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 src/mat/matimpl.h
8: /* Logging support */
9: PetscCookie MAT_FDCOLORING_COOKIE = 0;
13: PetscErrorCode MatFDColoringSetF(MatFDColoring fd,Vec F)
14: {
16: fd->F = F;
17: return(0);
18: }
22: static PetscErrorCode MatFDColoringView_Draw_Zoom(PetscDraw draw,void *Aa)
23: {
24: MatFDColoring fd = (MatFDColoring)Aa;
26: PetscInt i,j;
27: PetscReal x,y;
31: /* loop over colors */
32: for (i=0; i<fd->ncolors; i++) {
33: for (j=0; j<fd->nrows[i]; j++) {
34: y = fd->M - fd->rows[i][j] - fd->rstart;
35: x = fd->columnsforrow[i][j];
36: PetscDrawRectangle(draw,x,y,x+1,y+1,i+1,i+1,i+1,i+1);
37: }
38: }
39: return(0);
40: }
44: static PetscErrorCode MatFDColoringView_Draw(MatFDColoring fd,PetscViewer viewer)
45: {
47: PetscTruth isnull;
48: PetscDraw draw;
49: PetscReal xr,yr,xl,yl,h,w;
52: PetscViewerDrawGetDraw(viewer,0,&draw);
53: PetscDrawIsNull(draw,&isnull); if (isnull) return(0);
55: PetscObjectCompose((PetscObject)fd,"Zoomviewer",(PetscObject)viewer);
57: xr = fd->N; yr = fd->M; h = yr/10.0; w = xr/10.0;
58: xr += w; yr += h; xl = -w; yl = -h;
59: PetscDrawSetCoordinates(draw,xl,yl,xr,yr);
60: PetscDrawZoom(draw,MatFDColoringView_Draw_Zoom,fd);
61: PetscObjectCompose((PetscObject)fd,"Zoomviewer",PETSC_NULL);
62: return(0);
63: }
67: /*@C
68: MatFDColoringView - Views a finite difference coloring context.
70: Collective on MatFDColoring
72: Input Parameters:
73: + c - the coloring context
74: - viewer - visualization context
76: Level: intermediate
78: Notes:
79: The available visualization contexts include
80: + PETSC_VIEWER_STDOUT_SELF - standard output (default)
81: . PETSC_VIEWER_STDOUT_WORLD - synchronized standard
82: output where only the first processor opens
83: the file. All other processors send their
84: data to the first processor to print.
85: - PETSC_VIEWER_DRAW_WORLD - graphical display of nonzero structure
87: Notes:
88: Since PETSc uses only a small number of basic colors (currently 33), if the coloring
89: involves more than 33 then some seemingly identical colors are displayed making it look
90: like an illegal coloring. This is just a graphical artifact.
92: .seealso: MatFDColoringCreate()
94: .keywords: Mat, finite differences, coloring, view
95: @*/
96: PetscErrorCode MatFDColoringView(MatFDColoring c,PetscViewer viewer)
97: {
98: PetscErrorCode ierr;
99: PetscInt i,j;
100: PetscTruth isdraw,iascii;
101: PetscViewerFormat format;
105: if (!viewer) viewer = PETSC_VIEWER_STDOUT_(c->comm);
109: PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_DRAW,&isdraw);
110: PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_ASCII,&iascii);
111: if (isdraw) {
112: MatFDColoringView_Draw(c,viewer);
113: } else if (iascii) {
114: PetscViewerASCIIPrintf(viewer,"MatFDColoring Object:\n");
115: PetscViewerASCIIPrintf(viewer," Error tolerance=%g\n",c->error_rel);
116: PetscViewerASCIIPrintf(viewer," Umin=%g\n",c->umin);
117: PetscViewerASCIIPrintf(viewer," Number of colors=%D\n",c->ncolors);
119: PetscViewerGetFormat(viewer,&format);
120: if (format != PETSC_VIEWER_ASCII_INFO) {
121: for (i=0; i<c->ncolors; i++) {
122: PetscViewerASCIIPrintf(viewer," Information for color %D\n",i);
123: PetscViewerASCIIPrintf(viewer," Number of columns %D\n",c->ncolumns[i]);
124: for (j=0; j<c->ncolumns[i]; j++) {
125: PetscViewerASCIIPrintf(viewer," %D\n",c->columns[i][j]);
126: }
127: PetscViewerASCIIPrintf(viewer," Number of rows %D\n",c->nrows[i]);
128: for (j=0; j<c->nrows[i]; j++) {
129: PetscViewerASCIIPrintf(viewer," %D %D \n",c->rows[i][j],c->columnsforrow[i][j]);
130: }
131: }
132: }
133: PetscViewerFlush(viewer);
134: } else {
135: SETERRQ1(PETSC_ERR_SUP,"Viewer type %s not supported for MatFDColoring",((PetscObject)viewer)->type_name);
136: }
137: return(0);
138: }
142: /*@
143: MatFDColoringSetParameters - Sets the parameters for the sparse approximation of
144: a Jacobian matrix using finite differences.
