Date: 2025-03-29T05:58:35+00:00

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
    252: - fctx - the optional user-defined function context

    254:   Level: intermediate

    256: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringSetFunction()`, `MatFDColoringSetFromOptions()`
    257: @*/
    258: PetscErrorCode MatFDColoringGetFunction(MatFDColoring matfd, PetscErrorCode (**f)(void), 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
    275: - fctx  - the optional user-defined function context

    277:   Level: advanced

    279:   Note:
    280:   `f` has two possible calling configurations\:
    281: $ PetscErrorCode f(SNES snes, Vec in, Vec out, void *fctx)
    282: + snes - the nonlinear solver `SNES` object
    283: . in   - the location where the Jacobian is to be computed
    284: . out  - the location to put the computed function value
    285: - fctx - the function context

    287:   and
    288: $ PetscErrorCode f(void *dummy, Vec in, Vec out, void *fctx)
    289: + dummy - an unused parameter
    290: . in    - the location where the Jacobian is to be computed
    291: . out   - the location to put the computed function value
    292: - fctx  - the function context

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

    298:   Fortran Notes:
    299:   In Fortran you must call `MatFDColoringSetFunction()` for a coloring object to
    300:   be used without `SNES` or within the `SNES` solvers.

    302: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringGetFunction()`, `MatFDColoringSetFromOptions()`
    303: @*/
    304: PetscErrorCode MatFDColoringSetFunction(MatFDColoring matfd, PetscErrorCode (*f)(void), void *fctx)
    305: {
    306:   PetscFunctionBegin;
    308:   matfd->f    = f;
    309:   matfd->fctx = fctx;
    310:   PetscFunctionReturn(PETSC_SUCCESS);
    311: }

    313: /*@
    314:   MatFDColoringSetFromOptions - Sets coloring finite difference parameters from
    315:   the options database.

    317:   Collective

    319:   The Jacobian, F'(u), is estimated with the differencing approximation
    320: .vb
    321:        F'(u)_{:,i} = [F(u+h*dx_{i}) - F(u)]/h where
    322:        h = error_rel*u[i]                 if  abs(u[i]) > umin
    323:          = +/- error_rel*umin             otherwise, with +/- determined by the sign of u[i]
    324:        dx_{i} = (0, ... 1, .... 0)
    325: .ve

    327:   Input Parameter:
    328: . matfd - the coloring context

    330:   Options Database Keys:
    331: + -mat_fd_coloring_err <err>         - Sets <err> (square root of relative error in the function)
    332: . -mat_fd_coloring_umin <umin>       - Sets umin, the minimum allowable u-value magnitude
    333: . -mat_fd_type                       - "wp" or "ds" (see `MATMFFD_WP` or `MATMFFD_DS`)
    334: . -mat_fd_coloring_view              - Activates basic viewing
    335: . -mat_fd_coloring_view ::ascii_info - Activates viewing info
    336: - -mat_fd_coloring_view draw         - Activates drawing

    338:   Level: intermediate

    340: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringView()`, `MatFDColoringSetParameters()`
    341: @*/
    342: PetscErrorCode MatFDColoringSetFromOptions(MatFDColoring matfd)
    343: {
    344:   PetscBool flg;
    345:   char      value[3];

    347:   PetscFunctionBegin;

    350:   PetscObjectOptionsBegin((PetscObject)matfd);
    351:   PetscCall(PetscOptionsReal("-mat_fd_coloring_err", "Square root of relative error in function", "MatFDColoringSetParameters", matfd->error_rel, &matfd->error_rel, NULL));
    352:   PetscCall(PetscOptionsReal("-mat_fd_coloring_umin", "Minimum allowable u magnitude", "MatFDColoringSetParameters", matfd->umin, &matfd->umin, NULL));
    353:   PetscCall(PetscOptionsString("-mat_fd_type", "Algorithm to compute h, wp or ds", "MatFDColoringCreate", matfd->htype, value, sizeof(value), &flg));
    354:   if (flg) {
    355:     if (value[0] == 'w' && value[1] == 'p') matfd->htype = "wp";
    356:     else if (value[0] == 'd' && value[1] == 's') matfd->htype = "ds";
    357:     else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unknown finite differencing type %s", value);
    358:   }
    359:   PetscCall(PetscOptionsInt("-mat_fd_coloring_brows", "Number of block rows", "MatFDColoringSetBlockSize", matfd->brows, &matfd->brows, NULL));
    360:   PetscCall(PetscOptionsInt("-mat_fd_coloring_bcols", "Number of block columns", "MatFDColoringSetBlockSize", matfd->bcols, &matfd->bcols, &flg));
    361:   if (flg && matfd->bcols > matfd->ncolors) {
    362:     /* input bcols cannot be > matfd->ncolors, thus set it as ncolors */
    363:     matfd->bcols = matfd->ncolors;
    364:   }

