);
1587:   MPIU_Allreduce(localDiff, diff, Nf, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)dm));
1588:   PetscFree(localDiff);
1589:   for (f = 0; f < Nf; ++f) diff[f] = PetscSqrtReal(diff[f]);
1590:   return(0);
1591: }

1593: /*@C
1594:   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.

1596:   Collective on dm

1598:   Input Parameters:
1599: + dm    - The DM
1600: . time  - The time
1601: . funcs - The functions to evaluate for each field component: NULL means that component does not contribute to error calculation
1602: . ctxs  - Optional array of contexts to pass to each function, or NULL.
1603: - X     - The coefficient vector u_h

1605:   Output Parameter:
1606: . D - A Vec which holds the difference ||u - u_h||_2 for each cell

1608:   Level: developer

1610: .seealso: DMProjectFunction(), DMComputeL2Diff(), DMPlexComputeL2FieldDiff(), DMComputeL2GradientDiff()
1611: @*/
1612: PetscErrorCode DMPlexComputeL2DiffVec(DM dm, PetscReal time, PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **ctxs, Vec X, Vec D)
1613: {
1614:   PetscSection     section;
1615:   PetscQuadrature  quad;
1616:   Vec              localX;
1617:   PetscFEGeom      fegeom;
1618:   PetscScalar     *funcVal, *interpolant;
1619:   PetscReal       *coords;
1620:   const PetscReal *quadPoints, *quadWeights;
1621:   PetscInt         dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, c, field, fieldOffset;
1622:   PetscErrorCode   ierr;

1625:   VecSet(D, 0.0);
1626:   DMGetDimension(dm, &dim);
1627:   DMGetCoordinateDim(dm, &coordDim);
1628:   DMGetLocalSection(dm, &section);
1629:   PetscSectionGetNumFields(section, &numFields);
1630:   DMGetLocalVector(dm, &localX);
1631:   DMProjectFunctionLocal(dm, time, funcs, ctxs, INSERT_BC_VALUES, localX);
1632:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);
1633:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);
1634:   for (field = 0; field < numFields; ++field) {
1635:     PetscObject  obj;
1636:     PetscClassId id;
1637:     PetscInt     Nc;

1639:     DMGetField(dm, field, NULL, &obj);
1640:     PetscObjectGetClassId(obj, &id);
1641:     if (id == PETSCFE_CLASSID) {
1642:       PetscFE fe = (PetscFE) obj;

1644:       PetscFEGetQuadrature(fe, &quad);
1645:       PetscFEGetNumComponents(fe, &Nc);
1646:     } else if (id == PETSCFV_CLASSID) {
1647:       PetscFV fv = (PetscFV) obj;

1649:       PetscFVGetQuadrature(fv, &quad);
1650:       PetscFVGetNumComponents(fv, &Nc);
1651:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1652:     numComponents += Nc;
1653:   }
1654:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);
1655:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
1656:   PetscMalloc6(numComponents,&funcVal,numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);
1657:   DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);
1658:   for (c = cStart; c < cEnd; ++c) {
1659:     PetscScalar *x = NULL;
1660:     PetscScalar  elemDiff = 0.0;
1661:     PetscInt     qc = 0;

1663:     DMPlexComputeCellGeometryFEM(dm, c, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1664:     DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);

1666:     for (field = 0, fieldOffset = 0; field < numFields; ++field) {
1667:       PetscObject  obj;
1668:       PetscClassId id;
1669:       void * const ctx = ctxs ? ctxs[field] : NULL;
1670:       PetscInt     Nb, Nc, q, fc;

1672:       DMGetField(dm, field, NULL, &obj);
1673:       PetscObjectGetClassId(obj, &id);
1674:       if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
1675:       else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
1676:       else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1677:       if (funcs[field]) {
1678:         for (q = 0; q < Nq; ++q) {
1679:           PetscFEGeom qgeom;

1681:           qgeom.dimEmbed = fegeom.dimEmbed;
1682:           qgeom.J        = &fegeom.J[q*coordDim*coordDim];
1683:           qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
1684:           qgeom.detJ     = &fegeom.detJ[q];
1685:           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);
1686:           (*funcs[field])(coordDim, time, &coords[q*coordDim], Nc, funcVal, ctx);
1687:           if (ierr) {
1688:             PetscErrorCode ierr2;
1689:             ierr2 = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr2);
1690:             ierr2 = PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
1691:             ierr2 = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr2);
1692:             
1693:           }
1694:           if (id == PETSCFE_CLASSID)      {PetscFEInterpolate_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);}
1695:           else if (id == PETSCFV_CLASSID) {PetscFVInterpolate_Static((PetscFV) obj, &x[fieldOffset], q, interpolant);}
1696:           else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1697:           for (fc = 0; fc < Nc; ++fc) {
1698:             const PetscReal wt = quadWeights[q*qNc+(qNc == 1 ? 0 : qc+fc)];
1699:             elemDiff += PetscSqr(PetscRealPart(interpolant[fc] - funcVal[fc]))*wt*fegeom.detJ[q];
1700:           }
1701:         }
1702:       }
1703:       fieldOffset += Nb;
1704:       qc          += Nc;
1705:     }
1706:     DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);
1707:     VecSetValue(D, c - cStart, elemDiff, INSERT_VALUES);
1708:   }
1709:   PetscFree6(funcVal,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);
1710:   DMRestoreLocalVector(dm, &localX);
1711:   VecSqrtAbs(D);
1712:   return(0);
1713: }

1715: /*@C
1716:   DMPlexComputeGradientClementInterpolant - This function computes the L2 projection of the cellwise gradient of a function u onto P1, and stores it in a Vec.

1718:   Collective on dm

1720:   Input Parameters:
1721: + dm - The DM
1722: - LocX  - The coefficient vector u_h

1724:   Output Parameter:
1725: . locC - A Vec which holds the Clement interpolant of the gradient

1727:   Notes:
1728:     Add citation to (Clement, 1975) and definition of the interpolant
1729:   \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

1731:   Level: developer

1733: .seealso: DMProjectFunction(), DMComputeL2Diff(), DMPlexComputeL2FieldDiff(), DMComputeL2GradientDiff()
1734: @*/
1735: PetscErrorCode DMPlexComputeGradientClementInterpolant(DM dm, Vec locX, Vec locC)
1736: {
1737:   DM_Plex         *mesh  = (DM_Plex *) dm->data;
1738:   PetscInt         debug = mesh->printFEM;
1739:   DM               dmC;
1740:   PetscSection     section;
1741:   PetscQuadrature  quad;
1742:   PetscScalar     *interpolant, *gradsum;
1743:   PetscFEGeom      fegeom;
1744:   PetscReal       *coords;
1745:   const PetscReal *quadPoints, *quadWeights;
1746:   PetscInt         dim, coordDim, numFields, numComponents = 0, qNc, Nq, cStart, cEnd, vStart, vEnd, v, field, fieldOffset;
1747:   PetscErrorCode   ierr;

1750:   VecGetDM(locC, &dmC);
1751:   VecSet(locC, 0.0);
1752:   DMGetDimension(dm, &dim);
1753:   DMGetCoordinateDim(dm, &coordDim);
1754:   fegeom.dimEmbed = coordDim;
1755:   DMGetLocalSection(dm, &section);
1756:   PetscSectionGetNumFields(section, &numFields);
1757:   for (field = 0; field < numFields; ++field) {
1758:     PetscObject  obj;
1759:     PetscClassId id;
1760:     PetscInt     Nc;

1762:     DMGetField(dm, field, NULL, &obj);
1763:     PetscObjectGetClassId(obj, &id);
1764:     if (id == PETSCFE_CLASSID) {
1765:       PetscFE fe = (PetscFE) obj;

1767:       PetscFEGetQuadrature(fe, &quad);
1768:       PetscFEGetNumComponents(fe, &Nc);
1769:     } else if (id == PETSCFV_CLASSID) {
1770:       PetscFV fv = (PetscFV) obj;

1772:       PetscFVGetQuadrature(fv, &quad);
1773:       PetscFVGetNumComponents(fv, &Nc);
1774:     } else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1775:     numComponents += Nc;
1776:   }
1777:   PetscQuadratureGetData(quad, NULL, &qNc, &Nq, &quadPoints, &quadWeights);
1778:   if ((qNc != 1) && (qNc != numComponents)) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_SIZ, "Quadrature components %D != %D field components", qNc, numComponents);
1779:   PetscMalloc6(coordDim*numComponents*2,&gradsum,coordDim*numComponents,&interpolant,coordDim*Nq,&coords,Nq,&fegeom.detJ,coordDim*coordDim*Nq,&fegeom.J,coordDim*coordDim*Nq,&fegeom.invJ);
1780:   DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
1781:   DMPlexGetSimplexOrBoxCells(dm, 0, &cStart, &cEnd);
1782:   for (v = vStart; v < vEnd; ++v) {
1783:     PetscScalar volsum = 0.0;
1784:     PetscInt   *star = NULL;
1785:     PetscInt    starSize, st, d, fc;

1787:     PetscArrayzero(gradsum, coordDim*numComponents);
1788:     DMPlexGetTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);
1789:     for (st = 0; st < starSize*2; st += 2) {
1790:       const PetscInt cell = star[st];
1791:       PetscScalar   *grad = &gradsum[coordDim*numComponents];
1792:       PetscScalar   *x    = NULL;
1793:       PetscReal      vol  = 0.0;

1795:       if ((cell < cStart) || (cell >= cEnd)) continue;
1796:       DMPlexComputeCellGeometryFEM(dm, cell, quad, coords, fegeom.J, fegeom.invJ, fegeom.detJ);
1797:       DMPlexVecGetClosure(dm, NULL, locX, cell, NULL, &x);
1798:       for (field = 0, fieldOffset = 0; field < numFields; ++field) {
1799:         PetscObject  obj;
1800:         PetscClassId id;
1801:         PetscInt     Nb, Nc, q, qc = 0;

1803:         PetscArrayzero(grad, coordDim*numComponents);
1804:         DMGetField(dm, field, NULL, &obj);
1805:         PetscObjectGetClassId(obj, &id);
1806:         if (id == PETSCFE_CLASSID)      {PetscFEGetNumComponents((PetscFE) obj, &Nc);PetscFEGetDimension((PetscFE) obj, &Nb);}
1807:         else if (id == PETSCFV_CLASSID) {PetscFVGetNumComponents((PetscFV) obj, &Nc);Nb = 1;}
1808:         else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1809:         for (q = 0; q < Nq; ++q) {
1810:           PetscFEGeom qgeom;

1812:           qgeom.dimEmbed = fegeom.dimEmbed;
1813:           qgeom.J        = &fegeom.J[q*coordDim*coordDim];
1814:           qgeom.invJ     = &fegeom.invJ[q*coordDim*coordDim];
1815:           qgeom.detJ     = &fegeom.detJ[q];
1816:           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);
1817:           if (ierr) {
1818:             PetscErrorCode ierr2;
1819:             ierr2 = DMPlexVecRestoreClosure(dm, NULL, locX, cell, NULL, &x);CHKERRQ(ierr2);
1820:             ierr2 = DMPlexRestoreTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr2);
1821:             ierr2 = PetscFree6(gradsum,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);CHKERRQ(ierr2);
1822:             
1823:           }
1824:           if (id == PETSCFE_CLASSID)      {PetscFEInterpolateGradient_Static((PetscFE) obj, &x[fieldOffset], &qgeom, q, interpolant);}
1825:           else SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", field);
1826:           for (fc = 0; fc < Nc; ++fc) {
1827:             const PetscReal wt = quadWeights[q*qNc+qc+fc];

1829:             for (d = 0; d < coordDim; ++d) grad[fc*coordDim+d] += interpolant[fc*dim+d]*wt*fegeom.detJ[q];
1830:           }
1831:           vol += quadWeights[q*qNc]*fegeom.detJ[q];
1832:         }
1833:         fieldOffset += Nb;
1834:         qc          += Nc;
1835:       }
1836:       DMPlexVecRestoreClosure(dm, NULL, locX, cell, NULL, &x);
1837:       for (fc = 0; fc < numComponents; ++fc) {
1838:         for (d = 0; d < coordDim; ++d) {
1839:           gradsum[fc*coordDim+d] += grad[fc*coordDim+d];
1840:         }
1841:       }
1842:       volsum += vol;
1843:       if (debug) {
1844:         PetscPrintf(PETSC_COMM_SELF, "Cell %D gradient: [", cell);
1845:         for (fc = 0; fc < numComponents; ++fc) {
1846:           for (d = 0; d < coordDim; ++d) {
1847:             if (fc || d > 0) {PetscPrintf(PETSC_COMM_SELF, ", ");}
1848:             PetscPrintf(PETSC_COMM_SELF, "%g", (double)PetscRealPart(grad[fc*coordDim+d]));
1849:           }
1850:         }
1851:         PetscPrintf(PETSC_COMM_SELF, "]\n");
1852:       }
1853:     }
1854:     for (fc = 0; fc < numComponents; ++fc) {
1855:       for (d = 0; d < coordDim; ++d) gradsum[fc*coordDim+d] /= volsum;
1856:     }
1857:     DMPlexRestoreTransitiveClosure(dm, v, PETSC_FALSE, &starSize, &star);
1858:     DMPlexVecSetClosure(dmC, NULL, locC, v, gradsum, INSERT_VALUES);
1859:   }
1860:   PetscFree6(gradsum,interpolant,coords,fegeom.detJ,fegeom.J,fegeom.invJ);
1861:   return(0);
1862: }

1864: static PetscErrorCode DMPlexComputeIntegral_Internal(DM dm, Vec X, PetscInt cStart, PetscInt cEnd, PetscScalar *cintegral, void *user)
1865: {
1866:   DM                 dmAux = NULL;
1867:   PetscDS            prob,    probAux = NULL;
1868:   PetscSection       section, sectionAux;
1869:   Vec                locX,    locA;
1870:   PetscInt           dim, numCells = cEnd - cStart, c, f;
1871:   PetscBool          useFVM = PETSC_FALSE;
1872:   /* DS */
1873:   PetscInt           Nf,    totDim,    *uOff, *uOff_x, numConstants;
1874:   PetscInt           NfAux, totDimAux, *aOff;
1875:   PetscScalar       *u, *a;
1876:   const PetscScalar *constants;
1877:   /* Geometry */
1878:   PetscFEGeom       *cgeomFEM;
1879:   DM                 dmGrad;
1880:   PetscQuadrature    affineQuad = NULL;
1881:   Vec                cellGeometryFVM = NULL, faceGeometryFVM = NULL, locGrad = NULL;
1882:   PetscFVCellGeom   *cgeomFVM;
1883:   const PetscScalar *lgrad;
1884:   PetscInt           maxDegree;
1885:   DMField            coordField;
1886:   IS                 cellIS;
1887:   PetscErrorCode     ierr;

1890:   DMGetDS(dm, &prob);
1891:   DMGetDimension(dm, &dim);
1892:   DMGetLocalSection(dm, &section);
1893:   PetscSectionGetNumFields(section, &Nf);
1894:   /* Determine which discretizations we have */
1895:   for (f = 0; f < Nf; ++f) {
1896:     PetscObject  obj;
1897:     PetscClassId id;

1899:     PetscDSGetDiscretization(prob, f, &obj);
1900:     PetscObjectGetClassId(obj, &id);
1901:     if (id == PETSCFV_CLASSID) useFVM = PETSC_TRUE;
1902:   }
1903:   /* Get local solution with boundary values */
1904:   DMGetLocalVector(dm, &locX);
1905:   DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locX, 0.0, NULL, NULL, NULL);
1906:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);
1907:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);
1908:   /* Read DS information */
1909:   PetscDSGetTotalDimension(prob, &totDim);
1910:   PetscDSGetComponentOffsets(prob, &uOff);
1911:   PetscDSGetComponentDerivativeOffsets(prob, &uOff_x);
1912:   ISCreateStride(PETSC_COMM_SELF,numCells,cStart,1,&cellIS);
1913:   PetscDSGetConstants(prob, &numConstants, &constants);
1914:   /* Read Auxiliary DS information */
1915:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
1916:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
1917:   if (dmAux) {
1918:     DMGetDS(dmAux, &probAux);
1919:     PetscDSGetNumFields(probAux, &NfAux);
1920:     DMGetLocalSection(dmAux, &sectionAux);
1921:     PetscDSGetTotalDimension(probAux, &totDimAux);
1922:     PetscDSGetComponentOffsets(probAux, &aOff);
1923:   }
1924:   /* Allocate data  arrays */
1925:   PetscCalloc1(numCells*totDim, &u);
1926:   if (dmAux) {PetscMalloc1(numCells*totDimAux, &a);}
1927:   /* Read out geometry */
1928:   DMGetCoordinateField(dm,&coordField);
1929:   DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
1930:   if (maxDegree <= 1) {
1931:     DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);
1932:     if (affineQuad) {
1933:       DMFieldCreateFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&cgeomFEM);
1934:     }
1935:   }
1936:   if (useFVM) {
1937:     PetscFV   fv = NULL;
1938:     Vec       grad;
1939:     PetscInt  fStart, fEnd;
1940:     PetscBool compGrad;

1942:     for (f = 0; f < Nf; ++f) {
1943:       PetscObject  obj;
1944:       PetscClassId id;

1946:       PetscDSGetDiscretization(prob, f, &obj);
1947:       PetscObjectGetClassId(obj, &id);
1948:       if (id == PETSCFV_CLASSID) {fv = (PetscFV) obj; break;}
1949:     }
1950:     PetscFVGetComputeGradients(fv, &compGrad);
1951:     PetscFVSetComputeGradients(fv, PETSC_TRUE);
1952:     DMPlexComputeGeometryFVM(dm, &cellGeometryFVM, &faceGeometryFVM);
1953:     DMPlexComputeGradientFVM(dm, fv, faceGeometryFVM, cellGeometryFVM, &dmGrad);
1954:     PetscFVSetComputeGradients(fv, compGrad);
1955:     VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);
1956:     /* Reconstruct and limit cell gradients */
1957:     DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
1958:     DMGetGlobalVector(dmGrad, &grad);
1959:     DMPlexReconstructGradients_Internal(dm, fv, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);
1960:     /* Communicate gradient values */
1961:     DMGetLocalVector(dmGrad, &locGrad);
1962:     DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);
1963:     DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);
1964:     DMRestoreGlobalVector(dmGrad, &grad);
1965:     /* Handle non-essential (e.g. outflow) boundary values */
1966:     DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, 0.0, faceGeometryFVM, cellGeometryFVM, locGrad);
1967:     VecGetArrayRead(locGrad, &lgrad);
1968:   }
1969:   /* Read out data from inputs */
1970:   for (c = cStart; c < cEnd; ++c) {
1971:     PetscScalar *x = NULL;
1972:     PetscInt     i;

1974:     DMPlexVecGetClosure(dm, section, locX, c, NULL, &x);
1975:     for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i];
1976:     DMPlexVecRestoreClosure(dm, section, locX, c, NULL, &x);
1977:     if (dmAux) {
1978:       DMPlexVecGetClosure(dmAux, sectionAux, locA, c, NULL, &x);
1979:       for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i];
1980:       DMPlexVecRestoreClosure(dmAux, sectionAux, locA, c, NULL, &x);
1981:     }
1982:   }
1983:   /* Do integration for each field */
1984:   for (f = 0; f < Nf; ++f) {
1985:     PetscObject  obj;
1986:     PetscClassId id;
1987:     PetscInt     numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset;

1989:     PetscDSGetDiscretization(prob, f, &obj);
1990:     PetscObjectGetClassId(obj, &id);
1991:     if (id == PETSCFE_CLASSID) {
1992:       PetscFE         fe = (PetscFE) obj;
1993:       PetscQuadrature q;
1994:       PetscFEGeom     *chunkGeom = NULL;
1995:       PetscInt        Nq, Nb;

1997:       PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
1998:       PetscFEGetQuadrature(fe, &q);
1999:       PetscQuadratureGetData(q, NULL, NULL, &Nq, NULL, NULL);
2000:       PetscFEGetDimension(fe, &Nb);
2001:       blockSize = Nb*Nq;
2002:       batchSize = numBlocks * blockSize;
2003:       PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
2004:       numChunks = numCells / (numBatches*batchSize);
2005:       Ne        = numChunks*numBatches*batchSize;
2006:       Nr        = numCells % (numBatches*batchSize);
2007:       offset    = numCells - Nr;
2008:       if (!affineQuad) {
2009:         DMFieldCreateFEGeom(coordField,cellIS,q,PETSC_FALSE,&cgeomFEM);
2010:       }
2011:       PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);
2012:       PetscFEIntegrate(prob, f, Ne, chunkGeom, u, probAux, a, cintegral);
2013:       PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&chunkGeom);
2014:       PetscFEIntegrate(prob, f, Nr, chunkGeom, &u[offset*totDim], probAux, &a[offset*totDimAux], &cintegral[offset*Nf]);
2015:       PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&chunkGeom);
2016:       if (!affineQuad) {
2017:         PetscFEGeomDestroy(&cgeomFEM);
2018:       }
2019:     } else if (id == PETSCFV_CLASSID) {
2020:       PetscInt       foff;
2021:       PetscPointFunc obj_func;
2022:       PetscScalar    lint;

2024:       PetscDSGetObjective(prob, f, &obj_func);
2025:       PetscDSGetFieldOffset(prob, f, &foff);
2026:       if (obj_func) {
2027:         for (c = 0; c < numCells; ++c) {
2028:           PetscScalar *u_x;

