Actual source code: fdmatrix.c

  1: /*
  2:    This is where the abstract matrix operations are defined that are
  3:   used for finite difference computations of Jacobians using coloring.
  4: */

  6: #include <petsc/private/matimpl.h>
  7: #include <petsc/private/isimpl.h>

  9: PetscErrorCode MatFDColoringSetF(MatFDColoring fd, Vec F)
 10: {
 11:   PetscFunctionBegin;
 12:   if (F) {
 13:     PetscCall(VecCopy(F, fd->w1));
 14:     fd->fset = PETSC_TRUE;
 15:   } else {
 16:     fd->fset = PETSC_FALSE;
 17:   }
 18:   PetscFunctionReturn(PETSC_SUCCESS);
 19: }

 21: #include <petscdraw.h>
 22: static PetscErrorCode MatFDColoringView_Draw_Zoom(PetscDraw draw, void *Aa)
 23: {
 24:   MatFDColoring fd = (MatFDColoring)Aa;
 25:   PetscMPIInt   i, j, nz;
 26:   PetscInt      row;
 27:   PetscReal     x, y;
 28:   MatEntry     *Jentry = fd->matentry;

 30:   PetscFunctionBegin;
 31:   /* loop over colors  */
 32:   nz = 0;
 33:   for (i = 0; i < fd->ncolors; i++) {
 34:     for (j = 0; j < fd->nrows[i]; j++) {
 35:       row = Jentry[nz].row;
 36:       y   = fd->M - row - fd->rstart;
 37:       x   = (PetscReal)Jentry[nz++].col;
 38:       PetscCall(PetscDrawRectangle(draw, x, y, x + 1, y + 1, i + 1, i + 1, i + 1, i + 1));
 39:     }
 40:   }
 41:   PetscFunctionReturn(PETSC_SUCCESS);
 42: }

 44: static PetscErrorCode MatFDColoringView_Draw(MatFDColoring fd, PetscViewer viewer)
 45: {
 46:   PetscBool isnull;
 47:   PetscDraw draw;
 48:   PetscReal xr, yr, xl, yl, h, w;

 50:   PetscFunctionBegin;
 51:   PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw));
 52:   PetscCall(PetscDrawIsNull(draw, &isnull));
 53:   if (isnull) PetscFunctionReturn(PETSC_SUCCESS);

 55:   xr = fd->N;
 56:   yr = fd->M;
 57:   h  = yr / 10.0;
 58:   w  = xr / 10.0;
 59:   xr += w;
 60:   yr += h;
 61:   xl = -w;
 62:   yl = -h;
 63:   PetscCall(PetscDrawSetCoordinates(draw, xl, yl, xr, yr));
 64:   PetscCall(PetscObjectCompose((PetscObject)fd, "Zoomviewer", (PetscObject)viewer));
 65:   PetscCall(PetscDrawZoom(draw, MatFDColoringView_Draw_Zoom, fd));
 66:   PetscCall(PetscObjectCompose((PetscObject)fd, "Zoomviewer", NULL));
 67:   PetscCall(PetscDrawSave(draw));
 68:   PetscFunctionReturn(PETSC_SUCCESS);
 69: }

 71: /*@
 72:   MatFDColoringView - Views a finite difference coloring context.

 74:   Collective

 76:   Input Parameters:
 77: + c      - the coloring context
 78: - viewer - visualization context

 80:   Level: intermediate

 82:   Notes:
 83:   The available visualization contexts include
 84: +     `PETSC_VIEWER_STDOUT_SELF` - standard output (default)
 85: .     `PETSC_VIEWER_STDOUT_WORLD` - synchronized standard
 86:   output where only the first processor opens
 87:   the file.  All other processors send their
 88:   data to the first processor to print.
 89: -     `PETSC_VIEWER_DRAW_WORLD` - graphical display of nonzero structure

 91:   Since PETSc uses only a small number of basic colors (currently 33), if the coloring
 92:   involves more than 33 then some seemingly identical colors are displayed making it look
 93:   like an illegal coloring. This is just a graphical artifact.