146: Collective on MatFDColoring
148: The Jacobian is estimated with the differencing approximation
149: .vb
150: F'(u)_{:,i} = [F(u+h*dx_{i}) - F(u)]/h where
151: h = error_rel*u[i] if abs(u[i]) > umin
152: = +/- error_rel*umin otherwise, with +/- determined by the sign of u[i]
153: dx_{i} = (0, ... 1, .... 0)
154: .ve
156: Input Parameters:
157: + coloring - the coloring context
158: . error_rel - relative error
159: - umin - minimum allowable u-value magnitude
161: Level: advanced
163: .keywords: Mat, finite differences, coloring, set, parameters
165: .seealso: MatFDColoringCreate()
166: @*/
167: PetscErrorCode MatFDColoringSetParameters(MatFDColoring matfd,PetscReal error,PetscReal umin)
168: {
172: if (error != PETSC_DEFAULT) matfd->error_rel = error;
173: if (umin != PETSC_DEFAULT) matfd->umin = umin;
174: return(0);
175: }
179: /*@
180: MatFDColoringSetFrequency - Sets the frequency for computing new Jacobian
181: matrices.
183: Collective on MatFDColoring
185: Input Parameters:
186: + coloring - the coloring context
187: - freq - frequency (default is 1)
189: Options Database Keys:
190: . -mat_fd_coloring_freq <freq> - Sets coloring frequency
192: Level: advanced
194: Notes:
195: Using a modified Newton strategy, where the Jacobian remains fixed for several
196: iterations, can be cost effective in terms of overall nonlinear solution
197: efficiency. This parameter indicates that a new Jacobian will be computed every
198: <freq> nonlinear iterations.
200: .keywords: Mat, finite differences, coloring, set, frequency
202: .seealso: MatFDColoringCreate(), MatFDColoringGetFrequency(), MatFDColoringSetRecompute()
203: @*/
204: PetscErrorCode MatFDColoringSetFrequency(MatFDColoring matfd,PetscInt freq)
205: {
209: matfd->freq = freq;
210: return(0);
211: }
215: /*@
216: MatFDColoringGetFrequency - Gets the frequency for computing new Jacobian
217: matrices.
219: Not Collective
221: Input Parameters:
222: . coloring - the coloring context
224: Output Parameters:
225: . freq - frequency (default is 1)
227: Options Database Keys:
228: . -mat_fd_coloring_freq <freq> - Sets coloring frequency
230: Level: advanced
232: Notes:
233: Using a modified Newton strategy, where the Jacobian remains fixed for several
234: iterations, can be cost effective in terms of overall nonlinear solution
235: efficiency. This parameter indicates that a new Jacobian will be computed every
236: <freq> nonlinear iterations.
238: .keywords: Mat, finite differences, coloring, get, frequency
240: .seealso: MatFDColoringSetFrequency()
241: @*/
242: PetscErrorCode MatFDColoringGetFrequency(MatFDColoring matfd,PetscInt *freq)
243: {
246: *freq = matfd->freq;
247: return(0);
248: }
252: /*@C
253: MatFDColoringSetFunction - Sets the function to use for computing the Jacobian.
