Actual source code: dmplexsnes.c
petsc-3.11.4 2019-09-28
1: #include <petsc/private/dmpleximpl.h>
2: #include <petsc/private/snesimpl.h>
3: #include <petscds.h>
4: #include <petscblaslapack.h>
5: #include <petsc/private/petscimpl.h>
6: #include <petsc/private/petscfeimpl.h>
8: /************************** Interpolation *******************************/
10: static PetscErrorCode DMSNESConvertPlex(DM dm, DM *plex, PetscBool copy)
11: {
12: PetscBool isPlex;
16: PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);
17: if (isPlex) {
18: *plex = dm;
19: PetscObjectReference((PetscObject) dm);
20: } else {
21: PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);
22: if (!*plex) {
23: DMConvert(dm,DMPLEX,plex);
24: PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);
25: if (copy) {
26: PetscInt i;
27: PetscObject obj;
28: const char *comps[3] = {"A","dmAux","dmCh"};
30: DMCopyDMSNES(dm, *plex);
31: for (i = 0; i < 3; i++) {
32: PetscObjectQuery((PetscObject) dm, comps[i], &obj);
33: PetscObjectCompose((PetscObject) *plex, comps[i], obj);
34: }
35: }
36: } else {
37: PetscObjectReference((PetscObject) *plex);
38: }
39: }
40: return(0);
41: }
43: /*@C
44: DMInterpolationCreate - Creates a DMInterpolationInfo context
46: Collective on comm
48: Input Parameter:
49: . comm - the communicator
51: Output Parameter:
52: . ctx - the context
54: Level: beginner
56: .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationDestroy()
57: @*/
58: PetscErrorCode DMInterpolationCreate(MPI_Comm comm, DMInterpolationInfo *ctx)
59: {
64: PetscNew(ctx);
66: (*ctx)->comm = comm;
67: (*ctx)->dim = -1;
68: (*ctx)->nInput = 0;
69: (*ctx)->points = NULL;
70: (*ctx)->cells = NULL;
71: (*ctx)->n = -1;
72: (*ctx)->coords = NULL;
73: return(0);
74: }
76: /*@C
77: DMInterpolationSetDim - Sets the spatial dimension for the interpolation context
79: Not collective
81: Input Parameters:
82: + ctx - the context
83: - dim - the spatial dimension
85: Level: intermediate
87: .seealso: DMInterpolationGetDim(), DMInterpolationEvaluate(), DMInterpolationAddPoints()
88: @*/
89: PetscErrorCode DMInterpolationSetDim(DMInterpolationInfo ctx, PetscInt dim)
90: {
92: if ((dim < 1) || (dim > 3)) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension for points: %d", dim);
93: ctx->dim = dim;
94: return(0);
95: }
97: /*@C
98: DMInterpolationGetDim - Gets the spatial dimension for the interpolation context
100: Not collective
102: Input Parameter:
103: . ctx - the context
105: Output Parameter:
106: . dim - the spatial dimension
108: Level: intermediate
110: .seealso: DMInterpolationSetDim(), DMInterpolationEvaluate(), DMInterpolationAddPoints()
111: @*/
112: PetscErrorCode DMInterpolationGetDim(DMInterpolationInfo ctx, PetscInt *dim)
113: {
116: *dim = ctx->dim;
117: return(0);
118: }
120: /*@C
121: DMInterpolationSetDof - Sets the number of fields interpolated at a point for the interpolation context
123: Not collective
125: Input Parameters:
126: + ctx - the context
127: - dof - the number of fields
129: Level: intermediate
131: .seealso: DMInterpolationGetDof(), DMInterpolationEvaluate(), DMInterpolationAddPoints()
132: @*/
133: PetscErrorCode DMInterpolationSetDof(DMInterpolationInfo ctx, PetscInt dof)
134: {
136: if (dof < 1) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of components: %d", dof);
137: ctx->dof = dof;
138: return(0);
139: }
141: /*@C
142: DMInterpolationGetDof - Gets the number of fields interpolated at a point for the interpolation context
144: Not collective
146: Input Parameter:
147: . ctx - the context
149: Output Parameter:
150: . dof - the number of fields
152: Level: intermediate
154: .seealso: DMInterpolationSetDof(), DMInterpolationEvaluate(), DMInterpolationAddPoints()
155: @*/
156: PetscErrorCode DMInterpolationGetDof(DMInterpolationInfo ctx, PetscInt *dof)
157: {
160: *dof = ctx->dof;
161: return(0);
162: }
164: /*@C
165: DMInterpolationAddPoints - Add points at which we will interpolate the fields
167: Not collective
169: Input Parameters:
170: + ctx - the context
171: . n - the number of points
172: - points - the coordinates for each point, an array of size n * dim
174: Note: The coordinate information is copied.
176: Level: intermediate
178: .seealso: DMInterpolationSetDim(), DMInterpolationEvaluate(), DMInterpolationCreate()
179: @*/
180: PetscErrorCode DMInterpolationAddPoints(DMInterpolationInfo ctx, PetscInt n, PetscReal points[])
181: {
185: if (ctx->dim < 0) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set");
186: if (ctx->points) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "Cannot add points multiple times yet");
187: ctx->nInput = n;
189: PetscMalloc1(n*ctx->dim, &ctx->points);
190: PetscMemcpy(ctx->points, points, n*ctx->dim * sizeof(PetscReal));
191: return(0);
192: }
194: /*@C
195: DMInterpolationSetUp - Computea spatial indices that add in point location during interpolation
197: Collective on ctx
199: Input Parameters:
200: + ctx - the context
201: . dm - the DM for the function space used for interpolation
202: - redundantPoints - If PETSC_TRUE, all processes are passing in the same array of points. Otherwise, points need to be communicated among processes.
204: Level: intermediate
206: .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate()
207: @*/
208: PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints)
209: {
210: MPI_Comm comm = ctx->comm;
211: PetscScalar *a;
212: PetscInt p, q, i;
213: PetscMPIInt rank, size;
214: PetscErrorCode ierr;
215: Vec pointVec;
216: PetscSF cellSF;
217: PetscLayout layout;
218: PetscReal *globalPoints;
219: PetscScalar *globalPointsScalar;
220: const PetscInt *ranges;
221: PetscMPIInt *counts, *displs;
222: const PetscSFNode *foundCells;
223: const PetscInt *foundPoints;
224: PetscMPIInt *foundProcs, *globalProcs;
225: PetscInt n, N, numFound;
229: MPI_Comm_size(comm, &size);
230: MPI_Comm_rank(comm, &rank);
231: if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set");
232: /* Locate points */
233: n = ctx->nInput;
234: if (!redundantPoints) {
235: PetscLayoutCreate(comm, &layout);
236: PetscLayoutSetBlockSize(layout, 1);
237: PetscLayoutSetLocalSize(layout, n);
238: PetscLayoutSetUp(layout);
239: PetscLayoutGetSize(layout, &N);
240: /* Communicate all points to all processes */
241: PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);
242: PetscLayoutGetRanges(layout, &ranges);
243: for (p = 0; p < size; ++p) {
244: counts[p] = (ranges[p+1] - ranges[p])*ctx->dim;
245: displs[p] = ranges[p]*ctx->dim;
246: }
247: MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);
248: } else {
249: N = n;
250: globalPoints = ctx->points;
251: counts = displs = NULL;
252: layout = NULL;
253: }
254: #if 0
255: PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);
256: /* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */
257: #else
258: #if defined(PETSC_USE_COMPLEX)
259: PetscMalloc1(N*ctx->dim,&globalPointsScalar);
260: for (i=0; i<N*ctx->dim; i++) globalPointsScalar[i] = globalPoints[i];
261: #else
262: globalPointsScalar = globalPoints;
263: #endif
264: VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);
265: PetscMalloc2(N,&foundProcs,N,&globalProcs);
266: for (p = 0; p < N; ++p) {foundProcs[p] = size;}
267: cellSF = NULL;
268: DMLocatePoints(dm, pointVec, DM_POINTLOCATION_REMOVE, &cellSF);
269: PetscSFGetGraph(cellSF,NULL,&numFound,&foundPoints,&foundCells);
270: #endif
271: for (p = 0; p < numFound; ++p) {
272: if (foundCells[p].index >= 0) foundProcs[foundPoints ? foundPoints[p] : p] = rank;
273: }
274: /* Let the lowest rank process own each point */
275: MPIU_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);
276: ctx->n = 0;
277: for (p = 0; p < N; ++p) {
278: if (globalProcs[p] == size) SETERRQ4(comm, PETSC_ERR_PLIB, "Point %d: %g %g %g not located in mesh", p, (double)globalPoints[p*ctx->dim+0], (double)(ctx->dim > 1 ? globalPoints[p*ctx->dim+1] : 0.0), (double)(ctx->dim > 2 ? globalPoints[p*ctx->dim+2] : 0.0));
279: else if (globalProcs[p] == rank) ctx->n++;
280: }
281: /* Create coordinates vector and array of owned cells */
282: PetscMalloc1(ctx->n, &ctx->cells);
283: VecCreate(comm, &ctx->coords);
284: VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);
285: VecSetBlockSize(ctx->coords, ctx->dim);
286: VecSetType(ctx->coords,VECSTANDARD);
287: VecGetArray(ctx->coords, &a);
288: for (p = 0, q = 0, i = 0; p < N; ++p) {
289: if (globalProcs[p] == rank) {
290: PetscInt d;
292: for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d];
293: ctx->cells[q] = foundCells[q].index;
294: ++q;
295: }
296: }
297: VecRestoreArray(ctx->coords, &a);
298: #if 0
299: PetscFree3(foundCells,foundProcs,globalProcs);
300: #else
301: PetscFree2(foundProcs,globalProcs);
302: PetscSFDestroy(&cellSF);
303: VecDestroy(&pointVec);
304: #endif
305: if ((void*)globalPointsScalar != (void*)globalPoints) {PetscFree(globalPointsScalar);}
306: if (!redundantPoints) {PetscFree3(globalPoints,counts,displs);}
307: PetscLayoutDestroy(&layout);
308: return(0);
309: }
311: /*@C
312: DMInterpolationGetCoordinates - Gets a Vec with the coordinates of each interpolation point
314: Collective on ctx
316: Input Parameter:
317: . ctx - the context
319: Output Parameter:
320: . coordinates - the coordinates of interpolation points
322: Note: The local vector entries correspond to interpolation points lying on this process, according to the associated DM. This is a borrowed vector that the user should not destroy.
324: Level: intermediate
326: .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate()
327: @*/
328: PetscErrorCode DMInterpolationGetCoordinates(DMInterpolationInfo ctx, Vec *coordinates)
329: {
332: if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup.");
333: *coordinates = ctx->coords;
334: return(0);
335: }
337: /*@C
338: DMInterpolationGetVector - Gets a Vec which can hold all the interpolated field values
340: Collective on ctx
342: Input Parameter:
343: . ctx - the context
345: Output Parameter:
346: . v - a vector capable of holding the interpolated field values
348: Note: This vector should be returned using DMInterpolationRestoreVector().