 95: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`
 96: @*/
 97: PetscErrorCode MatFDColoringView(MatFDColoring c, PetscViewer viewer)
 98: {
 99:   PetscInt          i, j;
100:   PetscBool         isdraw, iascii;
101:   PetscViewerFormat format;

103:   PetscFunctionBegin;
105:   if (!viewer) PetscCall(PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)c), &viewer));
107:   PetscCheckSameComm(c, 1, viewer, 2);

109:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw));
110:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii));
111:   if (isdraw) {
112:     PetscCall(MatFDColoringView_Draw(c, viewer));
113:   } else if (iascii) {
114:     PetscCall(PetscObjectPrintClassNamePrefixType((PetscObject)c, viewer));
115:     PetscCall(PetscViewerASCIIPrintf(viewer, "  Error tolerance=%g\n", (double)c->error_rel));
116:     PetscCall(PetscViewerASCIIPrintf(viewer, "  Umin=%g\n", (double)c->umin));
117:     PetscCall(PetscViewerASCIIPrintf(viewer, "  Number of colors=%" PetscInt_FMT "\n", c->ncolors));

119:     PetscCall(PetscViewerGetFormat(viewer, &format));
120:     if (format != PETSC_VIEWER_ASCII_INFO) {
121:       PetscInt row, col, nz;
122:       nz = 0;
123:       for (i = 0; i < c->ncolors; i++) {
124:         PetscCall(PetscViewerASCIIPrintf(viewer, "  Information for color %" PetscInt_FMT "\n", i));
125:         PetscCall(PetscViewerASCIIPrintf(viewer, "    Number of columns %" PetscInt_FMT "\n", c->ncolumns[i]));
126:         for (j = 0; j < c->ncolumns[i]; j++) PetscCall(PetscViewerASCIIPrintf(viewer, "      %" PetscInt_FMT "\n", c->columns[i][j]));
127:         PetscCall(PetscViewerASCIIPrintf(viewer, "    Number of rows %" PetscInt_FMT "\n", c->nrows[i]));
128:         if (c->matentry) {
129:           for (j = 0; j < c->nrows[i]; j++) {
130:             row = c->matentry[nz].row;
131:             col = c->matentry[nz++].col;
132:             PetscCall(PetscViewerASCIIPrintf(viewer, "      %" PetscInt_FMT " %" PetscInt_FMT " \n", row, col));
133:           }
134:         }
135:       }
136:     }
137:     PetscCall(PetscViewerFlush(viewer));
138:   }
139:   PetscFunctionReturn(PETSC_SUCCESS);
140: }

142: /*@
143:   MatFDColoringSetParameters - Sets the parameters for the approximation of
144:   a sparse Jacobian matrix using finite differences and matrix coloring

146:   Logically Collective

148:   Input Parameters:
149: + matfd - the coloring context
150: . error - relative error
151: - umin  - minimum allowable u-value magnitude

153:   Level: advanced

155:   Note:
156:   The Jacobian is estimated with the differencing approximation
157: .vb
158:        F'(u)_{:,i} = [F(u+h*dx_{i}) - F(u)]/h where
159:        htype = 'ds':
160:          h = error_rel*u[i]                 if  abs(u[i]) > umin
161:            = +/- error_rel*umin             otherwise, with +/- determined by the sign of u[i]
162:          dx_{i} = (0, ... 1, .... 0)

164:        htype = 'wp':
165:          h = error_rel * sqrt(1 + ||u||)
166: .ve

168: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringSetFromOptions()`
169: @*/
170: PetscErrorCode MatFDColoringSetParameters(MatFDColoring matfd, PetscReal error, PetscReal umin)
171: {
172:   PetscFunctionBegin;
176:   if (error != (PetscReal)PETSC_DEFAULT) matfd->error_rel = error;
177:   if (umin != (PetscReal)PETSC_DEFAULT) matfd->umin = umin;
178:   PetscFunctionReturn(PETSC_SUCCESS);
179: }

181: /*@
182:   MatFDColoringSetBlockSize - Sets block size for efficient inserting entries of Jacobian matrix.