255: Collective on MatFDColoring
257: Input Parameters:
258: + coloring - the coloring context
259: . f - the function
260: - fctx - the optional user-defined function context
262: Level: intermediate
264: Notes:
265: In Fortran you must call MatFDColoringSetFunctionSNES() for a coloring object to
266: be used with the SNES solvers and MatFDColoringSetFunctionTS() if it is to be used
267: with the TS solvers.
269: .keywords: Mat, Jacobian, finite differences, set, function
270: @*/
271: PetscErrorCode MatFDColoringSetFunction(MatFDColoring matfd,PetscErrorCode (*f)(void),void *fctx)
272: {
275: matfd->f = f;
276: matfd->fctx = fctx;
277: return(0);
278: }
282: /*@
283: MatFDColoringSetFromOptions - Sets coloring finite difference parameters from
284: the options database.
286: Collective on MatFDColoring
288: The Jacobian, F'(u), is estimated with the differencing approximation
289: .vb
290: F'(u)_{:,i} = [F(u+h*dx_{i}) - F(u)]/h where
291: h = error_rel*u[i] if abs(u[i]) > umin
292: = +/- error_rel*umin otherwise, with +/- determined by the sign of u[i]
293: dx_{i} = (0, ... 1, .... 0)
294: .ve
296: Input Parameter:
297: . coloring - the coloring context
299: Options Database Keys:
300: + -mat_fd_coloring_err <err> - Sets <err> (square root
301: of relative error in the function)
302: . -mat_fd_coloring_umin <umin> - Sets umin, the minimum allowable u-value magnitude
303: . -mat_fd_coloring_freq <freq> - Sets frequency of computing a new Jacobian
304: . -mat_fd_coloring_view - Activates basic viewing
305: . -mat_fd_coloring_view_info - Activates viewing info
306: - -mat_fd_coloring_view_draw - Activates drawing
308: Level: intermediate
310: .keywords: Mat, finite differences, parameters
312: .seealso: MatFDColoringCreate(), MatFDColoringView(), MatFDColoringSetParameters()
314: @*/
315: PetscErrorCode MatFDColoringSetFromOptions(MatFDColoring matfd)
316: {
322: PetscOptionsBegin(matfd->comm,matfd->prefix,"Jacobian computation via finite differences option","MatFD");
323: PetscOptionsReal("-mat_fd_coloring_err","Square root of relative error in function","MatFDColoringSetParameters",matfd->error_rel,&matfd->error_rel,0);
324: PetscOptionsReal("-mat_fd_coloring_umin","Minimum allowable u magnitude","MatFDColoringSetParameters",matfd->umin,&matfd->umin,0);
325: PetscOptionsInt("-mat_fd_coloring_freq","How often Jacobian is recomputed","MatFDColoringSetFrequency",matfd->freq,&matfd->freq,0);
326: /* not used here; but so they are presented in the GUI */
327: PetscOptionsName("-mat_fd_coloring_view","Print entire datastructure used for Jacobian","None",0);
328: PetscOptionsName("-mat_fd_coloring_view_info","Print number of colors etc for Jacobian","None",0);
329: PetscOptionsName("-mat_fd_coloring_view_draw","Plot nonzero structure ofJacobian","None",0);
330: PetscOptionsEnd();
331: return(0);
332: }
336: PetscErrorCode MatFDColoringView_Private(MatFDColoring fd)
337: {
339: PetscTruth flg;
342: PetscOptionsHasName(PETSC_NULL,"-mat_fd_coloring_view",&flg);
343: if (flg) {
344: MatFDColoringView(fd,PETSC_VIEWER_STDOUT_(fd->comm));
345: }
346: PetscOptionsHasName(PETSC_NULL,"-mat_fd_coloring_view_info",&flg);
347: if (flg) {
348: PetscViewerPushFormat(PETSC_VIEWER_STDOUT_(fd->comm),PETSC_VIEWER_ASCII_INFO);
349: MatFDColoringView(fd,PETSC_VIEWER_STDOUT_(fd->comm));
350: PetscViewerPopFormat(PETSC_VIEWER_STDOUT_(fd->comm));
351: }
352: PetscOptionsHasName(PETSC_NULL,"-mat_fd_coloring_view_draw",&flg);
353: if (flg) {
354: MatFDColoringView(fd,PETSC_VIEWER_DRAW_(fd->comm));
355: PetscViewerFlush(PETSC_VIEWER_DRAW_(fd->comm));
356: }
357: return(0);
358: }
362: /*@C
363: MatFDColoringCreate - Creates a matrix coloring context for finite difference
364: computation of Jacobians.