350: Level: intermediate
352: .seealso: DMInterpolationRestoreVector(), DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate()
353: @*/
354: PetscErrorCode DMInterpolationGetVector(DMInterpolationInfo ctx, Vec *v)
355: {
360: if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup.");
361: VecCreate(ctx->comm, v);
362: VecSetSizes(*v, ctx->n*ctx->dof, PETSC_DECIDE);
363: VecSetBlockSize(*v, ctx->dof);
364: VecSetType(*v,VECSTANDARD);
365: return(0);
366: }
368: /*@C
369: DMInterpolationRestoreVector - Returns a Vec which can hold all the interpolated field values
371: Collective on ctx
373: Input Parameters:
374: + ctx - the context
375: - v - a vector capable of holding the interpolated field values
377: Level: intermediate
379: .seealso: DMInterpolationGetVector(), DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate()
380: @*/
381: PetscErrorCode DMInterpolationRestoreVector(DMInterpolationInfo ctx, Vec *v)
382: {
387: if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup.");
388: VecDestroy(v);
389: return(0);
390: }
392: PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Triangle_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v)
393: {
394: PetscReal *v0, *J, *invJ, detJ;
395: const PetscScalar *coords;
396: PetscScalar *a;
397: PetscInt p;
401: PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);
402: VecGetArrayRead(ctx->coords, &coords);
403: VecGetArray(v, &a);
404: for (p = 0; p < ctx->n; ++p) {
405: PetscInt c = ctx->cells[p];
406: PetscScalar *x = NULL;
407: PetscReal xi[4];
408: PetscInt d, f, comp;
410: DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);
411: if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", (double)detJ, c);
412: DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);
413: for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp];
415: for (d = 0; d < ctx->dim; ++d) {
416: xi[d] = 0.0;
417: for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]);
418: for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[(d+1)*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d];
419: }
420: DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);
421: }
422: VecRestoreArray(v, &a);
423: VecRestoreArrayRead(ctx->coords, &coords);
424: PetscFree3(v0, J, invJ);
425: return(0);
426: }
428: PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Tetrahedron_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v)
429: {
430: PetscReal *v0, *J, *invJ, detJ;
431: const PetscScalar *coords;
432: PetscScalar *a;
433: PetscInt p;
437: PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);
438: VecGetArrayRead(ctx->coords, &coords);
439: VecGetArray(v, &a);
440: for (p = 0; p < ctx->n; ++p) {
441: PetscInt c = ctx->cells[p];
442: const PetscInt order[3] = {2, 1, 3};
443: PetscScalar *x = NULL;
444: PetscReal xi[4];
445: PetscInt d, f, comp;
447: DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);
448: if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", (double)detJ, c);
449: DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);
450: for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp];
452: for (d = 0; d < ctx->dim; ++d) {
453: xi[d] = 0.0;
454: for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]);
455: for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[order[d]*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d];
456: }
457: DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);
458: }
459: VecRestoreArray(v, &a);
460: VecRestoreArrayRead(ctx->coords, &coords);
461: PetscFree3(v0, J, invJ);
462: return(0);
463: }
465: PETSC_STATIC_INLINE PetscErrorCode QuadMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx)
466: {
467: const PetscScalar *vertices = (const PetscScalar*) ctx;
468: const PetscScalar x0 = vertices[0];
469: const PetscScalar y0 = vertices[1];
470: const PetscScalar x1 = vertices[2];
471: const PetscScalar y1 = vertices[3];
472: const PetscScalar x2 = vertices[4];
473: const PetscScalar y2 = vertices[5];
474: const PetscScalar x3 = vertices[6];
475: const PetscScalar y3 = vertices[7];
476: const PetscScalar f_1 = x1 - x0;
477: const PetscScalar g_1 = y1 - y0;
478: const PetscScalar f_3 = x3 - x0;
479: const PetscScalar g_3 = y3 - y0;
480: const PetscScalar f_01 = x2 - x1 - x3 + x0;
481: const PetscScalar g_01 = y2 - y1 - y3 + y0;
482: const PetscScalar *ref;
483: PetscScalar *real;
484: PetscErrorCode ierr;
487: VecGetArrayRead(Xref, &ref);
488: VecGetArray(Xreal, &real);
489: {
490: const PetscScalar p0 = ref[0];
491: const PetscScalar p1 = ref[1];
493: real[0] = x0 + f_1 * p0 + f_3 * p1 + f_01 * p0 * p1;
494: real[1] = y0 + g_1 * p0 + g_3 * p1 + g_01 * p0 * p1;
495: }
496: PetscLogFlops(28);
497: VecRestoreArrayRead(Xref, &ref);
498: VecRestoreArray(Xreal, &real);
499: return(0);
500: }
502: #include <petsc/private/dmimpl.h>
503: PETSC_STATIC_INLINE PetscErrorCode QuadJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx)
504: {
505: const PetscScalar *vertices = (const PetscScalar*) ctx;
506: const PetscScalar x0 = vertices[0];
507: const PetscScalar y0 = vertices[1];
508: const PetscScalar x1 = vertices[2];
509: const PetscScalar y1 = vertices[3];
510: const PetscScalar x2 = vertices[4];
511: const PetscScalar y2 = vertices[5];
512: const PetscScalar x3 = vertices[6];
513: const PetscScalar y3 = vertices[7];
514: const PetscScalar f_01 = x2 - x1 - x3 + x0;
515: const PetscScalar g_01 = y2 - y1 - y3 + y0;
516: const PetscScalar *ref;
517: PetscErrorCode ierr;
520: VecGetArrayRead(Xref, &ref);
521: {
522: const PetscScalar x = ref[0];
523: const PetscScalar y = ref[1];
524: const PetscInt rows[2] = {0, 1};
525: PetscScalar values[4];
527: values[0] = (x1 - x0 + f_01*y) * 0.5; values[1] = (x3 - x0 + f_01*x) * 0.5;
528: values[2] = (y1 - y0 + g_01*y) * 0.5; values[3] = (y3 - y0 + g_01*x) * 0.5;
529: MatSetValues(J, 2, rows, 2, rows, values, INSERT_VALUES);
530: }
531: PetscLogFlops(30);
532: VecRestoreArrayRead(Xref, &ref);
533: MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);
534: MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);
535: return(0);
536: }
538: PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Quad_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v)
539: {
540: DM dmCoord;
541: PetscFE fem = NULL;
542: SNES snes;
543: KSP ksp;
544: PC pc;
545: Vec coordsLocal, r, ref, real;
546: Mat J;
547: const PetscScalar *coords;
548: PetscScalar *a;
549: PetscInt Nf, p;
550: const PetscInt dof = ctx->dof;
554: DMGetNumFields(dm, &Nf);
555: if (Nf) {DMGetField(dm, 0, NULL, (PetscObject *) &fem);}
556: DMGetCoordinatesLocal(dm, &coordsLocal);
557: DMGetCoordinateDM(dm, &dmCoord);
558: SNESCreate(PETSC_COMM_SELF, &snes);
559: SNESSetOptionsPrefix(snes, "quad_interp_");
560: VecCreate(PETSC_COMM_SELF, &r);
561: VecSetSizes(r, 2, 2);
562: VecSetType(r,dm->vectype);
563: VecDuplicate(r, &ref);
564: VecDuplicate(r, &real);
565: MatCreate(PETSC_COMM_SELF, &J);
566: MatSetSizes(J, 2, 2, 2, 2);
567: MatSetType(J, MATSEQDENSE);
568: MatSetUp(J);
569: SNESSetFunction(snes, r, QuadMap_Private, NULL);
570: SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);
571: SNESGetKSP(snes, &ksp);
572: KSPGetPC(ksp, &pc);
573: PCSetType(pc, PCLU);
574: SNESSetFromOptions(snes);
576: VecGetArrayRead(ctx->coords, &coords);
577: VecGetArray(v, &a);
578: for (p = 0; p < ctx->n; ++p) {
579: PetscScalar *x = NULL, *vertices = NULL;
580: PetscScalar *xi;
581: PetscReal xir[2];
582: PetscInt c = ctx->cells[p], comp, coordSize, xSize;
584: /* Can make this do all points at once */
585: DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);
586: if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 4*2);
587: DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);
588: SNESSetFunction(snes, NULL, NULL, (void*) vertices);
589: SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);
590: VecGetArray(real, &xi);
591: xi[0] = coords[p*ctx->dim+0];
592: xi[1] = coords[p*ctx->dim+1];
593: VecRestoreArray(real, &xi);
594: SNESSolve(snes, real, ref);
595: VecGetArray(ref, &xi);
596: xir[0] = PetscRealPart(xi[0]);
597: xir[1] = PetscRealPart(xi[1]);
598: if (4*dof != xSize) {
599: PetscReal *B;
600: PetscInt d;
602: xir[0] = 2.0*xir[0] - 1.0; xir[1] = 2.0*xir[1] - 1.0;
603: PetscFEGetTabulation(fem, 1, xir, &B, NULL, NULL);
604: for (comp = 0; comp < dof; ++comp) {
605: a[p*dof+comp] = 0.0;
606: for (d = 0; d < xSize/dof; ++d) {
607: a[p*dof+comp] += x[d*dof+comp]*B[d*dof+comp];
608: }
609: }
610: PetscFERestoreTabulation(fem, 1, xir, &B, NULL, NULL);
611: } else {
612: for (comp = 0; comp < dof; ++comp)
613: a[p*dof+comp] = x[0*dof+comp]*(1 - xir[0])*(1 - xir[1]) + x[1*dof+comp]*xir[0]*(1 - xir[1]) + x[2*dof+comp]*xir[0]*xir[1] + x[3*dof+comp]*(1 - xir[0])*xir[1];
614: }
615: VecRestoreArray(ref, &xi);
616: DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);
617: DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);
618: }
619: VecRestoreArray(v, &a);
620: VecRestoreArrayRead(ctx->coords, &coords);
622: SNESDestroy(&snes);
623: VecDestroy(&r);
624: VecDestroy(&ref);
625: VecDestroy(&real);
626: MatDestroy(&J);
627: return(0);
628: }
630: PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx)
631: {
632: const PetscScalar *vertices = (const PetscScalar*) ctx;
633: const PetscScalar x0 = vertices[0];
634: const PetscScalar y0 = vertices[1];
635: const PetscScalar z0 = vertices[2];
636: const PetscScalar x1 = vertices[9];
637: const PetscScalar y1 = vertices[10];
638: const PetscScalar z1 = vertices[11];
639: const PetscScalar x2 = vertices[6];
640: const PetscScalar y2 = vertices[7];
641: const PetscScalar z2 = vertices[8];
642: const PetscScalar x3 = vertices[3];
643: const PetscScalar y3 = vertices[4];
644: const PetscScalar z3 = vertices[5];
645: const PetscScalar x4 = vertices[12];
646: const PetscScalar y4 = vertices[13];
647: const PetscScalar z4 = vertices[14];
648: const PetscScalar x5 = vertices[15];
649: const PetscScalar y5 = vertices[16];
650: const PetscScalar z5 = vertices[17];
651: const PetscScalar x6 = vertices[18];