184:   Logically Collective

186:   Input Parameters:
187: + matfd - the coloring context
188: . brows - number of rows in the block
189: - bcols - number of columns in the block

191:   Level: intermediate

193: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringSetFromOptions()`
194: @*/
195: PetscErrorCode MatFDColoringSetBlockSize(MatFDColoring matfd, PetscInt brows, PetscInt bcols)
196: {
197:   PetscFunctionBegin;
201:   if (brows != PETSC_DEFAULT) matfd->brows = brows;
202:   if (bcols != PETSC_DEFAULT) matfd->bcols = bcols;
203:   PetscFunctionReturn(PETSC_SUCCESS);
204: }

206: /*@
207:   MatFDColoringSetUp - Sets up the internal data structures of matrix coloring context for the later use.

209:   Collective

211:   Input Parameters:
212: + mat        - the matrix containing the nonzero structure of the Jacobian
213: . iscoloring - the coloring of the matrix; usually obtained with `MatGetColoring()` or `DMCreateColoring()`
214: - color      - the matrix coloring context

216:   Level: beginner

218:   Notes:
219:   When the coloring type is `IS_COLORING_LOCAL` the coloring is in the local ordering of the unknowns.

221: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringDestroy()`
222: @*/
223: PetscErrorCode MatFDColoringSetUp(Mat mat, ISColoring iscoloring, MatFDColoring color)
224: {
225:   PetscBool eq;

227:   PetscFunctionBegin;
230:   if (color->setupcalled) PetscFunctionReturn(PETSC_SUCCESS);
231:   PetscCall(PetscObjectCompareId((PetscObject)mat, color->matid, &eq));
232:   PetscCheck(eq, PetscObjectComm((PetscObject)mat), PETSC_ERR_ARG_WRONG, "Matrix used with MatFDColoringSetUp() must be that used with MatFDColoringCreate()");

234:   PetscCall(PetscLogEventBegin(MAT_FDColoringSetUp, mat, 0, 0, 0));
235:   PetscUseTypeMethod(mat, fdcoloringsetup, iscoloring, color);

237:   color->setupcalled = PETSC_TRUE;
238:   PetscCall(PetscLogEventEnd(MAT_FDColoringSetUp, mat, 0, 0, 0));
239:   PetscFunctionReturn(PETSC_SUCCESS);
240: }

242: /*@C
243:   MatFDColoringGetFunction - Gets the function to use for computing the Jacobian.

245:   Not Collective

247:   Input Parameter:
248: . matfd - the coloring context

250:   Output Parameters:
251: + f    - the function, see `MatFDColoringFn` for the calling sequence
252: - fctx - the optional user-defined function context

254:   Level: intermediate

256: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringSetFunction()`, `MatFDColoringSetFromOptions()`, `MatFDColoringFn`
257: @*/
258: PetscErrorCode MatFDColoringGetFunction(MatFDColoring matfd, MatFDColoringFn **f, void **fctx)
259: {
260:   PetscFunctionBegin;
262:   if (f) *f = matfd->f;
263:   if (fctx) *fctx = matfd->fctx;
264:   PetscFunctionReturn(PETSC_SUCCESS);
265: }

267: /*@C
268:   MatFDColoringSetFunction - Sets the function to use for computing the Jacobian.

270:   Logically Collective

272:   Input Parameters:
273: + matfd - the coloring context
274: . f     - the function, see `MatFDColoringFn` for the calling sequence
275: - fctx  - the optional user-defined function context

277:   Level: advanced

279:   Note:
280:   This function is usually used automatically by `SNES` (when one uses `SNESSetJacobian()` with the argument
281:   `SNESComputeJacobianDefaultColor()`) and only needs to be used by someone computing a matrix via coloring directly by
282:   calling `MatFDColoringApply()`

284:   Fortran Note:
285:   In Fortran you must call `MatFDColoringSetFunction()` for a coloring object to
286:   be used without `SNES` or within the `SNES` solvers.