366: Collective on Mat
368: Input Parameters:
369: + mat - the matrix containing the nonzero structure of the Jacobian
370: - iscoloring - the coloring of the matrix
372: Output Parameter:
373: . color - the new coloring context
374:
375: Level: intermediate
377: .seealso: MatFDColoringDestroy(),SNESDefaultComputeJacobianColor(), ISColoringCreate(),
378: MatFDColoringSetFunction(), MatFDColoringSetFromOptions(), MatFDColoringApply(),
379: MatFDColoringSetFrequency(), MatFDColoringSetRecompute(), MatFDColoringView(),
380: MatFDColoringSetParameters()
381: @*/
382: PetscErrorCode MatFDColoringCreate(Mat mat,ISColoring iscoloring,MatFDColoring *color)
383: {
384: MatFDColoring c;
385: MPI_Comm comm;
387: PetscInt M,N;
390: PetscLogEventBegin(MAT_FDColoringCreate,mat,0,0,0);
391: MatGetSize(mat,&M,&N);
392: if (M != N) SETERRQ(PETSC_ERR_SUP,"Only for square matrices");
394: PetscObjectGetComm((PetscObject)mat,&comm);
395: PetscHeaderCreate(c,_p_MatFDColoring,int,MAT_FDCOLORING_COOKIE,0,"MatFDColoring",comm,MatFDColoringDestroy,MatFDColoringView);
396: PetscLogObjectCreate(c);
398: if (mat->ops->fdcoloringcreate) {
399: (*mat->ops->fdcoloringcreate)(mat,iscoloring,c);
400: } else {
401: SETERRQ(PETSC_ERR_SUP,"Code not yet written for this matrix type");
402: }
404: c->error_rel = PETSC_SQRT_MACHINE_EPSILON;
405: c->umin = 100.0*PETSC_SQRT_MACHINE_EPSILON;
406: c->freq = 1;
407: c->usersetsrecompute = PETSC_FALSE;
408: c->recompute = PETSC_FALSE;
409: c->currentcolor = -1;
411: *color = c;
412: PetscLogEventEnd(MAT_FDColoringCreate,mat,0,0,0);
413: return(0);
414: }
418: /*@C
419: MatFDColoringDestroy - Destroys a matrix coloring context that was created
420: via MatFDColoringCreate().
422: Collective on MatFDColoring
424: Input Parameter:
425: . c - coloring context
427: Level: intermediate
429: .seealso: MatFDColoringCreate()
430: @*/
431: PetscErrorCode MatFDColoringDestroy(MatFDColoring c)
432: {
434: PetscInt i;
437: if (--c->refct > 0) return(0);
439: for (i=0; i<c->ncolors; i++) {
440: if (c->columns[i]) {PetscFree(c->columns[i]);}
441: if (c->rows[i]) {PetscFree(c->rows[i]);}
442: if (c->columnsforrow[i]) {PetscFree(c->columnsforrow[i]);}
443: if (c->vscaleforrow && c->vscaleforrow[i]) {PetscFree(c->vscaleforrow[i]);}
444: }
445: PetscFree(c->ncolumns);
446: PetscFree(c->columns);
447: PetscFree(c->nrows);
448: PetscFree(c->rows);
449: PetscFree(c->columnsforrow);
450: if (c->vscaleforrow) {PetscFree(c->vscaleforrow);}
451: if (c->vscale) {VecDestroy(c->vscale);}
452: if (c->w1) {
453: VecDestroy(c->w1);
454: VecDestroy(c->w2);
455: VecDestroy(c->w3);
456: }
457: PetscLogObjectDestroy(c);
458: PetscHeaderDestroy(c);
459: return(0);
460: }
464: /*@C
465: MatFDColoringGetPerturbedColumns - Returns the indices of the columns that
466: that are currently being perturbed.
