Actual source code: plextree.c
petsc-3.9.4 2018-09-11
1: #include <petsc/private/dmpleximpl.h>
2: #include <petsc/private/isimpl.h>
3: #include <petsc/private/petscfeimpl.h>
4: #include <petscsf.h>
5: #include <petscds.h>
7: /** hierarchy routines */
9: /*@
10: DMPlexSetReferenceTree - set the reference tree for hierarchically non-conforming meshes.
12: Not collective
14: Input Parameters:
15: + dm - The DMPlex object
16: - ref - The reference tree DMPlex object
18: Level: intermediate
20: .seealso: DMPlexGetReferenceTree(), DMPlexCreateDefaultReferenceTree()
21: @*/
22: PetscErrorCode DMPlexSetReferenceTree(DM dm, DM ref)
23: {
24: DM_Plex *mesh = (DM_Plex *)dm->data;
25: PetscErrorCode ierr;
30: PetscObjectReference((PetscObject)ref);
31: DMDestroy(&mesh->referenceTree);
32: mesh->referenceTree = ref;
33: return(0);
34: }
36: /*@
37: DMPlexGetReferenceTree - get the reference tree for hierarchically non-conforming meshes.
39: Not collective
41: Input Parameters:
42: . dm - The DMPlex object
44: Output Parameters
45: . ref - The reference tree DMPlex object
47: Level: intermediate
49: .seealso: DMPlexSetReferenceTree(), DMPlexCreateDefaultReferenceTree()
50: @*/
51: PetscErrorCode DMPlexGetReferenceTree(DM dm, DM *ref)
52: {
53: DM_Plex *mesh = (DM_Plex *)dm->data;
58: *ref = mesh->referenceTree;
59: return(0);
60: }
62: static PetscErrorCode DMPlexReferenceTreeGetChildSymmetry_Default(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB)
63: {
64: PetscInt coneSize, dStart, dEnd, dim, ABswap, oAvert, oBvert, ABswapVert;
68: if (parentOrientA == parentOrientB) {
69: if (childOrientB) *childOrientB = childOrientA;
70: if (childB) *childB = childA;
71: return(0);
72: }
73: for (dim = 0; dim < 3; dim++) {
74: DMPlexGetDepthStratum(dm,dim,&dStart,&dEnd);
75: if (parent >= dStart && parent <= dEnd) {
76: break;
77: }
78: }
79: if (dim > 2) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot perform child symmetry for %d-cells",dim);
80: if (!dim) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"A vertex has no children");
81: if (childA < dStart || childA >= dEnd) {
82: /* this is a lower-dimensional child: bootstrap */
83: PetscInt size, i, sA = -1, sB, sOrientB, sConeSize;
84: const PetscInt *supp, *coneA, *coneB, *oA, *oB;
86: DMPlexGetSupportSize(dm,childA,&size);
87: DMPlexGetSupport(dm,childA,&supp);
89: /* find a point sA in supp(childA) that has the same parent */
90: for (i = 0; i < size; i++) {
91: PetscInt sParent;
93: sA = supp[i];
94: if (sA == parent) continue;
95: DMPlexGetTreeParent(dm,sA,&sParent,NULL);
96: if (sParent == parent) {
97: break;
98: }
99: }
100: if (i == size) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"could not find support in children");
101: /* find out which point sB is in an equivalent position to sA under
102: * parentOrientB */
103: DMPlexReferenceTreeGetChildSymmetry_Default(dm,parent,parentOrientA,0,sA,parentOrientB,&sOrientB,&sB);
104: DMPlexGetConeSize(dm,sA,&sConeSize);
105: DMPlexGetCone(dm,sA,&coneA);
106: DMPlexGetCone(dm,sB,&coneB);
107: DMPlexGetConeOrientation(dm,sA,&oA);
108: DMPlexGetConeOrientation(dm,sB,&oB);
109: /* step through the cone of sA in natural order */
110: for (i = 0; i < sConeSize; i++) {
111: if (coneA[i] == childA) {
112: /* if childA is at position i in coneA,
113: * then we want the point that is at sOrientB*i in coneB */
114: PetscInt j = (sOrientB >= 0) ? ((sOrientB + i) % sConeSize) : ((sConeSize -(sOrientB+1) - i) % sConeSize);
115: if (childB) *childB = coneB[j];
116: if (childOrientB) {
117: PetscInt oBtrue;
119: DMPlexGetConeSize(dm,childA,&coneSize);
120: /* compose sOrientB and oB[j] */
121: if (coneSize != 0 && coneSize != 2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Expected a vertex or an edge");
122: /* we may have to flip an edge */
123: oBtrue = coneSize ? ((sOrientB >= 0) ? oB[j] : -(oB[j] + 2)) : 0;
124: ABswap = DihedralSwap(coneSize,oA[i],oBtrue);
125: *childOrientB = DihedralCompose(coneSize,childOrientA,ABswap);
126: }
127: break;
128: }
129: }
130: if (i == sConeSize) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"support cone mismatch");
131: return(0);
132: }
133: /* get the cone size and symmetry swap */
134: DMPlexGetConeSize(dm,parent,&coneSize);
135: ABswap = DihedralSwap(coneSize, parentOrientA, parentOrientB);
136: if (dim == 2) {
137: /* orientations refer to cones: we want them to refer to vertices:
138: * if it's a rotation, they are the same, but if the order is reversed, a
139: * permutation that puts side i first does *not* put vertex i first */
140: oAvert = (parentOrientA >= 0) ? parentOrientA : -((-parentOrientA % coneSize) + 1);
141: oBvert = (parentOrientB >= 0) ? parentOrientB : -((-parentOrientB % coneSize) + 1);
142: ABswapVert = DihedralSwap(coneSize, oAvert, oBvert);
143: } else {
144: ABswapVert = ABswap;
145: }
146: if (childB) {
147: /* assume that each child corresponds to a vertex, in the same order */
148: PetscInt p, posA = -1, numChildren, i;
149: const PetscInt *children;
151: /* count which position the child is in */
152: DMPlexGetTreeChildren(dm,parent,&numChildren,&children);
153: for (i = 0; i < numChildren; i++) {
154: p = children[i];
155: if (p == childA) {
156: posA = i;
157: break;
158: }
159: }
160: if (posA >= coneSize) {
161: /* this is the triangle in the middle of a uniformly refined triangle: it
162: * is invariant */
163: if (dim != 2 || posA != 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Expected a middle triangle, got something else");
164: *childB = childA;
165: }
166: else {
167: /* figure out position B by applying ABswapVert */
168: PetscInt posB;
170: posB = (ABswapVert >= 0) ? ((ABswapVert + posA) % coneSize) : ((coneSize -(ABswapVert + 1) - posA) % coneSize);
171: if (childB) *childB = children[posB];
172: }
173: }
174: if (childOrientB) *childOrientB = DihedralCompose(coneSize,childOrientA,ABswap);
175: return(0);
176: }
178: /*@
179: DMPlexReferenceTreeGetChildSymmetry - Given a reference tree, transform a childid and orientation from one parent frame to another
181: Input Parameters:
182: + dm - the reference tree DMPlex object
183: . parent - the parent point
184: . parentOrientA - the reference orientation for describing the parent
185: . childOrientA - the reference orientation for describing the child
186: . childA - the reference childID for describing the child
187: - parentOrientB - the new orientation for describing the parent
189: Output Parameters:
190: + childOrientB - if not NULL, set to the new oreintation for describing the child
191: - childB - if not NULL, the new childID for describing the child
193: Level: developer
195: .seealso: DMPlexGetReferenceTree(), DMPlexSetReferenceTree(), DMPlexSetTree()
196: @*/
197: PetscErrorCode DMPlexReferenceTreeGetChildSymmetry(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB)
198: {
199: DM_Plex *mesh = (DM_Plex *)dm->data;
204: if (!mesh->getchildsymmetry) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"DMPlexReferenceTreeGetChildSymmetry not implemented");
205: mesh->getchildsymmetry(dm,parent,parentOrientA,childOrientA,childA,parentOrientB,childOrientB,childB);
206: return(0);
207: }
209: static PetscErrorCode DMPlexSetTree_Internal(DM,PetscSection,PetscInt*,PetscInt*,PetscBool,PetscBool);
211: PetscErrorCode DMPlexCreateReferenceTree_Union(DM K, DM Kref, const char *labelName, DM *ref)
212: {
213: MPI_Comm comm;
214: PetscInt dim, p, pStart, pEnd, pRefStart, pRefEnd, d, offset, parentSize, *parents, *childIDs;
215: PetscInt *permvals, *unionCones, *coneSizes, *unionOrientations, numUnionPoints, *numDimPoints, numCones, numVerts;
216: DMLabel identity, identityRef;
217: PetscSection unionSection, unionConeSection, parentSection;
218: PetscScalar *unionCoords;
219: IS perm;
223: comm = PetscObjectComm((PetscObject)K);
224: DMGetDimension(K, &dim);
225: DMPlexGetChart(K, &pStart, &pEnd);
226: DMGetLabel(K, labelName, &identity);
227: DMGetLabel(Kref, labelName, &identityRef);
228: DMPlexGetChart(Kref, &pRefStart, &pRefEnd);
229: PetscSectionCreate(comm, &unionSection);
230: PetscSectionSetChart(unionSection, 0, (pEnd - pStart) + (pRefEnd - pRefStart));
231: /* count points that will go in the union */
232: for (p = pStart; p < pEnd; p++) {
233: PetscSectionSetDof(unionSection, p - pStart, 1);
234: }
235: for (p = pRefStart; p < pRefEnd; p++) {
236: PetscInt q, qSize;
237: DMLabelGetValue(identityRef, p, &q);
238: DMLabelGetStratumSize(identityRef, q, &qSize);
239: if (qSize > 1) {
240: PetscSectionSetDof(unionSection, p - pRefStart + (pEnd - pStart), 1);
241: }
242: }
243: PetscMalloc1(pEnd - pStart + pRefEnd - pRefStart,&permvals);
244: offset = 0;
245: /* stratify points in the union by topological dimension */
246: for (d = 0; d <= dim; d++) {
247: PetscInt cStart, cEnd, c;
249: DMPlexGetHeightStratum(K, d, &cStart, &cEnd);
250: for (c = cStart; c < cEnd; c++) {
251: permvals[offset++] = c;
252: }
254: DMPlexGetHeightStratum(Kref, d, &cStart, &cEnd);
255: for (c = cStart; c < cEnd; c++) {
256: permvals[offset++] = c + (pEnd - pStart);
257: }
258: }
259: ISCreateGeneral(comm, (pEnd - pStart) + (pRefEnd - pRefStart), permvals, PETSC_OWN_POINTER, &perm);
260: PetscSectionSetPermutation(unionSection,perm);
261: PetscSectionSetUp(unionSection);
262: PetscSectionGetStorageSize(unionSection,&numUnionPoints);
263: PetscMalloc2(numUnionPoints,&coneSizes,dim+1,&numDimPoints);
264: /* count dimension points */
265: for (d = 0; d <= dim; d++) {
266: PetscInt cStart, cOff, cOff2;
267: DMPlexGetHeightStratum(K,d,&cStart,NULL);
268: PetscSectionGetOffset(unionSection,cStart-pStart,&cOff);
269: if (d < dim) {
270: DMPlexGetHeightStratum(K,d+1,&cStart,NULL);
271: PetscSectionGetOffset(unionSection,cStart-pStart,&cOff2);
272: }
273: else {
274: cOff2 = numUnionPoints;
275: }
276: numDimPoints[dim - d] = cOff2 - cOff;
277: }
278: PetscSectionCreate(comm, &unionConeSection);
279: PetscSectionSetChart(unionConeSection, 0, numUnionPoints);
280: /* count the cones in the union */
281: for (p = pStart; p < pEnd; p++) {
282: PetscInt dof, uOff;
284: DMPlexGetConeSize(K, p, &dof);
285: PetscSectionGetOffset(unionSection, p - pStart,&uOff);
286: PetscSectionSetDof(unionConeSection, uOff, dof);
287: coneSizes[uOff] = dof;
288: }
289: for (p = pRefStart; p < pRefEnd; p++) {
290: PetscInt dof, uDof, uOff;
292: DMPlexGetConeSize(Kref, p, &dof);
293: PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
294: PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
295: if (uDof) {
296: PetscSectionSetDof(unionConeSection, uOff, dof);
297: coneSizes[uOff] = dof;
298: }
299: }
300: PetscSectionSetUp(unionConeSection);
301: PetscSectionGetStorageSize(unionConeSection,&numCones);
302: PetscMalloc2(numCones,&unionCones,numCones,&unionOrientations);
303: /* write the cones in the union */
304: for (p = pStart; p < pEnd; p++) {
305: PetscInt dof, uOff, c, cOff;
306: const PetscInt *cone, *orientation;
308: DMPlexGetConeSize(K, p, &dof);
309: DMPlexGetCone(K, p, &cone);
310: DMPlexGetConeOrientation(K, p, &orientation);
311: PetscSectionGetOffset(unionSection, p - pStart,&uOff);
312: PetscSectionGetOffset(unionConeSection,uOff,&cOff);
313: for (c = 0; c < dof; c++) {
314: PetscInt e, eOff;
315: e = cone[c];
316: PetscSectionGetOffset(unionSection, e - pStart, &eOff);
317: unionCones[cOff + c] = eOff;
318: unionOrientations[cOff + c] = orientation[c];
319: }
320: }
321: for (p = pRefStart; p < pRefEnd; p++) {
322: PetscInt dof, uDof, uOff, c, cOff;
323: const PetscInt *cone, *orientation;
325: DMPlexGetConeSize(Kref, p, &dof);
326: DMPlexGetCone(Kref, p, &cone);
327: DMPlexGetConeOrientation(Kref, p, &orientation);
328: PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
329: PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
330: if (uDof) {
331: PetscSectionGetOffset(unionConeSection,uOff,&cOff);
332: for (c = 0; c < dof; c++) {
333: PetscInt e, eOff, eDof;
335: e = cone[c];
336: PetscSectionGetDof(unionSection, e - pRefStart + (pEnd - pStart),&eDof);
337: if (eDof) {
338: PetscSectionGetOffset(unionSection, e - pRefStart + (pEnd - pStart), &eOff);
339: }
340: else {
341: DMLabelGetValue(identityRef, e, &e);
342: PetscSectionGetOffset(unionSection, e - pStart, &eOff);
343: }
344: unionCones[cOff + c] = eOff;
345: unionOrientations[cOff + c] = orientation[c];
346: }
347: }
348: }
349: /* get the coordinates */
350: {
351: PetscInt vStart, vEnd, vRefStart, vRefEnd, v, vDof, vOff;
352: PetscSection KcoordsSec, KrefCoordsSec;
353: Vec KcoordsVec, KrefCoordsVec;
354: PetscScalar *Kcoords;
356: DMGetCoordinateSection(K, &KcoordsSec);
357: DMGetCoordinatesLocal(K, &KcoordsVec);
358: DMGetCoordinateSection(Kref, &KrefCoordsSec);
359: DMGetCoordinatesLocal(Kref, &KrefCoordsVec);
361: numVerts = numDimPoints[0];
362: PetscMalloc1(numVerts * dim,&unionCoords);
363: DMPlexGetDepthStratum(K,0,&vStart,&vEnd);
365: offset = 0;
366: for (v = vStart; v < vEnd; v++) {
367: PetscSectionGetOffset(unionSection,v - pStart,&vOff);
368: VecGetValuesSection(KcoordsVec, KcoordsSec, v, &Kcoords);
369: for (d = 0; d < dim; d++) {
370: unionCoords[offset * dim + d] = Kcoords[d];
371: }
372: offset++;
373: }
374: DMPlexGetDepthStratum(Kref,0,&vRefStart,&vRefEnd);
375: for (v = vRefStart; v < vRefEnd; v++) {
376: PetscSectionGetDof(unionSection,v - pRefStart + (pEnd - pStart),&vDof);
377: PetscSectionGetOffset(unionSection,v - pRefStart + (pEnd - pStart),&vOff);
378: VecGetValuesSection(KrefCoordsVec, KrefCoordsSec, v, &Kcoords);
379: if (vDof) {
380: for (d = 0; d < dim; d++) {
381: unionCoords[offset * dim + d] = Kcoords[d];
382: }
383: offset++;
384: }
385: }
386: }
387: DMCreate(comm,ref);
388: DMSetType(*ref,DMPLEX);
389: DMSetDimension(*ref,dim);
390: DMPlexCreateFromDAG(*ref,dim,numDimPoints,coneSizes,unionCones,unionOrientations,unionCoords);
391: /* set the tree */
392: PetscSectionCreate(comm,&parentSection);
393: PetscSectionSetChart(parentSection,0,numUnionPoints);
394: for (p = pRefStart; p < pRefEnd; p++) {
395: PetscInt uDof, uOff;
397: PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
398: PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
399: if (uDof) {
400: PetscSectionSetDof(parentSection,uOff,1);
401: }
402: }
403: PetscSectionSetUp(parentSection);
404: PetscSectionGetStorageSize(parentSection,&parentSize);
405: PetscMalloc2(parentSize,&parents,parentSize,&childIDs);
406: for (p = pRefStart; p < pRefEnd; p++) {
407: PetscInt uDof, uOff;
409: PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
410: PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
411: if (uDof) {
412: PetscInt pOff, parent, parentU;
413: PetscSectionGetOffset(parentSection,uOff,&pOff);
414: DMLabelGetValue(identityRef,p,&parent);
415: PetscSectionGetOffset(unionSection, parent - pStart,&parentU);
416: parents[pOff] = parentU;
417: childIDs[pOff] = uOff;
418: }
419: }
420: DMPlexSetTree_Internal(*ref,parentSection,parents,childIDs,PETSC_TRUE,PETSC_FALSE);
421: PetscSectionDestroy(&parentSection);
422: PetscFree2(parents,childIDs);
424: /* clean up */
425: PetscSectionDestroy(&unionSection);
426: PetscSectionDestroy(&unionConeSection);
427: ISDestroy(&perm);
428: PetscFree(unionCoords);
429: PetscFree2(unionCones,unionOrientations);
430: PetscFree2(coneSizes,numDimPoints);
431: return(0);
432: }
434: /*@
435: DMPlexCreateDefaultReferenceTree - create a reference tree for isotropic hierarchical mesh refinement.