2030:           DMPlexPointLocalRead(dmGrad, c, lgrad, &u_x);
2031:           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);
2032:           cintegral[c*Nf+f] += PetscRealPart(lint)*cgeomFVM[c].volume;
2033:         }
2034:       }
2035:     } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f);
2036:   }
2037:   /* Cleanup data arrays */
2038:   if (useFVM) {
2039:     VecRestoreArrayRead(locGrad, &lgrad);
2040:     VecRestoreArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);
2041:     DMRestoreLocalVector(dmGrad, &locGrad);
2042:     VecDestroy(&faceGeometryFVM);
2043:     VecDestroy(&cellGeometryFVM);
2044:     DMDestroy(&dmGrad);
2045:   }
2046:   if (dmAux) {PetscFree(a);}
2047:   PetscFree(u);
2048:   /* Cleanup */
2049:   if (affineQuad) {
2050:     PetscFEGeomDestroy(&cgeomFEM);
2051:   }
2052:   PetscQuadratureDestroy(&affineQuad);
2053:   ISDestroy(&cellIS);
2054:   DMRestoreLocalVector(dm, &locX);
2055:   return(0);
2056: }

2058: /*@
2059:   DMPlexComputeIntegralFEM - Form the integral over the domain from the global input X using pointwise functions specified by the user

2061:   Input Parameters:
2062: + dm - The mesh
2063: . X  - Global input vector
2064: - user - The user context

2066:   Output Parameter:
2067: . integral - Integral for each field

2069:   Level: developer

2071: .seealso: DMPlexComputeResidualFEM()
2072: @*/
2073: PetscErrorCode DMPlexComputeIntegralFEM(DM dm, Vec X, PetscScalar *integral, void *user)
2074: {
2075:   DM_Plex       *mesh = (DM_Plex *) dm->data;
2076:   PetscScalar   *cintegral, *lintegral;
2077:   PetscInt       Nf, f, cellHeight, cStart, cEnd, cell;

2084:   PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);
2085:   DMGetNumFields(dm, &Nf);
2086:   DMPlexGetVTKCellHeight(dm, &cellHeight);
2087:   DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);
2088:   /* TODO Introduce a loop over large chunks (right now this is a single chunk) */
2089:   PetscCalloc2(Nf, &lintegral, (cEnd-cStart)*Nf, &cintegral);
2090:   DMPlexComputeIntegral_Internal(dm, X, cStart, cEnd, cintegral, user);
2091:   /* Sum up values */
2092:   for (cell = cStart; cell < cEnd; ++cell) {
2093:     const PetscInt c = cell - cStart;

2095:     if (mesh->printFEM > 1) {DMPrintCellVector(cell, "Cell Integral", Nf, &cintegral[c*Nf]);}
2096:     for (f = 0; f < Nf; ++f) lintegral[f] += cintegral[c*Nf+f];
2097:   }
2098:   MPIU_Allreduce(lintegral, integral, Nf, MPIU_SCALAR, MPIU_SUM, PetscObjectComm((PetscObject) dm));
2099:   if (mesh->printFEM) {
2100:     PetscPrintf(PetscObjectComm((PetscObject) dm), "Integral:");
2101:     for (f = 0; f < Nf; ++f) {PetscPrintf(PetscObjectComm((PetscObject) dm), " %g", (double) PetscRealPart(integral[f]));}
2102:     PetscPrintf(PetscObjectComm((PetscObject) dm), "\n");
2103:   }
2104:   PetscFree2(lintegral, cintegral);
2105:   PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);
2106:   return(0);
2107: }

2109: /*@
2110:   DMPlexComputeCellwiseIntegralFEM - Form the vector of cellwise integrals F from the global input X using pointwise functions specified by the user

2112:   Input Parameters:
2113: + dm - The mesh
2114: . X  - Global input vector
2115: - user - The user context

2117:   Output Parameter:
2118: . integral - Cellwise integrals for each field

2120:   Level: developer

2122: .seealso: DMPlexComputeResidualFEM()
2123: @*/
2124: PetscErrorCode DMPlexComputeCellwiseIntegralFEM(DM dm, Vec X, Vec F, void *user)
2125: {
2126:   DM_Plex       *mesh = (DM_Plex *) dm->data;
2127:   DM             dmF;
2128:   PetscSection   sectionF;
2129:   PetscScalar   *cintegral, *af;
2130:   PetscInt       Nf, f, cellHeight, cStart, cEnd, cell;

2137:   PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);
2138:   DMGetNumFields(dm, &Nf);
2139:   DMPlexGetVTKCellHeight(dm, &cellHeight);
2140:   DMPlexGetSimplexOrBoxCells(dm, cellHeight, &cStart, &cEnd);
2141:   /* TODO Introduce a loop over large chunks (right now this is a single chunk) */
2142:   PetscCalloc1((cEnd-cStart)*Nf, &cintegral);
2143:   DMPlexComputeIntegral_Internal(dm, X, cStart, cEnd, cintegral, user);
2144:   /* Put values in F*/
2145:   VecGetDM(F, &dmF);
2146:   DMGetLocalSection(dmF, &sectionF);
2147:   VecGetArray(F, &af);
2148:   for (cell = cStart; cell < cEnd; ++cell) {
2149:     const PetscInt c = cell - cStart;
2150:     PetscInt       dof, off;

2152:     if (mesh->printFEM > 1) {DMPrintCellVector(cell, "Cell Integral", Nf, &cintegral[c*Nf]);}
2153:     PetscSectionGetDof(sectionF, cell, &dof);
2154:     PetscSectionGetOffset(sectionF, cell, &off);
2155:     if (dof != Nf) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "The number of cell dofs %D != %D", dof, Nf);
2156:     for (f = 0; f < Nf; ++f) af[off+f] = cintegral[c*Nf+f];
2157:   }
2158:   VecRestoreArray(F, &af);
2159:   PetscFree(cintegral);
2160:   PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);
2161:   return(0);
2162: }

2164: static PetscErrorCode DMPlexComputeBdIntegral_Internal(DM dm, Vec locX, IS pointIS,
2165:                                                        void (*func)(PetscInt, PetscInt, PetscInt,
2166:                                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
2167:                                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
2168:                                                                     PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]),
2169:                                                        PetscScalar *fintegral, void *user)
2170: {
2171:   DM                 plex = NULL, plexA = NULL;
2172:   DMEnclosureType    encAux;
2173:   PetscDS            prob, probAux = NULL;
2174:   PetscSection       section, sectionAux = NULL;
2175:   Vec                locA = NULL;
2176:   DMField            coordField;
2177:   PetscInt           Nf,        totDim,        *uOff, *uOff_x;
2178:   PetscInt           NfAux = 0, totDimAux = 0, *aOff = NULL;
2179:   PetscScalar       *u, *a = NULL;
2180:   const PetscScalar *constants;
2181:   PetscInt           numConstants, f;
2182:   PetscErrorCode     ierr;

2185:   DMGetCoordinateField(dm, &coordField);
2186:   DMConvert(dm, DMPLEX, &plex);
2187:   DMGetDS(dm, &prob);
2188:   DMGetLocalSection(dm, &section);
2189:   PetscSectionGetNumFields(section, &Nf);
2190:   /* Determine which discretizations we have */
2191:   for (f = 0; f < Nf; ++f) {
2192:     PetscObject  obj;
2193:     PetscClassId id;

2195:     PetscDSGetDiscretization(prob, f, &obj);
2196:     PetscObjectGetClassId(obj, &id);
2197:     if (id == PETSCFV_CLASSID) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Not supported for FVM (field %D)", f);
2198:   }
2199:   /* Read DS information */
2200:   PetscDSGetTotalDimension(prob, &totDim);
2201:   PetscDSGetComponentOffsets(prob, &uOff);
2202:   PetscDSGetComponentDerivativeOffsets(prob, &uOff_x);
2203:   PetscDSGetConstants(prob, &numConstants, &constants);
2204:   /* Read Auxiliary DS information */
2205:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
2206:   if (locA) {
2207:     DM dmAux;

2209:     VecGetDM(locA, &dmAux);
2210:     DMGetEnclosureRelation(dmAux, dm, &encAux);
2211:     DMConvert(dmAux, DMPLEX, &plexA);
2212:     DMGetDS(dmAux, &probAux);
2213:     PetscDSGetNumFields(probAux, &NfAux);
2214:     DMGetLocalSection(dmAux, &sectionAux);
2215:     PetscDSGetTotalDimension(probAux, &totDimAux);
2216:     PetscDSGetComponentOffsets(probAux, &aOff);
2217:   }
2218:   /* Integrate over points */
2219:   {
2220:     PetscFEGeom    *fgeom, *chunkGeom = NULL;
2221:     PetscInt        maxDegree;
2222:     PetscQuadrature qGeom = NULL;
2223:     const PetscInt *points;
2224:     PetscInt        numFaces, face, Nq, field;
2225:     PetscInt        numChunks, chunkSize, chunk, Nr, offset;

2227:     ISGetLocalSize(pointIS, &numFaces);
2228:     ISGetIndices(pointIS, &points);
2229:     PetscCalloc2(numFaces*totDim, &u, locA ? numFaces*totDimAux : 0, &a);
2230:     DMFieldGetDegree(coordField, pointIS, NULL, &maxDegree);
2231:     for (field = 0; field < Nf; ++field) {
2232:       PetscFE fe;

2234:       PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);
2235:       if (maxDegree <= 1) {DMFieldCreateDefaultQuadrature(coordField, pointIS, &qGeom);}
2236:       if (!qGeom) {
2237:         PetscFEGetFaceQuadrature(fe, &qGeom);
2238:         PetscObjectReference((PetscObject) qGeom);
2239:       }
2240:       PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
2241:       DMPlexGetFEGeom(coordField, pointIS, qGeom, PETSC_TRUE, &fgeom);
2242:       for (face = 0; face < numFaces; ++face) {
2243:         const PetscInt point = points[face], *support;
2244:         PetscScalar    *x    = NULL;
2245:         PetscInt       i;

2247:         DMPlexGetSupport(dm, point, &support);
2248:         DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);
2249:         for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i];
2250:         DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);
2251:         if (locA) {
2252:           PetscInt subp;
2253:           DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);
2254:           DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);
2255:           for (i = 0; i < totDimAux; ++i) a[f*totDimAux+i] = x[i];
2256:           DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);
2257:         }
2258:       }
2259:       /* Get blocking */
2260:       {
2261:         PetscQuadrature q;
2262:         PetscInt        numBatches, batchSize, numBlocks, blockSize;
2263:         PetscInt        Nq, Nb;

2265:         PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
2266:         PetscFEGetQuadrature(fe, &q);
2267:         PetscQuadratureGetData(q, NULL, NULL, &Nq, NULL, NULL);
2268:         PetscFEGetDimension(fe, &Nb);
2269:         blockSize = Nb*Nq;
2270:         batchSize = numBlocks * blockSize;
2271:         chunkSize = numBatches*batchSize;
2272:         PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
2273:         numChunks = numFaces / chunkSize;
2274:         Nr        = numFaces % chunkSize;
2275:         offset    = numFaces - Nr;
2276:       }
2277:       /* Do integration for each field */
2278:       for (chunk = 0; chunk < numChunks; ++chunk) {
2279:         PetscFEGeomGetChunk(fgeom, chunk*chunkSize, (chunk+1)*chunkSize, &chunkGeom);
2280:         PetscFEIntegrateBd(prob, field, func, chunkSize, chunkGeom, u, probAux, a, fintegral);
2281:         PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);
2282:       }
2283:       PetscFEGeomGetChunk(fgeom, offset, numFaces, &chunkGeom);
2284:       PetscFEIntegrateBd(prob, field, func, Nr, chunkGeom, &u[offset*totDim], probAux, a ? &a[offset*totDimAux] : NULL, &fintegral[offset*Nf]);
2285:       PetscFEGeomRestoreChunk(fgeom, offset, numFaces, &chunkGeom);
2286:       /* Cleanup data arrays */
2287:       DMPlexRestoreFEGeom(coordField, pointIS, qGeom, PETSC_TRUE, &fgeom);
2288:       PetscQuadratureDestroy(&qGeom);
2289:       PetscFree2(u, a);
2290:       ISRestoreIndices(pointIS, &points);
2291:     }
2292:   }
2293:   if (plex)  {DMDestroy(&plex);}
2294:   if (plexA) {DMDestroy(&plexA);}
2295:   return(0);
2296: }

2298: /*@
2299:   DMPlexComputeBdIntegral - Form the integral over the specified boundary from the global input X using pointwise functions specified by the user

2301:   Input Parameters:
2302: + dm      - The mesh
2303: . X       - Global input vector
2304: . label   - The boundary DMLabel
2305: . numVals - The number of label values to use, or PETSC_DETERMINE for all values
2306: . vals    - The label values to use, or PETSC_NULL for all values
2307: . func    = The function to integrate along the boundary
2308: - user    - The user context

2310:   Output Parameter:
2311: . integral - Integral for each field

2313:   Level: developer

2315: .seealso: DMPlexComputeIntegralFEM(), DMPlexComputeBdResidualFEM()
2316: @*/
2317: PetscErrorCode DMPlexComputeBdIntegral(DM dm, Vec X, DMLabel label, PetscInt numVals, const PetscInt vals[],
2318:                                        void (*func)(PetscInt, PetscInt, PetscInt,
2319:                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
2320:                                                     const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
2321:                                                     PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]),
2322:                                        PetscScalar *integral, void *user)
2323: {
2324:   Vec            locX;
2325:   PetscSection   section;
2326:   DMLabel        depthLabel;
2327:   IS             facetIS;
2328:   PetscInt       dim, Nf, f, v;

2337:   PetscLogEventBegin(DMPLEX_IntegralFEM,dm,0,0,0);
2338:   DMPlexGetDepthLabel(dm, &depthLabel);
2339:   DMGetDimension(dm, &dim);
2340:   DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
2341:   DMGetLocalSection(dm, &section);
2342:   PetscSectionGetNumFields(section, &Nf);
2343:   /* Get local solution with boundary values */
2344:   DMGetLocalVector(dm, &locX);
2345:   DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locX, 0.0, NULL, NULL, NULL);
2346:   DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);
2347:   DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);
2348:   /* Loop over label values */
2349:   PetscArrayzero(integral, Nf);
2350:   for (v = 0; v < numVals; ++v) {
2351:     IS           pointIS;
2352:     PetscInt     numFaces, face;
2353:     PetscScalar *fintegral;

2355:     DMLabelGetStratumIS(label, vals[v], &pointIS);
2356:     if (!pointIS) continue; /* No points with that id on this process */
2357:     {
2358:       IS isectIS;

2360:       /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */
2361:       ISIntersect_Caching_Internal(facetIS, pointIS, &isectIS);
2362:       ISDestroy(&pointIS);
2363:       pointIS = isectIS;
2364:     }
2365:     ISGetLocalSize(pointIS, &numFaces);
2366:     PetscCalloc1(numFaces*Nf, &fintegral);
2367:     DMPlexComputeBdIntegral_Internal(dm, locX, pointIS, func, fintegral, user);
2368:     /* Sum point contributions into integral */
2369:     for (f = 0; f < Nf; ++f) for (face = 0; face < numFaces; ++face) integral[f] += fintegral[face*Nf+f];
2370:     PetscFree(fintegral);
2371:     ISDestroy(&pointIS);
2372:   }
2373:   DMRestoreLocalVector(dm, &locX);
2374:   ISDestroy(&facetIS);
2375:   PetscLogEventEnd(DMPLEX_IntegralFEM,dm,0,0,0);
2376:   return(0);
2377: }

2379: /*@
2380:   DMPlexComputeInterpolatorNested - Form the local portion of the interpolation matrix I from the coarse DM to a uniformly refined DM.

2382:   Input Parameters:
2383: + dmc  - The coarse mesh
2384: . dmf  - The fine mesh
2385: . isRefined - Flag indicating regular refinement, rather than the same topology
2386: - user - The user context

2388:   Output Parameter:
2389: . In  - The interpolation matrix

2391:   Level: developer

2393: .seealso: DMPlexComputeInterpolatorGeneral(), DMPlexComputeJacobianFEM()
2394: @*/
2395: PetscErrorCode DMPlexComputeInterpolatorNested(DM dmc, DM dmf, PetscBool isRefined, Mat In, void *user)
2396: {
2397:   DM_Plex          *mesh  = (DM_Plex *) dmc->data;
2398:   const char       *name  = "Interpolator";
2399:   PetscDS           cds, rds;
2400:   PetscFE          *feRef;
2401:   PetscFV          *fvRef;
2402:   PetscSection      fsection, fglobalSection;
2403:   PetscSection      csection, cglobalSection;
2404:   PetscScalar      *elemMat;
2405:   PetscInt          dim, Nf, f, fieldI, fieldJ, offsetI, offsetJ, cStart, cEnd, c;
2406:   PetscInt          cTotDim, rTotDim = 0;
2407:   PetscErrorCode    ierr;

2410:   PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
2411:   DMGetDimension(dmf, &dim);
2412:   DMGetLocalSection(dmf, &fsection);
2413:   DMGetGlobalSection(dmf, &fglobalSection);
2414:   DMGetLocalSection(dmc, &csection);
2415:   DMGetGlobalSection(dmc, &cglobalSection);
2416:   PetscSectionGetNumFields(fsection, &Nf);
2417:   DMPlexGetSimplexOrBoxCells(dmc, 0, &cStart, &cEnd);
2418:   DMGetDS(dmc, &cds);
2419:   DMGetDS(dmf, &rds);
2420:   PetscCalloc2(Nf, &feRef, Nf, &fvRef);
2421:   for (f = 0; f < Nf; ++f) {
2422:     PetscObject  obj;
2423:     PetscClassId id;
2424:     PetscInt     rNb = 0, Nc = 0;

2426:     PetscDSGetDiscretization(rds, f, &obj);
2427:     PetscObjectGetClassId(obj, &id);
2428:     if (id == PETSCFE_CLASSID) {
2429:       PetscFE fe = (PetscFE) obj;

2431:       if (isRefined) {
2432:         PetscFERefine(fe, &feRef[f]);
2433:       } else {
2434:         PetscObjectReference((PetscObject) fe);
2435:         feRef[f] = fe;
2436:       }
2437:       PetscFEGetDimension(feRef[f], &rNb);
2438:       PetscFEGetNumComponents(fe, &Nc);
2439:     } else if (id == PETSCFV_CLASSID) {
2440:       PetscFV        fv = (PetscFV) obj;
2441:       PetscDualSpace Q;

2443:       if (isRefined) {
2444:         PetscFVRefine(fv, &fvRef[f]);
2445:       } else {
2446:         PetscObjectReference((PetscObject) fv);
2447:         fvRef[f] = fv;
2448:       }
2449:       PetscFVGetDualSpace(fvRef[f], &Q);
2450:       PetscDualSpaceGetDimension(Q, &rNb);
2451:       PetscFVGetNumComponents(fv, &Nc);
2452:     }
2453:     rTotDim += rNb;
2454:   }
2455:   PetscDSGetTotalDimension(cds, &cTotDim);
2456:   PetscMalloc1(rTotDim*cTotDim,&elemMat);
2457:   PetscArrayzero(elemMat, rTotDim*cTotDim);
2458:   for (fieldI = 0, offsetI = 0; fieldI < Nf; ++fieldI) {
2459:     PetscDualSpace   Qref;
2460:     PetscQuadrature  f;
2461:     const PetscReal *qpoints, *qweights;
2462:     PetscReal       *points;
2463:     PetscInt         npoints = 0, Nc, Np, fpdim, i, k, p, d;

2465:     /* Compose points from all dual basis functionals */
2466:     if (feRef[fieldI]) {
2467:       PetscFEGetDualSpace(feRef[fieldI], &Qref);
2468:       PetscFEGetNumComponents(feRef[fieldI], &Nc);
2469:     } else {
2470:       PetscFVGetDualSpace(fvRef[fieldI], &Qref);
2471:       PetscFVGetNumComponents(fvRef[fieldI], &Nc);
2472:     }
2473:     PetscDualSpaceGetDimension(Qref, &fpdim);
2474:     for (i = 0; i < fpdim; ++i) {
2475:       PetscDualSpaceGetFunctional(Qref, i, &f);
2476:       PetscQuadratureGetData(f, NULL, NULL, &Np, NULL, NULL);
2477:       npoints += Np;
2478:     }
2479:     PetscMalloc1(npoints*dim,&points);
2480:     for (i = 0, k = 0; i < fpdim; ++i) {
2481:       PetscDualSpaceGetFunctional(Qref, i, &f);
2482:       PetscQuadratureGetData(f, NULL, NULL, &Np, &qpoints, NULL);
2483:       for (p = 0; p < Np; ++p, ++k) for (d = 0; d < dim; ++d) points[k*dim+d] = qpoints[p*dim+d];
2484:     }

2486:     for (fieldJ = 0, offsetJ = 0; fieldJ < Nf; ++fieldJ) {
2487:       PetscObject  obj;
2488:       PetscClassId id;
2489:       PetscInt     NcJ = 0, cpdim = 0, j, qNc;

2491:       PetscDSGetDiscretization(cds, fieldJ, &obj);
2492:       PetscObjectGetClassId(obj, &id);
2493:       if (id == PETSCFE_CLASSID) {
2494:         PetscFE           fe = (PetscFE) obj;
2495:         PetscTabulation T  = NULL;

2497:         /* Evaluate basis at points */
2498:         PetscFEGetNumComponents(fe, &NcJ);
2499:         PetscFEGetDimension(fe, &cpdim);
2500:         /* For now, fields only interpolate themselves */
2501:         if (fieldI == fieldJ) {
2502:           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);
2503:           PetscFECreateTabulation(fe, 1, npoints, points, 0, &T);
2504:           for (i = 0, k = 0; i < fpdim; ++i) {
2505:             PetscDualSpaceGetFunctional(Qref, i, &f);
2506:             PetscQuadratureGetData(f, NULL, &qNc, &Np, NULL, &qweights);
2507:             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);
2508:             for (p = 0; p < Np; ++p, ++k) {
2509:               for (j = 0; j < cpdim; ++j) {
2510:                 /*
2511:                    cTotDim:            Total columns in element interpolation matrix, sum of number of dual basis functionals in each field
2512:                    offsetI, offsetJ:   Offsets into the larger element interpolation matrix for different fields
2513:                    fpdim, i, cpdim, j: Dofs for fine and coarse grids, correspond to dual space basis functionals
2514:                    qNC, Nc, Ncj, c:    Number of components in this field
2515:                    Np, p:              Number of quad points in the fine grid functional i
2516:                    k:                  i*Np + p, overall point number for the interpolation
2517:                 */
2518:                 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i)*cTotDim + offsetJ + j] += T->T[0][k*cpdim*NcJ+j*Nc+c]*qweights[p*qNc+c];
2519:               }
2520:             }
2521:           }
2522:           PetscTabulationDestroy(&T);
2523:         }
2524:       } else if (id == PETSCFV_CLASSID) {
2525:         PetscFV        fv = (PetscFV) obj;