652: const PetscScalar y6 = vertices[19];
653: const PetscScalar z6 = vertices[20];
654: const PetscScalar x7 = vertices[21];
655: const PetscScalar y7 = vertices[22];
656: const PetscScalar z7 = vertices[23];
657: const PetscScalar f_1 = x1 - x0;
658: const PetscScalar g_1 = y1 - y0;
659: const PetscScalar h_1 = z1 - z0;
660: const PetscScalar f_3 = x3 - x0;
661: const PetscScalar g_3 = y3 - y0;
662: const PetscScalar h_3 = z3 - z0;
663: const PetscScalar f_4 = x4 - x0;
664: const PetscScalar g_4 = y4 - y0;
665: const PetscScalar h_4 = z4 - z0;
666: const PetscScalar f_01 = x2 - x1 - x3 + x0;
667: const PetscScalar g_01 = y2 - y1 - y3 + y0;
668: const PetscScalar h_01 = z2 - z1 - z3 + z0;
669: const PetscScalar f_12 = x7 - x3 - x4 + x0;
670: const PetscScalar g_12 = y7 - y3 - y4 + y0;
671: const PetscScalar h_12 = z7 - z3 - z4 + z0;
672: const PetscScalar f_02 = x5 - x1 - x4 + x0;
673: const PetscScalar g_02 = y5 - y1 - y4 + y0;
674: const PetscScalar h_02 = z5 - z1 - z4 + z0;
675: const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7;
676: const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7;
677: const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7;
678: const PetscScalar *ref;
679: PetscScalar *real;
680: PetscErrorCode ierr;
683: VecGetArrayRead(Xref, &ref);
684: VecGetArray(Xreal, &real);
685: {
686: const PetscScalar p0 = ref[0];
687: const PetscScalar p1 = ref[1];
688: const PetscScalar p2 = ref[2];
690: real[0] = x0 + f_1*p0 + f_3*p1 + f_4*p2 + f_01*p0*p1 + f_12*p1*p2 + f_02*p0*p2 + f_012*p0*p1*p2;
691: real[1] = y0 + g_1*p0 + g_3*p1 + g_4*p2 + g_01*p0*p1 + g_01*p0*p1 + g_12*p1*p2 + g_02*p0*p2 + g_012*p0*p1*p2;
692: real[2] = z0 + h_1*p0 + h_3*p1 + h_4*p2 + h_01*p0*p1 + h_01*p0*p1 + h_12*p1*p2 + h_02*p0*p2 + h_012*p0*p1*p2;
693: }
694: PetscLogFlops(114);
695: VecRestoreArrayRead(Xref, &ref);
696: VecRestoreArray(Xreal, &real);
697: return(0);
698: }
700: PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx)
701: {
702: const PetscScalar *vertices = (const PetscScalar*) ctx;
703: const PetscScalar x0 = vertices[0];
704: const PetscScalar y0 = vertices[1];
705: const PetscScalar z0 = vertices[2];
706: const PetscScalar x1 = vertices[9];
707: const PetscScalar y1 = vertices[10];
708: const PetscScalar z1 = vertices[11];
709: const PetscScalar x2 = vertices[6];
710: const PetscScalar y2 = vertices[7];
711: const PetscScalar z2 = vertices[8];
712: const PetscScalar x3 = vertices[3];
713: const PetscScalar y3 = vertices[4];
714: const PetscScalar z3 = vertices[5];
715: const PetscScalar x4 = vertices[12];
716: const PetscScalar y4 = vertices[13];
717: const PetscScalar z4 = vertices[14];
718: const PetscScalar x5 = vertices[15];
719: const PetscScalar y5 = vertices[16];
720: const PetscScalar z5 = vertices[17];
721: const PetscScalar x6 = vertices[18];
722: const PetscScalar y6 = vertices[19];
723: const PetscScalar z6 = vertices[20];
724: const PetscScalar x7 = vertices[21];
725: const PetscScalar y7 = vertices[22];
726: const PetscScalar z7 = vertices[23];
727: const PetscScalar f_xy = x2 - x1 - x3 + x0;
728: const PetscScalar g_xy = y2 - y1 - y3 + y0;
729: const PetscScalar h_xy = z2 - z1 - z3 + z0;
730: const PetscScalar f_yz = x7 - x3 - x4 + x0;
731: const PetscScalar g_yz = y7 - y3 - y4 + y0;
732: const PetscScalar h_yz = z7 - z3 - z4 + z0;
733: const PetscScalar f_xz = x5 - x1 - x4 + x0;
734: const PetscScalar g_xz = y5 - y1 - y4 + y0;
735: const PetscScalar h_xz = z5 - z1 - z4 + z0;
736: const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7;
737: const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7;
738: const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7;
739: const PetscScalar *ref;
740: PetscErrorCode ierr;
743: VecGetArrayRead(Xref, &ref);
744: {
745: const PetscScalar x = ref[0];
746: const PetscScalar y = ref[1];
747: const PetscScalar z = ref[2];
748: const PetscInt rows[3] = {0, 1, 2};
749: PetscScalar values[9];
751: values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0;
752: values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0;
753: values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0;
754: values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0;
755: values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0;
756: values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0;
757: values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0;
758: values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0;
759: values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0;
761: MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);
762: }
763: PetscLogFlops(152);
764: VecRestoreArrayRead(Xref, &ref);
765: MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);
766: MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);
767: return(0);
768: }
770: PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v)
771: {
772: DM dmCoord;
773: SNES snes;
774: KSP ksp;
775: PC pc;
776: Vec coordsLocal, r, ref, real;
777: Mat J;
778: const PetscScalar *coords;
779: PetscScalar *a;
780: PetscInt p;
784: DMGetCoordinatesLocal(dm, &coordsLocal);
785: DMGetCoordinateDM(dm, &dmCoord);
786: SNESCreate(PETSC_COMM_SELF, &snes);
787: SNESSetOptionsPrefix(snes, "hex_interp_");
788: VecCreate(PETSC_COMM_SELF, &r);
789: VecSetSizes(r, 3, 3);
790: VecSetType(r,dm->vectype);
791: VecDuplicate(r, &ref);
792: VecDuplicate(r, &real);
793: MatCreate(PETSC_COMM_SELF, &J);
794: MatSetSizes(J, 3, 3, 3, 3);
795: MatSetType(J, MATSEQDENSE);
796: MatSetUp(J);
797: SNESSetFunction(snes, r, HexMap_Private, NULL);
798: SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);
799: SNESGetKSP(snes, &ksp);
800: KSPGetPC(ksp, &pc);
801: PCSetType(pc, PCLU);
802: SNESSetFromOptions(snes);
804: VecGetArrayRead(ctx->coords, &coords);
805: VecGetArray(v, &a);
806: for (p = 0; p < ctx->n; ++p) {
807: PetscScalar *x = NULL, *vertices = NULL;
808: PetscScalar *xi;
809: PetscReal xir[3];
810: PetscInt c = ctx->cells[p], comp, coordSize, xSize;
812: /* Can make this do all points at once */
813: DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);
814: if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 8*3);
815: DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);
816: if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 8*ctx->dof);
817: SNESSetFunction(snes, NULL, NULL, (void*) vertices);
818: SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);
819: VecGetArray(real, &xi);
820: xi[0] = coords[p*ctx->dim+0];
821: xi[1] = coords[p*ctx->dim+1];
822: xi[2] = coords[p*ctx->dim+2];
823: VecRestoreArray(real, &xi);
824: SNESSolve(snes, real, ref);
825: VecGetArray(ref, &xi);
826: xir[0] = PetscRealPart(xi[0]);
827: xir[1] = PetscRealPart(xi[1]);
828: xir[2] = PetscRealPart(xi[2]);
829: for (comp = 0; comp < ctx->dof; ++comp) {
830: a[p*ctx->dof+comp] =
831: x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) +
832: x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) +
833: x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) +
834: x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) +
835: x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] +
836: x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] +
837: x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] +
838: x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2];
839: }
840: VecRestoreArray(ref, &xi);
841: DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);
842: DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);
843: }
844: VecRestoreArray(v, &a);
845: VecRestoreArrayRead(ctx->coords, &coords);
847: SNESDestroy(&snes);
848: VecDestroy(&r);
849: VecDestroy(&ref);
850: VecDestroy(&real);
851: MatDestroy(&J);
852: return(0);
853: }
855: /*@C
856: DMInterpolationEvaluate - Using the input from dm and x, calculates interpolated field values at the interpolation points.
858: Input Parameters:
859: + ctx - The DMInterpolationInfo context
860: . dm - The DM
861: - x - The local vector containing the field to be interpolated
863: Output Parameters:
864: . v - The vector containing the interpolated values
866: Note: A suitable v can be obtained using DMInterpolationGetVector().
868: Level: beginner
870: .seealso: DMInterpolationGetVector(), DMInterpolationAddPoints(), DMInterpolationCreate()
871: @*/
872: PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v)
873: {
874: PetscInt dim, coneSize, n;
881: VecGetLocalSize(v, &n);
882: if (n != ctx->n*ctx->dof) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid input vector size %d should be %d", n, ctx->n*ctx->dof);
883: if (n) {
884: DMGetDimension(dm, &dim);
885: DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);
886: if (dim == 2) {
887: if (coneSize == 3) {
888: DMInterpolate_Triangle_Private(ctx, dm, x, v);
889: } else if (coneSize == 4) {
890: DMInterpolate_Quad_Private(ctx, dm, x, v);
891: } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim);
892: } else if (dim == 3) {
893: if (coneSize == 4) {
894: DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);
895: } else {
896: DMInterpolate_Hex_Private(ctx, dm, x, v);
897: }
898: } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim);
899: }
900: return(0);
901: }
903: /*@C
904: DMInterpolationDestroy - Destroys a DMInterpolationInfo context
906: Collective on ctx
908: Input Parameter:
909: . ctx - the context
911: Level: beginner
913: .seealso: DMInterpolationEvaluate(), DMInterpolationAddPoints(), DMInterpolationCreate()
914: @*/
915: PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx)
916: {
921: VecDestroy(&(*ctx)->coords);
922: PetscFree((*ctx)->points);
923: PetscFree((*ctx)->cells);
924: PetscFree(*ctx);
925: *ctx = NULL;
926: return(0);
927: }
929: /*@C
930: SNESMonitorFields - Monitors the residual for each field separately
932: Collective on SNES
934: Input Parameters:
935: + snes - the SNES context
936: . its - iteration number
937: . fgnorm - 2-norm of residual
938: - vf - PetscViewerAndFormat of type ASCII
940: Notes:
941: This routine prints the residual norm at each iteration.