437: Collective on comm
439: Input Parameters:
440: + comm - the MPI communicator
441: . dim - the spatial dimension
442: - simplex - Flag for simplex, otherwise use a tensor-product cell
444: Output Parameters:
445: . ref - the reference tree DMPlex object
447: Level: intermediate
449: .keywords: reference cell
450: .seealso: DMPlexSetReferenceTree(), DMPlexGetReferenceTree()
451: @*/
452: PetscErrorCode DMPlexCreateDefaultReferenceTree(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *ref)
453: {
454: DM_Plex *mesh;
455: DM K, Kref;
456: PetscInt p, pStart, pEnd;
457: DMLabel identity;
461: #if 1
462: comm = PETSC_COMM_SELF;
463: #endif
464: /* create a reference element */
465: DMPlexCreateReferenceCell(comm, dim, simplex, &K);
466: DMCreateLabel(K, "identity");
467: DMGetLabel(K, "identity", &identity);
468: DMPlexGetChart(K, &pStart, &pEnd);
469: for (p = pStart; p < pEnd; p++) {
470: DMLabelSetValue(identity, p, p);
471: }
472: /* refine it */
473: DMRefine(K,comm,&Kref);
475: /* the reference tree is the union of these two, without duplicating
476: * points that appear in both */
477: DMPlexCreateReferenceTree_Union(K, Kref, "identity", ref);
478: mesh = (DM_Plex *) (*ref)->data;
479: mesh->getchildsymmetry = DMPlexReferenceTreeGetChildSymmetry_Default;
480: DMDestroy(&K);
481: DMDestroy(&Kref);
482: return(0);
483: }
485: static PetscErrorCode DMPlexTreeSymmetrize(DM dm)
486: {
487: DM_Plex *mesh = (DM_Plex *)dm->data;
488: PetscSection childSec, pSec;
489: PetscInt p, pSize, cSize, parMax = PETSC_MIN_INT, parMin = PETSC_MAX_INT;
490: PetscInt *offsets, *children, pStart, pEnd;
495: PetscSectionDestroy(&mesh->childSection);
496: PetscFree(mesh->children);
497: pSec = mesh->parentSection;
498: if (!pSec) return(0);
499: PetscSectionGetStorageSize(pSec,&pSize);
500: for (p = 0; p < pSize; p++) {
501: PetscInt par = mesh->parents[p];
503: parMax = PetscMax(parMax,par+1);
504: parMin = PetscMin(parMin,par);
505: }
506: if (parMin > parMax) {
507: parMin = -1;
508: parMax = -1;
509: }
510: PetscSectionCreate(PetscObjectComm((PetscObject)pSec),&childSec);
511: PetscSectionSetChart(childSec,parMin,parMax);
512: for (p = 0; p < pSize; p++) {
513: PetscInt par = mesh->parents[p];
515: PetscSectionAddDof(childSec,par,1);
516: }
517: PetscSectionSetUp(childSec);
518: PetscSectionGetStorageSize(childSec,&cSize);
519: PetscMalloc1(cSize,&children);
520: PetscCalloc1(parMax-parMin,&offsets);
521: PetscSectionGetChart(pSec,&pStart,&pEnd);
522: for (p = pStart; p < pEnd; p++) {
523: PetscInt dof, off, i;
525: PetscSectionGetDof(pSec,p,&dof);
526: PetscSectionGetOffset(pSec,p,&off);
527: for (i = 0; i < dof; i++) {
528: PetscInt par = mesh->parents[off + i], cOff;
530: PetscSectionGetOffset(childSec,par,&cOff);
531: children[cOff + offsets[par-parMin]++] = p;
532: }
533: }
534: mesh->childSection = childSec;
535: mesh->children = children;
536: PetscFree(offsets);
537: return(0);
538: }
540: static PetscErrorCode AnchorsFlatten (PetscSection section, IS is, PetscSection *sectionNew, IS *isNew)
541: {
542: PetscInt pStart, pEnd, size, sizeNew, i, p, *valsNew = NULL;
543: const PetscInt *vals;
544: PetscSection secNew;
545: PetscBool anyNew, globalAnyNew;
546: PetscBool compress;
550: PetscSectionGetChart(section,&pStart,&pEnd);
551: ISGetLocalSize(is,&size);
552: ISGetIndices(is,&vals);
553: PetscSectionCreate(PetscObjectComm((PetscObject)section),&secNew);
554: PetscSectionSetChart(secNew,pStart,pEnd);
555: for (i = 0; i < size; i++) {
556: PetscInt dof;
558: p = vals[i];
559: if (p < pStart || p >= pEnd) continue;
560: PetscSectionGetDof(section, p, &dof);
561: if (dof) break;
562: }
563: if (i == size) {
564: PetscSectionSetUp(secNew);
565: anyNew = PETSC_FALSE;
566: compress = PETSC_FALSE;
567: sizeNew = 0;
568: }
569: else {
570: anyNew = PETSC_TRUE;
571: for (p = pStart; p < pEnd; p++) {
572: PetscInt dof, off;
574: PetscSectionGetDof(section, p, &dof);
575: PetscSectionGetOffset(section, p, &off);
576: for (i = 0; i < dof; i++) {
577: PetscInt q = vals[off + i], qDof = 0;
579: if (q >= pStart && q < pEnd) {
580: PetscSectionGetDof(section, q, &qDof);
581: }
582: if (qDof) {
583: PetscSectionAddDof(secNew, p, qDof);
584: }
585: else {
586: PetscSectionAddDof(secNew, p, 1);
587: }
588: }
589: }
590: PetscSectionSetUp(secNew);
591: PetscSectionGetStorageSize(secNew,&sizeNew);
592: PetscMalloc1(sizeNew,&valsNew);
593: compress = PETSC_FALSE;
594: for (p = pStart; p < pEnd; p++) {
595: PetscInt dof, off, count, offNew, dofNew;
597: PetscSectionGetDof(section, p, &dof);
598: PetscSectionGetOffset(section, p, &off);
599: PetscSectionGetDof(secNew, p, &dofNew);
600: PetscSectionGetOffset(secNew, p, &offNew);
601: count = 0;
602: for (i = 0; i < dof; i++) {
603: PetscInt q = vals[off + i], qDof = 0, qOff = 0, j;
605: if (q >= pStart && q < pEnd) {
606: PetscSectionGetDof(section, q, &qDof);
607: PetscSectionGetOffset(section, q, &qOff);
608: }
609: if (qDof) {
610: PetscInt oldCount = count;
612: for (j = 0; j < qDof; j++) {
613: PetscInt k, r = vals[qOff + j];
615: for (k = 0; k < oldCount; k++) {
616: if (valsNew[offNew + k] == r) {
617: break;
618: }
619: }
620: if (k == oldCount) {
621: valsNew[offNew + count++] = r;
622: }
623: }
624: }
625: else {
626: PetscInt k, oldCount = count;
628: for (k = 0; k < oldCount; k++) {
629: if (valsNew[offNew + k] == q) {
630: break;
631: }
632: }
633: if (k == oldCount) {
634: valsNew[offNew + count++] = q;
635: }
636: }
637: }
638: if (count < dofNew) {
639: PetscSectionSetDof(secNew, p, count);
640: compress = PETSC_TRUE;
641: }
642: }
643: }
644: ISRestoreIndices(is,&vals);
645: MPIU_Allreduce(&anyNew,&globalAnyNew,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));
646: if (!globalAnyNew) {
647: PetscSectionDestroy(&secNew);
648: *sectionNew = NULL;
649: *isNew = NULL;
650: }
651: else {
652: PetscBool globalCompress;
654: MPIU_Allreduce(&compress,&globalCompress,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));
655: if (compress) {
656: PetscSection secComp;
657: PetscInt *valsComp = NULL;
659: PetscSectionCreate(PetscObjectComm((PetscObject)section),&secComp);
660: PetscSectionSetChart(secComp,pStart,pEnd);
661: for (p = pStart; p < pEnd; p++) {
662: PetscInt dof;
664: PetscSectionGetDof(secNew, p, &dof);
665: PetscSectionSetDof(secComp, p, dof);
666: }
667: PetscSectionSetUp(secComp);
668: PetscSectionGetStorageSize(secComp,&sizeNew);
669: PetscMalloc1(sizeNew,&valsComp);
670: for (p = pStart; p < pEnd; p++) {
671: PetscInt dof, off, offNew, j;
673: PetscSectionGetDof(secNew, p, &dof);
674: PetscSectionGetOffset(secNew, p, &off);
675: PetscSectionGetOffset(secComp, p, &offNew);
676: for (j = 0; j < dof; j++) {
677: valsComp[offNew + j] = valsNew[off + j];
678: }
679: }
680: PetscSectionDestroy(&secNew);
681: secNew = secComp;
682: PetscFree(valsNew);
683: valsNew = valsComp;
684: }
685: ISCreateGeneral(PetscObjectComm((PetscObject)is),sizeNew,valsNew,PETSC_OWN_POINTER,isNew);
686: }
687: return(0);
688: }
690: static PetscErrorCode DMPlexCreateAnchors_Tree(DM dm)
691: {
692: PetscInt p, pStart, pEnd, *anchors, size;
693: PetscInt aMin = PETSC_MAX_INT, aMax = PETSC_MIN_INT;
694: PetscSection aSec;
695: DMLabel canonLabel;
696: IS aIS;
701: DMPlexGetChart(dm,&pStart,&pEnd);
702: DMGetLabel(dm,"canonical",&canonLabel);
703: for (p = pStart; p < pEnd; p++) {
704: PetscInt parent;
706: if (canonLabel) {
707: PetscInt canon;
709: DMLabelGetValue(canonLabel,p,&canon);
710: if (p != canon) continue;
711: }
712: DMPlexGetTreeParent(dm,p,&parent,NULL);
713: if (parent != p) {
714: aMin = PetscMin(aMin,p);
715: aMax = PetscMax(aMax,p+1);
716: }
717: }
718: if (aMin > aMax) {
719: aMin = -1;
720: aMax = -1;
721: }
722: PetscSectionCreate(PETSC_COMM_SELF,&aSec);
723: PetscSectionSetChart(aSec,aMin,aMax);
724: for (p = aMin; p < aMax; p++) {
725: PetscInt parent, ancestor = p;
727: if (canonLabel) {
728: PetscInt canon;
730: DMLabelGetValue(canonLabel,p,&canon);
731: if (p != canon) continue;
732: }
733: DMPlexGetTreeParent(dm,p,&parent,NULL);
734: while (parent != ancestor) {
735: ancestor = parent;
736: DMPlexGetTreeParent(dm,ancestor,&parent,NULL);
737: }
738: if (ancestor != p) {
739: PetscInt closureSize, *closure = NULL;
741: DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
742: PetscSectionSetDof(aSec,p,closureSize);
743: DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
744: }
745: }
746: PetscSectionSetUp(aSec);
747: PetscSectionGetStorageSize(aSec,&size);
748: PetscMalloc1(size,&anchors);
749: for (p = aMin; p < aMax; p++) {
750: PetscInt parent, ancestor = p;
752: if (canonLabel) {
753: PetscInt canon;
755: DMLabelGetValue(canonLabel,p,&canon);
756: if (p != canon) continue;
757: }
758: DMPlexGetTreeParent(dm,p,&parent,NULL);
759: while (parent != ancestor) {
760: ancestor = parent;
761: DMPlexGetTreeParent(dm,ancestor,&parent,NULL);
762: }
763: if (ancestor != p) {
764: PetscInt j, closureSize, *closure = NULL, aOff;
766: PetscSectionGetOffset(aSec,p,&aOff);
768: DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
769: for (j = 0; j < closureSize; j++) {
770: anchors[aOff + j] = closure[2*j];
771: }
772: DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
773: }
774: }
775: ISCreateGeneral(PETSC_COMM_SELF,size,anchors,PETSC_OWN_POINTER,&aIS);
776: {
777: PetscSection aSecNew = aSec;
778: IS aISNew = aIS;
780: PetscObjectReference((PetscObject)aSec);
781: PetscObjectReference((PetscObject)aIS);
782: while (aSecNew) {
783: PetscSectionDestroy(&aSec);
784: ISDestroy(&aIS);
785: aSec = aSecNew;
786: aIS = aISNew;
787: aSecNew = NULL;
788: aISNew = NULL;
789: AnchorsFlatten(aSec,aIS,&aSecNew,&aISNew);
790: }
791: }
792: DMPlexSetAnchors(dm,aSec,aIS);
793: PetscSectionDestroy(&aSec);
794: ISDestroy(&aIS);
795: return(0);
796: }
798: static PetscErrorCode DMPlexGetTrueSupportSize(DM dm,PetscInt p,PetscInt *dof,PetscInt *numTrueSupp)
799: {
803: if (numTrueSupp[p] == -1) {
804: PetscInt i, alldof;
805: const PetscInt *supp;
806: PetscInt count = 0;
808: DMPlexGetSupportSize(dm,p,&alldof);
809: DMPlexGetSupport(dm,p,&supp);
810: for (i = 0; i < alldof; i++) {
811: PetscInt q = supp[i], numCones, j;
812: const PetscInt *cone;
814: DMPlexGetConeSize(dm,q,&numCones);
815: DMPlexGetCone(dm,q,&cone);
816: for (j = 0; j < numCones; j++) {
817: if (cone[j] == p) break;
818: }
819: if (j < numCones) count++;
820: }
821: numTrueSupp[p] = count;
822: }
823: *dof = numTrueSupp[p];
824: return(0);
825: }
827: static PetscErrorCode DMPlexTreeExchangeSupports(DM dm)
828: {
829: DM_Plex *mesh = (DM_Plex *)dm->data;
830: PetscSection newSupportSection;
831: PetscInt newSize, *newSupports, pStart, pEnd, p, d, depth;
832: PetscInt *numTrueSupp;
833: PetscInt *offsets;
838: /* symmetrize the hierarchy */
839: DMPlexGetDepth(dm,&depth);
840: PetscSectionCreate(PetscObjectComm((PetscObject)(mesh->supportSection)),&newSupportSection);
841: DMPlexGetChart(dm,&pStart,&pEnd);
842: PetscSectionSetChart(newSupportSection,pStart,pEnd);
843: PetscCalloc1(pEnd,&offsets);
844: PetscMalloc1(pEnd,&numTrueSupp);
845: for (p = 0; p < pEnd; p++) numTrueSupp[p] = -1;
846: /* if a point is in the (true) support of q, it should be in the support of
847: * parent(q) */
848: for (d = 0; d <= depth; d++) {
849: DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);
850: for (p = pStart; p < pEnd; ++p) {
851: PetscInt dof, q, qdof, parent;
853: DMPlexGetTrueSupportSize(dm,p,&dof,numTrueSupp);
854: PetscSectionAddDof(newSupportSection, p, dof);
855: q = p;
856: DMPlexGetTreeParent(dm,q,&parent,NULL);
857: while (parent != q && parent >= pStart && parent < pEnd) {
858: q = parent;
860: DMPlexGetTrueSupportSize(dm,q,&qdof,numTrueSupp);
861: PetscSectionAddDof(newSupportSection,p,qdof);
862: PetscSectionAddDof(newSupportSection,q,dof);
863: DMPlexGetTreeParent(dm,q,&parent,NULL);
864: }
865: }
866: }
867: PetscSectionSetUp(newSupportSection);
868: PetscSectionGetStorageSize(newSupportSection,&newSize);
869: PetscMalloc1(newSize,&newSupports);
870: for (d = 0; d <= depth; d++) {
871: DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);
872: for (p = pStart; p < pEnd; p++) {
873: PetscInt dof, off, q, qdof, qoff, newDof, newOff, newqOff, i, parent;
875: PetscSectionGetDof(mesh->supportSection, p, &dof);
876: PetscSectionGetOffset(mesh->supportSection, p, &off);
877: PetscSectionGetDof(newSupportSection, p, &newDof);
878: PetscSectionGetOffset(newSupportSection, p, &newOff);
879: for (i = 0; i < dof; i++) {
880: PetscInt numCones, j;
881: const PetscInt *cone;
882: PetscInt q = mesh->supports[off + i];
884: DMPlexGetConeSize(dm,q,&numCones);
885: DMPlexGetCone(dm,q,&cone);
886: for (j = 0; j < numCones; j++) {
887: if (cone[j] == p) break;
888: }
889: if (j < numCones) newSupports[newOff+offsets[p]++] = q;
890: }
891: mesh->maxSupportSize = PetscMax(mesh->maxSupportSize,newDof);
893: q = p;
894: DMPlexGetTreeParent(dm,q,&parent,NULL);
895: while (parent != q && parent >= pStart && parent < pEnd) {
896: q = parent;
897: PetscSectionGetDof(mesh->supportSection, q, &qdof);
898: PetscSectionGetOffset(mesh->supportSection, q, &qoff);
899: PetscSectionGetOffset(newSupportSection, q, &newqOff);
900: for (i = 0; i < qdof; i++) {
901: PetscInt numCones, j;
902: const PetscInt *cone;
903: PetscInt r = mesh->supports[qoff + i];
905: DMPlexGetConeSize(dm,r,&numCones);
906: DMPlexGetCone(dm,r,&cone);
907: for (j = 0; j < numCones; j++) {
908: if (cone[j] == q) break;
909: }
910: if (j < numCones) newSupports[newOff+offsets[p]++] = r;
911: }
912: for (i = 0; i < dof; i++) {
913: PetscInt numCones, j;
914: const PetscInt *cone;
915: PetscInt r = mesh->supports[off + i];
917: DMPlexGetConeSize(dm,r,&numCones);
918: DMPlexGetCone(dm,r,&cone);
919: for (j = 0; j < numCones; j++) {
920: if (cone[j] == p) break;
921: }
922: if (j < numCones) newSupports[newqOff+offsets[q]++] = r;
923: }
924: DMPlexGetTreeParent(dm,q,&parent,NULL);
925: }
926: }
927: }
928: PetscSectionDestroy(&mesh->supportSection);
929: mesh->supportSection = newSupportSection;
930: PetscFree(mesh->supports);
931: mesh->supports = newSupports;
932: PetscFree(offsets);
933: PetscFree(numTrueSupp);
935: return(0);
936: }
938: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM,PetscSection,PetscSection,Mat);
939: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM,PetscSection,PetscSection,Mat);
941: static PetscErrorCode DMPlexSetTree_Internal(DM dm, PetscSection parentSection, PetscInt *parents, PetscInt *childIDs, PetscBool computeCanonical, PetscBool exchangeSupports)
942: {
943: DM_Plex *mesh = (DM_Plex *)dm->data;
944: DM refTree;
945: PetscInt size;
951: PetscObjectReference((PetscObject)parentSection);
952: PetscSectionDestroy(&mesh->parentSection);
953: mesh->parentSection = parentSection;
954: PetscSectionGetStorageSize(parentSection,&size);
955: if (parents != mesh->parents) {
956: PetscFree(mesh->parents);
957: PetscMalloc1(size,&mesh->parents);
958: PetscMemcpy(mesh->parents, parents, size * sizeof(*parents));
959: }
960: if (childIDs != mesh->childIDs) {
961: PetscFree(mesh->childIDs);
962: PetscMalloc1(size,&mesh->childIDs);
963: PetscMemcpy(mesh->childIDs, childIDs, size * sizeof(*childIDs));
964: }
965: DMPlexGetReferenceTree(dm,&refTree);
966: if (refTree) {
967: DMLabel canonLabel;
969: DMGetLabel(refTree,"canonical",&canonLabel);
970: if (canonLabel) {
971: PetscInt i;
973: for (i = 0; i < size; i++) {
974: PetscInt canon;
975: DMLabelGetValue(canonLabel, mesh->childIDs[i], &canon);
976: if (canon >= 0) {
977: mesh->childIDs[i] = canon;
978: }
979: }
980: }
981: mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_FromReference;
982: }
983: else {
984: mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_Direct;
985: }
986: DMPlexTreeSymmetrize(dm);
987: if (computeCanonical) {
988: PetscInt d, dim;
990: /* add the canonical label */
991: DMGetDimension(dm,&dim);
992: DMCreateLabel(dm,"canonical");
993: for (d = 0; d <= dim; d++) {
994: PetscInt p, dStart, dEnd, canon = -1, cNumChildren;
995: const PetscInt *cChildren;
997: DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);
998: for (p = dStart; p < dEnd; p++) {
999: DMPlexGetTreeChildren(dm,p,&cNumChildren,&cChildren);
1000: if (cNumChildren) {
1001: canon = p;
1002: break;
1003: }
1004: }
1005: if (canon == -1) continue;
1006: for (p = dStart; p < dEnd; p++) {
1007: PetscInt numChildren, i;
1008: const PetscInt *children;
1010: DMPlexGetTreeChildren(dm,p,&numChildren,&children);
1011: if (numChildren) {
1012: if (numChildren != cNumChildren) SETERRQ2(PetscObjectComm((PetscObject)dm),PETSC_ERR_PLIB,"All parent points in a stratum should have the same number of children: %d != %d", numChildren, cNumChildren);
1013: DMSetLabelValue(dm,"canonical",p,canon);
1014: for (i = 0; i < numChildren; i++) {
1015: DMSetLabelValue(dm,"canonical",children[i],cChildren[i]);
1016: }
1017: }
1018: }
1019: }
1020: }
1021: if (exchangeSupports) {
1022: DMPlexTreeExchangeSupports(dm);
1023: }
1024: mesh->createanchors = DMPlexCreateAnchors_Tree;
1025: /* reset anchors */
1026: DMPlexSetAnchors(dm,NULL,NULL);
1027: return(0);
1028: }
1030: /*@
1031: DMPlexSetTree - set the tree that describes the hierarchy of non-conforming mesh points. This routine also creates
1032: the point-to-point constraints determined by the tree: a point is constained to the points in the closure of its
1033: tree root.
1035: Collective on dm
1037: Input Parameters:
1038: + dm - the DMPlex object
1039: . parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section
1040: offset indexes the parent and childID list; the reference count of parentSection is incremented
1041: . parents - a list of the point parents; copied, can be destroyed
1042: - childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then
1043: the child corresponds to the point in the reference tree with index childIDs; copied, can be destroyed
1045: Level: intermediate
1047: .seealso: DMPlexGetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren()
1048: @*/
1049: PetscErrorCode DMPlexSetTree(DM dm, PetscSection parentSection, PetscInt parents[], PetscInt childIDs[])
1050: {
1054: DMPlexSetTree_Internal(dm,parentSection,parents,childIDs,PETSC_FALSE,PETSC_TRUE);
1055: return(0);
1056: }
1058: /*@
1059: DMPlexGetTree - get the tree that describes the hierarchy of non-conforming mesh points.
1060: Collective on dm
1062: Input Parameters:
1063: . dm - the DMPlex object
1065: Output Parameters:
1066: + parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section
1067: offset indexes the parent and childID list
1068: . parents - a list of the point parents
1069: . childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then
1070: the child corresponds to the point in the reference tree with index childID
1071: . childSection - the inverse of the parent section
1072: - children - a list of the point children
1074: Level: intermediate
1076: .seealso: DMPlexSetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren()
1077: @*/
1078: PetscErrorCode DMPlexGetTree(DM dm, PetscSection *parentSection, PetscInt *parents[], PetscInt *childIDs[], PetscSection *childSection, PetscInt *children[])
1079: {
1080: DM_Plex *mesh = (DM_Plex *)dm->data;
1084: if (parentSection) *parentSection = mesh->parentSection;
1085: if (parents) *parents = mesh->parents;
1086: if (childIDs) *childIDs = mesh->childIDs;
1087: if (childSection) *childSection = mesh->childSection;
1088: if (children) *children = mesh->children;
1089: return(0);
1090: }
1092: /*@
1093: DMPlexGetTreeParent - get the parent of a point in the tree describing the point hierarchy (not the DAG)
1095: Input Parameters:
1096: + dm - the DMPlex object
1097: - point - the query point
1099: Output Parameters:
1100: + parent - if not NULL, set to the parent of the point, or the point itself if the point does not have a parent
1101: - childID - if not NULL, set to the child ID of the point with respect to its parent, or 0 if the point
1102: does not have a parent
1104: Level: intermediate
1106: .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeChildren()
1107: @*/
1108: PetscErrorCode DMPlexGetTreeParent(DM dm, PetscInt point, PetscInt *parent, PetscInt *childID)
1109: {
1110: DM_Plex *mesh = (DM_Plex *)dm->data;
1111: PetscSection pSec;
1116: pSec = mesh->parentSection;
1117: if (pSec && point >= pSec->pStart && point < pSec->pEnd) {
1118: PetscInt dof;
1120: PetscSectionGetDof (pSec, point, &dof);
1121: if (dof) {
1122: PetscInt off;
1124: PetscSectionGetOffset (pSec, point, &off);
1125: if (parent) *parent = mesh->parents[off];
1126: if (childID) *childID = mesh->childIDs[off];
1127: return(0);
1128: }
1129: }
1130: if (parent) {
1131: *parent = point;
1132: }
1133: if (childID) {
1134: *childID = 0;
1135: }
1136: return(0);
1137: }
1139: /*@C
1140: DMPlexGetTreeChildren - get the children of a point in the tree describing the point hierarchy (not the DAG)
1142: Input Parameters:
1143: + dm - the DMPlex object
1144: - point - the query point
1146: Output Parameters:
1147: + numChildren - if not NULL, set to the number of children
1148: - children - if not NULL, set to a list children, or set to NULL if the point has no children
1150: Level: intermediate
1152: Fortran Notes:
1153: Since it returns an array, this routine is only available in Fortran 90, and you must
1154: include petsc.h90 in your code.