    366:   /* process any options handlers added with PetscObjectAddOptionsHandler() */
    367:   PetscCall(PetscObjectProcessOptionsHandlers((PetscObject)matfd, PetscOptionsObject));
    368:   PetscOptionsEnd();
    369:   PetscFunctionReturn(PETSC_SUCCESS);
    370: }

    372: /*@
    373:   MatFDColoringSetType - Sets the approach for computing the finite difference parameter

    375:   Collective

    377:   Input Parameters:
    378: + matfd - the coloring context
    379: - type  - either `MATMFFD_WP` or `MATMFFD_DS`

    381:   Options Database Key:
    382: . -mat_fd_type - "wp" or "ds"

    384:   Level: intermediate

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

    391: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringView()`, `MatFDColoringSetParameters()`
    392: @*/
    393: PetscErrorCode MatFDColoringSetType(MatFDColoring matfd, MatMFFDType type)
    394: {
    395:   PetscFunctionBegin;
    397:   /*
    398:      It is goofy to handle the strings this way but currently there is no code to free a dynamically created matfd->htype
    399:      and this function is being provided as patch for a release so it shouldn't change the implementation
    400:   */
    401:   if (type[0] == 'w' && type[1] == 'p') matfd->htype = "wp";
    402:   else if (type[0] == 'd' && type[1] == 's') matfd->htype = "ds";
    403:   else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unknown finite differencing type %s", type);
    404:   PetscCall(PetscObjectChangeTypeName((PetscObject)matfd, type));
    405:   PetscFunctionReturn(PETSC_SUCCESS);
    406: }

    408: static PetscErrorCode MatFDColoringViewFromOptions(MatFDColoring fd, const char prefix[], const char optionname[])
    409: {
    410:   PetscBool         flg;
    411:   PetscViewer       viewer;
    412:   PetscViewerFormat format;

    414:   PetscFunctionBegin;
    415:   if (prefix) {
    416:     PetscCall(PetscOptionsCreateViewer(PetscObjectComm((PetscObject)fd), ((PetscObject)fd)->options, prefix, optionname, &viewer, &format, &flg));
    417:   } else {
    418:     PetscCall(PetscOptionsCreateViewer(PetscObjectComm((PetscObject)fd), ((PetscObject)fd)->options, ((PetscObject)fd)->prefix, optionname, &viewer, &format, &flg));
    419:   }
    420:   if (flg) {
    421:     PetscCall(PetscViewerPushFormat(viewer, format));
    422:     PetscCall(MatFDColoringView(fd, viewer));
    423:     PetscCall(PetscViewerPopFormat(viewer));
    424:     PetscCall(PetscViewerDestroy(&viewer));
    425:   }
    426:   PetscFunctionReturn(PETSC_SUCCESS);
    427: }

    429: /*@
    430:   MatFDColoringCreate - Creates a matrix coloring context for finite difference
    431:   computation of Jacobians.

