xref: /petsc/src/snes/interface/snes.c (revision ea73f9d272377cf48e653e196e120b5857de3c28)
1 
2 #include <petsc/private/snesimpl.h>      /*I "petscsnes.h"  I*/
3 #include <petscdmshell.h>
4 #include <petscdraw.h>
5 
6 PetscBool         SNESRegisterAllCalled = PETSC_FALSE;
7 PetscFunctionList SNESList              = NULL;
8 
9 /* Logging support */
10 PetscClassId  SNES_CLASSID, DMSNES_CLASSID;
11 PetscLogEvent SNES_Solve, SNES_FunctionEval, SNES_JacobianEval, SNES_NGSEval, SNES_NGSFuncEval, SNES_NPCSolve, SNES_ObjectiveEval;
12 
13 #undef __FUNCT__
14 #define __FUNCT__ "SNESSetErrorIfNotConverged"
15 /*@
16    SNESSetErrorIfNotConverged - Causes SNESSolve() to generate an error if the solver has not converged.
17 
18    Logically Collective on SNES
19 
20    Input Parameters:
21 +  snes - iterative context obtained from SNESCreate()
22 -  flg - PETSC_TRUE indicates you want the error generated
23 
24    Options database keys:
25 .  -snes_error_if_not_converged : this takes an optional truth value (0/1/no/yes/true/false)
26 
27    Level: intermediate
28 
29    Notes:
30     Normally PETSc continues if a linear solver fails to converge, you can call SNESGetConvergedReason() after a SNESSolve()
31     to determine if it has converged.
32 
33 .keywords: SNES, set, initial guess, nonzero
34 
35 .seealso: SNESGetErrorIfNotConverged(), KSPGetErrorIfNotConverged(), KSPSetErrorIFNotConverged()
36 @*/
37 PetscErrorCode  SNESSetErrorIfNotConverged(SNES snes,PetscBool flg)
38 {
39   PetscFunctionBegin;
40   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
41   PetscValidLogicalCollectiveBool(snes,flg,2);
42   snes->errorifnotconverged = flg;
43   PetscFunctionReturn(0);
44 }
45 
46 #undef __FUNCT__
47 #define __FUNCT__ "SNESGetErrorIfNotConverged"
48 /*@
49    SNESGetErrorIfNotConverged - Will SNESSolve() generate an error if the solver does not converge?
50 
51    Not Collective
52 
53    Input Parameter:
54 .  snes - iterative context obtained from SNESCreate()
55 
56    Output Parameter:
57 .  flag - PETSC_TRUE if it will generate an error, else PETSC_FALSE
58 
59    Level: intermediate
60 
61 .keywords: SNES, set, initial guess, nonzero
62 
63 .seealso:  SNESSetErrorIfNotConverged(), KSPGetErrorIfNotConverged(), KSPSetErrorIFNotConverged()
64 @*/
65 PetscErrorCode  SNESGetErrorIfNotConverged(SNES snes,PetscBool  *flag)
66 {
67   PetscFunctionBegin;
68   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
69   PetscValidPointer(flag,2);
70   *flag = snes->errorifnotconverged;
71   PetscFunctionReturn(0);
72 }
73 
74 #undef __FUNCT__
75 #define __FUNCT__ "SNESSetAlwaysComputesFinalResidual"
76 /*@
77     SNESSetAlwaysComputesFinalResidual - does the SNES always compute the residual at the final solution?
78 
79    Logically Collective on SNES
80 
81     Input Parameters:
82 +   snes - the shell SNES
83 -   flg - is the residual computed?
84 
85    Level: advanced
86 
87 .seealso: SNESGetAlwaysComputesFinalResidual()
88 @*/
89 PetscErrorCode  SNESSetAlwaysComputesFinalResidual(SNES snes, PetscBool flg)
90 {
91   PetscFunctionBegin;
92   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
93   snes->alwayscomputesfinalresidual = flg;
94   PetscFunctionReturn(0);
95 }
96 
97 #undef __FUNCT__
98 #define __FUNCT__ "SNESGetAlwaysComputesFinalResidual"
99 /*@
100     SNESGetAlwaysComputesFinalResidual - does the SNES always compute the residual at the final solution?
101 
102    Logically Collective on SNES
103 
104     Input Parameter:
105 .   snes - the shell SNES
106 
107     Output Parameter:
108 .   flg - is the residual computed?
109 
110    Level: advanced
111 
112 .seealso: SNESSetAlwaysComputesFinalResidual()
113 @*/
114 PetscErrorCode  SNESGetAlwaysComputesFinalResidual(SNES snes, PetscBool *flg)
115 {
116   PetscFunctionBegin;
117   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
118   *flg = snes->alwayscomputesfinalresidual;
119   PetscFunctionReturn(0);
120 }
121 
122 #undef __FUNCT__
123 #define __FUNCT__ "SNESSetFunctionDomainError"
124 /*@
125    SNESSetFunctionDomainError - tells SNES that the input vector to your SNESFunction is not
126      in the functions domain. For example, negative pressure.
127 
128    Logically Collective on SNES
129 
130    Input Parameters:
131 .  snes - the SNES context
132 
133    Level: advanced
134 
135 .keywords: SNES, view
136 
137 .seealso: SNESCreate(), SNESSetFunction(), SNESFunction
138 @*/
139 PetscErrorCode  SNESSetFunctionDomainError(SNES snes)
140 {
141   PetscFunctionBegin;
142   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
143   if (snes->errorifnotconverged) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"User code indicates input vector is not in the function domain");
144   snes->domainerror = PETSC_TRUE;
145   PetscFunctionReturn(0);
146 }
147 
148 #undef __FUNCT__
149 #define __FUNCT__ "SNESGetFunctionDomainError"
150 /*@
151    SNESGetFunctionDomainError - Gets the status of the domain error after a call to SNESComputeFunction;
152 
153    Logically Collective on SNES
154 
155    Input Parameters:
156 .  snes - the SNES context
157 
158    Output Parameters:
159 .  domainerror - Set to PETSC_TRUE if there's a domain error; PETSC_FALSE otherwise.
160 
161    Level: advanced
162 
163 .keywords: SNES, view
164 
165 .seealso: SNESSetFunctionDomainError(), SNESComputeFunction()
166 @*/
167 PetscErrorCode  SNESGetFunctionDomainError(SNES snes, PetscBool *domainerror)
168 {
169   PetscFunctionBegin;
170   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
171   PetscValidPointer(domainerror, 2);
172   *domainerror = snes->domainerror;
173   PetscFunctionReturn(0);
174 }
175 
176 #undef __FUNCT__
177 #define __FUNCT__ "SNESLoad"
178 /*@C
179   SNESLoad - Loads a SNES that has been stored in binary  with SNESView().
180 
181   Collective on PetscViewer
182 
183   Input Parameters:
184 + newdm - the newly loaded SNES, this needs to have been created with SNESCreate() or
185            some related function before a call to SNESLoad().
186 - viewer - binary file viewer, obtained from PetscViewerBinaryOpen()
187 
188    Level: intermediate
189 
190   Notes:
191    The type is determined by the data in the file, any type set into the SNES before this call is ignored.
192 
193   Notes for advanced users:
194   Most users should not need to know the details of the binary storage
195   format, since SNESLoad() and TSView() completely hide these details.
196   But for anyone who's interested, the standard binary matrix storage
197   format is
198 .vb
199      has not yet been determined
200 .ve
201 
202 .seealso: PetscViewerBinaryOpen(), SNESView(), MatLoad(), VecLoad()
203 @*/
204 PetscErrorCode  SNESLoad(SNES snes, PetscViewer viewer)
205 {
206   PetscErrorCode ierr;
207   PetscBool      isbinary;
208   PetscInt       classid;
209   char           type[256];
210   KSP            ksp;
211   DM             dm;
212   DMSNES         dmsnes;
213 
214   PetscFunctionBegin;
215   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
216   PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,2);
217   ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr);
218   if (!isbinary) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid viewer; open viewer with PetscViewerBinaryOpen()");
219 
220   ierr = PetscViewerBinaryRead(viewer,&classid,1,NULL,PETSC_INT);CHKERRQ(ierr);
221   if (classid != SNES_FILE_CLASSID) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_WRONG,"Not SNES next in file");
222   ierr = PetscViewerBinaryRead(viewer,type,256,NULL,PETSC_CHAR);CHKERRQ(ierr);
223   ierr = SNESSetType(snes, type);CHKERRQ(ierr);
224   if (snes->ops->load) {
225     ierr = (*snes->ops->load)(snes,viewer);CHKERRQ(ierr);
226   }
227   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
228   ierr = DMGetDMSNES(dm,&dmsnes);CHKERRQ(ierr);
229   ierr = DMSNESLoad(dmsnes,viewer);CHKERRQ(ierr);
230   ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
231   ierr = KSPLoad(ksp,viewer);CHKERRQ(ierr);
232   PetscFunctionReturn(0);
233 }
234 
235 #include <petscdraw.h>
236 #if defined(PETSC_HAVE_SAWS)
237 #include <petscviewersaws.h>
238 #endif
239 #undef __FUNCT__
240 #define __FUNCT__ "SNESView"
241 /*@C
242    SNESView - Prints the SNES data structure.
243 
244    Collective on SNES
245 
246    Input Parameters:
247 +  SNES - the SNES context
248 -  viewer - visualization context
249 
250    Options Database Key:
251 .  -snes_view - Calls SNESView() at end of SNESSolve()
252 
253    Notes:
254    The available visualization contexts include
255 +     PETSC_VIEWER_STDOUT_SELF - standard output (default)
256 -     PETSC_VIEWER_STDOUT_WORLD - synchronized standard
257          output where only the first processor opens
258          the file.  All other processors send their
259          data to the first processor to print.
260 
261    The user can open an alternative visualization context with
262    PetscViewerASCIIOpen() - output to a specified file.
263 
264    Level: beginner
265 
266 .keywords: SNES, view
267 
268 .seealso: PetscViewerASCIIOpen()
269 @*/
270 PetscErrorCode  SNESView(SNES snes,PetscViewer viewer)
271 {
272   SNESKSPEW      *kctx;
273   PetscErrorCode ierr;
274   KSP            ksp;
275   SNESLineSearch linesearch;
276   PetscBool      iascii,isstring,isbinary,isdraw;
277   DMSNES         dmsnes;
278 #if defined(PETSC_HAVE_SAWS)
279   PetscBool      issaws;
280 #endif
281 
282   PetscFunctionBegin;
283   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
284   if (!viewer) {
285     ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)snes),&viewer);CHKERRQ(ierr);
286   }
287   PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,2);
288   PetscCheckSameComm(snes,1,viewer,2);
289 
290   ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
291   ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSTRING,&isstring);CHKERRQ(ierr);
292   ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr);
293   ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr);
294 #if defined(PETSC_HAVE_SAWS)
295   ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSAWS,&issaws);CHKERRQ(ierr);
296 #endif
297   if (iascii) {
298     SNESNormSchedule normschedule;
299 
300     ierr = PetscObjectPrintClassNamePrefixType((PetscObject)snes,viewer);CHKERRQ(ierr);
301     if (!snes->setupcalled) {
302       ierr = PetscViewerASCIIPrintf(viewer,"  SNES has not been set up so information may be incomplete\n");CHKERRQ(ierr);
303     }
304     if (snes->ops->view) {
305       ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
306       ierr = (*snes->ops->view)(snes,viewer);CHKERRQ(ierr);
307       ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
308     }
309     ierr = PetscViewerASCIIPrintf(viewer,"  maximum iterations=%D, maximum function evaluations=%D\n",snes->max_its,snes->max_funcs);CHKERRQ(ierr);
310     ierr = PetscViewerASCIIPrintf(viewer,"  tolerances: relative=%g, absolute=%g, solution=%g\n",(double)snes->rtol,(double)snes->abstol,(double)snes->stol);CHKERRQ(ierr);
311     ierr = PetscViewerASCIIPrintf(viewer,"  total number of linear solver iterations=%D\n",snes->linear_its);CHKERRQ(ierr);
312     ierr = PetscViewerASCIIPrintf(viewer,"  total number of function evaluations=%D\n",snes->nfuncs);CHKERRQ(ierr);
313     ierr = SNESGetNormSchedule(snes, &normschedule);CHKERRQ(ierr);
314     if (normschedule > 0) {ierr = PetscViewerASCIIPrintf(viewer,"  norm schedule %s\n",SNESNormSchedules[normschedule]);CHKERRQ(ierr);}
315     if (snes->gridsequence) {
316       ierr = PetscViewerASCIIPrintf(viewer,"  total number of grid sequence refinements=%D\n",snes->gridsequence);CHKERRQ(ierr);
317     }
318     if (snes->ksp_ewconv) {
319       kctx = (SNESKSPEW*)snes->kspconvctx;
320       if (kctx) {
321         ierr = PetscViewerASCIIPrintf(viewer,"  Eisenstat-Walker computation of KSP relative tolerance (version %D)\n",kctx->version);CHKERRQ(ierr);
322         ierr = PetscViewerASCIIPrintf(viewer,"    rtol_0=%g, rtol_max=%g, threshold=%g\n",(double)kctx->rtol_0,(double)kctx->rtol_max,(double)kctx->threshold);CHKERRQ(ierr);
323         ierr = PetscViewerASCIIPrintf(viewer,"    gamma=%g, alpha=%g, alpha2=%g\n",(double)kctx->gamma,(double)kctx->alpha,(double)kctx->alpha2);CHKERRQ(ierr);
324       }
325     }
326     if (snes->lagpreconditioner == -1) {
327       ierr = PetscViewerASCIIPrintf(viewer,"  Preconditioned is never rebuilt\n");CHKERRQ(ierr);
328     } else if (snes->lagpreconditioner > 1) {
329       ierr = PetscViewerASCIIPrintf(viewer,"  Preconditioned is rebuilt every %D new Jacobians\n",snes->lagpreconditioner);CHKERRQ(ierr);
330     }
331     if (snes->lagjacobian == -1) {
332       ierr = PetscViewerASCIIPrintf(viewer,"  Jacobian is never rebuilt\n");CHKERRQ(ierr);
333     } else if (snes->lagjacobian > 1) {
334       ierr = PetscViewerASCIIPrintf(viewer,"  Jacobian is rebuilt every %D SNES iterations\n",snes->lagjacobian);CHKERRQ(ierr);
335     }
336   } else if (isstring) {
337     const char *type;
338     ierr = SNESGetType(snes,&type);CHKERRQ(ierr);
339     ierr = PetscViewerStringSPrintf(viewer," %-3.3s",type);CHKERRQ(ierr);
340   } else if (isbinary) {
341     PetscInt    classid = SNES_FILE_CLASSID;
342     MPI_Comm    comm;
343     PetscMPIInt rank;
344     char        type[256];
345 
346     ierr = PetscObjectGetComm((PetscObject)snes,&comm);CHKERRQ(ierr);
347     ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
348     if (!rank) {
349       ierr = PetscViewerBinaryWrite(viewer,&classid,1,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
350       ierr = PetscStrncpy(type,((PetscObject)snes)->type_name,sizeof(type));CHKERRQ(ierr);
351       ierr = PetscViewerBinaryWrite(viewer,type,sizeof(type),PETSC_CHAR,PETSC_FALSE);CHKERRQ(ierr);
352     }
353     if (snes->ops->view) {
354       ierr = (*snes->ops->view)(snes,viewer);CHKERRQ(ierr);
355     }
356   } else if (isdraw) {
357     PetscDraw draw;
358     char      str[36];
359     PetscReal x,y,bottom,h;
360 
361     ierr   = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
362     ierr   = PetscDrawGetCurrentPoint(draw,&x,&y);CHKERRQ(ierr);
363     ierr   = PetscStrcpy(str,"SNES: ");CHKERRQ(ierr);
364     ierr   = PetscStrcat(str,((PetscObject)snes)->type_name);CHKERRQ(ierr);
365     ierr   = PetscDrawStringBoxed(draw,x,y,PETSC_DRAW_BLUE,PETSC_DRAW_BLACK,str,NULL,&h);CHKERRQ(ierr);
366     bottom = y - h;
367     ierr   = PetscDrawPushCurrentPoint(draw,x,bottom);CHKERRQ(ierr);
368     if (snes->ops->view) {
369       ierr = (*snes->ops->view)(snes,viewer);CHKERRQ(ierr);
370     }
371 #if defined(PETSC_HAVE_SAWS)
372   } else if (issaws) {
373     PetscMPIInt rank;
374     const char *name;
375 
376     ierr = PetscObjectGetName((PetscObject)snes,&name);CHKERRQ(ierr);
377     ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
378     if (!((PetscObject)snes)->amsmem && !rank) {
379       char       dir[1024];
380 
381       ierr = PetscObjectViewSAWs((PetscObject)snes,viewer);CHKERRQ(ierr);
382       ierr = PetscSNPrintf(dir,1024,"/PETSc/Objects/%s/its",name);CHKERRQ(ierr);
383       PetscStackCallSAWs(SAWs_Register,(dir,&snes->iter,1,SAWs_READ,SAWs_INT));
384       if (!snes->conv_hist) {
385         ierr = SNESSetConvergenceHistory(snes,NULL,NULL,PETSC_DECIDE,PETSC_TRUE);CHKERRQ(ierr);
386       }
387       ierr = PetscSNPrintf(dir,1024,"/PETSc/Objects/%s/conv_hist",name);CHKERRQ(ierr);
388       PetscStackCallSAWs(SAWs_Register,(dir,snes->conv_hist,10,SAWs_READ,SAWs_DOUBLE));
389     }
390 #endif
391   }
392   if (snes->linesearch) {
393     ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
394     ierr = SNESGetLineSearch(snes, &linesearch);CHKERRQ(ierr);
395     ierr = SNESLineSearchView(linesearch, viewer);CHKERRQ(ierr);
396     ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
397   }
398   if (snes->pc && snes->usespc) {
399     ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
400     ierr = SNESView(snes->pc, viewer);CHKERRQ(ierr);
401     ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
402   }
403   ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
404   ierr = DMGetDMSNES(snes->dm,&dmsnes);CHKERRQ(ierr);
405   ierr = DMSNESView(dmsnes, viewer);CHKERRQ(ierr);
406   ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
407   if (snes->usesksp) {
408     ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
409     ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
410     ierr = KSPView(ksp,viewer);CHKERRQ(ierr);
411     ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
412   }
413   if (isdraw) {
414     PetscDraw draw;
415     ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
416     ierr = PetscDrawPopCurrentPoint(draw);CHKERRQ(ierr);
417   }
418   PetscFunctionReturn(0);
419 }
420 
421 /*
422   We retain a list of functions that also take SNES command
423   line options. These are called at the end SNESSetFromOptions()
424 */
425 #define MAXSETFROMOPTIONS 5
426 static PetscInt numberofsetfromoptions;
427 static PetscErrorCode (*othersetfromoptions[MAXSETFROMOPTIONS])(SNES);
428 
429 #undef __FUNCT__
430 #define __FUNCT__ "SNESAddOptionsChecker"
431 /*@C
432   SNESAddOptionsChecker - Adds an additional function to check for SNES options.
433 
434   Not Collective
435 
436   Input Parameter:
437 . snescheck - function that checks for options
438 
439   Level: developer
440 
441 .seealso: SNESSetFromOptions()
442 @*/
443 PetscErrorCode  SNESAddOptionsChecker(PetscErrorCode (*snescheck)(SNES))
444 {
445   PetscFunctionBegin;
446   if (numberofsetfromoptions >= MAXSETFROMOPTIONS) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Too many options checkers, only %D allowed", MAXSETFROMOPTIONS);
447   othersetfromoptions[numberofsetfromoptions++] = snescheck;
448   PetscFunctionReturn(0);
449 }
450 
451 extern PetscErrorCode  SNESDefaultMatrixFreeCreate2(SNES,Vec,Mat*);
452 
453 #undef __FUNCT__
454 #define __FUNCT__ "SNESSetUpMatrixFree_Private"
455 static PetscErrorCode SNESSetUpMatrixFree_Private(SNES snes, PetscBool hasOperator, PetscInt version)
456 {
457   Mat            J;
458   KSP            ksp;
459   PC             pc;
460   PetscBool      match;
461   PetscErrorCode ierr;
462   MatNullSpace   nullsp;
463 
464   PetscFunctionBegin;
465   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
466 
467   if (!snes->vec_func && (snes->jacobian || snes->jacobian_pre)) {
468     Mat A = snes->jacobian, B = snes->jacobian_pre;
469     ierr = MatCreateVecs(A ? A : B, NULL,&snes->vec_func);CHKERRQ(ierr);
470   }
471 
472   if (version == 1) {
473     ierr = MatCreateSNESMF(snes,&J);CHKERRQ(ierr);
474     ierr = MatMFFDSetOptionsPrefix(J,((PetscObject)snes)->prefix);CHKERRQ(ierr);
475     ierr = MatSetFromOptions(J);CHKERRQ(ierr);
476   } else if (version == 2) {
477     if (!snes->vec_func) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SNESSetFunction() must be called first");
478 #if !defined(PETSC_USE_COMPLEX) && !defined(PETSC_USE_REAL_SINGLE) && !defined(PETSC_USE_REAL___FLOAT128)
479     ierr = SNESDefaultMatrixFreeCreate2(snes,snes->vec_func,&J);CHKERRQ(ierr);
480 #else
481     SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP, "matrix-free operator rutines (version 2)");
482 #endif
483   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "matrix-free operator rutines, only version 1 and 2");
484 
485   /* attach any user provided null space that was on Amat to the newly created matrix free matrix */
486   if (snes->jacobian) {
487     ierr = MatGetNullSpace(snes->jacobian,&nullsp);CHKERRQ(ierr);
488     if (nullsp) {
489       ierr = MatSetNullSpace(J,nullsp);CHKERRQ(ierr);
490     }
491   }
492 
493   ierr = PetscInfo1(snes,"Setting default matrix-free operator routines (version %D)\n", version);CHKERRQ(ierr);
494   if (hasOperator) {
495 
496     /* This version replaces the user provided Jacobian matrix with a
497        matrix-free version but still employs the user-provided preconditioner matrix. */
498     ierr = SNESSetJacobian(snes,J,0,0,0);CHKERRQ(ierr);
499   } else {
500     /* This version replaces both the user-provided Jacobian and the user-
501      provided preconditioner Jacobian with the default matrix free version. */
502     if ((snes->pcside == PC_LEFT) && snes->pc) {
503       if (!snes->jacobian){ierr = SNESSetJacobian(snes,J,0,0,0);CHKERRQ(ierr);}
504     } else {
505       ierr = SNESSetJacobian(snes,J,J,MatMFFDComputeJacobian,0);CHKERRQ(ierr);
506     }
507     /* Force no preconditioner */
508     ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
509     ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
510     ierr = PetscObjectTypeCompare((PetscObject)pc,PCSHELL,&match);CHKERRQ(ierr);
511     if (!match) {
512       ierr = PetscInfo(snes,"Setting default matrix-free preconditioner routines\nThat is no preconditioner is being used\n");CHKERRQ(ierr);
513       ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr);
514     }
515   }
516   ierr = MatDestroy(&J);CHKERRQ(ierr);
517   PetscFunctionReturn(0);
518 }
519 
520 #undef __FUNCT__
521 #define __FUNCT__ "DMRestrictHook_SNESVecSol"
522 static PetscErrorCode DMRestrictHook_SNESVecSol(DM dmfine,Mat Restrict,Vec Rscale,Mat Inject,DM dmcoarse,void *ctx)
523 {
524   SNES           snes = (SNES)ctx;
525   PetscErrorCode ierr;
526   Vec            Xfine,Xfine_named = NULL,Xcoarse;
527 
528   PetscFunctionBegin;
529   if (PetscLogPrintInfo) {
530     PetscInt finelevel,coarselevel,fineclevel,coarseclevel;
531     ierr = DMGetRefineLevel(dmfine,&finelevel);CHKERRQ(ierr);
532     ierr = DMGetCoarsenLevel(dmfine,&fineclevel);CHKERRQ(ierr);
533     ierr = DMGetRefineLevel(dmcoarse,&coarselevel);CHKERRQ(ierr);
534     ierr = DMGetCoarsenLevel(dmcoarse,&coarseclevel);CHKERRQ(ierr);
535     ierr = PetscInfo4(dmfine,"Restricting SNES solution vector from level %D-%D to level %D-%D\n",finelevel,fineclevel,coarselevel,coarseclevel);CHKERRQ(ierr);
536   }
537   if (dmfine == snes->dm) Xfine = snes->vec_sol;
538   else {
539     ierr  = DMGetNamedGlobalVector(dmfine,"SNESVecSol",&Xfine_named);CHKERRQ(ierr);
540     Xfine = Xfine_named;
541   }
542   ierr = DMGetNamedGlobalVector(dmcoarse,"SNESVecSol",&Xcoarse);CHKERRQ(ierr);
543   if (Inject) {
544     ierr = MatRestrict(Inject,Xfine,Xcoarse);CHKERRQ(ierr);
545   } else {
546     ierr = MatRestrict(Restrict,Xfine,Xcoarse);CHKERRQ(ierr);
547     ierr = VecPointwiseMult(Xcoarse,Xcoarse,Rscale);CHKERRQ(ierr);
548   }
549   ierr = DMRestoreNamedGlobalVector(dmcoarse,"SNESVecSol",&Xcoarse);CHKERRQ(ierr);
550   if (Xfine_named) {ierr = DMRestoreNamedGlobalVector(dmfine,"SNESVecSol",&Xfine_named);CHKERRQ(ierr);}
551   PetscFunctionReturn(0);
552 }
553 
554 #undef __FUNCT__
555 #define __FUNCT__ "DMCoarsenHook_SNESVecSol"
556 static PetscErrorCode DMCoarsenHook_SNESVecSol(DM dm,DM dmc,void *ctx)
557 {
558   PetscErrorCode ierr;
559 
560   PetscFunctionBegin;
561   ierr = DMCoarsenHookAdd(dmc,DMCoarsenHook_SNESVecSol,DMRestrictHook_SNESVecSol,ctx);CHKERRQ(ierr);
562   PetscFunctionReturn(0);
563 }
564 
565 #undef __FUNCT__
566 #define __FUNCT__ "KSPComputeOperators_SNES"
567 /* This may be called to rediscretize the operator on levels of linear multigrid. The DM shuffle is so the user can
568  * safely call SNESGetDM() in their residual evaluation routine. */
569 static PetscErrorCode KSPComputeOperators_SNES(KSP ksp,Mat A,Mat B,void *ctx)
570 {
571   SNES           snes = (SNES)ctx;
572   PetscErrorCode ierr;
573   Mat            Asave = A,Bsave = B;
574   Vec            X,Xnamed = NULL;
575   DM             dmsave;
576   void           *ctxsave;
577   PetscErrorCode (*jac)(SNES,Vec,Mat,Mat,void*);
578 
579   PetscFunctionBegin;
580   dmsave = snes->dm;
581   ierr   = KSPGetDM(ksp,&snes->dm);CHKERRQ(ierr);
582   if (dmsave == snes->dm) X = snes->vec_sol; /* We are on the finest level */
583   else {                                     /* We are on a coarser level, this vec was initialized using a DM restrict hook */
584     ierr = DMGetNamedGlobalVector(snes->dm,"SNESVecSol",&Xnamed);CHKERRQ(ierr);
585     X    = Xnamed;
586     ierr = SNESGetJacobian(snes,NULL,NULL,&jac,&ctxsave);CHKERRQ(ierr);
587     /* If the DM's don't match up, the MatFDColoring context needed for the jacobian won't match up either -- fixit. */
588     if (jac == SNESComputeJacobianDefaultColor) {
589       ierr = SNESSetJacobian(snes,NULL,NULL,SNESComputeJacobianDefaultColor,0);CHKERRQ(ierr);
590     }
591   }
592   /* put the previous context back */
593 
594   ierr = SNESComputeJacobian(snes,X,A,B);CHKERRQ(ierr);
595   if (snes->dm != dmsave && jac == SNESComputeJacobianDefaultColor) {
596     ierr = SNESSetJacobian(snes,NULL,NULL,jac,ctxsave);CHKERRQ(ierr);
597   }
598 
599   if (A != Asave || B != Bsave) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_SUP,"No support for changing matrices at this time");
600   if (Xnamed) {
601     ierr = DMRestoreNamedGlobalVector(snes->dm,"SNESVecSol",&Xnamed);CHKERRQ(ierr);
602   }
603   snes->dm = dmsave;
604   PetscFunctionReturn(0);
605 }
606 
607 #undef __FUNCT__
608 #define __FUNCT__ "SNESSetUpMatrices"
609 /*@
610    SNESSetUpMatrices - ensures that matrices are available for SNES, to be called by SNESSetUp_XXX()
611 
612    Collective
613 
614    Input Arguments:
615 .  snes - snes to configure
616 
617    Level: developer
618 
619 .seealso: SNESSetUp()
620 @*/
621 PetscErrorCode SNESSetUpMatrices(SNES snes)
622 {
623   PetscErrorCode ierr;
624   DM             dm;
625   DMSNES         sdm;
626 
627   PetscFunctionBegin;
628   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
629   ierr = DMGetDMSNES(dm,&sdm);CHKERRQ(ierr);
630   if (!sdm->ops->computejacobian) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_PLIB,"DMSNES not properly configured");
631   else if (!snes->jacobian && snes->mf) {
632     Mat  J;
633     void *functx;
634     ierr = MatCreateSNESMF(snes,&J);CHKERRQ(ierr);
635     ierr = MatMFFDSetOptionsPrefix(J,((PetscObject)snes)->prefix);CHKERRQ(ierr);
636     ierr = MatSetFromOptions(J);CHKERRQ(ierr);
637     ierr = SNESGetFunction(snes,NULL,NULL,&functx);CHKERRQ(ierr);
638     ierr = SNESSetJacobian(snes,J,J,0,0);CHKERRQ(ierr);
639     ierr = MatDestroy(&J);CHKERRQ(ierr);
640   } else if (snes->mf_operator && !snes->jacobian_pre && !snes->jacobian) {
641     Mat J,B;
642     ierr = MatCreateSNESMF(snes,&J);CHKERRQ(ierr);
643     ierr = MatMFFDSetOptionsPrefix(J,((PetscObject)snes)->prefix);CHKERRQ(ierr);
644     ierr = MatSetFromOptions(J);CHKERRQ(ierr);
645     ierr = DMCreateMatrix(snes->dm,&B);CHKERRQ(ierr);
646     /* sdm->computejacobian was already set to reach here */
647     ierr = SNESSetJacobian(snes,J,B,NULL,NULL);CHKERRQ(ierr);
648     ierr = MatDestroy(&J);CHKERRQ(ierr);
649     ierr = MatDestroy(&B);CHKERRQ(ierr);
650   } else if (!snes->jacobian_pre) {
651     Mat J,B;
652     J    = snes->jacobian;
653     ierr = DMCreateMatrix(snes->dm,&B);CHKERRQ(ierr);
654     ierr = SNESSetJacobian(snes,J ? J : B,B,NULL,NULL);CHKERRQ(ierr);
655     ierr = MatDestroy(&B);CHKERRQ(ierr);
656   }
657   {
658     KSP ksp;
659     ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
660     ierr = KSPSetComputeOperators(ksp,KSPComputeOperators_SNES,snes);CHKERRQ(ierr);
661     ierr = DMCoarsenHookAdd(snes->dm,DMCoarsenHook_SNESVecSol,DMRestrictHook_SNESVecSol,snes);CHKERRQ(ierr);
662   }
663   PetscFunctionReturn(0);
664 }
665 
666 #undef __FUNCT__
667 #define __FUNCT__ "SNESMonitorSetFromOptions"
668 /*@C
669    SNESMonitorSetFromOptions - Sets a monitor function and viewer appropriate for the type indicated by the user
670 
671    Collective on SNES
672 
673    Input Parameters:
674 +  snes - SNES object you wish to monitor
675 .  name - the monitor type one is seeking
676 .  help - message indicating what monitoring is done
677 .  manual - manual page for the monitor
678 .  monitor - the monitor function
679 -  monitorsetup - a function that is called once ONLY if the user selected this monitor that may set additional features of the SNES or PetscViewer objects
680 
681    Level: developer
682 
683 .seealso: PetscOptionsGetViewer(), PetscOptionsGetReal(), PetscOptionsHasName(), PetscOptionsGetString(),
684           PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool()
685           PetscOptionsInt(), PetscOptionsString(), PetscOptionsReal(), PetscOptionsBool(),
686           PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
687           PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
688           PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
689           PetscOptionsFList(), PetscOptionsEList()
690 @*/
691 PetscErrorCode  SNESMonitorSetFromOptions(SNES snes,const char name[],const char help[], const char manual[],PetscErrorCode (*monitor)(SNES,PetscInt,PetscReal,PetscViewerAndFormat*),PetscErrorCode (*monitorsetup)(SNES,PetscViewerAndFormat*))
692 {
693   PetscErrorCode    ierr;
694   PetscViewer       viewer;
695   PetscViewerFormat format;
696   PetscBool         flg;
697 
698   PetscFunctionBegin;
699   ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,name,&viewer,&format,&flg);CHKERRQ(ierr);
700   if (flg) {
701     PetscViewerAndFormat *vf;
702     ierr = PetscViewerAndFormatCreate(viewer,format,&vf);CHKERRQ(ierr);
703     ierr = PetscObjectDereference((PetscObject)viewer);CHKERRQ(ierr);
704     if (monitorsetup) {
705       ierr = (*monitorsetup)(snes,vf);CHKERRQ(ierr);
706     }
707     ierr = SNESMonitorSet(snes,(PetscErrorCode (*)(SNES,PetscInt,PetscReal,void*))monitor,vf,(PetscErrorCode (*)(void**))PetscViewerAndFormatDestroy);CHKERRQ(ierr);
708   }
709   PetscFunctionReturn(0);
710 }
711 
712 #undef __FUNCT__
713 #define __FUNCT__ "SNESSetFromOptions"