1156: .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeParent()
1157: @*/
1158: PetscErrorCode DMPlexGetTreeChildren(DM dm, PetscInt point, PetscInt *numChildren, const PetscInt *children[])
1159: {
1160: DM_Plex *mesh = (DM_Plex *)dm->data;
1161: PetscSection childSec;
1162: PetscInt dof = 0;
1167: childSec = mesh->childSection;
1168: if (childSec && point >= childSec->pStart && point < childSec->pEnd) {
1169: PetscSectionGetDof (childSec, point, &dof);
1170: }
1171: if (numChildren) *numChildren = dof;
1172: if (children) {
1173: if (dof) {
1174: PetscInt off;
1176: PetscSectionGetOffset (childSec, point, &off);
1177: *children = &mesh->children[off];
1178: }
1179: else {
1180: *children = NULL;
1181: }
1182: }
1183: return(0);
1184: }
1186: static PetscErrorCode EvaluateBasis(PetscSpace space, PetscInt nBasis, PetscInt nFunctionals, PetscInt nComps, PetscInt nPoints, const PetscInt *pointsPerFn, const PetscReal *points, const PetscReal *weights, PetscReal *work, Mat basisAtPoints)
1187: {
1188: PetscInt f, b, p, c, offset, qPoints;
1192: PetscSpaceEvaluate(space,nPoints,points,work,NULL,NULL);
1193: for (f = 0, offset = 0; f < nFunctionals; f++) {
1194: qPoints = pointsPerFn[f];
1195: for (b = 0; b < nBasis; b++) {
1196: PetscScalar val = 0.;
1198: for (p = 0; p < qPoints; p++) {
1199: for (c = 0; c < nComps; c++) {
1200: val += work[((offset + p) * nBasis + b) * nComps + c] * weights[(offset + p) * nComps + c];
1201: }
1202: }
1203: MatSetValue(basisAtPoints,b,f,val,INSERT_VALUES);
1204: }
1205: offset += qPoints;
1206: }
1207: MatAssemblyBegin(basisAtPoints,MAT_FINAL_ASSEMBLY);
1208: MatAssemblyEnd(basisAtPoints,MAT_FINAL_ASSEMBLY);
1209: return(0);
1210: }
1212: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM dm, PetscSection section, PetscSection cSec, Mat cMat)
1213: {
1214: PetscDS ds;
1215: PetscInt spdim;
1216: PetscInt numFields, f, c, cStart, cEnd, pStart, pEnd, conStart, conEnd;
1217: const PetscInt *anchors;
1218: PetscSection aSec;
1219: PetscReal *v0, *v0parent, *vtmp, *J, *Jparent, *invJparent, detJ, detJparent;
1220: IS aIS;
1224: DMPlexGetChart(dm,&pStart,&pEnd);
1225: DMGetDS(dm,&ds);
1226: PetscDSGetNumFields(ds,&numFields);
1227: DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);
1228: DMPlexGetAnchors(dm,&aSec,&aIS);
1229: ISGetIndices(aIS,&anchors);
1230: PetscSectionGetChart(cSec,&conStart,&conEnd);
1231: DMGetDimension(dm,&spdim);
1232: PetscMalloc6(spdim,&v0,spdim,&v0parent,spdim,&vtmp,spdim*spdim,&J,spdim*spdim,&Jparent,spdim*spdim,&invJparent);
1234: for (f = 0; f < numFields; f++) {
1235: PetscObject disc;
1236: PetscClassId id;
1237: PetscSpace bspace;
1238: PetscDualSpace dspace;
1239: PetscInt i, j, k, nPoints, Nc, offset;
1240: PetscInt fSize, maxDof;
1241: PetscReal *weights, *pointsRef, *pointsReal, *work;
1242: PetscScalar *scwork, *X;
1243: PetscInt *sizes, *workIndRow, *workIndCol;
1244: Mat Amat, Bmat, Xmat;
1245: const PetscInt *numDof = NULL;
1246: const PetscInt ***perms = NULL;
1247: const PetscScalar ***flips = NULL;
1249: PetscDSGetDiscretization(ds,f,&disc);
1250: PetscObjectGetClassId(disc,&id);
1251: if (id == PETSCFE_CLASSID) {
1252: PetscFE fe = (PetscFE) disc;
1254: PetscFEGetBasisSpace(fe,&bspace);
1255: PetscFEGetDualSpace(fe,&dspace);
1256: PetscDualSpaceGetDimension(dspace,&fSize);
1257: PetscFEGetNumComponents(fe,&Nc);
1258: }
1259: else if (id == PETSCFV_CLASSID) {
1260: PetscFV fv = (PetscFV) disc;
1262: PetscFVGetNumComponents(fv,&Nc);
1263: PetscSpaceCreate(PetscObjectComm((PetscObject)fv),&bspace);
1264: PetscSpaceSetType(bspace,PETSCSPACEPOLYNOMIAL);
1265: PetscSpaceSetOrder(bspace,0);
1266: PetscSpaceSetNumComponents(bspace,Nc);
1267: PetscSpacePolynomialSetNumVariables(bspace,spdim);
1268: PetscSpaceSetUp(bspace);
1269: PetscFVGetDualSpace(fv,&dspace);
1270: PetscDualSpaceGetDimension(dspace,&fSize);
1271: }
1272: else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id);
1273: PetscDualSpaceGetNumDof(dspace,&numDof);
1274: for (i = 0, maxDof = 0; i <= spdim; i++) {maxDof = PetscMax(maxDof,numDof[i]);}
1275: PetscDualSpaceGetSymmetries(dspace,&perms,&flips);
1277: MatCreate(PETSC_COMM_SELF,&Amat);
1278: MatSetSizes(Amat,fSize,fSize,fSize,fSize);
1279: MatSetType(Amat,MATSEQDENSE);
1280: MatSetUp(Amat);
1281: MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Bmat);
1282: MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Xmat);
1283: nPoints = 0;
1284: for (i = 0; i < fSize; i++) {
1285: PetscInt qPoints, thisNc;
1286: PetscQuadrature quad;
1288: PetscDualSpaceGetFunctional(dspace,i,&quad);
1289: PetscQuadratureGetData(quad,NULL,&thisNc,&qPoints,NULL,NULL);
1290: if (thisNc != Nc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Functional dim %D does not much basis dim %D\n",thisNc,Nc);
1291: nPoints += qPoints;
1292: }
1293: PetscMalloc7(fSize,&sizes,nPoints*Nc,&weights,spdim*nPoints,&pointsRef,spdim*nPoints,&pointsReal,nPoints*fSize*Nc,&work,maxDof,&workIndRow,maxDof,&workIndCol);
1294: PetscMalloc1(maxDof * maxDof,&scwork);
1295: offset = 0;
1296: for (i = 0; i < fSize; i++) {
1297: PetscInt qPoints;
1298: const PetscReal *p, *w;
1299: PetscQuadrature quad;
1301: PetscDualSpaceGetFunctional(dspace,i,&quad);
1302: PetscQuadratureGetData(quad,NULL,NULL,&qPoints,&p,&w);
1303: PetscMemcpy(weights+Nc*offset,w,Nc*qPoints*sizeof(*w));
1304: PetscMemcpy(pointsRef+spdim*offset,p,spdim*qPoints*sizeof(*p));
1305: sizes[i] = qPoints;
1306: offset += qPoints;
1307: }
1308: EvaluateBasis(bspace,fSize,fSize,Nc,nPoints,sizes,pointsRef,weights,work,Amat);
1309: MatLUFactor(Amat,NULL,NULL,NULL);
1310: for (c = cStart; c < cEnd; c++) {
1311: PetscInt parent;
1312: PetscInt closureSize, closureSizeP, *closure = NULL, *closureP = NULL;
1313: PetscInt *childOffsets, *parentOffsets;
1315: DMPlexGetTreeParent(dm,c,&parent,NULL);
1316: if (parent == c) continue;
1317: DMPlexGetTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
1318: for (i = 0; i < closureSize; i++) {
1319: PetscInt p = closure[2*i];
1320: PetscInt conDof;
1322: if (p < conStart || p >= conEnd) continue;
1323: if (numFields) {
1324: PetscSectionGetFieldDof(cSec,p,f,&conDof);
1325: }
1326: else {
1327: PetscSectionGetDof(cSec,p,&conDof);
1328: }
1329: if (conDof) break;
1330: }
1331: if (i == closureSize) {
1332: DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
1333: continue;
1334: }
1336: DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, NULL, &detJ);
1337: DMPlexComputeCellGeometryFEM(dm, parent, NULL, v0parent, Jparent, invJparent, &detJparent);
1338: for (i = 0; i < nPoints; i++) {
1339: CoordinatesRefToReal(spdim, spdim, v0, J, &pointsRef[i*spdim],vtmp);
1340: CoordinatesRealToRef(spdim, spdim, v0parent, invJparent, vtmp, &pointsReal[i*spdim]);
1341: }
1342: EvaluateBasis(bspace,fSize,fSize,Nc,nPoints,sizes,pointsReal,weights,work,Bmat);
1343: MatMatSolve(Amat,Bmat,Xmat);
1344: MatDenseGetArray(Xmat,&X);
1345: DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);
1346: PetscMalloc2(closureSize+1,&childOffsets,closureSizeP+1,&parentOffsets);
1347: childOffsets[0] = 0;
1348: for (i = 0; i < closureSize; i++) {
1349: PetscInt p = closure[2*i];
1350: PetscInt dof;
1352: if (numFields) {
1353: PetscSectionGetFieldDof(section,p,f,&dof);
1354: }
1355: else {
1356: PetscSectionGetDof(section,p,&dof);
1357: }
1358: childOffsets[i+1]=childOffsets[i]+dof;
1359: }
1360: parentOffsets[0] = 0;
1361: for (i = 0; i < closureSizeP; i++) {
1362: PetscInt p = closureP[2*i];
1363: PetscInt dof;
1365: if (numFields) {
1366: PetscSectionGetFieldDof(section,p,f,&dof);
1367: }
1368: else {
1369: PetscSectionGetDof(section,p,&dof);
1370: }
1371: parentOffsets[i+1]=parentOffsets[i]+dof;
1372: }
1373: for (i = 0; i < closureSize; i++) {
1374: PetscInt conDof, conOff, aDof, aOff, nWork;
1375: PetscInt p = closure[2*i];
1376: PetscInt o = closure[2*i+1];
1377: const PetscInt *perm;
1378: const PetscScalar *flip;
1380: if (p < conStart || p >= conEnd) continue;
1381: if (numFields) {
1382: PetscSectionGetFieldDof(cSec,p,f,&conDof);
1383: PetscSectionGetFieldOffset(cSec,p,f,&conOff);
1384: }
1385: else {
1386: PetscSectionGetDof(cSec,p,&conDof);
1387: PetscSectionGetOffset(cSec,p,&conOff);
1388: }
1389: if (!conDof) continue;
1390: perm = (perms && perms[i]) ? perms[i][o] : NULL;
1391: flip = (flips && flips[i]) ? flips[i][o] : NULL;
1392: PetscSectionGetDof(aSec,p,&aDof);
1393: PetscSectionGetOffset(aSec,p,&aOff);
1394: nWork = childOffsets[i+1]-childOffsets[i];
1395: for (k = 0; k < aDof; k++) {
1396: PetscInt a = anchors[aOff + k];
1397: PetscInt aSecDof, aSecOff;
1399: if (numFields) {
1400: PetscSectionGetFieldDof(section,a,f,&aSecDof);
1401: PetscSectionGetFieldOffset(section,a,f,&aSecOff);
1402: }
1403: else {
1404: PetscSectionGetDof(section,a,&aSecDof);
1405: PetscSectionGetOffset(section,a,&aSecOff);
1406: }
1407: if (!aSecDof) continue;
1409: for (j = 0; j < closureSizeP; j++) {
1410: PetscInt q = closureP[2*j];
1411: PetscInt oq = closureP[2*j+1];
1413: if (q == a) {
1414: PetscInt r, s, nWorkP;
1415: const PetscInt *permP;
1416: const PetscScalar *flipP;
1418: permP = (perms && perms[j]) ? perms[j][oq] : NULL;
1419: flipP = (flips && flips[j]) ? flips[j][oq] : NULL;
1420: nWorkP = parentOffsets[j+1]-parentOffsets[j];
1421: /* get a copy of the child-to-anchor portion of the matrix, and transpose so that rows correspond to the
1422: * child and columns correspond to the anchor: BUT the maxrix returned by MatDenseGetArray is
1423: * column-major, so transpose-transpose = do nothing */
1424: for (r = 0; r < nWork; r++) {
1425: for (s = 0; s < nWorkP; s++) {
1426: scwork[r * nWorkP + s] = X[fSize * (r + childOffsets[i]) + (s + parentOffsets[j])];
1427: }
1428: }
1429: for (r = 0; r < nWork; r++) {workIndRow[perm ? perm[r] : r] = conOff + r;}
1430: for (s = 0; s < nWorkP; s++) {workIndCol[permP ? permP[s] : s] = aSecOff + s;}
1431: if (flip) {
1432: for (r = 0; r < nWork; r++) {
1433: for (s = 0; s < nWorkP; s++) {
1434: scwork[r * nWorkP + s] *= flip[r];
1435: }
1436: }
1437: }
1438: if (flipP) {
1439: for (r = 0; r < nWork; r++) {
1440: for (s = 0; s < nWorkP; s++) {
1441: scwork[r * nWorkP + s] *= flipP[s];
1442: }
1443: }
1444: }
1445: MatSetValues(cMat,nWork,workIndRow,nWorkP,workIndCol,scwork,INSERT_VALUES);
1446: break;
1447: }
1448: }
1449: }
1450: }
1451: MatDenseRestoreArray(Xmat,&X);
1452: PetscFree2(childOffsets,parentOffsets);
1453: DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
1454: DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);
1455: }
1456: MatDestroy(&Amat);
1457: MatDestroy(&Bmat);
1458: MatDestroy(&Xmat);
1459: PetscFree(scwork);
1460: PetscFree7(sizes,weights,pointsRef,pointsReal,work,workIndRow,workIndCol);
1461: if (id == PETSCFV_CLASSID) {
1462: PetscSpaceDestroy(&bspace);
1463: }
1464: }
1465: MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);
1466: MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);
1467: PetscFree6(v0,v0parent,vtmp,J,Jparent,invJparent);
1468: ISRestoreIndices(aIS,&anchors);
1470: return(0);
1471: }
1473: static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN)
1474: {
1475: Mat refCmat;
1476: PetscDS ds;
1477: PetscInt numFields, maxFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof, maxAnDof, **refPointFieldN;
1478: PetscScalar ***refPointFieldMats;
1479: PetscSection refConSec, refAnSec, refSection;
1480: IS refAnIS;
1481: const PetscInt *refAnchors;
1482: const PetscInt **perms;
1483: const PetscScalar **flips;
1484: PetscErrorCode ierr;
1487: DMGetDS(refTree,&ds);
1488: PetscDSGetNumFields(ds,&numFields);
1489: maxFields = PetscMax(1,numFields);
1490: DMGetDefaultConstraints(refTree,&refConSec,&refCmat);
1491: DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);
1492: ISGetIndices(refAnIS,&refAnchors);
1493: DMGetDefaultSection(refTree,&refSection);
1494: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
1495: PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);
1496: PetscMalloc1(pRefEnd-pRefStart,&refPointFieldN);
1497: PetscSectionGetMaxDof(refConSec,&maxDof);
1498: PetscSectionGetMaxDof(refAnSec,&maxAnDof);
1499: PetscMalloc1(maxDof,&rows);
1500: PetscMalloc1(maxDof*maxAnDof,&cols);
1501: for (p = pRefStart; p < pRefEnd; p++) {
1502: PetscInt parent, closureSize, *closure = NULL, pDof;
1504: DMPlexGetTreeParent(refTree,p,&parent,NULL);
1505: PetscSectionGetDof(refConSec,p,&pDof);
1506: if (!pDof || parent == p) continue;
1508: PetscMalloc1(maxFields,&refPointFieldMats[p-pRefStart]);
1509: PetscCalloc1(maxFields,&refPointFieldN[p-pRefStart]);
1510: DMPlexGetTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);
1511: for (f = 0; f < maxFields; f++) {
1512: PetscInt cDof, cOff, numCols, r, i;
1514: if (f < numFields) {
1515: PetscSectionGetFieldDof(refConSec,p,f,&cDof);
1516: PetscSectionGetFieldOffset(refConSec,p,f,&cOff);
1517: PetscSectionGetFieldPointSyms(refSection,f,closureSize,closure,&perms,&flips);
1518: } else {
1519: PetscSectionGetDof(refConSec,p,&cDof);
1520: PetscSectionGetOffset(refConSec,p,&cOff);
1521: PetscSectionGetPointSyms(refSection,closureSize,closure,&perms,&flips);
1522: }
1524: for (r = 0; r < cDof; r++) {
1525: rows[r] = cOff + r;
1526: }
1527: numCols = 0;
1528: for (i = 0; i < closureSize; i++) {
1529: PetscInt q = closure[2*i];
1530: PetscInt aDof, aOff, j;
1531: const PetscInt *perm = perms ? perms[i] : NULL;
1533: if (numFields) {
1534: PetscSectionGetFieldDof(refSection,q,f,&aDof);
1535: PetscSectionGetFieldOffset(refSection,q,f,&aOff);
1536: }
1537: else {
1538: PetscSectionGetDof(refSection,q,&aDof);
1539: PetscSectionGetOffset(refSection,q,&aOff);
1540: }
1542: for (j = 0; j < aDof; j++) {
1543: cols[numCols++] = aOff + (perm ? perm[j] : j);
1544: }
1545: }
1546: refPointFieldN[p-pRefStart][f] = numCols;
1547: PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);
1548: MatGetValues(refCmat,cDof,rows,numCols,cols,refPointFieldMats[p-pRefStart][f]);
1549: if (flips) {
1550: PetscInt colOff = 0;
1552: for (i = 0; i < closureSize; i++) {
1553: PetscInt q = closure[2*i];
1554: PetscInt aDof, aOff, j;
1555: const PetscScalar *flip = flips ? flips[i] : NULL;
1557: if (numFields) {
1558: PetscSectionGetFieldDof(refSection,q,f,&aDof);
1559: PetscSectionGetFieldOffset(refSection,q,f,&aOff);
1560: }
1561: else {
1562: PetscSectionGetDof(refSection,q,&aDof);
1563: PetscSectionGetOffset(refSection,q,&aOff);
1564: }
1565: if (flip) {
1566: PetscInt k;
1567: for (k = 0; k < cDof; k++) {
1568: for (j = 0; j < aDof; j++) {
1569: refPointFieldMats[p-pRefStart][f][k * numCols + colOff + j] *= flip[j];
1570: }
1571: }
1572: }
1573: colOff += aDof;
1574: }
1575: }
1576: if (numFields) {
1577: PetscSectionRestoreFieldPointSyms(refSection,f,closureSize,closure,&perms,&flips);
1578: } else {
1579: PetscSectionRestorePointSyms(refSection,closureSize,closure,&perms,&flips);
1580: }
1581: }
1582: DMPlexRestoreTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);
1583: }
1584: *childrenMats = refPointFieldMats;
1585: *childrenN = refPointFieldN;
1586: ISRestoreIndices(refAnIS,&refAnchors);
1587: PetscFree(rows);
1588: PetscFree(cols);
1589: return(0);
1590: }
1592: static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN)
1593: {
1594: PetscDS ds;
1595: PetscInt **refPointFieldN;
1596: PetscScalar ***refPointFieldMats;
1597: PetscInt numFields, maxFields, pRefStart, pRefEnd, p, f;
1598: PetscSection refConSec;
1602: refPointFieldN = *childrenN;
1603: *childrenN = NULL;
1604: refPointFieldMats = *childrenMats;
1605: *childrenMats = NULL;
1606: DMGetDS(refTree,&ds);
1607: PetscDSGetNumFields(ds,&numFields);
1608: maxFields = PetscMax(1,numFields);
1609: DMGetDefaultConstraints(refTree,&refConSec,NULL);
1610: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
1611: for (p = pRefStart; p < pRefEnd; p++) {
1612: PetscInt parent, pDof;
1614: DMPlexGetTreeParent(refTree,p,&parent,NULL);
1615: PetscSectionGetDof(refConSec,p,&pDof);
1616: if (!pDof || parent == p) continue;
1618: for (f = 0; f < maxFields; f++) {
1619: PetscInt cDof;
1621: if (numFields) {
1622: PetscSectionGetFieldDof(refConSec,p,f,&cDof);
1623: }
1624: else {
1625: PetscSectionGetDof(refConSec,p,&cDof);
1626: }
1628: PetscFree(refPointFieldMats[p - pRefStart][f]);
1629: }
1630: PetscFree(refPointFieldMats[p - pRefStart]);
1631: PetscFree(refPointFieldN[p - pRefStart]);
1632: }
1633: PetscFree(refPointFieldMats);
1634: PetscFree(refPointFieldN);
1635: return(0);
1636: }
1638: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM dm, PetscSection section, PetscSection conSec, Mat cMat)
1639: {
1640: DM refTree;
1641: PetscDS ds;
1642: Mat refCmat;
1643: PetscInt numFields, maxFields, f, pRefStart, pRefEnd, p, maxDof, maxAnDof, *perm, *iperm, pStart, pEnd, conStart, conEnd, **refPointFieldN;
1644: PetscScalar ***refPointFieldMats, *pointWork;
1645: PetscSection refConSec, refAnSec, anSec;
1646: IS refAnIS, anIS;
1647: const PetscInt *anchors;
1652: DMGetDS(dm,&ds);
1653: PetscDSGetNumFields(ds,&numFields);
1654: maxFields = PetscMax(1,numFields);
1655: DMPlexGetReferenceTree(dm,&refTree);
1656: DMSetDS(refTree,ds);
1657: DMGetDefaultConstraints(refTree,&refConSec,&refCmat);
1658: DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);
1659: DMPlexGetAnchors(dm,&anSec,&anIS);
1660: ISGetIndices(anIS,&anchors);
1661: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
1662: PetscSectionGetChart(conSec,&conStart,&conEnd);
1663: PetscSectionGetMaxDof(refConSec,&maxDof);
1664: PetscSectionGetMaxDof(refAnSec,&maxAnDof);
1665: PetscMalloc1(maxDof*maxDof*maxAnDof,&pointWork);
1667: /* step 1: get submats for every constrained point in the reference tree */
1668: DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
1670: /* step 2: compute the preorder */
1671: DMPlexGetChart(dm,&pStart,&pEnd);
1672: PetscMalloc2(pEnd-pStart,&perm,pEnd-pStart,&iperm);
1673: for (p = pStart; p < pEnd; p++) {
1674: perm[p - pStart] = p;
1675: iperm[p - pStart] = p-pStart;
1676: }
1677: for (p = 0; p < pEnd - pStart;) {
1678: PetscInt point = perm[p];
1679: PetscInt parent;
1681: DMPlexGetTreeParent(dm,point,&parent,NULL);
1682: if (parent == point) {
1683: p++;
1684: }
1685: else {
1686: PetscInt size, closureSize, *closure = NULL, i;
1688: DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1689: for (i = 0; i < closureSize; i++) {
1690: PetscInt q = closure[2*i];
1691: if (iperm[q-pStart] > iperm[point-pStart]) {
1692: /* swap */
1693: perm[p] = q;
1694: perm[iperm[q-pStart]] = point;
1695: iperm[point-pStart] = iperm[q-pStart];
1696: iperm[q-pStart] = p;
1697: break;
1698: }
1699: }
1700: size = closureSize;
1701: DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1702: if (i == size) {
1703: p++;
1704: }
1705: }
1706: }
1708: /* step 3: fill the constraint matrix */
1709: /* we are going to use a preorder progressive fill strategy. Mat doesn't
1710: * allow progressive fill without assembly, so we are going to set up the
1711: * values outside of the Mat first.