    433:   Collective

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

    439:   Output Parameter:
    440: . color - the new coloring context

    442:   Level: intermediate

    444: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringDestroy()`, `SNESComputeJacobianDefaultColor()`, `ISColoringCreate()`,
    445:           `MatFDColoringSetFunction()`, `MatFDColoringSetFromOptions()`, `MatFDColoringApply()`,
    446:           `MatFDColoringView()`, `MatFDColoringSetParameters()`, `MatColoringCreate()`, `DMCreateColoring()`, `MatFDColoringSetValues()`
    447: @*/
    448: PetscErrorCode MatFDColoringCreate(Mat mat, ISColoring iscoloring, MatFDColoring *color)
    449: {
    450:   MatFDColoring c;
    451:   MPI_Comm      comm;
    452:   PetscInt      M, N;

    454:   PetscFunctionBegin;
    456:   PetscAssertPointer(color, 3);
    457:   PetscCheck(mat->assembled, PetscObjectComm((PetscObject)mat), PETSC_ERR_ARG_WRONGSTATE, "Matrix must be assembled by calls to MatAssemblyBegin/End();");
    458:   PetscCall(PetscLogEventBegin(MAT_FDColoringCreate, mat, 0, 0, 0));
    459:   PetscCall(MatGetSize(mat, &M, &N));
    460:   PetscCheck(M == N, PetscObjectComm((PetscObject)mat), PETSC_ERR_SUP, "Only for square matrices");
    461:   PetscCall(PetscObjectGetComm((PetscObject)mat, &comm));
    462:   PetscCall(PetscHeaderCreate(c, MAT_FDCOLORING_CLASSID, "MatFDColoring", "Jacobian computation via finite differences with coloring", "Mat", comm, MatFDColoringDestroy, MatFDColoringView));

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

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

    469:   PetscCall(MatCreateVecs(mat, NULL, &c->w1));
    470:   /* Vec is used intensively in particular piece of scalar CPU code; won't benefit from bouncing back and forth to the GPU */
    471:   PetscCall(VecBindToCPU(c->w1, PETSC_TRUE));
    472:   PetscCall(VecDuplicate(c->w1, &c->w2));
    473:   /* Vec is used intensively in particular piece of scalar CPU code; won't benefit from bouncing back and forth to the GPU */
    474:   PetscCall(VecBindToCPU(c->w2, PETSC_TRUE));

    476:   c->error_rel    = PETSC_SQRT_MACHINE_EPSILON;
    477:   c->umin         = 100.0 * PETSC_SQRT_MACHINE_EPSILON;
    478:   c->currentcolor = -1;
    479:   c->htype        = "wp";
    480:   c->fset         = PETSC_FALSE;
    481:   c->setupcalled  = PETSC_FALSE;

    483:   *color = c;
    484:   PetscCall(PetscObjectCompose((PetscObject)mat, "SNESMatFDColoring", (PetscObject)c));
    485:   PetscCall(PetscLogEventEnd(MAT_FDColoringCreate, mat, 0, 0, 0));
    486:   PetscFunctionReturn(PETSC_SUCCESS);
    487: }

    489: /*@
    490:   MatFDColoringDestroy - Destroys a matrix coloring context that was created
    491:   via `MatFDColoringCreate()`.

    493:   Collective

    495:   Input Parameter:
    496: . c - coloring context

    498:   Level: intermediate

    500: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`
    501: @*/
    502: PetscErrorCode MatFDColoringDestroy(MatFDColoring *c)
    503: {
    504:   PetscInt      i;
    505:   MatFDColoring color = *c;

    507:   PetscFunctionBegin;
    508:   if (!*c) PetscFunctionReturn(PETSC_SUCCESS);
    509:   if (--((PetscObject)color)->refct > 0) {
    510:     *c = NULL;
    511:     PetscFunctionReturn(PETSC_SUCCESS);
    512:   }

    514:   /* we do not free the column arrays since their entries are owned by the ISs in color->isa */
    515:   for (i = 0; i < color->ncolors; i++) PetscCall(ISDestroy(&color->isa[i]));
    516:   PetscCall(PetscFree(color->isa));
    517:   PetscCall(PetscFree2(color->ncolumns, color->columns));
    518:   PetscCall(PetscFree(color->nrows));
    519:   if (color->htype[0] == 'w') {
    520:     PetscCall(PetscFree(color->matentry2));
    521:   } else {
    522:     PetscCall(PetscFree(color->matentry));
    523:   }
    524:   PetscCall(PetscFree(color->dy));
    525:   if (color->vscale) PetscCall(VecDestroy(&color->vscale));
    526:   PetscCall(VecDestroy(&color->w1));
    527:   PetscCall(VecDestroy(&color->w2));
    528:   PetscCall(VecDestroy(&color->w3));
    529:   PetscCall(PetscHeaderDestroy(c));
    530:   PetscFunctionReturn(PETSC_SUCCESS);
    531: }

    533: /*@C
    534:   MatFDColoringGetPerturbedColumns - Returns the indices of the columns that
    535:   that are currently being perturbed.