2527:         /* Evaluate constant function at points */
2528:         PetscFVGetNumComponents(fv, &NcJ);
2529:         cpdim = 1;
2530:         /* For now, fields only interpolate themselves */
2531:         if (fieldI == fieldJ) {
2532:           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);
2533:           for (i = 0, k = 0; i < fpdim; ++i) {
2534:             PetscDualSpaceGetFunctional(Qref, i, &f);
2535:             PetscQuadratureGetData(f, NULL, &qNc, &Np, NULL, &qweights);
2536:             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);
2537:             for (p = 0; p < Np; ++p, ++k) {
2538:               for (j = 0; j < cpdim; ++j) {
2539:                 for (c = 0; c < Nc; ++c) elemMat[(offsetI + i)*cTotDim + offsetJ + j] += 1.0*qweights[p*qNc+c];
2540:               }
2541:             }
2542:           }
2543:         }
2544:       }
2545:       offsetJ += cpdim;
2546:     }
2547:     offsetI += fpdim;
2548:     PetscFree(points);
2549:   }
2550:   if (mesh->printFEM > 1) {DMPrintCellMatrix(0, name, rTotDim, cTotDim, elemMat);}
2551:   /* Preallocate matrix */
2552:   {
2553:     Mat          preallocator;
2554:     PetscScalar *vals;
2555:     PetscInt    *cellCIndices, *cellFIndices;
2556:     PetscInt     locRows, locCols, cell;

2558:     MatGetLocalSize(In, &locRows, &locCols);
2559:     MatCreate(PetscObjectComm((PetscObject) In), &preallocator);
2560:     MatSetType(preallocator, MATPREALLOCATOR);
2561:     MatSetSizes(preallocator, locRows, locCols, PETSC_DETERMINE, PETSC_DETERMINE);
2562:     MatSetUp(preallocator);
2563:     PetscCalloc3(rTotDim*cTotDim, &vals,cTotDim,&cellCIndices,rTotDim,&cellFIndices);
2564:     for (cell = cStart; cell < cEnd; ++cell) {
2565:       if (isRefined) {
2566:         DMPlexMatGetClosureIndicesRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, cell, cellCIndices, cellFIndices);
2567:         MatSetValues(preallocator, rTotDim, cellFIndices, cTotDim, cellCIndices, vals, INSERT_VALUES);
2568:       } else {
2569:         DMPlexMatSetClosureGeneral(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, preallocator, cell, vals, INSERT_VALUES);
2570:       }
2571:     }
2572:     PetscFree3(vals,cellCIndices,cellFIndices);
2573:     MatAssemblyBegin(preallocator, MAT_FINAL_ASSEMBLY);
2574:     MatAssemblyEnd(preallocator, MAT_FINAL_ASSEMBLY);
2575:     MatPreallocatorPreallocate(preallocator, PETSC_TRUE, In);
2576:     MatDestroy(&preallocator);
2577:   }
2578:   /* Fill matrix */
2579:   MatZeroEntries(In);
2580:   for (c = cStart; c < cEnd; ++c) {
2581:     if (isRefined) {
2582:       DMPlexMatSetClosureRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);
2583:     } else {
2584:       DMPlexMatSetClosureGeneral(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, In, c, elemMat, INSERT_VALUES);
2585:     }
2586:   }
2587:   for (f = 0; f < Nf; ++f) {PetscFEDestroy(&feRef[f]);}
2588:   PetscFree2(feRef,fvRef);
2589:   PetscFree(elemMat);
2590:   MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);
2591:   MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);
2592:   if (mesh->printFEM) {
2593:     PetscPrintf(PetscObjectComm((PetscObject)In), "%s:\n", name);
2594:     MatChop(In, 1.0e-10);
2595:     MatView(In, NULL);
2596:   }
2597:   PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
2598:   return(0);
2599: }

2601: PetscErrorCode DMPlexComputeMassMatrixNested(DM dmc, DM dmf, Mat mass, void *user)
2602: {
2603:   SETERRQ(PetscObjectComm((PetscObject) dmc), PETSC_ERR_SUP, "Laziness");
2604: }

2606: /*@
2607:   DMPlexComputeInterpolatorGeneral - Form the local portion of the interpolation matrix I from the coarse DM to a non-nested fine DM.

2609:   Input Parameters:
2610: + dmf  - The fine mesh
2611: . dmc  - The coarse mesh
2612: - user - The user context

2614:   Output Parameter:
2615: . In  - The interpolation matrix

2617:   Level: developer

2619: .seealso: DMPlexComputeInterpolatorNested(), DMPlexComputeJacobianFEM()
2620: @*/
2621: PetscErrorCode DMPlexComputeInterpolatorGeneral(DM dmc, DM dmf, Mat In, void *user)
2622: {
2623:   DM_Plex       *mesh = (DM_Plex *) dmf->data;
2624:   const char    *name = "Interpolator";
2625:   PetscDS        prob;
2626:   PetscSection   fsection, csection, globalFSection, globalCSection;
2627:   PetscHSetIJ    ht;
2628:   PetscLayout    rLayout;
2629:   PetscInt      *dnz, *onz;
2630:   PetscInt       locRows, rStart, rEnd;
2631:   PetscReal     *x, *v0, *J, *invJ, detJ;
2632:   PetscReal     *v0c, *Jc, *invJc, detJc;
2633:   PetscScalar   *elemMat;
2634:   PetscInt       dim, Nf, field, totDim, cStart, cEnd, cell, ccell;

2638:   PetscLogEventBegin(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
2639:   DMGetCoordinateDim(dmc, &dim);
2640:   DMGetDS(dmc, &prob);
2641:   PetscDSGetWorkspace(prob, &x, NULL, NULL, NULL, NULL);
2642:   PetscDSGetNumFields(prob, &Nf);
2643:   PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);
2644:   PetscMalloc3(dim,&v0c,dim*dim,&Jc,dim*dim,&invJc);
2645:   DMGetLocalSection(dmf, &fsection);
2646:   DMGetGlobalSection(dmf, &globalFSection);
2647:   DMGetLocalSection(dmc, &csection);
2648:   DMGetGlobalSection(dmc, &globalCSection);
2649:   DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);
2650:   PetscDSGetTotalDimension(prob, &totDim);
2651:   PetscMalloc1(totDim, &elemMat);

2653:   MatGetLocalSize(In, &locRows, NULL);
2654:   PetscLayoutCreate(PetscObjectComm((PetscObject) In), &rLayout);
2655:   PetscLayoutSetLocalSize(rLayout, locRows);
2656:   PetscLayoutSetBlockSize(rLayout, 1);
2657:   PetscLayoutSetUp(rLayout);
2658:   PetscLayoutGetRange(rLayout, &rStart, &rEnd);
2659:   PetscLayoutDestroy(&rLayout);
2660:   PetscCalloc2(locRows,&dnz,locRows,&onz);
2661:   PetscHSetIJCreate(&ht);
2662:   for (field = 0; field < Nf; ++field) {
2663:     PetscObject      obj;
2664:     PetscClassId     id;
2665:     PetscDualSpace   Q = NULL;
2666:     PetscQuadrature  f;
2667:     const PetscReal *qpoints;
2668:     PetscInt         Nc, Np, fpdim, i, d;

2670:     PetscDSGetDiscretization(prob, field, &obj);
2671:     PetscObjectGetClassId(obj, &id);
2672:     if (id == PETSCFE_CLASSID) {
2673:       PetscFE fe = (PetscFE) obj;

2675:       PetscFEGetDualSpace(fe, &Q);
2676:       PetscFEGetNumComponents(fe, &Nc);
2677:     } else if (id == PETSCFV_CLASSID) {
2678:       PetscFV fv = (PetscFV) obj;

2680:       PetscFVGetDualSpace(fv, &Q);
2681:       Nc   = 1;
2682:     }
2683:     PetscDualSpaceGetDimension(Q, &fpdim);
2684:     /* For each fine grid cell */
2685:     for (cell = cStart; cell < cEnd; ++cell) {
2686:       PetscInt *findices,   *cindices;
2687:       PetscInt  numFIndices, numCIndices;

2689:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
2690:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
2691:       if (numFIndices != fpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of fine indices %D != %D dual basis vecs", numFIndices, fpdim);
2692:       for (i = 0; i < fpdim; ++i) {
2693:         Vec             pointVec;
2694:         PetscScalar    *pV;
2695:         PetscSF         coarseCellSF = NULL;
2696:         const PetscSFNode *coarseCells;
2697:         PetscInt        numCoarseCells, q, c;

2699:         /* Get points from the dual basis functional quadrature */
2700:         PetscDualSpaceGetFunctional(Q, i, &f);
2701:         PetscQuadratureGetData(f, NULL, NULL, &Np, &qpoints, NULL);
2702:         VecCreateSeq(PETSC_COMM_SELF, Np*dim, &pointVec);
2703:         VecSetBlockSize(pointVec, dim);
2704:         VecGetArray(pointVec, &pV);
2705:         for (q = 0; q < Np; ++q) {
2706:           const PetscReal xi0[3] = {-1., -1., -1.};

2708:           /* Transform point to real space */
2709:           CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
2710:           for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
2711:         }
2712:         VecRestoreArray(pointVec, &pV);
2713:         /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
2714:         /* OPT: Pack all quad points from fine cell */
2715:         DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
2716:         PetscSFViewFromOptions(coarseCellSF, NULL, "-interp_sf_view");
2717:         /* Update preallocation info */
2718:         PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
2719:         if (numCoarseCells != Np) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
2720:         {
2721:           PetscHashIJKey key;
2722:           PetscBool      missing;

2724:           key.i = findices[i];
2725:           if (key.i >= 0) {
2726:             /* Get indices for coarse elements */
2727:             for (ccell = 0; ccell < numCoarseCells; ++ccell) {
2728:               DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
2729:               for (c = 0; c < numCIndices; ++c) {
2730:                 key.j = cindices[c];
2731:                 if (key.j < 0) continue;
2732:                 PetscHSetIJQueryAdd(ht, key, &missing);
2733:                 if (missing) {
2734:                   if ((key.j >= rStart) && (key.j < rEnd)) ++dnz[key.i-rStart];
2735:                   else                                     ++onz[key.i-rStart];
2736:                 }
2737:               }
2738:               DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
2739:             }
2740:           }
2741:         }
2742:         PetscSFDestroy(&coarseCellSF);
2743:         VecDestroy(&pointVec);
2744:       }
2745:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
2746:     }
2747:   }
2748:   PetscHSetIJDestroy(&ht);
2749:   MatXAIJSetPreallocation(In, 1, dnz, onz, NULL, NULL);
2750:   MatSetOption(In, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
2751:   PetscFree2(dnz,onz);
2752:   for (field = 0; field < Nf; ++field) {
2753:     PetscObject       obj;
2754:     PetscClassId      id;
2755:     PetscDualSpace    Q = NULL;
2756:     PetscTabulation T = NULL;
2757:     PetscQuadrature   f;
2758:     const PetscReal  *qpoints, *qweights;
2759:     PetscInt          Nc, qNc, Np, fpdim, i, d;

2761:     PetscDSGetDiscretization(prob, field, &obj);
2762:     PetscObjectGetClassId(obj, &id);
2763:     if (id == PETSCFE_CLASSID) {
2764:       PetscFE fe = (PetscFE) obj;

2766:       PetscFEGetDualSpace(fe, &Q);
2767:       PetscFEGetNumComponents(fe, &Nc);
2768:       PetscFECreateTabulation(fe, 1, 1, x, 0, &T);
2769:     } else if (id == PETSCFV_CLASSID) {
2770:       PetscFV fv = (PetscFV) obj;

2772:       PetscFVGetDualSpace(fv, &Q);
2773:       Nc   = 1;
2774:     } else SETERRQ1(PetscObjectComm((PetscObject)dmc),PETSC_ERR_ARG_WRONG,"Unknown discretization type for field %D",field);
2775:     PetscDualSpaceGetDimension(Q, &fpdim);
2776:     /* For each fine grid cell */
2777:     for (cell = cStart; cell < cEnd; ++cell) {
2778:       PetscInt *findices,   *cindices;
2779:       PetscInt  numFIndices, numCIndices;

2781:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
2782:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
2783:       if (numFIndices != fpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of fine indices %D != %D dual basis vecs", numFIndices, fpdim);
2784:       for (i = 0; i < fpdim; ++i) {
2785:         Vec             pointVec;
2786:         PetscScalar    *pV;
2787:         PetscSF         coarseCellSF = NULL;
2788:         const PetscSFNode *coarseCells;
2789:         PetscInt        numCoarseCells, cpdim, q, c, j;

2791:         /* Get points from the dual basis functional quadrature */
2792:         PetscDualSpaceGetFunctional(Q, i, &f);
2793:         PetscQuadratureGetData(f, NULL, &qNc, &Np, &qpoints, &qweights);
2794:         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);
2795:         VecCreateSeq(PETSC_COMM_SELF, Np*dim, &pointVec);
2796:         VecSetBlockSize(pointVec, dim);
2797:         VecGetArray(pointVec, &pV);
2798:         for (q = 0; q < Np; ++q) {
2799:           const PetscReal xi0[3] = {-1., -1., -1.};

2801:           /* Transform point to real space */
2802:           CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
2803:           for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
2804:         }
2805:         VecRestoreArray(pointVec, &pV);
2806:         /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
2807:         /* OPT: Read this out from preallocation information */
2808:         DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
2809:         /* Update preallocation info */
2810:         PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
2811:         if (numCoarseCells != Np) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
2812:         VecGetArray(pointVec, &pV);
2813:         for (ccell = 0; ccell < numCoarseCells; ++ccell) {
2814:           PetscReal pVReal[3];
2815:           const PetscReal xi0[3] = {-1., -1., -1.};

2817:           DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
2818:           /* Transform points from real space to coarse reference space */
2819:           DMPlexComputeCellGeometryFEM(dmc, coarseCells[ccell].index, NULL, v0c, Jc, invJc, &detJc);
2820:           for (d = 0; d < dim; ++d) pVReal[d] = PetscRealPart(pV[ccell*dim+d]);
2821:           CoordinatesRealToRef(dim, dim, xi0, v0c, invJc, pVReal, x);

2823:           if (id == PETSCFE_CLASSID) {
2824:             PetscFE fe = (PetscFE) obj;

2826:             /* Evaluate coarse basis on contained point */
2827:             PetscFEGetDimension(fe, &cpdim);
2828:             PetscFEComputeTabulation(fe, 1, x, 0, T);
2829:             PetscArrayzero(elemMat, cpdim);
2830:             /* Get elemMat entries by multiplying by weight */
2831:             for (j = 0; j < cpdim; ++j) {
2832:               for (c = 0; c < Nc; ++c) elemMat[j] += T->T[0][j*Nc + c]*qweights[ccell*qNc + c];
2833:             }
2834:           } else {
2835:             cpdim = 1;
2836:             for (j = 0; j < cpdim; ++j) {
2837:               for (c = 0; c < Nc; ++c) elemMat[j] += 1.0*qweights[ccell*qNc + c];
2838:             }
2839:           }
2840:           /* Update interpolator */
2841:           if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
2842:           if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim);
2843:           MatSetValues(In, 1, &findices[i], numCIndices, cindices, elemMat, INSERT_VALUES);
2844:           DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
2845:         }
2846:         VecRestoreArray(pointVec, &pV);
2847:         PetscSFDestroy(&coarseCellSF);
2848:         VecDestroy(&pointVec);
2849:       }
2850:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
2851:     }
2852:     if (id == PETSCFE_CLASSID) {PetscTabulationDestroy(&T);}
2853:   }
2854:   PetscFree3(v0,J,invJ);
2855:   PetscFree3(v0c,Jc,invJc);
2856:   PetscFree(elemMat);
2857:   MatAssemblyBegin(In, MAT_FINAL_ASSEMBLY);
2858:   MatAssemblyEnd(In, MAT_FINAL_ASSEMBLY);
2859:   PetscLogEventEnd(DMPLEX_InterpolatorFEM,dmc,dmf,0,0);
2860:   return(0);
2861: }

2863: /*@
2864:   DMPlexComputeMassMatrixGeneral - Form the local portion of the mass matrix M from the coarse DM to a non-nested fine DM.

2866:   Input Parameters:
2867: + dmf  - The fine mesh
2868: . dmc  - The coarse mesh
2869: - user - The user context

2871:   Output Parameter:
2872: . mass  - The mass matrix

2874:   Level: developer

2876: .seealso: DMPlexComputeMassMatrixNested(), DMPlexComputeInterpolatorNested(), DMPlexComputeInterpolatorGeneral(), DMPlexComputeJacobianFEM()
2877: @*/
2878: PetscErrorCode DMPlexComputeMassMatrixGeneral(DM dmc, DM dmf, Mat mass, void *user)
2879: {
2880:   DM_Plex       *mesh = (DM_Plex *) dmf->data;
2881:   const char    *name = "Mass Matrix";
2882:   PetscDS        prob;
2883:   PetscSection   fsection, csection, globalFSection, globalCSection;
2884:   PetscHSetIJ    ht;
2885:   PetscLayout    rLayout;
2886:   PetscInt      *dnz, *onz;
2887:   PetscInt       locRows, rStart, rEnd;
2888:   PetscReal     *x, *v0, *J, *invJ, detJ;
2889:   PetscReal     *v0c, *Jc, *invJc, detJc;
2890:   PetscScalar   *elemMat;
2891:   PetscInt       dim, Nf, field, totDim, cStart, cEnd, cell, ccell;

2895:   DMGetCoordinateDim(dmc, &dim);
2896:   DMGetDS(dmc, &prob);
2897:   PetscDSGetWorkspace(prob, &x, NULL, NULL, NULL, NULL);
2898:   PetscDSGetNumFields(prob, &Nf);
2899:   PetscMalloc3(dim,&v0,dim*dim,&J,dim*dim,&invJ);
2900:   PetscMalloc3(dim,&v0c,dim*dim,&Jc,dim*dim,&invJc);
2901:   DMGetLocalSection(dmf, &fsection);
2902:   DMGetGlobalSection(dmf, &globalFSection);
2903:   DMGetLocalSection(dmc, &csection);
2904:   DMGetGlobalSection(dmc, &globalCSection);
2905:   DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);
2906:   PetscDSGetTotalDimension(prob, &totDim);
2907:   PetscMalloc1(totDim, &elemMat);

2909:   MatGetLocalSize(mass, &locRows, NULL);
2910:   PetscLayoutCreate(PetscObjectComm((PetscObject) mass), &rLayout);
2911:   PetscLayoutSetLocalSize(rLayout, locRows);
2912:   PetscLayoutSetBlockSize(rLayout, 1);
2913:   PetscLayoutSetUp(rLayout);
2914:   PetscLayoutGetRange(rLayout, &rStart, &rEnd);
2915:   PetscLayoutDestroy(&rLayout);
2916:   PetscCalloc2(locRows,&dnz,locRows,&onz);
2917:   PetscHSetIJCreate(&ht);
2918:   for (field = 0; field < Nf; ++field) {
2919:     PetscObject      obj;
2920:     PetscClassId     id;
2921:     PetscQuadrature  quad;
2922:     const PetscReal *qpoints;
2923:     PetscInt         Nq, Nc, i, d;

2925:     PetscDSGetDiscretization(prob, field, &obj);
2926:     PetscObjectGetClassId(obj, &id);
2927:     if (id == PETSCFE_CLASSID) {PetscFEGetQuadrature((PetscFE) obj, &quad);}
2928:     else                       {PetscFVGetQuadrature((PetscFV) obj, &quad);}
2929:     PetscQuadratureGetData(quad, NULL, &Nc, &Nq, &qpoints, NULL);
2930:     /* For each fine grid cell */
2931:     for (cell = cStart; cell < cEnd; ++cell) {
2932:       Vec                pointVec;
2933:       PetscScalar       *pV;
2934:       PetscSF            coarseCellSF = NULL;
2935:       const PetscSFNode *coarseCells;
2936:       PetscInt           numCoarseCells, q, c;
2937:       PetscInt          *findices,   *cindices;
2938:       PetscInt           numFIndices, numCIndices;

2940:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
2941:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
2942:       /* Get points from the quadrature */
2943:       VecCreateSeq(PETSC_COMM_SELF, Nq*dim, &pointVec);
2944:       VecSetBlockSize(pointVec, dim);
2945:       VecGetArray(pointVec, &pV);
2946:       for (q = 0; q < Nq; ++q) {
2947:         const PetscReal xi0[3] = {-1., -1., -1.};

2949:         /* Transform point to real space */
2950:         CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
2951:         for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
2952:       }
2953:       VecRestoreArray(pointVec, &pV);
2954:       /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
2955:       DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
2956:       PetscSFViewFromOptions(coarseCellSF, NULL, "-interp_sf_view");
2957:       /* Update preallocation info */
2958:       PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
2959:       if (numCoarseCells != Nq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
2960:       {
2961:         PetscHashIJKey key;
2962:         PetscBool      missing;