1712: */
1713: {
1714: PetscInt nRows, row, nnz;
1715: PetscBool done;
1716: const PetscInt *ia, *ja;
1717: PetscScalar *vals;
1719: MatGetRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);
1720: if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not get RowIJ of constraint matrix");
1721: nnz = ia[nRows];
1722: /* malloc and then zero rows right before we fill them: this way valgrind
1723: * can tell if we are doing progressive fill in the wrong order */
1724: PetscMalloc1(nnz,&vals);
1725: for (p = 0; p < pEnd - pStart; p++) {
1726: PetscInt parent, childid, closureSize, *closure = NULL;
1727: PetscInt point = perm[p], pointDof;
1729: DMPlexGetTreeParent(dm,point,&parent,&childid);
1730: if ((point < conStart) || (point >= conEnd) || (parent == point)) continue;
1731: PetscSectionGetDof(conSec,point,&pointDof);
1732: if (!pointDof) continue;
1733: DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1734: for (f = 0; f < maxFields; f++) {
1735: PetscInt cDof, cOff, numCols, numFillCols, i, r, matOffset, offset;
1736: PetscScalar *pointMat;
1737: const PetscInt **perms;
1738: const PetscScalar **flips;
1740: if (numFields) {
1741: PetscSectionGetFieldDof(conSec,point,f,&cDof);
1742: PetscSectionGetFieldOffset(conSec,point,f,&cOff);
1743: }
1744: else {
1745: PetscSectionGetDof(conSec,point,&cDof);
1746: PetscSectionGetOffset(conSec,point,&cOff);
1747: }
1748: if (!cDof) continue;
1749: if (numFields) {PetscSectionGetFieldPointSyms(section,f,closureSize,closure,&perms,&flips);}
1750: else {PetscSectionGetPointSyms(section,closureSize,closure,&perms,&flips);}
1752: /* make sure that every row for this point is the same size */
1753: #if defined(PETSC_USE_DEBUG)
1754: for (r = 0; r < cDof; r++) {
1755: if (cDof > 1 && r) {
1756: if ((ia[cOff+r+1]-ia[cOff+r]) != (ia[cOff+r]-ia[cOff+r-1])) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Two point rows have different nnz: %D vs. %D", (ia[cOff+r+1]-ia[cOff+r]), (ia[cOff+r]-ia[cOff+r-1]));
1757: }
1758: }
1759: #endif
1760: /* zero rows */
1761: for (i = ia[cOff] ; i< ia[cOff+cDof];i++) {
1762: vals[i] = 0.;
1763: }
1764: matOffset = ia[cOff];
1765: numFillCols = ia[cOff+1] - matOffset;
1766: pointMat = refPointFieldMats[childid-pRefStart][f];
1767: numCols = refPointFieldN[childid-pRefStart][f];
1768: offset = 0;
1769: for (i = 0; i < closureSize; i++) {
1770: PetscInt q = closure[2*i];
1771: PetscInt aDof, aOff, j, k, qConDof, qConOff;
1772: const PetscInt *perm = perms ? perms[i] : NULL;
1773: const PetscScalar *flip = flips ? flips[i] : NULL;
1775: qConDof = qConOff = 0;
1776: if (numFields) {
1777: PetscSectionGetFieldDof(section,q,f,&aDof);
1778: PetscSectionGetFieldOffset(section,q,f,&aOff);
1779: if (q >= conStart && q < conEnd) {
1780: PetscSectionGetFieldDof(conSec,q,f,&qConDof);
1781: PetscSectionGetFieldOffset(conSec,q,f,&qConOff);
1782: }
1783: }
1784: else {
1785: PetscSectionGetDof(section,q,&aDof);
1786: PetscSectionGetOffset(section,q,&aOff);
1787: if (q >= conStart && q < conEnd) {
1788: PetscSectionGetDof(conSec,q,&qConDof);
1789: PetscSectionGetOffset(conSec,q,&qConOff);
1790: }
1791: }
1792: if (!aDof) continue;
1793: if (qConDof) {
1794: /* this point has anchors: its rows of the matrix should already
1795: * be filled, thanks to preordering */
1796: /* first multiply into pointWork, then set in matrix */
1797: PetscInt aMatOffset = ia[qConOff];
1798: PetscInt aNumFillCols = ia[qConOff + 1] - aMatOffset;
1799: for (r = 0; r < cDof; r++) {
1800: for (j = 0; j < aNumFillCols; j++) {
1801: PetscScalar inVal = 0;
1802: for (k = 0; k < aDof; k++) {
1803: PetscInt col = perm ? perm[k] : k;
1805: inVal += pointMat[r * numCols + offset + col] * vals[aMatOffset + aNumFillCols * k + j] * (flip ? flip[col] : 1.);
1806: }
1807: pointWork[r * aNumFillCols + j] = inVal;
1808: }
1809: }
1810: /* assume that the columns are sorted, spend less time searching */
1811: for (j = 0, k = 0; j < aNumFillCols; j++) {
1812: PetscInt col = ja[aMatOffset + j];
1813: for (;k < numFillCols; k++) {
1814: if (ja[matOffset + k] == col) {
1815: break;
1816: }
1817: }
1818: if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, col);
1819: for (r = 0; r < cDof; r++) {
1820: vals[matOffset + numFillCols * r + k] = pointWork[r * aNumFillCols + j];
1821: }
1822: }
1823: }
1824: else {
1825: /* find where to put this portion of pointMat into the matrix */
1826: for (k = 0; k < numFillCols; k++) {
1827: if (ja[matOffset + k] == aOff) {
1828: break;
1829: }
1830: }
1831: if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, aOff);
1832: for (r = 0; r < cDof; r++) {
1833: for (j = 0; j < aDof; j++) {
1834: PetscInt col = perm ? perm[j] : j;
1836: vals[matOffset + numFillCols * r + k + col] += pointMat[r * numCols + offset + j] * (flip ? flip[col] : 1.);
1837: }
1838: }
1839: }
1840: offset += aDof;
1841: }
1842: if (numFields) {
1843: PetscSectionRestoreFieldPointSyms(section,f,closureSize,closure,&perms,&flips);
1844: } else {
1845: PetscSectionRestorePointSyms(section,closureSize,closure,&perms,&flips);
1846: }
1847: }
1848: DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1849: }
1850: for (row = 0; row < nRows; row++) {
1851: MatSetValues(cMat,1,&row,ia[row+1]-ia[row],&ja[ia[row]],&vals[ia[row]],INSERT_VALUES);
1852: }
1853: MatRestoreRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);
1854: if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not restore RowIJ of constraint matrix");
1855: MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);
1856: MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);
1857: PetscFree(vals);
1858: }
1860: /* clean up */
1861: ISRestoreIndices(anIS,&anchors);
1862: PetscFree2(perm,iperm);
1863: PetscFree(pointWork);
1864: DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
1865: return(0);
1866: }
1868: /* refine a single cell on rank 0: this is not intended to provide good local refinement, only to create an example of
1869: * a non-conforming mesh. Local refinement comes later */
1870: PetscErrorCode DMPlexTreeRefineCell (DM dm, PetscInt cell, DM *ncdm)
1871: {
1872: DM K;
1873: PetscMPIInt rank;
1874: PetscInt dim, *pNewStart, *pNewEnd, *pNewCount, *pOldStart, *pOldEnd, offset, d, pStart, pEnd;
1875: PetscInt numNewCones, *newConeSizes, *newCones, *newOrientations;
1876: PetscInt *Kembedding;
1877: PetscInt *cellClosure=NULL, nc;
1878: PetscScalar *newVertexCoords;
1879: PetscInt numPointsWithParents, *parents, *childIDs, *perm, *iperm, *preOrient, pOffset;
1880: PetscSection parentSection;
1884: MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);
1885: DMGetDimension(dm,&dim);
1886: DMPlexCreate(PetscObjectComm((PetscObject)dm), ncdm);
1887: DMSetDimension(*ncdm,dim);
1889: DMPlexGetChart(dm, &pStart, &pEnd);
1890: PetscSectionCreate(PetscObjectComm((PetscObject)dm),&parentSection);
1891: DMPlexGetReferenceTree(dm,&K);
1892: if (!rank) {
1893: /* compute the new charts */
1894: PetscMalloc5(dim+1,&pNewCount,dim+1,&pNewStart,dim+1,&pNewEnd,dim+1,&pOldStart,dim+1,&pOldEnd);
1895: offset = 0;
1896: for (d = 0; d <= dim; d++) {
1897: PetscInt pOldCount, kStart, kEnd, k;
1899: pNewStart[d] = offset;
1900: DMPlexGetHeightStratum(dm,d,&pOldStart[d],&pOldEnd[d]);
1901: DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
1902: pOldCount = pOldEnd[d] - pOldStart[d];
1903: /* adding the new points */
1904: pNewCount[d] = pOldCount + kEnd - kStart;
1905: if (!d) {
1906: /* removing the cell */
1907: pNewCount[d]--;
1908: }
1909: for (k = kStart; k < kEnd; k++) {
1910: PetscInt parent;
1911: DMPlexGetTreeParent(K,k,&parent,NULL);
1912: if (parent == k) {
1913: /* avoid double counting points that won't actually be new */
1914: pNewCount[d]--;
1915: }
1916: }
1917: pNewEnd[d] = pNewStart[d] + pNewCount[d];
1918: offset = pNewEnd[d];
1920: }
1921: if (cell < pOldStart[0] || cell >= pOldEnd[0]) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"%d not in cell range [%d, %d)", cell, pOldStart[0], pOldEnd[0]);
1922: /* get the current closure of the cell that we are removing */
1923: DMPlexGetTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);
1925: PetscMalloc1(pNewEnd[dim],&newConeSizes);
1926: {
1927: PetscInt kStart, kEnd, k, closureSizeK, *closureK = NULL, j;
1929: DMPlexGetChart(K,&kStart,&kEnd);
1930: PetscMalloc4(kEnd-kStart,&Kembedding,kEnd-kStart,&perm,kEnd-kStart,&iperm,kEnd-kStart,&preOrient);
1932: for (k = kStart; k < kEnd; k++) {
1933: perm[k - kStart] = k;
1934: iperm [k - kStart] = k - kStart;
1935: preOrient[k - kStart] = 0;
1936: }
1938: DMPlexGetTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);
1939: for (j = 1; j < closureSizeK; j++) {
1940: PetscInt parentOrientA = closureK[2*j+1];
1941: PetscInt parentOrientB = cellClosure[2*j+1];
1942: PetscInt p, q;
1944: p = closureK[2*j];
1945: q = cellClosure[2*j];
1946: for (d = 0; d <= dim; d++) {
1947: if (q >= pOldStart[d] && q < pOldEnd[d]) {
1948: Kembedding[p] = (q - pOldStart[d]) + pNewStart[d];
1949: }
1950: }
1951: if (parentOrientA != parentOrientB) {
1952: PetscInt numChildren, i;
1953: const PetscInt *children;
1955: DMPlexGetTreeChildren(K,p,&numChildren,&children);
1956: for (i = 0; i < numChildren; i++) {
1957: PetscInt kPerm, oPerm;
1959: k = children[i];
1960: DMPlexReferenceTreeGetChildSymmetry(K,p,parentOrientA,0,k,parentOrientB,&oPerm,&kPerm);
1961: /* perm = what refTree position I'm in */
1962: perm[kPerm-kStart] = k;
1963: /* iperm = who is at this position */
1964: iperm[k-kStart] = kPerm-kStart;
1965: preOrient[kPerm-kStart] = oPerm;
1966: }
1967: }
1968: }
1969: DMPlexRestoreTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);
1970: }
1971: PetscSectionSetChart(parentSection,0,pNewEnd[dim]);
1972: offset = 0;
1973: numNewCones = 0;
1974: for (d = 0; d <= dim; d++) {
1975: PetscInt kStart, kEnd, k;
1976: PetscInt p;
1977: PetscInt size;
1979: for (p = pOldStart[d]; p < pOldEnd[d]; p++) {
1980: /* skip cell 0 */
1981: if (p == cell) continue;
1982: /* old cones to new cones */
1983: DMPlexGetConeSize(dm,p,&size);
1984: newConeSizes[offset++] = size;
1985: numNewCones += size;
1986: }
1988: DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
1989: for (k = kStart; k < kEnd; k++) {
1990: PetscInt kParent;
1992: DMPlexGetTreeParent(K,k,&kParent,NULL);
1993: if (kParent != k) {
1994: Kembedding[k] = offset;
1995: DMPlexGetConeSize(K,k,&size);
1996: newConeSizes[offset++] = size;
1997: numNewCones += size;
1998: if (kParent != 0) {
1999: PetscSectionSetDof(parentSection,Kembedding[k],1);
2000: }
2001: }
2002: }
2003: }
2005: PetscSectionSetUp(parentSection);
2006: PetscSectionGetStorageSize(parentSection,&numPointsWithParents);
2007: PetscMalloc2(numNewCones,&newCones,numNewCones,&newOrientations);
2008: PetscMalloc2(numPointsWithParents,&parents,numPointsWithParents,&childIDs);
2010: /* fill new cones */
2011: offset = 0;
2012: for (d = 0; d <= dim; d++) {
2013: PetscInt kStart, kEnd, k, l;
2014: PetscInt p;
2015: PetscInt size;
2016: const PetscInt *cone, *orientation;
2018: for (p = pOldStart[d]; p < pOldEnd[d]; p++) {
2019: /* skip cell 0 */
2020: if (p == cell) continue;
2021: /* old cones to new cones */
2022: DMPlexGetConeSize(dm,p,&size);
2023: DMPlexGetCone(dm,p,&cone);
2024: DMPlexGetConeOrientation(dm,p,&orientation);
2025: for (l = 0; l < size; l++) {
2026: newCones[offset] = (cone[l] - pOldStart[d + 1]) + pNewStart[d + 1];
2027: newOrientations[offset++] = orientation[l];
2028: }
2029: }
2031: DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
2032: for (k = kStart; k < kEnd; k++) {
2033: PetscInt kPerm = perm[k], kParent;
2034: PetscInt preO = preOrient[k];
2036: DMPlexGetTreeParent(K,k,&kParent,NULL);
2037: if (kParent != k) {
2038: /* embed new cones */
2039: DMPlexGetConeSize(K,k,&size);
2040: DMPlexGetCone(K,kPerm,&cone);
2041: DMPlexGetConeOrientation(K,kPerm,&orientation);
2042: for (l = 0; l < size; l++) {
2043: PetscInt q, m = (preO >= 0) ? ((preO + l) % size) : ((size -(preO + 1) - l) % size);
2044: PetscInt newO, lSize, oTrue;
2046: q = iperm[cone[m]];
2047: newCones[offset] = Kembedding[q];
2048: DMPlexGetConeSize(K,q,&lSize);
2049: oTrue = orientation[m];
2050: oTrue = ((!lSize) || (preOrient[k] >= 0)) ? oTrue : -(oTrue + 2);
2051: newO = DihedralCompose(lSize,oTrue,preOrient[q]);
2052: newOrientations[offset++] = newO;
2053: }
2054: if (kParent != 0) {
2055: PetscInt newPoint = Kembedding[kParent];
2056: PetscSectionGetOffset(parentSection,Kembedding[k],&pOffset);
2057: parents[pOffset] = newPoint;
2058: childIDs[pOffset] = k;
2059: }
2060: }
2061: }
2062: }
2064: PetscMalloc1(dim*(pNewEnd[dim]-pNewStart[dim]),&newVertexCoords);
2066: /* fill coordinates */
2067: offset = 0;
2068: {
2069: PetscInt kStart, kEnd, l;
2070: PetscSection vSection;
2071: PetscInt v;
2072: Vec coords;
2073: PetscScalar *coordvals;
2074: PetscInt dof, off;
2075: PetscReal v0[3], J[9], detJ;
2077: #if defined(PETSC_USE_DEBUG)
2078: {
2079: PetscInt k;
2080: DMPlexGetHeightStratum(K,0,&kStart,&kEnd);
2081: for (k = kStart; k < kEnd; k++) {
2082: DMPlexComputeCellGeometryFEM(K, k, NULL, v0, J, NULL, &detJ);
2083: if (detJ <= 0.) SETERRQ1 (PETSC_COMM_SELF,PETSC_ERR_PLIB,"reference tree cell %d has bad determinant",k);
2084: }
2085: }
2086: #endif
2087: DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, NULL, &detJ);
2088: DMGetCoordinateSection(dm,&vSection);
2089: DMGetCoordinatesLocal(dm,&coords);
2090: VecGetArray(coords,&coordvals);
2091: for (v = pOldStart[dim]; v < pOldEnd[dim]; v++) {
2093: PetscSectionGetDof(vSection,v,&dof);
2094: PetscSectionGetOffset(vSection,v,&off);
2095: for (l = 0; l < dof; l++) {
2096: newVertexCoords[offset++] = coordvals[off + l];
2097: }
2098: }
2099: VecRestoreArray(coords,&coordvals);
2101: DMGetCoordinateSection(K,&vSection);
2102: DMGetCoordinatesLocal(K,&coords);
2103: VecGetArray(coords,&coordvals);
2104: DMPlexGetDepthStratum(K,0,&kStart,&kEnd);
2105: for (v = kStart; v < kEnd; v++) {
2106: PetscReal coord[3], newCoord[3];
2107: PetscInt vPerm = perm[v];
2108: PetscInt kParent;
2110: DMPlexGetTreeParent(K,v,&kParent,NULL);
2111: if (kParent != v) {
2112: /* this is a new vertex */
2113: PetscSectionGetOffset(vSection,vPerm,&off);
2114: for (l = 0; l < dim; ++l) coord[l] = PetscRealPart(coordvals[off+l]);
2115: CoordinatesRefToReal(dim, dim, v0, J, coord, newCoord);
2116: for (l = 0; l < dim; ++l) newVertexCoords[offset+l] = newCoord[l];
2117: offset += dim;
2118: }
2119: }
2120: VecRestoreArray(coords,&coordvals);
2121: }
2123: /* need to reverse the order of pNewCount: vertices first, cells last */
2124: for (d = 0; d < (dim + 1) / 2; d++) {
2125: PetscInt tmp;
2127: tmp = pNewCount[d];
2128: pNewCount[d] = pNewCount[dim - d];
2129: pNewCount[dim - d] = tmp;
2130: }
2132: DMPlexCreateFromDAG(*ncdm,dim,pNewCount,newConeSizes,newCones,newOrientations,newVertexCoords);
2133: DMPlexSetReferenceTree(*ncdm,K);
2134: DMPlexSetTree(*ncdm,parentSection,parents,childIDs);
2136: /* clean up */
2137: DMPlexRestoreTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);
2138: PetscFree5(pNewCount,pNewStart,pNewEnd,pOldStart,pOldEnd);
2139: PetscFree(newConeSizes);
2140: PetscFree2(newCones,newOrientations);
2141: PetscFree(newVertexCoords);
2142: PetscFree2(parents,childIDs);
2143: PetscFree4(Kembedding,perm,iperm,preOrient);
2144: }
2145: else {
2146: PetscInt p, counts[4];
2147: PetscInt *coneSizes, *cones, *orientations;
2148: Vec coordVec;
2149: PetscScalar *coords;
2151: for (d = 0; d <= dim; d++) {
2152: PetscInt dStart, dEnd;
2154: DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);
2155: counts[d] = dEnd - dStart;
2156: }
2157: PetscMalloc1(pEnd-pStart,&coneSizes);
2158: for (p = pStart; p < pEnd; p++) {
2159: DMPlexGetConeSize(dm,p,&coneSizes[p-pStart]);
2160: }
2161: DMPlexGetCones(dm, &cones);
2162: DMPlexGetConeOrientations(dm, &orientations);
2163: DMGetCoordinatesLocal(dm,&coordVec);
2164: VecGetArray(coordVec,&coords);
2166: PetscSectionSetChart(parentSection,pStart,pEnd);
2167: PetscSectionSetUp(parentSection);
2168: DMPlexCreateFromDAG(*ncdm,dim,counts,coneSizes,cones,orientations,NULL);
2169: DMPlexSetReferenceTree(*ncdm,K);
2170: DMPlexSetTree(*ncdm,parentSection,NULL,NULL);
2171: VecRestoreArray(coordVec,&coords);
2172: }
2173: PetscSectionDestroy(&parentSection);
2175: return(0);
2176: }
2178: PetscErrorCode DMPlexComputeInterpolatorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat)
2179: {
2180: PetscSF coarseToFineEmbedded;
2181: PetscSection globalCoarse, globalFine;
2182: PetscSection localCoarse, localFine;
2183: PetscSection aSec, cSec;
2184: PetscSection rootIndicesSec, rootMatricesSec;
2185: PetscSection leafIndicesSec, leafMatricesSec;
2186: PetscInt *rootIndices, *leafIndices;
2187: PetscScalar *rootMatrices, *leafMatrices;
2188: IS aIS;
2189: const PetscInt *anchors;
2190: Mat cMat;
2191: PetscInt numFields, maxFields;
2192: PetscInt pStartC, pEndC, pStartF, pEndF, p;
2193: PetscInt aStart, aEnd, cStart, cEnd;
2194: PetscInt *maxChildIds;
2195: PetscInt *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO;
2196: const PetscInt ***perms;
2197: const PetscScalar ***flips;
2198: PetscErrorCode ierr;
2201: DMPlexGetChart(coarse,&pStartC,&pEndC);
2202: DMPlexGetChart(fine,&pStartF,&pEndF);
2203: DMGetDefaultGlobalSection(fine,&globalFine);
2204: { /* winnow fine points that don't have global dofs out of the sf */
2205: PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, nleaves, l;
2206: const PetscInt *leaves;
2208: PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);
2209: for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) {
2210: p = leaves ? leaves[l] : l;
2211: PetscSectionGetDof(globalFine,p,&dof);
2212: PetscSectionGetConstraintDof(globalFine,p,&cdof);
2213: if ((dof - cdof) > 0) {
2214: numPointsWithDofs++;
2215: }
2216: }
2217: PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
2218: for (l = 0, offset = 0; l < nleaves; l++) {
2219: p = leaves ? leaves[l] : l;
2220: PetscSectionGetDof(globalFine,p,&dof);
2221: PetscSectionGetConstraintDof(globalFine,p,&cdof);
2222: if ((dof - cdof) > 0) {
2223: pointsWithDofs[offset++] = l;
2224: }
2225: }
2226: PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
2227: PetscFree(pointsWithDofs);
2228: }
2229: /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */
2230: PetscMalloc1(pEndC-pStartC,&maxChildIds);
2231: for (p = pStartC; p < pEndC; p++) {
2232: maxChildIds[p - pStartC] = -2;
2233: }
2234: PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);
2235: PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);
2237: DMGetDefaultSection(coarse,&localCoarse);
2238: DMGetDefaultGlobalSection(coarse,&globalCoarse);
2240: DMPlexGetAnchors(coarse,&aSec,&aIS);
2241: ISGetIndices(aIS,&anchors);
2242: PetscSectionGetChart(aSec,&aStart,&aEnd);
2244: DMGetDefaultConstraints(coarse,&cSec,&cMat);
2245: PetscSectionGetChart(cSec,&cStart,&cEnd);
2247: /* create sections that will send to children the indices and matrices they will need to construct the interpolator */
2248: PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);
2249: PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootMatricesSec);
2250: PetscSectionSetChart(rootIndicesSec,pStartC,pEndC);
2251: PetscSectionSetChart(rootMatricesSec,pStartC,pEndC);
2252: PetscSectionGetNumFields(localCoarse,&numFields);
2253: maxFields = PetscMax(1,numFields);
2254: PetscMalloc7(maxFields+1,&offsets,maxFields+1,&offsetsCopy,maxFields+1,&newOffsets,maxFields+1,&newOffsetsCopy,maxFields+1,&rowOffsets,maxFields+1,&numD,maxFields+1,&numO);
2255: PetscMalloc2(maxFields+1,(PetscInt****)&perms,maxFields+1,(PetscScalar****)&flips);
2256: PetscMemzero((void *) perms, (maxFields+1) * sizeof(const PetscInt **));
2257: PetscMemzero((void *) flips, (maxFields+1) * sizeof(const PetscScalar **));
2259: for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */
2260: PetscInt dof, matSize = 0;
2261: PetscInt aDof = 0;
2262: PetscInt cDof = 0;
2263: PetscInt maxChildId = maxChildIds[p - pStartC];
2264: PetscInt numRowIndices = 0;
2265: PetscInt numColIndices = 0;
2266: PetscInt f;
2268: PetscSectionGetDof(globalCoarse,p,&dof);
2269: if (dof < 0) {
2270: dof = -(dof + 1);
2271: }
2272: if (p >= aStart && p < aEnd) {
2273: PetscSectionGetDof(aSec,p,&aDof);
2274: }
2275: if (p >= cStart && p < cEnd) {
2276: PetscSectionGetDof(cSec,p,&cDof);
2277: }
2278: for (f = 0; f <= numFields; f++) offsets[f] = 0;
2279: for (f = 0; f <= numFields; f++) newOffsets[f] = 0;
2280: if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */
2281: PetscInt *closure = NULL, closureSize, cl;
2283: DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
2284: for (cl = 0; cl < closureSize; cl++) { /* get the closure */
2285: PetscInt c = closure[2 * cl], clDof;