468: Not Collective
470: Input Parameters:
471: . coloring - coloring context created with MatFDColoringCreate()
473: Output Parameters:
474: + n - the number of local columns being perturbed
475: - cols - the column indices, in global numbering
477: Level: intermediate
479: .seealso: MatFDColoringCreate(), MatFDColoringDestroy(), MatFDColoringView(), MatFDColoringApply()
481: .keywords: coloring, Jacobian, finite differences
482: @*/
483: EXTERN PetscErrorCode MatFDColoringGetPerturbedColumns(MatFDColoring coloring,PetscInt *n,PetscInt *cols[])
484: {
486: if (coloring->currentcolor >= 0) {
487: *n = coloring->ncolumns[coloring->currentcolor];
488: *cols = coloring->columns[coloring->currentcolor];
489: } else {
490: *n = 0;
491: }
492: return(0);
493: }
497: /*@
498: MatFDColoringApply - Given a matrix for which a MatFDColoring context
499: has been created, computes the Jacobian for a function via finite differences.
501: Collective on MatFDColoring
503: Input Parameters:
504: + mat - location to store Jacobian
505: . coloring - coloring context created with MatFDColoringCreate()
506: . x1 - location at which Jacobian is to be computed
507: - sctx - optional context required by function (actually a SNES context)
509: Options Database Keys:
510: + -mat_fd_coloring_freq <freq> - Sets coloring frequency
511: . -mat_fd_coloring_view - Activates basic viewing or coloring
512: . -mat_fd_coloring_view_draw - Activates drawing of coloring
513: - -mat_fd_coloring_view_info - Activates viewing of coloring info
515: Level: intermediate
517: .seealso: MatFDColoringCreate(), MatFDColoringDestroy(), MatFDColoringView()
519: .keywords: coloring, Jacobian, finite differences
520: @*/
521: PetscErrorCode MatFDColoringApply(Mat J,MatFDColoring coloring,Vec x1,MatStructure *flag,void *sctx)
522: {
523: PetscErrorCode (*f)(void*,Vec,Vec,void*) = (PetscErrorCode (*)(void*,Vec,Vec,void *))coloring->f;
525: PetscInt k,N,start,end,l,row,col,srow,**vscaleforrow,m1,m2;
526: PetscScalar dx,mone = -1.0,*y,*xx,*w3_array;
527: PetscScalar *vscale_array;
528: PetscReal epsilon = coloring->error_rel,umin = coloring->umin;
529: Vec w1,w2,w3;
530: void *fctx = coloring->fctx;
531: PetscTruth flg;
539: if (coloring->usersetsrecompute) {
540: if (!coloring->recompute) {
541: *flag = SAME_PRECONDITIONER;
542: PetscLogInfo(J,"MatFDColoringApply:Skipping Jacobian, since user called MatFDColorSetRecompute()\n");
543: return(0);
544: } else {
545: coloring->recompute = PETSC_FALSE;
546: }
547: }
549: PetscLogEventBegin(MAT_FDColoringApply,coloring,J,x1,0);
550: if (J->ops->fdcoloringapply) {
551: (*J->ops->fdcoloringapply)(J,coloring,x1,flag,sctx);
552: } else {
554: if (!coloring->w1) {
555: VecDuplicate(x1,&coloring->w1);
556: PetscLogObjectParent(coloring,coloring->w1);
557: VecDuplicate(x1,&coloring->w2);
558: PetscLogObjectParent(coloring,coloring->w2);