943: Level: intermediate
945: .keywords: SNES, nonlinear, default, monitor, norm
946: .seealso: SNESMonitorSet(), SNESMonitorDefault()
947: @*/
948: PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, PetscViewerAndFormat *vf)
949: {
950: PetscViewer viewer = vf->viewer;
951: Vec res;
952: DM dm;
953: PetscSection s;
954: const PetscScalar *r;
955: PetscReal *lnorms, *norms;
956: PetscInt numFields, f, pStart, pEnd, p;
957: PetscErrorCode ierr;
961: SNESGetFunction(snes, &res, 0, 0);
962: SNESGetDM(snes, &dm);
963: DMGetSection(dm, &s);
964: PetscSectionGetNumFields(s, &numFields);
965: PetscSectionGetChart(s, &pStart, &pEnd);
966: PetscCalloc2(numFields, &lnorms, numFields, &norms);
967: VecGetArrayRead(res, &r);
968: for (p = pStart; p < pEnd; ++p) {
969: for (f = 0; f < numFields; ++f) {
970: PetscInt fdof, foff, d;
972: PetscSectionGetFieldDof(s, p, f, &fdof);
973: PetscSectionGetFieldOffset(s, p, f, &foff);
974: for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d]));
975: }
976: }
977: VecRestoreArrayRead(res, &r);
978: MPIU_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject) dm));
979: PetscViewerPushFormat(viewer,vf->format);
980: PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);
981: PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);
982: for (f = 0; f < numFields; ++f) {
983: if (f > 0) {PetscViewerASCIIPrintf(viewer, ", ");}
984: PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));
985: }
986: PetscViewerASCIIPrintf(viewer, "]\n");
987: PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);
988: PetscViewerPopFormat(viewer);
989: PetscFree2(lnorms, norms);
990: return(0);
991: }
993: /********************* Residual Computation **************************/
996: /*@
997: DMPlexSNESGetGeometryFVM - Return precomputed geometric data
999: Input Parameter:
1000: . dm - The DM
1002: Output Parameters:
1003: + facegeom - The values precomputed from face geometry
1004: . cellgeom - The values precomputed from cell geometry
1005: - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell
1007: Level: developer
1009: .seealso: DMPlexTSSetRHSFunctionLocal()
1010: @*/
1011: PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius)
1012: {
1013: DM plex;
1018: DMSNESConvertPlex(dm,&plex,PETSC_TRUE);
1019: DMPlexGetDataFVM(plex, NULL, cellgeom, facegeom, NULL);
1020: if (minRadius) {DMPlexGetMinRadius(plex, minRadius);}
1021: DMDestroy(&plex);
1022: return(0);
1023: }
1025: /*@
1026: DMPlexSNESGetGradientDM - Return gradient data layout
1028: Input Parameters:
1029: + dm - The DM
1030: - fv - The PetscFV
1032: Output Parameter:
1033: . dmGrad - The layout for gradient values
1035: Level: developer
1037: .seealso: DMPlexSNESGetGeometryFVM()
1038: @*/
1039: PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad)
1040: {
1041: DM plex;
1042: PetscBool computeGradients;
1049: PetscFVGetComputeGradients(fv, &computeGradients);
1050: if (!computeGradients) {*dmGrad = NULL; return(0);}
1051: DMSNESConvertPlex(dm,&plex,PETSC_TRUE);
1052: DMPlexGetDataFVM(plex, fv, NULL, NULL, dmGrad);
1053: DMDestroy(&plex);
1054: return(0);
1055: }
1057: static PetscErrorCode DMPlexComputeBdResidual_Single_Internal(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF, DMField coordField, IS facetIS)
1058: {
1059: DM_Plex *mesh = (DM_Plex *) dm->data;
1060: DM plex = NULL, plexA = NULL;
1061: PetscDS prob, probAux = NULL;
1062: PetscSection section, sectionAux = NULL;
1063: Vec locA = NULL;
1064: PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL;
1065: PetscInt v;
1066: PetscInt totDim, totDimAux = 0;
1067: PetscErrorCode ierr;
1070: DMConvert(dm, DMPLEX, &plex);
1071: DMGetSection(dm, §ion);
1072: DMGetDS(dm, &prob);
1073: PetscDSGetTotalDimension(prob, &totDim);
1074: PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
1075: if (locA) {
1076: DM dmAux;
1078: VecGetDM(locA, &dmAux);
1079: DMConvert(dmAux, DMPLEX, &plexA);
1080: DMGetDS(plexA, &probAux);
1081: PetscDSGetTotalDimension(probAux, &totDimAux);
1082: DMGetSection(plexA, §ionAux);
1083: }
1084: for (v = 0; v < numValues; ++v) {
1085: PetscFEGeom *fgeom;
1086: PetscInt maxDegree;
1087: PetscQuadrature qGeom = NULL;
1088: IS pointIS;
1089: const PetscInt *points;
1090: PetscInt numFaces, face, Nq;
1092: DMLabelGetStratumIS(label, values[v], &pointIS);
1093: if (!pointIS) continue; /* No points with that id on this process */
1094: {
1095: IS isectIS;
1097: /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */
1098: ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);
1099: ISDestroy(&pointIS);
1100: pointIS = isectIS;
1101: }
1102: ISGetLocalSize(pointIS,&numFaces);
1103: ISGetIndices(pointIS,&points);
1104: PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);
1105: DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);
1106: if (maxDegree <= 1) {
1107: DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);
1108: }
1109: if (!qGeom) {
1110: PetscFE fe;
1112: PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);
1113: PetscFEGetFaceQuadrature(fe, &qGeom);
1114: PetscObjectReference((PetscObject)qGeom);
1115: }
1116: PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
1117: DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
1118: for (face = 0; face < numFaces; ++face) {
1119: const PetscInt point = points[face], *support, *cone;
1120: PetscScalar *x = NULL;
1121: PetscInt i, coneSize, faceLoc;
1123: DMPlexGetSupport(dm, point, &support);
1124: DMPlexGetConeSize(dm, support[0], &coneSize);
1125: DMPlexGetCone(dm, support[0], &cone);
1126: for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break;
1127: if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]);
1128: fgeom->face[face][0] = faceLoc;
1129: DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);
1130: for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i];
1131: DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);
1132: if (locX_t) {
1133: DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);
1134: for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i];
1135: DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);
1136: }
1137: if (locA) {
1138: PetscInt subp;
1140: DMPlexGetAuxiliaryPoint(plex, plexA, support[0], &subp);
1141: DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);
1142: for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i];
1143: DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);
1144: }
1145: }
1146: PetscMemzero(elemVec, numFaces*totDim * sizeof(PetscScalar));
1147: {
1148: PetscFE fe;
1149: PetscInt Nb;
1150: PetscFEGeom *chunkGeom = NULL;
1151: /* Conforming batches */
1152: PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
1153: /* Remainder */
1154: PetscInt Nr, offset;
1156: PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);
1157: PetscFEGetDimension(fe, &Nb);
1158: PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
1159: /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */
1160: blockSize = Nb;
1161: batchSize = numBlocks * blockSize;
1162: PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
1163: numChunks = numFaces / (numBatches*batchSize);
1164: Ne = numChunks*numBatches*batchSize;
1165: Nr = numFaces % (numBatches*batchSize);
1166: offset = numFaces - Nr;
1167: PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);
1168: PetscFEIntegrateBdResidual(fe, prob, field, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);
1169: PetscFEGeomRestoreChunk(fgeom, 0, offset, &chunkGeom);
1170: PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);
1171: PetscFEIntegrateBdResidual(fe, prob, field, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, &elemVec[offset*totDim]);
1172: PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);
1173: }
1174: for (face = 0; face < numFaces; ++face) {
1175: const PetscInt point = points[face], *support;
1177: if (mesh->printFEM > 1) {DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);}
1178: DMPlexGetSupport(plex, point, &support);
1179: DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);
1180: }
1181: DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
1182: PetscQuadratureDestroy(&qGeom);
1183: ISRestoreIndices(pointIS, &points);
1184: ISDestroy(&pointIS);
1185: PetscFree4(u, u_t, elemVec, a);
1186: }
1187: if (plex) {DMDestroy(&plex);}
1188: if (plexA) {DMDestroy(&plexA);}
1189: return(0);
1190: }
1192: PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF)
1193: {
1194: DMField coordField;
1195: DMLabel depthLabel;
1196: IS facetIS;
1197: PetscInt dim;
1201: DMGetDimension(dm, &dim);
1202: DMPlexGetDepthLabel(dm, &depthLabel);
1203: DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
1204: DMGetCoordinateField(dm, &coordField);
1205: DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);
1206: return(0);
1207: }
1209: PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user)
1210: {
1211: PetscDS prob;
1212: PetscInt numBd, bd;
1213: DMField coordField = NULL;
1214: IS facetIS = NULL;
1215: DMLabel depthLabel;
1216: PetscInt dim;
1220: DMGetDS(dm, &prob);
1221: DMPlexGetDepthLabel(dm, &depthLabel);
1222: DMGetDimension(dm, &dim);
1223: DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);
1224: PetscDSGetNumBoundary(prob, &numBd);
1225: for (bd = 0; bd < numBd; ++bd) {
1226: DMBoundaryConditionType type;
1227: const char *bdLabel;
1228: DMLabel label;
1229: const PetscInt *values;
1230: PetscInt field, numValues;
1231: PetscObject obj;
1232: PetscClassId id;
1234: PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);
1235: PetscDSGetDiscretization(prob, field, &obj);
1236: PetscObjectGetClassId(obj, &id);
1237: if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue;
1238: if (!facetIS) {
1239: DMLabel depthLabel;
1240: PetscInt dim;
1242: DMPlexGetDepthLabel(dm, &depthLabel);
1243: DMGetDimension(dm, &dim);
1244: DMLabelGetStratumIS(depthLabel, dim - 1, &facetIS);
1245: }
1246: DMGetCoordinateField(dm, &coordField);
1247: DMGetLabel(dm, bdLabel, &label);
1248: DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);
1249: }
1250: ISDestroy(&facetIS);
1251: return(0);
1252: }
1254: PetscErrorCode DMPlexComputeResidual_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user)
1255: {
1256: DM_Plex *mesh = (DM_Plex *) dm->data;
1257: const char *name = "Residual";
1258: DM dmAux = NULL;
1259: DM dmGrad = NULL;
1260: DMLabel ghostLabel = NULL;
1261: PetscDS prob = NULL;
1262: PetscDS probAux = NULL;
1263: PetscSection section = NULL;
1264: PetscBool useFEM = PETSC_FALSE;
1265: PetscBool useFVM = PETSC_FALSE;
1266: PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE;
1267: PetscFV fvm = NULL;
1268: PetscFVCellGeom *cgeomFVM = NULL;
1269: PetscFVFaceGeom *fgeomFVM = NULL;
1270: DMField coordField = NULL;
1271: Vec locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL;
1272: PetscScalar *u = NULL, *u_t, *a, *uL, *uR;
1273: IS chunkIS;
1274: const PetscInt *cells;
1275: PetscInt cStart, cEnd, numCells;
1276: PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd;
1277: PetscInt maxDegree = PETSC_MAX_INT;
1278: PetscQuadrature affineQuad = NULL, *quads = NULL;
1279: PetscFEGeom *affineGeom = NULL, **geoms = NULL;
1280: PetscErrorCode ierr;
1283: PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);
1284: /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */
1285: /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */
1286: /* FEM+FVM */
1287: ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
1288: DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
1289: /* 1: Get sizes from dm and dmAux */
1290: DMGetSection(dm, §ion);
1291: DMGetLabel(dm, "ghost", &ghostLabel);
1292: DMGetCellDS(dm, cStart, &prob);
1293: PetscDSGetNumFields(prob, &Nf);
1294: PetscDSGetTotalDimension(prob, &totDim);