2287: PetscSectionGetDof(localCoarse,c,&clDof);
2288: numRowIndices += clDof;
2289: for (f = 0; f < numFields; f++) {
2290: PetscSectionGetFieldDof(localCoarse,c,f,&clDof);
2291: offsets[f + 1] += clDof;
2292: }
2293: }
2294: for (f = 0; f < numFields; f++) {
2295: offsets[f + 1] += offsets[f];
2296: newOffsets[f + 1] = offsets[f + 1];
2297: }
2298: /* get the number of indices needed and their field offsets */
2299: DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,NULL,NULL,NULL,&numColIndices,NULL,NULL,newOffsets,PETSC_FALSE);
2300: DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
2301: if (!numColIndices) { /* there are no hanging constraint modifications, so the matrix is just the identity: do not send it */
2302: numColIndices = numRowIndices;
2303: matSize = 0;
2304: }
2305: else if (numFields) { /* we send one submat for each field: sum their sizes */
2306: matSize = 0;
2307: for (f = 0; f < numFields; f++) {
2308: PetscInt numRow, numCol;
2310: numRow = offsets[f + 1] - offsets[f];
2311: numCol = newOffsets[f + 1] - newOffsets[f];
2312: matSize += numRow * numCol;
2313: }
2314: }
2315: else {
2316: matSize = numRowIndices * numColIndices;
2317: }
2318: } else if (maxChildId == -1) {
2319: if (cDof > 0) { /* this point's dofs are interpolated via cMat: get the submatrix of cMat */
2320: PetscInt aOff, a;
2322: PetscSectionGetOffset(aSec,p,&aOff);
2323: for (f = 0; f < numFields; f++) {
2324: PetscInt fDof;
2326: PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
2327: offsets[f+1] = fDof;
2328: }
2329: for (a = 0; a < aDof; a++) {
2330: PetscInt anchor = anchors[a + aOff], aLocalDof;
2332: PetscSectionGetDof(localCoarse,anchor,&aLocalDof);
2333: numColIndices += aLocalDof;
2334: for (f = 0; f < numFields; f++) {
2335: PetscInt fDof;
2337: PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);
2338: newOffsets[f+1] += fDof;
2339: }
2340: }
2341: if (numFields) {
2342: matSize = 0;
2343: for (f = 0; f < numFields; f++) {
2344: matSize += offsets[f+1] * newOffsets[f+1];
2345: }
2346: }
2347: else {
2348: matSize = numColIndices * dof;
2349: }
2350: }
2351: else { /* no children, and no constraints on dofs: just get the global indices */
2352: numColIndices = dof;
2353: matSize = 0;
2354: }
2355: }
2356: /* we will pack the column indices with the field offsets */
2357: PetscSectionSetDof(rootIndicesSec,p,numColIndices ? numColIndices+2*numFields : 0);
2358: PetscSectionSetDof(rootMatricesSec,p,matSize);
2359: }
2360: PetscSectionSetUp(rootIndicesSec);
2361: PetscSectionSetUp(rootMatricesSec);
2362: {
2363: PetscInt numRootIndices, numRootMatrices;
2365: PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);
2366: PetscSectionGetStorageSize(rootMatricesSec,&numRootMatrices);
2367: PetscMalloc2(numRootIndices,&rootIndices,numRootMatrices,&rootMatrices);
2368: for (p = pStartC; p < pEndC; p++) {
2369: PetscInt numRowIndices, numColIndices, matSize, dof;
2370: PetscInt pIndOff, pMatOff, f;
2371: PetscInt *pInd;
2372: PetscInt maxChildId = maxChildIds[p - pStartC];
2373: PetscScalar *pMat = NULL;
2375: PetscSectionGetDof(rootIndicesSec,p,&numColIndices);
2376: if (!numColIndices) {
2377: continue;
2378: }
2379: for (f = 0; f <= numFields; f++) {
2380: offsets[f] = 0;
2381: newOffsets[f] = 0;
2382: offsetsCopy[f] = 0;
2383: newOffsetsCopy[f] = 0;
2384: }
2385: numColIndices -= 2 * numFields;
2386: PetscSectionGetOffset(rootIndicesSec,p,&pIndOff);
2387: pInd = &(rootIndices[pIndOff]);
2388: PetscSectionGetDof(rootMatricesSec,p,&matSize);
2389: if (matSize) {
2390: PetscSectionGetOffset(rootMatricesSec,p,&pMatOff);
2391: pMat = &rootMatrices[pMatOff];
2392: }
2393: PetscSectionGetDof(globalCoarse,p,&dof);
2394: if (dof < 0) {
2395: dof = -(dof + 1);
2396: }
2397: if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */
2398: PetscInt i, j;
2399: PetscInt numRowIndices = matSize / numColIndices;
2401: if (!numRowIndices) { /* don't need to calculate the mat, just the indices */
2402: PetscInt numIndices, *indices;
2403: DMPlexGetClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);
2404: if (numIndices != numColIndices) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"mismatching constraint indices calculations");
2405: for (i = 0; i < numColIndices; i++) {
2406: pInd[i] = indices[i];
2407: }
2408: for (i = 0; i < numFields; i++) {
2409: pInd[numColIndices + i] = offsets[i+1];
2410: pInd[numColIndices + numFields + i] = offsets[i+1];
2411: }
2412: DMPlexRestoreClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);
2413: }
2414: else {
2415: PetscInt closureSize, *closure = NULL, cl;
2416: PetscScalar *pMatIn, *pMatModified;
2417: PetscInt numPoints,*points;
2419: DMGetWorkArray(coarse,numRowIndices * numRowIndices,MPIU_SCALAR,&pMatIn);
2420: for (i = 0; i < numRowIndices; i++) { /* initialize to the identity */
2421: for (j = 0; j < numRowIndices; j++) {
2422: pMatIn[i * numRowIndices + j] = (i == j) ? 1. : 0.;
2423: }
2424: }
2425: DMPlexGetTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);
2426: for (f = 0; f < maxFields; f++) {
2427: if (numFields) {PetscSectionGetFieldPointSyms(localCoarse,f,closureSize,closure,&perms[f],&flips[f]);}
2428: else {PetscSectionGetPointSyms(localCoarse,closureSize,closure,&perms[f],&flips[f]);}
2429: }
2430: if (numFields) {
2431: for (cl = 0; cl < closureSize; cl++) {
2432: PetscInt c = closure[2 * cl];
2434: for (f = 0; f < numFields; f++) {
2435: PetscInt fDof;
2437: PetscSectionGetFieldDof(localCoarse,c,f,&fDof);
2438: offsets[f + 1] += fDof;
2439: }
2440: }
2441: for (f = 0; f < numFields; f++) {
2442: offsets[f + 1] += offsets[f];
2443: newOffsets[f + 1] = offsets[f + 1];
2444: }
2445: }
2446: /* TODO : flips here ? */
2447: /* apply hanging node constraints on the right, get the new points and the new offsets */
2448: DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,perms,pMatIn,&numPoints,NULL,&points,&pMatModified,newOffsets,PETSC_FALSE);
2449: for (f = 0; f < maxFields; f++) {
2450: if (numFields) {PetscSectionRestoreFieldPointSyms(localCoarse,f,closureSize,closure,&perms[f],&flips[f]);}
2451: else {PetscSectionRestorePointSyms(localCoarse,closureSize,closure,&perms[f],&flips[f]);}
2452: }
2453: for (f = 0; f < maxFields; f++) {
2454: if (numFields) {PetscSectionGetFieldPointSyms(localCoarse,f,numPoints,points,&perms[f],&flips[f]);}
2455: else {PetscSectionGetPointSyms(localCoarse,numPoints,points,&perms[f],&flips[f]);}
2456: }
2457: if (!numFields) {
2458: for (i = 0; i < numRowIndices * numColIndices; i++) {
2459: pMat[i] = pMatModified[i];
2460: }
2461: }
2462: else {
2463: PetscInt i, j, count;
2464: for (f = 0, count = 0; f < numFields; f++) {
2465: for (i = offsets[f]; i < offsets[f+1]; i++) {
2466: for (j = newOffsets[f]; j < newOffsets[f+1]; j++, count++) {
2467: pMat[count] = pMatModified[i * numColIndices + j];
2468: }
2469: }
2470: }
2471: }
2472: DMRestoreWorkArray(coarse,numRowIndices * numColIndices,MPIU_SCALAR,&pMatModified);
2473: DMPlexRestoreTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);
2474: DMRestoreWorkArray(coarse,numRowIndices * numColIndices,MPIU_SCALAR,&pMatIn);
2475: if (numFields) {
2476: for (f = 0; f < numFields; f++) {
2477: pInd[numColIndices + f] = offsets[f+1];
2478: pInd[numColIndices + numFields + f] = newOffsets[f+1];
2479: }
2480: for (cl = 0; cl < numPoints; cl++) {
2481: PetscInt globalOff, c = points[2*cl];
2482: PetscSectionGetOffset(globalCoarse, c, &globalOff);
2483: DMPlexGetIndicesPointFields_Internal(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, perms, cl, pInd);
2484: }
2485: } else {
2486: for (cl = 0; cl < numPoints; cl++) {
2487: PetscInt c = points[2*cl], globalOff;
2488: const PetscInt *perm = perms[0] ? perms[0][cl] : NULL;
2490: PetscSectionGetOffset(globalCoarse, c, &globalOff);
2491: DMPlexGetIndicesPoint_Internal(localCoarse, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, perm, pInd);
2492: }
2493: }
2494: for (f = 0; f < maxFields; f++) {
2495: if (numFields) {PetscSectionRestoreFieldPointSyms(localCoarse,f,numPoints,points,&perms[f],&flips[f]);}
2496: else {PetscSectionRestorePointSyms(localCoarse,numPoints,points,&perms[f],&flips[f]);}
2497: }
2498: DMRestoreWorkArray(coarse,numPoints,MPIU_SCALAR,&points);
2499: }
2500: }
2501: else if (matSize) {
2502: PetscInt cOff;
2503: PetscInt *rowIndices, *colIndices, a, aDof, aOff;
2505: numRowIndices = matSize / numColIndices;
2506: if (numRowIndices != dof) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Miscounted dofs");
2507: DMGetWorkArray(coarse,numRowIndices,MPIU_INT,&rowIndices);
2508: DMGetWorkArray(coarse,numColIndices,MPIU_INT,&colIndices);
2509: PetscSectionGetOffset(cSec,p,&cOff);
2510: PetscSectionGetDof(aSec,p,&aDof);
2511: PetscSectionGetOffset(aSec,p,&aOff);
2512: if (numFields) {
2513: for (f = 0; f < numFields; f++) {
2514: PetscInt fDof;
2516: PetscSectionGetFieldDof(cSec,p,f,&fDof);
2517: offsets[f + 1] = fDof;
2518: for (a = 0; a < aDof; a++) {
2519: PetscInt anchor = anchors[a + aOff];
2520: PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);
2521: newOffsets[f + 1] += fDof;
2522: }
2523: }
2524: for (f = 0; f < numFields; f++) {
2525: offsets[f + 1] += offsets[f];
2526: offsetsCopy[f + 1] = offsets[f + 1];
2527: newOffsets[f + 1] += newOffsets[f];
2528: newOffsetsCopy[f + 1] = newOffsets[f + 1];
2529: }
2530: DMPlexGetIndicesPointFields_Internal(cSec,p,cOff,offsetsCopy,PETSC_TRUE,NULL,-1,rowIndices);
2531: for (a = 0; a < aDof; a++) {
2532: PetscInt anchor = anchors[a + aOff], lOff;
2533: PetscSectionGetOffset(localCoarse,anchor,&lOff);
2534: DMPlexGetIndicesPointFields_Internal(localCoarse,anchor,lOff,newOffsetsCopy,PETSC_TRUE,NULL,-1,colIndices);
2535: }
2536: }
2537: else {
2538: DMPlexGetIndicesPoint_Internal(cSec,p,cOff,offsetsCopy,PETSC_TRUE,NULL,rowIndices);
2539: for (a = 0; a < aDof; a++) {
2540: PetscInt anchor = anchors[a + aOff], lOff;
2541: PetscSectionGetOffset(localCoarse,anchor,&lOff);
2542: DMPlexGetIndicesPoint_Internal(localCoarse,anchor,lOff,newOffsetsCopy,PETSC_TRUE,NULL,colIndices);
2543: }
2544: }
2545: if (numFields) {
2546: PetscInt count, a;
2548: for (f = 0, count = 0; f < numFields; f++) {
2549: PetscInt iSize = offsets[f + 1] - offsets[f];
2550: PetscInt jSize = newOffsets[f + 1] - newOffsets[f];
2551: MatGetValues(cMat,iSize,&rowIndices[offsets[f]],jSize,&colIndices[newOffsets[f]],&pMat[count]);
2552: count += iSize * jSize;
2553: pInd[numColIndices + f] = offsets[f+1];
2554: pInd[numColIndices + numFields + f] = newOffsets[f+1];
2555: }
2556: for (a = 0; a < aDof; a++) {
2557: PetscInt anchor = anchors[a + aOff];
2558: PetscInt gOff;
2559: PetscSectionGetOffset(globalCoarse,anchor,&gOff);
2560: DMPlexGetIndicesPointFields_Internal(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,NULL,-1,pInd);
2561: }
2562: }
2563: else {
2564: PetscInt a;
2565: MatGetValues(cMat,numRowIndices,rowIndices,numColIndices,colIndices,pMat);
2566: for (a = 0; a < aDof; a++) {
2567: PetscInt anchor = anchors[a + aOff];
2568: PetscInt gOff;
2569: PetscSectionGetOffset(globalCoarse,anchor,&gOff);
2570: DMPlexGetIndicesPoint_Internal(localCoarse,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,NULL,pInd);
2571: }
2572: }
2573: DMRestoreWorkArray(coarse,numColIndices,MPIU_INT,&colIndices);
2574: DMRestoreWorkArray(coarse,numRowIndices,MPIU_INT,&rowIndices);
2575: }
2576: else {
2577: PetscInt gOff;
2579: PetscSectionGetOffset(globalCoarse,p,&gOff);
2580: if (numFields) {
2581: for (f = 0; f < numFields; f++) {
2582: PetscInt fDof;
2583: PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
2584: offsets[f + 1] = fDof + offsets[f];
2585: }
2586: for (f = 0; f < numFields; f++) {
2587: pInd[numColIndices + f] = offsets[f+1];
2588: pInd[numColIndices + numFields + f] = offsets[f+1];
2589: }
2590: DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL,-1,pInd);
2591: }
2592: else {
2593: DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL,pInd);
2594: }
2595: }
2596: }
2597: PetscFree(maxChildIds);
2598: }
2599: {
2600: PetscSF indicesSF, matricesSF;
2601: PetscInt *remoteOffsetsIndices, *remoteOffsetsMatrices, numLeafIndices, numLeafMatrices;
2603: PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);
2604: PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafMatricesSec);
2605: PetscSFDistributeSection(coarseToFineEmbedded,rootIndicesSec,&remoteOffsetsIndices,leafIndicesSec);
2606: PetscSFDistributeSection(coarseToFineEmbedded,rootMatricesSec,&remoteOffsetsMatrices,leafMatricesSec);
2607: PetscSFCreateSectionSF(coarseToFineEmbedded,rootIndicesSec,remoteOffsetsIndices,leafIndicesSec,&indicesSF);
2608: PetscSFCreateSectionSF(coarseToFineEmbedded,rootMatricesSec,remoteOffsetsMatrices,leafMatricesSec,&matricesSF);
2609: PetscSFDestroy(&coarseToFineEmbedded);
2610: PetscFree(remoteOffsetsIndices);
2611: PetscFree(remoteOffsetsMatrices);
2612: PetscSectionGetStorageSize(leafIndicesSec,&numLeafIndices);
2613: PetscSectionGetStorageSize(leafMatricesSec,&numLeafMatrices);
2614: PetscMalloc2(numLeafIndices,&leafIndices,numLeafMatrices,&leafMatrices);
2615: PetscSFBcastBegin(indicesSF,MPIU_INT,rootIndices,leafIndices);
2616: PetscSFBcastBegin(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);
2617: PetscSFBcastEnd(indicesSF,MPIU_INT,rootIndices,leafIndices);
2618: PetscSFBcastEnd(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);
2619: PetscSFDestroy(&matricesSF);
2620: PetscSFDestroy(&indicesSF);
2621: PetscFree2(rootIndices,rootMatrices);
2622: PetscSectionDestroy(&rootIndicesSec);
2623: PetscSectionDestroy(&rootMatricesSec);
2624: }
2625: /* count to preallocate */
2626: DMGetDefaultSection(fine,&localFine);
2627: {
2628: PetscInt nGlobal;
2629: PetscInt *dnnz, *onnz;
2630: PetscLayout rowMap, colMap;
2631: PetscInt rowStart, rowEnd, colStart, colEnd;
2632: PetscInt maxDof;
2633: PetscInt *rowIndices;
2634: DM refTree;
2635: PetscInt **refPointFieldN;
2636: PetscScalar ***refPointFieldMats;
2637: PetscSection refConSec, refAnSec;
2638: PetscInt pRefStart,pRefEnd,maxConDof,maxColumns,leafStart,leafEnd;
2639: PetscScalar *pointWork;
2641: PetscSectionGetConstrainedStorageSize(globalFine,&nGlobal);
2642: PetscCalloc2(nGlobal,&dnnz,nGlobal,&onnz);
2643: MatGetLayouts(mat,&rowMap,&colMap);
2644: PetscLayoutSetUp(rowMap);
2645: PetscLayoutSetUp(colMap);
2646: PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
2647: PetscLayoutGetRange(colMap,&colStart,&colEnd);
2648: PetscSectionGetMaxDof(globalFine,&maxDof);
2649: PetscSectionGetChart(leafIndicesSec,&leafStart,&leafEnd);
2650: DMGetWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
2651: for (p = leafStart; p < leafEnd; p++) {
2652: PetscInt gDof, gcDof, gOff;
2653: PetscInt numColIndices, pIndOff, *pInd;
2654: PetscInt matSize;
2655: PetscInt i;
2657: PetscSectionGetDof(globalFine,p,&gDof);
2658: PetscSectionGetConstraintDof(globalFine,p,&gcDof);
2659: if ((gDof - gcDof) <= 0) {
2660: continue;
2661: }
2662: PetscSectionGetOffset(globalFine,p,&gOff);
2663: if (gOff < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I though having global dofs meant a non-negative offset");
2664: if ((gOff < rowStart) || ((gOff + gDof - gcDof) > rowEnd)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I thought the row map would constrain the global dofs");
2665: PetscSectionGetDof(leafIndicesSec,p,&numColIndices);
2666: PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);
2667: numColIndices -= 2 * numFields;
2668: if (numColIndices <= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"global fine dof with no dofs to interpolate from");
2669: pInd = &leafIndices[pIndOff];
2670: offsets[0] = 0;
2671: offsetsCopy[0] = 0;
2672: newOffsets[0] = 0;
2673: newOffsetsCopy[0] = 0;
2674: if (numFields) {
2675: PetscInt f;
2676: for (f = 0; f < numFields; f++) {
2677: PetscInt rowDof;
2679: PetscSectionGetFieldDof(localFine,p,f,&rowDof);
2680: offsets[f + 1] = offsets[f] + rowDof;
2681: offsetsCopy[f + 1] = offsets[f + 1];
2682: newOffsets[f + 1] = pInd[numColIndices + numFields + f];
2683: numD[f] = 0;
2684: numO[f] = 0;
2685: }
2686: DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,-1,rowIndices);
2687: for (f = 0; f < numFields; f++) {
2688: PetscInt colOffset = newOffsets[f];
2689: PetscInt numFieldCols = newOffsets[f + 1] - newOffsets[f];
2691: for (i = 0; i < numFieldCols; i++) {
2692: PetscInt gInd = pInd[i + colOffset];
2694: if (gInd >= colStart && gInd < colEnd) {
2695: numD[f]++;
2696: }
2697: else if (gInd >= 0) { /* negative means non-entry */
2698: numO[f]++;
2699: }
2700: }
2701: }
2702: }
2703: else {
2704: DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,rowIndices);
2705: numD[0] = 0;
2706: numO[0] = 0;
2707: for (i = 0; i < numColIndices; i++) {
2708: PetscInt gInd = pInd[i];
2710: if (gInd >= colStart && gInd < colEnd) {
2711: numD[0]++;
2712: }
2713: else if (gInd >= 0) { /* negative means non-entry */
2714: numO[0]++;
2715: }
2716: }
2717: }
2718: PetscSectionGetDof(leafMatricesSec,p,&matSize);
2719: if (!matSize) { /* incoming matrix is identity */
2720: PetscInt childId;
2722: childId = childIds[p-pStartF];
2723: if (childId < 0) { /* no child interpolation: one nnz per */
2724: if (numFields) {
2725: PetscInt f;
2726: for (f = 0; f < numFields; f++) {
2727: PetscInt numRows = offsets[f+1] - offsets[f], row;
2728: for (row = 0; row < numRows; row++) {
2729: PetscInt gIndCoarse = pInd[newOffsets[f] + row];
2730: PetscInt gIndFine = rowIndices[offsets[f] + row];
2731: if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */
2732: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2733: dnnz[gIndFine - rowStart] = 1;
2734: }
2735: else if (gIndCoarse >= 0) { /* remote */
2736: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2737: onnz[gIndFine - rowStart] = 1;
2738: }
2739: else { /* constrained */
2740: if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2741: }
2742: }
2743: }
2744: }
2745: else {
2746: PetscInt i;
2747: for (i = 0; i < gDof; i++) {
2748: PetscInt gIndCoarse = pInd[i];
2749: PetscInt gIndFine = rowIndices[i];
2750: if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */
2751: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2752: dnnz[gIndFine - rowStart] = 1;
2753: }
2754: else if (gIndCoarse >= 0) { /* remote */
2755: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2756: onnz[gIndFine - rowStart] = 1;
2757: }
2758: else { /* constrained */
2759: if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2760: }
2761: }
2762: }
2763: }
2764: else { /* interpolate from all */
2765: if (numFields) {
2766: PetscInt f;
2767: for (f = 0; f < numFields; f++) {
2768: PetscInt numRows = offsets[f+1] - offsets[f], row;
2769: for (row = 0; row < numRows; row++) {
2770: PetscInt gIndFine = rowIndices[offsets[f] + row];
2771: if (gIndFine >= 0) {
2772: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2773: dnnz[gIndFine - rowStart] = numD[f];
2774: onnz[gIndFine - rowStart] = numO[f];
2775: }
2776: }
2777: }
2778: }
2779: else {
2780: PetscInt i;
2781: for (i = 0; i < gDof; i++) {
2782: PetscInt gIndFine = rowIndices[i];
2783: if (gIndFine >= 0) {
2784: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2785: dnnz[gIndFine - rowStart] = numD[0];
2786: onnz[gIndFine - rowStart] = numO[0];
2787: }
2788: }
2789: }
2790: }
2791: }
2792: else { /* interpolate from all */
2793: if (numFields) {
2794: PetscInt f;
2795: for (f = 0; f < numFields; f++) {
2796: PetscInt numRows = offsets[f+1] - offsets[f], row;
2797: for (row = 0; row < numRows; row++) {
2798: PetscInt gIndFine = rowIndices[offsets[f] + row];
2799: if (gIndFine >= 0) {
2800: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2801: dnnz[gIndFine - rowStart] = numD[f];
2802: onnz[gIndFine - rowStart] = numO[f];
2803: }
2804: }
2805: }
2806: }
2807: else { /* every dof get a full row */
2808: PetscInt i;
2809: for (i = 0; i < gDof; i++) {
2810: PetscInt gIndFine = rowIndices[i];
2811: if (gIndFine >= 0) {
2812: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2813: dnnz[gIndFine - rowStart] = numD[0];
2814: onnz[gIndFine - rowStart] = numO[0];
2815: }
2816: }
2817: }
2818: }
2819: }
2820: MatXAIJSetPreallocation(mat,1,dnnz,onnz,NULL,NULL);
2821: PetscFree2(dnnz,onnz);
2823: DMPlexGetReferenceTree(fine,&refTree);
2824: DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
2825: DMGetDefaultConstraints(refTree,&refConSec,NULL);
2826: DMPlexGetAnchors(refTree,&refAnSec,NULL);
2827: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
2828: PetscSectionGetMaxDof(refConSec,&maxConDof);
2829: PetscSectionGetMaxDof(leafIndicesSec,&maxColumns);
2830: PetscMalloc1(maxConDof*maxColumns,&pointWork);
2831: for (p = leafStart; p < leafEnd; p++) {