2964:         for (i = 0; i < numFIndices; ++i) {
2965:           key.i = findices[i];
2966:           if (key.i >= 0) {
2967:             /* Get indices for coarse elements */
2968:             for (ccell = 0; ccell < numCoarseCells; ++ccell) {
2969:               DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
2970:               for (c = 0; c < numCIndices; ++c) {
2971:                 key.j = cindices[c];
2972:                 if (key.j < 0) continue;
2973:                 PetscHSetIJQueryAdd(ht, key, &missing);
2974:                 if (missing) {
2975:                   if ((key.j >= rStart) && (key.j < rEnd)) ++dnz[key.i-rStart];
2976:                   else                                     ++onz[key.i-rStart];
2977:                 }
2978:               }
2979:               DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
2980:             }
2981:           }
2982:         }
2983:       }
2984:       PetscSFDestroy(&coarseCellSF);
2985:       VecDestroy(&pointVec);
2986:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
2987:     }
2988:   }
2989:   PetscHSetIJDestroy(&ht);
2990:   MatXAIJSetPreallocation(mass, 1, dnz, onz, NULL, NULL);
2991:   MatSetOption(mass, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
2992:   PetscFree2(dnz,onz);
2993:   for (field = 0; field < Nf; ++field) {
2994:     PetscObject       obj;
2995:     PetscClassId      id;
2996:     PetscTabulation T, Tfine;
2997:     PetscQuadrature   quad;
2998:     const PetscReal  *qpoints, *qweights;
2999:     PetscInt          Nq, Nc, i, d;

3001:     PetscDSGetDiscretization(prob, field, &obj);
3002:     PetscObjectGetClassId(obj, &id);
3003:     if (id == PETSCFE_CLASSID) {
3004:       PetscFEGetQuadrature((PetscFE) obj, &quad);
3005:       PetscFEGetCellTabulation((PetscFE) obj, &Tfine);
3006:       PetscFECreateTabulation((PetscFE) obj, 1, 1, x, 0, &T);
3007:     } else {
3008:       PetscFVGetQuadrature((PetscFV) obj, &quad);
3009:     }
3010:     PetscQuadratureGetData(quad, NULL, &Nc, &Nq, &qpoints, &qweights);
3011:     /* For each fine grid cell */
3012:     for (cell = cStart; cell < cEnd; ++cell) {
3013:       Vec                pointVec;
3014:       PetscScalar       *pV;
3015:       PetscSF            coarseCellSF = NULL;
3016:       const PetscSFNode *coarseCells;
3017:       PetscInt           numCoarseCells, cpdim, q, c, j;
3018:       PetscInt          *findices,   *cindices;
3019:       PetscInt           numFIndices, numCIndices;

3021:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
3022:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
3023:       /* Get points from the quadrature */
3024:       VecCreateSeq(PETSC_COMM_SELF, Nq*dim, &pointVec);
3025:       VecSetBlockSize(pointVec, dim);
3026:       VecGetArray(pointVec, &pV);
3027:       for (q = 0; q < Nq; ++q) {
3028:         const PetscReal xi0[3] = {-1., -1., -1.};

3030:         /* Transform point to real space */
3031:         CoordinatesRefToReal(dim, dim, xi0, v0, J, &qpoints[q*dim], x);
3032:         for (d = 0; d < dim; ++d) pV[q*dim+d] = x[d];
3033:       }
3034:       VecRestoreArray(pointVec, &pV);
3035:       /* Get set of coarse cells that overlap points (would like to group points by coarse cell) */
3036:       DMLocatePoints(dmc, pointVec, DM_POINTLOCATION_NEAREST, &coarseCellSF);
3037:       /* Update matrix */
3038:       PetscSFGetGraph(coarseCellSF, NULL, &numCoarseCells, NULL, &coarseCells);
3039:       if (numCoarseCells != Nq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Not all closure points located");
3040:       VecGetArray(pointVec, &pV);
3041:       for (ccell = 0; ccell < numCoarseCells; ++ccell) {
3042:         PetscReal pVReal[3];
3043:         const PetscReal xi0[3] = {-1., -1., -1.};


3046:         DMPlexGetClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
3047:         /* Transform points from real space to coarse reference space */
3048:         DMPlexComputeCellGeometryFEM(dmc, coarseCells[ccell].index, NULL, v0c, Jc, invJc, &detJc);
3049:         for (d = 0; d < dim; ++d) pVReal[d] = PetscRealPart(pV[ccell*dim+d]);
3050:         CoordinatesRealToRef(dim, dim, xi0, v0c, invJc, pVReal, x);

3052:         if (id == PETSCFE_CLASSID) {
3053:           PetscFE fe = (PetscFE) obj;

3055:           /* Evaluate coarse basis on contained point */
3056:           PetscFEGetDimension(fe, &cpdim);
3057:           PetscFEComputeTabulation(fe, 1, x, 0, T);
3058:           /* Get elemMat entries by multiplying by weight */
3059:           for (i = 0; i < numFIndices; ++i) {
3060:             PetscArrayzero(elemMat, cpdim);
3061:             for (j = 0; j < cpdim; ++j) {
3062:               for (c = 0; c < Nc; ++c) elemMat[j] += T->T[0][j*Nc + c]*Tfine->T[0][(ccell*numFIndices + i)*Nc + c]*qweights[ccell*Nc + c]*detJ;
3063:             }
3064:             /* Update interpolator */
3065:             if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
3066:             if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim);
3067:             MatSetValues(mass, 1, &findices[i], numCIndices, cindices, elemMat, ADD_VALUES);
3068:           }
3069:         } else {
3070:           cpdim = 1;
3071:           for (i = 0; i < numFIndices; ++i) {
3072:             PetscArrayzero(elemMat, cpdim);
3073:             for (j = 0; j < cpdim; ++j) {
3074:               for (c = 0; c < Nc; ++c) elemMat[j] += 1.0*1.0*qweights[ccell*Nc + c]*detJ;
3075:             }
3076:             /* Update interpolator */
3077:             if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
3078:             PetscPrintf(PETSC_COMM_SELF, "Nq: %D %D Nf: %D %D Nc: %D %D\n", ccell, Nq, i, numFIndices, j, numCIndices);
3079:             if (numCIndices != cpdim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of element matrix columns %D != %D", numCIndices, cpdim);
3080:             MatSetValues(mass, 1, &findices[i], numCIndices, cindices, elemMat, ADD_VALUES);
3081:           }
3082:         }
3083:         DMPlexRestoreClosureIndices(dmc, csection, globalCSection, coarseCells[ccell].index, PETSC_FALSE, &numCIndices, &cindices, NULL, NULL);
3084:       }
3085:       VecRestoreArray(pointVec, &pV);
3086:       PetscSFDestroy(&coarseCellSF);
3087:       VecDestroy(&pointVec);
3088:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
3089:     }
3090:     if (id == PETSCFE_CLASSID) {PetscTabulationDestroy(&T);}
3091:   }
3092:   PetscFree3(v0,J,invJ);
3093:   PetscFree3(v0c,Jc,invJc);
3094:   PetscFree(elemMat);
3095:   MatAssemblyBegin(mass, MAT_FINAL_ASSEMBLY);
3096:   MatAssemblyEnd(mass, MAT_FINAL_ASSEMBLY);
3097:   return(0);
3098: }

3100: /*@
3101:   DMPlexComputeInjectorFEM - Compute a mapping from coarse unknowns to fine unknowns

3103:   Input Parameters:
3104: + dmc  - The coarse mesh
3105: - dmf  - The fine mesh
3106: - user - The user context

3108:   Output Parameter:
3109: . sc   - The mapping

3111:   Level: developer

3113: .seealso: DMPlexComputeInterpolatorNested(), DMPlexComputeJacobianFEM()
3114: @*/
3115: PetscErrorCode DMPlexComputeInjectorFEM(DM dmc, DM dmf, VecScatter *sc, void *user)
3116: {
3117:   PetscDS        prob;
3118:   PetscFE       *feRef;
3119:   PetscFV       *fvRef;
3120:   Vec            fv, cv;
3121:   IS             fis, cis;
3122:   PetscSection   fsection, fglobalSection, csection, cglobalSection;
3123:   PetscInt      *cmap, *cellCIndices, *cellFIndices, *cindices, *findices;
3124:   PetscInt       cTotDim, fTotDim = 0, Nf, f, field, cStart, cEnd, c, dim, d, startC, endC, offsetC, offsetF, m;
3125:   PetscBool     *needAvg;

3129:   PetscLogEventBegin(DMPLEX_InjectorFEM,dmc,dmf,0,0);
3130:   DMGetDimension(dmf, &dim);
3131:   DMGetLocalSection(dmf, &fsection);
3132:   DMGetGlobalSection(dmf, &fglobalSection);
3133:   DMGetLocalSection(dmc, &csection);
3134:   DMGetGlobalSection(dmc, &cglobalSection);
3135:   PetscSectionGetNumFields(fsection, &Nf);
3136:   DMPlexGetSimplexOrBoxCells(dmc, 0, &cStart, &cEnd);
3137:   DMGetDS(dmc, &prob);
3138:   PetscCalloc3(Nf,&feRef,Nf,&fvRef,Nf,&needAvg);
3139:   for (f = 0; f < Nf; ++f) {
3140:     PetscObject  obj;
3141:     PetscClassId id;
3142:     PetscInt     fNb = 0, Nc = 0;

3144:     PetscDSGetDiscretization(prob, f, &obj);
3145:     PetscObjectGetClassId(obj, &id);
3146:     if (id == PETSCFE_CLASSID) {
3147:       PetscFE    fe = (PetscFE) obj;
3148:       PetscSpace sp;
3149:       PetscInt   maxDegree;

3151:       PetscFERefine(fe, &feRef[f]);
3152:       PetscFEGetDimension(feRef[f], &fNb);
3153:       PetscFEGetNumComponents(fe, &Nc);
3154:       PetscFEGetBasisSpace(fe, &sp);
3155:       PetscSpaceGetDegree(sp, NULL, &maxDegree);
3156:       if (!maxDegree) needAvg[f] = PETSC_TRUE;
3157:     } else if (id == PETSCFV_CLASSID) {
3158:       PetscFV        fv = (PetscFV) obj;
3159:       PetscDualSpace Q;

3161:       PetscFVRefine(fv, &fvRef[f]);
3162:       PetscFVGetDualSpace(fvRef[f], &Q);
3163:       PetscDualSpaceGetDimension(Q, &fNb);
3164:       PetscFVGetNumComponents(fv, &Nc);
3165:       needAvg[f] = PETSC_TRUE;
3166:     }
3167:     fTotDim += fNb;
3168:   }
3169:   PetscDSGetTotalDimension(prob, &cTotDim);
3170:   PetscMalloc1(cTotDim,&cmap);
3171:   for (field = 0, offsetC = 0, offsetF = 0; field < Nf; ++field) {
3172:     PetscFE        feC;
3173:     PetscFV        fvC;
3174:     PetscDualSpace QF, QC;
3175:     PetscInt       order = -1, NcF, NcC, fpdim, cpdim;

3177:     if (feRef[field]) {
3178:       PetscDSGetDiscretization(prob, field, (PetscObject *) &feC);
3179:       PetscFEGetNumComponents(feC, &NcC);
3180:       PetscFEGetNumComponents(feRef[field], &NcF);
3181:       PetscFEGetDualSpace(feRef[field], &QF);
3182:       PetscDualSpaceGetOrder(QF, &order);
3183:       PetscDualSpaceGetDimension(QF, &fpdim);
3184:       PetscFEGetDualSpace(feC, &QC);
3185:       PetscDualSpaceGetDimension(QC, &cpdim);
3186:     } else {
3187:       PetscDSGetDiscretization(prob, field, (PetscObject *) &fvC);
3188:       PetscFVGetNumComponents(fvC, &NcC);
3189:       PetscFVGetNumComponents(fvRef[field], &NcF);
3190:       PetscFVGetDualSpace(fvRef[field], &QF);
3191:       PetscDualSpaceGetDimension(QF, &fpdim);
3192:       PetscFVGetDualSpace(fvC, &QC);
3193:       PetscDualSpaceGetDimension(QC, &cpdim);
3194:     }
3195:     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);
3196:     for (c = 0; c < cpdim; ++c) {
3197:       PetscQuadrature  cfunc;
3198:       const PetscReal *cqpoints, *cqweights;
3199:       PetscInt         NqcC, NpC;
3200:       PetscBool        found = PETSC_FALSE;

3202:       PetscDualSpaceGetFunctional(QC, c, &cfunc);
3203:       PetscQuadratureGetData(cfunc, NULL, &NqcC, &NpC, &cqpoints, &cqweights);
3204:       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);
3205:       if (NpC != 1 && feRef[field]) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Do not know how to do injection for moments");
3206:       for (f = 0; f < fpdim; ++f) {
3207:         PetscQuadrature  ffunc;
3208:         const PetscReal *fqpoints, *fqweights;
3209:         PetscReal        sum = 0.0;
3210:         PetscInt         NqcF, NpF;

3212:         PetscDualSpaceGetFunctional(QF, f, &ffunc);
3213:         PetscQuadratureGetData(ffunc, NULL, &NqcF, &NpF, &fqpoints, &fqweights);
3214:         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);
3215:         if (NpC != NpF) continue;
3216:         for (d = 0; d < dim; ++d) sum += PetscAbsReal(cqpoints[d] - fqpoints[d]);
3217:         if (sum > 1.0e-9) continue;
3218:         for (d = 0; d < NcC; ++d) sum += PetscAbsReal(cqweights[d]*fqweights[d]);
3219:         if (sum < 1.0e-9) continue;
3220:         cmap[offsetC+c] = offsetF+f;
3221:         found = PETSC_TRUE;
3222:         break;
3223:       }
3224:       if (!found) {
3225:         /* TODO We really want the average here, but some asshole put VecScatter in the interface */
3226:         if (fvRef[field] || (feRef[field] && order == 0)) {
3227:           cmap[offsetC+c] = offsetF+0;
3228:         } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not locate matching functional for injection");
3229:       }
3230:     }
3231:     offsetC += cpdim;
3232:     offsetF += fpdim;
3233:   }
3234:   for (f = 0; f < Nf; ++f) {PetscFEDestroy(&feRef[f]);PetscFVDestroy(&fvRef[f]);}
3235:   PetscFree3(feRef,fvRef,needAvg);

3237:   DMGetGlobalVector(dmf, &fv);
3238:   DMGetGlobalVector(dmc, &cv);
3239:   VecGetOwnershipRange(cv, &startC, &endC);
3240:   PetscSectionGetConstrainedStorageSize(cglobalSection, &m);
3241:   PetscMalloc2(cTotDim,&cellCIndices,fTotDim,&cellFIndices);
3242:   PetscMalloc1(m,&cindices);
3243:   PetscMalloc1(m,&findices);
3244:   for (d = 0; d < m; ++d) cindices[d] = findices[d] = -1;
3245:   for (c = cStart; c < cEnd; ++c) {
3246:     DMPlexMatGetClosureIndicesRefined(dmf, fsection, fglobalSection, dmc, csection, cglobalSection, c, cellCIndices, cellFIndices);
3247:     for (d = 0; d < cTotDim; ++d) {
3248:       if ((cellCIndices[d] < startC) || (cellCIndices[d] >= endC)) continue;
3249:       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]]);
3250:       cindices[cellCIndices[d]-startC] = cellCIndices[d];
3251:       findices[cellCIndices[d]-startC] = cellFIndices[cmap[d]];
3252:     }
3253:   }
3254:   PetscFree(cmap);
3255:   PetscFree2(cellCIndices,cellFIndices);

3257:   ISCreateGeneral(PETSC_COMM_SELF, m, cindices, PETSC_OWN_POINTER, &cis);
3258:   ISCreateGeneral(PETSC_COMM_SELF, m, findices, PETSC_OWN_POINTER, &fis);
3259:   VecScatterCreate(cv, cis, fv, fis, sc);
3260:   ISDestroy(&cis);
3261:   ISDestroy(&fis);
3262:   DMRestoreGlobalVector(dmf, &fv);
3263:   DMRestoreGlobalVector(dmc, &cv);
3264:   PetscLogEventEnd(DMPLEX_InjectorFEM,dmc,dmf,0,0);
3265:   return(0);
3266: }

3268: /*@C
3269:   DMPlexGetCellFields - Retrieve the field values values for a chunk of cells

3271:   Input Parameters:
3272: + dm     - The DM
3273: . cellIS - The cells to include
3274: . locX   - A local vector with the solution fields
3275: . locX_t - A local vector with solution field time derivatives, or NULL
3276: - locA   - A local vector with auxiliary fields, or NULL

3278:   Output Parameters:
3279: + u   - The field coefficients
3280: . u_t - The fields derivative coefficients
3281: - a   - The auxiliary field coefficients

3283:   Level: developer

3285: .seealso: DMPlexGetFaceFields()
3286: @*/
3287: PetscErrorCode DMPlexGetCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a)
3288: {
3289:   DM              plex, plexA = NULL;
3290:   DMEnclosureType encAux;
3291:   PetscSection    section, sectionAux;
3292:   PetscDS         prob;
3293:   const PetscInt *cells;
3294:   PetscInt        cStart, cEnd, numCells, totDim, totDimAux, c;
3295:   PetscErrorCode  ierr;

3305:   DMPlexConvertPlex(dm, &plex, PETSC_FALSE);
3306:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
3307:   DMGetLocalSection(dm, &section);
3308:   DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);
3309:   PetscDSGetTotalDimension(prob, &totDim);
3310:   if (locA) {
3311:     DM      dmAux;
3312:     PetscDS probAux;

3314:     VecGetDM(locA, &dmAux);
3315:     DMGetEnclosureRelation(dmAux, dm, &encAux);
3316:     DMPlexConvertPlex(dmAux, &plexA, PETSC_FALSE);
3317:     DMGetLocalSection(dmAux, &sectionAux);
3318:     DMGetDS(dmAux, &probAux);
3319:     PetscDSGetTotalDimension(probAux, &totDimAux);
3320:   }
3321:   numCells = cEnd - cStart;
3322:   DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u);
3323:   if (locX_t) {DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u_t);} else {*u_t = NULL;}
3324:   if (locA)   {DMGetWorkArray(dm, numCells*totDimAux, MPIU_SCALAR, a);} else {*a = NULL;}
3325:   for (c = cStart; c < cEnd; ++c) {
3326:     const PetscInt cell = cells ? cells[c] : c;
3327:     const PetscInt cind = c - cStart;
3328:     PetscScalar   *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a;
3329:     PetscInt       i;

3331:     DMPlexVecGetClosure(plex, section, locX, cell, NULL, &x);
3332:     for (i = 0; i < totDim; ++i) ul[cind*totDim+i] = x[i];
3333:     DMPlexVecRestoreClosure(plex, section, locX, cell, NULL, &x);
3334:     if (locX_t) {
3335:       DMPlexVecGetClosure(plex, section, locX_t, cell, NULL, &x_t);
3336:       for (i = 0; i < totDim; ++i) ul_t[cind*totDim+i] = x_t[i];
3337:       DMPlexVecRestoreClosure(plex, section, locX_t, cell, NULL, &x_t);
3338:     }
3339:     if (locA) {
3340:       PetscInt subcell;
3341:       DMGetEnclosurePoint(plexA, dm, encAux, cell, &subcell);
3342:       DMPlexVecGetClosure(plexA, sectionAux, locA, subcell, NULL, &x);
3343:       for (i = 0; i < totDimAux; ++i) al[cind*totDimAux+i] = x[i];
3344:       DMPlexVecRestoreClosure(plexA, sectionAux, locA, subcell, NULL, &x);
3345:     }
3346:   }
3347:   DMDestroy(&plex);
3348:   if (locA) {DMDestroy(&plexA);}
3349:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
3350:   return(0);
3351: }

3353: /*@C
3354:   DMPlexRestoreCellFields - Restore the field values values for a chunk of cells

3356:   Input Parameters:
3357: + dm     - The DM
3358: . cellIS - The cells to include
3359: . locX   - A local vector with the solution fields
3360: . locX_t - A local vector with solution field time derivatives, or NULL
3361: - locA   - A local vector with auxiliary fields, or NULL

3363:   Output Parameters:
3364: + u   - The field coefficients
3365: . u_t - The fields derivative coefficients
3366: - a   - The auxiliary field coefficients

3368:   Level: developer

3370: .seealso: DMPlexGetFaceFields()
3371: @*/
3372: PetscErrorCode DMPlexRestoreCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a)
3373: {

3377:   DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u);
3378:   if (locX_t) {DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u_t);}
3379:   if (locA)   {DMRestoreWorkArray(dm, 0, MPIU_SCALAR, a);}
3380:   return(0);
3381: }

3383: /*@C
3384:   DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces

3386:   Input Parameters:
3387: + dm     - The DM
3388: . fStart - The first face to include
3389: . fEnd   - The first face to exclude
3390: . locX   - A local vector with the solution fields
3391: . locX_t - A local vector with solution field time derivatives, or NULL
3392: . faceGeometry - A local vector with face geometry
3393: . cellGeometry - A local vector with cell geometry
3394: - locaGrad - A local vector with field gradients, or NULL

3396:   Output Parameters:
3397: + Nface - The number of faces with field values
3398: . uL - The field values at the left side of the face
3399: - uR - The field values at the right side of the face

3401:   Level: developer

3403: .seealso: DMPlexGetCellFields()
3404: @*/
3405: 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)
3406: {
3407:   DM                 dmFace, dmCell, dmGrad = NULL;
3408:   PetscSection       section;
3409:   PetscDS            prob;
3410:   DMLabel            ghostLabel;
3411:   const PetscScalar *facegeom, *cellgeom, *x, *lgrad;
3412:   PetscBool         *isFE;
3413:   PetscInt           dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face;
3414:   PetscErrorCode     ierr;

3425:   DMGetDimension(dm, &dim);
3426:   DMGetDS(dm, &prob);
3427:   DMGetLocalSection(dm, &section);
3428:   PetscDSGetNumFields(prob, &Nf);
3429:   PetscDSGetTotalComponents(prob, &Nc);
3430:   PetscMalloc1(Nf, &isFE);
3431:   for (f = 0; f < Nf; ++f) {
3432:     PetscObject  obj;
3433:     PetscClassId id;