714 /*@
715    SNESSetFromOptions - Sets various SNES and KSP parameters from user options.
716 
717    Collective on SNES
718 
719    Input Parameter:
720 .  snes - the SNES context
721 
722    Options Database Keys:
723 +  -snes_type <type> - newtonls, newtontr, ngmres, ncg, nrichardson, qn, vi, fas, SNESType for complete list
724 .  -snes_stol - convergence tolerance in terms of the norm
725                 of the change in the solution between steps
726 .  -snes_atol <abstol> - absolute tolerance of residual norm
727 .  -snes_rtol <rtol> - relative decrease in tolerance norm from initial
728 .  -snes_max_it <max_it> - maximum number of iterations
729 .  -snes_max_funcs <max_funcs> - maximum number of function evaluations
730 .  -snes_max_fail <max_fail> - maximum number of line search failures allowed before stopping, default is none
731 .  -snes_max_linear_solve_fail - number of linear solver failures before SNESSolve() stops
732 .  -snes_lag_preconditioner <lag> - how often preconditioner is rebuilt (use -1 to never rebuild)
733 .  -snes_lag_jacobian <lag> - how often Jacobian is rebuilt (use -1 to never rebuild)
734 .  -snes_trtol <trtol> - trust region tolerance
735 .  -snes_no_convergence_test - skip convergence test in nonlinear
736                                solver; hence iterations will continue until max_it
737                                or some other criterion is reached. Saves expense
738                                of convergence test
739 .  -snes_monitor [ascii][:filename][:viewer format] - prints residual norm at each iteration. if no filename given prints to stdout
740 .  -snes_monitor_solution [ascii binary draw][:filename][:viewer format] - plots solution at each iteration
741 .  -snes_monitor_residual [ascii binary draw][:filename][:viewer format] - plots residual (not its norm) at each iteration
742 .  -snes_monitor_solution_update [ascii binary draw][:filename][:viewer format] - plots update to solution at each iteration
743 .  -snes_monitor_lg_residualnorm - plots residual norm at each iteration
744 .  -snes_monitor_lg_range - plots residual norm at each iteration
745 .  -snes_fd - use finite differences to compute Jacobian; very slow, only for testing
746 .  -snes_fd_color - use finite differences with coloring to compute Jacobian
747 .  -snes_mf_ksp_monitor - if using matrix-free multiply then print h at each KSP iteration
748 -  -snes_converged_reason - print the reason for convergence/divergence after each solve
749 
750     Options Database for Eisenstat-Walker method:
751 +  -snes_ksp_ew - use Eisenstat-Walker method for determining linear system convergence
752 .  -snes_ksp_ew_version ver - version of  Eisenstat-Walker method
753 .  -snes_ksp_ew_rtol0 <rtol0> - Sets rtol0
754 .  -snes_ksp_ew_rtolmax <rtolmax> - Sets rtolmax
755 .  -snes_ksp_ew_gamma <gamma> - Sets gamma
756 .  -snes_ksp_ew_alpha <alpha> - Sets alpha
757 .  -snes_ksp_ew_alpha2 <alpha2> - Sets alpha2
758 -  -snes_ksp_ew_threshold <threshold> - Sets threshold
759 
760    Notes:
761    To see all options, run your program with the -help option or consult
762    Users-Manual: ch_snes
763 
764    Level: beginner
765 
766 .keywords: SNES, nonlinear, set, options, database
767 
768 .seealso: SNESSetOptionsPrefix()
769 @*/
770 PetscErrorCode  SNESSetFromOptions(SNES snes)
771 {
772   PetscBool      flg,pcset,persist,set;
773   PetscInt       i,indx,lag,grids;
774   const char     *deft        = SNESNEWTONLS;
775   const char     *convtests[] = {"default","skip"};
776   SNESKSPEW      *kctx        = NULL;
777   char           type[256], monfilename[PETSC_MAX_PATH_LEN];
778   PetscErrorCode ierr;
779   PCSide         pcside;
780   const char     *optionsprefix;
781 
782   PetscFunctionBegin;
783   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
784   ierr = SNESRegisterAll();CHKERRQ(ierr);
785   ierr = PetscObjectOptionsBegin((PetscObject)snes);CHKERRQ(ierr);
786   if (((PetscObject)snes)->type_name) deft = ((PetscObject)snes)->type_name;
787   ierr = PetscOptionsFList("-snes_type","Nonlinear solver method","SNESSetType",SNESList,deft,type,256,&flg);CHKERRQ(ierr);
788   if (flg) {
789     ierr = SNESSetType(snes,type);CHKERRQ(ierr);
790   } else if (!((PetscObject)snes)->type_name) {
791     ierr = SNESSetType(snes,deft);CHKERRQ(ierr);
792   }
793   ierr = PetscOptionsReal("-snes_stol","Stop if step length less than","SNESSetTolerances",snes->stol,&snes->stol,NULL);CHKERRQ(ierr);
794   ierr = PetscOptionsReal("-snes_atol","Stop if function norm less than","SNESSetTolerances",snes->abstol,&snes->abstol,NULL);CHKERRQ(ierr);
795 
796   ierr = PetscOptionsReal("-snes_rtol","Stop if decrease in function norm less than","SNESSetTolerances",snes->rtol,&snes->rtol,NULL);CHKERRQ(ierr);
797   ierr = PetscOptionsInt("-snes_max_it","Maximum iterations","SNESSetTolerances",snes->max_its,&snes->max_its,NULL);CHKERRQ(ierr);
798   ierr = PetscOptionsInt("-snes_max_funcs","Maximum function evaluations","SNESSetTolerances",snes->max_funcs,&snes->max_funcs,NULL);CHKERRQ(ierr);
799   ierr = PetscOptionsInt("-snes_max_fail","Maximum nonlinear step failures","SNESSetMaxNonlinearStepFailures",snes->maxFailures,&snes->maxFailures,NULL);CHKERRQ(ierr);
800   ierr = PetscOptionsInt("-snes_max_linear_solve_fail","Maximum failures in linear solves allowed","SNESSetMaxLinearSolveFailures",snes->maxLinearSolveFailures,&snes->maxLinearSolveFailures,NULL);CHKERRQ(ierr);
801   ierr = PetscOptionsBool("-snes_error_if_not_converged","Generate error if solver does not converge","SNESSetErrorIfNotConverged",snes->errorifnotconverged,&snes->errorifnotconverged,NULL);CHKERRQ(ierr);
802 
803   ierr = PetscOptionsInt("-snes_lag_preconditioner","How often to rebuild preconditioner","SNESSetLagPreconditioner",snes->lagpreconditioner,&lag,&flg);CHKERRQ(ierr);
804   if (flg) {
805     ierr = SNESSetLagPreconditioner(snes,lag);CHKERRQ(ierr);
806   }
807   ierr = PetscOptionsBool("-snes_lag_preconditioner_persists","Preconditioner lagging through multiple solves","SNESSetLagPreconditionerPersists",snes->lagjac_persist,&persist,&flg);CHKERRQ(ierr);
808   if (flg) {
809     ierr = SNESSetLagPreconditionerPersists(snes,persist);CHKERRQ(ierr);
810   }
811   ierr = PetscOptionsInt("-snes_lag_jacobian","How often to rebuild Jacobian","SNESSetLagJacobian",snes->lagjacobian,&lag,&flg);CHKERRQ(ierr);
812   if (flg) {
813     ierr = SNESSetLagJacobian(snes,lag);CHKERRQ(ierr);
814   }
815   ierr = PetscOptionsBool("-snes_lag_jacobian_persists","Jacobian lagging through multiple solves","SNESSetLagJacobianPersists",snes->lagjac_persist,&persist,&flg);CHKERRQ(ierr);
816   if (flg) {
817     ierr = SNESSetLagJacobianPersists(snes,persist);CHKERRQ(ierr);
818   }
819 
820   ierr = PetscOptionsInt("-snes_grid_sequence","Use grid sequencing to generate initial guess","SNESSetGridSequence",snes->gridsequence,&grids,&flg);CHKERRQ(ierr);
821   if (flg) {
822     ierr = SNESSetGridSequence(snes,grids);CHKERRQ(ierr);
823   }
824 
825   ierr = PetscOptionsEList("-snes_convergence_test","Convergence test","SNESSetConvergenceTest",convtests,2,"default",&indx,&flg);CHKERRQ(ierr);
826   if (flg) {
827     switch (indx) {
828     case 0: ierr = SNESSetConvergenceTest(snes,SNESConvergedDefault,NULL,NULL);CHKERRQ(ierr); break;
829     case 1: ierr = SNESSetConvergenceTest(snes,SNESConvergedSkip,NULL,NULL);CHKERRQ(ierr);    break;
830     }
831   }
832 
833   ierr = PetscOptionsEList("-snes_norm_schedule","SNES Norm schedule","SNESSetNormSchedule",SNESNormSchedules,5,"function",&indx,&flg);CHKERRQ(ierr);
834   if (flg) { ierr = SNESSetNormSchedule(snes,(SNESNormSchedule)indx);CHKERRQ(ierr); }
835 
836   ierr = PetscOptionsEList("-snes_function_type","SNES Norm schedule","SNESSetFunctionType",SNESFunctionTypes,2,"unpreconditioned",&indx,&flg);CHKERRQ(ierr);
837   if (flg) { ierr = SNESSetFunctionType(snes,(SNESFunctionType)indx);CHKERRQ(ierr); }
838 
839   kctx = (SNESKSPEW*)snes->kspconvctx;
840 
841   ierr = PetscOptionsBool("-snes_ksp_ew","Use Eisentat-Walker linear system convergence test","SNESKSPSetUseEW",snes->ksp_ewconv,&snes->ksp_ewconv,NULL);CHKERRQ(ierr);
842 
843   ierr = PetscOptionsInt("-snes_ksp_ew_version","Version 1, 2 or 3","SNESKSPSetParametersEW",kctx->version,&kctx->version,NULL);CHKERRQ(ierr);
844   ierr = PetscOptionsReal("-snes_ksp_ew_rtol0","0 <= rtol0 < 1","SNESKSPSetParametersEW",kctx->rtol_0,&kctx->rtol_0,NULL);CHKERRQ(ierr);
845   ierr = PetscOptionsReal("-snes_ksp_ew_rtolmax","0 <= rtolmax < 1","SNESKSPSetParametersEW",kctx->rtol_max,&kctx->rtol_max,NULL);CHKERRQ(ierr);
846   ierr = PetscOptionsReal("-snes_ksp_ew_gamma","0 <= gamma <= 1","SNESKSPSetParametersEW",kctx->gamma,&kctx->gamma,NULL);CHKERRQ(ierr);
847   ierr = PetscOptionsReal("-snes_ksp_ew_alpha","1 < alpha <= 2","SNESKSPSetParametersEW",kctx->alpha,&kctx->alpha,NULL);CHKERRQ(ierr);
848   ierr = PetscOptionsReal("-snes_ksp_ew_alpha2","alpha2","SNESKSPSetParametersEW",kctx->alpha2,&kctx->alpha2,NULL);CHKERRQ(ierr);
849   ierr = PetscOptionsReal("-snes_ksp_ew_threshold","0 < threshold < 1","SNESKSPSetParametersEW",kctx->threshold,&kctx->threshold,NULL);CHKERRQ(ierr);
850 
851   flg  = PETSC_FALSE;
852   ierr = PetscOptionsBool("-snes_check_jacobian","Check each Jacobian with a differenced one","SNESUpdateCheckJacobian",flg,&flg,&set);CHKERRQ(ierr);
853   if (set && flg) {
854     ierr = SNESSetUpdate(snes,SNESUpdateCheckJacobian);CHKERRQ(ierr);
855   }
856 
857   flg  = PETSC_FALSE;
858   ierr = PetscOptionsBool("-snes_monitor_cancel","Remove all monitors","SNESMonitorCancel",flg,&flg,&set);CHKERRQ(ierr);
859   if (set && flg) {ierr = SNESMonitorCancel(snes);CHKERRQ(ierr);}
860 
861   ierr = SNESMonitorSetFromOptions(snes,"-snes_monitor","Monitor norm of function","SNESMonitorDefault",SNESMonitorDefault,NULL);CHKERRQ(ierr);
862   ierr = SNESMonitorSetFromOptions(snes,"-snes_monitor_short","Monitor norm of function with fewer digits","SNESMonitorDefaultShort",SNESMonitorDefaultShort,NULL);CHKERRQ(ierr);
863   ierr = SNESMonitorSetFromOptions(snes,"-snes_monitor_range","Monitor range of elements of function","SNESMonitorRange",SNESMonitorRange,NULL);CHKERRQ(ierr);
864 
865   ierr = SNESMonitorSetFromOptions(snes,"-snes_monitor_ratio","Monitor ratios of the norm of function for consecutive steps","SNESMonitorRatio",SNESMonitorRatio,SNESMonitorRatioSetUp);CHKERRQ(ierr);
866   ierr = SNESMonitorSetFromOptions(snes,"-snes_monitor_field","Monitor norm of function (split into fields)","SNESMonitorDefaultField",SNESMonitorDefaultField,NULL);CHKERRQ(ierr);
867   ierr = SNESMonitorSetFromOptions(snes,"-snes_monitor_solution","View solution at each iteration","SNESMonitorSolution",SNESMonitorSolution,NULL);CHKERRQ(ierr);
868   ierr = SNESMonitorSetFromOptions(snes,"-snes_monitor_solution_update","View correction at each iteration","SNESMonitorSolutionUpdate",SNESMonitorSolutionUpdate,NULL);CHKERRQ(ierr);
869   ierr = SNESMonitorSetFromOptions(snes,"-snes_monitor_residual","View residual at each iteration","SNESMonitorResidual",SNESMonitorResidual,NULL);CHKERRQ(ierr);
870   ierr = SNESMonitorSetFromOptions(snes,"-snes_monitor_jacupdate_spectrum","Print the change in the spectrum of the Jacobian","SNESMonitorJacUpdateSpectrum",SNESMonitorJacUpdateSpectrum,NULL);CHKERRQ(ierr);
871   ierr = SNESMonitorSetFromOptions(snes,"-snes_monitor_fields","Monitor norm of function per field","SNESMonitorSet",SNESMonitorFields,NULL);CHKERRQ(ierr);
872 
873   ierr = PetscOptionsString("-snes_monitor_python","Use Python function","SNESMonitorSet",0,monfilename,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
874   if (flg) {ierr = PetscPythonMonitorSet((PetscObject)snes,monfilename);CHKERRQ(ierr);}
875 
876 
877   flg  = PETSC_FALSE;
878   ierr = PetscOptionsBool("-snes_monitor_lg_residualnorm","Plot function norm at each iteration","SNESMonitorLGResidualNorm",flg,&flg,NULL);CHKERRQ(ierr);
879   if (flg) {
880     PetscDrawLG ctx;
881 
882     ierr = SNESMonitorLGCreate(PetscObjectComm((PetscObject)snes),NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,&ctx);CHKERRQ(ierr);
883     ierr = SNESMonitorSet(snes,SNESMonitorLGResidualNorm,ctx,(PetscErrorCode (*)(void**))PetscDrawLGDestroy);CHKERRQ(ierr);
884   }
885   flg  = PETSC_FALSE;
886   ierr = PetscOptionsBool("-snes_monitor_lg_range","Plot function range at each iteration","SNESMonitorLGRange",flg,&flg,NULL);CHKERRQ(ierr);
887   if (flg) {
888     PetscViewer ctx;
889 
890     ierr = PetscViewerDrawOpen(PetscObjectComm((PetscObject)snes),NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,&ctx);CHKERRQ(ierr);
891     ierr = SNESMonitorSet(snes,SNESMonitorLGRange,ctx,(PetscErrorCode (*)(void**))PetscViewerDestroy);CHKERRQ(ierr);
892   }
893 
894 
895 
896   flg  = PETSC_FALSE;
897   ierr = PetscOptionsBool("-snes_fd","Use finite differences (slow) to compute Jacobian","SNESComputeJacobianDefault",flg,&flg,NULL);CHKERRQ(ierr);
898   if (flg) {
899     void *functx;
900     ierr = SNESGetFunction(snes,NULL,NULL,&functx);CHKERRQ(ierr);
901     ierr = SNESSetJacobian(snes,snes->jacobian,snes->jacobian_pre,SNESComputeJacobianDefault,functx);CHKERRQ(ierr);
902     ierr = PetscInfo(snes,"Setting default finite difference Jacobian matrix\n");CHKERRQ(ierr);
903   }
904 
905   flg  = PETSC_FALSE;
906   ierr = PetscOptionsBool("-snes_fd_function","Use finite differences (slow) to compute function from user objective","SNESObjectiveComputeFunctionDefaultFD",flg,&flg,NULL);CHKERRQ(ierr);
907   if (flg) {
908     ierr = SNESSetFunction(snes,NULL,SNESObjectiveComputeFunctionDefaultFD,NULL);CHKERRQ(ierr);
909   }
910 
911   flg  = PETSC_FALSE;
912   ierr = PetscOptionsBool("-snes_fd_color","Use finite differences with coloring to compute Jacobian","SNESComputeJacobianDefaultColor",flg,&flg,NULL);CHKERRQ(ierr);
913   if (flg) {
914     DM             dm;
915     DMSNES         sdm;
916     ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
917     ierr = DMGetDMSNES(dm,&sdm);CHKERRQ(ierr);
918     sdm->jacobianctx = NULL;
919     ierr = SNESSetJacobian(snes,snes->jacobian,snes->jacobian_pre,SNESComputeJacobianDefaultColor,0);CHKERRQ(ierr);
920     ierr = PetscInfo(snes,"Setting default finite difference coloring Jacobian matrix\n");CHKERRQ(ierr);
921   }
922 
923   flg  = PETSC_FALSE;
924   ierr = PetscOptionsBool("-snes_mf_operator","Use a Matrix-Free Jacobian with user-provided preconditioner matrix","MatCreateSNESMF",PETSC_FALSE,&snes->mf_operator,&flg);CHKERRQ(ierr);
925   if (flg && snes->mf_operator) {
926     snes->mf_operator = PETSC_TRUE;
927     snes->mf          = PETSC_TRUE;
928   }
929   flg  = PETSC_FALSE;
930   ierr = PetscOptionsBool("-snes_mf","Use a Matrix-Free Jacobian with no preconditioner matrix","MatCreateSNESMF",PETSC_FALSE,&snes->mf,&flg);CHKERRQ(ierr);
931   if (!flg && snes->mf_operator) snes->mf = PETSC_TRUE;
932   ierr = PetscOptionsInt("-snes_mf_version","Matrix-Free routines version 1 or 2","None",snes->mf_version,&snes->mf_version,0);CHKERRQ(ierr);
933 
934   flg  = PETSC_FALSE;
935   ierr = SNESGetNPCSide(snes,&pcside);CHKERRQ(ierr);
936   ierr = PetscOptionsEnum("-snes_npc_side","SNES nonlinear preconditioner side","SNESSetNPCSide",PCSides,(PetscEnum)pcside,(PetscEnum*)&pcside,&flg);CHKERRQ(ierr);
937   if (flg) {ierr = SNESSetNPCSide(snes,pcside);CHKERRQ(ierr);}
938 
939 #if defined(PETSC_HAVE_SAWS)
940   /*
941     Publish convergence information using SAWs
942   */
943   flg  = PETSC_FALSE;
944   ierr = PetscOptionsBool("-snes_monitor_saws","Publish SNES progress using SAWs","SNESMonitorSet",flg,&flg,NULL);CHKERRQ(ierr);
945   if (flg) {
946     void *ctx;
947     ierr = SNESMonitorSAWsCreate(snes,&ctx);CHKERRQ(ierr);
948     ierr = SNESMonitorSet(snes,SNESMonitorSAWs,ctx,SNESMonitorSAWsDestroy);CHKERRQ(ierr);
949   }
950 #endif
951 #if defined(PETSC_HAVE_SAWS)
952   {
953   PetscBool set;
954   flg  = PETSC_FALSE;
955   ierr = PetscOptionsBool("-snes_saws_block","Block for SAWs at end of SNESSolve","PetscObjectSAWsBlock",((PetscObject)snes)->amspublishblock,&flg,&set);CHKERRQ(ierr);
956   if (set) {
957     ierr = PetscObjectSAWsSetBlock((PetscObject)snes,flg);CHKERRQ(ierr);
958   }
959   }
960 #endif
961 
962   for (i = 0; i < numberofsetfromoptions; i++) {
963     ierr = (*othersetfromoptions[i])(snes);CHKERRQ(ierr);
964   }
965 
966   if (snes->ops->setfromoptions) {
967     ierr = (*snes->ops->setfromoptions)(PetscOptionsObject,snes);CHKERRQ(ierr);
968   }
969 
970   /* process any options handlers added with PetscObjectAddOptionsHandler() */
971   ierr = PetscObjectProcessOptionsHandlers(PetscOptionsObject,(PetscObject)snes);CHKERRQ(ierr);
972   ierr = PetscOptionsEnd();CHKERRQ(ierr);
973 
974   if (!snes->linesearch) {
975     ierr = SNESGetLineSearch(snes, &snes->linesearch);CHKERRQ(ierr);
976   }
977   ierr = SNESLineSearchSetFromOptions(snes->linesearch);CHKERRQ(ierr);
978 
979   if (!snes->ksp) {ierr = SNESGetKSP(snes,&snes->ksp);CHKERRQ(ierr);}
980   ierr = KSPSetOperators(snes->ksp,snes->jacobian,snes->jacobian_pre);CHKERRQ(ierr);
981   ierr = KSPSetFromOptions(snes->ksp);CHKERRQ(ierr);
982 
983   /* if someone has set the SNES NPC type, create it. */
984   ierr = SNESGetOptionsPrefix(snes, &optionsprefix);CHKERRQ(ierr);
985   ierr = PetscOptionsHasName(((PetscObject)snes)->options,optionsprefix, "-npc_snes_type", &pcset);CHKERRQ(ierr);
986   if (pcset && (!snes->pc)) {
987     ierr = SNESGetNPC(snes, &snes->pc);CHKERRQ(ierr);
988   }
989   PetscFunctionReturn(0);
990 }
991 
992 #undef __FUNCT__
993 #define __FUNCT__ "SNESSetComputeApplicationContext"
994 /*@C
995    SNESSetComputeApplicationContext - Sets an optional function to compute a user-defined context for
996    the nonlinear solvers.
997 
998    Logically Collective on SNES
999 
1000    Input Parameters:
1001 +  snes - the SNES context
1002 .  compute - function to compute the context
1003 -  destroy - function to destroy the context
1004 
1005    Level: intermediate
1006 
1007    Notes:
1008    This function is currently not available from Fortran.
1009 
1010 .keywords: SNES, nonlinear, set, application, context
1011 
1012 .seealso: SNESGetApplicationContext(), SNESSetComputeApplicationContext(), SNESGetApplicationContext()
1013 @*/
1014 PetscErrorCode  SNESSetComputeApplicationContext(SNES snes,PetscErrorCode (*compute)(SNES,void**),PetscErrorCode (*destroy)(void**))
1015 {
1016   PetscFunctionBegin;
1017   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1018   snes->ops->usercompute = compute;
1019   snes->ops->userdestroy = destroy;
1020   PetscFunctionReturn(0);
1021 }
1022 
1023 #undef __FUNCT__
1024 #define __FUNCT__ "SNESSetApplicationContext"
1025 /*@
1026    SNESSetApplicationContext - Sets the optional user-defined context for
1027    the nonlinear solvers.
1028 
1029    Logically Collective on SNES
1030 
1031    Input Parameters:
1032 +  snes - the SNES context
1033 -  usrP - optional user context
1034 
1035    Level: intermediate
1036 
1037    Fortran Notes: To use this from Fortran you must write a Fortran interface definition for this
1038     function that tells Fortran the Fortran derived data type that you are passing in as the ctx argument.
1039 
1040 .keywords: SNES, nonlinear, set, application, context
1041 
1042 .seealso: SNESGetApplicationContext()
1043 @*/
1044 PetscErrorCode  SNESSetApplicationContext(SNES snes,void *usrP)
1045 {
1046   PetscErrorCode ierr;
1047   KSP            ksp;
1048 
1049   PetscFunctionBegin;
1050   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1051   ierr       = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
1052   ierr       = KSPSetApplicationContext(ksp,usrP);CHKERRQ(ierr);
1053   snes->user = usrP;
1054   PetscFunctionReturn(0);
1055 }
1056 
1057 #undef __FUNCT__
1058 #define __FUNCT__ "SNESGetApplicationContext"
1059 /*@
1060    SNESGetApplicationContext - Gets the user-defined context for the
1061    nonlinear solvers.
1062 
1063    Not Collective
1064 
1065    Input Parameter:
1066 .  snes - SNES context
1067 
1068    Output Parameter:
1069 .  usrP - user context
1070 
1071    Fortran Notes: To use this from Fortran you must write a Fortran interface definition for this
1072     function that tells Fortran the Fortran derived data type that you are passing in as the ctx argument.
1073 
1074    Level: intermediate
1075 
1076 .keywords: SNES, nonlinear, get, application, context
1077 
1078 .seealso: SNESSetApplicationContext()
1079 @*/
1080 PetscErrorCode  SNESGetApplicationContext(SNES snes,void *usrP)
1081 {
1082   PetscFunctionBegin;
1083   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1084   *(void**)usrP = snes->user;
1085   PetscFunctionReturn(0);
1086 }
1087 
1088 #undef __FUNCT__
1089 #define __FUNCT__ "SNESGetIterationNumber"
1090 /*@
1091    SNESGetIterationNumber - Gets the number of nonlinear iterations completed
1092    at this time.
1093 
1094    Not Collective
1095 
1096    Input Parameter:
1097 .  snes - SNES context
1098 
1099    Output Parameter:
1100 .  iter - iteration number
1101 
1102    Notes:
1103    For example, during the computation of iteration 2 this would return 1.
1104 
1105    This is useful for using lagged Jacobians (where one does not recompute the
1106    Jacobian at each SNES iteration). For example, the code
1107 .vb
1108       ierr = SNESGetIterationNumber(snes,&it);
1109       if (!(it % 2)) {
1110         [compute Jacobian here]
1111       }
1112 .ve
1113    can be used in your ComputeJacobian() function to cause the Jacobian to be
1114    recomputed every second SNES iteration.
1115 
1116    Level: intermediate
1117 
1118 .keywords: SNES, nonlinear, get, iteration, number,
1119 
1120 .seealso:   SNESGetLinearSolveIterations()
1121 @*/
1122 PetscErrorCode  SNESGetIterationNumber(SNES snes,PetscInt *iter)
1123 {
1124   PetscFunctionBegin;
1125   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1126   PetscValidIntPointer(iter,2);
1127   *iter = snes->iter;
1128   PetscFunctionReturn(0);
1129 }
1130 
1131 #undef __FUNCT__
1132 #define __FUNCT__ "SNESSetIterationNumber"
1133 /*@
1134    SNESSetIterationNumber - Sets the current iteration number.
1135 
1136    Not Collective
1137 
1138    Input Parameter:
1139 .  snes - SNES context
1140 .  iter - iteration number
1141 
1142    Level: developer
1143 
1144 .keywords: SNES, nonlinear, set, iteration, number,
1145 
1146 .seealso:   SNESGetLinearSolveIterations()
1147 @*/
1148 PetscErrorCode  SNESSetIterationNumber(SNES snes,PetscInt iter)
1149 {
1150   PetscErrorCode ierr;
1151 
1152   PetscFunctionBegin;
1153   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1154   ierr       = PetscObjectSAWsTakeAccess((PetscObject)snes);CHKERRQ(ierr);
1155   snes->iter = iter;
1156   ierr       = PetscObjectSAWsGrantAccess((PetscObject)snes);CHKERRQ(ierr);
1157   PetscFunctionReturn(0);
1158 }
1159 
1160 #undef __FUNCT__
1161 #define __FUNCT__ "SNESGetNonlinearStepFailures"
1162 /*@
1163    SNESGetNonlinearStepFailures - Gets the number of unsuccessful steps
1164    attempted by the nonlinear solver.
1165 
1166    Not Collective
1167 
1168    Input Parameter:
1169 .  snes - SNES context
1170 
1171    Output Parameter:
1172 .  nfails - number of unsuccessful steps attempted
1173 
1174    Notes:
1175    This counter is reset to zero for each successive call to SNESSolve().
1176 
1177    Level: intermediate
1178 
1179 .keywords: SNES, nonlinear, get, number, unsuccessful, steps
1180 
1181 .seealso: SNESGetMaxLinearSolveFailures(), SNESGetLinearSolveIterations(), SNESSetMaxLinearSolveFailures(), SNESGetLinearSolveFailures(),
1182           SNESSetMaxNonlinearStepFailures(), SNESGetMaxNonlinearStepFailures()
1183 @*/
1184 PetscErrorCode  SNESGetNonlinearStepFailures(SNES snes,PetscInt *nfails)
1185 {
1186   PetscFunctionBegin;
1187   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1188   PetscValidIntPointer(nfails,2);
1189   *nfails = snes->numFailures;
1190   PetscFunctionReturn(0);
1191 }
1192 
1193 #undef __FUNCT__
1194 #define __FUNCT__ "SNESSetMaxNonlinearStepFailures"
1195 /*@
1196    SNESSetMaxNonlinearStepFailures - Sets the maximum number of unsuccessful steps
1197    attempted by the nonlinear solver before it gives up.
1198 
1199    Not Collective
1200 
1201    Input Parameters:
1202 +  snes     - SNES context
1203 -  maxFails - maximum of unsuccessful steps
1204 
1205    Level: intermediate
1206 
1207 .keywords: SNES, nonlinear, set, maximum, unsuccessful, steps
1208 
1209 .seealso: SNESGetMaxLinearSolveFailures(), SNESGetLinearSolveIterations(), SNESSetMaxLinearSolveFailures(), SNESGetLinearSolveFailures(),
1210           SNESGetMaxNonlinearStepFailures(), SNESGetNonlinearStepFailures()
1211 @*/
1212 PetscErrorCode  SNESSetMaxNonlinearStepFailures(SNES snes, PetscInt maxFails)
1213 {
1214   PetscFunctionBegin;
1215   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1216   snes->maxFailures = maxFails;
1217   PetscFunctionReturn(0);
1218 }
1219 
1220 #undef __FUNCT__
1221 #define __FUNCT__ "SNESGetMaxNonlinearStepFailures"
1222 /*@
1223    SNESGetMaxNonlinearStepFailures - Gets the maximum number of unsuccessful steps
1224    attempted by the nonlinear solver before it gives up.
1225 
1226    Not Collective
1227 
1228    Input Parameter:
1229 .  snes     - SNES context
1230 
1231    Output Parameter:
1232 .  maxFails - maximum of unsuccessful steps
1233 
1234    Level: intermediate
1235 
1236 .keywords: SNES, nonlinear, get, maximum, unsuccessful, steps
1237 
1238 .seealso: SNESGetMaxLinearSolveFailures(), SNESGetLinearSolveIterations(), SNESSetMaxLinearSolveFailures(), SNESGetLinearSolveFailures(),
1239           SNESSetMaxNonlinearStepFailures(), SNESGetNonlinearStepFailures()
1240 
1241 @*/
1242 PetscErrorCode  SNESGetMaxNonlinearStepFailures(SNES snes, PetscInt *maxFails)
1243 {
1244   PetscFunctionBegin;
1245   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1246   PetscValidIntPointer(maxFails,2);
1247   *maxFails = snes->maxFailures;
1248   PetscFunctionReturn(0);
1249 }
1250 
1251 #undef __FUNCT__
1252 #define __FUNCT__ "SNESGetNumberFunctionEvals"
1253 /*@
1254    SNESGetNumberFunctionEvals - Gets the number of user provided function evaluations
1255      done by SNES.