2832: PetscInt gDof, gcDof, gOff;
2833: PetscInt numColIndices, pIndOff, *pInd;
2834: PetscInt matSize;
2835: PetscInt childId;
2838: PetscSectionGetDof(globalFine,p,&gDof);
2839: PetscSectionGetConstraintDof(globalFine,p,&gcDof);
2840: if ((gDof - gcDof) <= 0) {
2841: continue;
2842: }
2843: childId = childIds[p-pStartF];
2844: PetscSectionGetOffset(globalFine,p,&gOff);
2845: PetscSectionGetDof(leafIndicesSec,p,&numColIndices);
2846: PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);
2847: numColIndices -= 2 * numFields;
2848: pInd = &leafIndices[pIndOff];
2849: offsets[0] = 0;
2850: offsetsCopy[0] = 0;
2851: newOffsets[0] = 0;
2852: newOffsetsCopy[0] = 0;
2853: rowOffsets[0] = 0;
2854: if (numFields) {
2855: PetscInt f;
2856: for (f = 0; f < numFields; f++) {
2857: PetscInt rowDof;
2859: PetscSectionGetFieldDof(localFine,p,f,&rowDof);
2860: offsets[f + 1] = offsets[f] + rowDof;
2861: offsetsCopy[f + 1] = offsets[f + 1];
2862: rowOffsets[f + 1] = pInd[numColIndices + f];
2863: newOffsets[f + 1] = pInd[numColIndices + numFields + f];
2864: }
2865: DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,-1,rowIndices);
2866: }
2867: else {
2868: DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,rowIndices);
2869: }
2870: PetscSectionGetDof(leafMatricesSec,p,&matSize);
2871: if (!matSize) { /* incoming matrix is identity */
2872: if (childId < 0) { /* no child interpolation: scatter */
2873: if (numFields) {
2874: PetscInt f;
2875: for (f = 0; f < numFields; f++) {
2876: PetscInt numRows = offsets[f+1] - offsets[f], row;
2877: for (row = 0; row < numRows; row++) {
2878: MatSetValue(mat,rowIndices[offsets[f]+row],pInd[newOffsets[f]+row],1.,INSERT_VALUES);
2879: }
2880: }
2881: }
2882: else {
2883: PetscInt numRows = gDof, row;
2884: for (row = 0; row < numRows; row++) {
2885: MatSetValue(mat,rowIndices[row],pInd[row],1.,INSERT_VALUES);
2886: }
2887: }
2888: }
2889: else { /* interpolate from all */
2890: if (numFields) {
2891: PetscInt f;
2892: for (f = 0; f < numFields; f++) {
2893: PetscInt numRows = offsets[f+1] - offsets[f];
2894: PetscInt numCols = newOffsets[f + 1] - newOffsets[f];
2895: MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],refPointFieldMats[childId - pRefStart][f],INSERT_VALUES);
2896: }
2897: }
2898: else {
2899: MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,refPointFieldMats[childId - pRefStart][0],INSERT_VALUES);
2900: }
2901: }
2902: }
2903: else { /* interpolate from all */
2904: PetscInt pMatOff;
2905: PetscScalar *pMat;
2907: PetscSectionGetOffset(leafMatricesSec,p,&pMatOff);
2908: pMat = &leafMatrices[pMatOff];
2909: if (childId < 0) { /* copy the incoming matrix */
2910: if (numFields) {
2911: PetscInt f, count;
2912: for (f = 0, count = 0; f < numFields; f++) {
2913: PetscInt numRows = offsets[f+1]-offsets[f];
2914: PetscInt numCols = newOffsets[f+1]-newOffsets[f];
2915: PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f];
2916: PetscScalar *inMat = &pMat[count];
2918: MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],inMat,INSERT_VALUES);
2919: count += numCols * numInRows;
2920: }
2921: }
2922: else {
2923: MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,pMat,INSERT_VALUES);
2924: }
2925: }
2926: else { /* multiply the incoming matrix by the child interpolation */
2927: if (numFields) {
2928: PetscInt f, count;
2929: for (f = 0, count = 0; f < numFields; f++) {
2930: PetscInt numRows = offsets[f+1]-offsets[f];
2931: PetscInt numCols = newOffsets[f+1]-newOffsets[f];
2932: PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f];
2933: PetscScalar *inMat = &pMat[count];
2934: PetscInt i, j, k;
2935: if (refPointFieldN[childId - pRefStart][f] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch");
2936: for (i = 0; i < numRows; i++) {
2937: for (j = 0; j < numCols; j++) {
2938: PetscScalar val = 0.;
2939: for (k = 0; k < numInRows; k++) {
2940: val += refPointFieldMats[childId - pRefStart][f][i * numInRows + k] * inMat[k * numCols + j];
2941: }
2942: pointWork[i * numCols + j] = val;
2943: }
2944: }
2945: MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],pointWork,INSERT_VALUES);
2946: count += numCols * numInRows;
2947: }
2948: }
2949: else { /* every dof gets a full row */
2950: PetscInt numRows = gDof;
2951: PetscInt numCols = numColIndices;
2952: PetscInt numInRows = matSize / numColIndices;
2953: PetscInt i, j, k;
2954: if (refPointFieldN[childId - pRefStart][0] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch");
2955: for (i = 0; i < numRows; i++) {
2956: for (j = 0; j < numCols; j++) {
2957: PetscScalar val = 0.;
2958: for (k = 0; k < numInRows; k++) {
2959: val += refPointFieldMats[childId - pRefStart][0][i * numInRows + k] * pMat[k * numCols + j];
2960: }
2961: pointWork[i * numCols + j] = val;
2962: }
2963: }
2964: MatSetValues(mat,numRows,rowIndices,numCols,pInd,pointWork,INSERT_VALUES);
2965: }
2966: }
2967: }
2968: }
2969: DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
2970: DMRestoreWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
2971: PetscFree(pointWork);
2972: }
2973: MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
2974: MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
2975: PetscSectionDestroy(&leafIndicesSec);
2976: PetscSectionDestroy(&leafMatricesSec);
2977: PetscFree2(leafIndices,leafMatrices);
2978: PetscFree2(*(PetscInt****)&perms,*(PetscScalar****)&flips);
2979: PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);
2980: ISRestoreIndices(aIS,&anchors);
2981: return(0);
2982: }
2984: /*
2985: * Assuming a nodal basis (w.r.t. the dual basis) basis:
2986: *
2987: * for each coarse dof \phi^c_i:
2988: * for each quadrature point (w_l,x_l) in the dual basis definition of \phi^c_i:
2989: * for each fine dof \phi^f_j;
2990: * a_{i,j} = 0;
2991: * for each fine dof \phi^f_k:
2992: * a_{i,j} += interp_{i,k} * \phi^f_k(x_l) * \phi^f_j(x_l) * w_l
2993: * [^^^ this is = \phi^c_i ^^^]
2994: */
2995: PetscErrorCode DMPlexComputeInjectorReferenceTree(DM refTree, Mat *inj)
2996: {
2997: PetscDS ds;
2998: PetscSection section, cSection;
2999: DMLabel canonical, depth;
3000: Mat cMat, mat;
3001: PetscInt *nnz;
3002: PetscInt f, dim, numFields, numSecFields, p, pStart, pEnd, cStart, cEnd;
3003: PetscInt m, n;
3004: PetscScalar *pointScalar;
3005: PetscReal *v0, *v0parent, *vtmp, *J, *Jparent, *invJ, *pointRef, detJ, detJparent;
3009: DMGetDefaultSection(refTree,§ion);
3010: DMGetDimension(refTree, &dim);
3011: PetscMalloc6(dim,&v0,dim,&v0parent,dim,&vtmp,dim*dim,&J,dim*dim,&Jparent,dim*dim,&invJ);
3012: PetscMalloc2(dim,&pointScalar,dim,&pointRef);
3013: DMGetDS(refTree,&ds);
3014: PetscDSGetNumFields(ds,&numFields);
3015: PetscSectionGetNumFields(section,&numSecFields);
3016: DMGetLabel(refTree,"canonical",&canonical);
3017: DMGetLabel(refTree,"depth",&depth);
3018: DMGetDefaultConstraints(refTree,&cSection,&cMat);
3019: DMPlexGetChart(refTree, &pStart, &pEnd);
3020: DMPlexGetHeightStratum(refTree, 0, &cStart, &cEnd);
3021: MatGetSize(cMat,&n,&m); /* the injector has transpose sizes from the constraint matrix */
3022: /* Step 1: compute non-zero pattern. A proper subset of constraint matrix non-zero */
3023: PetscCalloc1(m,&nnz);
3024: for (p = pStart; p < pEnd; p++) { /* a point will have non-zeros if it is canonical, it has dofs, and its children have dofs */
3025: const PetscInt *children;
3026: PetscInt numChildren;
3027: PetscInt i, numChildDof, numSelfDof;
3029: if (canonical) {
3030: PetscInt pCanonical;
3031: DMLabelGetValue(canonical,p,&pCanonical);
3032: if (p != pCanonical) continue;
3033: }
3034: DMPlexGetTreeChildren(refTree,p,&numChildren,&children);
3035: if (!numChildren) continue;
3036: for (i = 0, numChildDof = 0; i < numChildren; i++) {
3037: PetscInt child = children[i];
3038: PetscInt dof;
3040: PetscSectionGetDof(section,child,&dof);
3041: numChildDof += dof;
3042: }
3043: PetscSectionGetDof(section,p,&numSelfDof);
3044: if (!numChildDof || !numSelfDof) continue;
3045: for (f = 0; f < numFields; f++) {
3046: PetscInt selfOff;
3048: if (numSecFields) { /* count the dofs for just this field */
3049: for (i = 0, numChildDof = 0; i < numChildren; i++) {
3050: PetscInt child = children[i];
3051: PetscInt dof;
3053: PetscSectionGetFieldDof(section,child,f,&dof);
3054: numChildDof += dof;
3055: }
3056: PetscSectionGetFieldDof(section,p,f,&numSelfDof);
3057: PetscSectionGetFieldOffset(section,p,f,&selfOff);
3058: }
3059: else {
3060: PetscSectionGetOffset(section,p,&selfOff);
3061: }
3062: for (i = 0; i < numSelfDof; i++) {
3063: nnz[selfOff + i] = numChildDof;
3064: }
3065: }
3066: }
3067: MatCreateAIJ(PETSC_COMM_SELF,m,n,m,n,-1,nnz,-1,NULL,&mat);
3068: PetscFree(nnz);
3069: /* Setp 2: compute entries */
3070: for (p = pStart; p < pEnd; p++) {
3071: const PetscInt *children;
3072: PetscInt numChildren;
3073: PetscInt i, numChildDof, numSelfDof;
3075: /* same conditions about when entries occur */
3076: if (canonical) {
3077: PetscInt pCanonical;
3078: DMLabelGetValue(canonical,p,&pCanonical);
3079: if (p != pCanonical) continue;
3080: }
3081: DMPlexGetTreeChildren(refTree,p,&numChildren,&children);
3082: if (!numChildren) continue;
3083: for (i = 0, numChildDof = 0; i < numChildren; i++) {
3084: PetscInt child = children[i];
3085: PetscInt dof;
3087: PetscSectionGetDof(section,child,&dof);
3088: numChildDof += dof;
3089: }
3090: PetscSectionGetDof(section,p,&numSelfDof);
3091: if (!numChildDof || !numSelfDof) continue;
3093: for (f = 0; f < numFields; f++) {
3094: PetscInt selfOff, Nc, parentCell;
3095: PetscInt cellShapeOff;
3096: PetscObject disc;
3097: PetscDualSpace dsp;
3098: PetscClassId classId;
3099: PetscScalar *pointMat;
3100: PetscInt *matRows, *matCols;
3101: PetscInt pO = PETSC_MIN_INT;
3102: const PetscInt *depthNumDof;
3104: if (numSecFields) {
3105: for (i = 0, numChildDof = 0; i < numChildren; i++) {
3106: PetscInt child = children[i];
3107: PetscInt dof;
3109: PetscSectionGetFieldDof(section,child,f,&dof);
3110: numChildDof += dof;
3111: }
3112: PetscSectionGetFieldDof(section,p,f,&numSelfDof);
3113: PetscSectionGetFieldOffset(section,p,f,&selfOff);
3114: }
3115: else {
3116: PetscSectionGetOffset(section,p,&selfOff);
3117: }
3119: /* find a cell whose closure contains p */
3120: if (p >= cStart && p < cEnd) {
3121: parentCell = p;
3122: }
3123: else {
3124: PetscInt *star = NULL;
3125: PetscInt numStar;
3127: parentCell = -1;
3128: DMPlexGetTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);
3129: for (i = numStar - 1; i >= 0; i--) {
3130: PetscInt c = star[2 * i];
3132: if (c >= cStart && c < cEnd) {
3133: parentCell = c;
3134: break;
3135: }
3136: }
3137: DMPlexRestoreTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);
3138: }
3139: /* determine the offset of p's shape functions withing parentCell's shape functions */
3140: PetscDSGetDiscretization(ds,f,&disc);
3141: PetscObjectGetClassId(disc,&classId);
3142: if (classId == PETSCFE_CLASSID) {
3143: PetscFEGetDualSpace((PetscFE)disc,&dsp);
3144: }
3145: else if (classId == PETSCFV_CLASSID) {
3146: PetscFVGetDualSpace((PetscFV)disc,&dsp);
3147: }
3148: else {
3149: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unsupported discretization object");
3150: }
3151: PetscDualSpaceGetNumDof(dsp,&depthNumDof);
3152: PetscDualSpaceGetNumComponents(dsp,&Nc);
3153: {
3154: PetscInt *closure = NULL;
3155: PetscInt numClosure;
3157: DMPlexGetTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);
3158: for (i = 0, cellShapeOff = 0; i < numClosure; i++) {
3159: PetscInt point = closure[2 * i], pointDepth;
3161: pO = closure[2 * i + 1];
3162: if (point == p) break;
3163: DMLabelGetValue(depth,point,&pointDepth);
3164: cellShapeOff += depthNumDof[pointDepth];
3165: }
3166: DMPlexRestoreTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);
3167: }
3169: DMGetWorkArray(refTree, numSelfDof * numChildDof, MPIU_SCALAR,&pointMat);
3170: DMGetWorkArray(refTree, numSelfDof + numChildDof, MPIU_INT,&matRows);
3171: matCols = matRows + numSelfDof;
3172: for (i = 0; i < numSelfDof; i++) {
3173: matRows[i] = selfOff + i;
3174: }
3175: for (i = 0; i < numSelfDof * numChildDof; i++) pointMat[i] = 0.;
3176: {
3177: PetscInt colOff = 0;
3179: for (i = 0; i < numChildren; i++) {
3180: PetscInt child = children[i];
3181: PetscInt dof, off, j;
3183: if (numSecFields) {
3184: PetscSectionGetFieldDof(cSection,child,f,&dof);
3185: PetscSectionGetFieldOffset(cSection,child,f,&off);
3186: }
3187: else {
3188: PetscSectionGetDof(cSection,child,&dof);
3189: PetscSectionGetOffset(cSection,child,&off);
3190: }
3192: for (j = 0; j < dof; j++) {
3193: matCols[colOff++] = off + j;
3194: }
3195: }
3196: }
3197: if (classId == PETSCFE_CLASSID) {
3198: PetscFE fe = (PetscFE) disc;
3199: PetscInt fSize;
3201: PetscFEGetDualSpace(fe,&dsp);
3202: PetscDualSpaceGetDimension(dsp,&fSize);
3203: for (i = 0; i < numSelfDof; i++) { /* for every shape function */
3204: PetscQuadrature q;
3205: PetscInt dim, thisNc, numPoints, j, k;
3206: const PetscReal *points;
3207: const PetscReal *weights;
3208: PetscInt *closure = NULL;
3209: PetscInt numClosure;
3210: PetscInt parentCellShapeDof = cellShapeOff + (pO < 0 ? (numSelfDof - 1 - i) : i);
3211: PetscReal *Bparent;
3213: PetscDualSpaceGetFunctional(dsp,parentCellShapeDof,&q);
3214: PetscQuadratureGetData(q,&dim,&thisNc,&numPoints,&points,&weights);
3215: if (thisNc != Nc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Functional dim %D does not much basis dim %D\n",thisNc,Nc);
3216: PetscFEGetTabulation(fe,numPoints,points,&Bparent,NULL,NULL); /* I'm expecting a nodal basis: weights[:]' * Bparent[:,cellShapeDof] = 1. */
3217: for (j = 0; j < numPoints; j++) {
3218: PetscInt childCell = -1;
3219: PetscReal *parentValAtPoint;
3220: const PetscReal *pointReal = &points[dim * j];
3221: const PetscScalar *point;
3222: PetscReal *Bchild;
3223: PetscInt childCellShapeOff, pointMatOff;
3224: #if defined(PETSC_USE_COMPLEX)
3225: PetscInt d;
3227: for (d = 0; d < dim; d++) {
3228: pointScalar[d] = points[dim * j + d];
3229: }
3230: point = pointScalar;
3231: #else
3232: point = pointReal;
3233: #endif
3235: parentValAtPoint = &Bparent[(fSize * j + parentCellShapeDof) * Nc];
3237: for (k = 0; k < numChildren; k++) { /* locate the point in a child's star cell*/
3238: PetscInt child = children[k];
3239: PetscInt *star = NULL;
3240: PetscInt numStar, s;
3242: DMPlexGetTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);
3243: for (s = numStar - 1; s >= 0; s--) {
3244: PetscInt c = star[2 * s];
3246: if (c < cStart || c >= cEnd) continue;
3247: DMPlexLocatePoint_Internal(refTree,dim,point,c,&childCell);
3248: if (childCell >= 0) break;
3249: }
3250: DMPlexRestoreTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);
3251: if (childCell >= 0) break;
3252: }
3253: if (childCell < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Could not locate quadrature point");
3254: DMPlexComputeCellGeometryFEM(refTree, childCell, NULL, v0, J, invJ, &detJ);
3255: DMPlexComputeCellGeometryFEM(refTree, parentCell, NULL, v0parent, Jparent, NULL, &detJparent);
3256: CoordinatesRefToReal(dim, dim, v0parent, Jparent, pointReal, vtmp);
3257: CoordinatesRealToRef(dim, dim, v0, invJ, vtmp, pointRef);
3259: PetscFEGetTabulation(fe,1,pointRef,&Bchild,NULL,NULL);
3260: DMPlexGetTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);
3261: for (k = 0, pointMatOff = 0; k < numChildren; k++) { /* point is located in cell => child dofs support at point are in closure of cell */
3262: PetscInt child = children[k], childDepth, childDof, childO = PETSC_MIN_INT;
3263: PetscInt l;
3265: DMLabelGetValue(depth,child,&childDepth);
3266: childDof = depthNumDof[childDepth];
3267: for (l = 0, childCellShapeOff = 0; l < numClosure; l++) {
3268: PetscInt point = closure[2 * l];
3269: PetscInt pointDepth;
3271: childO = closure[2 * l + 1];
3272: if (point == child) break;
3273: DMLabelGetValue(depth,point,&pointDepth);
3274: childCellShapeOff += depthNumDof[pointDepth];
3275: }
3276: if (l == numClosure) {
3277: pointMatOff += childDof;
3278: continue; /* child is not in the closure of the cell: has nothing to contribute to this point */
3279: }
3280: for (l = 0; l < childDof; l++) {
3281: PetscInt childCellDof = childCellShapeOff + (childO ? (childDof - 1 - l) : l), m;
3282: PetscReal *childValAtPoint;
3283: PetscReal val = 0.;
3285: childValAtPoint = &Bchild[childCellDof * Nc];
3286: for (m = 0; m < Nc; m++) {
3287: val += weights[j * Nc + m] * parentValAtPoint[m] * childValAtPoint[m];
3288: }
3290: pointMat[i * numChildDof + pointMatOff + l] += val;
3291: }
3292: pointMatOff += childDof;
3293: }
3294: DMPlexRestoreTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);
3295: PetscFERestoreTabulation(fe,1,pointRef,&Bchild,NULL,NULL);
3296: }
3297: PetscFERestoreTabulation(fe,numPoints,points,&Bparent,NULL,NULL);
3298: }
3299: }
3300: else { /* just the volume-weighted averages of the children */
3301: PetscReal parentVol;
3302: PetscInt childCell;
3304: DMPlexComputeCellGeometryFVM(refTree, p, &parentVol, NULL, NULL);
3305: for (i = 0, childCell = 0; i < numChildren; i++) {
3306: PetscInt child = children[i], j;
3307: PetscReal childVol;
3309: if (child < cStart || child >= cEnd) continue;
3310: DMPlexComputeCellGeometryFVM(refTree, child, &childVol, NULL, NULL);
3311: for (j = 0; j < Nc; j++) {
3312: pointMat[j * numChildDof + Nc * childCell + j] = childVol / parentVol;
3313: }
3314: childCell++;
3315: }
3316: }
3317: /* Insert pointMat into mat */
3318: MatSetValues(mat,numSelfDof,matRows,numChildDof,matCols,pointMat,INSERT_VALUES);
3319: DMRestoreWorkArray(refTree, numSelfDof + numChildDof, MPIU_INT,&matRows);
3320: DMRestoreWorkArray(refTree, numSelfDof * numChildDof, MPIU_SCALAR,&pointMat);
3321: }
3322: }
3323: PetscFree6(v0,v0parent,vtmp,J,Jparent,invJ);
3324: PetscFree2(pointScalar,pointRef);
3325: MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
3326: MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
3327: *inj = mat;
3328: return(0);
3329: }
3331: static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats)
3332: {
3333: PetscDS ds;
3334: PetscInt numFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof;
3335: PetscScalar ***refPointFieldMats;
3336: PetscSection refConSec, refSection;
3340: DMGetDS(refTree,&ds);
3341: PetscDSGetNumFields(ds,&numFields);
3342: DMGetDefaultConstraints(refTree,&refConSec,NULL);
3343: DMGetDefaultSection(refTree,&refSection);
3344: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
3345: PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);
3346: PetscSectionGetMaxDof(refConSec,&maxDof);
3347: PetscMalloc1(maxDof,&rows);
3348: PetscMalloc1(maxDof*maxDof,&cols);
3349: for (p = pRefStart; p < pRefEnd; p++) {
3350: PetscInt parent, pDof, parentDof;
3352: DMPlexGetTreeParent(refTree,p,&parent,NULL);
3353: PetscSectionGetDof(refConSec,p,&pDof);
3354: PetscSectionGetDof(refSection,parent,&parentDof);
3355: if (!pDof || !parentDof || parent == p) continue;
3357: PetscMalloc1(numFields,&refPointFieldMats[p-pRefStart]);
3358: for (f = 0; f < numFields; f++) {
3359: PetscInt cDof, cOff, numCols, r;
3361: if (numFields > 1) {
3362: PetscSectionGetFieldDof(refConSec,p,f,&cDof);
3363: PetscSectionGetFieldOffset(refConSec,p,f,&cOff);
3364: }
3365: else {
3366: PetscSectionGetDof(refConSec,p,&cDof);
3367: PetscSectionGetOffset(refConSec,p,&cOff);
3368: }
3370: for (r = 0; r < cDof; r++) {
3371: rows[r] = cOff + r;
3372: }
3373: numCols = 0;
3374: {
3375: PetscInt aDof, aOff, j;
3377: if (numFields > 1) {
3378: PetscSectionGetFieldDof(refSection,parent,f,&aDof);
3379: PetscSectionGetFieldOffset(refSection,parent,f,&aOff);
3380: }
3381: else {
3382: PetscSectionGetDof(refSection,parent,&aDof);
3383: PetscSectionGetOffset(refSection,parent,&aOff);
3384: }
3386: for (j = 0; j < aDof; j++) {
3387: cols[numCols++] = aOff + j;
3388: }
3389: }
3390: PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);
3391: /* transpose of constraint matrix */
3392: MatGetValues(inj,numCols,cols,cDof,rows,refPointFieldMats[p-pRefStart][f]);
3393: }
3394: }
3395: *childrenMats = refPointFieldMats;
3396: PetscFree(rows);
3397: PetscFree(cols);
3398: return(0);
3399: }
3401: static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats)
3402: {
3403: PetscDS ds;
3404: PetscScalar ***refPointFieldMats;
3405: PetscInt numFields, pRefStart, pRefEnd, p, f;
3406: PetscSection refConSec, refSection;
3410: refPointFieldMats = *childrenMats;
3411: *childrenMats = NULL;
3412: DMGetDS(refTree,&ds);
3413: DMGetDefaultSection(refTree,&refSection);
3414: PetscDSGetNumFields(ds,&numFields);
3415: DMGetDefaultConstraints(refTree,&refConSec,NULL);
3416: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