288: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringGetFunction()`, `MatFDColoringSetFromOptions()`, `MatFDColoringFn`
289: @*/
290: PetscErrorCode MatFDColoringSetFunction(MatFDColoring matfd, MatFDColoringFn *f, void *fctx)
291: {
292:   PetscFunctionBegin;
294:   matfd->f    = f;
295:   matfd->fctx = fctx;
296:   PetscFunctionReturn(PETSC_SUCCESS);
297: }

299: /*@
300:   MatFDColoringSetFromOptions - Sets coloring finite difference parameters from
301:   the options database.

303:   Collective

305:   The Jacobian, F'(u), is estimated with the differencing approximation
306: .vb
307:        F'(u)_{:,i} = [F(u+h*dx_{i}) - F(u)]/h where
308:        h = error_rel*u[i]                 if  abs(u[i]) > umin
309:          = +/- error_rel*umin             otherwise, with +/- determined by the sign of u[i]
310:        dx_{i} = (0, ... 1, .... 0)
311: .ve

313:   Input Parameter:
314: . matfd - the coloring context

316:   Options Database Keys:
317: + -mat_fd_coloring_err <err>         - Sets <err> (square root of relative error in the function)
318: . -mat_fd_coloring_umin <umin>       - Sets umin, the minimum allowable u-value magnitude
319: . -mat_fd_type                       - "wp" or "ds" (see `MATMFFD_WP` or `MATMFFD_DS`)
320: . -mat_fd_coloring_view              - Activates basic viewing
321: . -mat_fd_coloring_view ::ascii_info - Activates viewing info
322: - -mat_fd_coloring_view draw         - Activates drawing

324:   Level: intermediate

326: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringView()`, `MatFDColoringSetParameters()`
327: @*/
328: PetscErrorCode MatFDColoringSetFromOptions(MatFDColoring matfd)
329: {
330:   PetscBool flg;
331:   char      value[3];

333:   PetscFunctionBegin;

336:   PetscObjectOptionsBegin((PetscObject)matfd);
337:   PetscCall(PetscOptionsReal("-mat_fd_coloring_err", "Square root of relative error in function", "MatFDColoringSetParameters", matfd->error_rel, &matfd->error_rel, NULL));
338:   PetscCall(PetscOptionsReal("-mat_fd_coloring_umin", "Minimum allowable u magnitude", "MatFDColoringSetParameters", matfd->umin, &matfd->umin, NULL));
339:   PetscCall(PetscOptionsString("-mat_fd_type", "Algorithm to compute h, wp or ds", "MatFDColoringCreate", matfd->htype, value, sizeof(value), &flg));
340:   if (flg) {
341:     if (value[0] == 'w' && value[1] == 'p') matfd->htype = "wp";
342:     else if (value[0] == 'd' && value[1] == 's') matfd->htype = "ds";
343:     else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unknown finite differencing type %s", value);
344:   }
345:   PetscCall(PetscOptionsInt("-mat_fd_coloring_brows", "Number of block rows", "MatFDColoringSetBlockSize", matfd->brows, &matfd->brows, NULL));
346:   PetscCall(PetscOptionsInt("-mat_fd_coloring_bcols", "Number of block columns", "MatFDColoringSetBlockSize", matfd->bcols, &matfd->bcols, &flg));
347:   if (flg && matfd->bcols > matfd->ncolors) {
348:     /* input bcols cannot be > matfd->ncolors, thus set it as ncolors */
349:     matfd->bcols = matfd->ncolors;
350:   }

352:   /* process any options handlers added with PetscObjectAddOptionsHandler() */
353:   PetscCall(PetscObjectProcessOptionsHandlers((PetscObject)matfd, PetscOptionsObject));
354:   PetscOptionsEnd();
355:   PetscFunctionReturn(PETSC_SUCCESS);
356: }