1256 
1257    Not Collective
1258 
1259    Input Parameter:
1260 .  snes     - SNES context
1261 
1262    Output Parameter:
1263 .  nfuncs - number of evaluations
1264 
1265    Level: intermediate
1266 
1267    Notes: Reset every time SNESSolve is called unless SNESSetCountersReset() is used.
1268 
1269 .keywords: SNES, nonlinear, get, maximum, unsuccessful, steps
1270 
1271 .seealso: SNESGetMaxLinearSolveFailures(), SNESGetLinearSolveIterations(), SNESSetMaxLinearSolveFailures(), SNESGetLinearSolveFailures(), SNESSetCountersReset()
1272 @*/
1273 PetscErrorCode  SNESGetNumberFunctionEvals(SNES snes, PetscInt *nfuncs)
1274 {
1275   PetscFunctionBegin;
1276   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1277   PetscValidIntPointer(nfuncs,2);
1278   *nfuncs = snes->nfuncs;
1279   PetscFunctionReturn(0);
1280 }
1281 
1282 #undef __FUNCT__
1283 #define __FUNCT__ "SNESGetLinearSolveFailures"
1284 /*@
1285    SNESGetLinearSolveFailures - Gets the number of failed (non-converged)
1286    linear solvers.
1287 
1288    Not Collective
1289 
1290    Input Parameter:
1291 .  snes - SNES context
1292 
1293    Output Parameter:
1294 .  nfails - number of failed solves
1295 
1296    Level: intermediate
1297 
1298    Options Database Keys:
1299 . -snes_max_linear_solve_fail <num> - The number of failures before the solve is terminated
1300 
1301    Notes:
1302    This counter is reset to zero for each successive call to SNESSolve().
1303 
1304 .keywords: SNES, nonlinear, get, number, unsuccessful, steps
1305 
1306 .seealso: SNESGetMaxLinearSolveFailures(), SNESGetLinearSolveIterations(), SNESSetMaxLinearSolveFailures()
1307 @*/
1308 PetscErrorCode  SNESGetLinearSolveFailures(SNES snes,PetscInt *nfails)
1309 {
1310   PetscFunctionBegin;
1311   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1312   PetscValidIntPointer(nfails,2);
1313   *nfails = snes->numLinearSolveFailures;
1314   PetscFunctionReturn(0);
1315 }
1316 
1317 #undef __FUNCT__
1318 #define __FUNCT__ "SNESSetMaxLinearSolveFailures"
1319 /*@
1320    SNESSetMaxLinearSolveFailures - the number of failed linear solve attempts
1321    allowed before SNES returns with a diverged reason of SNES_DIVERGED_LINEAR_SOLVE
1322 
1323    Logically Collective on SNES
1324 
1325    Input Parameters:
1326 +  snes     - SNES context
1327 -  maxFails - maximum allowed linear solve failures
1328 
1329    Level: intermediate
1330 
1331    Options Database Keys:
1332 . -snes_max_linear_solve_fail <num> - The number of failures before the solve is terminated
1333 
1334    Notes: By default this is 0; that is SNES returns on the first failed linear solve
1335 
1336 .keywords: SNES, nonlinear, set, maximum, unsuccessful, steps
1337 
1338 .seealso: SNESGetLinearSolveFailures(), SNESGetMaxLinearSolveFailures(), SNESGetLinearSolveIterations()
1339 @*/
1340 PetscErrorCode  SNESSetMaxLinearSolveFailures(SNES snes, PetscInt maxFails)
1341 {
1342   PetscFunctionBegin;
1343   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1344   PetscValidLogicalCollectiveInt(snes,maxFails,2);
1345   snes->maxLinearSolveFailures = maxFails;
1346   PetscFunctionReturn(0);
1347 }
1348 
1349 #undef __FUNCT__
1350 #define __FUNCT__ "SNESGetMaxLinearSolveFailures"
1351 /*@
1352    SNESGetMaxLinearSolveFailures - gets the maximum number of linear solve failures that
1353      are allowed before SNES terminates
1354 
1355    Not Collective
1356 
1357    Input Parameter:
1358 .  snes     - SNES context
1359 
1360    Output Parameter:
1361 .  maxFails - maximum of unsuccessful solves allowed
1362 
1363    Level: intermediate
1364 
1365    Notes: By default this is 1; that is SNES returns on the first failed linear solve
1366 
1367 .keywords: SNES, nonlinear, get, maximum, unsuccessful, steps
1368 
1369 .seealso: SNESGetLinearSolveFailures(), SNESGetLinearSolveIterations(), SNESSetMaxLinearSolveFailures(),
1370 @*/
1371 PetscErrorCode  SNESGetMaxLinearSolveFailures(SNES snes, PetscInt *maxFails)
1372 {
1373   PetscFunctionBegin;
1374   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1375   PetscValidIntPointer(maxFails,2);
1376   *maxFails = snes->maxLinearSolveFailures;
1377   PetscFunctionReturn(0);
1378 }
1379 
1380 #undef __FUNCT__
1381 #define __FUNCT__ "SNESGetLinearSolveIterations"
1382 /*@
1383    SNESGetLinearSolveIterations - Gets the total number of linear iterations
1384    used by the nonlinear solver.
1385 
1386    Not Collective
1387 
1388    Input Parameter:
1389 .  snes - SNES context
1390 
1391    Output Parameter:
1392 .  lits - number of linear iterations
1393 
1394    Notes:
1395    This counter is reset to zero for each successive call to SNESSolve() unless SNESSetCountersReset() is used.
1396 
1397    If the linear solver fails inside the SNESSolve() the iterations for that call to the linear solver are not included. If you wish to count them
1398    then call KSPGetIterationNumber() after the failed solve.
1399 
1400    Level: intermediate
1401 
1402 .keywords: SNES, nonlinear, get, number, linear, iterations
1403 
1404 .seealso:  SNESGetIterationNumber(), SNESGetLinearSolveFailures(), SNESGetMaxLinearSolveFailures(), SNESSetCountersReset()
1405 @*/
1406 PetscErrorCode  SNESGetLinearSolveIterations(SNES snes,PetscInt *lits)
1407 {
1408   PetscFunctionBegin;
1409   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1410   PetscValidIntPointer(lits,2);
1411   *lits = snes->linear_its;
1412   PetscFunctionReturn(0);
1413 }
1414 
1415 #undef __FUNCT__
1416 #define __FUNCT__ "SNESSetCountersReset"
1417 /*@
1418    SNESSetCountersReset - Sets whether or not the counters for linear iterations and function evaluations
1419    are reset every time SNESSolve() is called.
1420 
1421    Logically Collective on SNES
1422 
1423    Input Parameter:
1424 +  snes - SNES context
1425 -  reset - whether to reset the counters or not
1426 
1427    Notes:
1428    This defaults to PETSC_TRUE
1429 
1430    Level: developer
1431 
1432 .keywords: SNES, nonlinear, set, reset, number, linear, iterations
1433 
1434 .seealso:  SNESGetNumberFunctionEvals(), SNESGetLinearSolveIterations(), SNESGetNPC()
1435 @*/
1436 PetscErrorCode  SNESSetCountersReset(SNES snes,PetscBool reset)
1437 {
1438   PetscFunctionBegin;
1439   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1440   PetscValidLogicalCollectiveBool(snes,reset,2);
1441   snes->counters_reset = reset;
1442   PetscFunctionReturn(0);
1443 }
1444 
1445 
1446 #undef __FUNCT__
1447 #define __FUNCT__ "SNESSetKSP"
1448 /*@
1449    SNESSetKSP - Sets a KSP context for the SNES object to use
1450 
1451    Not Collective, but the SNES and KSP objects must live on the same MPI_Comm
1452 
1453    Input Parameters:
1454 +  snes - the SNES context
1455 -  ksp - the KSP context
1456 
1457    Notes:
1458    The SNES object already has its KSP object, you can obtain with SNESGetKSP()
1459    so this routine is rarely needed.
1460 
1461    The KSP object that is already in the SNES object has its reference count
1462    decreased by one.
1463 
1464    Level: developer
1465 
1466 .keywords: SNES, nonlinear, get, KSP, context
1467 
1468 .seealso: KSPGetPC(), SNESCreate(), KSPCreate(), SNESSetKSP()
1469 @*/
1470 PetscErrorCode  SNESSetKSP(SNES snes,KSP ksp)
1471 {
1472   PetscErrorCode ierr;
1473 
1474   PetscFunctionBegin;
1475   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1476   PetscValidHeaderSpecific(ksp,KSP_CLASSID,2);
1477   PetscCheckSameComm(snes,1,ksp,2);
1478   ierr = PetscObjectReference((PetscObject)ksp);CHKERRQ(ierr);
1479   if (snes->ksp) {ierr = PetscObjectDereference((PetscObject)snes->ksp);CHKERRQ(ierr);}
1480   snes->ksp = ksp;
1481   PetscFunctionReturn(0);
1482 }
1483 
1484 /* -----------------------------------------------------------*/
1485 #undef __FUNCT__
1486 #define __FUNCT__ "SNESCreate"
1487 /*@
1488    SNESCreate - Creates a nonlinear solver context.
1489 
1490    Collective on MPI_Comm
1491 
1492    Input Parameters:
1493 .  comm - MPI communicator
1494 
1495    Output Parameter:
1496 .  outsnes - the new SNES context
1497 
1498    Options Database Keys:
1499 +   -snes_mf - Activates default matrix-free Jacobian-vector products,
1500                and no preconditioning matrix
1501 .   -snes_mf_operator - Activates default matrix-free Jacobian-vector
1502                products, and a user-provided preconditioning matrix
1503                as set by SNESSetJacobian()
1504 -   -snes_fd - Uses (slow!) finite differences to compute Jacobian
1505 
1506    Level: beginner
1507 
1508 .keywords: SNES, nonlinear, create, context
1509 
1510 .seealso: SNESSolve(), SNESDestroy(), SNES, SNESSetLagPreconditioner()
1511 
1512 @*/
1513 PetscErrorCode  SNESCreate(MPI_Comm comm,SNES *outsnes)
1514 {
1515   PetscErrorCode ierr;
1516   SNES           snes;
1517   SNESKSPEW      *kctx;
1518 
1519   PetscFunctionBegin;
1520   PetscValidPointer(outsnes,2);
1521   *outsnes = NULL;
1522   ierr = SNESInitializePackage();CHKERRQ(ierr);
1523 
1524   ierr = PetscHeaderCreate(snes,SNES_CLASSID,"SNES","Nonlinear solver","SNES",comm,SNESDestroy,SNESView);CHKERRQ(ierr);
1525 
1526   snes->ops->converged    = SNESConvergedDefault;
1527   snes->usesksp           = PETSC_TRUE;
1528   snes->tolerancesset     = PETSC_FALSE;
1529   snes->max_its           = 50;
1530   snes->max_funcs         = 10000;
1531   snes->norm              = 0.0;
1532   snes->normschedule      = SNES_NORM_ALWAYS;
1533   snes->functype          = SNES_FUNCTION_DEFAULT;
1534 #if defined(PETSC_USE_REAL_SINGLE)
1535   snes->rtol              = 1.e-5;
1536 #else
1537   snes->rtol              = 1.e-8;
1538 #endif
1539   snes->ttol              = 0.0;
1540 #if defined(PETSC_USE_REAL_SINGLE)
1541   snes->abstol            = 1.e-25;
1542 #else
1543   snes->abstol            = 1.e-50;
1544 #endif
1545 #if defined(PETSC_USE_REAL_SINGLE)
1546   snes->stol              = 1.e-5;
1547 #else
1548   snes->stol              = 1.e-8;
1549 #endif
1550 #if defined(PETSC_USE_REAL_SINGLE)
1551   snes->deltatol          = 1.e-6;
1552 #else
1553   snes->deltatol          = 1.e-12;
1554 #endif
1555   snes->nfuncs            = 0;
1556   snes->numFailures       = 0;
1557   snes->maxFailures       = 1;
1558   snes->linear_its        = 0;
1559   snes->lagjacobian       = 1;
1560   snes->jac_iter          = 0;
1561   snes->lagjac_persist    = PETSC_FALSE;
1562   snes->lagpreconditioner = 1;
1563   snes->pre_iter          = 0;
1564   snes->lagpre_persist    = PETSC_FALSE;
1565   snes->numbermonitors    = 0;
1566   snes->data              = 0;
1567   snes->setupcalled       = PETSC_FALSE;
1568   snes->ksp_ewconv        = PETSC_FALSE;
1569   snes->nwork             = 0;
1570   snes->work              = 0;
1571   snes->nvwork            = 0;
1572   snes->vwork             = 0;
1573   snes->conv_hist_len     = 0;
1574   snes->conv_hist_max     = 0;
1575   snes->conv_hist         = NULL;
1576   snes->conv_hist_its     = NULL;
1577   snes->conv_hist_reset   = PETSC_TRUE;
1578   snes->counters_reset    = PETSC_TRUE;
1579   snes->vec_func_init_set = PETSC_FALSE;
1580   snes->reason            = SNES_CONVERGED_ITERATING;
1581   snes->pcside            = PC_RIGHT;
1582 
1583   snes->mf          = PETSC_FALSE;
1584   snes->mf_operator = PETSC_FALSE;
1585   snes->mf_version  = 1;
1586 
1587   snes->numLinearSolveFailures = 0;
1588   snes->maxLinearSolveFailures = 1;
1589 
1590   snes->vizerotolerance = 1.e-8;
1591 
1592   /* Set this to true if the implementation of SNESSolve_XXX does compute the residual at the final solution. */
1593   snes->alwayscomputesfinalresidual = PETSC_FALSE;
1594 
1595   /* Create context to compute Eisenstat-Walker relative tolerance for KSP */
1596   ierr = PetscNewLog(snes,&kctx);CHKERRQ(ierr);
1597 
1598   snes->kspconvctx  = (void*)kctx;
1599   kctx->version     = 2;
1600   kctx->rtol_0      = .3; /* Eisenstat and Walker suggest rtol_0=.5, but
1601                              this was too large for some test cases */
1602   kctx->rtol_last   = 0.0;
1603   kctx->rtol_max    = .9;
1604   kctx->gamma       = 1.0;
1605   kctx->alpha       = .5*(1.0 + PetscSqrtReal(5.0));
1606   kctx->alpha2      = kctx->alpha;
1607   kctx->threshold   = .1;
1608   kctx->lresid_last = 0.0;
1609   kctx->norm_last   = 0.0;
1610 
1611   *outsnes = snes;
1612   PetscFunctionReturn(0);
1613 }
1614 
1615 /*MC
1616     SNESFunction - Functional form used to convey the nonlinear function to be solved by SNES
1617 
1618      Synopsis:
1619      #include "petscsnes.h"
1620      PetscErrorCode SNESFunction(SNES snes,Vec x,Vec f,void *ctx);
1621 
1622      Input Parameters:
1623 +     snes - the SNES context
1624 .     x    - state at which to evaluate residual
1625 -     ctx     - optional user-defined function context, passed in with SNESSetFunction()
1626 
1627      Output Parameter:
1628 .     f  - vector to put residual (function value)
1629 
1630    Level: intermediate
1631 
1632 .seealso:   SNESSetFunction(), SNESGetFunction()
1633 M*/
1634 
1635 #undef __FUNCT__
1636 #define __FUNCT__ "SNESSetFunction"
1637 /*@C
1638    SNESSetFunction - Sets the function evaluation routine and function
1639    vector for use by the SNES routines in solving systems of nonlinear
1640    equations.
1641 
1642    Logically Collective on SNES
1643 
1644    Input Parameters:
1645 +  snes - the SNES context
1646 .  r - vector to store function value
1647 .  f - function evaluation routine; see SNESFunction for calling sequence details
1648 -  ctx - [optional] user-defined context for private data for the
1649          function evaluation routine (may be NULL)
1650 
1651    Notes:
1652    The Newton-like methods typically solve linear systems of the form
1653 $      f'(x) x = -f(x),
1654    where f'(x) denotes the Jacobian matrix and f(x) is the function.
1655 
1656    Level: beginner
1657 
1658 .keywords: SNES, nonlinear, set, function
1659 
1660 .seealso: SNESGetFunction(), SNESComputeFunction(), SNESSetJacobian(), SNESSetPicard(), SNESFunction
1661 @*/
1662 PetscErrorCode  SNESSetFunction(SNES snes,Vec r,PetscErrorCode (*f)(SNES,Vec,Vec,void*),void *ctx)
1663 {
1664   PetscErrorCode ierr;
1665   DM             dm;
1666 
1667   PetscFunctionBegin;
1668   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1669   if (r) {
1670     PetscValidHeaderSpecific(r,VEC_CLASSID,2);
1671     PetscCheckSameComm(snes,1,r,2);
1672     ierr = PetscObjectReference((PetscObject)r);CHKERRQ(ierr);
1673     ierr = VecDestroy(&snes->vec_func);CHKERRQ(ierr);
1674 
1675     snes->vec_func = r;
1676   }
1677   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
1678   ierr = DMSNESSetFunction(dm,f,ctx);CHKERRQ(ierr);
1679   PetscFunctionReturn(0);
1680 }
1681 
1682 
1683 #undef __FUNCT__
1684 #define __FUNCT__ "SNESSetInitialFunction"
1685 /*@C
1686    SNESSetInitialFunction - Sets the function vector to be used as the
1687    function norm at the initialization of the method.  In some
1688    instances, the user has precomputed the function before calling
1689    SNESSolve.  This function allows one to avoid a redundant call
1690    to SNESComputeFunction in that case.
1691 
1692    Logically Collective on SNES
1693 
1694    Input Parameters:
1695 +  snes - the SNES context
1696 -  f - vector to store function value
1697 
1698    Notes:
1699    This should not be modified during the solution procedure.
1700 
1701    This is used extensively in the SNESFAS hierarchy and in nonlinear preconditioning.
1702 
1703    Level: developer
1704 
1705 .keywords: SNES, nonlinear, set, function
1706 
1707 .seealso: SNESSetFunction(), SNESComputeFunction(), SNESSetInitialFunctionNorm()
1708 @*/
1709 PetscErrorCode  SNESSetInitialFunction(SNES snes, Vec f)
1710 {
1711   PetscErrorCode ierr;
1712   Vec            vec_func;
1713 
1714   PetscFunctionBegin;
1715   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1716   PetscValidHeaderSpecific(f,VEC_CLASSID,2);
1717   PetscCheckSameComm(snes,1,f,2);
1718   if (snes->pcside == PC_LEFT && snes->functype == SNES_FUNCTION_PRECONDITIONED) {
1719     snes->vec_func_init_set = PETSC_FALSE;
1720     PetscFunctionReturn(0);
1721   }
1722   ierr = SNESGetFunction(snes,&vec_func,NULL,NULL);CHKERRQ(ierr);
1723   ierr = VecCopy(f, vec_func);CHKERRQ(ierr);
1724 
1725   snes->vec_func_init_set = PETSC_TRUE;
1726   PetscFunctionReturn(0);
1727 }
1728 
1729 #undef __FUNCT__
1730 #define __FUNCT__ "SNESSetNormSchedule"
1731 /*@
1732    SNESSetNormSchedule - Sets the SNESNormSchedule used in covergence and monitoring
1733    of the SNES method.
1734 
1735    Logically Collective on SNES
1736 
1737    Input Parameters:
1738 +  snes - the SNES context
1739 -  normschedule - the frequency of norm computation
1740 
1741    Options Database Key:
1742 .  -snes_norm_schedule <none, always, initialonly, finalonly, initalfinalonly>
1743 
1744    Notes:
1745    Only certain SNES methods support certain SNESNormSchedules.  Most require evaluation
1746    of the nonlinear function and the taking of its norm at every iteration to
1747    even ensure convergence at all.  However, methods such as custom Gauss-Seidel methods
1748    (SNESNGS) and the like do not require the norm of the function to be computed, and therfore
1749    may either be monitored for convergence or not.  As these are often used as nonlinear
1750    preconditioners, monitoring the norm of their error is not a useful enterprise within
1751    their solution.
1752 
1753    Level: developer
1754 
1755 .keywords: SNES, nonlinear, set, function, norm, type
1756 
1757 .seealso: SNESGetNormSchedule(), SNESComputeFunction(), VecNorm(), SNESSetFunction(), SNESSetInitialFunction(), SNESNormSchedule
1758 @*/
1759 PetscErrorCode  SNESSetNormSchedule(SNES snes, SNESNormSchedule normschedule)
1760 {
1761   PetscFunctionBegin;
1762   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1763   snes->normschedule = normschedule;
1764   PetscFunctionReturn(0);
1765 }
1766 
1767 
1768 #undef __FUNCT__
1769 #define __FUNCT__ "SNESGetNormSchedule"
1770 /*@
1771    SNESGetNormSchedule - Gets the SNESNormSchedule used in covergence and monitoring
1772    of the SNES method.
1773 
1774    Logically Collective on SNES
1775 
1776    Input Parameters:
1777 +  snes - the SNES context
1778 -  normschedule - the type of the norm used
1779 
1780    Level: advanced
1781 
1782 .keywords: SNES, nonlinear, set, function, norm, type
1783 
1784 .seealso: SNESSetNormSchedule(), SNESComputeFunction(), VecNorm(), SNESSetFunction(), SNESSetInitialFunction(), SNESNormSchedule
1785 @*/
1786 PetscErrorCode  SNESGetNormSchedule(SNES snes, SNESNormSchedule *normschedule)
1787 {
1788   PetscFunctionBegin;
1789   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1790   *normschedule = snes->normschedule;
1791   PetscFunctionReturn(0);
1792 }
1793 
1794 
1795 #undef __FUNCT__
1796 #define __FUNCT__ "SNESSetFunctionNorm"
1797 /*@
1798   SNESSetFunctionNorm - Sets the last computed residual norm.
1799 
1800   Logically Collective on SNES
1801 
1802   Input Parameters:
1803 + snes - the SNES context
1804 
1805 - normschedule - the frequency of norm computation
1806 
1807   Level: developer
1808 
1809 .keywords: SNES, nonlinear, set, function, norm, type
1810 .seealso: SNESGetNormSchedule(), SNESComputeFunction(), VecNorm(), SNESSetFunction(), SNESSetInitialFunction(), SNESNormSchedule
1811 @*/
1812 PetscErrorCode SNESSetFunctionNorm(SNES snes, PetscReal norm)
1813 {
1814   PetscFunctionBegin;
1815   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1816   snes->norm = norm;
1817   PetscFunctionReturn(0);
1818 }
1819 
1820 #undef __FUNCT__
1821 #define __FUNCT__ "SNESGetFunctionNorm"
1822 /*@
1823   SNESGetFunctionNorm - Gets the last computed norm of the residual
1824 
1825   Not Collective
1826 
1827   Input Parameter:
1828 . snes - the SNES context
1829 
1830   Output Parameter:
1831 . norm - the last computed residual norm
1832 
1833   Level: developer
1834 
1835 .keywords: SNES, nonlinear, set, function, norm, type
1836 .seealso: SNESSetNormSchedule(), SNESComputeFunction(), VecNorm(), SNESSetFunction(), SNESSetInitialFunction(), SNESNormSchedule
1837 @*/
1838 PetscErrorCode SNESGetFunctionNorm(SNES snes, PetscReal *norm)
1839 {
1840   PetscFunctionBegin;
1841   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1842   PetscValidPointer(norm, 2);
1843   *norm = snes->norm;
1844   PetscFunctionReturn(0);
1845 }
1846 
1847 #undef __FUNCT__
1848 #define __FUNCT__ "SNESSetFunctionType"
1849 /*@C
1850    SNESSetFunctionType - Sets the SNESNormSchedule used in covergence and monitoring
1851    of the SNES method.
1852 
1853    Logically Collective on SNES
1854 
1855    Input Parameters:
1856 +  snes - the SNES context
1857 -  normschedule - the frequency of norm computation
1858 
1859    Notes:
1860    Only certain SNES methods support certain SNESNormSchedules.  Most require evaluation
1861    of the nonlinear function and the taking of its norm at every iteration to
1862    even ensure convergence at all.  However, methods such as custom Gauss-Seidel methods
1863    (SNESNGS) and the like do not require the norm of the function to be computed, and therfore
1864    may either be monitored for convergence or not.  As these are often used as nonlinear
1865    preconditioners, monitoring the norm of their error is not a useful enterprise within
1866    their solution.
1867 
1868    Level: developer
1869 
1870 .keywords: SNES, nonlinear, set, function, norm, type
1871 
1872 .seealso: SNESGetNormSchedule(), SNESComputeFunction(), VecNorm(), SNESSetFunction(), SNESSetInitialFunction(), SNESNormSchedule
1873 @*/
1874 PetscErrorCode  SNESSetFunctionType(SNES snes, SNESFunctionType type)
1875 {
1876   PetscFunctionBegin;
1877   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1878   snes->functype = type;
1879   PetscFunctionReturn(0);
1880 }
1881 
1882 
1883 #undef __FUNCT__
1884 #define __FUNCT__ "SNESGetFunctionType"
1885 /*@C
1886    SNESGetFunctionType - Gets the SNESNormSchedule used in covergence and monitoring
1887    of the SNES method.
1888 
1889    Logically Collective on SNES
1890 
1891    Input Parameters:
1892 +  snes - the SNES context
1893 -  normschedule - the type of the norm used
1894 
1895    Level: advanced
1896 
1897 .keywords: SNES, nonlinear, set, function, norm, type
1898 
1899 .seealso: SNESSetNormSchedule(), SNESComputeFunction(), VecNorm(), SNESSetFunction(), SNESSetInitialFunction(), SNESNormSchedule
1900 @*/
1901 PetscErrorCode  SNESGetFunctionType(SNES snes, SNESFunctionType *type)
1902 {
1903   PetscFunctionBegin;
1904   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1905   *type = snes->functype;
1906   PetscFunctionReturn(0);
1907 }
1908 
1909 /*MC
1910     SNESNGSFunction - function used to convey a Gauss-Seidel sweep on the nonlinear function
1911 
1912      Synopsis:
1913      #include <petscsnes.h>
1914 $    SNESNGSFunction(SNES snes,Vec x,Vec b,void *ctx);
1915 
1916 +  X   - solution vector
1917 .  B   - RHS vector
1918 -  ctx - optional user-defined Gauss-Seidel context
1919 
1920    Level: intermediate
1921 
1922 .seealso:   SNESSetNGS(), SNESGetNGS()
1923 M*/
1924 
1925 #undef __FUNCT__
1926 #define __FUNCT__ "SNESSetNGS"
1927 /*@C
1928    SNESSetNGS - Sets the user nonlinear Gauss-Seidel routine for
1929    use with composed nonlinear solvers.
1930 
1931    Input Parameters:
1932 +  snes   - the SNES context
1933 .  f - function evaluation routine to apply Gauss-Seidel see SNESNGSFunction
1934 -  ctx    - [optional] user-defined context for private data for the
1935             smoother evaluation routine (may be NULL)
1936 
1937    Notes:
1938    The NGS routines are used by the composed nonlinear solver to generate
1939     a problem appropriate update to the solution, particularly FAS.
1940 
1941    Level: intermediate
1942 
1943 .keywords: SNES, nonlinear, set, Gauss-Seidel
1944 
1945 .seealso: SNESGetFunction(), SNESComputeNGS()
1946 @*/
1947 PetscErrorCode SNESSetNGS(SNES snes,PetscErrorCode (*f)(SNES,Vec,Vec,void*),void *ctx)
1948 {
1949   PetscErrorCode ierr;
1950   DM             dm;
1951 
1952   PetscFunctionBegin;
1953   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
1954   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
1955   ierr = DMSNESSetNGS(dm,f,ctx);CHKERRQ(ierr);
1956   PetscFunctionReturn(0);
1957 }
1958 
1959 #undef __FUNCT__
1960 #define __FUNCT__ "SNESPicardComputeFunction"
1961 PETSC_EXTERN PetscErrorCode SNESPicardComputeFunction(SNES snes,Vec x,Vec f,void *ctx)
1962 {
1963   PetscErrorCode ierr;
1964   DM             dm;
1965   DMSNES         sdm;
1966 
1967   PetscFunctionBegin;
1968   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
1969   ierr = DMGetDMSNES(dm,&sdm);CHKERRQ(ierr);
1970   /*  A(x)*x - b(x) */
1971   if (sdm->ops->computepfunction) {
1972     ierr = (*sdm->ops->computepfunction)(snes,x,f,sdm->pctx);CHKERRQ(ierr);
1973   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Must call SNESSetPicard() to provide Picard function.");
1974 
1975   if (sdm->ops->computepjacobian) {
1976     ierr = (*sdm->ops->computepjacobian)(snes,x,snes->jacobian,snes->jacobian_pre,sdm->pctx);CHKERRQ(ierr);
1977   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Must call SNESSetPicard() to provide Picard matrix.");
1978   ierr = VecScale(f,-1.0);CHKERRQ(ierr);
1979   ierr = MatMultAdd(snes->jacobian,x,f,f);CHKERRQ(ierr);
1980   PetscFunctionReturn(0);
1981 }
1982 
1983 #undef __FUNCT__
1984 #define __FUNCT__ "SNESPicardComputeJacobian"
1985 PETSC_EXTERN PetscErrorCode SNESPicardComputeJacobian(SNES snes,Vec x1,Mat J,Mat B,void *ctx)
1986 {
1987   PetscFunctionBegin;
1988   /* the jacobian matrix should be pre-filled in SNESPicardComputeFunction */
1989   PetscFunctionReturn(0);
1990 }
1991 
1992 #undef __FUNCT__
1993 #define __FUNCT__ "SNESSetPicard"
1994 /*@C
1995    SNESSetPicard - Use SNES to solve the semilinear-system A(x) x = b(x) via a Picard type iteration (Picard linearization)
1996 
1997    Logically Collective on SNES
1998 
1999    Input Parameters:
2000 +  snes - the SNES context
2001 .  r - vector to store function value
2002 .  b - function evaluation routine
2003 .  Amat - matrix with which A(x) x - b(x) is to be computed
2004 .  Pmat - matrix from which preconditioner is computed (usually the same as Amat)
2005 .  J  - function to compute matrix value, see SNESJacobianFunction for details on its calling sequence
2006 -  ctx - [optional] user-defined context for private data for the
2007          function evaluation routine (may be NULL)
2008 
2009    Notes:
2010     We do not recomemend using this routine. It is far better to provide the nonlinear function F() and some approximation to the Jacobian and use
2011     an approximate Newton solver. This interface is provided to allow porting/testing a previous Picard based code in PETSc before converting it to approximate Newton.
2012 
2013     One can call SNESSetPicard() or SNESSetFunction() (and possibly SNESSetJacobian()) but cannot call both
2014 
2015 $     Solves the equation A(x) x = b(x) via the defect correction algorithm A(x^{n}) (x^{n+1} - x^{n}) = b(x^{n}) - A(x^{n})x^{n}
2016 $     Note that when an exact solver is used this corresponds to the "classic" Picard A(x^{n}) x^{n+1} = b(x^{n}) iteration.
2017 
2018      Run with -snes_mf_operator to solve the system with Newton's method using A(x^{n}) to construct the preconditioner.
2019 
2020    We implement the defect correction form of the Picard iteration because it converges much more generally when inexact linear solvers are used then
2021    the direct Picard iteration A(x^n) x^{n+1} = b(x^n)
2022 
2023    There is some controversity over the definition of a Picard iteration for nonlinear systems but almost everyone agrees that it involves a linear solve and some
2024    believe it is the iteration  A(x^{n}) x^{n+1} = b(x^{n}) hence we use the name Picard. If anyone has an authoritative  reference that defines the Picard iteration
2025    different please contact us at petsc-dev@mcs.anl.gov and we'll have an entirely new argument :-).
2026 
2027    Level: intermediate
2028 
2029 .keywords: SNES, nonlinear, set, function
2030 
2031 .seealso: SNESGetFunction(), SNESSetFunction(), SNESComputeFunction(), SNESSetJacobian(), SNESGetPicard(), SNESLineSearchPreCheckPicard(), SNESJacobianFunction
2032 @*/
2033 PetscErrorCode  SNESSetPicard(SNES snes,Vec r,PetscErrorCode (*b)(SNES,Vec,Vec,void*),Mat Amat, Mat Pmat, PetscErrorCode (*J)(SNES,Vec,Mat,Mat,void*),void *ctx)
2034 {
2035   PetscErrorCode ierr;
2036   DM             dm;
2037 
2038   PetscFunctionBegin;
2039   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2040   ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr);
2041   ierr = DMSNESSetPicard(dm,b,J,ctx);CHKERRQ(ierr);
2042   ierr = SNESSetFunction(snes,r,SNESPicardComputeFunction,ctx);CHKERRQ(ierr);
2043   ierr = SNESSetJacobian(snes,Amat,Pmat,SNESPicardComputeJacobian,ctx);CHKERRQ(ierr);
2044   PetscFunctionReturn(0);
2045 }
2046 
2047 #undef __FUNCT__
2048 #define __FUNCT__ "SNESGetPicard"
2049 /*@C
2050    SNESGetPicard - Returns the context for the Picard iteration
2051 
2052    Not Collective, but Vec is parallel if SNES is parallel. Collective if Vec is requested, but has not been created yet.