1295: PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
1296: if (locA) {
1297: PetscInt subcell;
1298: DMPlexGetAuxiliaryPoint(dm, dmAux, cStart, &subcell);
1299: VecGetDM(locA, &dmAux);
1300: DMGetCellDS(dmAux, subcell, &probAux);
1301: PetscDSGetTotalDimension(probAux, &totDimAux);
1302: }
1303: /* 2: Get geometric data */
1304: for (f = 0; f < Nf; ++f) {
1305: PetscObject obj;
1306: PetscClassId id;
1307: PetscBool fimp;
1309: PetscDSGetImplicit(prob, f, &fimp);
1310: if (isImplicit != fimp) continue;
1311: PetscDSGetDiscretization(prob, f, &obj);
1312: PetscObjectGetClassId(obj, &id);
1313: if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;}
1314: if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;}
1315: }
1316: if (useFEM) {
1317: DMGetCoordinateField(dm, &coordField);
1318: DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
1319: if (maxDegree <= 1) {
1320: DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);
1321: if (affineQuad) {
1322: DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
1323: }
1324: } else {
1325: PetscCalloc2(Nf,&quads,Nf,&geoms);
1326: for (f = 0; f < Nf; ++f) {
1327: PetscObject obj;
1328: PetscClassId id;
1329: PetscBool fimp;
1331: PetscDSGetImplicit(prob, f, &fimp);
1332: if (isImplicit != fimp) continue;
1333: PetscDSGetDiscretization(prob, f, &obj);
1334: PetscObjectGetClassId(obj, &id);
1335: if (id == PETSCFE_CLASSID) {
1336: PetscFE fe = (PetscFE) obj;
1338: PetscFEGetQuadrature(fe, &quads[f]);
1339: PetscObjectReference((PetscObject)quads[f]);
1340: DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
1341: }
1342: }
1343: }
1344: }
1345: if (useFVM) {
1346: DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);
1347: VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);
1348: VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);
1349: /* Reconstruct and limit cell gradients */
1350: DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);
1351: if (dmGrad) {
1352: DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
1353: DMGetGlobalVector(dmGrad, &grad);
1354: DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);
1355: /* Communicate gradient values */
1356: DMGetLocalVector(dmGrad, &locGrad);
1357: DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);
1358: DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);
1359: DMRestoreGlobalVector(dmGrad, &grad);
1360: }
1361: /* Handle non-essential (e.g. outflow) boundary values */
1362: DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);
1363: }
1364: /* Loop over chunks */
1365: if (useFEM) {ISCreate(PETSC_COMM_SELF, &chunkIS);}
1366: numCells = cEnd - cStart;
1367: numChunks = 1;
1368: cellChunkSize = numCells/numChunks;
1369: faceChunkSize = (fEnd - fStart)/numChunks;
1370: numChunks = PetscMin(1,numCells);
1371: for (chunk = 0; chunk < numChunks; ++chunk) {
1372: PetscScalar *elemVec, *fluxL, *fluxR;
1373: PetscReal *vol;
1374: PetscFVFaceGeom *fgeom;
1375: PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c;
1376: PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face;
1378: /* Extract field coefficients */
1379: if (useFEM) {
1380: ISGetPointSubrange(chunkIS, cS, cE, cells);
1381: DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
1382: DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
1383: PetscMemzero(elemVec, numCells*totDim * sizeof(PetscScalar));
1384: }
1385: if (useFVM) {
1386: DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);
1387: DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);
1388: DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);
1389: DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);
1390: PetscMemzero(fluxL, numFaces*totDim * sizeof(PetscScalar));
1391: PetscMemzero(fluxR, numFaces*totDim * sizeof(PetscScalar));
1392: }
1393: /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */
1394: /* Loop over fields */
1395: for (f = 0; f < Nf; ++f) {
1396: PetscObject obj;
1397: PetscClassId id;
1398: PetscBool fimp;
1399: PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset;
1401: PetscDSGetImplicit(prob, f, &fimp);
1402: if (isImplicit != fimp) continue;
1403: PetscDSGetDiscretization(prob, f, &obj);
1404: PetscObjectGetClassId(obj, &id);
1405: if (id == PETSCFE_CLASSID) {
1406: PetscFE fe = (PetscFE) obj;
1407: PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f];
1408: PetscFEGeom *chunkGeom = NULL;
1409: PetscQuadrature quad = affineQuad ? affineQuad : quads[f];
1410: PetscInt Nq, Nb;
1412: PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
1413: PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);
1414: PetscFEGetDimension(fe, &Nb);
1415: blockSize = Nb;
1416: batchSize = numBlocks * blockSize;
1417: PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
1418: numChunks = numCells / (numBatches*batchSize);
1419: Ne = numChunks*numBatches*batchSize;
1420: Nr = numCells % (numBatches*batchSize);
1421: offset = numCells - Nr;
1422: /* Integrate FE residual to get elemVec (need fields at quadrature points) */
1423: /* For FV, I think we use a P0 basis and the cell coefficients (for subdivided cells, we can tweak the basis tabulation to be the indicator function) */
1424: PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);
1425: PetscFEIntegrateResidual(fe, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);
1426: PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);
1427: PetscFEIntegrateResidual(fe, prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);
1428: PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);
1429: } else if (id == PETSCFV_CLASSID) {
1430: PetscFV fv = (PetscFV) obj;
1432: Ne = numFaces;
1433: /* Riemann solve over faces (need fields at face centroids) */
1434: /* We need to evaluate FE fields at those coordinates */
1435: PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);
1436: } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %d", f);
1437: }
1438: /* Loop over domain */
1439: if (useFEM) {
1440: /* Add elemVec to locX */
1441: for (c = cS; c < cE; ++c) {
1442: const PetscInt cell = cells ? cells[c] : c;
1443: const PetscInt cind = c - cStart;
1445: if (mesh->printFEM > 1) {DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);}
1446: if (ghostLabel) {
1447: PetscInt ghostVal;
1449: DMLabelGetValue(ghostLabel,cell,&ghostVal);
1450: if (ghostVal > 0) continue;
1451: }
1452: DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);
1453: }
1454: }
1455: if (useFVM) {
1456: PetscScalar *fa;
1457: PetscInt iface;
1459: VecGetArray(locF, &fa);
1460: for (f = 0; f < Nf; ++f) {
1461: PetscFV fv;
1462: PetscObject obj;
1463: PetscClassId id;
1464: PetscInt foff, pdim;
1466: PetscDSGetDiscretization(prob, f, &obj);
1467: PetscDSGetFieldOffset(prob, f, &foff);
1468: PetscObjectGetClassId(obj, &id);
1469: if (id != PETSCFV_CLASSID) continue;
1470: fv = (PetscFV) obj;
1471: PetscFVGetNumComponents(fv, &pdim);
1472: /* Accumulate fluxes to cells */
1473: for (face = fS, iface = 0; face < fE; ++face) {
1474: const PetscInt *scells;
1475: PetscScalar *fL = NULL, *fR = NULL;
1476: PetscInt ghost, d, nsupp, nchild;
1478: DMLabelGetValue(ghostLabel, face, &ghost);
1479: DMPlexGetSupportSize(dm, face, &nsupp);
1480: DMPlexGetTreeChildren(dm, face, &nchild, NULL);
1481: if (ghost >= 0 || nsupp > 2 || nchild > 0) continue;
1482: DMPlexGetSupport(dm, face, &scells);
1483: DMLabelGetValue(ghostLabel,scells[0],&ghost);
1484: if (ghost <= 0) {DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);}
1485: DMLabelGetValue(ghostLabel,scells[1],&ghost);
1486: if (ghost <= 0) {DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);}
1487: for (d = 0; d < pdim; ++d) {
1488: if (fL) fL[d] -= fluxL[iface*totDim+foff+d];
1489: if (fR) fR[d] += fluxR[iface*totDim+foff+d];
1490: }
1491: ++iface;
1492: }
1493: }
1494: VecRestoreArray(locF, &fa);
1495: }
1496: /* Handle time derivative */
1497: if (locX_t) {
1498: PetscScalar *x_t, *fa;
1500: VecGetArray(locF, &fa);
1501: VecGetArray(locX_t, &x_t);
1502: for (f = 0; f < Nf; ++f) {
1503: PetscFV fv;
1504: PetscObject obj;
1505: PetscClassId id;
1506: PetscInt pdim, d;
1508: PetscDSGetDiscretization(prob, f, &obj);
1509: PetscObjectGetClassId(obj, &id);
1510: if (id != PETSCFV_CLASSID) continue;
1511: fv = (PetscFV) obj;
1512: PetscFVGetNumComponents(fv, &pdim);
1513: for (c = cS; c < cE; ++c) {
1514: const PetscInt cell = cells ? cells[c] : c;
1515: PetscScalar *u_t, *r;
1517: if (ghostLabel) {
1518: PetscInt ghostVal;
1520: DMLabelGetValue(ghostLabel, cell, &ghostVal);
1521: if (ghostVal > 0) continue;
1522: }
1523: DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);
1524: DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);
1525: for (d = 0; d < pdim; ++d) r[d] += u_t[d];
1526: }
1527: }
1528: VecRestoreArray(locX_t, &x_t);
1529: VecRestoreArray(locF, &fa);
1530: }
1531: if (useFEM) {
1532: DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);
1533: DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);
1534: }
1535: if (useFVM) {
1536: DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);
1537: DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);
1538: DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);
1539: DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);
1540: if (dmGrad) {DMRestoreLocalVector(dmGrad, &locGrad);}
1541: }
1542: }
1543: if (useFEM) {ISDestroy(&chunkIS);}
1544: ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
1546: if (useFEM) {
1547: DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);
1549: if (maxDegree <= 1) {
1550: DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);
1551: PetscQuadratureDestroy(&affineQuad);
1552: } else {
1553: for (f = 0; f < Nf; ++f) {
1554: DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);
1555: PetscQuadratureDestroy(&quads[f]);
1556: }
1557: PetscFree2(quads,geoms);
1558: }
1559: }
1561: /* FEM */
1562: /* 1: Get sizes from dm and dmAux */
1563: /* 2: Get geometric data */
1564: /* 3: Handle boundary values */
1565: /* 4: Loop over domain */
1566: /* Extract coefficients */
1567: /* Loop over fields */
1568: /* Set tiling for FE*/
1569: /* Integrate FE residual to get elemVec */
1570: /* Loop over subdomain */
1571: /* Loop over quad points */
1572: /* Transform coords to real space */
1573: /* Evaluate field and aux fields at point */
1574: /* Evaluate residual at point */
1575: /* Transform residual to real space */
1576: /* Add residual to elemVec */
1577: /* Loop over domain */
1578: /* Add elemVec to locX */
1580: /* FVM */
1581: /* Get geometric data */
1582: /* If using gradients */
1583: /* Compute gradient data */
1584: /* Loop over domain faces */
1585: /* Count computational faces */
1586: /* Reconstruct cell gradient */
1587: /* Loop over domain cells */
1588: /* Limit cell gradients */
1589: /* Handle boundary values */
1590: /* Loop over domain faces */
1591: /* Read out field, centroid, normal, volume for each side of face */
1592: /* Riemann solve over faces */
1593: /* Loop over domain faces */
1594: /* Accumulate fluxes to cells */
1595: /* TODO Change printFEM to printDisc here */
1596: if (mesh->printFEM) {
1597: Vec locFbc;
1598: PetscInt pStart, pEnd, p, maxDof;
1599: PetscScalar *zeroes;
1601: VecDuplicate(locF,&locFbc);
1602: VecCopy(locF,locFbc);
1603: PetscSectionGetChart(section,&pStart,&pEnd);
1604: PetscSectionGetMaxDof(section,&maxDof);
1605: PetscCalloc1(maxDof,&zeroes);
1606: for (p = pStart; p < pEnd; p++) {
1607: VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);
1608: }
1609: PetscFree(zeroes);
1610: DMPrintLocalVec(dm, name, mesh->printTol, locFbc);
1611: VecDestroy(&locFbc);
1612: }
1613: PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);
1614: return(0);
1615: }
1617: static PetscErrorCode DMPlexComputeResidualFEM_Check_Internal(DM dm, Vec X, Vec X_t, PetscReal t, Vec F, void *user)