358: /*@
359:   MatFDColoringSetType - Sets the approach for computing the finite difference parameter

361:   Collective

363:   Input Parameters:
364: + matfd - the coloring context
365: - type  - either `MATMFFD_WP` or `MATMFFD_DS`

367:   Options Database Key:
368: . -mat_fd_type - "wp" or "ds"

370:   Level: intermediate

372:   Note:
373:   It is goofy that the argument type is `MatMFFDType` since the `MatFDColoring` actually computes the matrix entries
374:   but the process of computing the entries is the same as with the `MATMFFD` operation so we should reuse the names instead of
375:   introducing another one.

377: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringView()`, `MatFDColoringSetParameters()`
378: @*/
379: PetscErrorCode MatFDColoringSetType(MatFDColoring matfd, MatMFFDType type)
380: {
381:   PetscFunctionBegin;
383:   /*
384:      It is goofy to handle the strings this way but currently there is no code to free a dynamically created matfd->htype
385:      and this function is being provided as patch for a release so it shouldn't change the implementation
386:   */
387:   if (type[0] == 'w' && type[1] == 'p') matfd->htype = "wp";
388:   else if (type[0] == 'd' && type[1] == 's') matfd->htype = "ds";
389:   else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unknown finite differencing type %s", type);
390:   PetscCall(PetscObjectChangeTypeName((PetscObject)matfd, type));
391:   PetscFunctionReturn(PETSC_SUCCESS);
392: }

394: static PetscErrorCode MatFDColoringViewFromOptions(MatFDColoring fd, const char prefix[], const char optionname[])
395: {
396:   PetscBool         flg;
397:   PetscViewer       viewer;
398:   PetscViewerFormat format;

400:   PetscFunctionBegin;
401:   if (prefix) {
402:     PetscCall(PetscOptionsCreateViewer(PetscObjectComm((PetscObject)fd), ((PetscObject)fd)->options, prefix, optionname, &viewer, &format, &flg));
403:   } else {
404:     PetscCall(PetscOptionsCreateViewer(PetscObjectComm((PetscObject)fd), ((PetscObject)fd)->options, ((PetscObject)fd)->prefix, optionname, &viewer, &format, &flg));
405:   }
406:   if (flg) {
407:     PetscCall(PetscViewerPushFormat(viewer, format));
408:     PetscCall(MatFDColoringView(fd, viewer));
409:     PetscCall(PetscViewerPopFormat(viewer));
410:     PetscCall(PetscViewerDestroy(&viewer));
411:   }
412:   PetscFunctionReturn(PETSC_SUCCESS);
413: }

415: /*@
416:   MatFDColoringCreate - Creates a matrix coloring context for finite difference
417:   computation of Jacobians.

419:   Collective

421:   Input Parameters:
422: + mat        - the matrix containing the nonzero structure of the Jacobian
423: - iscoloring - the coloring of the matrix; usually obtained with `MatColoringCreate()` or `DMCreateColoring()`

425:   Output Parameter:
426: . color - the new coloring context

428:   Level: intermediate

430: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringDestroy()`, `SNESComputeJacobianDefaultColor()`, `ISColoringCreate()`,
431:           `MatFDColoringSetFunction()`, `MatFDColoringSetFromOptions()`, `MatFDColoringApply()`,
432:           `MatFDColoringView()`, `MatFDColoringSetParameters()`, `MatColoringCreate()`, `DMCreateColoring()`, `MatFDColoringSetValues()`
433: @*/
434: PetscErrorCode MatFDColoringCreate(Mat mat, ISColoring iscoloring, MatFDColoring *color)
435: {
436:   MatFDColoring c;
437:   MPI_Comm      comm;
438:   PetscInt      M, N;