2053 
2054    Input Parameter:
2055 .  snes - the SNES context
2056 
2057    Output Parameter:
2058 +  r - the function (or NULL)
2059 .  f - the function (or NULL); see SNESFunction for calling sequence details
2060 .  Amat - the matrix used to defined the operation A(x) x - b(x) (or NULL)
2061 .  Pmat  - the matrix from which the preconditioner will be constructed (or NULL)
2062 .  J - the function for matrix evaluation (or NULL); see SNESJacobianFunction for calling sequence details
2063 -  ctx - the function context (or NULL)
2064 
2065    Level: advanced
2066 
2067 .keywords: SNES, nonlinear, get, function
2068 
2069 .seealso: SNESSetPicard(), SNESGetFunction(), SNESGetJacobian(), SNESGetDM(), SNESFunction, SNESJacobianFunction
2070 @*/
2071 PetscErrorCode  SNESGetPicard(SNES snes,Vec *r,PetscErrorCode (**f)(SNES,Vec,Vec,void*),Mat *Amat, Mat *Pmat, PetscErrorCode (**J)(SNES,Vec,Mat,Mat,void*),void **ctx)
2072 {
2073   PetscErrorCode ierr;
2074   DM             dm;
2075 
2076   PetscFunctionBegin;
2077   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2078   ierr = SNESGetFunction(snes,r,NULL,NULL);CHKERRQ(ierr);
2079   ierr = SNESGetJacobian(snes,Amat,Pmat,NULL,NULL);CHKERRQ(ierr);
2080   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
2081   ierr = DMSNESGetPicard(dm,f,J,ctx);CHKERRQ(ierr);
2082   PetscFunctionReturn(0);
2083 }
2084 
2085 #undef __FUNCT__
2086 #define __FUNCT__ "SNESSetComputeInitialGuess"
2087 /*@C
2088    SNESSetComputeInitialGuess - Sets a routine used to compute an initial guess for the problem
2089 
2090    Logically Collective on SNES
2091 
2092    Input Parameters:
2093 +  snes - the SNES context
2094 .  func - function evaluation routine
2095 -  ctx - [optional] user-defined context for private data for the
2096          function evaluation routine (may be NULL)
2097 
2098    Calling sequence of func:
2099 $    func (SNES snes,Vec x,void *ctx);
2100 
2101 .  f - function vector
2102 -  ctx - optional user-defined function context
2103 
2104    Level: intermediate
2105 
2106 .keywords: SNES, nonlinear, set, function
2107 
2108 .seealso: SNESGetFunction(), SNESComputeFunction(), SNESSetJacobian()
2109 @*/
2110 PetscErrorCode  SNESSetComputeInitialGuess(SNES snes,PetscErrorCode (*func)(SNES,Vec,void*),void *ctx)
2111 {
2112   PetscFunctionBegin;
2113   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2114   if (func) snes->ops->computeinitialguess = func;
2115   if (ctx)  snes->initialguessP            = ctx;
2116   PetscFunctionReturn(0);
2117 }
2118 
2119 /* --------------------------------------------------------------- */
2120 #undef __FUNCT__
2121 #define __FUNCT__ "SNESGetRhs"
2122 /*@C
2123    SNESGetRhs - Gets the vector for solving F(x) = rhs. If rhs is not set
2124    it assumes a zero right hand side.
2125 
2126    Logically Collective on SNES
2127 
2128    Input Parameter:
2129 .  snes - the SNES context
2130 
2131    Output Parameter:
2132 .  rhs - the right hand side vector or NULL if the right hand side vector is null
2133 
2134    Level: intermediate
2135 
2136 .keywords: SNES, nonlinear, get, function, right hand side
2137 
2138 .seealso: SNESGetSolution(), SNESGetFunction(), SNESComputeFunction(), SNESSetJacobian(), SNESSetFunction()
2139 @*/
2140 PetscErrorCode  SNESGetRhs(SNES snes,Vec *rhs)
2141 {
2142   PetscFunctionBegin;
2143   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2144   PetscValidPointer(rhs,2);
2145   *rhs = snes->vec_rhs;
2146   PetscFunctionReturn(0);
2147 }
2148 
2149 #undef __FUNCT__
2150 #define __FUNCT__ "SNESComputeFunction"
2151 /*@
2152    SNESComputeFunction - Calls the function that has been set with SNESSetFunction().
2153 
2154    Collective on SNES
2155 
2156    Input Parameters:
2157 +  snes - the SNES context
2158 -  x - input vector
2159 
2160    Output Parameter:
2161 .  y - function vector, as set by SNESSetFunction()
2162 
2163    Notes:
2164    SNESComputeFunction() is typically used within nonlinear solvers
2165    implementations, so most users would not generally call this routine
2166    themselves.
2167 
2168    Level: developer
2169 
2170 .keywords: SNES, nonlinear, compute, function
2171 
2172 .seealso: SNESSetFunction(), SNESGetFunction()
2173 @*/
2174 PetscErrorCode  SNESComputeFunction(SNES snes,Vec x,Vec y)
2175 {
2176   PetscErrorCode ierr;
2177   DM             dm;
2178   DMSNES         sdm;
2179 
2180   PetscFunctionBegin;
2181   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2182   PetscValidHeaderSpecific(x,VEC_CLASSID,2);
2183   PetscValidHeaderSpecific(y,VEC_CLASSID,3);
2184   PetscCheckSameComm(snes,1,x,2);
2185   PetscCheckSameComm(snes,1,y,3);
2186   ierr = VecValidValues(x,2,PETSC_TRUE);CHKERRQ(ierr);
2187 
2188   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
2189   ierr = DMGetDMSNES(dm,&sdm);CHKERRQ(ierr);
2190   if (sdm->ops->computefunction) {
2191     if (sdm->ops->computefunction != SNESObjectiveComputeFunctionDefaultFD) {
2192       ierr = PetscLogEventBegin(SNES_FunctionEval,snes,x,y,0);CHKERRQ(ierr);
2193     }
2194     ierr = VecLockPush(x);CHKERRQ(ierr);
2195     PetscStackPush("SNES user function");
2196     ierr = (*sdm->ops->computefunction)(snes,x,y,sdm->functionctx);CHKERRQ(ierr);
2197     PetscStackPop;
2198     ierr = VecLockPop(x);CHKERRQ(ierr);
2199     if (sdm->ops->computefunction != SNESObjectiveComputeFunctionDefaultFD) {
2200       ierr = PetscLogEventEnd(SNES_FunctionEval,snes,x,y,0);CHKERRQ(ierr);
2201     }
2202   } else if (snes->vec_rhs) {
2203     ierr = MatMult(snes->jacobian, x, y);CHKERRQ(ierr);
2204   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Must call SNESSetFunction() or SNESSetDM() before SNESComputeFunction(), likely called from SNESSolve().");
2205   if (snes->vec_rhs) {
2206     ierr = VecAXPY(y,-1.0,snes->vec_rhs);CHKERRQ(ierr);
2207   }
2208   snes->nfuncs++;
2209   /*
2210      domainerror might not be set on all processes; so we tag vector locally with Inf and the next inner product or norm will
2211      propagate the value to all processes
2212   */
2213   if (snes->domainerror) {
2214     ierr = VecSetInf(y);CHKERRQ(ierr);
2215   }
2216   PetscFunctionReturn(0);
2217 }
2218 
2219 #undef __FUNCT__
2220 #define __FUNCT__ "SNESComputeNGS"
2221 /*@
2222    SNESComputeNGS - Calls the Gauss-Seidel function that has been set with  SNESSetNGS().
2223 
2224    Collective on SNES
2225 
2226    Input Parameters:
2227 +  snes - the SNES context
2228 .  x - input vector
2229 -  b - rhs vector
2230 
2231    Output Parameter:
2232 .  x - new solution vector
2233 
2234    Notes:
2235    SNESComputeNGS() is typically used within composed nonlinear solver
2236    implementations, so most users would not generally call this routine
2237    themselves.
2238 
2239    Level: developer
2240 
2241 .keywords: SNES, nonlinear, compute, function
2242 
2243 .seealso: SNESSetNGS(), SNESComputeFunction()
2244 @*/
2245 PetscErrorCode  SNESComputeNGS(SNES snes,Vec b,Vec x)
2246 {
2247   PetscErrorCode ierr;
2248   DM             dm;
2249   DMSNES         sdm;
2250 
2251   PetscFunctionBegin;
2252   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2253   PetscValidHeaderSpecific(x,VEC_CLASSID,2);
2254   if (b) PetscValidHeaderSpecific(b,VEC_CLASSID,3);
2255   PetscCheckSameComm(snes,1,x,2);
2256   if (b) PetscCheckSameComm(snes,1,b,3);
2257   if (b) {ierr = VecValidValues(b,2,PETSC_TRUE);CHKERRQ(ierr);}
2258   ierr = PetscLogEventBegin(SNES_NGSEval,snes,x,b,0);CHKERRQ(ierr);
2259   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
2260   ierr = DMGetDMSNES(dm,&sdm);CHKERRQ(ierr);
2261   if (sdm->ops->computegs) {
2262     if (b) {ierr = VecLockPush(b);CHKERRQ(ierr);}
2263     PetscStackPush("SNES user NGS");
2264     ierr = (*sdm->ops->computegs)(snes,x,b,sdm->gsctx);CHKERRQ(ierr);
2265     PetscStackPop;
2266     if (b) {ierr = VecLockPop(b);CHKERRQ(ierr);}
2267   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Must call SNESSetNGS() before SNESComputeNGS(), likely called from SNESSolve().");
2268   ierr = PetscLogEventEnd(SNES_NGSEval,snes,x,b,0);CHKERRQ(ierr);
2269   PetscFunctionReturn(0);
2270 }
2271 
2272 #undef __FUNCT__
2273 #define __FUNCT__ "SNESComputeJacobian"
2274 /*@
2275    SNESComputeJacobian - Computes the Jacobian matrix that has been set with SNESSetJacobian().
2276 
2277    Collective on SNES and Mat
2278 
2279    Input Parameters:
2280 +  snes - the SNES context
2281 -  x - input vector
2282 
2283    Output Parameters:
2284 +  A - Jacobian matrix
2285 -  B - optional preconditioning matrix
2286 
2287   Options Database Keys:
2288 +    -snes_lag_preconditioner <lag>
2289 .    -snes_lag_jacobian <lag>
2290 .    -snes_compare_explicit - Compare the computed Jacobian to the finite difference Jacobian and output the differences
2291 .    -snes_compare_explicit_draw  - Compare the computed Jacobian to the finite difference Jacobian and draw the result
2292 .    -snes_compare_explicit_contour  - Compare the computed Jacobian to the finite difference Jacobian and draw a contour plot with the result
2293 .    -snes_compare_operator  - Make the comparison options above use the operator instead of the preconditioning matrix
2294 .    -snes_compare_coloring - Compute the finite difference Jacobian using coloring and display norms of difference
2295 .    -snes_compare_coloring_display - Compute the finite differece Jacobian using coloring and display verbose differences
2296 .    -snes_compare_coloring_threshold - Display only those matrix entries that differ by more than a given threshold
2297 .    -snes_compare_coloring_threshold_atol - Absolute tolerance for difference in matrix entries to be displayed by -snes_compare_coloring_threshold
2298 .    -snes_compare_coloring_threshold_rtol - Relative tolerance for difference in matrix entries to be displayed by -snes_compare_coloring_threshold
2299 .    -snes_compare_coloring_draw - Compute the finite differece Jacobian using coloring and draw differences
2300 -    -snes_compare_coloring_draw_contour - Compute the finite differece Jacobian using coloring and show contours of matrices and differences
2301 
2302 
2303    Notes:
2304    Most users should not need to explicitly call this routine, as it
2305    is used internally within the nonlinear solvers.
2306 
2307    Level: developer
2308 
2309 .keywords: SNES, compute, Jacobian, matrix
2310 
2311 .seealso:  SNESSetJacobian(), KSPSetOperators(), MatStructure, SNESSetLagPreconditioner(), SNESSetLagJacobian()
2312 @*/
2313 PetscErrorCode  SNESComputeJacobian(SNES snes,Vec X,Mat A,Mat B)
2314 {
2315   PetscErrorCode ierr;
2316   PetscBool      flag;
2317   DM             dm;
2318   DMSNES         sdm;
2319   KSP            ksp;
2320 
2321   PetscFunctionBegin;
2322   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2323   PetscValidHeaderSpecific(X,VEC_CLASSID,2);
2324   PetscCheckSameComm(snes,1,X,2);
2325   ierr = VecValidValues(X,2,PETSC_TRUE);CHKERRQ(ierr);
2326   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
2327   ierr = DMGetDMSNES(dm,&sdm);CHKERRQ(ierr);
2328 
2329   if (!sdm->ops->computejacobian) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_USER,"Must call SNESSetJacobian(), DMSNESSetJacobian(), DMDASNESSetJacobianLocal(), etc");
2330 
2331   /* make sure that MatAssemblyBegin/End() is called on A matrix if it is matrix free */
2332 
2333   if (snes->lagjacobian == -2) {
2334     snes->lagjacobian = -1;
2335 
2336     ierr = PetscInfo(snes,"Recomputing Jacobian/preconditioner because lag is -2 (means compute Jacobian, but then never again) \n");CHKERRQ(ierr);
2337   } else if (snes->lagjacobian == -1) {
2338     ierr = PetscInfo(snes,"Reusing Jacobian/preconditioner because lag is -1\n");CHKERRQ(ierr);
2339     ierr = PetscObjectTypeCompare((PetscObject)A,MATMFFD,&flag);CHKERRQ(ierr);
2340     if (flag) {
2341       ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2342       ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2343     }
2344     PetscFunctionReturn(0);
2345   } else if (snes->lagjacobian > 1 && (snes->iter + snes->jac_iter) % snes->lagjacobian) {
2346     ierr = PetscInfo2(snes,"Reusing Jacobian/preconditioner because lag is %D and SNES iteration is %D\n",snes->lagjacobian,snes->iter);CHKERRQ(ierr);
2347     ierr = PetscObjectTypeCompare((PetscObject)A,MATMFFD,&flag);CHKERRQ(ierr);
2348     if (flag) {
2349       ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2350       ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2351     }
2352     PetscFunctionReturn(0);
2353   }
2354   if (snes->pc && snes->pcside == PC_LEFT) {
2355       ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2356       ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2357       PetscFunctionReturn(0);
2358   }
2359 
2360   ierr = PetscLogEventBegin(SNES_JacobianEval,snes,X,A,B);CHKERRQ(ierr);
2361   ierr = VecLockPush(X);CHKERRQ(ierr);
2362   PetscStackPush("SNES user Jacobian function");
2363   ierr = (*sdm->ops->computejacobian)(snes,X,A,B,sdm->jacobianctx);CHKERRQ(ierr);
2364   PetscStackPop;
2365   ierr = VecLockPop(X);CHKERRQ(ierr);
2366   ierr = PetscLogEventEnd(SNES_JacobianEval,snes,X,A,B);CHKERRQ(ierr);
2367 
2368   /* the next line ensures that snes->ksp exists */
2369   ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
2370   if (snes->lagpreconditioner == -2) {
2371     ierr = PetscInfo(snes,"Rebuilding preconditioner exactly once since lag is -2\n");CHKERRQ(ierr);
2372     ierr = KSPSetReusePreconditioner(snes->ksp,PETSC_FALSE);CHKERRQ(ierr);
2373     snes->lagpreconditioner = -1;
2374   } else if (snes->lagpreconditioner == -1) {
2375     ierr = PetscInfo(snes,"Reusing preconditioner because lag is -1\n");CHKERRQ(ierr);
2376     ierr = KSPSetReusePreconditioner(snes->ksp,PETSC_TRUE);CHKERRQ(ierr);
2377   } else if (snes->lagpreconditioner > 1 && (snes->iter + snes->pre_iter) % snes->lagpreconditioner) {
2378     ierr = PetscInfo2(snes,"Reusing preconditioner because lag is %D and SNES iteration is %D\n",snes->lagpreconditioner,snes->iter);CHKERRQ(ierr);
2379     ierr = KSPSetReusePreconditioner(snes->ksp,PETSC_TRUE);CHKERRQ(ierr);
2380   } else {
2381     ierr = PetscInfo(snes,"Rebuilding preconditioner\n");CHKERRQ(ierr);
2382     ierr = KSPSetReusePreconditioner(snes->ksp,PETSC_FALSE);CHKERRQ(ierr);
2383   }
2384 
2385   /* make sure user returned a correct Jacobian and preconditioner */
2386   /* PetscValidHeaderSpecific(A,MAT_CLASSID,3);
2387     PetscValidHeaderSpecific(B,MAT_CLASSID,4);   */
2388   {
2389     PetscBool flag = PETSC_FALSE,flag_draw = PETSC_FALSE,flag_contour = PETSC_FALSE,flag_operator = PETSC_FALSE;
2390     ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_compare_explicit",NULL,NULL,&flag);CHKERRQ(ierr);
2391     ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_compare_explicit_draw",NULL,NULL,&flag_draw);CHKERRQ(ierr);
2392     ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_compare_explicit_draw_contour",NULL,NULL,&flag_contour);CHKERRQ(ierr);
2393     ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_compare_operator",NULL,NULL,&flag_operator);CHKERRQ(ierr);
2394     if (flag || flag_draw || flag_contour) {
2395       Mat          Bexp_mine = NULL,Bexp,FDexp;
2396       PetscViewer  vdraw,vstdout;
2397       PetscBool    flg;
2398       if (flag_operator) {
2399         ierr = MatComputeExplicitOperator(A,&Bexp_mine);CHKERRQ(ierr);
2400         Bexp = Bexp_mine;
2401       } else {
2402         /* See if the preconditioning matrix can be viewed and added directly */
2403         ierr = PetscObjectTypeCompareAny((PetscObject)B,&flg,MATSEQAIJ,MATMPIAIJ,MATSEQDENSE,MATMPIDENSE,MATSEQBAIJ,MATMPIBAIJ,MATSEQSBAIJ,MATMPIBAIJ,"");CHKERRQ(ierr);
2404         if (flg) Bexp = B;
2405         else {
2406           /* If the "preconditioning" matrix is itself MATSHELL or some other type without direct support */
2407           ierr = MatComputeExplicitOperator(B,&Bexp_mine);CHKERRQ(ierr);
2408           Bexp = Bexp_mine;
2409         }
2410       }
2411       ierr = MatConvert(Bexp,MATSAME,MAT_INITIAL_MATRIX,&FDexp);CHKERRQ(ierr);
2412       ierr = SNESComputeJacobianDefault(snes,X,FDexp,FDexp,NULL);CHKERRQ(ierr);
2413       ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)snes),&vstdout);CHKERRQ(ierr);
2414       if (flag_draw || flag_contour) {
2415         ierr = PetscViewerDrawOpen(PetscObjectComm((PetscObject)snes),0,"Explicit Jacobians",PETSC_DECIDE,PETSC_DECIDE,300,300,&vdraw);CHKERRQ(ierr);
2416         if (flag_contour) {ierr = PetscViewerPushFormat(vdraw,PETSC_VIEWER_DRAW_CONTOUR);CHKERRQ(ierr);}
2417       } else vdraw = NULL;
2418       ierr = PetscViewerASCIIPrintf(vstdout,"Explicit %s\n",flag_operator ? "Jacobian" : "preconditioning Jacobian");CHKERRQ(ierr);
2419       if (flag) {ierr = MatView(Bexp,vstdout);CHKERRQ(ierr);}
2420       if (vdraw) {ierr = MatView(Bexp,vdraw);CHKERRQ(ierr);}
2421       ierr = PetscViewerASCIIPrintf(vstdout,"Finite difference Jacobian\n");CHKERRQ(ierr);
2422       if (flag) {ierr = MatView(FDexp,vstdout);CHKERRQ(ierr);}
2423       if (vdraw) {ierr = MatView(FDexp,vdraw);CHKERRQ(ierr);}
2424       ierr = MatAYPX(FDexp,-1.0,Bexp,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
2425       ierr = PetscViewerASCIIPrintf(vstdout,"User-provided matrix minus finite difference Jacobian\n");CHKERRQ(ierr);
2426       if (flag) {ierr = MatView(FDexp,vstdout);CHKERRQ(ierr);}
2427       if (vdraw) {              /* Always use contour for the difference */
2428         ierr = PetscViewerPushFormat(vdraw,PETSC_VIEWER_DRAW_CONTOUR);CHKERRQ(ierr);
2429         ierr = MatView(FDexp,vdraw);CHKERRQ(ierr);
2430         ierr = PetscViewerPopFormat(vdraw);CHKERRQ(ierr);
2431       }
2432       if (flag_contour) {ierr = PetscViewerPopFormat(vdraw);CHKERRQ(ierr);}
2433       ierr = PetscViewerDestroy(&vdraw);CHKERRQ(ierr);
2434       ierr = MatDestroy(&Bexp_mine);CHKERRQ(ierr);
2435       ierr = MatDestroy(&FDexp);CHKERRQ(ierr);
2436     }
2437   }
2438   {
2439     PetscBool flag = PETSC_FALSE,flag_display = PETSC_FALSE,flag_draw = PETSC_FALSE,flag_contour = PETSC_FALSE,flag_threshold = PETSC_FALSE;
2440     PetscReal threshold_atol = PETSC_SQRT_MACHINE_EPSILON,threshold_rtol = 10*PETSC_SQRT_MACHINE_EPSILON;
2441     ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_compare_coloring",NULL,NULL,&flag);CHKERRQ(ierr);
2442     ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_compare_coloring_display",NULL,NULL,&flag_display);CHKERRQ(ierr);
2443     ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_compare_coloring_draw",NULL,NULL,&flag_draw);CHKERRQ(ierr);
2444     ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_compare_coloring_draw_contour",NULL,NULL,&flag_contour);CHKERRQ(ierr);
2445     ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_compare_coloring_threshold",NULL,NULL,&flag_threshold);CHKERRQ(ierr);
2446     if (flag_threshold) {
2447       ierr = PetscOptionsGetReal(((PetscObject)snes)->options,((PetscObject)snes)->prefix,"-snes_compare_coloring_threshold_rtol",&threshold_rtol,NULL);CHKERRQ(ierr);
2448       ierr = PetscOptionsGetReal(((PetscObject)snes)->options,((PetscObject)snes)->prefix,"-snes_compare_coloring_threshold_atol",&threshold_atol,NULL);CHKERRQ(ierr);
2449     }
2450     if (flag || flag_display || flag_draw || flag_contour || flag_threshold) {
2451       Mat            Bfd;
2452       PetscViewer    vdraw,vstdout;
2453       MatColoring    coloring;
2454       ISColoring     iscoloring;
2455       MatFDColoring  matfdcoloring;
2456       PetscErrorCode (*func)(SNES,Vec,Vec,void*);
2457       void           *funcctx;
2458       PetscReal      norm1,norm2,normmax;
2459 
2460       ierr = MatDuplicate(B,MAT_DO_NOT_COPY_VALUES,&Bfd);CHKERRQ(ierr);
2461       ierr = MatColoringCreate(Bfd,&coloring);CHKERRQ(ierr);
2462       ierr = MatColoringSetType(coloring,MATCOLORINGSL);CHKERRQ(ierr);
2463       ierr = MatColoringSetFromOptions(coloring);CHKERRQ(ierr);
2464       ierr = MatColoringApply(coloring,&iscoloring);CHKERRQ(ierr);
2465       ierr = MatColoringDestroy(&coloring);CHKERRQ(ierr);
2466       ierr = MatFDColoringCreate(Bfd,iscoloring,&matfdcoloring);CHKERRQ(ierr);
2467       ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
2468       ierr = MatFDColoringSetUp(Bfd,iscoloring,matfdcoloring);CHKERRQ(ierr);
2469       ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
2470 
2471       /* This method of getting the function is currently unreliable since it doesn't work for DM local functions. */
2472       ierr = SNESGetFunction(snes,NULL,&func,&funcctx);CHKERRQ(ierr);
2473       ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))func,funcctx);CHKERRQ(ierr);
2474       ierr = PetscObjectSetOptionsPrefix((PetscObject)matfdcoloring,((PetscObject)snes)->prefix);CHKERRQ(ierr);
2475       ierr = PetscObjectAppendOptionsPrefix((PetscObject)matfdcoloring,"coloring_");CHKERRQ(ierr);
2476       ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
2477       ierr = MatFDColoringApply(Bfd,matfdcoloring,X,snes);CHKERRQ(ierr);
2478       ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr);
2479 
2480       ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)snes),&vstdout);CHKERRQ(ierr);
2481       if (flag_draw || flag_contour) {
2482         ierr = PetscViewerDrawOpen(PetscObjectComm((PetscObject)snes),0,"Colored Jacobians",PETSC_DECIDE,PETSC_DECIDE,300,300,&vdraw);CHKERRQ(ierr);
2483         if (flag_contour) {ierr = PetscViewerPushFormat(vdraw,PETSC_VIEWER_DRAW_CONTOUR);CHKERRQ(ierr);}
2484       } else vdraw = NULL;
2485       ierr = PetscViewerASCIIPrintf(vstdout,"Explicit preconditioning Jacobian\n");CHKERRQ(ierr);
2486       if (flag_display) {ierr = MatView(B,vstdout);CHKERRQ(ierr);}
2487       if (vdraw) {ierr = MatView(B,vdraw);CHKERRQ(ierr);}
2488       ierr = PetscViewerASCIIPrintf(vstdout,"Colored Finite difference Jacobian\n");CHKERRQ(ierr);
2489       if (flag_display) {ierr = MatView(Bfd,vstdout);CHKERRQ(ierr);}
2490       if (vdraw) {ierr = MatView(Bfd,vdraw);CHKERRQ(ierr);}
2491       ierr = MatAYPX(Bfd,-1.0,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
2492       ierr = MatNorm(Bfd,NORM_1,&norm1);CHKERRQ(ierr);
2493       ierr = MatNorm(Bfd,NORM_FROBENIUS,&norm2);CHKERRQ(ierr);
2494       ierr = MatNorm(Bfd,NORM_MAX,&normmax);CHKERRQ(ierr);
2495       ierr = PetscViewerASCIIPrintf(vstdout,"User-provided matrix minus finite difference Jacobian, norm1=%g normFrob=%g normmax=%g\n",(double)norm1,(double)norm2,(double)normmax);CHKERRQ(ierr);
2496       if (flag_display) {ierr = MatView(Bfd,vstdout);CHKERRQ(ierr);}
2497       if (vdraw) {              /* Always use contour for the difference */
2498         ierr = PetscViewerPushFormat(vdraw,PETSC_VIEWER_DRAW_CONTOUR);CHKERRQ(ierr);
2499         ierr = MatView(Bfd,vdraw);CHKERRQ(ierr);
2500         ierr = PetscViewerPopFormat(vdraw);CHKERRQ(ierr);
2501       }
2502       if (flag_contour) {ierr = PetscViewerPopFormat(vdraw);CHKERRQ(ierr);}
2503 
2504       if (flag_threshold) {
2505         PetscInt bs,rstart,rend,i;
2506         ierr = MatGetBlockSize(B,&bs);CHKERRQ(ierr);
2507         ierr = MatGetOwnershipRange(B,&rstart,&rend);CHKERRQ(ierr);
2508         for (i=rstart; i<rend; i++) {
2509           const PetscScalar *ba,*ca;
2510           const PetscInt    *bj,*cj;
2511           PetscInt          bn,cn,j,maxentrycol = -1,maxdiffcol = -1,maxrdiffcol = -1;
2512           PetscReal         maxentry = 0,maxdiff = 0,maxrdiff = 0;
2513           ierr = MatGetRow(B,i,&bn,&bj,&ba);CHKERRQ(ierr);
2514           ierr = MatGetRow(Bfd,i,&cn,&cj,&ca);CHKERRQ(ierr);
2515           if (bn != cn) SETERRQ(((PetscObject)A)->comm,PETSC_ERR_PLIB,"Unexpected different nonzero pattern in -snes_compare_coloring_threshold");
2516           for (j=0; j<bn; j++) {
2517             PetscReal rdiff = PetscAbsScalar(ca[j]) / (threshold_atol + threshold_rtol*PetscAbsScalar(ba[j]));
2518             if (PetscAbsScalar(ba[j]) > PetscAbs(maxentry)) {
2519               maxentrycol = bj[j];
2520               maxentry    = PetscRealPart(ba[j]);
2521             }
2522             if (PetscAbsScalar(ca[j]) > PetscAbs(maxdiff)) {
2523               maxdiffcol = bj[j];
2524               maxdiff    = PetscRealPart(ca[j]);
2525             }
2526             if (rdiff > maxrdiff) {
2527               maxrdiffcol = bj[j];
2528               maxrdiff    = rdiff;
2529             }
2530           }
2531           if (maxrdiff > 1) {
2532             ierr = PetscViewerASCIIPrintf(vstdout,"row %D (maxentry=%g at %D, maxdiff=%g at %D, maxrdiff=%g at %D):",i,(double)maxentry,maxentrycol,(double)maxdiff,maxdiffcol,(double)maxrdiff,maxrdiffcol);CHKERRQ(ierr);
2533             for (j=0; j<bn; j++) {
2534               PetscReal rdiff;
2535               rdiff = PetscAbsScalar(ca[j]) / (threshold_atol + threshold_rtol*PetscAbsScalar(ba[j]));
2536               if (rdiff > 1) {
2537                 ierr = PetscViewerASCIIPrintf(vstdout," (%D,%g:%g)",bj[j],(double)PetscRealPart(ba[j]),(double)PetscRealPart(ca[j]));CHKERRQ(ierr);
2538               }
2539             }
2540             ierr = PetscViewerASCIIPrintf(vstdout,"\n",i,maxentry,maxdiff,maxrdiff);CHKERRQ(ierr);
2541           }
2542           ierr = MatRestoreRow(B,i,&bn,&bj,&ba);CHKERRQ(ierr);
2543           ierr = MatRestoreRow(Bfd,i,&cn,&cj,&ca);CHKERRQ(ierr);
2544         }
2545       }
2546       ierr = PetscViewerDestroy(&vdraw);CHKERRQ(ierr);
2547       ierr = MatDestroy(&Bfd);CHKERRQ(ierr);
2548     }
2549   }
2550   PetscFunctionReturn(0);
2551 }
2552 
2553 /*MC
2554     SNESJacobianFunction - Function used to convey the nonlinear Jacobian of the function to be solved by SNES
2555 
2556      Synopsis:
2557      #include "petscsnes.h"
2558      PetscErrorCode SNESJacobianFunction(SNES snes,Vec x,Mat Amat,Mat Pmat,void *ctx);
2559 
2560 +  x - input vector
2561 .  Amat - the matrix that defines the (approximate) Jacobian
2562 .  Pmat - the matrix to be used in constructing the preconditioner, usually the same as Amat.
2563 -  ctx - [optional] user-defined Jacobian context
2564 
2565    Level: intermediate
2566 
2567 .seealso:   SNESSetFunction(), SNESGetFunction(), SNESSetJacobian(), SNESGetJacobian()
2568 M*/
2569 
2570 #undef __FUNCT__
2571 #define __FUNCT__ "SNESSetJacobian"
2572 /*@C
2573    SNESSetJacobian - Sets the function to compute Jacobian as well as the
2574    location to store the matrix.
2575 
2576    Logically Collective on SNES and Mat
2577 
2578    Input Parameters:
2579 +  snes - the SNES context
2580 .  Amat - the matrix that defines the (approximate) Jacobian
2581 .  Pmat - the matrix to be used in constructing the preconditioner, usually the same as Amat.
2582 .  J - Jacobian evaluation routine (if NULL then SNES retains any previously set value), see SNESJacobianFunction for details
2583 -  ctx - [optional] user-defined context for private data for the
2584          Jacobian evaluation routine (may be NULL) (if NULL then SNES retains any previously set value)
2585 
2586    Notes:
2587    If the Amat matrix and Pmat matrix are different you must call MatAssemblyBegin/End() on
2588    each matrix.
2589 
2590    If you know the operator Amat has a null space you can use MatSetNullSpace() and MatSetTransposeNullSpace() to supply the null
2591    space to Amat and the KSP solvers will automatically use that null space as needed during the solution process.
2592 
2593    If using SNESComputeJacobianDefaultColor() to assemble a Jacobian, the ctx argument
2594    must be a MatFDColoring.
2595 
2596    Other defect-correction schemes can be used by computing a different matrix in place of the Jacobian.  One common
2597    example is to use the "Picard linearization" which only differentiates through the highest order parts of each term.