1618: {
1619: DM dmCh, dmAux;
1620: Vec A;
1621: DMField coordField = NULL;
1622: PetscDS prob, probCh, probAux = NULL;
1623: PetscSection section, sectionAux;
1624: PetscScalar *elemVec, *elemVecCh, *u, *u_t, *a = NULL;
1625: PetscInt Nf, f, numCells, cStart, cEnd, c;
1626: PetscInt totDim, totDimAux = 0, diffCell = 0;
1627: PetscInt depth;
1628: PetscInt maxDegree;
1629: IS cellIS;
1630: DMLabel depthLabel;
1631: PetscErrorCode ierr;
1634: DMGetSection(dm, §ion);
1635: DMGetDS(dm, &prob);
1636: PetscDSGetTotalDimension(prob, &totDim);
1637: PetscSectionGetNumFields(section, &Nf);
1638: DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
1639: numCells = cEnd - cStart;
1640: PetscObjectQuery((PetscObject) dm, "dmCh", (PetscObject *) &dmCh);
1641: DMGetDS(dmCh, &probCh);
1642: PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
1643: PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
1644: if (dmAux) {
1645: DMGetSection(dmAux, §ionAux);
1646: DMGetDS(dmAux, &probAux);
1647: PetscDSGetTotalDimension(probAux, &totDimAux);
1648: }
1649: VecSet(F, 0.0);
1650: PetscMalloc3(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim,&elemVec);
1651: PetscMalloc1(numCells*totDim,&elemVecCh);
1652: if (dmAux) {PetscMalloc1(numCells*totDimAux, &a);}
1653: DMPlexGetDepthLabel(dm, &depthLabel);
1654: DMPlexGetDepth(dm,&depth);
1655: DMLabelGetStratumIS(depthLabel,depth,&cellIS);
1656: DMGetCoordinateField(dm, &coordField);
1657: for (c = cStart; c < cEnd; ++c) {
1658: PetscScalar *x = NULL, *x_t = NULL;
1659: PetscInt i;
1661: DMPlexVecGetClosure(dm, section, X, c, NULL, &x);
1662: for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i];
1663: DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);
1664: if (X_t) {
1665: DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);
1666: for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i];
1667: DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);
1668: }
1669: if (dmAux) {
1670: DM dmAuxPlex;
1672: DMSNESConvertPlex(dmAux,&dmAuxPlex, PETSC_FALSE);
1673: DMPlexVecGetClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);
1674: for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i];
1675: DMPlexVecRestoreClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);
1676: DMDestroy(&dmAuxPlex);
1677: }
1678: }
1679: for (f = 0; f < Nf; ++f) {
1680: PetscFE fe, feCh;
1681: PetscInt Nq, Nb;
1682: /* Conforming batches */
1683: PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
1684: /* Remainder */
1685: PetscInt Nr, offset;
1686: PetscQuadrature qGeom = NULL;
1687: PetscFEGeom *cgeomFEM, *chunkGeom = NULL;
1689: PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);
1690: PetscDSGetDiscretization(probCh, f, (PetscObject *) &feCh);
1691: PetscFEGetDimension(fe, &Nb);
1692: PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
1693: DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
1694: if (maxDegree <= 1) {
1695: DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);
1696: }
1697: if (!qGeom) {
1698: PetscFEGetQuadrature(fe, &qGeom);
1699: PetscObjectReference((PetscObject)qGeom);
1700: }
1701: PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
1702: DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);
1703: blockSize = Nb;
1704: batchSize = numBlocks * blockSize;
1705: PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
1706: numChunks = numCells / (numBatches*batchSize);
1707: Ne = numChunks*numBatches*batchSize;
1708: Nr = numCells % (numBatches*batchSize);
1709: offset = numCells - Nr;
1710: PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);
1711: PetscFEIntegrateResidual(fe, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);
1712: PetscFEIntegrateResidual(feCh, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVecCh);
1713: PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&chunkGeom);
1714: PetscFEIntegrateResidual(fe, prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);
1715: PetscFEIntegrateResidual(feCh, prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVecCh[offset*totDim]);
1716: PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&chunkGeom);
1717: DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);
1718: PetscQuadratureDestroy(&qGeom);
1719: }
1720: ISDestroy(&cellIS);
1721: for (c = cStart; c < cEnd; ++c) {
1722: PetscBool diff = PETSC_FALSE;
1723: PetscInt d;
1725: for (d = 0; d < totDim; ++d) if (PetscAbsScalar(elemVec[c*totDim+d] - elemVecCh[c*totDim+d]) > 1.0e-7) {diff = PETSC_TRUE;break;}
1726: if (diff) {
1727: PetscPrintf(PetscObjectComm((PetscObject) dm), "Different cell %d\n", c);
1728: DMPrintCellVector(c, "Residual", totDim, &elemVec[c*totDim]);
1729: DMPrintCellVector(c, "Check Residual", totDim, &elemVecCh[c*totDim]);
1730: ++diffCell;
1731: }
1732: if (diffCell > 9) break;
1733: DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*totDim], ADD_ALL_VALUES);
1734: }
1735: PetscFree3(u,u_t,elemVec);
1736: PetscFree(elemVecCh);
1737: if (dmAux) {PetscFree(a);}
1738: return(0);
1739: }
1741: /*@
1742: DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user
1744: Input Parameters:
1745: + dm - The mesh
1746: . X - Local solution
1747: - user - The user context
1749: Output Parameter:
1750: . F - Local output vector
1752: Level: developer
1754: .seealso: DMPlexComputeJacobianAction()
1755: @*/
1756: PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user)
1757: {
1758: PetscObject check;
1759: DM plex;
1760: IS cellIS;
1761: PetscInt depth;
1765: DMSNESConvertPlex(dm,&plex,PETSC_TRUE);
1766: DMPlexGetDepth(plex, &depth);
1767: DMGetStratumIS(plex, "dim", depth, &cellIS);
1768: if (!cellIS) {
1769: DMGetStratumIS(plex, "depth", depth, &cellIS);
1770: }
1771: /* The dmCh is used to check two mathematically equivalent discretizations for computational equivalence */
1772: PetscObjectQuery((PetscObject) plex, "dmCh", &check);
1773: if (check) {DMPlexComputeResidualFEM_Check_Internal(plex, X, NULL, 0.0, F, user);}
1774: else {DMPlexComputeResidual_Internal(plex, cellIS, PETSC_MIN_REAL, X, NULL, 0.0, F, user);}
1775: ISDestroy(&cellIS);
1776: DMDestroy(&plex);
1777: return(0);
1778: }
1780: /*@
1781: DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X
1783: Input Parameters:
1784: + dm - The mesh
1785: - user - The user context
1787: Output Parameter:
1788: . X - Local solution
1790: Level: developer
1792: .seealso: DMPlexComputeJacobianAction()
1793: @*/
1794: PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user)
1795: {
1796: DM plex;
1800: DMSNESConvertPlex(dm,&plex,PETSC_TRUE);
1801: DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);
1802: DMDestroy(&plex);
1803: return(0);
1804: }
1806: PetscErrorCode DMPlexComputeBdJacobian_Single_Internal(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt fieldI, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP, DMField coordField, IS facetIS)
1807: {
1808: DM_Plex *mesh = (DM_Plex *) dm->data;
1809: DM plex = NULL, plexA = NULL;
1810: PetscDS prob, probAux = NULL;
1811: PetscSection section, sectionAux = NULL;
1812: PetscSection globalSection, subSection = NULL;
1813: Vec locA = NULL;
1814: PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL;
1815: PetscInt v;
1816: PetscInt Nf, totDim, totDimAux = 0;
1817: PetscBool isMatISP;
1821: DMConvert(dm, DMPLEX, &plex);
1822: DMGetSection(dm, §ion);
1823: DMGetDS(dm, &prob);
1824: PetscDSGetNumFields(prob, &Nf);
1825: PetscDSGetTotalDimension(prob, &totDim);
1826: PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);
1827: if (locA) {
1828: DM dmAux;
1830: VecGetDM(locA, &dmAux);
1831: DMConvert(dmAux, DMPLEX, &plexA);
1832: DMGetDS(plexA, &probAux);
1833: PetscDSGetTotalDimension(probAux, &totDimAux);
1834: DMGetSection(plexA, §ionAux);
1835: }
1837: PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
1838: DMGetGlobalSection(dm, &globalSection);
1839: if (isMatISP) {DMPlexGetSubdomainSection(dm, &subSection);}
1840: for (v = 0; v < numValues; ++v) {
1841: PetscFEGeom *fgeom;
1842: PetscInt maxDegree;
1843: PetscQuadrature qGeom = NULL;
1844: IS pointIS;
1845: const PetscInt *points;
1846: PetscInt numFaces, face, Nq;
1848: DMLabelGetStratumIS(label, values[v], &pointIS);
1849: if (!pointIS) continue; /* No points with that id on this process */
1850: {
1851: IS isectIS;
1853: /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */
1854: ISIntersect_Caching_Internal(facetIS,pointIS,&isectIS);
1855: ISDestroy(&pointIS);
1856: pointIS = isectIS;
1857: }
1858: ISGetLocalSize(pointIS, &numFaces);
1859: ISGetIndices(pointIS, &points);
1860: PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim*totDim, &elemMat, locA ? numFaces*totDimAux : 0, &a);
1861: DMFieldGetDegree(coordField,pointIS,NULL,&maxDegree);
1862: if (maxDegree <= 1) {
1863: DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);
1864: }
1865: if (!qGeom) {
1866: PetscFE fe;
1868: PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
1869: PetscFEGetFaceQuadrature(fe, &qGeom);
1870: PetscObjectReference((PetscObject)qGeom);
1871: }
1872: PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
1873: DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
1874: for (face = 0; face < numFaces; ++face) {
1875: const PetscInt point = points[face], *support, *cone;
1876: PetscScalar *x = NULL;
1877: PetscInt i, coneSize, faceLoc;
1879: DMPlexGetSupport(dm, point, &support);
1880: DMPlexGetConeSize(dm, support[0], &coneSize);
1881: DMPlexGetCone(dm, support[0], &cone);
1882: for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break;
1883: if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of support[0] %d", point, support[0]);
1884: fgeom->face[face][0] = faceLoc;
1885: DMPlexVecGetClosure(plex, section, locX, support[0], NULL, &x);
1886: for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i];
1887: DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);
1888: if (locX_t) {
1889: DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);
1890: for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i];
1891: DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);
1892: }
1893: if (locA) {
1894: PetscInt subp;
1895: DMPlexGetSubpoint(plexA, support[0], &subp);
1896: DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);
1897: for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i];
1898: DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);
1899: }
1900: }
1901: PetscMemzero(elemMat, numFaces*totDim*totDim * sizeof(PetscScalar));
1902: {
1903: PetscFE fe;
1904: PetscInt Nb;
1905: /* Conforming batches */
1906: PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
1907: /* Remainder */
1908: PetscFEGeom *chunkGeom = NULL;
1909: PetscInt fieldJ, Nr, offset;
1911: PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
1912: PetscFEGetDimension(fe, &Nb);
1913: PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
1914: blockSize = Nb;
1915: batchSize = numBlocks * blockSize;
1916: PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
1917: numChunks = numFaces / (numBatches*batchSize);
1918: Ne = numChunks*numBatches*batchSize;
1919: Nr = numFaces % (numBatches*batchSize);
1920: offset = numFaces - Nr;
1921: PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);
1922: for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
1923: PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);
1924: }
1925: PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);
1926: for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
1927: PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, X_tShift, &elemMat[offset*totDim*totDim]);
1928: }
1929: PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);
1930: }
1931: for (face = 0; face < numFaces; ++face) {
1932: const PetscInt point = points[face], *support;