3417: for (p = pRefStart; p < pRefEnd; p++) {
3418: PetscInt parent, pDof, parentDof;
3420: DMPlexGetTreeParent(refTree,p,&parent,NULL);
3421: PetscSectionGetDof(refConSec,p,&pDof);
3422: PetscSectionGetDof(refSection,parent,&parentDof);
3423: if (!pDof || !parentDof || parent == p) continue;
3425: for (f = 0; f < numFields; f++) {
3426: PetscInt cDof;
3428: if (numFields > 1) {
3429: PetscSectionGetFieldDof(refConSec,p,f,&cDof);
3430: }
3431: else {
3432: PetscSectionGetDof(refConSec,p,&cDof);
3433: }
3435: PetscFree(refPointFieldMats[p - pRefStart][f]);
3436: }
3437: PetscFree(refPointFieldMats[p - pRefStart]);
3438: }
3439: PetscFree(refPointFieldMats);
3440: return(0);
3441: }
3443: static PetscErrorCode DMPlexReferenceTreeGetInjector(DM refTree,Mat *injRef)
3444: {
3445: Mat cMatRef;
3446: PetscObject injRefObj;
3450: DMGetDefaultConstraints(refTree,NULL,&cMatRef);
3451: PetscObjectQuery((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",&injRefObj);
3452: *injRef = (Mat) injRefObj;
3453: if (!*injRef) {
3454: DMPlexComputeInjectorReferenceTree(refTree,injRef);
3455: PetscObjectCompose((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",(PetscObject)*injRef);
3456: /* there is now a reference in cMatRef, which should be the only one for symmetry with the above case */
3457: PetscObjectDereference((PetscObject)*injRef);
3458: }
3459: return(0);
3460: }
3462: static PetscErrorCode DMPlexTransferInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, const PetscInt *childIds, Vec fineVec, PetscInt numFields, PetscInt *offsets, PetscSection *rootMultiSec, PetscSection *multiLeafSec, PetscInt **gatheredIndices, PetscScalar **gatheredValues)
3463: {
3464: PetscInt pStartF, pEndF, pStartC, pEndC, p, maxDof, numMulti;
3465: PetscSection globalCoarse, globalFine;
3466: PetscSection localCoarse, localFine, leafIndicesSec;
3467: PetscSection multiRootSec, rootIndicesSec;
3468: PetscInt *leafInds, *rootInds = NULL;
3469: const PetscInt *rootDegrees;
3470: PetscScalar *leafVals = NULL, *rootVals = NULL;
3471: PetscSF coarseToFineEmbedded;
3475: DMPlexGetChart(coarse,&pStartC,&pEndC);
3476: DMPlexGetChart(fine,&pStartF,&pEndF);
3477: DMGetDefaultSection(fine,&localFine);
3478: DMGetDefaultGlobalSection(fine,&globalFine);
3479: PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);
3480: PetscSectionSetChart(leafIndicesSec,pStartF, pEndF);
3481: PetscSectionGetMaxDof(localFine,&maxDof);
3482: { /* winnow fine points that don't have global dofs out of the sf */
3483: PetscInt l, nleaves, dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, numIndices;
3484: const PetscInt *leaves;
3486: PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);
3487: for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) {
3488: p = leaves ? leaves[l] : l;
3489: PetscSectionGetDof(globalFine,p,&dof);
3490: PetscSectionGetConstraintDof(globalFine,p,&cdof);
3491: if ((dof - cdof) > 0) {
3492: numPointsWithDofs++;
3494: PetscSectionGetDof(localFine,p,&dof);
3495: PetscSectionSetDof(leafIndicesSec,p,dof + 1);
3496: }
3497: }
3498: PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
3499: PetscSectionSetUp(leafIndicesSec);
3500: PetscSectionGetStorageSize(leafIndicesSec,&numIndices);
3501: PetscMalloc1(gatheredIndices ? numIndices : (maxDof + 1),&leafInds);
3502: if (gatheredValues) {PetscMalloc1(numIndices,&leafVals);}
3503: for (l = 0, offset = 0; l < nleaves; l++) {
3504: p = leaves ? leaves[l] : l;
3505: PetscSectionGetDof(globalFine,p,&dof);
3506: PetscSectionGetConstraintDof(globalFine,p,&cdof);
3507: if ((dof - cdof) > 0) {
3508: PetscInt off, gOff;
3509: PetscInt *pInd;
3510: PetscScalar *pVal = NULL;
3512: pointsWithDofs[offset++] = l;
3514: PetscSectionGetOffset(leafIndicesSec,p,&off);
3516: pInd = gatheredIndices ? (&leafInds[off + 1]) : leafInds;
3517: if (gatheredValues) {
3518: PetscInt i;
3520: pVal = &leafVals[off + 1];
3521: for (i = 0; i < dof; i++) pVal[i] = 0.;
3522: }
3523: PetscSectionGetOffset(globalFine,p,&gOff);
3525: offsets[0] = 0;
3526: if (numFields) {
3527: PetscInt f;
3529: for (f = 0; f < numFields; f++) {
3530: PetscInt fDof;
3531: PetscSectionGetFieldDof(localFine,p,f,&fDof);
3532: offsets[f + 1] = fDof + offsets[f];
3533: }
3534: DMPlexGetIndicesPointFields_Internal(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL,-1,pInd);
3535: }
3536: else {
3537: DMPlexGetIndicesPoint_Internal(localFine,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL,pInd);
3538: }
3539: if (gatheredValues) {VecGetValues(fineVec,dof,pInd,pVal);}
3540: }
3541: }
3542: PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
3543: PetscFree(pointsWithDofs);
3544: }
3546: DMPlexGetChart(coarse,&pStartC,&pEndC);
3547: DMGetDefaultSection(coarse,&localCoarse);
3548: DMGetDefaultGlobalSection(coarse,&globalCoarse);
3550: { /* there may be the case where an sf root has a parent: broadcast parents back to children */
3551: MPI_Datatype threeInt;
3552: PetscMPIInt rank;
3553: PetscInt (*parentNodeAndIdCoarse)[3];
3554: PetscInt (*parentNodeAndIdFine)[3];
3555: PetscInt p, nleaves, nleavesToParents;
3556: PetscSF pointSF, sfToParents;
3557: const PetscInt *ilocal;
3558: const PetscSFNode *iremote;
3559: PetscSFNode *iremoteToParents;
3560: PetscInt *ilocalToParents;
3562: MPI_Comm_rank(PetscObjectComm((PetscObject)coarse),&rank);
3563: MPI_Type_contiguous(3,MPIU_INT,&threeInt);
3564: MPI_Type_commit(&threeInt);
3565: PetscMalloc2(pEndC-pStartC,&parentNodeAndIdCoarse,pEndF-pStartF,&parentNodeAndIdFine);
3566: DMGetPointSF(coarse,&pointSF);
3567: PetscSFGetGraph(pointSF,NULL,&nleaves,&ilocal,&iremote);
3568: for (p = pStartC; p < pEndC; p++) {
3569: PetscInt parent, childId;
3570: DMPlexGetTreeParent(coarse,p,&parent,&childId);
3571: parentNodeAndIdCoarse[p - pStartC][0] = rank;
3572: parentNodeAndIdCoarse[p - pStartC][1] = parent - pStartC;
3573: parentNodeAndIdCoarse[p - pStartC][2] = (p == parent) ? -1 : childId;
3574: if (nleaves > 0) {
3575: PetscInt leaf = -1;
3577: if (ilocal) {
3578: PetscFindInt(parent,nleaves,ilocal,&leaf);
3579: }
3580: else {
3581: leaf = p - pStartC;
3582: }
3583: if (leaf >= 0) {
3584: parentNodeAndIdCoarse[p - pStartC][0] = iremote[leaf].rank;
3585: parentNodeAndIdCoarse[p - pStartC][1] = iremote[leaf].index;
3586: }
3587: }
3588: }
3589: for (p = pStartF; p < pEndF; p++) {
3590: parentNodeAndIdFine[p - pStartF][0] = -1;
3591: parentNodeAndIdFine[p - pStartF][1] = -1;
3592: parentNodeAndIdFine[p - pStartF][2] = -1;
3593: }
3594: PetscSFBcastBegin(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);
3595: PetscSFBcastEnd(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);
3596: for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) {
3597: PetscInt dof;
3599: PetscSectionGetDof(leafIndicesSec,p,&dof);
3600: if (dof) {
3601: PetscInt off;
3603: PetscSectionGetOffset(leafIndicesSec,p,&off);
3604: if (gatheredIndices) {
3605: leafInds[off] = PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]);
3606: } else if (gatheredValues) {
3607: leafVals[off] = (PetscScalar) PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]);
3608: }
3609: }
3610: if (parentNodeAndIdFine[p-pStartF][0] >= 0) {
3611: nleavesToParents++;
3612: }
3613: }
3614: PetscMalloc1(nleavesToParents,&ilocalToParents);
3615: PetscMalloc1(nleavesToParents,&iremoteToParents);
3616: for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) {
3617: if (parentNodeAndIdFine[p-pStartF][0] >= 0) {
3618: ilocalToParents[nleavesToParents] = p - pStartF;
3619: iremoteToParents[nleavesToParents].rank = parentNodeAndIdFine[p-pStartF][0];
3620: iremoteToParents[nleavesToParents].index = parentNodeAndIdFine[p-pStartF][1];
3621: nleavesToParents++;
3622: }
3623: }
3624: PetscSFCreate(PetscObjectComm((PetscObject)coarse),&sfToParents);
3625: PetscSFSetGraph(sfToParents,pEndC-pStartC,nleavesToParents,ilocalToParents,PETSC_OWN_POINTER,iremoteToParents,PETSC_OWN_POINTER);
3626: PetscSFDestroy(&coarseToFineEmbedded);
3628: coarseToFineEmbedded = sfToParents;
3630: PetscFree2(parentNodeAndIdCoarse,parentNodeAndIdFine);
3631: MPI_Type_free(&threeInt);
3632: }
3634: { /* winnow out coarse points that don't have dofs */
3635: PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs;
3636: PetscSF sfDofsOnly;
3638: for (p = pStartC, numPointsWithDofs = 0; p < pEndC; p++) {
3639: PetscSectionGetDof(globalCoarse,p,&dof);
3640: PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
3641: if ((dof - cdof) > 0) {
3642: numPointsWithDofs++;
3643: }
3644: }
3645: PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
3646: for (p = pStartC, offset = 0; p < pEndC; p++) {
3647: PetscSectionGetDof(globalCoarse,p,&dof);
3648: PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
3649: if ((dof - cdof) > 0) {
3650: pointsWithDofs[offset++] = p - pStartC;
3651: }
3652: }
3653: PetscSFCreateEmbeddedSF(coarseToFineEmbedded, numPointsWithDofs, pointsWithDofs, &sfDofsOnly);
3654: PetscSFDestroy(&coarseToFineEmbedded);
3655: PetscFree(pointsWithDofs);
3656: coarseToFineEmbedded = sfDofsOnly;
3657: }
3659: /* communicate back to the coarse mesh which coarse points have children (that may require injection) */
3660: PetscSFComputeDegreeBegin(coarseToFineEmbedded,&rootDegrees);
3661: PetscSFComputeDegreeEnd(coarseToFineEmbedded,&rootDegrees);
3662: PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&multiRootSec);
3663: PetscSectionSetChart(multiRootSec,pStartC,pEndC);
3664: for (p = pStartC; p < pEndC; p++) {
3665: PetscSectionSetDof(multiRootSec,p,rootDegrees[p-pStartC]);
3666: }
3667: PetscSectionSetUp(multiRootSec);
3668: PetscSectionGetStorageSize(multiRootSec,&numMulti);
3669: PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);
3670: { /* distribute the leaf section */
3671: PetscSF multi, multiInv, indicesSF;
3672: PetscInt *remoteOffsets, numRootIndices;
3674: PetscSFGetMultiSF(coarseToFineEmbedded,&multi);
3675: PetscSFCreateInverseSF(multi,&multiInv);
3676: PetscSFDistributeSection(multiInv,leafIndicesSec,&remoteOffsets,rootIndicesSec);
3677: PetscSFCreateSectionSF(multiInv,leafIndicesSec,remoteOffsets,rootIndicesSec,&indicesSF);
3678: PetscFree(remoteOffsets);
3679: PetscSFDestroy(&multiInv);
3680: PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);
3681: if (gatheredIndices) {
3682: PetscMalloc1(numRootIndices,&rootInds);
3683: PetscSFBcastBegin(indicesSF,MPIU_INT,leafInds,rootInds);
3684: PetscSFBcastEnd(indicesSF,MPIU_INT,leafInds,rootInds);
3685: }
3686: if (gatheredValues) {
3687: PetscMalloc1(numRootIndices,&rootVals);
3688: PetscSFBcastBegin(indicesSF,MPIU_SCALAR,leafVals,rootVals);
3689: PetscSFBcastEnd(indicesSF,MPIU_SCALAR,leafVals,rootVals);
3690: }
3691: PetscSFDestroy(&indicesSF);
3692: }
3693: PetscSectionDestroy(&leafIndicesSec);
3694: PetscFree(leafInds);
3695: PetscFree(leafVals);
3696: PetscSFDestroy(&coarseToFineEmbedded);
3697: *rootMultiSec = multiRootSec;
3698: *multiLeafSec = rootIndicesSec;
3699: if (gatheredIndices) *gatheredIndices = rootInds;
3700: if (gatheredValues) *gatheredValues = rootVals;
3701: return(0);
3702: }
3704: PetscErrorCode DMPlexComputeInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat)
3705: {
3706: DM refTree;
3707: PetscSection multiRootSec, rootIndicesSec;
3708: PetscSection globalCoarse, globalFine;
3709: PetscSection localCoarse, localFine;
3710: PetscSection cSecRef;
3711: PetscInt *rootIndices, *parentIndices, pRefStart, pRefEnd;
3712: Mat injRef;
3713: PetscInt numFields, maxDof;
3714: PetscInt pStartC, pEndC, pStartF, pEndF, p;
3715: PetscInt *offsets, *offsetsCopy, *rowOffsets;
3716: PetscLayout rowMap, colMap;
3717: PetscInt rowStart, rowEnd, colStart, colEnd, *nnzD, *nnzO;
3718: PetscScalar ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */
3723: /* get the templates for the fine-to-coarse injection from the reference tree */
3724: DMPlexGetReferenceTree(coarse,&refTree);
3725: DMGetDefaultConstraints(refTree,&cSecRef,NULL);
3726: PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);
3727: DMPlexReferenceTreeGetInjector(refTree,&injRef);
3729: DMPlexGetChart(fine,&pStartF,&pEndF);
3730: DMGetDefaultSection(fine,&localFine);
3731: DMGetDefaultGlobalSection(fine,&globalFine);
3732: PetscSectionGetNumFields(localFine,&numFields);
3733: DMPlexGetChart(coarse,&pStartC,&pEndC);
3734: DMGetDefaultSection(coarse,&localCoarse);
3735: DMGetDefaultGlobalSection(coarse,&globalCoarse);
3736: PetscSectionGetMaxDof(localCoarse,&maxDof);
3737: {
3738: PetscInt maxFields = PetscMax(1,numFields) + 1;
3739: PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);
3740: }
3742: DMPlexTransferInjectorTree(coarse,fine,coarseToFine,childIds,NULL,numFields,offsets,&multiRootSec,&rootIndicesSec,&rootIndices,NULL);
3744: PetscMalloc1(maxDof,&parentIndices);
3746: /* count indices */
3747: MatGetLayouts(mat,&rowMap,&colMap);
3748: PetscLayoutSetUp(rowMap);
3749: PetscLayoutSetUp(colMap);
3750: PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
3751: PetscLayoutGetRange(colMap,&colStart,&colEnd);
3752: PetscCalloc2(rowEnd-rowStart,&nnzD,rowEnd-rowStart,&nnzO);
3753: for (p = pStartC; p < pEndC; p++) {
3754: PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;
3756: PetscSectionGetDof(globalCoarse,p,&dof);
3757: PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
3758: if ((dof - cdof) <= 0) continue;
3759: PetscSectionGetOffset(globalCoarse,p,&gOff);
3761: rowOffsets[0] = 0;
3762: offsetsCopy[0] = 0;
3763: if (numFields) {
3764: PetscInt f;
3766: for (f = 0; f < numFields; f++) {
3767: PetscInt fDof;
3768: PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
3769: rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
3770: }
3771: DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,-1,parentIndices);
3772: }
3773: else {
3774: DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,parentIndices);
3775: rowOffsets[1] = offsetsCopy[0];
3776: }
3778: PetscSectionGetDof(multiRootSec,p,&numLeaves);
3779: PetscSectionGetOffset(multiRootSec,p,&leafStart);
3780: leafEnd = leafStart + numLeaves;
3781: for (l = leafStart; l < leafEnd; l++) {
3782: PetscInt numIndices, childId, offset;
3783: const PetscInt *childIndices;
3785: PetscSectionGetDof(rootIndicesSec,l,&numIndices);
3786: PetscSectionGetOffset(rootIndicesSec,l,&offset);
3787: childId = rootIndices[offset++];
3788: childIndices = &rootIndices[offset];
3789: numIndices--;
3791: if (childId == -1) { /* equivalent points: scatter */
3792: PetscInt i;
3794: for (i = 0; i < numIndices; i++) {
3795: PetscInt colIndex = childIndices[i];
3796: PetscInt rowIndex = parentIndices[i];
3797: if (rowIndex < 0) continue;
3798: if (colIndex < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Unconstrained fine and constrained coarse");
3799: if (colIndex >= colStart && colIndex < colEnd) {
3800: nnzD[rowIndex - rowStart] = 1;
3801: }
3802: else {
3803: nnzO[rowIndex - rowStart] = 1;
3804: }
3805: }
3806: }
3807: else {
3808: PetscInt parentId, f, lim;
3810: DMPlexGetTreeParent(refTree,childId,&parentId,NULL);
3812: lim = PetscMax(1,numFields);
3813: offsets[0] = 0;
3814: if (numFields) {
3815: PetscInt f;
3817: for (f = 0; f < numFields; f++) {
3818: PetscInt fDof;
3819: PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);
3821: offsets[f + 1] = fDof + offsets[f];
3822: }
3823: }
3824: else {
3825: PetscInt cDof;
3827: PetscSectionGetDof(cSecRef,childId,&cDof);
3828: offsets[1] = cDof;
3829: }
3830: for (f = 0; f < lim; f++) {
3831: PetscInt parentStart = rowOffsets[f], parentEnd = rowOffsets[f + 1];
3832: PetscInt childStart = offsets[f], childEnd = offsets[f + 1];
3833: PetscInt i, numD = 0, numO = 0;
3835: for (i = childStart; i < childEnd; i++) {
3836: PetscInt colIndex = childIndices[i];
3838: if (colIndex < 0) continue;
3839: if (colIndex >= colStart && colIndex < colEnd) {
3840: numD++;
3841: }
3842: else {
3843: numO++;
3844: }
3845: }
3846: for (i = parentStart; i < parentEnd; i++) {
3847: PetscInt rowIndex = parentIndices[i];
3849: if (rowIndex < 0) continue;
3850: nnzD[rowIndex - rowStart] += numD;
3851: nnzO[rowIndex - rowStart] += numO;
3852: }
3853: }
3854: }
3855: }
3856: }
3857: /* preallocate */
3858: MatXAIJSetPreallocation(mat,1,nnzD,nnzO,NULL,NULL);
3859: PetscFree2(nnzD,nnzO);
3860: /* insert values */
3861: DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);
3862: for (p = pStartC; p < pEndC; p++) {
3863: PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;
3865: PetscSectionGetDof(globalCoarse,p,&dof);
3866: PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
3867: if ((dof - cdof) <= 0) continue;
3868: PetscSectionGetOffset(globalCoarse,p,&gOff);
3870: rowOffsets[0] = 0;
3871: offsetsCopy[0] = 0;
3872: if (numFields) {
3873: PetscInt f;
3875: for (f = 0; f < numFields; f++) {
3876: PetscInt fDof;
3877: PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
3878: rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
3879: }
3880: DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,-1,parentIndices);
3881: }
3882: else {
3883: DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,parentIndices);
3884: rowOffsets[1] = offsetsCopy[0];
3885: }
3887: PetscSectionGetDof(multiRootSec,p,&numLeaves);
3888: PetscSectionGetOffset(multiRootSec,p,&leafStart);
3889: leafEnd = leafStart + numLeaves;
3890: for (l = leafStart; l < leafEnd; l++) {
3891: PetscInt numIndices, childId, offset;
3892: const PetscInt *childIndices;
3894: PetscSectionGetDof(rootIndicesSec,l,&numIndices);
3895: PetscSectionGetOffset(rootIndicesSec,l,&offset);
3896: childId = rootIndices[offset++];
3897: childIndices = &rootIndices[offset];
3898: numIndices--;
3900: if (childId == -1) { /* equivalent points: scatter */
3901: PetscInt i;
3903: for (i = 0; i < numIndices; i++) {
3904: MatSetValue(mat,parentIndices[i],childIndices[i],1.,INSERT_VALUES);
3905: }
3906: }
3907: else {
3908: PetscInt parentId, f, lim;
3910: DMPlexGetTreeParent(refTree,childId,&parentId,NULL);
3912: lim = PetscMax(1,numFields);
3913: offsets[0] = 0;
3914: if (numFields) {
3915: PetscInt f;
3917: for (f = 0; f < numFields; f++) {
3918: PetscInt fDof;
3919: PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);
3921: offsets[f + 1] = fDof + offsets[f];
3922: }
3923: }
3924: else {
3925: PetscInt cDof;
3927: PetscSectionGetDof(cSecRef,childId,&cDof);
3928: offsets[1] = cDof;
3929: }
3930: for (f = 0; f < lim; f++) {
3931: PetscScalar *childMat = &childrenMats[childId - pRefStart][f][0];
3932: PetscInt *rowIndices = &parentIndices[rowOffsets[f]];
3933: const PetscInt *colIndices = &childIndices[offsets[f]];
3935: MatSetValues(mat,rowOffsets[f+1]-rowOffsets[f],rowIndices,offsets[f+1]-offsets[f],colIndices,childMat,INSERT_VALUES);
3936: }
3937: }
3938: }
3939: }
3940: PetscSectionDestroy(&multiRootSec);
3941: PetscSectionDestroy(&rootIndicesSec);
3942: PetscFree(parentIndices);
3943: DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);
3944: PetscFree(rootIndices);
3945: PetscFree3(offsets,offsetsCopy,rowOffsets);
3947: MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
3948: MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
3949: return(0);
3950: }
3952: static PetscErrorCode DMPlexTransferVecTree_Interpolate(DM coarse, Vec vecCoarseLocal, DM fine, Vec vecFine, PetscSF coarseToFine, PetscInt *cids, Vec grad, Vec cellGeom)
3953: {
3954: PetscDS ds;
3955: PetscSF coarseToFineEmbedded;
3956: PetscSection globalCoarse, globalFine;
3957: PetscSection localCoarse, localFine;
3958: PetscSection aSec, cSec;
3959: PetscSection rootValuesSec;
3960: PetscSection leafValuesSec;
3961: PetscScalar *rootValues, *leafValues;
3962: IS aIS;
3963: const PetscInt *anchors;
3964: Mat cMat;
3965: PetscInt numFields;
3966: PetscInt pStartC, pEndC, pStartF, pEndF, p, cellStart, cellEnd, cellEndInterior;
3967: PetscInt aStart, aEnd, cStart, cEnd;
3968: PetscInt *maxChildIds;
3969: PetscInt *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO;
3970: PetscFV fv = NULL;
3971: PetscInt dim, numFVcomps = -1, fvField = -1;
3972: DM cellDM = NULL, gradDM = NULL;
3973: const PetscScalar *cellGeomArray = NULL;
3974: const PetscScalar *gradArray = NULL;
3975: PetscErrorCode ierr;
3978: VecSetOption(vecFine,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);
3979: DMPlexGetChart(coarse,&pStartC,&pEndC);
3980: DMPlexGetHeightStratum(coarse,0,&cellStart,&cellEnd);
3981: DMPlexGetHybridBounds(coarse,&cellEndInterior,NULL,NULL,NULL);
3982: cellEnd = (cellEndInterior < 0) ? cellEnd : cellEndInterior;
3983: DMPlexGetChart(fine,&pStartF,&pEndF);
3984: DMGetDefaultGlobalSection(fine,&globalFine);
3985: DMGetCoordinateDim(coarse,&dim);
3986: { /* winnow fine points that don't have global dofs out of the sf */
3987: PetscInt nleaves, l;
3988: const PetscInt *leaves;