2598 
2599    Level: beginner
2600 
2601 .keywords: SNES, nonlinear, set, Jacobian, matrix
2602 
2603 .seealso: KSPSetOperators(), SNESSetFunction(), MatMFFDComputeJacobian(), SNESComputeJacobianDefaultColor(), MatStructure, J,
2604           SNESSetPicard(), SNESJacobianFunction
2605 @*/
2606 PetscErrorCode  SNESSetJacobian(SNES snes,Mat Amat,Mat Pmat,PetscErrorCode (*J)(SNES,Vec,Mat,Mat,void*),void *ctx)
2607 {
2608   PetscErrorCode ierr;
2609   DM             dm;
2610 
2611   PetscFunctionBegin;
2612   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2613   if (Amat) PetscValidHeaderSpecific(Amat,MAT_CLASSID,2);
2614   if (Pmat) PetscValidHeaderSpecific(Pmat,MAT_CLASSID,3);
2615   if (Amat) PetscCheckSameComm(snes,1,Amat,2);
2616   if (Pmat) PetscCheckSameComm(snes,1,Pmat,3);
2617   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
2618   ierr = DMSNESSetJacobian(dm,J,ctx);CHKERRQ(ierr);
2619   if (Amat) {
2620     ierr = PetscObjectReference((PetscObject)Amat);CHKERRQ(ierr);
2621     ierr = MatDestroy(&snes->jacobian);CHKERRQ(ierr);
2622 
2623     snes->jacobian = Amat;
2624   }
2625   if (Pmat) {
2626     ierr = PetscObjectReference((PetscObject)Pmat);CHKERRQ(ierr);
2627     ierr = MatDestroy(&snes->jacobian_pre);CHKERRQ(ierr);
2628 
2629     snes->jacobian_pre = Pmat;
2630   }
2631   PetscFunctionReturn(0);
2632 }
2633 
2634 #undef __FUNCT__
2635 #define __FUNCT__ "SNESGetJacobian"
2636 /*@C
2637    SNESGetJacobian - Returns the Jacobian matrix and optionally the user
2638    provided context for evaluating the Jacobian.
2639 
2640    Not Collective, but Mat object will be parallel if SNES object is
2641 
2642    Input Parameter:
2643 .  snes - the nonlinear solver context
2644 
2645    Output Parameters:
2646 +  Amat - location to stash (approximate) Jacobian matrix (or NULL)
2647 .  Pmat - location to stash matrix used to compute the preconditioner (or NULL)
2648 .  J - location to put Jacobian function (or NULL), see SNESJacobianFunction for details on its calling sequence
2649 -  ctx - location to stash Jacobian ctx (or NULL)
2650 
2651    Level: advanced
2652 
2653 .seealso: SNESSetJacobian(), SNESComputeJacobian(), SNESJacobianFunction, SNESGetFunction()
2654 @*/
2655 PetscErrorCode SNESGetJacobian(SNES snes,Mat *Amat,Mat *Pmat,PetscErrorCode (**J)(SNES,Vec,Mat,Mat,void*),void **ctx)
2656 {
2657   PetscErrorCode ierr;
2658   DM             dm;
2659   DMSNES         sdm;
2660 
2661   PetscFunctionBegin;
2662   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2663   if (Amat) *Amat = snes->jacobian;
2664   if (Pmat) *Pmat = snes->jacobian_pre;
2665   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
2666   ierr = DMGetDMSNES(dm,&sdm);CHKERRQ(ierr);
2667   if (J) *J = sdm->ops->computejacobian;
2668   if (ctx) *ctx = sdm->jacobianctx;
2669   PetscFunctionReturn(0);
2670 }
2671 
2672 #undef __FUNCT__
2673 #define __FUNCT__ "SNESSetUp"
2674 /*@
2675    SNESSetUp - Sets up the internal data structures for the later use
2676    of a nonlinear solver.
2677 
2678    Collective on SNES
2679 
2680    Input Parameters:
2681 .  snes - the SNES context
2682 
2683    Notes:
2684    For basic use of the SNES solvers the user need not explicitly call
2685    SNESSetUp(), since these actions will automatically occur during
2686    the call to SNESSolve().  However, if one wishes to control this
2687    phase separately, SNESSetUp() should be called after SNESCreate()
2688    and optional routines of the form SNESSetXXX(), but before SNESSolve().
2689 
2690    Level: advanced
2691 
2692 .keywords: SNES, nonlinear, setup
2693 
2694 .seealso: SNESCreate(), SNESSolve(), SNESDestroy()
2695 @*/
2696 PetscErrorCode  SNESSetUp(SNES snes)
2697 {
2698   PetscErrorCode ierr;
2699   DM             dm;
2700   DMSNES         sdm;
2701   SNESLineSearch linesearch, pclinesearch;
2702   void           *lsprectx,*lspostctx;
2703   PetscErrorCode (*precheck)(SNESLineSearch,Vec,Vec,PetscBool*,void*);
2704   PetscErrorCode (*postcheck)(SNESLineSearch,Vec,Vec,Vec,PetscBool*,PetscBool*,void*);
2705   PetscErrorCode (*func)(SNES,Vec,Vec,void*);
2706   Vec            f,fpc;
2707   void           *funcctx;
2708   PetscErrorCode (*jac)(SNES,Vec,Mat,Mat,void*);
2709   void           *jacctx,*appctx;
2710   Mat            j,jpre;
2711 
2712   PetscFunctionBegin;
2713   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2714   if (snes->setupcalled) PetscFunctionReturn(0);
2715 
2716   if (!((PetscObject)snes)->type_name) {
2717     ierr = SNESSetType(snes,SNESNEWTONLS);CHKERRQ(ierr);
2718   }
2719 
2720   ierr = SNESGetFunction(snes,&snes->vec_func,NULL,NULL);CHKERRQ(ierr);
2721 
2722   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
2723   ierr = DMGetDMSNES(dm,&sdm);CHKERRQ(ierr);
2724   if (!sdm->ops->computefunction) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_ARG_WRONGSTATE,"Function never provided to SNES object");
2725   if (!sdm->ops->computejacobian) {
2726     ierr = DMSNESSetJacobian(dm,SNESComputeJacobianDefaultColor,NULL);CHKERRQ(ierr);
2727   }
2728   if (!snes->vec_func) {
2729     ierr = DMCreateGlobalVector(dm,&snes->vec_func);CHKERRQ(ierr);
2730   }
2731 
2732   if (!snes->ksp) {
2733     ierr = SNESGetKSP(snes, &snes->ksp);CHKERRQ(ierr);
2734   }
2735 
2736   if (!snes->linesearch) {
2737     ierr = SNESGetLineSearch(snes, &snes->linesearch);CHKERRQ(ierr);
2738   }
2739   ierr = SNESLineSearchSetFunction(snes->linesearch,SNESComputeFunction);CHKERRQ(ierr);
2740 
2741   if (snes->pc && (snes->pcside == PC_LEFT)) {
2742     snes->mf          = PETSC_TRUE;
2743     snes->mf_operator = PETSC_FALSE;
2744   }
2745 
2746   if (snes->pc) {
2747     /* copy the DM over */
2748     ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
2749     ierr = SNESSetDM(snes->pc,dm);CHKERRQ(ierr);
2750 
2751     ierr = SNESGetFunction(snes,&f,&func,&funcctx);CHKERRQ(ierr);
2752     ierr = VecDuplicate(f,&fpc);CHKERRQ(ierr);
2753     ierr = SNESSetFunction(snes->pc,fpc,func,funcctx);CHKERRQ(ierr);
2754     ierr = SNESGetJacobian(snes,&j,&jpre,&jac,&jacctx);CHKERRQ(ierr);
2755     ierr = SNESSetJacobian(snes->pc,j,jpre,jac,jacctx);CHKERRQ(ierr);
2756     ierr = SNESGetApplicationContext(snes,&appctx);CHKERRQ(ierr);
2757     ierr = SNESSetApplicationContext(snes->pc,appctx);CHKERRQ(ierr);
2758     ierr = VecDestroy(&fpc);CHKERRQ(ierr);
2759 
2760     /* copy the function pointers over */
2761     ierr = PetscObjectCopyFortranFunctionPointers((PetscObject)snes,(PetscObject)snes->pc);CHKERRQ(ierr);
2762 
2763     /* default to 1 iteration */
2764     ierr = SNESSetTolerances(snes->pc,0.0,0.0,0.0,1,snes->pc->max_funcs);CHKERRQ(ierr);
2765     if (snes->pcside==PC_RIGHT) {
2766       ierr = SNESSetNormSchedule(snes->pc,SNES_NORM_FINAL_ONLY);CHKERRQ(ierr);
2767     } else {
2768       ierr = SNESSetNormSchedule(snes->pc,SNES_NORM_NONE);CHKERRQ(ierr);
2769     }
2770     ierr = SNESSetFromOptions(snes->pc);CHKERRQ(ierr);
2771 
2772     /* copy the line search context over */
2773     ierr = SNESGetLineSearch(snes,&linesearch);CHKERRQ(ierr);
2774     ierr = SNESGetLineSearch(snes->pc,&pclinesearch);CHKERRQ(ierr);
2775     ierr = SNESLineSearchGetPreCheck(linesearch,&precheck,&lsprectx);CHKERRQ(ierr);
2776     ierr = SNESLineSearchGetPostCheck(linesearch,&postcheck,&lspostctx);CHKERRQ(ierr);
2777     ierr = SNESLineSearchSetPreCheck(pclinesearch,precheck,lsprectx);CHKERRQ(ierr);
2778     ierr = SNESLineSearchSetPostCheck(pclinesearch,postcheck,lspostctx);CHKERRQ(ierr);
2779     ierr = PetscObjectCopyFortranFunctionPointers((PetscObject)linesearch, (PetscObject)pclinesearch);CHKERRQ(ierr);
2780   }
2781   if (snes->mf) {
2782     ierr = SNESSetUpMatrixFree_Private(snes, snes->mf_operator, snes->mf_version);CHKERRQ(ierr);
2783   }
2784   if (snes->ops->usercompute && !snes->user) {
2785     ierr = (*snes->ops->usercompute)(snes,(void**)&snes->user);CHKERRQ(ierr);
2786   }
2787 
2788   snes->jac_iter = 0;
2789   snes->pre_iter = 0;
2790 
2791   if (snes->ops->setup) {
2792     ierr = (*snes->ops->setup)(snes);CHKERRQ(ierr);
2793   }
2794 
2795   if (snes->pc && (snes->pcside == PC_LEFT)) {
2796     if (snes->functype == SNES_FUNCTION_PRECONDITIONED) {
2797       ierr = SNESGetLineSearch(snes,&linesearch);CHKERRQ(ierr);
2798       ierr = SNESLineSearchSetFunction(linesearch,SNESComputeFunctionDefaultNPC);CHKERRQ(ierr);
2799     }
2800   }
2801 
2802   snes->setupcalled = PETSC_TRUE;
2803   PetscFunctionReturn(0);
2804 }
2805 
2806 #undef __FUNCT__
2807 #define __FUNCT__ "SNESReset"
2808 /*@
2809    SNESReset - Resets a SNES context to the snessetupcalled = 0 state and removes any allocated Vecs and Mats
2810 
2811    Collective on SNES
2812 
2813    Input Parameter:
2814 .  snes - iterative context obtained from SNESCreate()
2815 
2816    Level: intermediate
2817 
2818    Notes: Also calls the application context destroy routine set with SNESSetComputeApplicationContext()
2819 
2820 .keywords: SNES, destroy
2821 
2822 .seealso: SNESCreate(), SNESSetUp(), SNESSolve()
2823 @*/
2824 PetscErrorCode  SNESReset(SNES snes)
2825 {
2826   PetscErrorCode ierr;
2827 
2828   PetscFunctionBegin;
2829   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2830   if (snes->ops->userdestroy && snes->user) {
2831     ierr       = (*snes->ops->userdestroy)((void**)&snes->user);CHKERRQ(ierr);
2832     snes->user = NULL;
2833   }
2834   if (snes->pc) {
2835     ierr = SNESReset(snes->pc);CHKERRQ(ierr);
2836   }
2837 
2838   if (snes->ops->reset) {
2839     ierr = (*snes->ops->reset)(snes);CHKERRQ(ierr);
2840   }
2841   if (snes->ksp) {
2842     ierr = KSPReset(snes->ksp);CHKERRQ(ierr);
2843   }
2844 
2845   if (snes->linesearch) {
2846     ierr = SNESLineSearchReset(snes->linesearch);CHKERRQ(ierr);
2847   }
2848 
2849   ierr = VecDestroy(&snes->vec_rhs);CHKERRQ(ierr);
2850   ierr = VecDestroy(&snes->vec_sol);CHKERRQ(ierr);
2851   ierr = VecDestroy(&snes->vec_sol_update);CHKERRQ(ierr);
2852   ierr = VecDestroy(&snes->vec_func);CHKERRQ(ierr);
2853   ierr = MatDestroy(&snes->jacobian);CHKERRQ(ierr);
2854   ierr = MatDestroy(&snes->jacobian_pre);CHKERRQ(ierr);
2855   ierr = VecDestroyVecs(snes->nwork,&snes->work);CHKERRQ(ierr);
2856   ierr = VecDestroyVecs(snes->nvwork,&snes->vwork);CHKERRQ(ierr);
2857 
2858   snes->alwayscomputesfinalresidual = PETSC_FALSE;
2859 
2860   snes->nwork       = snes->nvwork = 0;
2861   snes->setupcalled = PETSC_FALSE;
2862   PetscFunctionReturn(0);
2863 }
2864 
2865 #undef __FUNCT__
2866 #define __FUNCT__ "SNESDestroy"
2867 /*@
2868    SNESDestroy - Destroys the nonlinear solver context that was created
2869    with SNESCreate().
2870 
2871    Collective on SNES
2872 
2873    Input Parameter:
2874 .  snes - the SNES context
2875 
2876    Level: beginner
2877 
2878 .keywords: SNES, nonlinear, destroy
2879 
2880 .seealso: SNESCreate(), SNESSolve()
2881 @*/
2882 PetscErrorCode  SNESDestroy(SNES *snes)
2883 {
2884   PetscErrorCode ierr;
2885 
2886   PetscFunctionBegin;
2887   if (!*snes) PetscFunctionReturn(0);
2888   PetscValidHeaderSpecific((*snes),SNES_CLASSID,1);
2889   if (--((PetscObject)(*snes))->refct > 0) {*snes = 0; PetscFunctionReturn(0);}
2890 
2891   ierr = SNESReset((*snes));CHKERRQ(ierr);
2892   ierr = SNESDestroy(&(*snes)->pc);CHKERRQ(ierr);
2893 
2894   /* if memory was published with SAWs then destroy it */
2895   ierr = PetscObjectSAWsViewOff((PetscObject)*snes);CHKERRQ(ierr);
2896   if ((*snes)->ops->destroy) {ierr = (*((*snes))->ops->destroy)((*snes));CHKERRQ(ierr);}
2897 
2898   ierr = DMDestroy(&(*snes)->dm);CHKERRQ(ierr);
2899   ierr = KSPDestroy(&(*snes)->ksp);CHKERRQ(ierr);
2900   ierr = SNESLineSearchDestroy(&(*snes)->linesearch);CHKERRQ(ierr);
2901 
2902   ierr = PetscFree((*snes)->kspconvctx);CHKERRQ(ierr);
2903   if ((*snes)->ops->convergeddestroy) {
2904     ierr = (*(*snes)->ops->convergeddestroy)((*snes)->cnvP);CHKERRQ(ierr);
2905   }
2906   if ((*snes)->conv_malloc) {
2907     ierr = PetscFree((*snes)->conv_hist);CHKERRQ(ierr);
2908     ierr = PetscFree((*snes)->conv_hist_its);CHKERRQ(ierr);
2909   }
2910   ierr = SNESMonitorCancel((*snes));CHKERRQ(ierr);
2911   ierr = PetscHeaderDestroy(snes);CHKERRQ(ierr);
2912   PetscFunctionReturn(0);
2913 }
2914 
2915 /* ----------- Routines to set solver parameters ---------- */
2916 
2917 #undef __FUNCT__
2918 #define __FUNCT__ "SNESSetLagPreconditioner"
2919 /*@
2920    SNESSetLagPreconditioner - Determines when the preconditioner is rebuilt in the nonlinear solve.
2921 
2922    Logically Collective on SNES
2923 
2924    Input Parameters:
2925 +  snes - the SNES context
2926 -  lag - -1 indicates NEVER rebuild, 1 means rebuild every time the Jacobian is computed within a single nonlinear solve, 2 means every second time
2927          the Jacobian is built etc. -2 indicates rebuild preconditioner at next chance but then never rebuild after that
2928 
2929    Options Database Keys:
2930 .    -snes_lag_preconditioner <lag>
2931 
2932    Notes:
2933    The default is 1
2934    The preconditioner is ALWAYS built in the first iteration of a nonlinear solve unless lag is -1
2935    If  -1 is used before the very first nonlinear solve the preconditioner is still built because there is no previous preconditioner to use
2936 
2937    Level: intermediate
2938 
2939 .keywords: SNES, nonlinear, set, convergence, tolerances
2940 
2941 .seealso: SNESSetTrustRegionTolerance(), SNESGetLagPreconditioner(), SNESSetLagJacobian(), SNESGetLagJacobian()
2942 
2943 @*/
2944 PetscErrorCode  SNESSetLagPreconditioner(SNES snes,PetscInt lag)
2945 {
2946   PetscFunctionBegin;
2947   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2948   if (lag < -2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Lag must be -2, -1, 1 or greater");
2949   if (!lag) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Lag cannot be 0");
2950   PetscValidLogicalCollectiveInt(snes,lag,2);
2951   snes->lagpreconditioner = lag;
2952   PetscFunctionReturn(0);
2953 }
2954 
2955 #undef __FUNCT__
2956 #define __FUNCT__ "SNESSetGridSequence"
2957 /*@
2958    SNESSetGridSequence - sets the number of steps of grid sequencing that SNES does
2959 
2960    Logically Collective on SNES
2961 
2962    Input Parameters:
2963 +  snes - the SNES context
2964 -  steps - the number of refinements to do, defaults to 0
2965 
2966    Options Database Keys:
2967 .    -snes_grid_sequence <steps>
2968 
2969    Level: intermediate
2970 
2971    Notes:
2972    Use SNESGetSolution() to extract the fine grid solution after grid sequencing.
2973 
2974 .keywords: SNES, nonlinear, set, convergence, tolerances
2975 
2976 .seealso: SNESSetTrustRegionTolerance(), SNESGetLagPreconditioner(), SNESSetLagJacobian(), SNESGetLagJacobian(), SNESGetGridSequence()
2977 
2978 @*/
2979 PetscErrorCode  SNESSetGridSequence(SNES snes,PetscInt steps)
2980 {
2981   PetscFunctionBegin;
2982   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
2983   PetscValidLogicalCollectiveInt(snes,steps,2);
2984   snes->gridsequence = steps;
2985   PetscFunctionReturn(0);
2986 }
2987 
2988 #undef __FUNCT__
2989 #define __FUNCT__ "SNESGetGridSequence"
2990 /*@
2991    SNESGetGridSequence - gets the number of steps of grid sequencing that SNES does
2992 
2993    Logically Collective on SNES
2994 
2995    Input Parameter:
2996 .  snes - the SNES context
2997 
2998    Output Parameter:
2999 .  steps - the number of refinements to do, defaults to 0
3000 
3001    Options Database Keys:
3002 .    -snes_grid_sequence <steps>
3003 
3004    Level: intermediate
3005 
3006    Notes:
3007    Use SNESGetSolution() to extract the fine grid solution after grid sequencing.
3008 
3009 .keywords: SNES, nonlinear, set, convergence, tolerances
3010 
3011 .seealso: SNESSetTrustRegionTolerance(), SNESGetLagPreconditioner(), SNESSetLagJacobian(), SNESGetLagJacobian(), SNESSetGridSequence()
3012 
3013 @*/
3014 PetscErrorCode  SNESGetGridSequence(SNES snes,PetscInt *steps)
3015 {
3016   PetscFunctionBegin;
3017   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3018   *steps = snes->gridsequence;
3019   PetscFunctionReturn(0);
3020 }
3021 
3022 #undef __FUNCT__
3023 #define __FUNCT__ "SNESGetLagPreconditioner"
3024 /*@
3025    SNESGetLagPreconditioner - Indicates how often the preconditioner is rebuilt
3026 
3027    Not Collective
3028 
3029    Input Parameter:
3030 .  snes - the SNES context
3031 
3032    Output Parameter:
3033 .   lag - -1 indicates NEVER rebuild, 1 means rebuild every time the Jacobian is computed within a single nonlinear solve, 2 means every second time
3034          the Jacobian is built etc. -2 indicates rebuild preconditioner at next chance but then never rebuild after that
3035 
3036    Options Database Keys:
3037 .    -snes_lag_preconditioner <lag>
3038 
3039    Notes:
3040    The default is 1
3041    The preconditioner is ALWAYS built in the first iteration of a nonlinear solve unless lag is -1
3042 
3043    Level: intermediate
3044 
3045 .keywords: SNES, nonlinear, set, convergence, tolerances
3046 
3047 .seealso: SNESSetTrustRegionTolerance(), SNESSetLagPreconditioner()
3048 
3049 @*/
3050 PetscErrorCode  SNESGetLagPreconditioner(SNES snes,PetscInt *lag)
3051 {
3052   PetscFunctionBegin;
3053   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3054   *lag = snes->lagpreconditioner;
3055   PetscFunctionReturn(0);
3056 }
3057 
3058 #undef __FUNCT__
3059 #define __FUNCT__ "SNESSetLagJacobian"
3060 /*@
3061    SNESSetLagJacobian - Determines when the Jacobian is rebuilt in the nonlinear solve. See SNESSetLagPreconditioner() for determining how
3062      often the preconditioner is rebuilt.
3063 
3064    Logically Collective on SNES
3065 
3066    Input Parameters:
3067 +  snes - the SNES context
3068 -  lag - -1 indicates NEVER rebuild, 1 means rebuild every time the Jacobian is computed within a single nonlinear solve, 2 means every second time
3069          the Jacobian is built etc. -2 means rebuild at next chance but then never again
3070 
3071    Options Database Keys:
3072 .    -snes_lag_jacobian <lag>
3073 
3074    Notes:
3075    The default is 1
3076    The Jacobian is ALWAYS built in the first iteration of a nonlinear solve unless lag is -1
3077    If  -1 is used before the very first nonlinear solve the CODE WILL FAIL! because no Jacobian is used, use -2 to indicate you want it recomputed
3078    at the next Newton step but never again (unless it is reset to another value)
3079 
3080    Level: intermediate
3081 
3082 .keywords: SNES, nonlinear, set, convergence, tolerances
3083 
3084 .seealso: SNESSetTrustRegionTolerance(), SNESGetLagPreconditioner(), SNESSetLagPreconditioner(), SNESGetLagJacobian()
3085 
3086 @*/
3087 PetscErrorCode  SNESSetLagJacobian(SNES snes,PetscInt lag)
3088 {
3089   PetscFunctionBegin;
3090   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3091   if (lag < -2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Lag must be -2, -1, 1 or greater");
3092   if (!lag) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Lag cannot be 0");
3093   PetscValidLogicalCollectiveInt(snes,lag,2);
3094   snes->lagjacobian = lag;
3095   PetscFunctionReturn(0);
3096 }
3097 
3098 #undef __FUNCT__
3099 #define __FUNCT__ "SNESGetLagJacobian"
3100 /*@
3101    SNESGetLagJacobian - Indicates how often the Jacobian is rebuilt. See SNESGetLagPreconditioner() to determine when the preconditioner is rebuilt
3102 
3103    Not Collective
3104 
3105    Input Parameter:
3106 .  snes - the SNES context
3107 
3108    Output Parameter:
3109 .   lag - -1 indicates NEVER rebuild, 1 means rebuild every time the Jacobian is computed within a single nonlinear solve, 2 means every second time
3110          the Jacobian is built etc.
3111 
3112    Options Database Keys:
3113 .    -snes_lag_jacobian <lag>
3114 
3115    Notes:
3116    The default is 1
3117    The jacobian is ALWAYS built in the first iteration of a nonlinear solve unless lag is -1
3118 
3119    Level: intermediate
3120 
3121 .keywords: SNES, nonlinear, set, convergence, tolerances
3122 
3123 .seealso: SNESSetTrustRegionTolerance(), SNESSetLagJacobian(), SNESSetLagPreconditioner(), SNESGetLagPreconditioner()
3124 
3125 @*/
3126 PetscErrorCode  SNESGetLagJacobian(SNES snes,PetscInt *lag)
3127 {
3128   PetscFunctionBegin;
3129   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3130   *lag = snes->lagjacobian;
3131   PetscFunctionReturn(0);
3132 }
3133 
3134 #undef __FUNCT__
3135 #define __FUNCT__ "SNESSetLagJacobianPersists"
3136 /*@
3137    SNESSetLagJacobianPersists - Set whether or not the Jacobian lagging persists through multiple solves
3138 
3139    Logically collective on SNES
3140 
3141    Input Parameter:
3142 +  snes - the SNES context
3143 -   flg - jacobian lagging persists if true
3144 
3145    Options Database Keys:
3146 .    -snes_lag_jacobian_persists <flg>
3147 
3148    Notes: This is useful both for nonlinear preconditioning, where it's appropriate to have the Jacobian be stale by
3149    several solves, and for implicit time-stepping, where Jacobian lagging in the inner nonlinear solve over several
3150    timesteps may present huge efficiency gains.
3151 
3152    Level: developer
3153 
3154 .keywords: SNES, nonlinear, lag
3155 
3156 .seealso: SNESSetLagPreconditionerPersists(), SNESSetLagJacobian(), SNESGetLagJacobian(), SNESGetNPC()
3157 
3158 @*/
3159 PetscErrorCode  SNESSetLagJacobianPersists(SNES snes,PetscBool flg)
3160 {
3161   PetscFunctionBegin;
3162   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3163   PetscValidLogicalCollectiveBool(snes,flg,2);
3164   snes->lagjac_persist = flg;
3165   PetscFunctionReturn(0);
3166 }
3167 
3168 #undef __FUNCT__
3169 #define __FUNCT__ "SNESSetLagPreconditionerPersists"
3170 /*@
3171    SNESSetLagPreconditionerPersists - Set whether or not the preconditioner lagging persists through multiple solves
3172 
3173    Logically Collective on SNES
3174 
3175    Input Parameter:
3176 +  snes - the SNES context
3177 -   flg - preconditioner lagging persists if true
3178 
3179    Options Database Keys:
3180 .    -snes_lag_jacobian_persists <flg>
3181 
3182    Notes: This is useful both for nonlinear preconditioning, where it's appropriate to have the preconditioner be stale
3183    by several solves, and for implicit time-stepping, where preconditioner lagging in the inner nonlinear solve over
3184    several timesteps may present huge efficiency gains.
3185 
3186    Level: developer
3187 
3188 .keywords: SNES, nonlinear, lag
3189 
3190 .seealso: SNESSetLagJacobianPersists(), SNESSetLagJacobian(), SNESGetLagJacobian(), SNESGetNPC()
3191 
3192 @*/
3193 PetscErrorCode  SNESSetLagPreconditionerPersists(SNES snes,PetscBool flg)
3194 {
3195   PetscFunctionBegin;
3196   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3197   PetscValidLogicalCollectiveBool(snes,flg,2);
3198   snes->lagpre_persist = flg;
3199   PetscFunctionReturn(0);
3200 }
3201 
3202 #undef __FUNCT__
3203 #define __FUNCT__ "SNESSetTolerances"
3204 /*@
3205    SNESSetTolerances - Sets various parameters used in convergence tests.
3206 
3207    Logically Collective on SNES
3208 
3209    Input Parameters:
3210 +  snes - the SNES context
3211 .  abstol - absolute convergence tolerance
3212 .  rtol - relative convergence tolerance
3213 .  stol -  convergence tolerance in terms of the norm of the change in the solution between steps,  || delta x || < stol*|| x ||
3214 .  maxit - maximum number of iterations
3215 -  maxf - maximum number of function evaluations
3216 
3217    Options Database Keys:
3218 +    -snes_atol <abstol> - Sets abstol
3219 .    -snes_rtol <rtol> - Sets rtol
3220 .    -snes_stol <stol> - Sets stol
3221 .    -snes_max_it <maxit> - Sets maxit
3222 -    -snes_max_funcs <maxf> - Sets maxf
3223 
3224    Notes:
3225    The default maximum number of iterations is 50.
3226    The default maximum number of function evaluations is 1000.
3227 
3228    Level: intermediate
3229 
3230 .keywords: SNES, nonlinear, set, convergence, tolerances
3231 
3232 .seealso: SNESSetTrustRegionTolerance()
3233 @*/
3234 PetscErrorCode  SNESSetTolerances(SNES snes,PetscReal abstol,PetscReal rtol,PetscReal stol,PetscInt maxit,PetscInt maxf)
3235 {
3236   PetscFunctionBegin;
3237   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3238   PetscValidLogicalCollectiveReal(snes,abstol,2);
3239   PetscValidLogicalCollectiveReal(snes,rtol,3);
3240   PetscValidLogicalCollectiveReal(snes,stol,4);
3241   PetscValidLogicalCollectiveInt(snes,maxit,5);
3242   PetscValidLogicalCollectiveInt(snes,maxf,6);
3243 
3244   if (abstol != PETSC_DEFAULT) {
3245     if (abstol < 0.0) SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_OUTOFRANGE,"Absolute tolerance %g must be non-negative",(double)abstol);
3246     snes->abstol = abstol;
3247   }
3248   if (rtol != PETSC_DEFAULT) {
3249     if (rtol < 0.0 || 1.0 <= rtol) SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_OUTOFRANGE,"Relative tolerance %g must be non-negative and less than 1.0",(double)rtol);
3250     snes->rtol = rtol;
3251   }
3252   if (stol != PETSC_DEFAULT) {
3253     if (stol < 0.0) SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_OUTOFRANGE,"Step tolerance %g must be non-negative",(double)stol);
3254     snes->stol = stol;
3255   }
3256   if (maxit != PETSC_DEFAULT) {
3257     if (maxit < 0) SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_OUTOFRANGE,"Maximum number of iterations %D must be non-negative",maxit);
3258     snes->max_its = maxit;
3259   }
3260   if (maxf != PETSC_DEFAULT) {
3261     if (maxf < 0) SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_OUTOFRANGE,"Maximum number of function evaluations %D must be non-negative",maxf);
3262     snes->max_funcs = maxf;
3263   }
3264   snes->tolerancesset = PETSC_TRUE;
3265   PetscFunctionReturn(0);
3266 }
3267 
3268 #undef __FUNCT__
3269 #define __FUNCT__ "SNESGetTolerances"
3270 /*@
3271    SNESGetTolerances - Gets various parameters used in convergence tests.
3272 
3273    Not Collective
3274 
3275    Input Parameters:
3276 +  snes - the SNES context
3277 .  atol - absolute convergence tolerance
3278 .  rtol - relative convergence tolerance
3279 .  stol -  convergence tolerance in terms of the norm
3280            of the change in the solution between steps
3281 .  maxit - maximum number of iterations
3282 -  maxf - maximum number of function evaluations
3283 
3284    Notes:
3285    The user can specify NULL for any parameter that is not needed.
3286 
3287    Level: intermediate
3288 
3289 .keywords: SNES, nonlinear, get, convergence, tolerances
3290 
3291 .seealso: SNESSetTolerances()
3292 @*/
3293 PetscErrorCode  SNESGetTolerances(SNES snes,PetscReal *atol,PetscReal *rtol,PetscReal *stol,PetscInt *maxit,PetscInt *maxf)
3294 {
3295   PetscFunctionBegin;
3296   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3297   if (atol)  *atol  = snes->abstol;
3298   if (rtol)  *rtol  = snes->rtol;
3299   if (stol)  *stol  = snes->stol;
3300   if (maxit) *maxit = snes->max_its;
3301   if (maxf)  *maxf  = snes->max_funcs;
3302   PetscFunctionReturn(0);
3303 }
3304 
3305 #undef __FUNCT__
3306 #define __FUNCT__ "SNESSetTrustRegionTolerance"