1934: if (mesh->printFEM > 1) {DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);}
1935: DMPlexGetSupport(plex, point, &support);
1936: if (!isMatISP) {
1937: DMPlexMatSetClosure(plex, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);
1938: } else {
1939: Mat lJ;
1941: MatISGetLocalMat(JacP, &lJ);
1942: DMPlexMatSetClosure(plex, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);
1943: }
1944: }
1945: DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);
1946: PetscQuadratureDestroy(&qGeom);
1947: ISRestoreIndices(pointIS, &points);
1948: ISDestroy(&pointIS);
1949: PetscFree4(u, u_t, elemMat, a);
1950: }
1951: if (plex) {DMDestroy(&plex);}
1952: if (plexA) {DMDestroy(&plexA);}
1953: return(0);
1954: }
1956: PetscErrorCode DMPlexComputeBdJacobianSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP)
1957: {
1958: DMField coordField;
1959: DMLabel depthLabel;
1960: IS facetIS;
1961: PetscInt dim;
1965: DMGetDimension(dm, &dim);
1966: DMPlexGetDepthLabel(dm, &depthLabel);
1967: DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
1968: DMGetCoordinateField(dm, &coordField);
1969: DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);
1970: return(0);
1971: }
1973: PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user)
1974: {
1975: PetscDS prob;
1976: PetscInt dim, numBd, bd;
1977: DMLabel depthLabel;
1978: DMField coordField = NULL;
1979: IS facetIS;
1980: PetscErrorCode ierr;
1983: DMGetDS(dm, &prob);
1984: DMPlexGetDepthLabel(dm, &depthLabel);
1985: DMGetDimension(dm, &dim);
1986: DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);
1987: PetscDSGetNumBoundary(prob, &numBd);
1988: DMGetCoordinateField(dm, &coordField);
1989: for (bd = 0; bd < numBd; ++bd) {
1990: DMBoundaryConditionType type;
1991: const char *bdLabel;
1992: DMLabel label;
1993: const PetscInt *values;
1994: PetscInt fieldI, numValues;
1995: PetscObject obj;
1996: PetscClassId id;
1998: PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &fieldI, NULL, NULL, NULL, &numValues, &values, NULL);
1999: PetscDSGetDiscretization(prob, fieldI, &obj);
2000: PetscObjectGetClassId(obj, &id);
2001: if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue;
2002: DMGetLabel(dm, bdLabel, &label);
2003: DMPlexComputeBdJacobian_Single_Internal(dm, t, label, numValues, values, fieldI, locX, locX_t, X_tShift, Jac, JacP, coordField, facetIS);
2004: }
2005: ISDestroy(&facetIS);
2006: return(0);
2007: }
2009: PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user)
2010: {
2011: DM_Plex *mesh = (DM_Plex *) dm->data;
2012: const char *name = "Jacobian";
2013: DM dmAux, plex;
2014: Vec A;
2015: DMField coordField;
2016: PetscDS prob, probAux = NULL;
2017: PetscSection section, globalSection, subSection, sectionAux;
2018: PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL;
2019: const PetscInt *cells;
2020: PetscInt Nf, fieldI, fieldJ;
2021: PetscInt totDim, totDimAux, cStart, cEnd, numCells, c;
2022: PetscBool isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE;
2023: PetscErrorCode ierr;
2026: PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);
2027: DMGetSection(dm, §ion);
2028: PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);
2029: DMGetGlobalSection(dm, &globalSection);
2030: if (isMatISP) {DMPlexGetSubdomainSection(dm, &subSection);}
2031: DMGetDS(dm, &prob);
2032: PetscDSGetTotalDimension(prob, &totDim);
2033: PetscDSHasJacobian(prob, &hasJac);
2034: PetscDSHasJacobianPreconditioner(prob, &hasPrec);
2035: PetscDSHasDynamicJacobian(prob, &hasDyn);
2036: hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE;
2037: PetscSectionGetNumFields(section, &Nf);
2038: ISGetLocalSize(cellIS, &numCells);
2039: ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
2040: PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
2041: PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
2042: if (dmAux) {
2043: DMConvert(dmAux, DMPLEX, &plex);
2044: DMGetSection(plex, §ionAux);
2045: DMGetDS(dmAux, &probAux);
2046: PetscDSGetTotalDimension(probAux, &totDimAux);
2047: }
2048: PetscMalloc5(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,hasJac ? numCells*totDim*totDim : 0,&elemMat,hasPrec ? numCells*totDim*totDim : 0, &elemMatP,hasDyn ? numCells*totDim*totDim : 0, &elemMatD);
2049: if (dmAux) {PetscMalloc1(numCells*totDimAux, &a);}
2050: DMGetCoordinateField(dm, &coordField);
2051: for (c = cStart; c < cEnd; ++c) {
2052: const PetscInt cell = cells ? cells[c] : c;
2053: const PetscInt cind = c - cStart;
2054: PetscScalar *x = NULL, *x_t = NULL;
2055: PetscInt i;
2057: DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);
2058: for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i];
2059: DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);
2060: if (X_t) {
2061: DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);
2062: for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i];
2063: DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);
2064: }
2065: if (dmAux) {
2066: PetscInt subcell;
2067: DMPlexGetAuxiliaryPoint(dm, dmAux, cell, &subcell);
2068: DMPlexVecGetClosure(plex, sectionAux, A, subcell, NULL, &x);
2069: for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i];
2070: DMPlexVecRestoreClosure(plex, sectionAux, A, subcell, NULL, &x);
2071: }
2072: }
2073: if (hasJac) {PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));}
2074: if (hasPrec) {PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));}
2075: if (hasDyn) {PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));}
2076: for (fieldI = 0; fieldI < Nf; ++fieldI) {
2077: PetscClassId id;
2078: PetscFE fe;
2079: PetscQuadrature qGeom = NULL;
2080: PetscInt Nb;
2081: /* Conforming batches */
2082: PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
2083: /* Remainder */
2084: PetscInt Nr, offset, Nq;
2085: PetscInt maxDegree;
2086: PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL;
2088: PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
2089: PetscObjectGetClassId((PetscObject) fe, &id);
2090: if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;}
2091: PetscFEGetDimension(fe, &Nb);
2092: PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
2093: DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
2094: if (maxDegree <= 1) {
2095: DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);
2096: }
2097: if (!qGeom) {
2098: PetscFEGetQuadrature(fe,&qGeom);
2099: PetscObjectReference((PetscObject)qGeom);
2100: }
2101: PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
2102: DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);
2103: blockSize = Nb;
2104: batchSize = numBlocks * blockSize;
2105: PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
2106: numChunks = numCells / (numBatches*batchSize);
2107: Ne = numChunks*numBatches*batchSize;
2108: Nr = numCells % (numBatches*batchSize);
2109: offset = numCells - Nr;
2110: PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);
2111: PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);
2112: for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
2113: if (hasJac) {
2114: PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);
2115: PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);
2116: }
2117: if (hasPrec) {
2118: PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);
2119: PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatP[offset*totDim*totDim]);
2120: }
2121: if (hasDyn) {
2122: PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);
2123: PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatD[offset*totDim*totDim]);
2124: }
2125: }
2126: PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);
2127: PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);
2128: DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);
2129: PetscQuadratureDestroy(&qGeom);
2130: }
2131: /* Add contribution from X_t */
2132: if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];}
2133: if (hasFV) {
2134: PetscClassId id;
2135: PetscFV fv;
2136: PetscInt offsetI, NcI, NbI = 1, fc, f;
2138: for (fieldI = 0; fieldI < Nf; ++fieldI) {
2139: PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);
2140: PetscDSGetFieldOffset(prob, fieldI, &offsetI);
2141: PetscObjectGetClassId((PetscObject) fv, &id);
2142: if (id != PETSCFV_CLASSID) continue;
2143: /* Put in the identity */
2144: PetscFVGetNumComponents(fv, &NcI);
2145: for (c = cStart; c < cEnd; ++c) {
2146: const PetscInt cind = c - cStart;
2147: const PetscInt eOffset = cind*totDim*totDim;
2148: for (fc = 0; fc < NcI; ++fc) {
2149: for (f = 0; f < NbI; ++f) {
2150: const PetscInt i = offsetI + f*NcI+fc;
2151: if (hasPrec) {
2152: if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;}
2153: elemMatP[eOffset+i*totDim+i] = 1.0;
2154: } else {elemMat[eOffset+i*totDim+i] = 1.0;}
2155: }
2156: }
2157: }
2158: }
2159: /* No allocated space for FV stuff, so ignore the zero entries */
2160: MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);
2161: }
2162: /* Insert values into matrix */
2163: isMatIS = PETSC_FALSE;
2164: if (hasPrec && hasJac) {
2165: PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);
2166: }
2167: if (isMatIS && !subSection) {
2168: DMPlexGetSubdomainSection(dm, &subSection);
2169: }
2170: for (c = cStart; c < cEnd; ++c) {
2171: const PetscInt cell = cells ? cells[c] : c;
2172: const PetscInt cind = c - cStart;
2174: if (hasPrec) {
2175: if (hasJac) {
2176: if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);}
2177: if (!isMatIS) {
2178: DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
2179: } else {
2180: Mat lJ;
2182: MatISGetLocalMat(Jac,&lJ);
2183: DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
2184: }
2185: }
2186: if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);}
2187: if (!isMatISP) {
2188: DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);
2189: } else {
2190: Mat lJ;
2192: MatISGetLocalMat(JacP,&lJ);
2193: DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);
2194: }
2195: } else {
2196: if (mesh->printFEM > 1) {DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);}
2197: if (!isMatISP) {
2198: DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
2199: } else {
2200: Mat lJ;
2202: MatISGetLocalMat(JacP,&lJ);
2203: DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);
2204: }
2205: }
2206: }
2207: ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);
2208: if (hasFV) {MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);}
2209: PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);
2210: if (dmAux) {
2211: PetscFree(a);
2212: DMDestroy(&plex);
2213: }
2214: /* Compute boundary integrals */
2215: DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);
2216: /* Assemble matrix */
2217: if (hasJac && hasPrec) {
2218: MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);
2219: MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);
2220: }
2221: MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);
2222: MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);
2223: PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);
2224: return(0);
2225: }
2227: /*@
2228: DMPlexComputeJacobianAction - Form the local portion of the Jacobian action Z = J(X) Y at the local solution X using pointwise functions specified by the user.
2230: Input Parameters:
2231: + dm - The mesh
2232: . cellIS -
2233: . t - The time
2234: . X_tShift - The multiplier for the Jacobian with repsect to X_t
2235: . X - Local solution vector
2236: . X_t - Time-derivative of the local solution vector
2237: . Y - Local input vector
2238: - user - The user context
2240: Output Parameter:
2241: . Z - Local output vector
2243: Note:
2244: We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator,
2245: like a GPU, or vectorize on a multicore machine.