3435:     PetscDSGetDiscretization(prob, f, &obj);
3436:     PetscObjectGetClassId(obj, &id);
3437:     if (id == PETSCFE_CLASSID)      {isFE[f] = PETSC_TRUE;}
3438:     else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;}
3439:     else                            {isFE[f] = PETSC_FALSE;}
3440:   }
3441:   DMGetLabel(dm, "ghost", &ghostLabel);
3442:   VecGetArrayRead(locX, &x);
3443:   VecGetDM(faceGeometry, &dmFace);
3444:   VecGetArrayRead(faceGeometry, &facegeom);
3445:   VecGetDM(cellGeometry, &dmCell);
3446:   VecGetArrayRead(cellGeometry, &cellgeom);
3447:   if (locGrad) {
3448:     VecGetDM(locGrad, &dmGrad);
3449:     VecGetArrayRead(locGrad, &lgrad);
3450:   }
3451:   DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uL);
3452:   DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uR);
3453:   /* Right now just eat the extra work for FE (could make a cell loop) */
3454:   for (face = fStart, iface = 0; face < fEnd; ++face) {
3455:     const PetscInt        *cells;
3456:     PetscFVFaceGeom       *fg;
3457:     PetscFVCellGeom       *cgL, *cgR;
3458:     PetscScalar           *xL, *xR, *gL, *gR;
3459:     PetscScalar           *uLl = *uL, *uRl = *uR;
3460:     PetscInt               ghost, nsupp, nchild;

3462:     DMLabelGetValue(ghostLabel, face, &ghost);
3463:     DMPlexGetSupportSize(dm, face, &nsupp);
3464:     DMPlexGetTreeChildren(dm, face, &nchild, NULL);
3465:     if (ghost >= 0 || nsupp > 2 || nchild > 0) continue;
3466:     DMPlexPointLocalRead(dmFace, face, facegeom, &fg);
3467:     DMPlexGetSupport(dm, face, &cells);
3468:     DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);
3469:     DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);
3470:     for (f = 0; f < Nf; ++f) {
3471:       PetscInt off;

3473:       PetscDSGetComponentOffset(prob, f, &off);
3474:       if (isFE[f]) {
3475:         const PetscInt *cone;
3476:         PetscInt        comp, coneSizeL, coneSizeR, faceLocL, faceLocR, ldof, rdof, d;

3478:         xL = xR = NULL;
3479:         PetscSectionGetFieldComponents(section, f, &comp);
3480:         DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);
3481:         DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);
3482:         DMPlexGetCone(dm, cells[0], &cone);
3483:         DMPlexGetConeSize(dm, cells[0], &coneSizeL);
3484:         for (faceLocL = 0; faceLocL < coneSizeL; ++faceLocL) if (cone[faceLocL] == face) break;
3485:         DMPlexGetCone(dm, cells[1], &cone);
3486:         DMPlexGetConeSize(dm, cells[1], &coneSizeR);
3487:         for (faceLocR = 0; faceLocR < coneSizeR; ++faceLocR) if (cone[faceLocR] == face) break;
3488:         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]);
3489:         /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */
3490:         /* TODO: this is a hack that might not be right for nonconforming */
3491:         if (faceLocL < coneSizeL) {
3492:           PetscFEEvaluateFaceFields_Internal(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);
3493:           if (rdof == ldof && faceLocR < coneSizeR) {PetscFEEvaluateFaceFields_Internal(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);}
3494:           else              {for (d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];}
3495:         }
3496:         else {
3497:           PetscFEEvaluateFaceFields_Internal(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);
3498:           PetscSectionGetFieldComponents(section, f, &comp);
3499:           for (d = 0; d < comp; ++d) uLl[iface*Nc+off+d] = uRl[iface*Nc+off+d];
3500:         }
3501:         DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);
3502:         DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);
3503:       } else {
3504:         PetscFV  fv;
3505:         PetscInt numComp, c;

3507:         PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);
3508:         PetscFVGetNumComponents(fv, &numComp);
3509:         DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);
3510:         DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);
3511:         if (dmGrad) {
3512:           PetscReal dxL[3], dxR[3];

3514:           DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);
3515:           DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);
3516:           DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL);
3517:           DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR);
3518:           for (c = 0; c < numComp; ++c) {
3519:             uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL);
3520:             uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR);
3521:           }
3522:         } else {
3523:           for (c = 0; c < numComp; ++c) {
3524:             uLl[iface*Nc+off+c] = xL[c];
3525:             uRl[iface*Nc+off+c] = xR[c];
3526:           }
3527:         }
3528:       }
3529:     }
3530:     ++iface;
3531:   }
3532:   *Nface = iface;
3533:   VecRestoreArrayRead(locX, &x);
3534:   VecRestoreArrayRead(faceGeometry, &facegeom);
3535:   VecRestoreArrayRead(cellGeometry, &cellgeom);
3536:   if (locGrad) {
3537:     VecRestoreArrayRead(locGrad, &lgrad);
3538:   }
3539:   PetscFree(isFE);
3540:   return(0);
3541: }

3543: /*@C
3544:   DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces

3546:   Input Parameters:
3547: + dm     - The DM
3548: . fStart - The first face to include
3549: . fEnd   - The first face to exclude
3550: . locX   - A local vector with the solution fields
3551: . locX_t - A local vector with solution field time derivatives, or NULL
3552: . faceGeometry - A local vector with face geometry
3553: . cellGeometry - A local vector with cell geometry
3554: - locaGrad - A local vector with field gradients, or NULL

3556:   Output Parameters:
3557: + Nface - The number of faces with field values
3558: . uL - The field values at the left side of the face
3559: - uR - The field values at the right side of the face

3561:   Level: developer

3563: .seealso: DMPlexGetFaceFields()
3564: @*/
3565: 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)
3566: {

3570:   DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uL);
3571:   DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uR);
3572:   return(0);
3573: }

3575: /*@C
3576:   DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces

3578:   Input Parameters:
3579: + dm     - The DM
3580: . fStart - The first face to include
3581: . fEnd   - The first face to exclude
3582: . faceGeometry - A local vector with face geometry
3583: - cellGeometry - A local vector with cell geometry

3585:   Output Parameters:
3586: + Nface - The number of faces with field values
3587: . fgeom - The extract the face centroid and normal
3588: - vol   - The cell volume

3590:   Level: developer

3592: .seealso: DMPlexGetCellFields()
3593: @*/
3594: PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol)
3595: {
3596:   DM                 dmFace, dmCell;
3597:   DMLabel            ghostLabel;
3598:   const PetscScalar *facegeom, *cellgeom;
3599:   PetscInt           dim, numFaces = fEnd - fStart, iface, face;
3600:   PetscErrorCode     ierr;

3608:   DMGetDimension(dm, &dim);
3609:   DMGetLabel(dm, "ghost", &ghostLabel);
3610:   VecGetDM(faceGeometry, &dmFace);
3611:   VecGetArrayRead(faceGeometry, &facegeom);
3612:   VecGetDM(cellGeometry, &dmCell);
3613:   VecGetArrayRead(cellGeometry, &cellgeom);
3614:   PetscMalloc1(numFaces, fgeom);
3615:   DMGetWorkArray(dm, numFaces*2, MPIU_SCALAR, vol);
3616:   for (face = fStart, iface = 0; face < fEnd; ++face) {
3617:     const PetscInt        *cells;
3618:     PetscFVFaceGeom       *fg;
3619:     PetscFVCellGeom       *cgL, *cgR;
3620:     PetscFVFaceGeom       *fgeoml = *fgeom;
3621:     PetscReal             *voll   = *vol;
3622:     PetscInt               ghost, d, nchild, nsupp;

3624:     DMLabelGetValue(ghostLabel, face, &ghost);
3625:     DMPlexGetSupportSize(dm, face, &nsupp);
3626:     DMPlexGetTreeChildren(dm, face, &nchild, NULL);
3627:     if (ghost >= 0 || nsupp > 2 || nchild > 0) continue;
3628:     DMPlexPointLocalRead(dmFace, face, facegeom, &fg);
3629:     DMPlexGetSupport(dm, face, &cells);
3630:     DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);
3631:     DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);
3632:     for (d = 0; d < dim; ++d) {
3633:       fgeoml[iface].centroid[d] = fg->centroid[d];
3634:       fgeoml[iface].normal[d]   = fg->normal[d];
3635:     }
3636:     voll[iface*2+0] = cgL->volume;
3637:     voll[iface*2+1] = cgR->volume;
3638:     ++iface;
3639:   }
3640:   *Nface = iface;
3641:   VecRestoreArrayRead(faceGeometry, &facegeom);
3642:   VecRestoreArrayRead(cellGeometry, &cellgeom);
3643:   return(0);
3644: }

3646: /*@C
3647:   DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces

3649:   Input Parameters:
3650: + dm     - The DM
3651: . fStart - The first face to include
3652: . fEnd   - The first face to exclude
3653: . faceGeometry - A local vector with face geometry
3654: - cellGeometry - A local vector with cell geometry

3656:   Output Parameters:
3657: + Nface - The number of faces with field values
3658: . fgeom - The extract the face centroid and normal
3659: - vol   - The cell volume

3661:   Level: developer

3663: .seealso: DMPlexGetFaceFields()
3664: @*/
3665: PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol)
3666: {

3670:   PetscFree(*fgeom);
3671:   DMRestoreWorkArray(dm, 0, MPIU_REAL, vol);
3672:   return(0);
3673: }

3675: PetscErrorCode DMSNESGetFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom)
3676: {
3677:   char            composeStr[33] = {0};
3678:   PetscObjectId   id;
3679:   PetscContainer  container;
3680:   PetscErrorCode  ierr;

3683:   PetscObjectGetId((PetscObject)quad,&id);
3684:   PetscSNPrintf(composeStr, 32, "DMSNESGetFEGeom_%x\n", id);
3685:   PetscObjectQuery((PetscObject) pointIS, composeStr, (PetscObject *) &container);
3686:   if (container) {
3687:     PetscContainerGetPointer(container, (void **) geom);
3688:   } else {
3689:     DMFieldCreateFEGeom(coordField, pointIS, quad, faceData, geom);
3690:     PetscContainerCreate(PETSC_COMM_SELF,&container);
3691:     PetscContainerSetPointer(container, (void *) *geom);
3692:     PetscContainerSetUserDestroy(container, PetscContainerUserDestroy_PetscFEGeom);
3693:     PetscObjectCompose((PetscObject) pointIS, composeStr, (PetscObject) container);
3694:     PetscContainerDestroy(&container);
3695:   }
3696:   return(0);
3697: }

3699: PetscErrorCode DMSNESRestoreFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom)
3700: {
3702:   *geom = NULL;
3703:   return(0);
3704: }

3706: PetscErrorCode DMPlexComputeResidual_Patch_Internal(DM dm, PetscSection section, IS cellIS, PetscReal t, Vec locX, Vec locX_t, Vec locF, void *user)
3707: {
3708:   DM_Plex         *mesh       = (DM_Plex *) dm->data;
3709:   const char      *name       = "Residual";
3710:   DM               dmAux      = NULL;
3711:   DMLabel          ghostLabel = NULL;
3712:   PetscDS          prob       = NULL;
3713:   PetscDS          probAux    = NULL;
3714:   PetscBool        useFEM     = PETSC_FALSE;
3715:   PetscBool        isImplicit = (locX_t || t == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE;
3716:   DMField          coordField = NULL;
3717:   Vec              locA;
3718:   PetscScalar     *u = NULL, *u_t, *a, *uL = NULL, *uR = NULL;
3719:   IS               chunkIS;
3720:   const PetscInt  *cells;
3721:   PetscInt         cStart, cEnd, numCells;
3722:   PetscInt         Nf, f, totDim, totDimAux, numChunks, cellChunkSize, chunk, fStart, fEnd;
3723:   PetscInt         maxDegree = PETSC_MAX_INT;
3724:   PetscQuadrature  affineQuad = NULL, *quads = NULL;
3725:   PetscFEGeom     *affineGeom = NULL, **geoms = NULL;
3726:   PetscErrorCode   ierr;

3729:   PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);
3730:   /* FEM+FVM */
3731:   /* 1: Get sizes from dm and dmAux */
3732:   DMGetLabel(dm, "ghost", &ghostLabel);
3733:   DMGetDS(dm, &prob);
3734:   PetscDSGetNumFields(prob, &Nf);
3735:   PetscDSGetTotalDimension(prob, &totDim);
3736:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
3737:   if (locA) {
3738:     VecGetDM(locA, &dmAux);
3739:     DMGetDS(dmAux, &probAux);
3740:     PetscDSGetTotalDimension(probAux, &totDimAux);
3741:   }
3742:   /* 2: Get geometric data */
3743:   for (f = 0; f < Nf; ++f) {
3744:     PetscObject  obj;
3745:     PetscClassId id;
3746:     PetscBool    fimp;

3748:     PetscDSGetImplicit(prob, f, &fimp);
3749:     if (isImplicit != fimp) continue;
3750:     PetscDSGetDiscretization(prob, f, &obj);
3751:     PetscObjectGetClassId(obj, &id);
3752:     if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;}
3753:     if (id == PETSCFV_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Use of FVM with PCPATCH not yet implemented");
3754:   }
3755:   if (useFEM) {
3756:     DMGetCoordinateField(dm, &coordField);
3757:     DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
3758:     if (maxDegree <= 1) {
3759:       DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);
3760:       if (affineQuad) {
3761:         DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
3762:       }
3763:     } else {
3764:       PetscCalloc2(Nf,&quads,Nf,&geoms);
3765:       for (f = 0; f < Nf; ++f) {
3766:         PetscObject  obj;
3767:         PetscClassId id;
3768:         PetscBool    fimp;

3770:         PetscDSGetImplicit(prob, f, &fimp);
3771:         if (isImplicit != fimp) continue;
3772:         PetscDSGetDiscretization(prob, f, &obj);
3773:         PetscObjectGetClassId(obj, &id);
3774:         if (id == PETSCFE_CLASSID) {
3775:           PetscFE fe = (PetscFE) obj;

3777:           PetscFEGetQuadrature(fe, &quads[f]);
3778:           PetscObjectReference((PetscObject)quads[f]);
3779:           DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
3780:         }
3781:       }
3782:     }
3783:   }
3784:   /* Loop over chunks */
3785:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
3786:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
3787:   if (useFEM) {ISCreate(PETSC_COMM_SELF, &chunkIS);}
3788:   numCells      = cEnd - cStart;
3789:   numChunks     = 1;
3790:   cellChunkSize = numCells/numChunks;
3791:   numChunks     = PetscMin(1,numCells);
3792:   for (chunk = 0; chunk < numChunks; ++chunk) {
3793:     PetscScalar     *elemVec, *fluxL = NULL, *fluxR = NULL;
3794:     PetscReal       *vol = NULL;
3795:     PetscFVFaceGeom *fgeom = NULL;
3796:     PetscInt         cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c;
3797:     PetscInt         numFaces = 0;

3799:     /* Extract field coefficients */
3800:     if (useFEM) {
3801:       ISGetPointSubrange(chunkIS, cS, cE, cells);
3802:       DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
3803:       DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
3804:       PetscArrayzero(elemVec, numCells*totDim);
3805:     }
3806:     /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */
3807:     /* Loop over fields */
3808:     for (f = 0; f < Nf; ++f) {
3809:       PetscObject  obj;
3810:       PetscClassId id;
3811:       PetscBool    fimp;
3812:       PetscInt     numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset;

3814:       PetscDSGetImplicit(prob, f, &fimp);
3815:       if (isImplicit != fimp) continue;
3816:       PetscDSGetDiscretization(prob, f, &obj);
3817:       PetscObjectGetClassId(obj, &id);
3818:       if (id == PETSCFE_CLASSID) {
3819:         PetscFE         fe = (PetscFE) obj;
3820:         PetscFEGeom    *geom = affineGeom ? affineGeom : geoms[f];
3821:         PetscFEGeom    *chunkGeom = NULL;
3822:         PetscQuadrature quad = affineQuad ? affineQuad : quads[f];
3823:         PetscInt        Nq, Nb;

3825:         PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
3826:         PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);
3827:         PetscFEGetDimension(fe, &Nb);
3828:         blockSize = Nb;
3829:         batchSize = numBlocks * blockSize;
3830:         PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
3831:         numChunks = numCells / (numBatches*batchSize);
3832:         Ne        = numChunks*numBatches*batchSize;
3833:         Nr        = numCells % (numBatches*batchSize);
3834:         offset    = numCells - Nr;
3835:         /* Integrate FE residual to get elemVec (need fields at quadrature points) */
3836:         /*   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) */
3837:         PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
3838:         PetscFEIntegrateResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);
3839:         PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);
3840:         PetscFEIntegrateResidual(prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);
3841:         PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);
3842:       } else if (id == PETSCFV_CLASSID) {
3843:         PetscFV fv = (PetscFV) obj;

3845:         Ne = numFaces;
3846:         /* Riemann solve over faces (need fields at face centroids) */
3847:         /*   We need to evaluate FE fields at those coordinates */
3848:         PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);
3849:       } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f);
3850:     }
3851:     /* Loop over domain */
3852:     if (useFEM) {
3853:       /* Add elemVec to locX */
3854:       for (c = cS; c < cE; ++c) {
3855:         const PetscInt cell = cells ? cells[c] : c;
3856:         const PetscInt cind = c - cStart;

3858:         if (mesh->printFEM > 1) {DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);}
3859:         if (ghostLabel) {
3860:           PetscInt ghostVal;

3862:           DMLabelGetValue(ghostLabel,cell,&ghostVal);
3863:           if (ghostVal > 0) continue;
3864:         }
3865:         DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);
3866:       }
3867:     }
3868:     /* Handle time derivative */
3869:     if (locX_t) {
3870:       PetscScalar *x_t, *fa;

3872:       VecGetArray(locF, &fa);
3873:       VecGetArray(locX_t, &x_t);
3874:       for (f = 0; f < Nf; ++f) {
3875:         PetscFV      fv;
3876:         PetscObject  obj;
3877:         PetscClassId id;
3878:         PetscInt     pdim, d;

3880:         PetscDSGetDiscretization(prob, f, &obj);
3881:         PetscObjectGetClassId(obj, &id);
3882:         if (id != PETSCFV_CLASSID) continue;
3883:         fv   = (PetscFV) obj;
3884:         PetscFVGetNumComponents(fv, &pdim);
3885:         for (c = cS; c < cE; ++c) {
3886:           const PetscInt cell = cells ? cells[c] : c;
3887:           PetscScalar   *u_t, *r;

3889:           if (ghostLabel) {
3890:             PetscInt ghostVal;

3892:             DMLabelGetValue(ghostLabel, cell, &ghostVal);
3893:             if (ghostVal > 0) continue;
3894:           }
3895:           DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);
3896:           DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);
3897:           for (d = 0; d < pdim; ++d) r[d] += u_t[d];
3898:         }
3899:       }
3900:       VecRestoreArray(locX_t, &x_t);
3901:       VecRestoreArray(locF, &fa);
3902:     }
3903:     if (useFEM) {
3904:       DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
3905:       DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
3906:     }
3907:   }
3908:   if (useFEM) {ISDestroy(&chunkIS);}
3909:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
3910:   /* TODO Could include boundary residual here (see DMPlexComputeResidual_Internal) */
3911:   if (useFEM) {
3912:     if (maxDegree <= 1) {
3913:       DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
3914:       PetscQuadratureDestroy(&affineQuad);
3915:     } else {
3916:       for (f = 0; f < Nf; ++f) {
3917:         DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
3918:         PetscQuadratureDestroy(&quads[f]);
3919:       }
3920:       PetscFree2(quads,geoms);
3921:     }
3922:   }
3923:   PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);
3924:   return(0);
3925: }

3927: /*
3928:   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

3930:   X   - The local solution vector
3931:   X_t - The local solution time derviative vector, or NULL
3932: */
3933: PetscErrorCode DMPlexComputeJacobian_Patch_Internal(DM dm, PetscSection section, PetscSection globalSection, IS cellIS,
3934:                                                     PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP, void *ctx)
3935: {
3936:   DM_Plex         *mesh  = (DM_Plex *) dm->data;
3937:   const char      *name = "Jacobian", *nameP = "JacobianPre";
3938:   DM               dmAux = NULL;
3939:   PetscDS          prob,   probAux = NULL;
3940:   PetscSection     sectionAux = NULL;
3941:   Vec              A;
3942:   DMField          coordField;
3943:   PetscFEGeom     *cgeomFEM;
3944:   PetscQuadrature  qGeom = NULL;
3945:   Mat              J = Jac, JP = JacP;
3946:   PetscScalar     *work, *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL, *elemMatP = NULL, *elemMatD = NULL;
3947:   PetscBool        hasJac, hasPrec, hasDyn, assembleJac, isMatIS, isMatISP, *isFE, hasFV = PETSC_FALSE;
3948:   const PetscInt  *cells;
3949:   PetscInt         Nf, fieldI, fieldJ, maxDegree, numCells, cStart, cEnd, numChunks, chunkSize, chunk, totDim, totDimAux = 0, sz, wsz, off = 0, offCell = 0;
3950:   PetscErrorCode   ierr;