559: VecDuplicate(x1,&coloring->w3);
560: PetscLogObjectParent(coloring,coloring->w3);
561: }
562: w1 = coloring->w1; w2 = coloring->w2; w3 = coloring->w3;
564: MatSetUnfactored(J);
565: PetscOptionsHasName(PETSC_NULL,"-mat_fd_coloring_dont_rezero",&flg);
566: if (flg) {
567: PetscLogInfo(coloring,"MatFDColoringApply: Not calling MatZeroEntries()\n");
568: } else {
569: PetscTruth assembled;
570: MatAssembled(J,&assembled);
571: if (assembled) {
572: MatZeroEntries(J);
573: }
574: }
576: VecGetOwnershipRange(x1,&start,&end);
577: VecGetSize(x1,&N);
578:
579: /*
580: This is a horrible, horrible, hack. See DMMGComputeJacobian_Multigrid() it inproperly sets
581: coloring->F for the coarser grids from the finest
582: */
583: if (coloring->F) {
584: VecGetLocalSize(coloring->F,&m1);
585: VecGetLocalSize(w1,&m2);
586: if (m1 != m2) {
587: coloring->F = 0;
588: }
589: }
591: if (coloring->F) {
592: w1 = coloring->F; /* use already computed value of function */
593: coloring->F = 0;
594: } else {
595: PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);
596: (*f)(sctx,x1,w1,fctx);
597: PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);
598: }
600: /*
601: Compute all the scale factors and share with other processors
602: */
603: VecGetArray(x1,&xx);xx = xx - start;
604: VecGetArray(coloring->vscale,&vscale_array);vscale_array = vscale_array - start;
605: for (k=0; k<coloring->ncolors; k++) {
606: /*
607: Loop over each column associated with color adding the
608: perturbation to the vector w3.
609: */
610: for (l=0; l<coloring->ncolumns[k]; l++) {
611: col = coloring->columns[k][l]; /* column of the matrix we are probing for */
612: dx = xx[col];
613: if (dx == 0.0) dx = 1.0;
614: #if !defined(PETSC_USE_COMPLEX)
615: if (dx < umin && dx >= 0.0) dx = umin;
616: else if (dx < 0.0 && dx > -umin) dx = -umin;
617: #else
618: if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0) dx = umin;
619: else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin;
620: #endif
621: dx *= epsilon;
622: vscale_array[col] = 1.0/dx;
623: }
624: }
625: vscale_array = vscale_array + start;VecRestoreArray(coloring->vscale,&vscale_array);
626: VecGhostUpdateBegin(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);
627: VecGhostUpdateEnd(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);
629: /* VecView(coloring->vscale,PETSC_VIEWER_STDOUT_WORLD);
630: VecView(x1,PETSC_VIEWER_STDOUT_WORLD);*/
632: if (coloring->vscaleforrow) vscaleforrow = coloring->vscaleforrow;
633: else vscaleforrow = coloring->columnsforrow;
635: VecGetArray(coloring->vscale,&vscale_array);
636: /*
637: Loop over each color
638: */
639: for (k=0; k<coloring->ncolors; k++) {
640: coloring->currentcolor = k;
641: VecCopy(x1,w3);
642: VecGetArray(w3,&w3_array);w3_array = w3_array - start;
643: /*
644: Loop over each column associated with color adding the
645: perturbation to the vector w3.