3307 /*@
3308    SNESSetTrustRegionTolerance - Sets the trust region parameter tolerance.
3309 
3310    Logically Collective on SNES
3311 
3312    Input Parameters:
3313 +  snes - the SNES context
3314 -  tol - tolerance
3315 
3316    Options Database Key:
3317 .  -snes_trtol <tol> - Sets tol
3318 
3319    Level: intermediate
3320 
3321 .keywords: SNES, nonlinear, set, trust region, tolerance
3322 
3323 .seealso: SNESSetTolerances()
3324 @*/
3325 PetscErrorCode  SNESSetTrustRegionTolerance(SNES snes,PetscReal tol)
3326 {
3327   PetscFunctionBegin;
3328   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3329   PetscValidLogicalCollectiveReal(snes,tol,2);
3330   snes->deltatol = tol;
3331   PetscFunctionReturn(0);
3332 }
3333 
3334 /*
3335    Duplicate the lg monitors for SNES from KSP; for some reason with
3336    dynamic libraries things don't work under Sun4 if we just use
3337    macros instead of functions
3338 */
3339 #undef __FUNCT__
3340 #define __FUNCT__ "SNESMonitorLGResidualNorm"
3341 PetscErrorCode  SNESMonitorLGResidualNorm(SNES snes,PetscInt it,PetscReal norm,void *ctx)
3342 {
3343   PetscErrorCode ierr;
3344 
3345   PetscFunctionBegin;
3346   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3347   ierr = KSPMonitorLGResidualNorm((KSP)snes,it,norm,ctx);CHKERRQ(ierr);
3348   PetscFunctionReturn(0);
3349 }
3350 
3351 #undef __FUNCT__
3352 #define __FUNCT__ "SNESMonitorLGCreate"
3353 PetscErrorCode  SNESMonitorLGCreate(MPI_Comm comm,const char host[],const char label[],int x,int y,int m,int n,PetscDrawLG *lgctx)
3354 {
3355   PetscErrorCode ierr;
3356 
3357   PetscFunctionBegin;
3358   ierr = KSPMonitorLGResidualNormCreate(comm,host,label,x,y,m,n,lgctx);CHKERRQ(ierr);
3359   PetscFunctionReturn(0);
3360 }
3361 
3362 PETSC_INTERN PetscErrorCode  SNESMonitorRange_Private(SNES,PetscInt,PetscReal*);
3363 
3364 #undef __FUNCT__
3365 #define __FUNCT__ "SNESMonitorLGRange"
3366 PetscErrorCode  SNESMonitorLGRange(SNES snes,PetscInt n,PetscReal rnorm,void *monctx)
3367 {
3368   PetscDrawLG      lg;
3369   PetscErrorCode   ierr;
3370   PetscReal        x,y,per;
3371   PetscViewer      v = (PetscViewer)monctx;
3372   static PetscReal prev; /* should be in the context */
3373   PetscDraw        draw;
3374 
3375   PetscFunctionBegin;
3376   PetscValidHeaderSpecific(v,PETSC_VIEWER_CLASSID,4);
3377   ierr = PetscViewerDrawGetDrawLG(v,0,&lg);CHKERRQ(ierr);
3378   if (!n) {ierr = PetscDrawLGReset(lg);CHKERRQ(ierr);}
3379   ierr = PetscDrawLGGetDraw(lg,&draw);CHKERRQ(ierr);
3380   ierr = PetscDrawSetTitle(draw,"Residual norm");CHKERRQ(ierr);
3381   x    = (PetscReal)n;
3382   if (rnorm > 0.0) y = PetscLog10Real(rnorm);
3383   else y = -15.0;
3384   ierr = PetscDrawLGAddPoint(lg,&x,&y);CHKERRQ(ierr);
3385   if (n < 20 || !(n % 5) || snes->reason) {
3386     ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
3387     ierr = PetscDrawLGSave(lg);CHKERRQ(ierr);
3388   }
3389 
3390   ierr = PetscViewerDrawGetDrawLG(v,1,&lg);CHKERRQ(ierr);
3391   if (!n) {ierr = PetscDrawLGReset(lg);CHKERRQ(ierr);}
3392   ierr = PetscDrawLGGetDraw(lg,&draw);CHKERRQ(ierr);
3393   ierr = PetscDrawSetTitle(draw,"% elemts > .2*max elemt");CHKERRQ(ierr);
3394   ierr =  SNESMonitorRange_Private(snes,n,&per);CHKERRQ(ierr);
3395   x    = (PetscReal)n;
3396   y    = 100.0*per;
3397   ierr = PetscDrawLGAddPoint(lg,&x,&y);CHKERRQ(ierr);
3398   if (n < 20 || !(n % 5) || snes->reason) {
3399     ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
3400     ierr = PetscDrawLGSave(lg);CHKERRQ(ierr);
3401   }
3402 
3403   ierr = PetscViewerDrawGetDrawLG(v,2,&lg);CHKERRQ(ierr);
3404   if (!n) {prev = rnorm;ierr = PetscDrawLGReset(lg);CHKERRQ(ierr);}
3405   ierr = PetscDrawLGGetDraw(lg,&draw);CHKERRQ(ierr);
3406   ierr = PetscDrawSetTitle(draw,"(norm -oldnorm)/oldnorm");CHKERRQ(ierr);
3407   x    = (PetscReal)n;
3408   y    = (prev - rnorm)/prev;
3409   ierr = PetscDrawLGAddPoint(lg,&x,&y);CHKERRQ(ierr);
3410   if (n < 20 || !(n % 5) || snes->reason) {
3411     ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
3412     ierr = PetscDrawLGSave(lg);CHKERRQ(ierr);
3413   }
3414 
3415   ierr = PetscViewerDrawGetDrawLG(v,3,&lg);CHKERRQ(ierr);
3416   if (!n) {ierr = PetscDrawLGReset(lg);CHKERRQ(ierr);}
3417   ierr = PetscDrawLGGetDraw(lg,&draw);CHKERRQ(ierr);
3418   ierr = PetscDrawSetTitle(draw,"(norm -oldnorm)/oldnorm*(% > .2 max)");CHKERRQ(ierr);
3419   x    = (PetscReal)n;
3420   y    = (prev - rnorm)/(prev*per);
3421   if (n > 2) { /*skip initial crazy value */
3422     ierr = PetscDrawLGAddPoint(lg,&x,&y);CHKERRQ(ierr);
3423   }
3424   if (n < 20 || !(n % 5) || snes->reason) {
3425     ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
3426     ierr = PetscDrawLGSave(lg);CHKERRQ(ierr);
3427   }
3428   prev = rnorm;
3429   PetscFunctionReturn(0);
3430 }
3431 
3432 #undef __FUNCT__
3433 #define __FUNCT__ "SNESMonitor"
3434 /*@
3435    SNESMonitor - runs the user provided monitor routines, if they exist
3436 
3437    Collective on SNES
3438 
3439    Input Parameters:
3440 +  snes - nonlinear solver context obtained from SNESCreate()
3441 .  iter - iteration number
3442 -  rnorm - relative norm of the residual
3443 
3444    Notes:
3445    This routine is called by the SNES implementations.
3446    It does not typically need to be called by the user.
3447 
3448    Level: developer
3449 
3450 .seealso: SNESMonitorSet()
3451 @*/
3452 PetscErrorCode  SNESMonitor(SNES snes,PetscInt iter,PetscReal rnorm)
3453 {
3454   PetscErrorCode ierr;
3455   PetscInt       i,n = snes->numbermonitors;
3456 
3457   PetscFunctionBegin;
3458   ierr = VecLockPush(snes->vec_sol);CHKERRQ(ierr);
3459   for (i=0; i<n; i++) {
3460     ierr = (*snes->monitor[i])(snes,iter,rnorm,snes->monitorcontext[i]);CHKERRQ(ierr);
3461   }
3462   ierr = VecLockPop(snes->vec_sol);CHKERRQ(ierr);
3463   PetscFunctionReturn(0);
3464 }
3465 
3466 /* ------------ Routines to set performance monitoring options ----------- */
3467 
3468 /*MC
3469     SNESMonitorFunction - functional form passed to SNESMonitorSet() to monitor convergence of nonlinear solver
3470 
3471      Synopsis:
3472      #include <petscsnes.h>
3473 $    PetscErrorCode SNESMonitorFunction(SNES snes,PetscInt its, PetscReal norm,void *mctx)
3474 
3475 +    snes - the SNES context
3476 .    its - iteration number
3477 .    norm - 2-norm function value (may be estimated)
3478 -    mctx - [optional] monitoring context
3479 
3480    Level: advanced
3481 
3482 .seealso:   SNESMonitorSet(), SNESMonitorGet()
3483 M*/
3484 
3485 #undef __FUNCT__
3486 #define __FUNCT__ "SNESMonitorSet"
3487 /*@C
3488    SNESMonitorSet - Sets an ADDITIONAL function that is to be used at every
3489    iteration of the nonlinear solver to display the iteration's
3490    progress.
3491 
3492    Logically Collective on SNES
3493 
3494    Input Parameters:
3495 +  snes - the SNES context
3496 .  f - the monitor function, see SNESMonitorFunction for the calling sequence
3497 .  mctx - [optional] user-defined context for private data for the
3498           monitor routine (use NULL if no context is desired)
3499 -  monitordestroy - [optional] routine that frees monitor context
3500           (may be NULL)
3501 
3502    Options Database Keys:
3503 +    -snes_monitor        - sets SNESMonitorDefault()
3504 .    -snes_monitor_lg_residualnorm    - sets line graph monitor,
3505                             uses SNESMonitorLGCreate()
3506 -    -snes_monitor_cancel - cancels all monitors that have
3507                             been hardwired into a code by
3508                             calls to SNESMonitorSet(), but
3509                             does not cancel those set via
3510                             the options database.
3511 
3512    Notes:
3513    Several different monitoring routines may be set by calling
3514    SNESMonitorSet() multiple times; all will be called in the
3515    order in which they were set.
3516 
3517    Fortran notes: Only a single monitor function can be set for each SNES object
3518 
3519    Level: intermediate
3520 
3521 .keywords: SNES, nonlinear, set, monitor
3522 
3523 .seealso: SNESMonitorDefault(), SNESMonitorCancel(), SNESMonitorFunction
3524 @*/
3525 PetscErrorCode  SNESMonitorSet(SNES snes,PetscErrorCode (*f)(SNES,PetscInt,PetscReal,void*),void *mctx,PetscErrorCode (*monitordestroy)(void**))
3526 {
3527   PetscInt       i;
3528   PetscErrorCode ierr;
3529   PetscBool      identical;
3530 
3531   PetscFunctionBegin;
3532   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3533   for (i=0; i<snes->numbermonitors;i++) {
3534     ierr = PetscMonitorCompare((PetscErrorCode (*)(void))f,mctx,monitordestroy,(PetscErrorCode (*)(void))snes->monitor[i],snes->monitorcontext[i],snes->monitordestroy[i],&identical);CHKERRQ(ierr);
3535     if (identical) PetscFunctionReturn(0);
3536   }
3537   if (snes->numbermonitors >= MAXSNESMONITORS) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Too many monitors set");
3538   snes->monitor[snes->numbermonitors]          = f;
3539   snes->monitordestroy[snes->numbermonitors]   = monitordestroy;
3540   snes->monitorcontext[snes->numbermonitors++] = (void*)mctx;
3541   PetscFunctionReturn(0);
3542 }
3543 
3544 #undef __FUNCT__
3545 #define __FUNCT__ "SNESMonitorCancel"
3546 /*@
3547    SNESMonitorCancel - Clears all the monitor functions for a SNES object.
3548 
3549    Logically Collective on SNES
3550 
3551    Input Parameters:
3552 .  snes - the SNES context
3553 
3554    Options Database Key:
3555 .  -snes_monitor_cancel - cancels all monitors that have been hardwired
3556     into a code by calls to SNESMonitorSet(), but does not cancel those
3557     set via the options database
3558 
3559    Notes:
3560    There is no way to clear one specific monitor from a SNES object.
3561 
3562    Level: intermediate
3563 
3564 .keywords: SNES, nonlinear, set, monitor
3565 
3566 .seealso: SNESMonitorDefault(), SNESMonitorSet()
3567 @*/
3568 PetscErrorCode  SNESMonitorCancel(SNES snes)
3569 {
3570   PetscErrorCode ierr;
3571   PetscInt       i;
3572 
3573   PetscFunctionBegin;
3574   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3575   for (i=0; i<snes->numbermonitors; i++) {
3576     if (snes->monitordestroy[i]) {
3577       ierr = (*snes->monitordestroy[i])(&snes->monitorcontext[i]);CHKERRQ(ierr);
3578     }
3579   }
3580   snes->numbermonitors = 0;
3581   PetscFunctionReturn(0);
3582 }
3583 
3584 /*MC
3585     SNESConvergenceTestFunction - functional form used for testing of convergence of nonlinear solver
3586 
3587      Synopsis:
3588      #include <petscsnes.h>
3589 $     PetscErrorCode SNESConvergenceTest(SNES snes,PetscInt it,PetscReal xnorm,PetscReal gnorm,PetscReal f,SNESConvergedReason *reason,void *cctx)
3590 
3591 +    snes - the SNES context
3592 .    it - current iteration (0 is the first and is before any Newton step)
3593 .    cctx - [optional] convergence context
3594 .    reason - reason for convergence/divergence
3595 .    xnorm - 2-norm of current iterate
3596 .    gnorm - 2-norm of current step
3597 -    f - 2-norm of function
3598 
3599    Level: intermediate
3600 
3601 .seealso:   SNESSetConvergenceTest(), SNESGetConvergenceTest()
3602 M*/
3603 
3604 #undef __FUNCT__
3605 #define __FUNCT__ "SNESSetConvergenceTest"
3606 /*@C
3607    SNESSetConvergenceTest - Sets the function that is to be used
3608    to test for convergence of the nonlinear iterative solution.
3609 
3610    Logically Collective on SNES
3611 
3612    Input Parameters:
3613 +  snes - the SNES context
3614 .  SNESConvergenceTestFunction - routine to test for convergence
3615 .  cctx - [optional] context for private data for the convergence routine  (may be NULL)
3616 -  destroy - [optional] destructor for the context (may be NULL; NULL_FUNCTION in Fortran)
3617 
3618    Level: advanced
3619 
3620 .keywords: SNES, nonlinear, set, convergence, test
3621 
3622 .seealso: SNESConvergedDefault(), SNESConvergedSkip(), SNESConvergenceTestFunction
3623 @*/
3624 PetscErrorCode  SNESSetConvergenceTest(SNES snes,PetscErrorCode (*SNESConvergenceTestFunction)(SNES,PetscInt,PetscReal,PetscReal,PetscReal,SNESConvergedReason*,void*),void *cctx,PetscErrorCode (*destroy)(void*))
3625 {
3626   PetscErrorCode ierr;
3627 
3628   PetscFunctionBegin;
3629   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3630   if (!SNESConvergenceTestFunction) SNESConvergenceTestFunction = SNESConvergedSkip;
3631   if (snes->ops->convergeddestroy) {
3632     ierr = (*snes->ops->convergeddestroy)(snes->cnvP);CHKERRQ(ierr);
3633   }
3634   snes->ops->converged        = SNESConvergenceTestFunction;
3635   snes->ops->convergeddestroy = destroy;
3636   snes->cnvP                  = cctx;
3637   PetscFunctionReturn(0);
3638 }
3639 
3640 #undef __FUNCT__
3641 #define __FUNCT__ "SNESGetConvergedReason"
3642 /*@
3643    SNESGetConvergedReason - Gets the reason the SNES iteration was stopped.
3644 
3645    Not Collective
3646 
3647    Input Parameter:
3648 .  snes - the SNES context
3649 
3650    Output Parameter:
3651 .  reason - negative value indicates diverged, positive value converged, see SNESConvergedReason or the
3652             manual pages for the individual convergence tests for complete lists
3653 
3654    Level: intermediate
3655 
3656    Notes: Can only be called after the call the SNESSolve() is complete.
3657 
3658 .keywords: SNES, nonlinear, set, convergence, test
3659 
3660 .seealso: SNESSetConvergenceTest(), SNESSetConvergedReason(), SNESConvergedReason
3661 @*/
3662 PetscErrorCode SNESGetConvergedReason(SNES snes,SNESConvergedReason *reason)
3663 {
3664   PetscFunctionBegin;
3665   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3666   PetscValidPointer(reason,2);
3667   *reason = snes->reason;
3668   PetscFunctionReturn(0);
3669 }
3670 
3671 #undef __FUNCT__
3672 #define __FUNCT__ "SNESSetConvergedReason"
3673 /*@
3674    SNESSetConvergedReason - Sets the reason the SNES iteration was stopped.
3675 
3676    Not Collective
3677 
3678    Input Parameters:
3679 +  snes - the SNES context
3680 -  reason - negative value indicates diverged, positive value converged, see SNESConvergedReason or the
3681             manual pages for the individual convergence tests for complete lists
3682 
3683    Level: intermediate
3684 
3685 .keywords: SNES, nonlinear, set, convergence, test
3686 .seealso: SNESGetConvergedReason(), SNESSetConvergenceTest(), SNESConvergedReason
3687 @*/
3688 PetscErrorCode SNESSetConvergedReason(SNES snes,SNESConvergedReason reason)
3689 {
3690   PetscFunctionBegin;
3691   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3692   snes->reason = reason;
3693   PetscFunctionReturn(0);
3694 }
3695 
3696 #undef __FUNCT__
3697 #define __FUNCT__ "SNESSetConvergenceHistory"
3698 /*@
3699    SNESSetConvergenceHistory - Sets the array used to hold the convergence history.
3700 
3701    Logically Collective on SNES
3702 
3703    Input Parameters:
3704 +  snes - iterative context obtained from SNESCreate()
3705 .  a   - array to hold history, this array will contain the function norms computed at each step
3706 .  its - integer array holds the number of linear iterations for each solve.
3707 .  na  - size of a and its
3708 -  reset - PETSC_TRUE indicates each new nonlinear solve resets the history counter to zero,
3709            else it continues storing new values for new nonlinear solves after the old ones
3710 
3711    Notes:
3712    If 'a' and 'its' are NULL then space is allocated for the history. If 'na' PETSC_DECIDE or PETSC_DEFAULT then a
3713    default array of length 10000 is allocated.
3714 
3715    This routine is useful, e.g., when running a code for purposes
3716    of accurate performance monitoring, when no I/O should be done
3717    during the section of code that is being timed.
3718 
3719    Level: intermediate
3720 
3721 .keywords: SNES, set, convergence, history
3722 
3723 .seealso: SNESGetConvergenceHistory()
3724 
3725 @*/
3726 PetscErrorCode  SNESSetConvergenceHistory(SNES snes,PetscReal a[],PetscInt its[],PetscInt na,PetscBool reset)
3727 {
3728   PetscErrorCode ierr;
3729 
3730   PetscFunctionBegin;
3731   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3732   if (a) PetscValidScalarPointer(a,2);
3733   if (its) PetscValidIntPointer(its,3);
3734   if (!a) {
3735     if (na == PETSC_DECIDE || na == PETSC_DEFAULT) na = 1000;
3736     ierr = PetscCalloc1(na,&a);CHKERRQ(ierr);
3737     ierr = PetscCalloc1(na,&its);CHKERRQ(ierr);
3738 
3739     snes->conv_malloc = PETSC_TRUE;
3740   }
3741   snes->conv_hist       = a;
3742   snes->conv_hist_its   = its;
3743   snes->conv_hist_max   = na;
3744   snes->conv_hist_len   = 0;
3745   snes->conv_hist_reset = reset;
3746   PetscFunctionReturn(0);
3747 }
3748 
3749 #if defined(PETSC_HAVE_MATLAB_ENGINE)
3750 #include <engine.h>   /* MATLAB include file */
3751 #include <mex.h>      /* MATLAB include file */
3752 
3753 #undef __FUNCT__
3754 #define __FUNCT__ "SNESGetConvergenceHistoryMatlab"
3755 PETSC_EXTERN mxArray *SNESGetConvergenceHistoryMatlab(SNES snes)
3756 {
3757   mxArray   *mat;
3758   PetscInt  i;
3759   PetscReal *ar;
3760 
3761   PetscFunctionBegin;
3762   mat = mxCreateDoubleMatrix(snes->conv_hist_len,1,mxREAL);
3763   ar  = (PetscReal*) mxGetData(mat);
3764   for (i=0; i<snes->conv_hist_len; i++) ar[i] = snes->conv_hist[i];
3765   PetscFunctionReturn(mat);
3766 }
3767 #endif
3768 
3769 #undef __FUNCT__
3770 #define __FUNCT__ "SNESGetConvergenceHistory"
3771 /*@C
3772    SNESGetConvergenceHistory - Gets the array used to hold the convergence history.
3773 
3774    Not Collective
3775 
3776    Input Parameter:
3777 .  snes - iterative context obtained from SNESCreate()
3778 
3779    Output Parameters:
3780 .  a   - array to hold history
3781 .  its - integer array holds the number of linear iterations (or
3782          negative if not converged) for each solve.
3783 -  na  - size of a and its
3784 
3785    Notes:
3786     The calling sequence for this routine in Fortran is
3787 $   call SNESGetConvergenceHistory(SNES snes, integer na, integer ierr)
3788 
3789    This routine is useful, e.g., when running a code for purposes
3790    of accurate performance monitoring, when no I/O should be done
3791    during the section of code that is being timed.
3792 
3793    Level: intermediate
3794 
3795 .keywords: SNES, get, convergence, history
3796 
3797 .seealso: SNESSetConvergencHistory()
3798 
3799 @*/
3800 PetscErrorCode  SNESGetConvergenceHistory(SNES snes,PetscReal *a[],PetscInt *its[],PetscInt *na)
3801 {
3802   PetscFunctionBegin;
3803   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3804   if (a)   *a   = snes->conv_hist;
3805   if (its) *its = snes->conv_hist_its;
3806   if (na)  *na  = snes->conv_hist_len;
3807   PetscFunctionReturn(0);
3808 }
3809 
3810 #undef __FUNCT__
3811 #define __FUNCT__ "SNESSetUpdate"
3812 /*@C
3813   SNESSetUpdate - Sets the general-purpose update function called
3814   at the beginning of every iteration of the nonlinear solve. Specifically
3815   it is called just before the Jacobian is "evaluated".
3816 
3817   Logically Collective on SNES
3818 
3819   Input Parameters:
3820 . snes - The nonlinear solver context
3821 . func - The function
3822 
3823   Calling sequence of func:
3824 . func (SNES snes, PetscInt step);
3825 
3826 . step - The current step of the iteration
3827 
3828   Level: advanced
3829 
3830   Note: This is NOT what one uses to update the ghost points before a function evaluation, that should be done at the beginning of your FormFunction()
3831         This is not used by most users.
3832 
3833 .keywords: SNES, update
3834 
3835 .seealso SNESSetJacobian(), SNESSolve()
3836 @*/
3837 PetscErrorCode  SNESSetUpdate(SNES snes, PetscErrorCode (*func)(SNES, PetscInt))
3838 {
3839   PetscFunctionBegin;
3840   PetscValidHeaderSpecific(snes, SNES_CLASSID,1);
3841   snes->ops->update = func;
3842   PetscFunctionReturn(0);
3843 }
3844 
3845 #undef __FUNCT__
3846 #define __FUNCT__ "SNESScaleStep_Private"
3847 /*
3848    SNESScaleStep_Private - Scales a step so that its length is less than the
3849    positive parameter delta.
3850 
3851     Input Parameters:
3852 +   snes - the SNES context
3853 .   y - approximate solution of linear system
3854 .   fnorm - 2-norm of current function
3855 -   delta - trust region size
3856 
3857     Output Parameters:
3858 +   gpnorm - predicted function norm at the new point, assuming local
3859     linearization.  The value is zero if the step lies within the trust
3860     region, and exceeds zero otherwise.
3861 -   ynorm - 2-norm of the step
3862 
3863     Note:
3864     For non-trust region methods such as SNESNEWTONLS, the parameter delta
3865     is set to be the maximum allowable step size.
3866 
3867 .keywords: SNES, nonlinear, scale, step
3868 */
3869 PetscErrorCode SNESScaleStep_Private(SNES snes,Vec y,PetscReal *fnorm,PetscReal *delta,PetscReal *gpnorm,PetscReal *ynorm)
3870 {
3871   PetscReal      nrm;
3872   PetscScalar    cnorm;
3873   PetscErrorCode ierr;
3874 
3875   PetscFunctionBegin;
3876   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
3877   PetscValidHeaderSpecific(y,VEC_CLASSID,2);
3878   PetscCheckSameComm(snes,1,y,2);
3879 
3880   ierr = VecNorm(y,NORM_2,&nrm);CHKERRQ(ierr);
3881   if (nrm > *delta) {
3882     nrm     = *delta/nrm;
3883     *gpnorm = (1.0 - nrm)*(*fnorm);
3884     cnorm   = nrm;
3885     ierr    = VecScale(y,cnorm);CHKERRQ(ierr);
3886     *ynorm  = *delta;
3887   } else {
3888     *gpnorm = 0.0;
3889     *ynorm  = nrm;
3890   }
3891   PetscFunctionReturn(0);
3892 }
3893 
3894 #undef __FUNCT__
3895 #define __FUNCT__ "SNESReasonView"
3896 /*@
3897    SNESReasonView - Displays the reason a SNES solve converged or diverged to a viewer
3898 
3899    Collective on SNES
3900 
3901    Parameter:
3902 +  snes - iterative context obtained from SNESCreate()
3903 -  viewer - the viewer to display the reason
3904 
3905 
3906    Options Database Keys:
3907 .  -snes_converged_reason - print reason for converged or diverged, also prints number of iterations
3908 
3909    Level: beginner
3910 
3911 .keywords: SNES, solve, linear system
3912 
3913 .seealso: SNESCreate(), SNESSetUp(), SNESDestroy(), SNESSetTolerances(), SNESConvergedDefault()
3914 
3915 @*/
3916 PetscErrorCode  SNESReasonView(SNES snes,PetscViewer viewer)
3917 {
3918   PetscErrorCode ierr;
3919   PetscBool      isAscii;
3920 
3921   PetscFunctionBegin;
3922   ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&isAscii);CHKERRQ(ierr);
3923   if (isAscii) {
3924     ierr = PetscViewerASCIIAddTab(viewer,((PetscObject)snes)->tablevel);CHKERRQ(ierr);
3925     if (snes->reason > 0) {
3926       if (((PetscObject) snes)->prefix) {
3927         ierr = PetscViewerASCIIPrintf(viewer,"Nonlinear %s solve converged due to %s iterations %D\n",((PetscObject) snes)->prefix,SNESConvergedReasons[snes->reason],snes->iter);CHKERRQ(ierr);
3928       } else {
3929         ierr = PetscViewerASCIIPrintf(viewer,"Nonlinear solve converged due to %s iterations %D\n",SNESConvergedReasons[snes->reason],snes->iter);CHKERRQ(ierr);
3930       }
3931     } else {
3932       if (((PetscObject) snes)->prefix) {
3933         ierr = PetscViewerASCIIPrintf(viewer,"Nonlinear %s solve did not converge due to %s iterations %D\n",((PetscObject) snes)->prefix,SNESConvergedReasons[snes->reason],snes->iter);CHKERRQ(ierr);
3934       } else {
3935         ierr = PetscViewerASCIIPrintf(viewer,"Nonlinear solve did not converge due to %s iterations %D\n",SNESConvergedReasons[snes->reason],snes->iter);CHKERRQ(ierr);
3936       }
3937     }
3938     ierr = PetscViewerASCIISubtractTab(viewer,((PetscObject)snes)->tablevel);CHKERRQ(ierr);
3939   }
3940   PetscFunctionReturn(0);
3941 }
3942 
3943 #undef __FUNCT__
3944 #define __FUNCT__ "SNESReasonViewFromOptions"
3945 /*@C
3946   SNESReasonViewFromOptions - Processes command line options to determine if/how a SNESReason is to be viewed.
3947 
3948   Collective on SNES
3949 
3950   Input Parameters:
3951 . snes   - the SNES object
3952 
3953   Level: intermediate
3954 
3955 @*/
3956 PetscErrorCode SNESReasonViewFromOptions(SNES snes)
3957 {
3958   PetscErrorCode    ierr;
3959   PetscViewer       viewer;
3960   PetscBool         flg;
3961   static PetscBool  incall = PETSC_FALSE;
3962   PetscViewerFormat format;
3963 
3964   PetscFunctionBegin;
3965   if (incall) PetscFunctionReturn(0);
3966   incall = PETSC_TRUE;
3967   ierr   = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_converged_reason",&viewer,&format,&flg);CHKERRQ(ierr);
3968   if (flg) {
3969     ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
3970     ierr = SNESReasonView(snes,viewer);CHKERRQ(ierr);
3971     ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
3972     ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
3973   }
3974   incall = PETSC_FALSE;
3975   PetscFunctionReturn(0);
3976 }
3977 
3978 #undef __FUNCT__
3979 #define __FUNCT__ "SNESSolve"
3980 /*@C
3981    SNESSolve - Solves a nonlinear system F(x) = b.
3982    Call SNESSolve() after calling SNESCreate() and optional routines of the form SNESSetXXX().
3983 
3984    Collective on SNES
3985 
3986    Input Parameters:
3987 +  snes - the SNES context
3988 .  b - the constant part of the equation F(x) = b, or NULL to use zero.
3989 -  x - the solution vector.
3990 
3991    Notes:
3992    The user should initialize the vector,x, with the initial guess
3993    for the nonlinear solve prior to calling SNESSolve.  In particular,
3994    to employ an initial guess of zero, the user should explicitly set
3995    this vector to zero by calling VecSet().
3996 
3997    Level: beginner
3998 
3999 .keywords: SNES, nonlinear, solve
4000 
4001 .seealso: SNESCreate(), SNESDestroy(), SNESSetFunction(), SNESSetJacobian(), SNESSetGridSequence(), SNESGetSolution()
4002 @*/
4003 PetscErrorCode  SNESSolve(SNES snes,Vec b,Vec x)
4004 {
4005   PetscErrorCode    ierr;
4006   PetscBool         flg;
4007   PetscInt          grid;
4008   Vec               xcreated = NULL;
4009   DM                dm;
4010 
4011   PetscFunctionBegin;
4012   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4013   if (x) PetscValidHeaderSpecific(x,VEC_CLASSID,3);
4014   if (x) PetscCheckSameComm(snes,1,x,3);
4015   if (b) PetscValidHeaderSpecific(b,VEC_CLASSID,2);
4016   if (b) PetscCheckSameComm(snes,1,b,2);
4017 
4018   if (!x) {
4019     ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
4020     ierr = DMCreateGlobalVector(dm,&xcreated);CHKERRQ(ierr);
4021     x    = xcreated;
4022   }
4023   ierr = SNESViewFromOptions(snes,NULL,"-snes_view_pre");CHKERRQ(ierr);
4024 
4025   for (grid=0; grid<snes->gridsequence; grid++) {ierr = PetscViewerASCIIPushTab(PETSC_VIEWER_STDOUT_(PetscObjectComm((PetscObject)snes)));CHKERRQ(ierr);}
4026   for (grid=0; grid<snes->gridsequence+1; grid++) {
4027 
4028     /* set solution vector */
4029     if (!grid) {ierr = PetscObjectReference((PetscObject)x);CHKERRQ(ierr);}
4030     ierr          = VecDestroy(&snes->vec_sol);CHKERRQ(ierr);
4031     snes->vec_sol = x;
4032     ierr          = SNESGetDM(snes,&dm);CHKERRQ(ierr);
4033 
4034     /* set affine vector if provided */
4035     if (b) { ierr = PetscObjectReference((PetscObject)b);CHKERRQ(ierr); }
4036     ierr          = VecDestroy(&snes->vec_rhs);CHKERRQ(ierr);
4037     snes->vec_rhs = b;
4038 
4039     if (snes->vec_func == snes->vec_sol) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_IDN,"Solution vector cannot be function vector");
4040     if (snes->vec_rhs  == snes->vec_sol) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_IDN,"Solution vector cannot be right hand side vector");
4041     if (!snes->vec_sol_update /* && snes->vec_sol */) {
4042       ierr = VecDuplicate(snes->vec_sol,&snes->vec_sol_update);CHKERRQ(ierr);
4043       ierr = PetscLogObjectParent((PetscObject)snes,(PetscObject)snes->vec_sol_update);CHKERRQ(ierr);
4044     }
4045     ierr = DMShellSetGlobalVector(dm,snes->vec_sol);CHKERRQ(ierr);
4046     ierr = SNESSetUp(snes);CHKERRQ(ierr);
4047 
4048     if (!grid) {
4049       if (snes->ops->computeinitialguess) {
4050         ierr = (*snes->ops->computeinitialguess)(snes,snes->vec_sol,snes->initialguessP);CHKERRQ(ierr);
4051       }
4052     }
4053 
4054     if (snes->conv_hist_reset) snes->conv_hist_len = 0;
4055     if (snes->counters_reset) {snes->nfuncs = 0; snes->linear_its = 0; snes->numFailures = 0;}
4056 
4057     ierr = PetscLogEventBegin(SNES_Solve,snes,0,0,0);CHKERRQ(ierr);
4058     ierr = (*snes->ops->solve)(snes);CHKERRQ(ierr);
4059     ierr = PetscLogEventEnd(SNES_Solve,snes,0,0,0);CHKERRQ(ierr);
4060     if (!snes->reason) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal error, solver returned without setting converged reason");
4061     snes->domainerror = PETSC_FALSE; /* clear the flag if it has been set */
4062 
4063     if (snes->lagjac_persist) snes->jac_iter += snes->iter;
4064     if (snes->lagpre_persist) snes->pre_iter += snes->iter;
4065 
4066     ierr   = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,"-snes_test_local_min",NULL,NULL,&flg);CHKERRQ(ierr);
4067     if (flg && !PetscPreLoadingOn) { ierr = SNESTestLocalMin(snes);CHKERRQ(ierr); }
4068     ierr = SNESReasonViewFromOptions(snes);CHKERRQ(ierr);
4069 
4070     if (snes->errorifnotconverged && snes->reason < 0) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_NOT_CONVERGED,"SNESSolve has not converged");
4071     if (snes->reason < 0) break;
4072     if (grid <  snes->gridsequence) {
4073       DM  fine;
4074       Vec xnew;
4075       Mat interp;
4076 
4077       ierr = DMRefine(snes->dm,PetscObjectComm((PetscObject)snes),&fine);CHKERRQ(ierr);
4078       if (!fine) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_INCOMP,"DMRefine() did not perform any refinement, cannot continue grid sequencing");
4079       ierr = DMCreateInterpolation(snes->dm,fine,&interp,NULL);CHKERRQ(ierr);
4080       ierr = DMCreateGlobalVector(fine,&xnew);CHKERRQ(ierr);
4081       ierr = MatInterpolate(interp,x,xnew);CHKERRQ(ierr);
4082       ierr = DMInterpolate(snes->dm,interp,fine);CHKERRQ(ierr);
4083       ierr = MatDestroy(&interp);CHKERRQ(ierr);
4084       x    = xnew;
4085 
4086       ierr = SNESReset(snes);CHKERRQ(ierr);
4087       ierr = SNESSetDM(snes,fine);CHKERRQ(ierr);
4088       ierr = DMDestroy(&fine);CHKERRQ(ierr);
4089       ierr = PetscViewerASCIIPopTab(PETSC_VIEWER_STDOUT_(PetscObjectComm((PetscObject)snes)));CHKERRQ(ierr);
4090     }
4091   }
4092   ierr = SNESViewFromOptions(snes,NULL,"-snes_view");CHKERRQ(ierr);
4093   ierr = VecViewFromOptions(snes->vec_sol,(PetscObject)snes,"-snes_view_solution");CHKERRQ(ierr);
4094 
4095   ierr = VecDestroy(&xcreated);CHKERRQ(ierr);
4096   ierr = PetscObjectSAWsBlock((PetscObject)snes);CHKERRQ(ierr);
4097   PetscFunctionReturn(0);
4098 }
4099 
4100 /* --------- Internal routines for SNES Package --------- */
4101 
4102 #undef __FUNCT__
4103 #define __FUNCT__ "SNESSetType"
4104 /*@C
4105    SNESSetType - Sets the method for the nonlinear solver.
4106 
4107    Collective on SNES
4108 
4109    Input Parameters:
4110 +  snes - the SNES context
4111 -  type - a known method
4112 
4113    Options Database Key:
4114 .  -snes_type <type> - Sets the method; use -help for a list
4115    of available methods (for instance, newtonls or newtontr)
4116 
4117    Notes:
4118    See "petsc/include/petscsnes.h" for available methods (for instance)
4119 +    SNESNEWTONLS - Newton's method with line search
4120      (systems of nonlinear equations)
4121 .    SNESNEWTONTR - Newton's method with trust region
4122      (systems of nonlinear equations)
4123 
4124   Normally, it is best to use the SNESSetFromOptions() command and then
4125   set the SNES solver type from the options database rather than by using
4126   this routine.  Using the options database provides the user with
4127   maximum flexibility in evaluating the many nonlinear solvers.