3953:   CHKMEMQ;
3954:   ISGetLocalSize(cellIS, &numCells);
3955:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
3956:   PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);
3957:   DMGetDS(dm, &prob);
3958:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
3959:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
3960:   if (dmAux) {
3961:     DMGetLocalSection(dmAux, &sectionAux);
3962:     DMGetDS(dmAux, &probAux);
3963:   }
3964:   /* Get flags */
3965:   PetscDSGetNumFields(prob, &Nf);
3966:   DMGetWorkArray(dm, Nf, MPIU_BOOL, &isFE);
3967:   for (fieldI = 0; fieldI < Nf; ++fieldI) {
3968:     PetscObject  disc;
3969:     PetscClassId id;
3970:     PetscDSGetDiscretization(prob, fieldI, &disc);
3971:     PetscObjectGetClassId(disc, &id);
3972:     if (id == PETSCFE_CLASSID)      {isFE[fieldI] = PETSC_TRUE;}
3973:     else if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; isFE[fieldI] = PETSC_FALSE;}
3974:   }
3975:   PetscDSHasJacobian(prob, &hasJac);
3976:   PetscDSHasJacobianPreconditioner(prob, &hasPrec);
3977:   PetscDSHasDynamicJacobian(prob, &hasDyn);
3978:   assembleJac = hasJac && hasPrec && (Jac != JacP) ? PETSC_TRUE : PETSC_FALSE;
3979:   hasDyn      = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE;
3980:   PetscObjectTypeCompare((PetscObject) Jac,  MATIS, &isMatIS);
3981:   PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
3982:   /* Setup input data and temp arrays (should be DMGetWorkArray) */
3983:   if (isMatISP || isMatISP) {DMPlexGetSubdomainSection(dm, &globalSection);}
3984:   if (isMatIS)  {MatISGetLocalMat(Jac,  &J);}
3985:   if (isMatISP) {MatISGetLocalMat(JacP, &JP);}
3986:   if (hasFV)    {MatSetOption(JP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);} /* No allocated space for FV stuff, so ignore the zero entries */
3987:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
3988:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
3989:   PetscDSGetTotalDimension(prob, &totDim);
3990:   if (probAux) {PetscDSGetTotalDimension(probAux, &totDimAux);}
3991:   CHKMEMQ;
3992:   /* Compute batch sizes */
3993:   if (isFE[0]) {
3994:     PetscFE         fe;
3995:     PetscQuadrature q;
3996:     PetscInt        numQuadPoints, numBatches, batchSize, numBlocks, blockSize, Nb;

3998:     PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);
3999:     PetscFEGetQuadrature(fe, &q);
4000:     PetscQuadratureGetData(q, NULL, NULL, &numQuadPoints, NULL, NULL);
4001:     PetscFEGetDimension(fe, &Nb);
4002:     PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
4003:     blockSize = Nb*numQuadPoints;
4004:     batchSize = numBlocks  * blockSize;
4005:     chunkSize = numBatches * batchSize;
4006:     numChunks = numCells / chunkSize + numCells % chunkSize;
4007:     PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
4008:   } else {
4009:     chunkSize = numCells;
4010:     numChunks = 1;
4011:   }
4012:   /* Get work space */
4013:   wsz  = (((X?1:0) + (X_t?1:0) + (dmAux?1:0))*totDim + ((hasJac?1:0) + (hasPrec?1:0) + (hasDyn?1:0))*totDim*totDim)*chunkSize;
4014:   DMGetWorkArray(dm, wsz, MPIU_SCALAR, &work);
4015:   PetscArrayzero(work, wsz);
4016:   off      = 0;
4017:   u        = X       ? (sz = chunkSize*totDim,        off += sz, work+off-sz) : NULL;
4018:   u_t      = X_t     ? (sz = chunkSize*totDim,        off += sz, work+off-sz) : NULL;
4019:   a        = dmAux   ? (sz = chunkSize*totDimAux,     off += sz, work+off-sz) : NULL;
4020:   elemMat  = hasJac  ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL;
4021:   elemMatP = hasPrec ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL;
4022:   elemMatD = hasDyn  ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL;
4023:   if (off != wsz) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Error is workspace size %D should be %D", off, wsz);
4024:   /* Setup geometry */
4025:   DMGetCoordinateField(dm, &coordField);
4026:   DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);
4027:   if (maxDegree <= 1) {DMFieldCreateDefaultQuadrature(coordField, cellIS, &qGeom);}
4028:   if (!qGeom) {
4029:     PetscFE fe;

4031:     PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);
4032:     PetscFEGetQuadrature(fe, &qGeom);
4033:     PetscObjectReference((PetscObject) qGeom);
4034:   }
4035:   DMSNESGetFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);
4036:   /* Compute volume integrals */
4037:   if (assembleJac) {MatZeroEntries(J);}
4038:   MatZeroEntries(JP);
4039:   for (chunk = 0; chunk < numChunks; ++chunk, offCell += chunkSize) {
4040:     const PetscInt   Ncell = PetscMin(chunkSize, numCells - offCell);
4041:     PetscInt         c;

4043:     /* Extract values */
4044:     for (c = 0; c < Ncell; ++c) {
4045:       const PetscInt cell = cells ? cells[c+offCell] : c+offCell;
4046:       PetscScalar   *x = NULL,  *x_t = NULL;
4047:       PetscInt       i;

4049:       if (X) {
4050:         DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);
4051:         for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i];
4052:         DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);
4053:       }
4054:       if (X_t) {
4055:         DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);
4056:         for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i];
4057:         DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);
4058:       }
4059:       if (dmAux) {
4060:         DMPlexVecGetClosure(dmAux, sectionAux, A, cell, NULL, &x);
4061:         for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i];
4062:         DMPlexVecRestoreClosure(dmAux, sectionAux, A, cell, NULL, &x);
4063:       }
4064:     }
4065:     CHKMEMQ;
4066:     for (fieldI = 0; fieldI < Nf; ++fieldI) {
4067:       PetscFE fe;
4068:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
4069:       for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
4070:         if (hasJac)  {PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN,     fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMat);}
4071:         if (hasPrec) {PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatP);}
4072:         if (hasDyn)  {PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatD);}
4073:       }
4074:       /* For finite volume, add the identity */
4075:       if (!isFE[fieldI]) {
4076:         PetscFV  fv;
4077:         PetscInt eOffset = 0, Nc, fc, foff;

4079:         PetscDSGetFieldOffset(prob, fieldI, &foff);
4080:         PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);
4081:         PetscFVGetNumComponents(fv, &Nc);
4082:         for (c = 0; c < chunkSize; ++c, eOffset += totDim*totDim) {
4083:           for (fc = 0; fc < Nc; ++fc) {
4084:             const PetscInt i = foff + fc;
4085:             if (hasJac)  {elemMat [eOffset+i*totDim+i] = 1.0;}
4086:             if (hasPrec) {elemMatP[eOffset+i*totDim+i] = 1.0;}
4087:           }
4088:         }
4089:       }
4090:     }
4091:     CHKMEMQ;
4092:     /*   Add contribution from X_t */
4093:     if (hasDyn) {for (c = 0; c < chunkSize*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];}
4094:     /* Insert values into matrix */
4095:     for (c = 0; c < Ncell; ++c) {
4096:       const PetscInt cell = cells ? cells[c+offCell] : c+offCell;
4097:       if (mesh->printFEM > 1) {
4098:         if (hasJac)  {DMPrintCellMatrix(cell, name,  totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);}
4099:         if (hasPrec) {DMPrintCellMatrix(cell, nameP, totDim, totDim, &elemMatP[(c-cStart)*totDim*totDim]);}
4100:       }
4101:       if (assembleJac) {DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);}
4102:       DMPlexMatSetClosure(dm, section, globalSection, JP, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);
4103:     }
4104:     CHKMEMQ;
4105:   }
4106:   /* Cleanup */
4107:   DMSNESRestoreFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);
4108:   PetscQuadratureDestroy(&qGeom);
4109:   if (hasFV) {MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);}
4110:   DMRestoreWorkArray(dm, Nf, MPIU_BOOL, &isFE);
4111:   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);
4112:   /* Compute boundary integrals */
4113:   /* DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, ctx); */
4114:   /* Assemble matrix */
4115:   if (assembleJac) {MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);}
4116:   MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);
4117:   PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);
4118:   CHKMEMQ;
4119:   return(0);
4120: }

4122: /******** FEM Assembly Function ********/

4124: static PetscErrorCode DMConvertPlex_Internal(DM dm, DM *plex, PetscBool copy)
4125: {
4126:   PetscBool      isPlex;

4130:   PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);
4131:   if (isPlex) {
4132:     *plex = dm;
4133:     PetscObjectReference((PetscObject) dm);
4134:   } else {
4135:     PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);
4136:     if (!*plex) {
4137:       DMConvert(dm,DMPLEX,plex);
4138:       PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);
4139:       if (copy) {
4140:         const char *comps[] = {"A", "dmAux"};
4141:         PetscObject obj;
4142:         PetscInt    i;

4144:         for (i = 0; i < 2; ++i) {
4145:           PetscObjectQuery((PetscObject) dm, comps[i], &obj);
4146:           PetscObjectCompose((PetscObject) *plex, comps[i], obj);
4147:         }
4148:       }
4149:     } else {
4150:       PetscObjectReference((PetscObject) *plex);
4151:     }
4152:   }
4153:   return(0);
4154: }

4156: /*@
4157:   DMPlexGetGeometryFVM - Return precomputed geometric data

4159:   Collective on DM

4161:   Input Parameter:
4162: . dm - The DM

4164:   Output Parameters:
4165: + facegeom - The values precomputed from face geometry
4166: . cellgeom - The values precomputed from cell geometry
4167: - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell

4169:   Level: developer

4171: .seealso: DMPlexTSSetRHSFunctionLocal()
4172: @*/
4173: PetscErrorCode DMPlexGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius)
4174: {
4175:   DM             plex;

4180:   DMConvertPlex_Internal(dm,&plex,PETSC_TRUE);
4181:   DMPlexGetDataFVM(plex, NULL, cellgeom, facegeom, NULL);
4182:   if (minRadius) {DMPlexGetMinRadius(plex, minRadius);}
4183:   DMDestroy(&plex);
4184:   return(0);
4185: }

4187: /*@
4188:   DMPlexGetGradientDM - Return gradient data layout

4190:   Collective on DM

4192:   Input Parameters:
4193: + dm - The DM
4194: - fv - The PetscFV

4196:   Output Parameter:
4197: . dmGrad - The layout for gradient values

4199:   Level: developer

4201: .seealso: DMPlexSNESGetGeometryFVM()
4202: @*/
4203: PetscErrorCode DMPlexGetGradientDM(DM dm, PetscFV fv, DM *dmGrad)
4204: {
4205:   DM             plex;
4206:   PetscBool      computeGradients;

4213:   PetscFVGetComputeGradients(fv, &computeGradients);
4214:   if (!computeGradients) {*dmGrad = NULL; return(0);}
4215:   DMConvertPlex_Internal(dm,&plex,PETSC_TRUE);
4216:   DMPlexGetDataFVM(plex, fv, NULL, NULL, dmGrad);
4217:   DMDestroy(&plex);
4218:   return(0);
4219: }

4221: static PetscErrorCode DMPlexComputeBdResidual_Single_Internal(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF, DMField coordField, IS facetIS)
4222: {
4223:   DM_Plex         *mesh = (DM_Plex *) dm->data;
4224:   DM               plex = NULL, plexA = NULL;
4225:   DMEnclosureType  encAux;
4226:   PetscDS          prob, probAux = NULL;
4227:   PetscSection     section, sectionAux = NULL;
4228:   Vec              locA = NULL;
4229:   PetscScalar     *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL;
4230:   PetscInt         v;
4231:   PetscInt         totDim, totDimAux = 0;
4232:   PetscErrorCode   ierr;

4235:   DMConvert(dm, DMPLEX, &plex);
4236:   DMGetLocalSection(dm, &section);
4237:   DMGetDS(dm, &prob);
4238:   PetscDSGetTotalDimension(prob, &totDim);
4239:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
4240:   if (locA) {
4241:     DM dmAux;

4243:     VecGetDM(locA, &dmAux);
4244:     DMGetEnclosureRelation(dmAux, dm, &encAux);
4245:     DMConvert(dmAux, DMPLEX, &plexA);
4246:     DMGetDS(plexA, &probAux);
4247:     PetscDSGetTotalDimension(probAux, &totDimAux);
4248:     DMGetLocalSection(plexA, &sectionAux);
4249:   }
4250:   for (v = 0; v < numValues; ++v) {
4251:     PetscFEGeom    *fgeom;
4252:     PetscInt        maxDegree;
4253:     PetscQuadrature qGeom = NULL;
4254:     IS              pointIS;
4255:     const PetscInt *points;
4256:     PetscInt        numFaces, face, Nq;

4258:     DMLabelGetStratumIS(label, values[v], &pointIS);
4259:     if (!pointIS) continue; /* No points with that id on this process */
4260:     {
4261:       IS isectIS;

4263:       /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */
4264:       ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);
4265:       ISDestroy(&pointIS);
4266:       pointIS = isectIS;
4267:     }
4268:     ISGetLocalSize(pointIS,&numFaces);
4269:     ISGetIndices(pointIS,&points);
4270:     PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);
4271:     DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);
4272:     if (maxDegree <= 1) {
4273:       DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);
4274:     }
4275:     if (!qGeom) {
4276:       PetscFE fe;

4278:       PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);
4279:       PetscFEGetFaceQuadrature(fe, &qGeom);
4280:       PetscObjectReference((PetscObject)qGeom);
4281:     }
4282:     PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
4283:     DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
4284:     for (face = 0; face < numFaces; ++face) {
4285:       const PetscInt point = points[face], *support;
4286:       PetscScalar   *x     = NULL;
4287:       PetscInt       i;

4289:       DMPlexGetSupport(dm, point, &support);
4290:       DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);
4291:       for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i];
4292:       DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);
4293:       if (locX_t) {
4294:         DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);
4295:         for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i];
4296:         DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);
4297:       }
4298:       if (locA) {
4299:         PetscInt subp;

4301:         DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);
4302:         DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);
4303:         for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i];
4304:         DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);
4305:       }
4306:     }
4307:     PetscArrayzero(elemVec, numFaces*totDim);
4308:     {
4309:       PetscFE         fe;
4310:       PetscInt        Nb;
4311:       PetscFEGeom     *chunkGeom = NULL;
4312:       /* Conforming batches */
4313:       PetscInt        numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
4314:       /* Remainder */
4315:       PetscInt        Nr, offset;

4317:       PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);
4318:       PetscFEGetDimension(fe, &Nb);
4319:       PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
4320:       /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */
4321:       blockSize = Nb;
4322:       batchSize = numBlocks * blockSize;
4323:        PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
4324:       numChunks = numFaces / (numBatches*batchSize);
4325:       Ne        = numChunks*numBatches*batchSize;
4326:       Nr        = numFaces % (numBatches*batchSize);
4327:       offset    = numFaces - Nr;
4328:       PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);
4329:       PetscFEIntegrateBdResidual(prob, field, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);
4330:       PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);
4331:       PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);
4332:       PetscFEIntegrateBdResidual(prob, field, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, &elemVec[offset*totDim]);
4333:       PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);
4334:     }
4335:     for (face = 0; face < numFaces; ++face) {
4336:       const PetscInt point = points[face], *support;

4338:       if (mesh->printFEM > 1) {DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);}
4339:       DMPlexGetSupport(plex, point, &support);
4340:       DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);
4341:     }
4342:     DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
4343:     PetscQuadratureDestroy(&qGeom);
4344:     ISRestoreIndices(pointIS, &points);
4345:     ISDestroy(&pointIS);
4346:     PetscFree4(u, u_t, elemVec, a);
4347:   }
4348:   DMDestroy(&plex);
4349:   DMDestroy(&plexA);
4350:   return(0);
4351: }

4353: PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF)
4354: {
4355:   DMField        coordField;
4356:   DMLabel        depthLabel;
4357:   IS             facetIS;
4358:   PetscInt       dim;

4362:   DMGetDimension(dm, &dim);
4363:   DMPlexGetDepthLabel(dm, &depthLabel);
4364:   DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
4365:   DMGetCoordinateField(dm, &coordField);
4366:   DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);
4367:   ISDestroy(&facetIS);
4368:   return(0);
4369: }

4371: PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user)
4372: {
4373:   PetscDS        prob;
4374:   PetscInt       numBd, bd;
4375:   DMField        coordField = NULL;
4376:   IS             facetIS    = NULL;
4377:   DMLabel        depthLabel;
4378:   PetscInt       dim;

4382:   DMGetDS(dm, &prob);
4383:   DMPlexGetDepthLabel(dm, &depthLabel);
4384:   DMGetDimension(dm, &dim);
4385:   DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);
4386:   PetscDSGetNumBoundary(prob, &numBd);
4387:   for (bd = 0; bd < numBd; ++bd) {
4388:     DMBoundaryConditionType type;
4389:     const char             *bdLabel;
4390:     DMLabel                 label;
4391:     const PetscInt         *values;
4392:     PetscInt                field, numValues;
4393:     PetscObject             obj;
4394:     PetscClassId            id;

4396:     PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &field, NULL, NULL, NULL, NULL, &numValues, &values, NULL);
4397:     PetscDSGetDiscretization(prob, field, &obj);
4398:     PetscObjectGetClassId(obj, &id);
4399:     if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue;
4400:     if (!facetIS) {
4401:       DMLabel  depthLabel;
4402:       PetscInt dim;

4404:       DMPlexGetDepthLabel(dm, &depthLabel);
4405:       DMGetDimension(dm, &dim);
4406:       DMLabelGetStratumIS(depthLabel, dim - 1, &facetIS);
4407:     }
4408:     DMGetCoordinateField(dm, &coordField);
4409:     DMGetLabel(dm, bdLabel, &label);
4410:     DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);
4411:   }
4412:   ISDestroy(&facetIS);
4413:   return(0);
4414: }

4416: PetscErrorCode DMPlexComputeResidual_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user)
4417: {
4418:   DM_Plex         *mesh       = (DM_Plex *) dm->data;
4419:   const char      *name       = "Residual";
4420:   DM               dmAux      = NULL;
4421:   DM               dmGrad     = NULL;
4422:   DMLabel          ghostLabel = NULL;
4423:   PetscDS          prob       = NULL;
4424:   PetscDS          probAux    = NULL;
4425:   PetscSection     section    = NULL;
4426:   PetscBool        useFEM     = PETSC_FALSE;
4427:   PetscBool        useFVM     = PETSC_FALSE;
4428:   PetscBool        isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE;
4429:   PetscFV          fvm        = NULL;
4430:   PetscFVCellGeom *cgeomFVM   = NULL;
4431:   PetscFVFaceGeom *fgeomFVM   = NULL;
4432:   DMField          coordField = NULL;
4433:   Vec              locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL;
4434:   PetscScalar     *u = NULL, *u_t, *a, *uL, *uR;
4435:   IS               chunkIS;
4436:   const PetscInt  *cells;
4437:   PetscInt         cStart, cEnd, numCells;
4438:   PetscInt         Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd;
4439:   PetscInt         maxDegree = PETSC_MAX_INT;
4440:   PetscQuadrature  affineQuad = NULL, *quads = NULL;
4441:   PetscFEGeom     *affineGeom = NULL, **geoms = NULL;
4442:   PetscErrorCode   ierr;

4445:   PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);
4446:   /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */
4447:   /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */
4448:   /* FEM+FVM */
4449:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
4450:   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
4451:   /* 1: Get sizes from dm and dmAux */
4452:   DMGetLocalSection(dm, &section);
4453:   DMGetLabel(dm, "ghost", &ghostLabel);
4454:   DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);
4455:   PetscDSGetNumFields(prob, &Nf);
4456:   PetscDSGetTotalDimension(prob, &totDim);
4457:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
4458:   if (locA) {
4459:     PetscInt subcell;
4460:     VecGetDM(locA, &dmAux);
4461:     DMGetEnclosurePoint(dmAux, dm, DM_ENC_UNKNOWN, cStart, &subcell);
4462:     DMGetCellDS(dmAux, subcell, &probAux);
4463:     PetscDSGetTotalDimension(probAux, &totDimAux);
4464:   }
4465:   /* 2: Get geometric data */
4466:   for (f = 0; f < Nf; ++f) {
4467:     PetscObject  obj;
4468:     PetscClassId id;
4469:     PetscBool    fimp;

4471:     PetscDSGetImplicit(prob, f, &fimp);
4472:     if (isImplicit != fimp) continue;
4473:     PetscDSGetDiscretization(prob, f, &obj);
4474:     PetscObjectGetClassId(obj, &id);
4475:     if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;}
4476:     if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;}
4477:   }
4478:   if (useFEM) {
4479:     DMGetCoordinateField(dm, &coordField);
4480:     DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
4481:     if (maxDegree <= 1) {
4482:       DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);
4483:       if (affineQuad) {
4484:         DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
4485:       }
4486:     } else {
4487:       PetscCalloc2(Nf,&quads,Nf,&geoms);
4488:       for (f = 0; f < Nf; ++f) {
4489:         PetscObject  obj;
4490:         PetscClassId id;
4491:         PetscBool    fimp;

4493:         PetscDSGetImplicit(prob, f, &fimp);
4494:         if (isImplicit != fimp) continue;
4495:         PetscDSGetDiscretization(prob, f, &obj);
4496:         PetscObjectGetClassId(obj, &id);
4497:         if (id == PETSCFE_CLASSID) {
4498:           PetscFE fe = (PetscFE) obj;