3989: PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs;
3991: PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);
3993: for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) {
3994: PetscInt p = leaves ? leaves[l] : l;
3996: PetscSectionGetDof(globalFine,p,&dof);
3997: PetscSectionGetConstraintDof(globalFine,p,&cdof);
3998: if ((dof - cdof) > 0) {
3999: numPointsWithDofs++;
4000: }
4001: }
4002: PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
4003: for (l = 0, offset = 0; l < nleaves; l++) {
4004: PetscInt p = leaves ? leaves[l] : l;
4006: PetscSectionGetDof(globalFine,p,&dof);
4007: PetscSectionGetConstraintDof(globalFine,p,&cdof);
4008: if ((dof - cdof) > 0) {
4009: pointsWithDofs[offset++] = l;
4010: }
4011: }
4012: PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
4013: PetscFree(pointsWithDofs);
4014: }
4015: /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */
4016: PetscMalloc1(pEndC-pStartC,&maxChildIds);
4017: for (p = pStartC; p < pEndC; p++) {
4018: maxChildIds[p - pStartC] = -2;
4019: }
4020: PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,cids,maxChildIds,MPIU_MAX);
4021: PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,cids,maxChildIds,MPIU_MAX);
4023: DMGetDefaultSection(coarse,&localCoarse);
4024: DMGetDefaultGlobalSection(coarse,&globalCoarse);
4026: DMPlexGetAnchors(coarse,&aSec,&aIS);
4027: ISGetIndices(aIS,&anchors);
4028: PetscSectionGetChart(aSec,&aStart,&aEnd);
4030: DMGetDefaultConstraints(coarse,&cSec,&cMat);
4031: PetscSectionGetChart(cSec,&cStart,&cEnd);
4033: /* create sections that will send to children the indices and matrices they will need to construct the interpolator */
4034: PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootValuesSec);
4035: PetscSectionSetChart(rootValuesSec,pStartC,pEndC);
4036: PetscSectionGetNumFields(localCoarse,&numFields);
4037: {
4038: PetscInt maxFields = PetscMax(1,numFields) + 1;
4039: PetscMalloc7(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&newOffsets,maxFields,&newOffsetsCopy,maxFields,&rowOffsets,maxFields,&numD,maxFields,&numO);
4040: }
4041: if (grad) {
4042: PetscInt i;
4044: VecGetDM(cellGeom,&cellDM);
4045: VecGetArrayRead(cellGeom,&cellGeomArray);
4046: VecGetDM(grad,&gradDM);
4047: VecGetArrayRead(grad,&gradArray);
4048: for (i = 0; i < PetscMax(1,numFields); i++) {
4049: PetscObject obj;
4050: PetscClassId id;
4052: DMGetField(coarse, i, &obj);
4053: PetscObjectGetClassId(obj,&id);
4054: if (id == PETSCFV_CLASSID) {
4055: fv = (PetscFV) obj;
4056: PetscFVGetNumComponents(fv,&numFVcomps);
4057: fvField = i;
4058: break;
4059: }
4060: }
4061: }
4063: for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */
4064: PetscInt dof;
4065: PetscInt maxChildId = maxChildIds[p - pStartC];
4066: PetscInt numValues = 0;
4068: PetscSectionGetDof(globalCoarse,p,&dof);
4069: if (dof < 0) {
4070: dof = -(dof + 1);
4071: }
4072: offsets[0] = 0;
4073: newOffsets[0] = 0;
4074: if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */
4075: PetscInt *closure = NULL, closureSize, cl;
4077: DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
4078: for (cl = 0; cl < closureSize; cl++) { /* get the closure */
4079: PetscInt c = closure[2 * cl], clDof;
4081: PetscSectionGetDof(localCoarse,c,&clDof);
4082: numValues += clDof;
4083: }
4084: DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
4085: }
4086: else if (maxChildId == -1) {
4087: PetscSectionGetDof(localCoarse,p,&numValues);
4088: }
4089: /* we will pack the column indices with the field offsets */
4090: if (maxChildId >= 0 && grad && p >= cellStart && p < cellEnd) {
4091: /* also send the centroid, and the gradient */
4092: numValues += dim * (1 + numFVcomps);
4093: }
4094: PetscSectionSetDof(rootValuesSec,p,numValues);
4095: }
4096: PetscSectionSetUp(rootValuesSec);
4097: {
4098: PetscInt numRootValues;
4099: const PetscScalar *coarseArray;
4101: PetscSectionGetStorageSize(rootValuesSec,&numRootValues);
4102: PetscMalloc1(numRootValues,&rootValues);
4103: VecGetArrayRead(vecCoarseLocal,&coarseArray);
4104: for (p = pStartC; p < pEndC; p++) {
4105: PetscInt numValues;
4106: PetscInt pValOff;
4107: PetscScalar *pVal;
4108: PetscInt maxChildId = maxChildIds[p - pStartC];
4110: PetscSectionGetDof(rootValuesSec,p,&numValues);
4111: if (!numValues) {
4112: continue;
4113: }
4114: PetscSectionGetOffset(rootValuesSec,p,&pValOff);
4115: pVal = &(rootValues[pValOff]);
4116: if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */
4117: PetscInt closureSize = numValues;
4118: DMPlexVecGetClosure(coarse,NULL,vecCoarseLocal,p,&closureSize,&pVal);
4119: if (grad && p >= cellStart && p < cellEnd) {
4120: PetscFVCellGeom *cg;
4121: PetscScalar *gradVals = NULL;
4122: PetscInt i;
4124: pVal += (numValues - dim * (1 + numFVcomps));
4126: DMPlexPointLocalRead(cellDM,p,cellGeomArray,(void *) &cg);
4127: for (i = 0; i < dim; i++) pVal[i] = cg->centroid[i];
4128: pVal += dim;
4129: DMPlexPointGlobalRead(gradDM,p,gradArray,(void *) &gradVals);
4130: for (i = 0; i < dim * numFVcomps; i++) pVal[i] = gradVals[i];
4131: }
4132: }
4133: else if (maxChildId == -1) {
4134: PetscInt lDof, lOff, i;
4136: PetscSectionGetDof(localCoarse,p,&lDof);
4137: PetscSectionGetOffset(localCoarse,p,&lOff);
4138: for (i = 0; i < lDof; i++) pVal[i] = coarseArray[lOff + i];
4139: }
4140: }
4141: VecRestoreArrayRead(vecCoarseLocal,&coarseArray);
4142: PetscFree(maxChildIds);
4143: }
4144: {
4145: PetscSF valuesSF;
4146: PetscInt *remoteOffsetsValues, numLeafValues;
4148: PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafValuesSec);
4149: PetscSFDistributeSection(coarseToFineEmbedded,rootValuesSec,&remoteOffsetsValues,leafValuesSec);
4150: PetscSFCreateSectionSF(coarseToFineEmbedded,rootValuesSec,remoteOffsetsValues,leafValuesSec,&valuesSF);
4151: PetscSFDestroy(&coarseToFineEmbedded);
4152: PetscFree(remoteOffsetsValues);
4153: PetscSectionGetStorageSize(leafValuesSec,&numLeafValues);
4154: PetscMalloc1(numLeafValues,&leafValues);
4155: PetscSFBcastBegin(valuesSF,MPIU_SCALAR,rootValues,leafValues);
4156: PetscSFBcastEnd(valuesSF,MPIU_SCALAR,rootValues,leafValues);
4157: PetscSFDestroy(&valuesSF);
4158: PetscFree(rootValues);
4159: PetscSectionDestroy(&rootValuesSec);
4160: }
4161: DMGetDefaultSection(fine,&localFine);
4162: {
4163: PetscInt maxDof;
4164: PetscInt *rowIndices;
4165: DM refTree;
4166: PetscInt **refPointFieldN;
4167: PetscScalar ***refPointFieldMats;
4168: PetscSection refConSec, refAnSec;
4169: PetscInt pRefStart,pRefEnd,leafStart,leafEnd;
4170: PetscScalar *pointWork;
4172: PetscSectionGetMaxDof(globalFine,&maxDof);
4173: DMGetWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
4174: DMGetWorkArray(fine,maxDof,MPIU_SCALAR,&pointWork);
4175: DMPlexGetReferenceTree(fine,&refTree);
4176: DMGetDS(fine,&ds);
4177: DMSetDS(refTree,ds);
4178: DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
4179: DMGetDefaultConstraints(refTree,&refConSec,NULL);
4180: DMPlexGetAnchors(refTree,&refAnSec,NULL);
4181: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
4182: PetscSectionGetChart(leafValuesSec,&leafStart,&leafEnd);
4183: DMPlexGetHeightStratum(fine,0,&cellStart,&cellEnd);
4184: DMPlexGetHybridBounds(fine,&cellEndInterior,NULL,NULL,NULL);
4185: cellEnd = (cellEndInterior < 0) ? cellEnd : cellEndInterior;
4186: for (p = leafStart; p < leafEnd; p++) {
4187: PetscInt gDof, gcDof, gOff, lDof;
4188: PetscInt numValues, pValOff;
4189: PetscInt childId;
4190: const PetscScalar *pVal;
4191: const PetscScalar *fvGradData = NULL;
4193: PetscSectionGetDof(globalFine,p,&gDof);
4194: PetscSectionGetDof(localFine,p,&lDof);
4195: PetscSectionGetConstraintDof(globalFine,p,&gcDof);
4196: if ((gDof - gcDof) <= 0) {
4197: continue;
4198: }
4199: PetscSectionGetOffset(globalFine,p,&gOff);
4200: PetscSectionGetDof(leafValuesSec,p,&numValues);
4201: if (!numValues) continue;
4202: PetscSectionGetOffset(leafValuesSec,p,&pValOff);
4203: pVal = &leafValues[pValOff];
4204: offsets[0] = 0;
4205: offsetsCopy[0] = 0;
4206: newOffsets[0] = 0;
4207: newOffsetsCopy[0] = 0;
4208: childId = cids[p - pStartF];
4209: if (numFields) {
4210: PetscInt f;
4211: for (f = 0; f < numFields; f++) {
4212: PetscInt rowDof;
4214: PetscSectionGetFieldDof(localFine,p,f,&rowDof);
4215: offsets[f + 1] = offsets[f] + rowDof;
4216: offsetsCopy[f + 1] = offsets[f + 1];
4217: /* TODO: closure indices */
4218: newOffsets[f + 1] = newOffsets[f] + ((childId == -1) ? rowDof : refPointFieldN[childId - pRefStart][f]);
4219: }
4220: DMPlexGetIndicesPointFields_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,-1,rowIndices);
4221: }
4222: else {
4223: offsets[0] = 0;
4224: offsets[1] = lDof;
4225: newOffsets[0] = 0;
4226: newOffsets[1] = (childId == -1) ? lDof : refPointFieldN[childId - pRefStart][0];
4227: DMPlexGetIndicesPoint_Internal(localFine,p,gOff,offsetsCopy,PETSC_FALSE,NULL,rowIndices);
4228: }
4229: if (childId == -1) { /* no child interpolation: one nnz per */
4230: VecSetValues(vecFine,numValues,rowIndices,pVal,INSERT_VALUES);
4231: } else {
4232: PetscInt f;
4234: if (grad && p >= cellStart && p < cellEnd) {
4235: numValues -= (dim * (1 + numFVcomps));
4236: fvGradData = &pVal[numValues];
4237: }
4238: for (f = 0; f < PetscMax(1,numFields); f++) {
4239: const PetscScalar *childMat = refPointFieldMats[childId - pRefStart][f];
4240: PetscInt numRows = offsets[f+1] - offsets[f];
4241: PetscInt numCols = newOffsets[f + 1] - newOffsets[f];
4242: const PetscScalar *cVal = &pVal[newOffsets[f]];
4243: PetscScalar *rVal = &pointWork[offsets[f]];
4244: PetscInt i, j;
4246: #if 0
4247: PetscInfo6(coarse,"field %D, numFields %D, childId %D, numRows %D, numCols %D, refPointFieldN %D\n",f,numFields,childId,numRows,numCols,refPointFieldN[childId - pRefStart][f]);
4248: #endif
4249: for (i = 0; i < numRows; i++) {
4250: PetscScalar val = 0.;
4251: for (j = 0; j < numCols; j++) {
4252: val += childMat[i * numCols + j] * cVal[j];
4253: }
4254: rVal[i] = val;
4255: }
4256: if (f == fvField && p >= cellStart && p < cellEnd) {
4257: PetscReal centroid[3];
4258: PetscScalar diff[3];
4259: const PetscScalar *parentCentroid = &fvGradData[0];
4260: const PetscScalar *gradient = &fvGradData[dim];
4262: DMPlexComputeCellGeometryFVM(fine,p,NULL,centroid,NULL);
4263: for (i = 0; i < dim; i++) {
4264: diff[i] = centroid[i] - parentCentroid[i];
4265: }
4266: for (i = 0; i < numFVcomps; i++) {
4267: PetscScalar val = 0.;
4269: for (j = 0; j < dim; j++) {
4270: val += gradient[dim * i + j] * diff[j];
4271: }
4272: rVal[i] += val;
4273: }
4274: }
4275: VecSetValues(vecFine,numRows,&rowIndices[offsets[f]],rVal,INSERT_VALUES);
4276: }
4277: }
4278: }
4279: DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
4280: DMRestoreWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
4281: DMRestoreWorkArray(fine,maxDof,MPIU_SCALAR,&pointWork);
4282: }
4283: PetscFree(leafValues);
4284: PetscSectionDestroy(&leafValuesSec);
4285: PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);
4286: ISRestoreIndices(aIS,&anchors);
4287: return(0);
4288: }
4290: static PetscErrorCode DMPlexTransferVecTree_Inject(DM fine, Vec vecFine, DM coarse, Vec vecCoarse, PetscSF coarseToFine, PetscInt *cids)
4291: {
4292: PetscDS ds;
4293: DM refTree;
4294: PetscSection multiRootSec, rootIndicesSec;
4295: PetscSection globalCoarse, globalFine;
4296: PetscSection localCoarse, localFine;
4297: PetscSection cSecRef;
4298: PetscInt *parentIndices, pRefStart, pRefEnd;
4299: PetscScalar *rootValues, *parentValues;
4300: Mat injRef;
4301: PetscInt numFields, maxDof;
4302: PetscInt pStartC, pEndC, pStartF, pEndF, p;
4303: PetscInt *offsets, *offsetsCopy, *rowOffsets;
4304: PetscLayout rowMap, colMap;
4305: PetscInt rowStart, rowEnd, colStart, colEnd;
4306: PetscScalar ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */
4311: /* get the templates for the fine-to-coarse injection from the reference tree */
4312: VecSetOption(vecFine,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);
4313: VecSetOption(vecCoarse,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);
4314: DMPlexGetReferenceTree(coarse,&refTree);
4315: DMGetDS(coarse,&ds);
4316: DMSetDS(refTree,ds);
4317: DMGetDefaultConstraints(refTree,&cSecRef,NULL);
4318: PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);
4319: DMPlexReferenceTreeGetInjector(refTree,&injRef);
4321: DMPlexGetChart(fine,&pStartF,&pEndF);
4322: DMGetDefaultSection(fine,&localFine);
4323: DMGetDefaultGlobalSection(fine,&globalFine);
4324: PetscSectionGetNumFields(localFine,&numFields);
4325: DMPlexGetChart(coarse,&pStartC,&pEndC);
4326: DMGetDefaultSection(coarse,&localCoarse);
4327: DMGetDefaultGlobalSection(coarse,&globalCoarse);
4328: PetscSectionGetMaxDof(localCoarse,&maxDof);
4329: {
4330: PetscInt maxFields = PetscMax(1,numFields) + 1;
4331: PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);
4332: }
4334: DMPlexTransferInjectorTree(coarse,fine,coarseToFine,cids,vecFine,numFields,offsets,&multiRootSec,&rootIndicesSec,NULL,&rootValues);
4336: PetscMalloc2(maxDof,&parentIndices,maxDof,&parentValues);
4338: /* count indices */
4339: VecGetLayout(vecFine,&colMap);
4340: VecGetLayout(vecCoarse,&rowMap);
4341: PetscLayoutSetUp(rowMap);
4342: PetscLayoutSetUp(colMap);
4343: PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
4344: PetscLayoutGetRange(colMap,&colStart,&colEnd);
4345: /* insert values */
4346: DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);
4347: for (p = pStartC; p < pEndC; p++) {
4348: PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;
4349: PetscBool contribute = PETSC_FALSE;
4351: PetscSectionGetDof(globalCoarse,p,&dof);
4352: PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
4353: if ((dof - cdof) <= 0) continue;
4354: PetscSectionGetDof(localCoarse,p,&dof);
4355: PetscSectionGetOffset(globalCoarse,p,&gOff);
4357: rowOffsets[0] = 0;
4358: offsetsCopy[0] = 0;
4359: if (numFields) {
4360: PetscInt f;
4362: for (f = 0; f < numFields; f++) {
4363: PetscInt fDof;
4364: PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
4365: rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
4366: }
4367: DMPlexGetIndicesPointFields_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,-1,parentIndices);
4368: }
4369: else {
4370: DMPlexGetIndicesPoint_Internal(localCoarse,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,parentIndices);
4371: rowOffsets[1] = offsetsCopy[0];
4372: }
4374: PetscSectionGetDof(multiRootSec,p,&numLeaves);
4375: PetscSectionGetOffset(multiRootSec,p,&leafStart);
4376: leafEnd = leafStart + numLeaves;
4377: for (l = 0; l < dof; l++) parentValues[l] = 0.;
4378: for (l = leafStart; l < leafEnd; l++) {
4379: PetscInt numIndices, childId, offset;
4380: const PetscScalar *childValues;
4382: PetscSectionGetDof(rootIndicesSec,l,&numIndices);
4383: PetscSectionGetOffset(rootIndicesSec,l,&offset);
4384: childId = (PetscInt) PetscRealPart(rootValues[offset++]);
4385: childValues = &rootValues[offset];
4386: numIndices--;
4388: if (childId == -2) { /* skip */
4389: continue;
4390: } else if (childId == -1) { /* equivalent points: scatter */
4391: PetscInt m;
4393: contribute = PETSC_TRUE;
4394: for (m = 0; m < numIndices; m++) parentValues[m] = childValues[m];
4395: } else { /* contributions from children: sum with injectors from reference tree */
4396: PetscInt parentId, f, lim;
4398: contribute = PETSC_TRUE;
4399: DMPlexGetTreeParent(refTree,childId,&parentId,NULL);
4401: lim = PetscMax(1,numFields);
4402: offsets[0] = 0;
4403: if (numFields) {
4404: PetscInt f;
4406: for (f = 0; f < numFields; f++) {
4407: PetscInt fDof;
4408: PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);
4410: offsets[f + 1] = fDof + offsets[f];
4411: }
4412: }
4413: else {
4414: PetscInt cDof;
4416: PetscSectionGetDof(cSecRef,childId,&cDof);
4417: offsets[1] = cDof;
4418: }
4419: for (f = 0; f < lim; f++) {
4420: PetscScalar *childMat = &childrenMats[childId - pRefStart][f][0];
4421: PetscInt n = offsets[f+1]-offsets[f];
4422: PetscInt m = rowOffsets[f+1]-rowOffsets[f];
4423: PetscInt i, j;
4424: const PetscScalar *colValues = &childValues[offsets[f]];
4426: for (i = 0; i < m; i++) {
4427: PetscScalar val = 0.;
4428: for (j = 0; j < n; j++) {
4429: val += childMat[n * i + j] * colValues[j];
4430: }
4431: parentValues[rowOffsets[f] + i] += val;
4432: }
4433: }
4434: }
4435: }
4436: if (contribute) {VecSetValues(vecCoarse,dof,parentIndices,parentValues,INSERT_VALUES);}
4437: }
4438: PetscSectionDestroy(&multiRootSec);
4439: PetscSectionDestroy(&rootIndicesSec);
4440: PetscFree2(parentIndices,parentValues);
4441: DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);
4442: PetscFree(rootValues);
4443: PetscFree3(offsets,offsetsCopy,rowOffsets);
4444: return(0);
4445: }
4447: /*@
4448: DMPlexTransferVecTree - transfer a vector between two meshes that differ from each other by refinement/coarsening
4449: that can be represented by a common reference tree used by both. This routine can be used for a combination of
4450: coarsening and refinement at the same time.
4452: collective
4454: Input Parameters:
4455: + dmIn - The DMPlex mesh for the input vector
4456: . vecIn - The input vector
4457: . sfRefine - A star forest indicating points in the mesh dmIn (roots in the star forest) that are parents to points in
4458: the mesh dmOut (leaves in the star forest), i.e. where dmOut is more refined than dmIn
4459: . sfCoarsen - A star forest indicating points in the mesh dmOut (roots in the star forest) that are parents to points in
4460: the mesh dmIn (leaves in the star forest), i.e. where dmOut is more coarsened than dmIn
4461: . cidsRefine - The childIds of the points in dmOut. These childIds relate back to the reference tree: childid[j] = k implies
4462: that mesh point j of dmOut was refined from a point in dmIn just as the mesh point k in the reference
4463: tree was refined from its parent. childid[j] = -1 indicates that the point j in dmOut is exactly
4464: equivalent to its root in dmIn, so no interpolation is necessary. childid[j] = -2 indicates that this
4465: point j in dmOut is not a leaf of sfRefine.
4466: . cidsCoarsen - The childIds of the points in dmIn. These childIds relate back to the reference tree: childid[j] = k implies
4467: that mesh point j of dmIn coarsens to a point in dmOut just as the mesh point k in the reference
4468: tree coarsens to its parent. childid[j] = -2 indicates that point j in dmOut is not a leaf in sfCoarsen.
4469: . useBCs - PETSC_TRUE indicates that boundary values should be inserted into vecIn before transfer.
4470: - time - Used if boundary values are time dependent.
4472: Output Parameters:
4473: . vecOut - Using interpolation and injection operators calculated on the reference tree, the transfered
4474: projection of vecIn from dmIn to dmOut. Note that any field discretized with a PetscFV finite volume
4475: method that uses gradient reconstruction will use reconstructed gradients when interpolating from
4476: coarse points to fine points.
4478: Level: developer
4480: .seealso(): DMPlexSetReferenceTree(), DMPlexGetReferenceTree(), PetscFVGetComputeGradients()
4481: @*/
4482: PetscErrorCode DMPlexTransferVecTree(DM dmIn, Vec vecIn, DM dmOut, Vec vecOut, PetscSF sfRefine, PetscSF sfCoarsen, PetscInt *cidsRefine, PetscInt *cidsCoarsen, PetscBool useBCs, PetscReal time)
4483: {
4487: VecSet(vecOut,0.0);
4488: if (sfRefine) {
4489: Vec vecInLocal;
4490: DM dmGrad = NULL;
4491: Vec faceGeom = NULL, cellGeom = NULL, grad = NULL;
4493: DMGetLocalVector(dmIn,&vecInLocal);
4494: VecSet(vecInLocal,0.0);
4495: {
4496: PetscInt numFields, i;
4498: DMGetNumFields(dmIn, &numFields);
4499: for (i = 0; i < numFields; i++) {
4500: PetscObject obj;
4501: PetscClassId classid;
4503: DMGetField(dmIn, i, &obj);
4504: PetscObjectGetClassId(obj, &classid);
4505: if (classid == PETSCFV_CLASSID) {
4506: DMPlexGetDataFVM(dmIn,(PetscFV)obj,&cellGeom,&faceGeom,&dmGrad);
4507: break;
4508: }
4509: }
4510: }
4511: if (useBCs) {
4512: DMPlexInsertBoundaryValues(dmIn,PETSC_TRUE,vecInLocal,time,faceGeom,cellGeom,NULL);
4513: }
4514: DMGlobalToLocalBegin(dmIn,vecIn,INSERT_VALUES,vecInLocal);
4515: DMGlobalToLocalEnd(dmIn,vecIn,INSERT_VALUES,vecInLocal);
4516: if (dmGrad) {
4517: DMGetGlobalVector(dmGrad,&grad);
4518: DMPlexReconstructGradientsFVM(dmIn,vecInLocal,grad);
4519: }
4520: DMPlexTransferVecTree_Interpolate(dmIn,vecInLocal,dmOut,vecOut,sfRefine,cidsRefine,grad,cellGeom);
4521: DMRestoreLocalVector(dmIn,&vecInLocal);
4522: if (dmGrad) {
4523: DMRestoreGlobalVector(dmGrad,&grad);
4524: }
4525: }
4526: if (sfCoarsen) {
4527: DMPlexTransferVecTree_Inject(dmIn,vecIn,dmOut,vecOut,sfCoarsen,cidsCoarsen);
4528: }
4529: VecAssemblyBegin(vecOut);
4530: VecAssemblyEnd(vecOut);
4531: return(0);
4532: }