440:   PetscFunctionBegin;
442:   PetscAssertPointer(color, 3);
443:   PetscCheck(mat->assembled, PetscObjectComm((PetscObject)mat), PETSC_ERR_ARG_WRONGSTATE, "Matrix must be assembled by calls to MatAssemblyBegin/End();");
444:   PetscCall(PetscLogEventBegin(MAT_FDColoringCreate, mat, 0, 0, 0));
445:   PetscCall(MatGetSize(mat, &M, &N));
446:   PetscCheck(M == N, PetscObjectComm((PetscObject)mat), PETSC_ERR_SUP, "Only for square matrices");
447:   PetscCall(PetscObjectGetComm((PetscObject)mat, &comm));
448:   PetscCall(PetscHeaderCreate(c, MAT_FDCOLORING_CLASSID, "MatFDColoring", "Jacobian computation via finite differences with coloring", "Mat", comm, MatFDColoringDestroy, MatFDColoringView));

450:   c->ctype = iscoloring->ctype;
451:   PetscCall(PetscObjectGetId((PetscObject)mat, &c->matid));

453:   PetscUseTypeMethod(mat, fdcoloringcreate, iscoloring, c);

455:   PetscCall(MatCreateVecs(mat, NULL, &c->w1));
456:   /* Vec is used intensively in particular piece of scalar CPU code; won't benefit from bouncing back and forth to the GPU */
457:   PetscCall(VecBindToCPU(c->w1, PETSC_TRUE));
458:   PetscCall(VecDuplicate(c->w1, &c->w2));
459:   /* Vec is used intensively in particular piece of scalar CPU code; won't benefit from bouncing back and forth to the GPU */
460:   PetscCall(VecBindToCPU(c->w2, PETSC_TRUE));

462:   c->error_rel    = PETSC_SQRT_MACHINE_EPSILON;
463:   c->umin         = 100.0 * PETSC_SQRT_MACHINE_EPSILON;
464:   c->currentcolor = -1;
465:   c->htype        = "wp";
466:   c->fset         = PETSC_FALSE;
467:   c->setupcalled  = PETSC_FALSE;

469:   *color = c;
470:   PetscCall(PetscObjectCompose((PetscObject)mat, "SNESMatFDColoring", (PetscObject)c));
471:   PetscCall(PetscLogEventEnd(MAT_FDColoringCreate, mat, 0, 0, 0));
472:   PetscFunctionReturn(PETSC_SUCCESS);
473: }

475: /*@
476:   MatFDColoringDestroy - Destroys a matrix coloring context that was created
477:   via `MatFDColoringCreate()`.

479:   Collective

481:   Input Parameter:
482: . c - coloring context

484:   Level: intermediate

486: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`
487: @*/
488: PetscErrorCode MatFDColoringDestroy(MatFDColoring *c)
489: {
490:   PetscInt      i;
491:   MatFDColoring color = *c;

493:   PetscFunctionBegin;
494:   if (!*c) PetscFunctionReturn(PETSC_SUCCESS);
495:   if (--((PetscObject)color)->refct > 0) {
496:     *c = NULL;
497:     PetscFunctionReturn(PETSC_SUCCESS);
498:   }

500:   /* we do not free the column arrays since their entries are owned by the ISs in color->isa */
501:   for (i = 0; i < color->ncolors; i++) PetscCall(ISDestroy(&color->isa[i]));
502:   PetscCall(PetscFree(color->isa));
503:   PetscCall(PetscFree2(color->ncolumns, color->columns));
504:   PetscCall(PetscFree(color->nrows));
505:   if (color->htype[0] == 'w') {
506:     PetscCall(PetscFree(color->matentry2));
507:   } else {
508:     PetscCall(PetscFree(color->matentry));
509:   }
510:   PetscCall(PetscFree(color->dy));
511:   if (color->vscale) PetscCall(VecDestroy(&color->vscale));
512:   PetscCall(VecDestroy(&color->w1));
513:   PetscCall(VecDestroy(&color->w2));
514:   PetscCall(VecDestroy(&color->w3));
515:   PetscCall(PetscHeaderDestroy(c));
516:   PetscFunctionReturn(PETSC_SUCCESS);
517: }

519: /*@C
520:   MatFDColoringGetPerturbedColumns - Returns the indices of the columns that
521:   that are currently being perturbed.