4500:           PetscFEGetQuadrature(fe, &quads[f]);
4501:           PetscObjectReference((PetscObject)quads[f]);
4502:           DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
4503:         }
4504:       }
4505:     }
4506:   }
4507:   if (useFVM) {
4508:     DMPlexGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);
4509:     VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);
4510:     VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);
4511:     /* Reconstruct and limit cell gradients */
4512:     DMPlexGetGradientDM(dm, fvm, &dmGrad);
4513:     if (dmGrad) {
4514:       DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
4515:       DMGetGlobalVector(dmGrad, &grad);
4516:       DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);
4517:       /* Communicate gradient values */
4518:       DMGetLocalVector(dmGrad, &locGrad);
4519:       DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);
4520:       DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);
4521:       DMRestoreGlobalVector(dmGrad, &grad);
4522:     }
4523:     /* Handle non-essential (e.g. outflow) boundary values */
4524:     DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);
4525:   }
4526:   /* Loop over chunks */
4527:   if (useFEM) {ISCreate(PETSC_COMM_SELF, &chunkIS);}
4528:   numCells      = cEnd - cStart;
4529:   numChunks     = 1;
4530:   cellChunkSize = numCells/numChunks;
4531:   faceChunkSize = (fEnd - fStart)/numChunks;
4532:   numChunks     = PetscMin(1,numCells);
4533:   for (chunk = 0; chunk < numChunks; ++chunk) {
4534:     PetscScalar     *elemVec, *fluxL, *fluxR;
4535:     PetscReal       *vol;
4536:     PetscFVFaceGeom *fgeom;
4537:     PetscInt         cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c;
4538:     PetscInt         fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face;

4540:     /* Extract field coefficients */
4541:     if (useFEM) {
4542:       ISGetPointSubrange(chunkIS, cS, cE, cells);
4543:       DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
4544:       DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
4545:       PetscArrayzero(elemVec, numCells*totDim);
4546:     }
4547:     if (useFVM) {
4548:       DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);
4549:       DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);
4550:       DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);
4551:       DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);
4552:       PetscArrayzero(fluxL, numFaces*totDim);
4553:       PetscArrayzero(fluxR, numFaces*totDim);
4554:     }
4555:     /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */
4556:     /* Loop over fields */
4557:     for (f = 0; f < Nf; ++f) {
4558:       PetscObject  obj;
4559:       PetscClassId id;
4560:       PetscBool    fimp;
4561:       PetscInt     numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset;

4563:       PetscDSGetImplicit(prob, f, &fimp);
4564:       if (isImplicit != fimp) continue;
4565:       PetscDSGetDiscretization(prob, f, &obj);
4566:       PetscObjectGetClassId(obj, &id);
4567:       if (id == PETSCFE_CLASSID) {
4568:         PetscFE         fe = (PetscFE) obj;
4569:         PetscFEGeom    *geom = affineGeom ? affineGeom : geoms[f];
4570:         PetscFEGeom    *chunkGeom = NULL;
4571:         PetscQuadrature quad = affineQuad ? affineQuad : quads[f];
4572:         PetscInt        Nq, Nb;

4574:         PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
4575:         PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);
4576:         PetscFEGetDimension(fe, &Nb);
4577:         blockSize = Nb;
4578:         batchSize = numBlocks * blockSize;
4579:         PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
4580:         numChunks = numCells / (numBatches*batchSize);
4581:         Ne        = numChunks*numBatches*batchSize;
4582:         Nr        = numCells % (numBatches*batchSize);
4583:         offset    = numCells - Nr;
4584:         /* Integrate FE residual to get elemVec (need fields at quadrature points) */
4585:         /*   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) */
4586:         PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
4587:         PetscFEIntegrateResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);
4588:         PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);
4589:         PetscFEIntegrateResidual(prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);
4590:         PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);
4591:       } else if (id == PETSCFV_CLASSID) {
4592:         PetscFV fv = (PetscFV) obj;

4594:         Ne = numFaces;
4595:         /* Riemann solve over faces (need fields at face centroids) */
4596:         /*   We need to evaluate FE fields at those coordinates */
4597:         PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);
4598:       } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %D", f);
4599:     }
4600:     /* Loop over domain */
4601:     if (useFEM) {
4602:       /* Add elemVec to locX */
4603:       for (c = cS; c < cE; ++c) {
4604:         const PetscInt cell = cells ? cells[c] : c;
4605:         const PetscInt cind = c - cStart;

4607:         if (mesh->printFEM > 1) {DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);}
4608:         if (ghostLabel) {
4609:           PetscInt ghostVal;

4611:           DMLabelGetValue(ghostLabel,cell,&ghostVal);
4612:           if (ghostVal > 0) continue;
4613:         }
4614:         DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);
4615:       }
4616:     }
4617:     if (useFVM) {
4618:       PetscScalar *fa;
4619:       PetscInt     iface;

4621:       VecGetArray(locF, &fa);
4622:       for (f = 0; f < Nf; ++f) {
4623:         PetscFV      fv;
4624:         PetscObject  obj;
4625:         PetscClassId id;
4626:         PetscInt     foff, pdim;

4628:         PetscDSGetDiscretization(prob, f, &obj);
4629:         PetscDSGetFieldOffset(prob, f, &foff);
4630:         PetscObjectGetClassId(obj, &id);
4631:         if (id != PETSCFV_CLASSID) continue;
4632:         fv   = (PetscFV) obj;
4633:         PetscFVGetNumComponents(fv, &pdim);
4634:         /* Accumulate fluxes to cells */
4635:         for (face = fS, iface = 0; face < fE; ++face) {
4636:           const PetscInt *scells;
4637:           PetscScalar    *fL = NULL, *fR = NULL;
4638:           PetscInt        ghost, d, nsupp, nchild;

4640:           DMLabelGetValue(ghostLabel, face, &ghost);
4641:           DMPlexGetSupportSize(dm, face, &nsupp);
4642:           DMPlexGetTreeChildren(dm, face, &nchild, NULL);
4643:           if (ghost >= 0 || nsupp > 2 || nchild > 0) continue;
4644:           DMPlexGetSupport(dm, face, &scells);
4645:           DMLabelGetValue(ghostLabel,scells[0],&ghost);
4646:           if (ghost <= 0) {DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);}
4647:           DMLabelGetValue(ghostLabel,scells[1],&ghost);
4648:           if (ghost <= 0) {DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);}
4649:           for (d = 0; d < pdim; ++d) {
4650:             if (fL) fL[d] -= fluxL[iface*totDim+foff+d];
4651:             if (fR) fR[d] += fluxR[iface*totDim+foff+d];
4652:           }
4653:           ++iface;
4654:         }
4655:       }
4656:       VecRestoreArray(locF, &fa);
4657:     }
4658:     /* Handle time derivative */
4659:     if (locX_t) {
4660:       PetscScalar *x_t, *fa;

4662:       VecGetArray(locF, &fa);
4663:       VecGetArray(locX_t, &x_t);
4664:       for (f = 0; f < Nf; ++f) {
4665:         PetscFV      fv;
4666:         PetscObject  obj;
4667:         PetscClassId id;
4668:         PetscInt     pdim, d;

4670:         PetscDSGetDiscretization(prob, f, &obj);
4671:         PetscObjectGetClassId(obj, &id);
4672:         if (id != PETSCFV_CLASSID) continue;
4673:         fv   = (PetscFV) obj;
4674:         PetscFVGetNumComponents(fv, &pdim);
4675:         for (c = cS; c < cE; ++c) {
4676:           const PetscInt cell = cells ? cells[c] : c;
4677:           PetscScalar   *u_t, *r;

4679:           if (ghostLabel) {
4680:             PetscInt ghostVal;

4682:             DMLabelGetValue(ghostLabel, cell, &ghostVal);
4683:             if (ghostVal > 0) continue;
4684:           }
4685:           DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);
4686:           DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);
4687:           for (d = 0; d < pdim; ++d) r[d] += u_t[d];
4688:         }
4689:       }
4690:       VecRestoreArray(locX_t, &x_t);
4691:       VecRestoreArray(locF, &fa);
4692:     }
4693:     if (useFEM) {
4694:       DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
4695:       DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
4696:     }
4697:     if (useFVM) {
4698:       DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);
4699:       DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);
4700:       DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);
4701:       DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);
4702:       if (dmGrad) {DMRestoreLocalVector(dmGrad, &locGrad);}
4703:     }
4704:   }
4705:   if (useFEM) {ISDestroy(&chunkIS);}
4706:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);

4708:   if (useFEM) {
4709:     DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);

4711:     if (maxDegree <= 1) {
4712:       DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
4713:       PetscQuadratureDestroy(&affineQuad);
4714:     } else {
4715:       for (f = 0; f < Nf; ++f) {
4716:         DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
4717:         PetscQuadratureDestroy(&quads[f]);
4718:       }
4719:       PetscFree2(quads,geoms);
4720:     }
4721:   }

4723:   /* FEM */
4724:   /* 1: Get sizes from dm and dmAux */
4725:   /* 2: Get geometric data */
4726:   /* 3: Handle boundary values */
4727:   /* 4: Loop over domain */
4728:   /*   Extract coefficients */
4729:   /* Loop over fields */
4730:   /*   Set tiling for FE*/
4731:   /*   Integrate FE residual to get elemVec */
4732:   /*     Loop over subdomain */
4733:   /*       Loop over quad points */
4734:   /*         Transform coords to real space */
4735:   /*         Evaluate field and aux fields at point */
4736:   /*         Evaluate residual at point */
4737:   /*         Transform residual to real space */
4738:   /*       Add residual to elemVec */
4739:   /* Loop over domain */
4740:   /*   Add elemVec to locX */

4742:   /* FVM */
4743:   /* Get geometric data */
4744:   /* If using gradients */
4745:   /*   Compute gradient data */
4746:   /*   Loop over domain faces */
4747:   /*     Count computational faces */
4748:   /*     Reconstruct cell gradient */
4749:   /*   Loop over domain cells */
4750:   /*     Limit cell gradients */
4751:   /* Handle boundary values */
4752:   /* Loop over domain faces */
4753:   /*   Read out field, centroid, normal, volume for each side of face */
4754:   /* Riemann solve over faces */
4755:   /* Loop over domain faces */
4756:   /*   Accumulate fluxes to cells */
4757:   /* TODO Change printFEM to printDisc here */
4758:   if (mesh->printFEM) {
4759:     Vec         locFbc;
4760:     PetscInt    pStart, pEnd, p, maxDof;
4761:     PetscScalar *zeroes;

4763:     VecDuplicate(locF,&locFbc);
4764:     VecCopy(locF,locFbc);
4765:     PetscSectionGetChart(section,&pStart,&pEnd);
4766:     PetscSectionGetMaxDof(section,&maxDof);
4767:     PetscCalloc1(maxDof,&zeroes);
4768:     for (p = pStart; p < pEnd; p++) {
4769:       VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);
4770:     }
4771:     PetscFree(zeroes);
4772:     DMPrintLocalVec(dm, name, mesh->printTol, locFbc);
4773:     VecDestroy(&locFbc);
4774:   }
4775:   PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);
4776:   return(0);
4777: }

4779: PetscErrorCode DMPlexComputeResidual_Hybrid_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user)
4780: {
4781:   DM_Plex         *mesh       = (DM_Plex *) dm->data;
4782:   const char      *name       = "Hybrid Residual";
4783:   DM               dmAux      = NULL;
4784:   DMLabel          ghostLabel = NULL;
4785:   PetscDS          prob       = NULL;
4786:   PetscDS          probAux    = NULL;
4787:   PetscSection     section    = NULL;
4788:   DMField          coordField = NULL;
4789:   Vec              locA;
4790:   PetscScalar     *u = NULL, *u_t, *a;
4791:   PetscScalar     *elemVec;
4792:   IS               chunkIS;
4793:   const PetscInt  *cells;
4794:   PetscInt        *faces;
4795:   PetscInt         cStart, cEnd, numCells;
4796:   PetscInt         Nf, f, totDim, totDimAux, numChunks, cellChunkSize, chunk;
4797:   PetscInt         maxDegree = PETSC_MAX_INT;
4798:   PetscQuadrature  affineQuad = NULL, *quads = NULL;
4799:   PetscFEGeom     *affineGeom = NULL, **geoms = NULL;
4800:   PetscErrorCode   ierr;

4803:   PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);
4804:   /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */
4805:   /* FEM */
4806:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
4807:   /* 1: Get sizes from dm and dmAux */
4808:   DMGetSection(dm, &section);
4809:   DMGetLabel(dm, "ghost", &ghostLabel);
4810:   DMGetCellDS(dm, cStart, &prob);
4811:   PetscDSGetNumFields(prob, &Nf);
4812:   PetscDSGetTotalDimension(prob, &totDim);
4813:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
4814:   if (locA) {
4815:     VecGetDM(locA, &dmAux);
4816:     DMGetCellDS(dmAux, cStart, &probAux);
4817:     PetscDSGetTotalDimension(probAux, &totDimAux);
4818:   }
4819:   /* 2: Setup geometric data */
4820:   DMGetCoordinateField(dm, &coordField);
4821:   DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);
4822:   if (maxDegree > 1) {
4823:     PetscCalloc2(Nf,&quads,Nf,&geoms);
4824:     for (f = 0; f < Nf; ++f) {
4825:       PetscFE fe;

4827:       PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);
4828:       if (fe) {
4829:         PetscFEGetQuadrature(fe, &quads[f]);
4830:         PetscObjectReference((PetscObject) quads[f]);
4831:       }
4832:     }
4833:   }
4834:   /* Loop over chunks */
4835:   numCells      = cEnd - cStart;
4836:   cellChunkSize = numCells;
4837:   numChunks     = !numCells ? 0 : PetscCeilReal(((PetscReal) numCells)/cellChunkSize);
4838:   PetscCalloc1(2*cellChunkSize, &faces);
4839:   ISCreateGeneral(PETSC_COMM_SELF, cellChunkSize, faces, PETSC_USE_POINTER, &chunkIS);
4840:   /* Extract field coefficients */
4841:   /* NOTE This needs the end cap faces to have identical orientations */
4842:   DMPlexGetCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);
4843:   DMGetWorkArray(dm, cellChunkSize*totDim, MPIU_SCALAR, &elemVec);
4844:   for (chunk = 0; chunk < numChunks; ++chunk) {
4845:     PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c;

4847:     PetscMemzero(elemVec, cellChunkSize*totDim * sizeof(PetscScalar));
4848:     /* Get faces */
4849:     for (c = cS; c < cE; ++c) {
4850:       const PetscInt  cell = cells ? cells[c] : c;
4851:       const PetscInt *cone;
4852:       DMPlexGetCone(dm, cell, &cone);
4853:       faces[(c-cS)*2+0] = cone[0];
4854:       faces[(c-cS)*2+1] = cone[1];
4855:     }
4856:     ISGeneralSetIndices(chunkIS, cellChunkSize, faces, PETSC_USE_POINTER);
4857:     /* Get geometric data */
4858:     if (maxDegree <= 1) {
4859:       if (!affineQuad) {DMFieldCreateDefaultQuadrature(coordField, chunkIS, &affineQuad);}
4860:       if (affineQuad)  {DMSNESGetFEGeom(coordField, chunkIS, affineQuad, PETSC_TRUE, &affineGeom);}
4861:     } else {
4862:       for (f = 0; f < Nf; ++f) {
4863:         if (quads[f]) {DMSNESGetFEGeom(coordField, chunkIS, quads[f], PETSC_TRUE, &geoms[f]);}
4864:       }
4865:     }
4866:     /* Loop over fields */
4867:     for (f = 0; f < Nf; ++f) {
4868:       PetscFE         fe;
4869:       PetscFEGeom    *geom = affineGeom ? affineGeom : geoms[f];
4870:       PetscFEGeom    *chunkGeom = NULL;
4871:       PetscQuadrature quad = affineQuad ? affineQuad : quads[f];
4872:       PetscInt        numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset, Nq, Nb;

4874:       PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);
4875:       if (!fe) continue;
4876:       PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
4877:       PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);
4878:       PetscFEGetDimension(fe, &Nb);
4879:       blockSize = Nb;
4880:       batchSize = numBlocks * blockSize;
4881:       PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
4882:       numChunks = numCells / (numBatches*batchSize);
4883:       Ne        = numChunks*numBatches*batchSize;
4884:       Nr        = numCells % (numBatches*batchSize);
4885:       offset    = numCells - Nr;
4886:       PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
4887:       PetscFEIntegrateHybridResidual(prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);
4888:       PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);
4889:       PetscFEIntegrateHybridResidual(prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);
4890:       PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);
4891:     }
4892:     /* Add elemVec to locX */
4893:     for (c = cS; c < cE; ++c) {
4894:       const PetscInt cell = cells ? cells[c] : c;
4895:       const PetscInt cind = c - cStart;

4897:       if (mesh->printFEM > 1) {DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);}
4898:       if (ghostLabel) {
4899:         PetscInt ghostVal;

4901:         DMLabelGetValue(ghostLabel,cell,&ghostVal);
4902:         if (ghostVal > 0) continue;
4903:       }
4904:       DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);
4905:     }
4906:   }
4907:   DMPlexRestoreCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);
4908:   DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
4909:   PetscFree(faces);
4910:   ISDestroy(&chunkIS);
4911:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
4912:   if (maxDegree <= 1) {
4913:     DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
4914:     PetscQuadratureDestroy(&affineQuad);
4915:   } else {
4916:     for (f = 0; f < Nf; ++f) {
4917:       if (geoms) {DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);}
4918:       if (quads) {PetscQuadratureDestroy(&quads[f]);}
4919:     }
4920:     PetscFree2(quads,geoms);
4921:   }
4922:   PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);
4923:   return(0);
4924: }

4926: PetscErrorCode DMPlexComputeBdJacobian_Single_Internal(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt fieldI, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP, DMField coordField, IS facetIS)
4927: {
4928:   DM_Plex        *mesh = (DM_Plex *) dm->data;
4929:   DM              plex = NULL, plexA = NULL, tdm;
4930:   DMEnclosureType encAux;
4931:   PetscDS         prob, probAux = NULL;
4932:   PetscSection    section, sectionAux = NULL;
4933:   PetscSection    globalSection, subSection = NULL;
4934:   Vec             locA = NULL, tv;
4935:   PetscScalar    *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL;
4936:   PetscInt        v;
4937:   PetscInt        Nf, totDim, totDimAux = 0;
4938:   PetscBool       isMatISP, transform;
4939:   PetscErrorCode  ierr;

4942:   DMConvert(dm, DMPLEX, &plex);
4943:   DMHasBasisTransform(dm, &transform);
4944:   DMGetBasisTransformDM_Internal(dm, &tdm);
4945:   DMGetBasisTransformVec_Internal(dm, &tv);
4946:   DMGetLocalSection(dm, &section);
4947:   DMGetDS(dm, &prob);
4948:   PetscDSGetNumFields(prob, &Nf);
4949:   PetscDSGetTotalDimension(prob, &totDim);
4950:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
4951:   if (locA) {
4952:     DM dmAux;

4954:     VecGetDM(locA, &dmAux);
4955:     DMGetEnclosureRelation(dmAux, dm, &encAux);
4956:     DMConvert(dmAux, DMPLEX, &plexA);
4957:     DMGetDS(plexA, &probAux);
4958:     PetscDSGetTotalDimension(probAux, &totDimAux);
4959:     DMGetLocalSection(plexA, &sectionAux);
4960:   }

4962:   PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
4963:   DMGetGlobalSection(dm, &globalSection);
4964:   if (isMatISP) {DMPlexGetSubdomainSection(dm, &subSection);}
4965:   for (v = 0; v < numValues; ++v) {
4966:     PetscFEGeom    *fgeom;
4967:     PetscInt        maxDegree;
4968:     PetscQuadrature qGeom = NULL;
4969:     IS              pointIS;
4970:     const PetscInt *points;
4971:     PetscInt        numFaces, face, Nq;

4973:     DMLabelGetStratumIS(label, values[v], &pointIS);
4974:     if (!pointIS) continue; /* No points with that id on this process */
4975:     {
4976:       IS isectIS;

4978:       /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */
4979:       ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);
4980:       ISDestroy(&pointIS);
4981:       pointIS = isectIS;
4982:     }
4983:     ISGetLocalSize(pointIS, &numFaces);
4984:     ISGetIndices(pointIS, &points);
4985:     PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim*totDim, &elemMat, locA ? numFaces*totDimAux : 0, &a);
4986:     DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);
4987:     if (maxDegree <= 1) {
4988:       DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);
4989:     }
4990:     if (!qGeom) {
4991:       PetscFE fe;

4993:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
4994:       PetscFEGetFaceQuadrature(fe, &qGeom);
4995:       PetscObjectReference((PetscObject)qGeom);
4996:     }
4997:     PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
4998:     DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
4999:     for (face = 0; face < numFaces; ++face) {
5000:       const PetscInt point = points[face], *support;
5001:       PetscScalar   *x     = NULL;
5002:       PetscInt       i;

5004:       DMPlexGetSupport(dm, point, &support);
5005:       DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);
5006:       for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i];
5007:       DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);
5008:       if (locX_t) {
5009:         DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);
5010:         for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i];
5011:         DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);
5012:       }
5013:       if (locA) {
5014:         PetscInt subp;
5015:         DMGetEnclosurePoint(plexA, dm, encAux, support[0], &subp);
5016:         DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);
5017:         for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i];
5018:         DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);
5019:       }
5020:     }
5021:     PetscArrayzero(elemMat, numFaces*totDim*totDim);
5022:     {
5023:       PetscFE         fe;
5024:       PetscInt        Nb;
5025:       /* Conforming batches */
5026:       PetscInt        numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
5027:       /* Remainder */
5028:       PetscFEGeom    *chunkGeom = NULL;
5029:       PetscInt        fieldJ, Nr, offset;

5031:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
5032:       PetscFEGetDimension(fe, &Nb);
5033:       PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
5034:       blockSize = Nb;
5035:       batchSize = numBlocks * blockSize;
5036:       PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
5037:       numChunks = numFaces / (numBatches*batchSize);
5038:       Ne        = numChunks*numBatches*batchSize;
5039:       Nr        = numFaces % (numBatches*batchSize);
5040:       offset    = numFaces - Nr;
5041:       PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);
5042:       for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
5043:         PetscFEIntegrateBdJacobian(prob, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);
5044:       }
5045:       PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);
5046:       for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
5047:         PetscFEIntegrateBdJacobian(prob, fieldI, fieldJ, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, X_tShift, &elemMat[offset*totDim*totDim]);
5048:       }
5049:       PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);
5050:     }
5051:     for (face = 0; face < numFaces; ++face) {
5052:       const PetscInt point = points[face], *support;

