Actual source code: fdmatrix.c
1: /*$Id: fdmatrix.c,v 1.92 2001/08/21 21:03:06 bsmith Exp $*/
3: /*
4: This is where the abstract matrix operations are defined that are
5: used for finite difference computations of Jacobians using coloring.
6: */
8: #include src/mat/matimpl.h
10: /* Logging support */
11: int MAT_FDCOLORING_COOKIE = 0;
15: int MatFDColoringSetF(MatFDColoring fd,Vec F)
16: {
18: fd->F = F;
19: return(0);
20: }
24: static int MatFDColoringView_Draw_Zoom(PetscDraw draw,void *Aa)
25: {
26: MatFDColoring fd = (MatFDColoring)Aa;
27: int ierr,i,j;
28: PetscReal x,y;
32: /* loop over colors */
33: for (i=0; i<fd->ncolors; i++) {
34: for (j=0; j<fd->nrows[i]; j++) {
35: y = fd->M - fd->rows[i][j] - fd->rstart;
36: x = fd->columnsforrow[i][j];
37: PetscDrawRectangle(draw,x,y,x+1,y+1,i+1,i+1,i+1,i+1);
38: }
39: }
40: return(0);
41: }
45: static int MatFDColoringView_Draw(MatFDColoring fd,PetscViewer viewer)
46: {
47: int ierr;
48: PetscTruth isnull;
49: PetscDraw draw;
50: PetscReal xr,yr,xl,yl,h,w;
53: PetscViewerDrawGetDraw(viewer,0,&draw);
54: PetscDrawIsNull(draw,&isnull); if (isnull) return(0);
56: PetscObjectCompose((PetscObject)fd,"Zoomviewer",(PetscObject)viewer);
58: xr = fd->N; yr = fd->M; h = yr/10.0; w = xr/10.0;
59: xr += w; yr += h; xl = -w; yl = -h;
60: PetscDrawSetCoordinates(draw,xl,yl,xr,yr);
61: PetscDrawZoom(draw,MatFDColoringView_Draw_Zoom,fd);
62: PetscObjectCompose((PetscObject)fd,"Zoomviewer",PETSC_NULL);
63: return(0);
64: }
68: /*@C
69: MatFDColoringView - Views a finite difference coloring context.
71: Collective on MatFDColoring
73: Input Parameters:
74: + c - the coloring context
75: - viewer - visualization context
77: Level: intermediate
79: Notes:
80: The available visualization contexts include
81: + PETSC_VIEWER_STDOUT_SELF - standard output (default)
82: . PETSC_VIEWER_STDOUT_WORLD - synchronized standard
83: output where only the first processor opens
84: the file. All other processors send their
85: data to the first processor to print.
86: - PETSC_VIEWER_DRAW_WORLD - graphical display of nonzero structure
88: Notes:
89: Since PETSc uses only a small number of basic colors (currently 33), if the coloring
90: involves more than 33 then some seemingly identical colors are displayed making it look
91: like an illegal coloring. This is just a graphical artifact.
93: .seealso: MatFDColoringCreate()
95: .keywords: Mat, finite differences, coloring, view
96: @*/
97: int MatFDColoringView(MatFDColoring c,PetscViewer viewer)
98: {
99: int i,j,ierr;
100: PetscTruth isdraw,isascii;
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,&isascii);
111: if (isdraw) {
112: MatFDColoringView_Draw(c,viewer);
113: } else if (isascii) {
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(1,"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: int 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: int MatFDColoringSetFrequency(MatFDColoring matfd,int 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: int MatFDColoringGetFrequency(MatFDColoring matfd,int *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: int MatFDColoringSetFunction(MatFDColoring matfd,int (*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: int MatFDColoringSetFromOptions(MatFDColoring matfd)
316: {
317: int ierr;
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: int MatFDColoringView_Private(MatFDColoring fd)
337: {
338: int ierr;
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: int MatFDColoringCreate(Mat mat,ISColoring iscoloring,MatFDColoring *color)
383: {
384: MatFDColoring c;
385: MPI_Comm comm;
386: int ierr,M,N;
389: PetscLogEventBegin(MAT_FDColoringCreate,mat,0,0,0);
390: MatGetSize(mat,&M,&N);
391: if (M != N) SETERRQ(PETSC_ERR_SUP,"Only for square matrices");
393: PetscObjectGetComm((PetscObject)mat,&comm);
394: PetscHeaderCreate(c,_p_MatFDColoring,int,MAT_FDCOLORING_COOKIE,0,"MatFDColoring",comm,MatFDColoringDestroy,MatFDColoringView);
395: PetscLogObjectCreate(c);
397: if (mat->ops->fdcoloringcreate) {
398: (*mat->ops->fdcoloringcreate)(mat,iscoloring,c);
399: } else {
400: SETERRQ(PETSC_ERR_SUP,"Code not yet written for this matrix type");
401: }
403: c->error_rel = PETSC_SQRT_MACHINE_EPSILON;
404: c->umin = 100.0*PETSC_SQRT_MACHINE_EPSILON;
405: c->freq = 1;
406: c->usersetsrecompute = PETSC_FALSE;
407: c->recompute = PETSC_FALSE;
408: c->currentcolor = -1;
410: *color = c;
411: PetscLogEventEnd(MAT_FDColoringCreate,mat,0,0,0);
412: return(0);
413: }
417: /*@C
418: MatFDColoringDestroy - Destroys a matrix coloring context that was created
419: via MatFDColoringCreate().