646: */
647: for (l=0; l<coloring->ncolumns[k]; l++) {
648: col = coloring->columns[k][l]; /* column of the matrix we are probing for */
649: dx = xx[col];
650: if (dx == 0.0) dx = 1.0;
651: #if !defined(PETSC_USE_COMPLEX)
652: if (dx < umin && dx >= 0.0) dx = umin;
653: else if (dx < 0.0 && dx > -umin) dx = -umin;
654: #else
655: if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0) dx = umin;
656: else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin;
657: #endif
658: dx *= epsilon;
659: if (!PetscAbsScalar(dx)) SETERRQ(PETSC_ERR_PLIB,"Computed 0 differencing parameter");
660: w3_array[col] += dx;
661: }
662: w3_array = w3_array + start; VecRestoreArray(w3,&w3_array);
664: /*
665: Evaluate function at x1 + dx (here dx is a vector of perturbations)
666: */
668: PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);
669: (*f)(sctx,w3,w2,fctx);
670: PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);
671: VecAXPY(&mone,w1,w2);
673: /*
674: Loop over rows of vector, putting results into Jacobian matrix
675: */
676: VecGetArray(w2,&y);
677: for (l=0; l<coloring->nrows[k]; l++) {
678: row = coloring->rows[k][l];
679: col = coloring->columnsforrow[k][l];
680: y[row] *= vscale_array[vscaleforrow[k][l]];
681: srow = row + start;
682: MatSetValues(J,1,&srow,1,&col,y+row,INSERT_VALUES);
683: }
684: VecRestoreArray(w2,&y);
685: }
686: coloring->currentcolor = -1;
687: VecRestoreArray(coloring->vscale,&vscale_array);
688: xx = xx + start; VecRestoreArray(x1,&xx);
689: MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);
690: MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);
691: }
692: PetscLogEventEnd(MAT_FDColoringApply,coloring,J,x1,0);
694: PetscOptionsHasName(PETSC_NULL,"-mat_null_space_test",&flg);
695: if (flg) {
696: MatNullSpaceTest(J->nullsp,J);
697: }
698: MatFDColoringView_Private(coloring);
700: return(0);
701: }
705: /*@
706: MatFDColoringApplyTS - Given a matrix for which a MatFDColoring context
707: has been created, computes the Jacobian for a function via finite differences.
709: Collective on Mat, MatFDColoring, and Vec
711: Input Parameters:
712: + mat - location to store Jacobian
713: . coloring - coloring context created with MatFDColoringCreate()
714: . x1 - location at which Jacobian is to be computed
715: - sctx - optional context required by function (actually a SNES context)
717: Options Database Keys:
718: . -mat_fd_coloring_freq <freq> - Sets coloring frequency
720: Level: intermediate
722: .seealso: MatFDColoringCreate(), MatFDColoringDestroy(), MatFDColoringView()
724: .keywords: coloring, Jacobian, finite differences
725: @*/
726: PetscErrorCode MatFDColoringApplyTS(Mat J,MatFDColoring coloring,PetscReal t,Vec x1,MatStructure *flag,void *sctx)
727: {
728: PetscErrorCode (*f)(void*,PetscReal,Vec,Vec,void*)=(PetscErrorCode (*)(void*,PetscReal,Vec,Vec,void *))coloring->f;
730: PetscInt k,N,start,end,l,row,col,srow,**vscaleforrow;
731: PetscScalar dx,mone = -1.0,*y,*xx,*w3_array;
732: PetscScalar *vscale_array;
733: PetscReal epsilon = coloring->error_rel,umin = coloring->umin;
734: Vec w1,w2,w3;
735: void *fctx = coloring->fctx;
736: PetscTruth flg;
743: PetscLogEventBegin(MAT_FDColoringApply,coloring,J,x1,0);
744: if (!coloring->w1) {
745: VecDuplicate(x1,&coloring->w1);
746: PetscLogObjectParent(coloring,coloring->w1);
747: VecDuplicate(x1,&coloring->w2);
748: PetscLogObjectParent(coloring,coloring->w2);
749: VecDuplicate(x1,&coloring->w3);
750: PetscLogObjectParent(coloring,coloring->w3);
751: }
752: w1 = coloring->w1; w2 = coloring->w2; w3 = coloring->w3;
754: MatSetUnfactored(J);
755: PetscOptionsHasName(PETSC_NULL,"-mat_fd_coloring_dont_rezero",&flg);
756: if (flg) {
757: PetscLogInfo(coloring,"MatFDColoringApply: Not calling MatZeroEntries()\n");
758: } else {
759: PetscTruth assembled;
760: MatAssembled(J,&assembled);
761: if (assembled) {
762: MatZeroEntries(J);
763: }
764: }
766: VecGetOwnershipRange(x1,&start,&end);
767: VecGetSize(x1,&N);
768: PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);
769: (*f)(sctx,t,x1,w1,fctx);
770: PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);
772: /*
773: Compute all the scale factors and share with other processors
774: */
775: VecGetArray(x1,&xx);xx = xx - start;
776: VecGetArray(coloring->vscale,&vscale_array);vscale_array = vscale_array - start;
777: for (k=0; k<coloring->ncolors; k++) {
778: /*
779: Loop over each column associated with color adding the
780: perturbation to the vector w3.