5054:       /* Transform to global basis before insertion in Jacobian */
5055:       DMPlexGetSupport(plex, point, &support);
5056:       if (transform) {DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, support[0], PETSC_TRUE, totDim, &elemMat[face*totDim*totDim]);}
5057:       if (mesh->printFEM > 1) {DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);}
5058:       if (!isMatISP) {
5059:         DMPlexMatSetClosure(plex, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);
5060:       } else {
5061:         Mat lJ;

5063:         MatISGetLocalMat(JacP, &lJ);
5064:         DMPlexMatSetClosure(plex, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);
5065:       }
5066:     }
5067:     DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
5068:     PetscQuadratureDestroy(&qGeom);
5069:     ISRestoreIndices(pointIS, &points);
5070:     ISDestroy(&pointIS);
5071:     PetscFree4(u, u_t, elemMat, a);
5072:   }
5073:   if (plex)  {DMDestroy(&plex);}
5074:   if (plexA) {DMDestroy(&plexA);}
5075:   return(0);
5076: }

5078: PetscErrorCode DMPlexComputeBdJacobianSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP)
5079: {
5080:   DMField        coordField;
5081:   DMLabel        depthLabel;
5082:   IS             facetIS;
5083:   PetscInt       dim;

5087:   DMGetDimension(dm, &dim);
5088:   DMPlexGetDepthLabel(dm, &depthLabel);
5089:   DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
5090:   DMGetCoordinateField(dm, &coordField);
5091:   DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);
5092:   ISDestroy(&facetIS);
5093:   return(0);
5094: }

5096: PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user)
5097: {
5098:   PetscDS          prob;
5099:   PetscInt         dim, numBd, bd;
5100:   DMLabel          depthLabel;
5101:   DMField          coordField = NULL;
5102:   IS               facetIS;
5103:   PetscErrorCode   ierr;

5106:   DMGetDS(dm, &prob);
5107:   DMPlexGetDepthLabel(dm, &depthLabel);
5108:   DMGetDimension(dm, &dim);
5109:   DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
5110:   PetscDSGetNumBoundary(prob, &numBd);
5111:   DMGetCoordinateField(dm, &coordField);
5112:   for (bd = 0; bd < numBd; ++bd) {
5113:     DMBoundaryConditionType type;
5114:     const char             *bdLabel;
5115:     DMLabel                 label;
5116:     const PetscInt         *values;
5117:     PetscInt                fieldI, numValues;
5118:     PetscObject             obj;
5119:     PetscClassId            id;

5121:     PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &fieldI, NULL, NULL, NULL, NULL, &numValues, &values, NULL);
5122:     PetscDSGetDiscretization(prob, fieldI, &obj);
5123:     PetscObjectGetClassId(obj, &id);
5124:     if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue;
5125:     DMGetLabel(dm, bdLabel, &label);
5126:     DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, fieldI, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);
5127:   }
5128:   ISDestroy(&facetIS);
5129:   return(0);
5130: }

5132: PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user)
5133: {
5134:   DM_Plex        *mesh  = (DM_Plex *) dm->data;
5135:   const char     *name  = "Jacobian";
5136:   DM              dmAux, plex, tdm;
5137:   DMEnclosureType encAux;
5138:   Vec             A, tv;
5139:   DMField         coordField;
5140:   PetscDS         prob, probAux = NULL;
5141:   PetscSection    section, globalSection, subSection, sectionAux;
5142:   PetscScalar    *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL;
5143:   const PetscInt *cells;
5144:   PetscInt        Nf, fieldI, fieldJ;
5145:   PetscInt        totDim, totDimAux, cStart, cEnd, numCells, c;
5146:   PetscBool       isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE, transform;
5147:   PetscErrorCode  ierr;

5150:   PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);
5151:   ISGetLocalSize(cellIS, &numCells);
5152:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
5153:   DMHasBasisTransform(dm, &transform);
5154:   DMGetBasisTransformDM_Internal(dm, &tdm);
5155:   DMGetBasisTransformVec_Internal(dm, &tv);
5156:   DMGetLocalSection(dm, &section);
5157:   PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
5158:   DMGetGlobalSection(dm, &globalSection);
5159:   if (isMatISP) {DMPlexGetSubdomainSection(dm, &subSection);}
5160:   ISGetLocalSize(cellIS, &numCells);
5161:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
5162:   DMGetCellDS(dm, cells ? cells[cStart] : cStart, &prob);
5163:   PetscDSGetNumFields(prob, &Nf);
5164:   PetscDSGetTotalDimension(prob, &totDim);
5165:   PetscDSHasJacobian(prob, &hasJac);
5166:   PetscDSHasJacobianPreconditioner(prob, &hasPrec);
5167:   /* user passed in the same matrix, avoid double contributions and
5168:      only assemble the Jacobian */
5169:   if (hasJac && Jac == JacP) hasPrec = PETSC_FALSE;
5170:   PetscDSHasDynamicJacobian(prob, &hasDyn);
5171:   hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE;
5172:   PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
5173:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
5174:   if (dmAux) {
5175:     DMGetEnclosureRelation(dmAux, dm, &encAux);
5176:     DMConvert(dmAux, DMPLEX, &plex);
5177:     DMGetLocalSection(plex, &sectionAux);
5178:     DMGetDS(dmAux, &probAux);
5179:     PetscDSGetTotalDimension(probAux, &totDimAux);
5180:   }
5181:   PetscMalloc5(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,hasJac ? numCells*totDim*totDim : 0,&elemMat,hasPrec ? numCells*totDim*totDim : 0, &elemMatP,hasDyn ? numCells*totDim*totDim : 0, &elemMatD);
5182:   if (dmAux) {PetscMalloc1(numCells*totDimAux, &a);}
5183:   DMGetCoordinateField(dm, &coordField);
5184:   for (c = cStart; c < cEnd; ++c) {
5185:     const PetscInt cell = cells ? cells[c] : c;
5186:     const PetscInt cind = c - cStart;
5187:     PetscScalar   *x = NULL,  *x_t = NULL;
5188:     PetscInt       i;

5190:     DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);
5191:     for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i];
5192:     DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);
5193:     if (X_t) {
5194:       DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);
5195:       for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i];
5196:       DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);
5197:     }
5198:     if (dmAux) {
5199:       PetscInt subcell;
5200:       DMGetEnclosurePoint(dmAux, dm, encAux, cell, &subcell);
5201:       DMPlexVecGetClosure(plex, sectionAux, A, subcell, NULL, &x);
5202:       for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i];
5203:       DMPlexVecRestoreClosure(plex, sectionAux, A, subcell, NULL, &x);
5204:     }
5205:   }
5206:   if (hasJac)  {PetscArrayzero(elemMat,  numCells*totDim*totDim);}
5207:   if (hasPrec) {PetscArrayzero(elemMatP, numCells*totDim*totDim);}
5208:   if (hasDyn)  {PetscArrayzero(elemMatD, numCells*totDim*totDim);}
5209:   for (fieldI = 0; fieldI < Nf; ++fieldI) {
5210:     PetscClassId    id;
5211:     PetscFE         fe;
5212:     PetscQuadrature qGeom = NULL;
5213:     PetscInt        Nb;
5214:     /* Conforming batches */
5215:     PetscInt        numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
5216:     /* Remainder */
5217:     PetscInt        Nr, offset, Nq;
5218:     PetscInt        maxDegree;
5219:     PetscFEGeom     *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL;

5221:     PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
5222:     PetscObjectGetClassId((PetscObject) fe, &id);
5223:     if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;}
5224:     PetscFEGetDimension(fe, &Nb);
5225:     PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
5226:     DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
5227:     if (maxDegree <= 1) {
5228:       DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);
5229:     }
5230:     if (!qGeom) {
5231:       PetscFEGetQuadrature(fe,&qGeom);
5232:       PetscObjectReference((PetscObject)qGeom);
5233:     }
5234:     PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
5235:     DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);
5236:     blockSize = Nb;
5237:     batchSize = numBlocks * blockSize;
5238:     PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
5239:     numChunks = numCells / (numBatches*batchSize);
5240:     Ne        = numChunks*numBatches*batchSize;
5241:     Nr        = numCells % (numBatches*batchSize);
5242:     offset    = numCells - Nr;
5243:     PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);
5244:     PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);
5245:     for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
5246:       if (hasJac) {
5247:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);
5248:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);
5249:       }
5250:       if (hasPrec) {
5251:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);
5252:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatP[offset*totDim*totDim]);
5253:       }
5254:       if (hasDyn) {
5255:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);
5256:         PetscFEIntegrateJacobian(prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatD[offset*totDim*totDim]);
5257:       }
5258:     }
5259:     PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);
5260:     PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);
5261:     DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);
5262:     PetscQuadratureDestroy(&qGeom);
5263:   }
5264:   /*   Add contribution from X_t */
5265:   if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];}
5266:   if (hasFV) {
5267:     PetscClassId id;
5268:     PetscFV      fv;
5269:     PetscInt     offsetI, NcI, NbI = 1, fc, f;

5271:     for (fieldI = 0; fieldI < Nf; ++fieldI) {
5272:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);
5273:       PetscDSGetFieldOffset(prob, fieldI, &offsetI);
5274:       PetscObjectGetClassId((PetscObject) fv, &id);
5275:       if (id != PETSCFV_CLASSID) continue;
5276:       /* Put in the identity */
5277:       PetscFVGetNumComponents(fv, &NcI);
5278:       for (c = cStart; c < cEnd; ++c) {
5279:         const PetscInt cind    = c - cStart;
5280:         const PetscInt eOffset = cind*totDim*totDim;
5281:         for (fc = 0; fc < NcI; ++fc) {
5282:           for (f = 0; f < NbI; ++f) {
5283:             const PetscInt i = offsetI + f*NcI+fc;
5284:             if (hasPrec) {
5285:               if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;}
5286:               elemMatP[eOffset+i*totDim+i] = 1.0;
5287:             } else {elemMat[eOffset+i*totDim+i] = 1.0;}
5288:           }
5289:         }
5290:       }
5291:     }
5292:     /* No allocated space for FV stuff, so ignore the zero entries */
5293:     MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);
5294:   }
5295:   /* Insert values into matrix */
5296:   isMatIS = PETSC_FALSE;
5297:   if (hasPrec && hasJac) {
5298:     PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);
5299:   }
5300:   if (isMatIS && !subSection) {
5301:     DMPlexGetSubdomainSection(dm, &subSection);
5302:   }
5303:   for (c = cStart; c < cEnd; ++c) {
5304:     const PetscInt cell = cells ? cells[c] : c;
5305:     const PetscInt cind = c - cStart;

5307:     /* Transform to global basis before insertion in Jacobian */
5308:     if (transform) {DMPlexBasisTransformPointTensor_Internal(dm, tdm, tv, cell, PETSC_TRUE, totDim, &elemMat[cind*totDim*totDim]);}
5309:     if (hasPrec) {
5310:       if (hasJac) {
5311:         if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);}
5312:         if (!isMatIS) {
5313:           DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
5314:         } else {
5315:           Mat lJ;

5317:           MatISGetLocalMat(Jac,&lJ);
5318:           DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
5319:         }
5320:       }
5321:       if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);}
5322:       if (!isMatISP) {
5323:         DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);
5324:       } else {
5325:         Mat lJ;

5327:         MatISGetLocalMat(JacP,&lJ);
5328:         DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);
5329:       }
5330:     } else {
5331:       if (hasJac) {
5332:         if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);}
5333:         if (!isMatISP) {
5334:           DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
5335:         } else {
5336:           Mat lJ;

5338:           MatISGetLocalMat(JacP,&lJ);
5339:           DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
5340:         }
5341:       }
5342:     }
5343:   }
5344:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
5345:   if (hasFV) {MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);}
5346:   PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);
5347:   if (dmAux) {
5348:     PetscFree(a);
5349:     DMDestroy(&plex);
5350:   }
5351:   /* Compute boundary integrals */
5352:   DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);
5353:   /* Assemble matrix */
5354:   if (hasJac && hasPrec) {
5355:     MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);
5356:     MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);
5357:   }
5358:   MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);
5359:   MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);
5360:   PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);
5361:   return(0);
5362: }

5364: PetscErrorCode DMPlexComputeJacobian_Hybrid_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec locX, Vec locX_t, Mat Jac, Mat JacP, void *user)
5365: {
5366:   DM_Plex         *mesh       = (DM_Plex *) dm->data;
5367:   const char      *name       = "Hybrid Jacobian";
5368:   DM               dmAux      = NULL;
5369:   DM               plex       = NULL;
5370:   DM               plexA      = NULL;
5371:   DMLabel          ghostLabel = NULL;
5372:   PetscDS          prob       = NULL;
5373:   PetscDS          probAux    = NULL;
5374:   PetscSection     section    = NULL;
5375:   DMField          coordField = NULL;
5376:   Vec              locA;
5377:   PetscScalar     *u = NULL, *u_t, *a = NULL;
5378:   PetscScalar     *elemMat, *elemMatP;
5379:   PetscSection     globalSection, subSection, sectionAux;
5380:   IS               chunkIS;
5381:   const PetscInt  *cells;
5382:   PetscInt        *faces;
5383:   PetscInt         cStart, cEnd, numCells;
5384:   PetscInt         Nf, fieldI, fieldJ, totDim, totDimAux, numChunks, cellChunkSize, chunk;
5385:   PetscInt         maxDegree = PETSC_MAX_INT;
5386:   PetscQuadrature  affineQuad = NULL, *quads = NULL;
5387:   PetscFEGeom     *affineGeom = NULL, **geoms = NULL;
5388:   PetscBool        isMatIS = PETSC_FALSE, isMatISP = PETSC_FALSE, hasBdJac, hasBdPrec;
5389:   PetscErrorCode   ierr;

5392:   PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);
5393:   ISGetLocalSize(cellIS, &numCells);
5394:   ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
5395:   DMConvert(dm, DMPLEX, &plex);
5396:   DMGetSection(dm, &section);
5397:   DMGetGlobalSection(dm, &globalSection);
5398:   DMGetLabel(dm, "ghost", &ghostLabel);
5399:   DMGetCellDS(dm, cStart, &prob);
5400:   PetscDSGetNumFields(prob, &Nf);
5401:   PetscDSGetTotalDimension(prob, &totDim);
5402:   PetscDSHasBdJacobian(prob, &hasBdJac);
5403:   PetscDSHasBdJacobianPreconditioner(prob, &hasBdPrec);
5404:   PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
5405:   if (isMatISP) {DMPlexGetSubdomainSection(plex, &subSection);}
5406:   if (hasBdPrec && hasBdJac) {PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);}
5407:   if (isMatIS && !subSection) {DMPlexGetSubdomainSection(plex, &subSection);}
5408:   PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
5409:   if (locA) {
5410:     VecGetDM(locA, &dmAux);
5411:     DMConvert(dmAux, DMPLEX, &plexA);
5412:     DMGetSection(dmAux, &sectionAux);
5413:     DMGetCellDS(dmAux, cStart, &probAux);
5414:     PetscDSGetTotalDimension(probAux, &totDimAux);
5415:   }
5416:   DMGetCoordinateField(dm, &coordField);
5417:   DMFieldGetDegree(coordField, cellIS, NULL, &maxDegree);
5418:   if (maxDegree > 1) {
5419:     PetscInt f;
5420:     PetscCalloc2(Nf,&quads,Nf,&geoms);
5421:     for (f = 0; f < Nf; ++f) {
5422:       PetscFE fe;

5424:       PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);
5425:       if (fe) {
5426:         PetscFEGetQuadrature(fe, &quads[f]);
5427:         PetscObjectReference((PetscObject) quads[f]);
5428:       }
5429:     }
5430:   }
5431:   cellChunkSize = numCells;
5432:   numChunks     = !numCells ? 0 : PetscCeilReal(((PetscReal) numCells)/cellChunkSize);
5433:   PetscCalloc1(2*cellChunkSize, &faces);
5434:   ISCreateGeneral(PETSC_COMM_SELF, cellChunkSize, faces, PETSC_USE_POINTER, &chunkIS);
5435:   DMPlexGetCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);
5436:   DMGetWorkArray(dm, hasBdJac  ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMat);
5437:   DMGetWorkArray(dm, hasBdPrec ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMatP);
5438:   for (chunk = 0; chunk < numChunks; ++chunk) {
5439:     PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c;

5441:     if (hasBdJac)  {PetscMemzero(elemMat,  numCells*totDim*totDim * sizeof(PetscScalar));}
5442:     if (hasBdPrec) {PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));}
5443:     /* Get faces */
5444:     for (c = cS; c < cE; ++c) {
5445:       const PetscInt  cell = cells ? cells[c] : c;
5446:       const PetscInt *cone;
5447:       DMPlexGetCone(plex, cell, &cone);
5448:       faces[(c-cS)*2+0] = cone[0];
5449:       faces[(c-cS)*2+1] = cone[1];
5450:     }
5451:     ISGeneralSetIndices(chunkIS, cellChunkSize, faces, PETSC_USE_POINTER);
5452:     if (maxDegree <= 1) {
5453:       if (!affineQuad) {DMFieldCreateDefaultQuadrature(coordField, chunkIS, &affineQuad);}
5454:       if (affineQuad)  {DMSNESGetFEGeom(coordField, chunkIS, affineQuad, PETSC_TRUE, &affineGeom);}
5455:     } else {
5456:       PetscInt f;
5457:       for (f = 0; f < Nf; ++f) {
5458:         if (quads[f]) {DMSNESGetFEGeom(coordField, chunkIS, quads[f], PETSC_TRUE, &geoms[f]);}
5459:       }
5460:     }

5462:     for (fieldI = 0; fieldI < Nf; ++fieldI) {
5463:       PetscFE         feI;
5464:       PetscFEGeom    *geom = affineGeom ? affineGeom : geoms[fieldI];
5465:       PetscFEGeom    *chunkGeom = NULL, *remGeom = NULL;
5466:       PetscQuadrature quad = affineQuad ? affineQuad : quads[fieldI];
5467:       PetscInt        numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset, Nq, Nb;

5469:       PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &feI);
5470:       if (!feI) continue;
5471:       PetscFEGetTileSizes(feI, NULL, &numBlocks, NULL, &numBatches);
5472:       PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);
5473:       PetscFEGetDimension(feI, &Nb);
5474:       blockSize = Nb;
5475:       batchSize = numBlocks * blockSize;
5476:       PetscFESetTileSizes(feI, blockSize, numBlocks, batchSize, numBatches);
5477:       numChunks = numCells / (numBatches*batchSize);
5478:       Ne        = numChunks*numBatches*batchSize;
5479:       Nr        = numCells % (numBatches*batchSize);
5480:       offset    = numCells - Nr;
5481:       PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
5482:       PetscFEGeomGetChunk(geom,offset,numCells,&remGeom);
5483:       for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
5484:         PetscFE feJ;

5486:         PetscDSGetDiscretization(prob, fieldJ, (PetscObject *) &feJ);
5487:         if (!feJ) continue;
5488:         if (hasBdJac) {
5489:           PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);
5490:           PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);
5491:         }
5492:         if (hasBdPrec) {
5493:           PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);
5494:           PetscFEIntegrateHybridJacobian(prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatP[offset*totDim*totDim]);
5495:         }
5496:       }
5497:       PetscFEGeomRestoreChunk(geom,offset,numCells,&remGeom);
5498:       PetscFEGeomRestoreChunk(geom,0,offset,&chunkGeom);
5499:     }
5500:     /* Insert values into matrix */
5501:     for (c = cS; c < cE; ++c) {
5502:       const PetscInt cell = cells ? cells[c] : c;
5503:       const PetscInt cind = c - cS;

5505:       if (hasBdPrec) {
5506:         if (hasBdJac) {
5507:           if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);}
5508:           if (!isMatIS) {
5509:             DMPlexMatSetClosure(plex, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
5510:           } else {
5511:             Mat lJ;

5513:             MatISGetLocalMat(Jac,&lJ);
5514:             DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
5515:           }
5516:         }
5517:         if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);}
5518:         if (!isMatISP) {
5519:           DMPlexMatSetClosure(plex, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);
5520:         } else {
5521:           Mat lJ;

5523:           MatISGetLocalMat(JacP,&lJ);
5524:           DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);
5525:         }
5526:       } else if (hasBdJac) {
5527:         if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);}
5528:         if (!isMatISP) {
5529:           DMPlexMatSetClosure(plex, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
5530:         } else {
5531:           Mat lJ;

5533:           MatISGetLocalMat(JacP,&lJ);
5534:           DMPlexMatSetClosure(plex, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
5535:         }
5536:       }
5537:     }
5538:   }
5539:   DMPlexRestoreCellFields(dm, cellIS, locX, locX_t, locA, &u, &u_t, &a);
5540:   DMRestoreWorkArray(dm, hasBdJac  ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMat);
5541:   DMRestoreWorkArray(dm, hasBdPrec ? cellChunkSize*totDim*totDim : 0, MPIU_SCALAR, &elemMatP);
5542:   PetscFree(faces);
5543:   ISDestroy(&chunkIS);
5544:   ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
5545:   if (maxDegree <= 1) {
5546:     DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
5547:     PetscQuadratureDestroy(&affineQuad);
5548:   } else {
5549:     PetscInt f;
5550:     for (f = 0; f < Nf; ++f) {
5551:       if (geoms) {DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE, &geoms[f]);}
5552:       if (quads) {PetscQuadratureDestroy(&quads[f]);}
5553:     }
5554:     PetscFree2(quads,geoms);
5555:   }
5556:   if (dmAux) {DMDestroy(&plexA);}
5557:   DMDestroy(&plex);
5558:   /* Assemble matrix */
5559:   if (hasBdJac && hasBdPrec) {
5560:     MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);
5561:     MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);
5562:   }
5563:   MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);
5564:   MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);
5565:   PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);
5566:   return(0);
5567: }