421: Collective on MatFDColoring
423: Input Parameter:
424: . c - coloring context
426: Level: intermediate
428: .seealso: MatFDColoringCreate()
429: @*/
430: int MatFDColoringDestroy(MatFDColoring c)
431: {
432: int i,ierr;
435: if (--c->refct > 0) return(0);
437: for (i=0; i<c->ncolors; i++) {
438: if (c->columns[i]) {PetscFree(c->columns[i]);}
439: if (c->rows[i]) {PetscFree(c->rows[i]);}
440: if (c->columnsforrow[i]) {PetscFree(c->columnsforrow[i]);}
441: if (c->vscaleforrow && c->vscaleforrow[i]) {PetscFree(c->vscaleforrow[i]);}
442: }
443: PetscFree(c->ncolumns);
444: PetscFree(c->columns);
445: PetscFree(c->nrows);
446: PetscFree(c->rows);
447: PetscFree(c->columnsforrow);
448: if (c->vscaleforrow) {PetscFree(c->vscaleforrow);}
449: if (c->vscale) {VecDestroy(c->vscale);}
450: if (c->w1) {
451: VecDestroy(c->w1);
452: VecDestroy(c->w2);
453: VecDestroy(c->w3);
454: }
455: PetscLogObjectDestroy(c);
456: PetscHeaderDestroy(c);
457: return(0);
458: }
462: /*@C
463: MatFDColoringGetPerturbedColumns - Returns the indices of the columns that
464: that are currently being perturbed.
466: Not Collective
468: Input Parameters:
469: . coloring - coloring context created with MatFDColoringCreate()
471: Output Parameters:
472: + n - the number of local columns being perturbed
473: - cols - the column indices, in global numbering
475: Level: intermediate
477: .seealso: MatFDColoringCreate(), MatFDColoringDestroy(), MatFDColoringView(), MatFDColoringApply()
479: .keywords: coloring, Jacobian, finite differences
480: @*/
481: EXTERN int MatFDColoringGetPerturbedColumns(MatFDColoring coloring,int *n,int *cols[])
482: {
484: if (coloring->currentcolor >= 0) {
485: *n = coloring->ncolumns[coloring->currentcolor];
486: *cols = coloring->columns[coloring->currentcolor];
487: } else {
488: *n = 0;
489: }
490: return(0);
491: }
495: /*@
496: MatFDColoringApply - Given a matrix for which a MatFDColoring context
497: has been created, computes the Jacobian for a function via finite differences.