2247: Level: developer
2249: .seealso: FormFunctionLocal()
2250: @*/
2251: PetscErrorCode DMPlexComputeJacobianAction(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user)
2252: {
2253: DM_Plex *mesh = (DM_Plex *) dm->data;
2254: const char *name = "Jacobian";
2255: DM dmAux, plex, plexAux = NULL;
2256: Vec A;
2257: PetscDS prob, probAux = NULL;
2258: PetscQuadrature quad;
2259: PetscSection section, globalSection, sectionAux;
2260: PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z;
2261: PetscInt Nf, fieldI, fieldJ;
2262: PetscInt totDim, totDimAux = 0;
2263: const PetscInt *cells;
2264: PetscInt cStart, cEnd, numCells, c;
2265: PetscBool hasDyn;
2266: DMField coordField;
2267: PetscErrorCode ierr;
2270: PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);
2271: DMSNESConvertPlex(dm, &plex, PETSC_TRUE);
2272: if (!cellIS) {
2273: PetscInt depth;
2275: DMPlexGetDepth(plex, &depth);
2276: DMGetStratumIS(plex, "dim", depth, &cellIS);
2277: if (!cellIS) {DMGetStratumIS(plex, "depth", depth, &cellIS);}
2278: } else {
2279: PetscObjectReference((PetscObject) cellIS);
2280: }
2281: DMGetSection(dm, §ion);
2282: DMGetGlobalSection(dm, &globalSection);
2283: DMGetDS(dm, &prob);
2284: PetscDSGetTotalDimension(prob, &totDim);
2285: PetscDSHasDynamicJacobian(prob, &hasDyn);
2286: hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE;
2287: PetscSectionGetNumFields(section, &Nf);
2288: ISGetLocalSize(cellIS, &numCells);
2289: ISGetPointRange(cellIS, &cStart, &cEnd, &cells);
2290: PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);
2291: PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);
2292: if (dmAux) {
2293: DMConvert(dmAux, DMPLEX, &plexAux);
2294: DMGetSection(plexAux, §ionAux);
2295: DMGetDS(dmAux, &probAux);
2296: PetscDSGetTotalDimension(probAux, &totDimAux);
2297: }
2298: VecSet(Z, 0.0);
2299: PetscMalloc6(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim*totDim,&elemMat,hasDyn ? numCells*totDim*totDim : 0, &elemMatD,numCells*totDim,&y,totDim,&z);
2300: if (dmAux) {PetscMalloc1(numCells*totDimAux, &a);}
2301: DMGetCoordinateField(dm, &coordField);
2302: for (c = cStart; c < cEnd; ++c) {
2303: const PetscInt cell = cells ? cells[c] : c;
2304: const PetscInt cind = c - cStart;
2305: PetscScalar *x = NULL, *x_t = NULL;
2306: PetscInt i;
2308: DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);
2309: for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i];
2310: DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);
2311: if (X_t) {
2312: DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);
2313: for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i];
2314: DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);
2315: }
2316: if (dmAux) {
2317: PetscInt subcell;
2318: DMPlexGetAuxiliaryPoint(dm, dmAux, cell, &subcell);
2319: DMPlexVecGetClosure(plexAux, sectionAux, A, subcell, NULL, &x);
2320: for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i];
2321: DMPlexVecRestoreClosure(plexAux, sectionAux, A, subcell, NULL, &x);
2322: }
2323: DMPlexVecGetClosure(dm, section, Y, cell, NULL, &x);
2324: for (i = 0; i < totDim; ++i) y[cind*totDim+i] = x[i];
2325: DMPlexVecRestoreClosure(dm, section, Y, cell, NULL, &x);
2326: }
2327: PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));
2328: if (hasDyn) {PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));}
2329: for (fieldI = 0; fieldI < Nf; ++fieldI) {
2330: PetscFE fe;
2331: PetscInt Nb;
2332: /* Conforming batches */
2333: PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize;
2334: /* Remainder */
2335: PetscInt Nr, offset, Nq;
2336: PetscQuadrature qGeom = NULL;
2337: PetscInt maxDegree;
2338: PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL;
2340: PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);
2341: PetscFEGetQuadrature(fe, &quad);
2342: PetscFEGetDimension(fe, &Nb);
2343: PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);
2344: DMFieldGetDegree(coordField,cellIS,NULL,&maxDegree);
2345: if (maxDegree <= 1) {DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);}
2346: if (!qGeom) {
2347: PetscFEGetQuadrature(fe,&qGeom);
2348: PetscObjectReference((PetscObject)qGeom);
2349: }
2350: PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);
2351: DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);
2352: blockSize = Nb;
2353: batchSize = numBlocks * blockSize;
2354: PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);
2355: numChunks = numCells / (numBatches*batchSize);
2356: Ne = numChunks*numBatches*batchSize;
2357: Nr = numCells % (numBatches*batchSize);
2358: offset = numCells - Nr;
2359: PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);
2360: PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);
2361: for (fieldJ = 0; fieldJ < Nf; ++fieldJ) {
2362: PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);
2363: PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);
2364: if (hasDyn) {
2365: PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);
2366: PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatD[offset*totDim*totDim]);
2367: }
2368: }
2369: PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);
2370: PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);
2371: DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);
2372: PetscQuadratureDestroy(&qGeom);
2373: }
2374: if (hasDyn) {
2375: for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];
2376: }
2377: for (c = cStart; c < cEnd; ++c) {
2378: const PetscInt cell = cells ? cells[c] : c;
2379: const PetscInt cind = c - cStart;
2380: const PetscBLASInt M = totDim, one = 1;
2381: const PetscScalar a = 1.0, b = 0.0;
2383: PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[cind*totDim*totDim], &M, &y[cind*totDim], &one, &b, z, &one));
2384: if (mesh->printFEM > 1) {
2385: DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[cind*totDim*totDim]);
2386: DMPrintCellVector(c, "Y", totDim, &y[cind*totDim]);
2387: DMPrintCellVector(c, "Z", totDim, z);
2388: }
2389: DMPlexVecSetClosure(dm, section, Z, cell, z, ADD_VALUES);
2390: }
2391: PetscFree6(u,u_t,elemMat,elemMatD,y,z);
2392: if (mesh->printFEM) {
2393: PetscPrintf(PETSC_COMM_WORLD, "Z:\n");
2394: VecView(Z, PETSC_VIEWER_STDOUT_WORLD);
2395: }
2396: PetscFree(a);
2397: ISDestroy(&cellIS);
2398: DMDestroy(&plexAux);
2399: DMDestroy(&plex);
2400: PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);
2401: return(0);
2402: }
2404: /*@
2405: DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user.
2407: Input Parameters:
2408: + dm - The mesh
2409: . X - Local input vector
2410: - user - The user context
2412: Output Parameter:
2413: . Jac - Jacobian matrix
2415: Note:
2416: We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator,
2417: like a GPU, or vectorize on a multicore machine.
2419: Level: developer
2421: .seealso: FormFunctionLocal()
2422: @*/
2423: PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user)
2424: {
2425: DM plex;
2426: PetscDS prob;
2427: IS cellIS;
2428: PetscBool hasJac, hasPrec;
2429: PetscInt depth;
2433: DMSNESConvertPlex(dm,&plex,PETSC_TRUE);
2434: DMPlexGetDepth(plex, &depth);
2435: DMGetStratumIS(plex, "dim", depth, &cellIS);
2436: if (!cellIS) {DMGetStratumIS(plex, "depth", depth, &cellIS);}
2437: DMGetDS(dm, &prob);
2438: PetscDSHasJacobian(prob, &hasJac);
2439: PetscDSHasJacobianPreconditioner(prob, &hasPrec);
2440: if (hasJac && hasPrec) {MatZeroEntries(Jac);}
2441: MatZeroEntries(JacP);
2442: DMPlexComputeJacobian_Internal(plex, cellIS, 0.0, 0.0, X, NULL, Jac, JacP, user);
2443: ISDestroy(&cellIS);
2444: DMDestroy(&plex);
2445: return(0);
2446: }
2448: /*@
2449: DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian.
2451: Input Parameters:
2452: + dm - The DM object
2453: . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see PetscDSAddBoundary())
2454: . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual())
2455: - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian())
2457: Level: developer
2458: @*/
2459: PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx)
2460: {
2464: DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);
2465: DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);
2466: DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);
2467: return(0);
2468: }
2470: PetscErrorCode DMSNESCheckFromOptions_Internal(SNES snes, DM dm, Vec u, PetscErrorCode (**exactFuncs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx), void **ctxs)
2471: {
2472: PetscErrorCode (**exacts)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx);
2473: PetscDS prob;
2474: Mat J, M;
2475: Vec r, b;
2476: MatNullSpace nullSpace;
2477: PetscReal *error, res = 0.0;
2478: PetscInt numFields;
2479: PetscBool hasJac, hasPrec;
2480: PetscInt Nf, f;
2484: DMGetNumFields(dm, &Nf);
2485: DMGetDS(dm, &prob);
2486: PetscMalloc1(Nf, &exacts);
2487: for (f = 0; f < Nf; ++f) {PetscDSGetExactSolution(prob, f, &exacts[f]);}
2488: VecDuplicate(u, &r);
2489: DMCreateMatrix(dm, &J);
2490: /* TODO Null space for J */
2491: /* Check discretization error */
2492: DMGetNumFields(dm, &numFields);
2493: PetscMalloc1(PetscMax(1, numFields), &error);
2494: DMProjectFunction(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs, INSERT_ALL_VALUES, u);
2495: if (numFields > 1) {
2496: PetscInt f;
2498: DMComputeL2FieldDiff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs, u, error);
2499: PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: [");
2500: for (f = 0; f < numFields; ++f) {
2501: if (f) {PetscPrintf(PETSC_COMM_WORLD, ", ");}
2502: if (error[f] >= 1.0e-11) {PetscPrintf(PETSC_COMM_WORLD, "%g", (double)error[f]);}
2503: else {PetscPrintf(PETSC_COMM_WORLD, "< 1.0e-11");}
2504: }
2505: PetscPrintf(PETSC_COMM_WORLD, "]\n");
2506: } else {
2507: DMComputeL2Diff(dm, 0.0, exactFuncs ? exactFuncs : exacts, ctxs, u, &error[0]);
2508: if (error[0] >= 1.0e-11) {PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", (double)error[0]);}
2509: else {PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");}
2510: }
2511: PetscFree(error);
2512: /* Check residual */
2513: SNESComputeFunction(snes, u, r);
2514: VecNorm(r, NORM_2, &res);
2515: PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", (double)res);
2516: VecChop(r, 1.0e-10);
2517: PetscObjectSetName((PetscObject) r, "Initial Residual");
2518: PetscObjectSetOptionsPrefix((PetscObject)r,"res_");
2519: VecViewFromOptions(r, NULL, "-vec_view");
2520: /* Check Jacobian */
2521: PetscDSHasJacobian(prob, &hasJac);
2522: PetscDSHasJacobianPreconditioner(prob, &hasPrec);
2523: if (hasJac && hasPrec) {
2524: DMCreateMatrix(dm, &M);
2525: SNESComputeJacobian(snes, u, J, M);
2526: PetscObjectSetOptionsPrefix((PetscObject) M, "jacpre_");
2527: MatViewFromOptions(M, NULL, "-mat_view");
2528: MatDestroy(&M);
2529: } else {
2530: SNESComputeJacobian(snes, u, J, J);
2531: }
2532: PetscObjectSetOptionsPrefix((PetscObject) J, "jac_");
2533: MatViewFromOptions(J, NULL, "-mat_view");
2534: MatGetNullSpace(J, &nullSpace);
2535: if (nullSpace) {
2536: PetscBool isNull;
2537: MatNullSpaceTest(nullSpace, J, &isNull);
2538: if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid.");
2539: }
2540: VecDuplicate(u, &b);
2541: VecSet(r, 0.0);
2542: SNESComputeFunction(snes, r, b);
2543: MatMult(J, u, r);
2544: VecAXPY(r, 1.0, b);
2545: VecDestroy(&b);
2546: VecNorm(r, NORM_2, &res);
2547: PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", (double)res);
2548: VecChop(r, 1.0e-10);
2549: PetscObjectSetName((PetscObject) r, "Au - b = Au + F(0)");
2550: PetscObjectSetOptionsPrefix((PetscObject)r,"linear_res_");
2551: VecViewFromOptions(r, NULL, "-vec_view");
2552: VecDestroy(&r);
2553: MatNullSpaceDestroy(&nullSpace);
2554: MatDestroy(&J);
2555: PetscFree(exacts);
2556: return(0);
2557: }
2559: /*@C
2560: DMSNESCheckFromOptions - Check the residual and Jacobian functions using the exact solution by outputting some diagnostic information
2562: Input Parameters:
2563: + snes - the SNES object
2564: . u - representative SNES vector
2565: . exactFuncs - pointwise functions of the exact solution for each field
2566: - ctxs - contexts for the functions
2568: Level: developer
2569: @*/
2570: PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs)
2571: {
2572: PetscErrorCode (**exact)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *) = NULL;
2573: DM dm;
2574: PetscDS prob;
2575: Vec sol;
2576: PetscBool check;
2577: PetscInt Nf, f;
2581: PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);
2582: if (!check) return(0);
2583: SNESGetDM(snes, &dm);
2584: DMGetDS(dm, &prob);
2585: if (!exactFuncs) {
2586: PetscDSGetNumFields(prob, &Nf);
2587: PetscMalloc1(Nf, &exact);
2588: for (f = 0; f < Nf; ++f) {PetscDSGetExactSolution(prob, f, &exact[f]);}
2589: }
2590: VecDuplicate(u, &sol);
2591: SNESSetSolution(snes, sol);
2592: DMSNESCheckFromOptions_Internal(snes, dm, sol, exactFuncs ? exactFuncs : exact, ctxs);
2593: VecDestroy(&sol);
2594: PetscFree(exact);
2595: return(0);
2596: }