4128   The SNESSetType() routine is provided for those situations where it
4129   is necessary to set the nonlinear solver independently of the command
4130   line or options database.  This might be the case, for example, when
4131   the choice of solver changes during the execution of the program,
4132   and the user's application is taking responsibility for choosing the
4133   appropriate method.
4134 
4135     Developer Notes: SNESRegister() adds a constructor for a new SNESType to SNESList, SNESSetType() locates
4136     the constructor in that list and calls it to create the spexific object.
4137 
4138   Level: intermediate
4139 
4140 .keywords: SNES, set, type
4141 
4142 .seealso: SNESType, SNESCreate(), SNESDestroy(), SNESGetType(), SNESSetFromOptions()
4143 
4144 @*/
4145 PetscErrorCode  SNESSetType(SNES snes,SNESType type)
4146 {
4147   PetscErrorCode ierr,(*r)(SNES);
4148   PetscBool      match;
4149 
4150   PetscFunctionBegin;
4151   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4152   PetscValidCharPointer(type,2);
4153 
4154   ierr = PetscObjectTypeCompare((PetscObject)snes,type,&match);CHKERRQ(ierr);
4155   if (match) PetscFunctionReturn(0);
4156 
4157   ierr =  PetscFunctionListFind(SNESList,type,&r);CHKERRQ(ierr);
4158   if (!r) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_UNKNOWN_TYPE,"Unable to find requested SNES type %s",type);
4159   /* Destroy the previous private SNES context */
4160   if (snes->ops->destroy) {
4161     ierr               = (*(snes)->ops->destroy)(snes);CHKERRQ(ierr);
4162     snes->ops->destroy = NULL;
4163   }
4164   /* Reinitialize function pointers in SNESOps structure */
4165   snes->ops->setup          = 0;
4166   snes->ops->solve          = 0;
4167   snes->ops->view           = 0;
4168   snes->ops->setfromoptions = 0;
4169   snes->ops->destroy        = 0;
4170   /* Call the SNESCreate_XXX routine for this particular Nonlinear solver */
4171   snes->setupcalled = PETSC_FALSE;
4172 
4173   ierr = PetscObjectChangeTypeName((PetscObject)snes,type);CHKERRQ(ierr);
4174   ierr = (*r)(snes);CHKERRQ(ierr);
4175   PetscFunctionReturn(0);
4176 }
4177 
4178 #undef __FUNCT__
4179 #define __FUNCT__ "SNESGetType"
4180 /*@C
4181    SNESGetType - Gets the SNES method type and name (as a string).
4182 
4183    Not Collective
4184 
4185    Input Parameter:
4186 .  snes - nonlinear solver context
4187 
4188    Output Parameter:
4189 .  type - SNES method (a character string)
4190 
4191    Level: intermediate
4192 
4193 .keywords: SNES, nonlinear, get, type, name
4194 @*/
4195 PetscErrorCode  SNESGetType(SNES snes,SNESType *type)
4196 {
4197   PetscFunctionBegin;
4198   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4199   PetscValidPointer(type,2);
4200   *type = ((PetscObject)snes)->type_name;
4201   PetscFunctionReturn(0);
4202 }
4203 
4204 #undef __FUNCT__
4205 #define __FUNCT__ "SNESSetSolution"
4206 /*@
4207   SNESSetSolution - Sets the solution vector for use by the SNES routines.
4208 
4209   Logically Collective on SNES and Vec
4210 
4211   Input Parameters:
4212 + snes - the SNES context obtained from SNESCreate()
4213 - u    - the solution vector
4214 
4215   Level: beginner
4216 
4217 .keywords: SNES, set, solution
4218 @*/
4219 PetscErrorCode SNESSetSolution(SNES snes, Vec u)
4220 {
4221   DM             dm;
4222   PetscErrorCode ierr;
4223 
4224   PetscFunctionBegin;
4225   PetscValidHeaderSpecific(snes, SNES_CLASSID, 1);
4226   PetscValidHeaderSpecific(u, VEC_CLASSID, 2);
4227   ierr = PetscObjectReference((PetscObject) u);CHKERRQ(ierr);
4228   ierr = VecDestroy(&snes->vec_sol);CHKERRQ(ierr);
4229 
4230   snes->vec_sol = u;
4231 
4232   ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr);
4233   ierr = DMShellSetGlobalVector(dm, u);CHKERRQ(ierr);
4234   PetscFunctionReturn(0);
4235 }
4236 
4237 #undef __FUNCT__
4238 #define __FUNCT__ "SNESGetSolution"
4239 /*@
4240    SNESGetSolution - Returns the vector where the approximate solution is
4241    stored. This is the fine grid solution when using SNESSetGridSequence().
4242 
4243    Not Collective, but Vec is parallel if SNES is parallel
4244 
4245    Input Parameter:
4246 .  snes - the SNES context
4247 
4248    Output Parameter:
4249 .  x - the solution
4250 
4251    Level: intermediate
4252 
4253 .keywords: SNES, nonlinear, get, solution
4254 
4255 .seealso:  SNESGetSolutionUpdate(), SNESGetFunction()
4256 @*/
4257 PetscErrorCode  SNESGetSolution(SNES snes,Vec *x)
4258 {
4259   PetscFunctionBegin;
4260   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4261   PetscValidPointer(x,2);
4262   *x = snes->vec_sol;
4263   PetscFunctionReturn(0);
4264 }
4265 
4266 #undef __FUNCT__
4267 #define __FUNCT__ "SNESGetSolutionUpdate"
4268 /*@
4269    SNESGetSolutionUpdate - Returns the vector where the solution update is
4270    stored.
4271 
4272    Not Collective, but Vec is parallel if SNES is parallel
4273 
4274    Input Parameter:
4275 .  snes - the SNES context
4276 
4277    Output Parameter:
4278 .  x - the solution update
4279 
4280    Level: advanced
4281 
4282 .keywords: SNES, nonlinear, get, solution, update
4283 
4284 .seealso: SNESGetSolution(), SNESGetFunction()
4285 @*/
4286 PetscErrorCode  SNESGetSolutionUpdate(SNES snes,Vec *x)
4287 {
4288   PetscFunctionBegin;
4289   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4290   PetscValidPointer(x,2);
4291   *x = snes->vec_sol_update;
4292   PetscFunctionReturn(0);
4293 }
4294 
4295 #undef __FUNCT__
4296 #define __FUNCT__ "SNESGetFunction"
4297 /*@C
4298    SNESGetFunction - Returns the vector where the function is stored.
4299 
4300    Not Collective, but Vec is parallel if SNES is parallel. Collective if Vec is requested, but has not been created yet.
4301 
4302    Input Parameter:
4303 .  snes - the SNES context
4304 
4305    Output Parameter:
4306 +  r - the vector that is used to store residuals (or NULL if you don't want it)
4307 .  f - the function (or NULL if you don't want it); see SNESFunction for calling sequence details
4308 -  ctx - the function context (or NULL if you don't want it)
4309 
4310    Level: advanced
4311 
4312 .keywords: SNES, nonlinear, get, function
4313 
4314 .seealso: SNESSetFunction(), SNESGetSolution(), SNESFunction
4315 @*/
4316 PetscErrorCode  SNESGetFunction(SNES snes,Vec *r,PetscErrorCode (**f)(SNES,Vec,Vec,void*),void **ctx)
4317 {
4318   PetscErrorCode ierr;
4319   DM             dm;
4320 
4321   PetscFunctionBegin;
4322   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4323   if (r) {
4324     if (!snes->vec_func) {
4325       if (snes->vec_rhs) {
4326         ierr = VecDuplicate(snes->vec_rhs,&snes->vec_func);CHKERRQ(ierr);
4327       } else if (snes->vec_sol) {
4328         ierr = VecDuplicate(snes->vec_sol,&snes->vec_func);CHKERRQ(ierr);
4329       } else if (snes->dm) {
4330         ierr = DMCreateGlobalVector(snes->dm,&snes->vec_func);CHKERRQ(ierr);
4331       }
4332     }
4333     *r = snes->vec_func;
4334   }
4335   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
4336   ierr = DMSNESGetFunction(dm,f,ctx);CHKERRQ(ierr);
4337   PetscFunctionReturn(0);
4338 }
4339 
4340 /*@C
4341    SNESGetNGS - Returns the NGS function and context.
4342 
4343    Input Parameter:
4344 .  snes - the SNES context
4345 
4346    Output Parameter:
4347 +  f - the function (or NULL) see SNESNGSFunction for details
4348 -  ctx    - the function context (or NULL)
4349 
4350    Level: advanced
4351 
4352 .keywords: SNES, nonlinear, get, function
4353 
4354 .seealso: SNESSetNGS(), SNESGetFunction()
4355 @*/
4356 
4357 #undef __FUNCT__
4358 #define __FUNCT__ "SNESGetNGS"
4359 PetscErrorCode SNESGetNGS (SNES snes, PetscErrorCode (**f)(SNES, Vec, Vec, void*), void ** ctx)
4360 {
4361   PetscErrorCode ierr;
4362   DM             dm;
4363 
4364   PetscFunctionBegin;
4365   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4366   ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
4367   ierr = DMSNESGetNGS(dm,f,ctx);CHKERRQ(ierr);
4368   PetscFunctionReturn(0);
4369 }
4370 
4371 #undef __FUNCT__
4372 #define __FUNCT__ "SNESSetOptionsPrefix"
4373 /*@C
4374    SNESSetOptionsPrefix - Sets the prefix used for searching for all
4375    SNES options in the database.
4376 
4377    Logically Collective on SNES
4378 
4379    Input Parameter:
4380 +  snes - the SNES context
4381 -  prefix - the prefix to prepend to all option names
4382 
4383    Notes:
4384    A hyphen (-) must NOT be given at the beginning of the prefix name.
4385    The first character of all runtime options is AUTOMATICALLY the hyphen.
4386 
4387    Level: advanced
4388 
4389 .keywords: SNES, set, options, prefix, database
4390 
4391 .seealso: SNESSetFromOptions()
4392 @*/
4393 PetscErrorCode  SNESSetOptionsPrefix(SNES snes,const char prefix[])
4394 {
4395   PetscErrorCode ierr;
4396 
4397   PetscFunctionBegin;
4398   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4399   ierr = PetscObjectSetOptionsPrefix((PetscObject)snes,prefix);CHKERRQ(ierr);
4400   if (!snes->ksp) {ierr = SNESGetKSP(snes,&snes->ksp);CHKERRQ(ierr);}
4401   if (snes->linesearch) {
4402     ierr = SNESGetLineSearch(snes,&snes->linesearch);CHKERRQ(ierr);
4403     ierr = PetscObjectSetOptionsPrefix((PetscObject)snes->linesearch,prefix);CHKERRQ(ierr);
4404   }
4405   ierr = KSPSetOptionsPrefix(snes->ksp,prefix);CHKERRQ(ierr);
4406   PetscFunctionReturn(0);
4407 }
4408 
4409 #undef __FUNCT__
4410 #define __FUNCT__ "SNESAppendOptionsPrefix"
4411 /*@C
4412    SNESAppendOptionsPrefix - Appends to the prefix used for searching for all
4413    SNES options in the database.
4414 
4415    Logically Collective on SNES
4416 
4417    Input Parameters:
4418 +  snes - the SNES context
4419 -  prefix - the prefix to prepend to all option names
4420 
4421    Notes:
4422    A hyphen (-) must NOT be given at the beginning of the prefix name.
4423    The first character of all runtime options is AUTOMATICALLY the hyphen.
4424 
4425    Level: advanced
4426 
4427 .keywords: SNES, append, options, prefix, database
4428 
4429 .seealso: SNESGetOptionsPrefix()
4430 @*/
4431 PetscErrorCode  SNESAppendOptionsPrefix(SNES snes,const char prefix[])
4432 {
4433   PetscErrorCode ierr;
4434 
4435   PetscFunctionBegin;
4436   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4437   ierr = PetscObjectAppendOptionsPrefix((PetscObject)snes,prefix);CHKERRQ(ierr);
4438   if (!snes->ksp) {ierr = SNESGetKSP(snes,&snes->ksp);CHKERRQ(ierr);}
4439   if (snes->linesearch) {
4440     ierr = SNESGetLineSearch(snes,&snes->linesearch);CHKERRQ(ierr);
4441     ierr = PetscObjectAppendOptionsPrefix((PetscObject)snes->linesearch,prefix);CHKERRQ(ierr);
4442   }
4443   ierr = KSPAppendOptionsPrefix(snes->ksp,prefix);CHKERRQ(ierr);
4444   PetscFunctionReturn(0);
4445 }
4446 
4447 #undef __FUNCT__
4448 #define __FUNCT__ "SNESGetOptionsPrefix"
4449 /*@C
4450    SNESGetOptionsPrefix - Sets the prefix used for searching for all
4451    SNES options in the database.
4452 
4453    Not Collective
4454 
4455    Input Parameter:
4456 .  snes - the SNES context
4457 
4458    Output Parameter:
4459 .  prefix - pointer to the prefix string used
4460 
4461    Notes: On the fortran side, the user should pass in a string 'prefix' of
4462    sufficient length to hold the prefix.
4463 
4464    Level: advanced
4465 
4466 .keywords: SNES, get, options, prefix, database
4467 
4468 .seealso: SNESAppendOptionsPrefix()
4469 @*/
4470 PetscErrorCode  SNESGetOptionsPrefix(SNES snes,const char *prefix[])
4471 {
4472   PetscErrorCode ierr;
4473 
4474   PetscFunctionBegin;
4475   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4476   ierr = PetscObjectGetOptionsPrefix((PetscObject)snes,prefix);CHKERRQ(ierr);
4477   PetscFunctionReturn(0);
4478 }
4479 
4480 
4481 #undef __FUNCT__
4482 #define __FUNCT__ "SNESRegister"
4483 /*@C
4484   SNESRegister - Adds a method to the nonlinear solver package.
4485 
4486    Not collective
4487 
4488    Input Parameters:
4489 +  name_solver - name of a new user-defined solver
4490 -  routine_create - routine to create method context
4491 
4492    Notes:
4493    SNESRegister() may be called multiple times to add several user-defined solvers.
4494 
4495    Sample usage:
4496 .vb
4497    SNESRegister("my_solver",MySolverCreate);
4498 .ve
4499 
4500    Then, your solver can be chosen with the procedural interface via
4501 $     SNESSetType(snes,"my_solver")
4502    or at runtime via the option
4503 $     -snes_type my_solver
4504 
4505    Level: advanced
4506 
4507     Note: If your function is not being put into a shared library then use SNESRegister() instead
4508 
4509 .keywords: SNES, nonlinear, register
4510 
4511 .seealso: SNESRegisterAll(), SNESRegisterDestroy()
4512 
4513   Level: advanced
4514 @*/
4515 PetscErrorCode  SNESRegister(const char sname[],PetscErrorCode (*function)(SNES))
4516 {
4517   PetscErrorCode ierr;
4518 
4519   PetscFunctionBegin;
4520   ierr = PetscFunctionListAdd(&SNESList,sname,function);CHKERRQ(ierr);
4521   PetscFunctionReturn(0);
4522 }
4523 
4524 #undef __FUNCT__
4525 #define __FUNCT__ "SNESTestLocalMin"
4526 PetscErrorCode  SNESTestLocalMin(SNES snes)
4527 {
4528   PetscErrorCode ierr;
4529   PetscInt       N,i,j;
4530   Vec            u,uh,fh;
4531   PetscScalar    value;
4532   PetscReal      norm;
4533 
4534   PetscFunctionBegin;
4535   ierr = SNESGetSolution(snes,&u);CHKERRQ(ierr);
4536   ierr = VecDuplicate(u,&uh);CHKERRQ(ierr);
4537   ierr = VecDuplicate(u,&fh);CHKERRQ(ierr);
4538 
4539   /* currently only works for sequential */
4540   ierr = PetscPrintf(PETSC_COMM_WORLD,"Testing FormFunction() for local min\n");CHKERRQ(ierr);
4541   ierr = VecGetSize(u,&N);CHKERRQ(ierr);
4542   for (i=0; i<N; i++) {
4543     ierr = VecCopy(u,uh);CHKERRQ(ierr);
4544     ierr = PetscPrintf(PETSC_COMM_WORLD,"i = %D\n",i);CHKERRQ(ierr);
4545     for (j=-10; j<11; j++) {
4546       value = PetscSign(j)*PetscExpReal(PetscAbs(j)-10.0);
4547       ierr  = VecSetValue(uh,i,value,ADD_VALUES);CHKERRQ(ierr);
4548       ierr  = SNESComputeFunction(snes,uh,fh);CHKERRQ(ierr);
4549       ierr  = VecNorm(fh,NORM_2,&norm);CHKERRQ(ierr);
4550       ierr  = PetscPrintf(PETSC_COMM_WORLD,"       j norm %D %18.16e\n",j,norm);CHKERRQ(ierr);
4551       value = -value;
4552       ierr  = VecSetValue(uh,i,value,ADD_VALUES);CHKERRQ(ierr);
4553     }
4554   }
4555   ierr = VecDestroy(&uh);CHKERRQ(ierr);
4556   ierr = VecDestroy(&fh);CHKERRQ(ierr);
4557   PetscFunctionReturn(0);
4558 }
4559 
4560 #undef __FUNCT__
4561 #define __FUNCT__ "SNESKSPSetUseEW"
4562 /*@
4563    SNESKSPSetUseEW - Sets SNES use Eisenstat-Walker method for
4564    computing relative tolerance for linear solvers within an inexact
4565    Newton method.
4566 
4567    Logically Collective on SNES
4568 
4569    Input Parameters:
4570 +  snes - SNES context
4571 -  flag - PETSC_TRUE or PETSC_FALSE
4572 
4573     Options Database:
4574 +  -snes_ksp_ew - use Eisenstat-Walker method for determining linear system convergence
4575 .  -snes_ksp_ew_version ver - version of  Eisenstat-Walker method
4576 .  -snes_ksp_ew_rtol0 <rtol0> - Sets rtol0
4577 .  -snes_ksp_ew_rtolmax <rtolmax> - Sets rtolmax
4578 .  -snes_ksp_ew_gamma <gamma> - Sets gamma
4579 .  -snes_ksp_ew_alpha <alpha> - Sets alpha
4580 .  -snes_ksp_ew_alpha2 <alpha2> - Sets alpha2
4581 -  -snes_ksp_ew_threshold <threshold> - Sets threshold
4582 
4583    Notes:
4584    Currently, the default is to use a constant relative tolerance for
4585    the inner linear solvers.  Alternatively, one can use the
4586    Eisenstat-Walker method, where the relative convergence tolerance
4587    is reset at each Newton iteration according progress of the nonlinear
4588    solver.
4589 
4590    Level: advanced
4591 
4592    Reference:
4593    S. C. Eisenstat and H. F. Walker, "Choosing the forcing terms in an
4594    inexact Newton method", SISC 17 (1), pp.16-32, 1996.
4595 
4596 .keywords: SNES, KSP, Eisenstat, Walker, convergence, test, inexact, Newton
4597 
4598 .seealso: SNESKSPGetUseEW(), SNESKSPGetParametersEW(), SNESKSPSetParametersEW()
4599 @*/
4600 PetscErrorCode  SNESKSPSetUseEW(SNES snes,PetscBool flag)
4601 {
4602   PetscFunctionBegin;
4603   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4604   PetscValidLogicalCollectiveBool(snes,flag,2);
4605   snes->ksp_ewconv = flag;
4606   PetscFunctionReturn(0);
4607 }
4608 
4609 #undef __FUNCT__
4610 #define __FUNCT__ "SNESKSPGetUseEW"
4611 /*@
4612    SNESKSPGetUseEW - Gets if SNES is using Eisenstat-Walker method
4613    for computing relative tolerance for linear solvers within an
4614    inexact Newton method.
4615 
4616    Not Collective
4617 
4618    Input Parameter:
4619 .  snes - SNES context
4620 
4621    Output Parameter:
4622 .  flag - PETSC_TRUE or PETSC_FALSE
4623 
4624    Notes:
4625    Currently, the default is to use a constant relative tolerance for
4626    the inner linear solvers.  Alternatively, one can use the
4627    Eisenstat-Walker method, where the relative convergence tolerance
4628    is reset at each Newton iteration according progress of the nonlinear
4629    solver.
4630 
4631    Level: advanced
4632 
4633    Reference:
4634    S. C. Eisenstat and H. F. Walker, "Choosing the forcing terms in an
4635    inexact Newton method", SISC 17 (1), pp.16-32, 1996.
4636 
4637 .keywords: SNES, KSP, Eisenstat, Walker, convergence, test, inexact, Newton
4638 
4639 .seealso: SNESKSPSetUseEW(), SNESKSPGetParametersEW(), SNESKSPSetParametersEW()
4640 @*/
4641 PetscErrorCode  SNESKSPGetUseEW(SNES snes, PetscBool  *flag)
4642 {
4643   PetscFunctionBegin;
4644   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4645   PetscValidPointer(flag,2);
4646   *flag = snes->ksp_ewconv;
4647   PetscFunctionReturn(0);
4648 }
4649 
4650 #undef __FUNCT__
4651 #define __FUNCT__ "SNESKSPSetParametersEW"
4652 /*@
4653    SNESKSPSetParametersEW - Sets parameters for Eisenstat-Walker
4654    convergence criteria for the linear solvers within an inexact
4655    Newton method.
4656 
4657    Logically Collective on SNES
4658 
4659    Input Parameters:
4660 +    snes - SNES context
4661 .    version - version 1, 2 (default is 2) or 3
4662 .    rtol_0 - initial relative tolerance (0 <= rtol_0 < 1)
4663 .    rtol_max - maximum relative tolerance (0 <= rtol_max < 1)
4664 .    gamma - multiplicative factor for version 2 rtol computation
4665              (0 <= gamma2 <= 1)
4666 .    alpha - power for version 2 rtol computation (1 < alpha <= 2)
4667 .    alpha2 - power for safeguard
4668 -    threshold - threshold for imposing safeguard (0 < threshold < 1)
4669 
4670    Note:
4671    Version 3 was contributed by Luis Chacon, June 2006.
4672 
4673    Use PETSC_DEFAULT to retain the default for any of the parameters.
4674 
4675    Level: advanced
4676 
4677    Reference:
4678    S. C. Eisenstat and H. F. Walker, "Choosing the forcing terms in an
4679    inexact Newton method", Utah State University Math. Stat. Dept. Res.
4680    Report 6/94/75, June, 1994, to appear in SIAM J. Sci. Comput.
4681 
4682 .keywords: SNES, KSP, Eisenstat, Walker, set, parameters
4683 
4684 .seealso: SNESKSPSetUseEW(), SNESKSPGetUseEW(), SNESKSPGetParametersEW()
4685 @*/
4686 PetscErrorCode  SNESKSPSetParametersEW(SNES snes,PetscInt version,PetscReal rtol_0,PetscReal rtol_max,PetscReal gamma,PetscReal alpha,PetscReal alpha2,PetscReal threshold)
4687 {
4688   SNESKSPEW *kctx;
4689 
4690   PetscFunctionBegin;
4691   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4692   kctx = (SNESKSPEW*)snes->kspconvctx;
4693   if (!kctx) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"No Eisenstat-Walker context existing");
4694   PetscValidLogicalCollectiveInt(snes,version,2);
4695   PetscValidLogicalCollectiveReal(snes,rtol_0,3);
4696   PetscValidLogicalCollectiveReal(snes,rtol_max,4);
4697   PetscValidLogicalCollectiveReal(snes,gamma,5);
4698   PetscValidLogicalCollectiveReal(snes,alpha,6);
4699   PetscValidLogicalCollectiveReal(snes,alpha2,7);
4700   PetscValidLogicalCollectiveReal(snes,threshold,8);
4701 
4702   if (version != PETSC_DEFAULT)   kctx->version   = version;
4703   if (rtol_0 != PETSC_DEFAULT)    kctx->rtol_0    = rtol_0;
4704   if (rtol_max != PETSC_DEFAULT)  kctx->rtol_max  = rtol_max;
4705   if (gamma != PETSC_DEFAULT)     kctx->gamma     = gamma;
4706   if (alpha != PETSC_DEFAULT)     kctx->alpha     = alpha;
4707   if (alpha2 != PETSC_DEFAULT)    kctx->alpha2    = alpha2;
4708   if (threshold != PETSC_DEFAULT) kctx->threshold = threshold;
4709 
4710   if (kctx->version < 1 || kctx->version > 3) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only versions 1, 2 and 3 are supported: %D",kctx->version);
4711   if (kctx->rtol_0 < 0.0 || kctx->rtol_0 >= 1.0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"0.0 <= rtol_0 < 1.0: %g",(double)kctx->rtol_0);
4712   if (kctx->rtol_max < 0.0 || kctx->rtol_max >= 1.0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"0.0 <= rtol_max (%g) < 1.0\n",(double)kctx->rtol_max);
4713   if (kctx->gamma < 0.0 || kctx->gamma > 1.0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"0.0 <= gamma (%g) <= 1.0\n",(double)kctx->gamma);
4714   if (kctx->alpha <= 1.0 || kctx->alpha > 2.0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"1.0 < alpha (%g) <= 2.0\n",(double)kctx->alpha);
4715   if (kctx->threshold <= 0.0 || kctx->threshold >= 1.0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"0.0 < threshold (%g) < 1.0\n",(double)kctx->threshold);
4716   PetscFunctionReturn(0);
4717 }
4718 
4719 #undef __FUNCT__
4720 #define __FUNCT__ "SNESKSPGetParametersEW"
4721 /*@
4722    SNESKSPGetParametersEW - Gets parameters for Eisenstat-Walker
4723    convergence criteria for the linear solvers within an inexact
4724    Newton method.
4725 
4726    Not Collective
4727 
4728    Input Parameters:
4729      snes - SNES context
4730 
4731    Output Parameters:
4732 +    version - version 1, 2 (default is 2) or 3
4733 .    rtol_0 - initial relative tolerance (0 <= rtol_0 < 1)
4734 .    rtol_max - maximum relative tolerance (0 <= rtol_max < 1)
4735 .    gamma - multiplicative factor for version 2 rtol computation (0 <= gamma2 <= 1)
4736 .    alpha - power for version 2 rtol computation (1 < alpha <= 2)
4737 .    alpha2 - power for safeguard
4738 -    threshold - threshold for imposing safeguard (0 < threshold < 1)
4739 
4740    Level: advanced
4741 
4742 .keywords: SNES, KSP, Eisenstat, Walker, get, parameters
4743 
4744 .seealso: SNESKSPSetUseEW(), SNESKSPGetUseEW(), SNESKSPSetParametersEW()
4745 @*/
4746 PetscErrorCode  SNESKSPGetParametersEW(SNES snes,PetscInt *version,PetscReal *rtol_0,PetscReal *rtol_max,PetscReal *gamma,PetscReal *alpha,PetscReal *alpha2,PetscReal *threshold)
4747 {
4748   SNESKSPEW *kctx;
4749 
4750   PetscFunctionBegin;
4751   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4752   kctx = (SNESKSPEW*)snes->kspconvctx;
4753   if (!kctx) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"No Eisenstat-Walker context existing");
4754   if (version)   *version   = kctx->version;
4755   if (rtol_0)    *rtol_0    = kctx->rtol_0;
4756   if (rtol_max)  *rtol_max  = kctx->rtol_max;
4757   if (gamma)     *gamma     = kctx->gamma;
4758   if (alpha)     *alpha     = kctx->alpha;
4759   if (alpha2)    *alpha2    = kctx->alpha2;
4760   if (threshold) *threshold = kctx->threshold;
4761   PetscFunctionReturn(0);
4762 }
4763 
4764 #undef __FUNCT__
4765 #define __FUNCT__ "KSPPreSolve_SNESEW"
4766  PetscErrorCode KSPPreSolve_SNESEW(KSP ksp, Vec b, Vec x, SNES snes)
4767 {
4768   PetscErrorCode ierr;
4769   SNESKSPEW      *kctx = (SNESKSPEW*)snes->kspconvctx;
4770   PetscReal      rtol  = PETSC_DEFAULT,stol;
4771 
4772   PetscFunctionBegin;
4773   if (!snes->ksp_ewconv) PetscFunctionReturn(0);
4774   if (!snes->iter) {
4775     rtol = kctx->rtol_0; /* first time in, so use the original user rtol */
4776     ierr = VecNorm(snes->vec_func,NORM_2,&kctx->norm_first);CHKERRQ(ierr);
4777   }
4778   else {
4779     if (kctx->version == 1) {
4780       rtol = (snes->norm - kctx->lresid_last)/kctx->norm_last;
4781       if (rtol < 0.0) rtol = -rtol;
4782       stol = PetscPowReal(kctx->rtol_last,kctx->alpha2);
4783       if (stol > kctx->threshold) rtol = PetscMax(rtol,stol);
4784     } else if (kctx->version == 2) {
4785       rtol = kctx->gamma * PetscPowReal(snes->norm/kctx->norm_last,kctx->alpha);
4786       stol = kctx->gamma * PetscPowReal(kctx->rtol_last,kctx->alpha);
4787       if (stol > kctx->threshold) rtol = PetscMax(rtol,stol);
4788     } else if (kctx->version == 3) { /* contributed by Luis Chacon, June 2006. */
4789       rtol = kctx->gamma * PetscPowReal(snes->norm/kctx->norm_last,kctx->alpha);
4790       /* safeguard: avoid sharp decrease of rtol */
4791       stol = kctx->gamma*PetscPowReal(kctx->rtol_last,kctx->alpha);
4792       stol = PetscMax(rtol,stol);
4793       rtol = PetscMin(kctx->rtol_0,stol);
4794       /* safeguard: avoid oversolving */
4795       stol = kctx->gamma*(kctx->norm_first*snes->rtol)/snes->norm;
4796       stol = PetscMax(rtol,stol);
4797       rtol = PetscMin(kctx->rtol_0,stol);
4798     } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only versions 1, 2 or 3 are supported: %D",kctx->version);
4799   }
4800   /* safeguard: avoid rtol greater than one */
4801   rtol = PetscMin(rtol,kctx->rtol_max);
4802   ierr = KSPSetTolerances(ksp,rtol,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRQ(ierr);
4803   ierr = PetscInfo3(snes,"iter %D, Eisenstat-Walker (version %D) KSP rtol=%g\n",snes->iter,kctx->version,(double)rtol);CHKERRQ(ierr);
4804   PetscFunctionReturn(0);
4805 }
4806 
4807 #undef __FUNCT__
4808 #define __FUNCT__ "KSPPostSolve_SNESEW"
4809 PetscErrorCode KSPPostSolve_SNESEW(KSP ksp, Vec b, Vec x, SNES snes)
4810 {
4811   PetscErrorCode ierr;
4812   SNESKSPEW      *kctx = (SNESKSPEW*)snes->kspconvctx;
4813   PCSide         pcside;
4814   Vec            lres;
4815 
4816   PetscFunctionBegin;
4817   if (!snes->ksp_ewconv) PetscFunctionReturn(0);
4818   ierr = KSPGetTolerances(ksp,&kctx->rtol_last,0,0,0);CHKERRQ(ierr);
4819   kctx->norm_last = snes->norm;
4820   if (kctx->version == 1) {
4821     PC        pc;
4822     PetscBool isNone;
4823 
4824     ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr);
4825     ierr = PetscObjectTypeCompare((PetscObject) pc, PCNONE, &isNone);CHKERRQ(ierr);
4826     ierr = KSPGetPCSide(ksp,&pcside);CHKERRQ(ierr);
4827      if (pcside == PC_RIGHT || isNone) { /* XXX Should we also test KSP_UNPRECONDITIONED_NORM ? */
4828       /* KSP residual is true linear residual */
4829       ierr = KSPGetResidualNorm(ksp,&kctx->lresid_last);CHKERRQ(ierr);
4830     } else {
4831       /* KSP residual is preconditioned residual */
4832       /* compute true linear residual norm */
4833       ierr = VecDuplicate(b,&lres);CHKERRQ(ierr);
4834       ierr = MatMult(snes->jacobian,x,lres);CHKERRQ(ierr);
4835       ierr = VecAYPX(lres,-1.0,b);CHKERRQ(ierr);
4836       ierr = VecNorm(lres,NORM_2,&kctx->lresid_last);CHKERRQ(ierr);
4837       ierr = VecDestroy(&lres);CHKERRQ(ierr);
4838     }
4839   }
4840   PetscFunctionReturn(0);
4841 }
4842 
4843 #undef __FUNCT__
4844 #define __FUNCT__ "SNESGetKSP"