499: Collective on MatFDColoring
501: Input Parameters:
502: + mat - location to store Jacobian
503: . coloring - coloring context created with MatFDColoringCreate()
504: . x1 - location at which Jacobian is to be computed
505: - sctx - optional context required by function (actually a SNES context)
507: Options Database Keys:
508: + -mat_fd_coloring_freq <freq> - Sets coloring frequency
509: . -mat_fd_coloring_view - Activates basic viewing or coloring
510: . -mat_fd_coloring_view_draw - Activates drawing of coloring
511: - -mat_fd_coloring_view_info - Activates viewing of coloring info
513: Level: intermediate
515: .seealso: MatFDColoringCreate(), MatFDColoringDestroy(), MatFDColoringView()
517: .keywords: coloring, Jacobian, finite differences
518: @*/
519: int MatFDColoringApply(Mat J,MatFDColoring coloring,Vec x1,MatStructure *flag,void *sctx)
520: {
521: int (*f)(void *,Vec,Vec,void*) = (int (*)(void *,Vec,Vec,void *))coloring->f;
522: int k,ierr,N,start,end,l,row,col,srow,**vscaleforrow,m1,m2;
523: PetscScalar dx,mone = -1.0,*y,*xx,*w3_array;
524: PetscScalar *vscale_array;
525: PetscReal epsilon = coloring->error_rel,umin = coloring->umin;
526: Vec w1,w2,w3;
527: void *fctx = coloring->fctx;
528: PetscTruth flg;
536: if (coloring->usersetsrecompute) {
537: if (!coloring->recompute) {
538: *flag = SAME_PRECONDITIONER;
539: PetscLogInfo(J,"MatFDColoringApply:Skipping Jacobian, since user called MatFDColorSetRecompute()\n");
540: return(0);
541: } else {
542: coloring->recompute = PETSC_FALSE;
543: }
544: }
546: PetscLogEventBegin(MAT_FDColoringApply,coloring,J,x1,0);
547: if (J->ops->fdcoloringapply) {
548: (*J->ops->fdcoloringapply)(J,coloring,x1,flag,sctx);
549: } else {
551: if (!coloring->w1) {
552: VecDuplicate(x1,&coloring->w1);
553: PetscLogObjectParent(coloring,coloring->w1);
554: VecDuplicate(x1,&coloring->w2);
555: PetscLogObjectParent(coloring,coloring->w2);
556: VecDuplicate(x1,&coloring->w3);
557: PetscLogObjectParent(coloring,coloring->w3);
558: }
559: w1 = coloring->w1; w2 = coloring->w2; w3 = coloring->w3;
561: MatSetUnfactored(J);
562: PetscOptionsHasName(PETSC_NULL,"-mat_fd_coloring_dont_rezero",&flg);
563: if (flg) {
564: PetscLogInfo(coloring,"MatFDColoringApply: Not calling MatZeroEntries()\n");
565: } else {
566: MatZeroEntries(J);
567: }
569: VecGetOwnershipRange(x1,&start,&end);
570: VecGetSize(x1,&N);
571:
572: /*
573: This is a horrible, horrible, hack. See DMMGComputeJacobian_Multigrid() it inproperly sets
574: coloring->F for the coarser grids from the finest
575: */
576: if (coloring->F) {
577: VecGetLocalSize(coloring->F,&m1);
578: VecGetLocalSize(w1,&m2);
579: if (m1 != m2) {
580: coloring->F = 0;
581: }
582: }
584: if (coloring->F) {
585: w1 = coloring->F; /* use already computed value of function */
586: coloring->F = 0;
587: } else {
588: PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);
589: (*f)(sctx,x1,w1,fctx);
590: PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);
591: }
593: /*
594: Compute all the scale factors and share with other processors
595: */
596: VecGetArray(x1,&xx);xx = xx - start;
597: VecGetArray(coloring->vscale,&vscale_array);vscale_array = vscale_array - start;
598: for (k=0; k<coloring->ncolors; k++) {
599: /*
600: Loop over each column associated with color adding the
601: perturbation to the vector w3.
602: */
603: for (l=0; l<coloring->ncolumns[k]; l++) {
604: col = coloring->columns[k][l]; /* column of the matrix we are probing for */
605: dx = xx[col];
606: if (dx == 0.0) dx = 1.0;
607: #if !defined(PETSC_USE_COMPLEX)
608: if (dx < umin && dx >= 0.0) dx = umin;
609: else if (dx < 0.0 && dx > -umin) dx = -umin;
610: #else
611: if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0) dx = umin;
612: else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin;
613: #endif
614: dx *= epsilon;
615: vscale_array[col] = 1.0/dx;
616: }
617: }
618: vscale_array = vscale_array + start;VecRestoreArray(coloring->vscale,&vscale_array);
619: VecGhostUpdateBegin(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);
620: VecGhostUpdateEnd(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);
622: /* VecView(coloring->vscale,PETSC_VIEWER_STDOUT_WORLD);
623: VecView(x1,PETSC_VIEWER_STDOUT_WORLD);*/
625: if (coloring->vscaleforrow) vscaleforrow = coloring->vscaleforrow;
626: else vscaleforrow = coloring->columnsforrow;
628: VecGetArray(coloring->vscale,&vscale_array);
629: /*
630: Loop over each color
631: */
632: for (k=0; k<coloring->ncolors; k++) {
633: coloring->currentcolor = k;
634: VecCopy(x1,w3);
635: VecGetArray(w3,&w3_array);w3_array = w3_array - start;
636: /*
637: Loop over each column associated with color adding the
638: perturbation to the vector w3.