781: */
782: for (l=0; l<coloring->ncolumns[k]; l++) {
783: col = coloring->columns[k][l]; /* column of the matrix we are probing for */
784: dx = xx[col];
785: if (dx == 0.0) dx = 1.0;
786: #if !defined(PETSC_USE_COMPLEX)
787: if (dx < umin && dx >= 0.0) dx = umin;
788: else if (dx < 0.0 && dx > -umin) dx = -umin;
789: #else
790: if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0) dx = umin;
791: else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin;
792: #endif
793: dx *= epsilon;
794: vscale_array[col] = 1.0/dx;
795: }
796: }
797: vscale_array = vscale_array - start;VecRestoreArray(coloring->vscale,&vscale_array);
798: VecGhostUpdateBegin(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);
799: VecGhostUpdateEnd(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);
801: if (coloring->vscaleforrow) vscaleforrow = coloring->vscaleforrow;
802: else vscaleforrow = coloring->columnsforrow;
804: VecGetArray(coloring->vscale,&vscale_array);
805: /*
806: Loop over each color
807: */
808: for (k=0; k<coloring->ncolors; k++) {
809: VecCopy(x1,w3);
810: VecGetArray(w3,&w3_array);w3_array = w3_array - start;
811: /*
812: Loop over each column associated with color adding the
813: perturbation to the vector w3.
814: */
815: for (l=0; l<coloring->ncolumns[k]; l++) {
816: col = coloring->columns[k][l]; /* column of the matrix we are probing for */
817: dx = xx[col];
818: if (dx == 0.0) dx = 1.0;
819: #if !defined(PETSC_USE_COMPLEX)
820: if (dx < umin && dx >= 0.0) dx = umin;
821: else if (dx < 0.0 && dx > -umin) dx = -umin;
822: #else
823: if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0) dx = umin;
824: else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin;
825: #endif
826: dx *= epsilon;
827: w3_array[col] += dx;
828: }
829: w3_array = w3_array + start; VecRestoreArray(w3,&w3_array);
831: /*
832: Evaluate function at x1 + dx (here dx is a vector of perturbations)
833: */
834: PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);
835: (*f)(sctx,t,w3,w2,fctx);
836: PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);
837: VecAXPY(&mone,w1,w2);
839: /*
840: Loop over rows of vector, putting results into Jacobian matrix
841: */
842: VecGetArray(w2,&y);
843: for (l=0; l<coloring->nrows[k]; l++) {
844: row = coloring->rows[k][l];
845: col = coloring->columnsforrow[k][l];
846: y[row] *= vscale_array[vscaleforrow[k][l]];
847: srow = row + start;
848: MatSetValues(J,1,&srow,1,&col,y+row,INSERT_VALUES);
849: }
850: VecRestoreArray(w2,&y);
851: }
852: VecRestoreArray(coloring->vscale,&vscale_array);
853: xx = xx + start; VecRestoreArray(x1,&xx);
854: MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);
855: MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);
856: PetscLogEventEnd(MAT_FDColoringApply,coloring,J,x1,0);
857: return(0);
858: }
863: /*@C
864: MatFDColoringSetRecompute - Indicates that the next time a Jacobian preconditioner
865: is needed it sholuld be recomputed. Once this is called and the new Jacobian is computed
866: no additional Jacobian's will be computed (the same one will be used) until this is
867: called again.
869: Collective on MatFDColoring
871: Input Parameters:
872: . c - the coloring context
874: Level: intermediate
876: Notes: The MatFDColoringSetFrequency() is ignored once this is called
878: .seealso: MatFDColoringCreate(), MatFDColoringSetFrequency()
880: .keywords: Mat, finite differences, coloring
881: @*/
882: PetscErrorCode MatFDColoringSetRecompute(MatFDColoring c)
883: {
886: c->usersetsrecompute = PETSC_TRUE;
887: c->recompute = PETSC_TRUE;
888: return(0);
889: }