4845 /*@
4846    SNESGetKSP - Returns the KSP context for a SNES solver.
4847 
4848    Not Collective, but if SNES object is parallel, then KSP object is parallel
4849 
4850    Input Parameter:
4851 .  snes - the SNES context
4852 
4853    Output Parameter:
4854 .  ksp - the KSP context
4855 
4856    Notes:
4857    The user can then directly manipulate the KSP context to set various
4858    options, etc.  Likewise, the user can then extract and manipulate the
4859    PC contexts as well.
4860 
4861    Level: beginner
4862 
4863 .keywords: SNES, nonlinear, get, KSP, context
4864 
4865 .seealso: KSPGetPC(), SNESCreate(), KSPCreate(), SNESSetKSP()
4866 @*/
4867 PetscErrorCode  SNESGetKSP(SNES snes,KSP *ksp)
4868 {
4869   PetscErrorCode ierr;
4870 
4871   PetscFunctionBegin;
4872   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4873   PetscValidPointer(ksp,2);
4874 
4875   if (!snes->ksp) {
4876     PetscBool monitor = PETSC_FALSE;
4877 
4878     ierr = KSPCreate(PetscObjectComm((PetscObject)snes),&snes->ksp);CHKERRQ(ierr);
4879     ierr = PetscObjectIncrementTabLevel((PetscObject)snes->ksp,(PetscObject)snes,1);CHKERRQ(ierr);
4880     ierr = PetscLogObjectParent((PetscObject)snes,(PetscObject)snes->ksp);CHKERRQ(ierr);
4881 
4882     ierr = KSPSetPreSolve(snes->ksp,(PetscErrorCode (*)(KSP,Vec,Vec,void*))KSPPreSolve_SNESEW,snes);CHKERRQ(ierr);
4883     ierr = KSPSetPostSolve(snes->ksp,(PetscErrorCode (*)(KSP,Vec,Vec,void*))KSPPostSolve_SNESEW,snes);CHKERRQ(ierr);
4884 
4885     ierr = PetscOptionsGetBool(((PetscObject)snes)->options,((PetscObject)snes)->prefix,"-ksp_monitor_snes",&monitor,NULL);CHKERRQ(ierr);
4886     if (monitor) {
4887       ierr = KSPMonitorSet(snes->ksp,KSPMonitorSNES,snes,NULL);CHKERRQ(ierr);
4888     }
4889     monitor = PETSC_FALSE;
4890     ierr = PetscOptionsGetBool(((PetscObject)snes)->options,((PetscObject)snes)->prefix,"-ksp_monitor_snes_lg",&monitor,NULL);CHKERRQ(ierr);
4891     if (monitor) {
4892       PetscObject *objs;
4893       ierr = KSPMonitorSNESLGResidualNormCreate(PetscObjectComm((PetscObject)snes),NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,600,600,&objs);CHKERRQ(ierr);
4894       objs[0] = (PetscObject) snes;
4895       ierr = KSPMonitorSet(snes->ksp,(PetscErrorCode (*)(KSP,PetscInt,PetscReal,void*))KSPMonitorSNESLGResidualNorm,objs,(PetscErrorCode (*)(void**))KSPMonitorSNESLGResidualNormDestroy);CHKERRQ(ierr);
4896     }
4897   }
4898   *ksp = snes->ksp;
4899   PetscFunctionReturn(0);
4900 }
4901 
4902 
4903 #include <petsc/private/dmimpl.h>
4904 #undef __FUNCT__
4905 #define __FUNCT__ "SNESSetDM"
4906 /*@
4907    SNESSetDM - Sets the DM that may be used by some nonlinear solvers or their underlying preconditioners
4908 
4909    Logically Collective on SNES
4910 
4911    Input Parameters:
4912 +  snes - the nonlinear solver context
4913 -  dm - the dm, cannot be NULL
4914 
4915    Level: intermediate
4916 
4917 .seealso: SNESGetDM(), KSPSetDM(), KSPGetDM()
4918 @*/
4919 PetscErrorCode  SNESSetDM(SNES snes,DM dm)
4920 {
4921   PetscErrorCode ierr;
4922   KSP            ksp;
4923   DMSNES         sdm;
4924 
4925   PetscFunctionBegin;
4926   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4927   PetscValidHeaderSpecific(dm,DM_CLASSID,2);
4928   ierr = PetscObjectReference((PetscObject)dm);CHKERRQ(ierr);
4929   if (snes->dm) {               /* Move the DMSNES context over to the new DM unless the new DM already has one */
4930     if (snes->dm->dmsnes && !dm->dmsnes) {
4931       ierr = DMCopyDMSNES(snes->dm,dm);CHKERRQ(ierr);
4932       ierr = DMGetDMSNES(snes->dm,&sdm);CHKERRQ(ierr);
4933       if (sdm->originaldm == snes->dm) sdm->originaldm = dm; /* Grant write privileges to the replacement DM */
4934     }
4935     ierr = DMDestroy(&snes->dm);CHKERRQ(ierr);
4936   }
4937   snes->dm     = dm;
4938   snes->dmAuto = PETSC_FALSE;
4939 
4940   ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
4941   ierr = KSPSetDM(ksp,dm);CHKERRQ(ierr);
4942   ierr = KSPSetDMActive(ksp,PETSC_FALSE);CHKERRQ(ierr);
4943   if (snes->pc) {
4944     ierr = SNESSetDM(snes->pc, snes->dm);CHKERRQ(ierr);
4945     ierr = SNESSetNPCSide(snes,snes->pcside);CHKERRQ(ierr);
4946   }
4947   PetscFunctionReturn(0);
4948 }
4949 
4950 #undef __FUNCT__
4951 #define __FUNCT__ "SNESGetDM"
4952 /*@
4953    SNESGetDM - Gets the DM that may be used by some preconditioners
4954 
4955    Not Collective but DM obtained is parallel on SNES
4956 
4957    Input Parameter:
4958 . snes - the preconditioner context
4959 
4960    Output Parameter:
4961 .  dm - the dm
4962 
4963    Level: intermediate
4964 
4965 .seealso: SNESSetDM(), KSPSetDM(), KSPGetDM()
4966 @*/
4967 PetscErrorCode  SNESGetDM(SNES snes,DM *dm)
4968 {
4969   PetscErrorCode ierr;
4970 
4971   PetscFunctionBegin;
4972   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
4973   if (!snes->dm) {
4974     ierr         = DMShellCreate(PetscObjectComm((PetscObject)snes),&snes->dm);CHKERRQ(ierr);
4975     snes->dmAuto = PETSC_TRUE;
4976   }
4977   *dm = snes->dm;
4978   PetscFunctionReturn(0);
4979 }
4980 
4981 #undef __FUNCT__
4982 #define __FUNCT__ "SNESSetNPC"
4983 /*@
4984   SNESSetNPC - Sets the nonlinear preconditioner to be used.
4985 
4986   Collective on SNES
4987 
4988   Input Parameters:
4989 + snes - iterative context obtained from SNESCreate()
4990 - pc   - the preconditioner object
4991 
4992   Notes:
4993   Use SNESGetNPC() to retrieve the preconditioner context (for example,
4994   to configure it using the API).
4995 
4996   Level: developer
4997 
4998 .keywords: SNES, set, precondition
4999 .seealso: SNESGetNPC(), SNESHasNPC()
5000 @*/
5001 PetscErrorCode SNESSetNPC(SNES snes, SNES pc)
5002 {
5003   PetscErrorCode ierr;
5004 
5005   PetscFunctionBegin;
5006   PetscValidHeaderSpecific(snes, SNES_CLASSID, 1);
5007   PetscValidHeaderSpecific(pc, SNES_CLASSID, 2);
5008   PetscCheckSameComm(snes, 1, pc, 2);
5009   ierr     = PetscObjectReference((PetscObject) pc);CHKERRQ(ierr);
5010   ierr     = SNESDestroy(&snes->pc);CHKERRQ(ierr);
5011   snes->pc = pc;
5012   ierr     = PetscLogObjectParent((PetscObject)snes, (PetscObject)snes->pc);CHKERRQ(ierr);
5013   PetscFunctionReturn(0);
5014 }
5015 
5016 #undef __FUNCT__
5017 #define __FUNCT__ "SNESGetNPC"
5018 /*@
5019   SNESGetNPC - Creates a nonlinear preconditioning solver (SNES) to be used to precondition the nonlinear solver.
5020 
5021   Not Collective
5022 
5023   Input Parameter:
5024 . snes - iterative context obtained from SNESCreate()
5025 
5026   Output Parameter:
5027 . pc - preconditioner context
5028 
5029   Notes: If a SNES was previously set with SNESSetNPC() then that SNES is returned.
5030 
5031   Level: developer
5032 
5033 .keywords: SNES, get, preconditioner
5034 .seealso: SNESSetNPC(), SNESHasNPC()
5035 @*/
5036 PetscErrorCode SNESGetNPC(SNES snes, SNES *pc)
5037 {
5038   PetscErrorCode ierr;
5039   const char     *optionsprefix;
5040 
5041   PetscFunctionBegin;
5042   PetscValidHeaderSpecific(snes, SNES_CLASSID, 1);
5043   PetscValidPointer(pc, 2);
5044   if (!snes->pc) {
5045     ierr = SNESCreate(PetscObjectComm((PetscObject)snes),&snes->pc);CHKERRQ(ierr);
5046     ierr = PetscObjectIncrementTabLevel((PetscObject)snes->pc,(PetscObject)snes,1);CHKERRQ(ierr);
5047     ierr = PetscLogObjectParent((PetscObject)snes,(PetscObject)snes->pc);CHKERRQ(ierr);
5048     ierr = SNESGetOptionsPrefix(snes,&optionsprefix);CHKERRQ(ierr);
5049     ierr = SNESSetOptionsPrefix(snes->pc,optionsprefix);CHKERRQ(ierr);
5050     ierr = SNESAppendOptionsPrefix(snes->pc,"npc_");CHKERRQ(ierr);
5051     ierr = SNESSetCountersReset(snes->pc,PETSC_FALSE);CHKERRQ(ierr);
5052   }
5053   *pc = snes->pc;
5054   PetscFunctionReturn(0);
5055 }
5056 
5057 #undef __FUNCT__
5058 #define __FUNCT__ "SNESHasNPC"
5059 /*@
5060   SNESHasNPC - Returns whether a nonlinear preconditioner exists
5061 
5062   Not Collective
5063 
5064   Input Parameter:
5065 . snes - iterative context obtained from SNESCreate()
5066 
5067   Output Parameter:
5068 . has_npc - whether the SNES has an NPC or not
5069 
5070   Level: developer
5071 
5072 .keywords: SNES, has, preconditioner
5073 .seealso: SNESSetNPC(), SNESGetNPC()
5074 @*/
5075 PetscErrorCode SNESHasNPC(SNES snes, PetscBool *has_npc)
5076 {
5077   PetscFunctionBegin;
5078   PetscValidHeaderSpecific(snes, SNES_CLASSID, 1);
5079   *has_npc = (PetscBool) (snes->pc ? PETSC_TRUE : PETSC_FALSE);
5080   PetscFunctionReturn(0);
5081 }
5082 
5083 #undef __FUNCT__
5084 #define __FUNCT__ "SNESSetNPCSide"
5085 /*@
5086     SNESSetNPCSide - Sets the preconditioning side.
5087 
5088     Logically Collective on SNES
5089 
5090     Input Parameter:
5091 .   snes - iterative context obtained from SNESCreate()
5092 
5093     Output Parameter:
5094 .   side - the preconditioning side, where side is one of
5095 .vb
5096       PC_LEFT - left preconditioning (default)
5097       PC_RIGHT - right preconditioning
5098 .ve
5099 
5100     Options Database Keys:
5101 .   -snes_pc_side <right,left>
5102 
5103     Level: intermediate
5104 
5105 .keywords: SNES, set, right, left, side, preconditioner, flag
5106 
5107 .seealso: SNESGetNPCSide(), KSPSetPCSide()
5108 @*/
5109 PetscErrorCode  SNESSetNPCSide(SNES snes,PCSide side)
5110 {
5111   PetscFunctionBegin;
5112   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
5113   PetscValidLogicalCollectiveEnum(snes,side,2);
5114   snes->pcside = side;
5115   PetscFunctionReturn(0);
5116 }
5117 
5118 #undef __FUNCT__
5119 #define __FUNCT__ "SNESGetNPCSide"
5120 /*@
5121     SNESGetNPCSide - Gets the preconditioning side.
5122 
5123     Not Collective
5124 
5125     Input Parameter:
5126 .   snes - iterative context obtained from SNESCreate()
5127 
5128     Output Parameter:
5129 .   side - the preconditioning side, where side is one of
5130 .vb
5131       PC_LEFT - left preconditioning (default)
5132       PC_RIGHT - right preconditioning
5133 .ve
5134 
5135     Level: intermediate
5136 
5137 .keywords: SNES, get, right, left, side, preconditioner, flag
5138 
5139 .seealso: SNESSetNPCSide(), KSPGetPCSide()
5140 @*/
5141 PetscErrorCode  SNESGetNPCSide(SNES snes,PCSide *side)
5142 {
5143   PetscFunctionBegin;
5144   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
5145   PetscValidPointer(side,2);
5146   *side = snes->pcside;
5147   PetscFunctionReturn(0);
5148 }
5149 
5150 #undef __FUNCT__
5151 #define __FUNCT__ "SNESSetLineSearch"
5152 /*@
5153   SNESSetLineSearch - Sets the linesearch on the SNES instance.
5154 
5155   Collective on SNES
5156 
5157   Input Parameters:
5158 + snes - iterative context obtained from SNESCreate()
5159 - linesearch   - the linesearch object
5160 
5161   Notes:
5162   Use SNESGetLineSearch() to retrieve the preconditioner context (for example,
5163   to configure it using the API).
5164 
5165   Level: developer
5166 
5167 .keywords: SNES, set, linesearch
5168 .seealso: SNESGetLineSearch()
5169 @*/
5170 PetscErrorCode SNESSetLineSearch(SNES snes, SNESLineSearch linesearch)
5171 {
5172   PetscErrorCode ierr;
5173 
5174   PetscFunctionBegin;
5175   PetscValidHeaderSpecific(snes, SNES_CLASSID, 1);
5176   PetscValidHeaderSpecific(linesearch, SNESLINESEARCH_CLASSID, 2);
5177   PetscCheckSameComm(snes, 1, linesearch, 2);
5178   ierr = PetscObjectReference((PetscObject) linesearch);CHKERRQ(ierr);
5179   ierr = SNESLineSearchDestroy(&snes->linesearch);CHKERRQ(ierr);
5180 
5181   snes->linesearch = linesearch;
5182 
5183   ierr = PetscLogObjectParent((PetscObject)snes, (PetscObject)snes->linesearch);CHKERRQ(ierr);
5184   PetscFunctionReturn(0);
5185 }
5186 
5187 #undef __FUNCT__
5188 #define __FUNCT__ "SNESGetLineSearch"
5189 /*@
5190   SNESGetLineSearch - Returns a pointer to the line search context set with SNESSetLineSearch()
5191   or creates a default line search instance associated with the SNES and returns it.
5192 
5193   Not Collective
5194 
5195   Input Parameter:
5196 . snes - iterative context obtained from SNESCreate()
5197 
5198   Output Parameter:
5199 . linesearch - linesearch context
5200 
5201   Level: beginner
5202 
5203 .keywords: SNES, get, linesearch
5204 .seealso: SNESSetLineSearch(), SNESLineSearchCreate()
5205 @*/
5206 PetscErrorCode SNESGetLineSearch(SNES snes, SNESLineSearch *linesearch)
5207 {
5208   PetscErrorCode ierr;
5209   const char     *optionsprefix;
5210 
5211   PetscFunctionBegin;
5212   PetscValidHeaderSpecific(snes, SNES_CLASSID, 1);
5213   PetscValidPointer(linesearch, 2);
5214   if (!snes->linesearch) {
5215     ierr = SNESGetOptionsPrefix(snes, &optionsprefix);CHKERRQ(ierr);
5216     ierr = SNESLineSearchCreate(PetscObjectComm((PetscObject)snes), &snes->linesearch);CHKERRQ(ierr);
5217     ierr = SNESLineSearchSetSNES(snes->linesearch, snes);CHKERRQ(ierr);
5218     ierr = SNESLineSearchAppendOptionsPrefix(snes->linesearch, optionsprefix);CHKERRQ(ierr);
5219     ierr = PetscObjectIncrementTabLevel((PetscObject) snes->linesearch, (PetscObject) snes, 1);CHKERRQ(ierr);
5220     ierr = PetscLogObjectParent((PetscObject)snes, (PetscObject)snes->linesearch);CHKERRQ(ierr);
5221   }
5222   *linesearch = snes->linesearch;
5223   PetscFunctionReturn(0);
5224 }
5225 
5226 #if defined(PETSC_HAVE_MATLAB_ENGINE)
5227 #include <mex.h>
5228 
5229 typedef struct {char *funcname; mxArray *ctx;} SNESMatlabContext;
5230 
5231 #undef __FUNCT__
5232 #define __FUNCT__ "SNESComputeFunction_Matlab"
5233 /*
5234    SNESComputeFunction_Matlab - Calls the function that has been set with SNESSetFunctionMatlab().
5235 
5236    Collective on SNES
5237 
5238    Input Parameters:
5239 +  snes - the SNES context
5240 -  x - input vector
5241 
5242    Output Parameter:
5243 .  y - function vector, as set by SNESSetFunction()
5244 
5245    Notes:
5246    SNESComputeFunction() is typically used within nonlinear solvers
5247    implementations, so most users would not generally call this routine
5248    themselves.
5249 
5250    Level: developer
5251 
5252 .keywords: SNES, nonlinear, compute, function
5253 
5254 .seealso: SNESSetFunction(), SNESGetFunction()
5255 */
5256 PetscErrorCode  SNESComputeFunction_Matlab(SNES snes,Vec x,Vec y, void *ctx)
5257 {
5258   PetscErrorCode    ierr;
5259   SNESMatlabContext *sctx = (SNESMatlabContext*)ctx;
5260   int               nlhs  = 1,nrhs = 5;
5261   mxArray           *plhs[1],*prhs[5];
5262   long long int     lx = 0,ly = 0,ls = 0;
5263 
5264   PetscFunctionBegin;
5265   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
5266   PetscValidHeaderSpecific(x,VEC_CLASSID,2);
5267   PetscValidHeaderSpecific(y,VEC_CLASSID,3);
5268   PetscCheckSameComm(snes,1,x,2);
5269   PetscCheckSameComm(snes,1,y,3);
5270 
5271   /* call Matlab function in ctx with arguments x and y */
5272 
5273   ierr    = PetscMemcpy(&ls,&snes,sizeof(snes));CHKERRQ(ierr);
5274   ierr    = PetscMemcpy(&lx,&x,sizeof(x));CHKERRQ(ierr);
5275   ierr    = PetscMemcpy(&ly,&y,sizeof(x));CHKERRQ(ierr);
5276   prhs[0] = mxCreateDoubleScalar((double)ls);
5277   prhs[1] = mxCreateDoubleScalar((double)lx);
5278   prhs[2] = mxCreateDoubleScalar((double)ly);
5279   prhs[3] = mxCreateString(sctx->funcname);
5280   prhs[4] = sctx->ctx;
5281   ierr    = mexCallMATLAB(nlhs,plhs,nrhs,prhs,"PetscSNESComputeFunctionInternal");CHKERRQ(ierr);
5282   ierr    = mxGetScalar(plhs[0]);CHKERRQ(ierr);
5283   mxDestroyArray(prhs[0]);
5284   mxDestroyArray(prhs[1]);
5285   mxDestroyArray(prhs[2]);
5286   mxDestroyArray(prhs[3]);
5287   mxDestroyArray(plhs[0]);
5288   PetscFunctionReturn(0);
5289 }
5290 
5291 #undef __FUNCT__
5292 #define __FUNCT__ "SNESSetFunctionMatlab"
5293 /*
5294    SNESSetFunctionMatlab - Sets the function evaluation routine and function
5295    vector for use by the SNES routines in solving systems of nonlinear
5296    equations from MATLAB. Here the function is a string containing the name of a MATLAB function
5297 
5298    Logically Collective on SNES
5299 
5300    Input Parameters:
5301 +  snes - the SNES context
5302 .  r - vector to store function value
5303 -  f - function evaluation routine
5304 
5305    Notes:
5306    The Newton-like methods typically solve linear systems of the form
5307 $      f'(x) x = -f(x),
5308    where f'(x) denotes the Jacobian matrix and f(x) is the function.
5309 
5310    Level: beginner
5311 
5312    Developer Note:  This bleeds the allocated memory SNESMatlabContext *sctx;
5313 
5314 .keywords: SNES, nonlinear, set, function
5315 
5316 .seealso: SNESGetFunction(), SNESComputeFunction(), SNESSetJacobian(), SNESSetFunction()
5317 */
5318 PetscErrorCode  SNESSetFunctionMatlab(SNES snes,Vec r,const char *f,mxArray *ctx)
5319 {
5320   PetscErrorCode    ierr;
5321   SNESMatlabContext *sctx;
5322 
5323   PetscFunctionBegin;
5324   /* currently sctx is memory bleed */
5325   ierr = PetscNew(&sctx);CHKERRQ(ierr);
5326   ierr = PetscStrallocpy(f,&sctx->funcname);CHKERRQ(ierr);
5327   /*
5328      This should work, but it doesn't
5329   sctx->ctx = ctx;
5330   mexMakeArrayPersistent(sctx->ctx);
5331   */
5332   sctx->ctx = mxDuplicateArray(ctx);
5333   ierr      = SNESSetFunction(snes,r,SNESComputeFunction_Matlab,sctx);CHKERRQ(ierr);
5334   PetscFunctionReturn(0);
5335 }
5336 
5337 #undef __FUNCT__
5338 #define __FUNCT__ "SNESComputeJacobian_Matlab"
5339 /*
5340    SNESComputeJacobian_Matlab - Calls the function that has been set with SNESSetJacobianMatlab().
5341 
5342    Collective on SNES
5343 
5344    Input Parameters:
5345 +  snes - the SNES context
5346 .  x - input vector
5347 .  A, B - the matrices
5348 -  ctx - user context
5349 
5350    Level: developer
5351 
5352 .keywords: SNES, nonlinear, compute, function
5353 
5354 .seealso: SNESSetFunction(), SNESGetFunction()
5355 @*/
5356 PetscErrorCode  SNESComputeJacobian_Matlab(SNES snes,Vec x,Mat A,Mat B,void *ctx)
5357 {
5358   PetscErrorCode    ierr;
5359   SNESMatlabContext *sctx = (SNESMatlabContext*)ctx;
5360   int               nlhs  = 2,nrhs = 6;
5361   mxArray           *plhs[2],*prhs[6];
5362   long long int     lx = 0,lA = 0,ls = 0, lB = 0;
5363 
5364   PetscFunctionBegin;
5365   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
5366   PetscValidHeaderSpecific(x,VEC_CLASSID,2);
5367 
5368   /* call Matlab function in ctx with arguments x and y */
5369 
5370   ierr    = PetscMemcpy(&ls,&snes,sizeof(snes));CHKERRQ(ierr);
5371   ierr    = PetscMemcpy(&lx,&x,sizeof(x));CHKERRQ(ierr);
5372   ierr    = PetscMemcpy(&lA,A,sizeof(x));CHKERRQ(ierr);
5373   ierr    = PetscMemcpy(&lB,B,sizeof(x));CHKERRQ(ierr);
5374   prhs[0] = mxCreateDoubleScalar((double)ls);
5375   prhs[1] = mxCreateDoubleScalar((double)lx);
5376   prhs[2] = mxCreateDoubleScalar((double)lA);
5377   prhs[3] = mxCreateDoubleScalar((double)lB);
5378   prhs[4] = mxCreateString(sctx->funcname);
5379   prhs[5] = sctx->ctx;
5380   ierr    = mexCallMATLAB(nlhs,plhs,nrhs,prhs,"PetscSNESComputeJacobianInternal");CHKERRQ(ierr);
5381   ierr    = mxGetScalar(plhs[0]);CHKERRQ(ierr);
5382   mxDestroyArray(prhs[0]);
5383   mxDestroyArray(prhs[1]);
5384   mxDestroyArray(prhs[2]);
5385   mxDestroyArray(prhs[3]);
5386   mxDestroyArray(prhs[4]);
5387   mxDestroyArray(plhs[0]);
5388   mxDestroyArray(plhs[1]);
5389   PetscFunctionReturn(0);
5390 }
5391 
5392 #undef __FUNCT__
5393 #define __FUNCT__ "SNESSetJacobianMatlab"
5394 /*
5395    SNESSetJacobianMatlab - Sets the Jacobian function evaluation routine and two empty Jacobian matrices
5396    vector for use by the SNES routines in solving systems of nonlinear
5397    equations from MATLAB. Here the function is a string containing the name of a MATLAB function
5398 
5399    Logically Collective on SNES
5400 
5401    Input Parameters:
5402 +  snes - the SNES context
5403 .  A,B - Jacobian matrices
5404 .  J - function evaluation routine
5405 -  ctx - user context
5406 
5407    Level: developer
5408 
5409    Developer Note:  This bleeds the allocated memory SNESMatlabContext *sctx;
5410 
5411 .keywords: SNES, nonlinear, set, function
5412 
5413 .seealso: SNESGetFunction(), SNESComputeFunction(), SNESSetJacobian(), SNESSetFunction(), J
5414 */
5415 PetscErrorCode  SNESSetJacobianMatlab(SNES snes,Mat A,Mat B,const char *J,mxArray *ctx)
5416 {
5417   PetscErrorCode    ierr;
5418   SNESMatlabContext *sctx;
5419 
5420   PetscFunctionBegin;
5421   /* currently sctx is memory bleed */
5422   ierr = PetscNew(&sctx);CHKERRQ(ierr);
5423   ierr = PetscStrallocpy(J,&sctx->funcname);CHKERRQ(ierr);
5424   /*
5425      This should work, but it doesn't
5426   sctx->ctx = ctx;
5427   mexMakeArrayPersistent(sctx->ctx);
5428   */
5429   sctx->ctx = mxDuplicateArray(ctx);
5430   ierr      = SNESSetJacobian(snes,A,B,SNESComputeJacobian_Matlab,sctx);CHKERRQ(ierr);
5431   PetscFunctionReturn(0);
5432 }
5433 
5434 #undef __FUNCT__
5435 #define __FUNCT__ "SNESMonitor_Matlab"
5436 /*
5437    SNESMonitor_Matlab - Calls the function that has been set with SNESMonitorSetMatlab().
5438 
5439    Collective on SNES
5440 
5441 .seealso: SNESSetFunction(), SNESGetFunction()
5442 @*/
5443 PetscErrorCode  SNESMonitor_Matlab(SNES snes,PetscInt it, PetscReal fnorm, void *ctx)
5444 {
5445   PetscErrorCode    ierr;
5446   SNESMatlabContext *sctx = (SNESMatlabContext*)ctx;
5447   int               nlhs  = 1,nrhs = 6;
5448   mxArray           *plhs[1],*prhs[6];
5449   long long int     lx = 0,ls = 0;
5450   Vec               x  = snes->vec_sol;
5451 
5452   PetscFunctionBegin;
5453   PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
5454 
5455   ierr    = PetscMemcpy(&ls,&snes,sizeof(snes));CHKERRQ(ierr);
5456   ierr    = PetscMemcpy(&lx,&x,sizeof(x));CHKERRQ(ierr);
5457   prhs[0] = mxCreateDoubleScalar((double)ls);
5458   prhs[1] = mxCreateDoubleScalar((double)it);
5459   prhs[2] = mxCreateDoubleScalar((double)fnorm);
5460   prhs[3] = mxCreateDoubleScalar((double)lx);
5461   prhs[4] = mxCreateString(sctx->funcname);
5462   prhs[5] = sctx->ctx;
5463   ierr    = mexCallMATLAB(nlhs,plhs,nrhs,prhs,"PetscSNESMonitorInternal");CHKERRQ(ierr);
5464   ierr    = mxGetScalar(plhs[0]);CHKERRQ(ierr);
5465   mxDestroyArray(prhs[0]);
5466   mxDestroyArray(prhs[1]);
5467   mxDestroyArray(prhs[2]);
5468   mxDestroyArray(prhs[3]);
5469   mxDestroyArray(prhs[4]);
5470   mxDestroyArray(plhs[0]);
5471   PetscFunctionReturn(0);
5472 }
5473 
5474 #undef __FUNCT__
5475 #define __FUNCT__ "SNESMonitorSetMatlab"
5476 /*
5477    SNESMonitorSetMatlab - Sets the monitor function from MATLAB
5478 
5479    Level: developer
5480 
5481    Developer Note:  This bleeds the allocated memory SNESMatlabContext *sctx;
5482 
5483 .keywords: SNES, nonlinear, set, function
5484 
5485 .seealso: SNESGetFunction(), SNESComputeFunction(), SNESSetJacobian(), SNESSetFunction()
5486 */
5487 PetscErrorCode  SNESMonitorSetMatlab(SNES snes,const char *f,mxArray *ctx)
5488 {
5489   PetscErrorCode    ierr;
5490   SNESMatlabContext *sctx;
5491 
5492   PetscFunctionBegin;
5493   /* currently sctx is memory bleed */
5494   ierr = PetscNew(&sctx);CHKERRQ(ierr);
5495   ierr = PetscStrallocpy(f,&sctx->funcname);CHKERRQ(ierr);
5496   /*
5497      This should work, but it doesn't
5498   sctx->ctx = ctx;
5499   mexMakeArrayPersistent(sctx->ctx);
5500   */
5501   sctx->ctx = mxDuplicateArray(ctx);
5502   ierr      = SNESMonitorSet(snes,SNESMonitor_Matlab,sctx,NULL);CHKERRQ(ierr);
5503   PetscFunctionReturn(0);
5504 }
5505 
5506 #endif
5507