639: */
640: for (l=0; l<coloring->ncolumns[k]; l++) {
641: col = coloring->columns[k][l]; /* column of the matrix we are probing for */
642: dx = xx[col];
643: if (dx == 0.0) dx = 1.0;
644: #if !defined(PETSC_USE_COMPLEX)
645: if (dx < umin && dx >= 0.0) dx = umin;
646: else if (dx < 0.0 && dx > -umin) dx = -umin;
647: #else
648: if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0) dx = umin;
649: else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin;
650: #endif
651: dx *= epsilon;
652: if (!PetscAbsScalar(dx)) SETERRQ(1,"Computed 0 differencing parameter");
653: w3_array[col] += dx;
654: }
655: w3_array = w3_array + start; VecRestoreArray(w3,&w3_array);
657: /*
658: Evaluate function at x1 + dx (here dx is a vector of perturbations)
659: */
661: PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);
662: (*f)(sctx,w3,w2,fctx);
663: PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);
664: VecAXPY(&mone,w1,w2);
666: /*
667: Loop over rows of vector, putting results into Jacobian matrix
668: */
669: VecGetArray(w2,&y);
670: for (l=0; l<coloring->nrows[k]; l++) {
671: row = coloring->rows[k][l];
672: col = coloring->columnsforrow[k][l];
673: y[row] *= vscale_array[vscaleforrow[k][l]];
674: srow = row + start;
675: MatSetValues(J,1,&srow,1,&col,y+row,INSERT_VALUES);
676: }
677: VecRestoreArray(w2,&y);
678: }
679: coloring->currentcolor = -1;
680: VecRestoreArray(coloring->vscale,&vscale_array);
681: xx = xx + start; VecRestoreArray(x1,&xx);
682: MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);
683: MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);
684: }
685: PetscLogEventEnd(MAT_FDColoringApply,coloring,J,x1,0);
687: PetscOptionsHasName(PETSC_NULL,"-mat_null_space_test",&flg);
688: if (flg) {
689: MatNullSpaceTest(J->nullsp,J);
690: }
691: MatFDColoringView_Private(coloring);
693: return(0);
694: }
698: /*@
699: MatFDColoringApplyTS - Given a matrix for which a MatFDColoring context
700: has been created, computes the Jacobian for a function via finite differences.
702: Collective on Mat, MatFDColoring, and Vec
704: Input Parameters:
705: + mat - location to store Jacobian
706: . coloring - coloring context created with MatFDColoringCreate()
707: . x1 - location at which Jacobian is to be computed
708: - sctx - optional context required by function (actually a SNES context)
710: Options Database Keys:
711: . -mat_fd_coloring_freq <freq> - Sets coloring frequency
713: Level: intermediate
715: .seealso: MatFDColoringCreate(), MatFDColoringDestroy(), MatFDColoringView()
717: .keywords: coloring, Jacobian, finite differences
718: @*/
719: int MatFDColoringApplyTS(Mat J,MatFDColoring coloring,PetscReal t,Vec x1,MatStructure *flag,void *sctx)
720: {
721: int (*f)(void *,PetscReal,Vec,Vec,void*)=(int (*)(void *,PetscReal,Vec,Vec,void *))coloring->f;
722: int k,ierr,N,start,end,l,row,col,srow,**vscaleforrow;
723: PetscScalar dx,mone = -1.0,*y,*xx,*w3_array;
724: PetscScalar *vscale_array;
725: PetscReal epsilon = coloring->error_rel,umin = coloring->umin;
726: Vec w1,w2,w3;
727: void *fctx = coloring->fctx;
728: PetscTruth flg;
735: PetscLogEventBegin(MAT_FDColoringApply,coloring,J,x1,0);
736: if (!coloring->w1) {
737: VecDuplicate(x1,&coloring->w1);
738: PetscLogObjectParent(coloring,coloring->w1);
739: VecDuplicate(x1,&coloring->w2);
740: PetscLogObjectParent(coloring,coloring->w2);
741: VecDuplicate(x1,&coloring->w3);
742: PetscLogObjectParent(coloring,coloring->w3);
743: }
744: w1 = coloring->w1; w2 = coloring->w2; w3 = coloring->w3;
746: MatSetUnfactored(J);
747: PetscOptionsHasName(PETSC_NULL,"-mat_fd_coloring_dont_rezero",&flg);
748: if (flg) {
749: PetscLogInfo(coloring,"MatFDColoringApply: Not calling MatZeroEntries()\n");
750: } else {
751: MatZeroEntries(J);
752: }
754: VecGetOwnershipRange(x1,&start,&end);
755: VecGetSize(x1,&N);
756: PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);
757: (*f)(sctx,t,x1,w1,fctx);
758: PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);
760: /*
761: Compute all the scale factors and share with other processors
762: */
763: VecGetArray(x1,&xx);xx = xx - start;
764: VecGetArray(coloring->vscale,&vscale_array);vscale_array = vscale_array - start;
765: for (k=0; k<coloring->ncolors; k++) {
766: /*
767: Loop over each column associated with color adding the
768: perturbation to the vector w3.