523:   Not Collective

525:   Input Parameter:
526: . coloring - coloring context created with `MatFDColoringCreate()`

528:   Output Parameters:
529: + n    - the number of local columns being perturbed
530: - cols - the column indices, in global numbering

532:   Level: advanced

534:   Note:
535:   IF the matrix type is `MATBAIJ`, then the block column indices are returned

537:   Fortran Note:
538: .vb
539:   PetscInt, pointer :: cols(:)
540: .ve
541:   Use `PETSC_NULL_INTEGER` if `n` is not needed

543: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringDestroy()`, `MatFDColoringView()`, `MatFDColoringApply()`
544: @*/
545: PetscErrorCode MatFDColoringGetPerturbedColumns(MatFDColoring coloring, PetscInt *n, const PetscInt *cols[])
546: {
547:   PetscFunctionBegin;
548:   if (coloring->currentcolor >= 0) {
549:     *n    = coloring->ncolumns[coloring->currentcolor];
550:     *cols = coloring->columns[coloring->currentcolor];
551:   } else {
552:     *n = 0;
553:   }
554:   PetscFunctionReturn(PETSC_SUCCESS);
555: }

557: /*@
558:   MatFDColoringApply - Given a matrix for which a `MatFDColoring` context
559:   has been created, computes the Jacobian for a function via finite differences.

561:   Collective

563:   Input Parameters:
564: + J        - matrix to store Jacobian entries into
565: . coloring - coloring context created with `MatFDColoringCreate()`
566: . x1       - location at which Jacobian is to be computed
567: - sctx     - context required by function, if this is being used with the `SNES` solver then it is `SNES` object, otherwise it is `NULL`

569:   Options Database Keys:
570: + -mat_fd_type                       - "wp" or "ds"  (see `MATMFFD_WP` or `MATMFFD_DS`)
571: . -mat_fd_coloring_view              - Activates basic viewing or coloring
572: . -mat_fd_coloring_view draw         - Activates drawing of coloring
573: - -mat_fd_coloring_view ::ascii_info - Activates viewing of coloring info

575:   Level: intermediate

577: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringDestroy()`, `MatFDColoringView()`, `MatFDColoringSetFunction()`, `MatFDColoringSetValues()`
578: @*/
579: PetscErrorCode MatFDColoringApply(Mat J, MatFDColoring coloring, Vec x1, void *sctx)
580: {
581:   PetscBool eq;

583:   PetscFunctionBegin;
587:   PetscCall(PetscObjectCompareId((PetscObject)J, coloring->matid, &eq));
588:   PetscCheck(eq, PetscObjectComm((PetscObject)J), PETSC_ERR_ARG_WRONG, "Matrix used with MatFDColoringApply() must be that used with MatFDColoringCreate()");
589:   PetscCheck(coloring->f, PetscObjectComm((PetscObject)J), PETSC_ERR_ARG_WRONGSTATE, "Must call MatFDColoringSetFunction()");
590:   PetscCheck(coloring->setupcalled, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Must call MatFDColoringSetUp()");

592:   PetscCall(MatSetUnfactored(J));
593:   PetscCall(PetscLogEventBegin(MAT_FDColoringApply, coloring, J, x1, 0));
594:   PetscUseTypeMethod(J, fdcoloringapply, coloring, x1, sctx);
595:   PetscCall(PetscLogEventEnd(MAT_FDColoringApply, coloring, J, x1, 0));
596:   if (!coloring->viewed) {
597:     PetscCall(MatFDColoringViewFromOptions(coloring, NULL, "-mat_fd_coloring_view"));
598:     coloring->viewed = PETSC_TRUE;
599:   }
600:   PetscFunctionReturn(PETSC_SUCCESS);
601: }