    537:   Not Collective

    539:   Input Parameter:
    540: . coloring - coloring context created with `MatFDColoringCreate()`

    542:   Output Parameters:
    543: + n    - the number of local columns being perturbed
    544: - cols - the column indices, in global numbering

    546:   Level: advanced

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

    551:   Fortran Note:
    552: .vb
    553:   PetscInt, pointer :: cols(:)
    554: .ve
    555:   Use `PETSC_NULL_INT` if `n` is not needed

    557: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringDestroy()`, `MatFDColoringView()`, `MatFDColoringApply()`
    558: @*/
    559: PetscErrorCode MatFDColoringGetPerturbedColumns(MatFDColoring coloring, PetscInt *n, const PetscInt *cols[])
    560: {
    561:   PetscFunctionBegin;
    562:   if (coloring->currentcolor >= 0) {
    563:     *n    = coloring->ncolumns[coloring->currentcolor];
    564:     *cols = coloring->columns[coloring->currentcolor];
    565:   } else {
    566:     *n = 0;
    567:   }
    568:   PetscFunctionReturn(PETSC_SUCCESS);
    569: }

    571: /*@
    572:   MatFDColoringApply - Given a matrix for which a `MatFDColoring` context
    573:   has been created, computes the Jacobian for a function via finite differences.

    575:   Collective

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

    583:   Options Database Keys:
    584: + -mat_fd_type                       - "wp" or "ds"  (see `MATMFFD_WP` or `MATMFFD_DS`)
    585: . -mat_fd_coloring_view              - Activates basic viewing or coloring
    586: . -mat_fd_coloring_view draw         - Activates drawing of coloring
    587: - -mat_fd_coloring_view ::ascii_info - Activates viewing of coloring info

    589:   Level: intermediate

    591: .seealso: `Mat`, `MatFDColoring`, `MatFDColoringCreate()`, `MatFDColoringDestroy()`, `MatFDColoringView()`, `MatFDColoringSetFunction()`, `MatFDColoringSetValues()`
    592: @*/
    593: PetscErrorCode MatFDColoringApply(Mat J, MatFDColoring coloring, Vec x1, void *sctx)
    594: {
    595:   PetscBool eq;

    597:   PetscFunctionBegin;
    601:   PetscCall(PetscObjectCompareId((PetscObject)J, coloring->matid, &eq));
    602:   PetscCheck(eq, PetscObjectComm((PetscObject)J), PETSC_ERR_ARG_WRONG, "Matrix used with MatFDColoringApply() must be that used with MatFDColoringCreate()");
    603:   PetscCheck(coloring->f, PetscObjectComm((PetscObject)J), PETSC_ERR_ARG_WRONGSTATE, "Must call MatFDColoringSetFunction()");
    604:   PetscCheck(coloring->setupcalled, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Must call MatFDColoringSetUp()");

    606:   PetscCall(MatSetUnfactored(J));
    607:   PetscCall(PetscLogEventBegin(MAT_FDColoringApply, coloring, J, x1, 0));
    608:   PetscUseTypeMethod(J, fdcoloringapply, coloring, x1, sctx);
    609:   PetscCall(PetscLogEventEnd(MAT_FDColoringApply, coloring, J, x1, 0));
    610:   if (!coloring->viewed) {
    611:     PetscCall(MatFDColoringViewFromOptions(coloring, NULL, "-mat_fd_coloring_view"));
    612:     coloring->viewed = PETSC_TRUE;
    613:   }
    614:   PetscFunctionReturn(PETSC_SUCCESS);
    615: }