769: */
770: for (l=0; l<coloring->ncolumns[k]; l++) {
771: col = coloring->columns[k][l]; /* column of the matrix we are probing for */
772: dx = xx[col];
773: if (dx == 0.0) dx = 1.0;
774: #if !defined(PETSC_USE_COMPLEX)
775: if (dx < umin && dx >= 0.0) dx = umin;
776: else if (dx < 0.0 && dx > -umin) dx = -umin;
777: #else
778: if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0) dx = umin;
779: else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin;
780: #endif
781: dx *= epsilon;
782: vscale_array[col] = 1.0/dx;
783: }
784: }
785: vscale_array = vscale_array - start;VecRestoreArray(coloring->vscale,&vscale_array);
786: VecGhostUpdateBegin(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);
787: VecGhostUpdateEnd(coloring->vscale,INSERT_VALUES,SCATTER_FORWARD);
789: if (coloring->vscaleforrow) vscaleforrow = coloring->vscaleforrow;
790: else vscaleforrow = coloring->columnsforrow;
792: VecGetArray(coloring->vscale,&vscale_array);
793: /*
794: Loop over each color
795: */
796: for (k=0; k<coloring->ncolors; k++) {
797: VecCopy(x1,w3);
798: VecGetArray(w3,&w3_array);w3_array = w3_array - start;
799: /*
800: Loop over each column associated with color adding the
801: perturbation to the vector w3.
802: */
803: for (l=0; l<coloring->ncolumns[k]; l++) {
804: col = coloring->columns[k][l]; /* column of the matrix we are probing for */
805: dx = xx[col];
806: if (dx == 0.0) dx = 1.0;
807: #if !defined(PETSC_USE_COMPLEX)
808: if (dx < umin && dx >= 0.0) dx = umin;
809: else if (dx < 0.0 && dx > -umin) dx = -umin;
810: #else
811: if (PetscAbsScalar(dx) < umin && PetscRealPart(dx) >= 0.0) dx = umin;
812: else if (PetscRealPart(dx) < 0.0 && PetscAbsScalar(dx) < umin) dx = -umin;
813: #endif
814: dx *= epsilon;
815: w3_array[col] += dx;
816: }
817: w3_array = w3_array + start; VecRestoreArray(w3,&w3_array);
819: /*
820: Evaluate function at x1 + dx (here dx is a vector of perturbations)
821: */
822: PetscLogEventBegin(MAT_FDColoringFunction,0,0,0,0);
823: (*f)(sctx,t,w3,w2,fctx);
824: PetscLogEventEnd(MAT_FDColoringFunction,0,0,0,0);
825: VecAXPY(&mone,w1,w2);
827: /*
828: Loop over rows of vector, putting results into Jacobian matrix
829: */
830: VecGetArray(w2,&y);
831: for (l=0; l<coloring->nrows[k]; l++) {
832: row = coloring->rows[k][l];
833: col = coloring->columnsforrow[k][l];
834: y[row] *= vscale_array[vscaleforrow[k][l]];
835: srow = row + start;
836: MatSetValues(J,1,&srow,1,&col,y+row,INSERT_VALUES);
837: }
838: VecRestoreArray(w2,&y);
839: }
840: VecRestoreArray(coloring->vscale,&vscale_array);
841: xx = xx + start; VecRestoreArray(x1,&xx);
842: MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);
843: MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);
844: PetscLogEventEnd(MAT_FDColoringApply,coloring,J,x1,0);
845: return(0);
846: }
851: /*@C
852: MatFDColoringSetRecompute - Indicates that the next time a Jacobian preconditioner
853: is needed it sholuld be recomputed. Once this is called and the new Jacobian is computed
854: no additional Jacobian's will be computed (the same one will be used) until this is
855: called again.
857: Collective on MatFDColoring
859: Input Parameters:
860: . c - the coloring context
862: Level: intermediate
864: Notes: The MatFDColoringSetFrequency() is ignored once this is called
866: .seealso: MatFDColoringCreate(), MatFDColoringSetFrequency()
868: .keywords: Mat, finite differences, coloring
869: @*/
870: int MatFDColoringSetRecompute(MatFDColoring c)
871: {
874: c->usersetsrecompute = PETSC_TRUE;
875: c->recompute = PETSC_TRUE;
876: return(0);
877: }